OSCR

Circulating microRNAs reveal egg-brain crosstalk and a brain-predominant microRNA linked to the onset of the next reproductive cycle in iteroparous salmonids.

Code ↔ Paper

3 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 3 matches
  1. [1] § Results › A single c-miRNA is associated with the onset of the next reproductive cycle ↔ askomics/create_datatables_askoR.R, lines 1–47 · score 0.74 · trunk kidney, head kidney, skin, spleen, gills, heart
  2. [2] § Results › A single c-miRNA is associated with the onset of the next reproductive cycle ↔ askomics/create_datatables_askoR.R, lines 1–47 · score 0.74 · trunk kidney, head kidney, skin, spleen, gills, heart
  3. [3] § Methods › sRNA-seq analysis ↔ prost_postprocess/projects/vim_details.R, lines 89–155 · score 0.66 · log fold changes, lfcShrink, DESeq2, apeglm, transformed, PCA

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

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The authors' code

R · 457 lines · 37 KB · no license · 2 matches

  1. library(tidyverse)
  2. library(prostPostprocess)
  3. library(readxl)
  5. data_path = "~/Documents/phenomir/data/askomics_data"
  6. datatables_path = "~/Documents/phenomir/askomics/datatables"
  8. miRnome_path = "~/Documents/phenomir/data/annotation/omy.mature.v3.fasta"
  10. # Organism
  12. organism <- tibble(Organism = "taxon:8022", organismName = "Oncorhynchus mykiss")#, taxonURI = "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=8022")
  13. organism %>%
  14. write_csv(paste(datatables_path, "Organism.csv", sep = "/"), na = "")
  16. # Organ
  18. organ <-
  19. tibble(`rdfs:label` = c(), Organ = c()) %>%
  20. add_row(`rdfs:label` = "plasma", Organ = "uberon:0001969") %>%
  21. add_row(`rdfs:label` = "ovarian fluid", Organ = "uberon:0036217") %>%
  22. add_row(`rdfs:label` = "mucus", Organ = "uberon:0000912") %>%
  23. add_row(`rdfs:label` = "seminal fluid", Organ = "uberon:0006530") %>%
  24. add_row(`rdfs:label` = "brain", Organ = "uberon:0000955") %>%
  25. add_row(`rdfs:label` = "egg", Organ = "uberon:egg") %>%
  26. add_row(`rdfs:label` = "gills", Organ = "uberon:gill") %>%
  27. add_row(`rdfs:label` = "gonad", Organ = "uberon:0000991") %>%
  28. add_row(`rdfs:label` = "head kidney", Organ = "uberon:0007132") %>%
  29. add_row(`rdfs:label` = "heart", Organ = "uberon:0000948") %>%
  30. add_row(`rdfs:label` = "intestine", Organ = "uberon:0000160") %>%
  31. add_row(`rdfs:label` = "leucocytes", Organ = "uberon:leucocytes") %>%
  32. add_row(`rdfs:label` = "liver", Organ = "uberon:0002107") %>%
  33. add_row(`rdfs:label` = "muscle", Organ = "uberon:0001630") %>%
  34. add_row(`rdfs:label` = "myoblast", Organ = "uberon:myoblast") %>%
  35. add_row(`rdfs:label` = "myotubes", Organ = "uberon:0014896") %>%
  36. add_row(`rdfs:label` = "ovary", Organ = "uberon:0000992") %>%
  37. add_row(`rdfs:label` = "pituitary", Organ = "uberon:pituiatary") %>%
  38. add_row(`rdfs:label` = "skin", Organ = "uberon:skin") %>%
  39. add_row(`rdfs:label` = "spermatogonia", Organ = "uberon:spermatogonia") %>%
  40. add_row(`rdfs:label` = "spleen", Organ = "uberon:0002106") %>%
  41. add_row(`rdfs:label` = "stomach", Organ = "uberon:0000945") %>%
  42. add_row(`rdfs:label` = "testis", Organ = "uberon:0000473") %>%
  43. add_row(`rdfs:label` = "trunk kidney", Organ = "uberon:trunkkidney") %>%
  44. add_row(`rdfs:label` = "whole embryo", Organ = "uberon:0000922") %>%
  45. select(Organ, `rdfs:label`)
  46. organ %>%
  47. write_csv(paste(datatables_path, "Organ.csv", sep = "/"), na = "")
  49. # MiRNA
  51. miRNA <- (read_lines(miRnome_path) %>%
  52. list(tibble(miRNAName = .[seq(1, length(.), 2)],
  53. sequence = .[seq(2, length(.), 2)])))[[2]] %>%
  54. mutate(miRNAName = str_replace(miRNAName, ">", "")) %>%
  55. #mutate(MiRNA = row_number()) %>%
  56. mutate(MiRNA = miRNAName) %>%
  57. select(MiRNA, sequence, miRNAName)
  58. miRNA
  59. miRNA %>%
  60. write_csv(paste(datatables_path, "MiRNA.csv", sep = "/"), na = "")
  62. # MiRNAOrigin
  63. miRNAOrigin <- read_tsv(paste(data_path, "average_count_by_tissue.tsv", sep = "/")) %>%
  64. dplyr::rename(`referenceLevelOf@MiRNA` = omy_miRNA) %>%
  65. pivot_longer(-`referenceLevelOf@MiRNA`, names_to = "organName", values_to = "referenceLevel") %>%
  66. mutate(organName = str_to_lower(organName)) %>%
  67. left_join(organ, by = c("organName" = "rdfs:label")) %>%
  68. dplyr::rename(`referenceLevelFrom@Organ` = Organ) %>%
  69. left_join(select(miRNA, MiRNA, miRNAName), by = c("referenceLevelOf@MiRNA" = "miRNAName")) %>%
  70. mutate(`referenceLevelOf@MiRNA` = MiRNA) %>%
  71. mutate(MiRNAOrigin = row_number()) %>%
  72. select(MiRNAOrigin, `referenceLevelOf@MiRNA`, referenceLevel, `referenceLevelFrom@Organ`)
  73. miRNAOrigin
  74. miRNAOrigin %>%
  75. write_csv(paste(datatables_path, "MiRNAOrigin.csv", sep = "/"), na = "")
  77. # Project
  78. project <- read_excel(paste(data_path, "biosample_attributes_extended.xlsx", sep = "/")) %>%
  79. select(projectName) %>%
  80. dplyr::distinct() %>%
  81. mutate(Project = projectName) %>%
  82. select(Project, projectName)
  83. project %>%
  84. write_csv(paste(datatables_path, "Project.csv", sep = "/"), na = "")
  86. # ExperimentalCondition
  87. experimentalCondition <- read_excel(paste(data_path, "biosample_attributes_extended.xlsx", sep = "/")) %>%
  88. select(projectName, description) %>%
  89. tidyr::separate(description, into = c("c1", "c2", "c3", "c4"), sep ="-", remove = F) %>%
  90. pivot_longer(cols = c("description", "c1", "c2", "c3", "c4"), names_to = "conditionGroup", values_to = "description") %>%
  91. mutate(description = str_trim(description, side = "both")) %>%
  92. na.omit() %>%
  93. filter(conditionGroup != "description" | grepl("-",description)) %>% #remove "description" conditionGroup if only one conditionGroup
  94. distinct() %>%
  95. mutate(conditionGroup = paste(projectName, conditionGroup) %>% as_factor %>% as.numeric()) %>%
  96. dplyr::rename(`conditionOf@Project` = projectName) %>%
  97. mutate(conditionType = case_when(
  100. description == "ovarian fluid" ~ "fluid",
  101. description == "plasma" ~ "fluid",
  102. description == "mucus" ~ "fluid",
  103. description == "pool of miRNA from mucus" ~ "fluid",
  104. description == "pool of miRNA from seminal fluid" ~ "fluid",
  105. description == "seminal fluid" ~ "fluid",
  107. description == "not stripped female" ~ "stripping",
  108. description == "stripped female" ~ "stripping",
  110. description == "control genetic line" ~ "genetic line",
  111. description == "selected genetic line" ~ "genetic line",
  112. description == "B57strain" ~ "genetic line",
  113. description == "AP2strain" ~ "genetic line",
  114. description == "A36strain" ~ "genetic line",
  116. description == "previtellogenesis" ~ "lifestage",
  117. description == "early vitellogenesis stage" ~ "lifestage",
  118. description == "mid vitellogenesis stage" ~ "lifestage",
  119. description == "late vitellogenesis stage" ~ "lifestage",
  120. description == "immature" ~ "lifestage",
  121. description == "mature" ~ "lifestage",
  122. description == "preovulated or prespermiant" ~ "lifestage",
  123. description == "ovulation" ~ "lifestage",
  124. description == "day of ovulation" ~ "lifestage",
  125. description == "21 days after ovulation" ~ "lifestage",
  126. description == "sampling days of ovulation" ~ "lifestage",
  127. description == "sampling 9 weeks after ovulation" ~ "lifestage",
  128. description == "sampling 18 weeks after ovulation" ~ "lifestage",
  130. description == "fish vaccinated twice against IPN virus" ~ "health",
  131. description == "control fish not infected" ~ "health",
  132. description == "vaccinated fish infected with VSHV virus" ~ "health",
  133. description == "fish infected with flavobacteria" ~ "health",
  134. description == "fish not infected control for flavobacteria" ~ "health",
  135. description == "fish not infected control for VHS" ~ "health",
  136. description == "fish infected with VSHV virus" ~ "health",
  138. description == "female" ~ "sex",
  139. description == "male" ~ "sex",
  141. description == "fish reared in enriched environment during 185 days" ~ "environment",
  142. description == "fish reared in non enriched environment during 185 days" ~ "environment",
  144. description == "male raised at 16°C for 8 months until they are spermiant" ~ "temperature",
  145. description == "male raised at 12°C for 8 months until they are spermiant" ~ "temperature",
  147. description == "fish reared in normoxia environment" ~ "oxygen",
  148. description == "fish reared in hypoxia environment" ~ "oxygen",
  150. description == "vegetal+yeast+insect+transformed animal proteins diet" ~ "nutrition",
  151. description == "commercial diet (fish meal+fish oil)" ~ "nutrition",
  152. description == "vegetal+yeast+insect diet" ~ "nutrition",
  153. description == "vegetal diet" ~ "nutrition",
  154. description == "commercial diet" ~ "nutrition",
  155. description == "vegetable diet" ~ "nutrition",
  156. description == "vegetable+microalgae diet" ~ "nutrition",
  157. description == "fingerling mother fed commercial diet" ~ "nutrition",
  158. description == "fingerling mother fed vegetable+microalgae diet" ~ "nutrition",
  159. description == "fingerling mother fed vegetable diet" ~ "nutrition",
  160. description == "challenged fish fed diet without carbohydrates at first feeding during 4 weeks" ~ "nutrition",
  161. description == "challenged fish fed diet without carbohydrate every other day at first feeding during 4 weeks" ~ "nutrition",
  162. description == "challenged fish fed diet with carbohydrates at first feeding during 4 weeks" ~ "nutrition",
  163. description == "fish fed with diet rich in carbohydrate during 4 weeks" ~ "nutrition",
  164. description == "fish fed with diet without carbohydrate during 4 weeks" ~ "nutrition",
  165. description == "classical feeding rate" ~ "nutrition",
  166. description == "restricted feeding rate" ~ "nutrition",
  167. description == "female fed adlibitum 5 months before ovulation" ~ "nutrition",
  168. description == "female fed at 80% of adlibitum (restricted) 5 months before ovulation" ~ "nutrition",
  170. description == "depigmented" ~ "flesh color",
  171. description == "pigmented" ~ "flesh color"
  172. )) %>%
  173. left_join(project %>% select(Project, projectName), by = c('conditionOf@Project' = 'projectName')) %>%
  174. mutate(`conditionOf@Project` = Project) %>%
  175. mutate(ExperimentalCondition = row_number()) %>%
  176. select(ExperimentalCondition, `conditionOf@Project`,
  177. conditionGroup,
  178. conditionType, description) #%>%
  179. #mutate(`isASubsetOf@ExperimentalCondition`)
  180. experimentalCondition
  181. #experimentalCondition %>%
  182. # write_csv(paste(datatables_path, "ExperimentalCondition.csv", sep = "/"), na = "")
  184. subsetsOfExperimentalCondition <- experimentalCondition %>%
  185. mutate(isASubset = grepl("-", description)) %>%
  186. tidyr::separate(description, into = c("c1", "c2", "c3", "c4"), sep ="-", remove = F) %>%
  187. pivot_longer(cols = c(c1, c2, c3, c4), values_drop_na = T) %>%
  188. select(-name) %>%
  189. mutate(value = if_else(isASubset, value, NA_character_)) %>%
  190. dplyr::rename(isASubsetOf = value) %>%
  191. select(ExperimentalCondition, `conditionOf@Project`, isASubsetOf) %>%
  192. left_join(experimentalCondition, by = c("isASubsetOf" = "description", "conditionOf@Project")) %>%
  193. select(ExperimentalCondition.x, ExperimentalCondition.y) %>%
  194. dplyr::rename(ExperimentalCondition = ExperimentalCondition.x) %>%
  195. dplyr::rename(`isASubsetOf@ExperimentalCondition` = ExperimentalCondition.y) %>%
  196. na.omit()
  198. subsetsOfExperimentalCondition
  199. #subsetsOfExperimentalCondition %>%
  200. # write_csv(paste(datatables_path, "SubsetOfExperimentalCondition.csv", sep = "/"), na = "")
  202. # Fish
  204. fish <- read_excel(paste(data_path, "biosample_attributes_extended.xlsx", sep = "/")) %>%
  205. select(sample_name, breedName, strain) %>%
  206. mutate(`organism@Organism` = 8022) %>%
  207. dplyr::rename(bioSampleName = sample_name) %>%
  208. tidyr::nest(names = bioSampleName) %>%
  209. mutate(Fish = row_number()) %>%
  210. tidyr::unnest(names) %>%
  211. select(Fish, `organism@Organism`, breedName, strain, bioSampleName)
  213. # Biosample
  215. bioSample <- read_excel(paste(data_path, "biosample_attributes_extended.xlsx", sep = "/")) %>%
  216. dplyr::select(sample_name, sameFishAs, tissue, ageInWeeks, lifeStage, reproductionStage, sex, weightInGrams, dietType,
  217. K, HSI, VSI, GSI, glucose, triglyceride, AATotal, prot, freeFattyAcid) %>%
  218. dplyr::rename(bioSampleName = sample_name) %>%
  219. left_join(select(organ, Organ, `rdfs:label`), by = c("tissue" = "rdfs:label")) %>%
  220. mutate(`sampledFluid@Organ` = Organ) %>%
  221. left_join(select(fish, Fish, bioSampleName), by = "bioSampleName") %>%
  222. dplyr::mutate(`sampledIn@Fish` = Fish) %>%
  223. dplyr::mutate(BioSample = row_number()) %>%
  224. select(BioSample, bioSampleName, sameFishAs, `sampledIn@Fish`, `sampledFluid@Organ`, ageInWeeks, lifeStage, reproductionStage,
  225. sex, weightInGrams, dietType, K, HSI, VSI, GSI, glucose, triglyceride, AATotal, prot, freeFattyAcid)
  227. fish <- fish %>%
  228. select(-bioSampleName) %>%
  229. distinct()
  231. fish
  232. fish %>%
  233. write_csv(paste(datatables_path, "Fish.csv", sep = "/"), na = "")
  234. bioSample
  235. bioSample %>%
  236. write_csv(paste(datatables_path, "BioSample.csv", sep = "/"), na = "")
  238. # link ExperimentalCondition and BioSample
  240. link_ExperimentalCondition_BioSample <- read_excel(paste(data_path, "biosample_attributes_extended.xlsx", sep = "/")) %>%
  241. select(sample_name, projectName, description) %>%
  242. #tidyr::separate_rows(description, sep = "-") %>%
  243. tidyr::separate(description, into = c("c1", "c2", "c3", "c4"), sep ="-", remove = F) %>%
  244. pivot_longer(cols = c("description", "c1", "c2", "c3", "c4"), names_to = "conditionGroup", values_to = "description") %>%
  245. na.omit() %>%
  246. mutate(description = str_trim(description, side = "both")) %>%
  247. na.omit() %>%
  248. filter(conditionGroup != "description" | grepl("-",description)) %>% #remove "description" conditionGroup if only one conditionGroup
  249. distinct() %>%
  250. left_join(select(project, Project, projectName), by = c("projectName" = "projectName")) %>%
  251. left_join(experimentalCondition, by = c("Project" = "conditionOf@Project", "description")) %>%
  252. left_join(bioSample, by = c("sample_name" = "bioSampleName")) %>%
  253. dplyr::rename(`isPartOf@ExperimentalCondition` = ExperimentalCondition) %>%
  254. select(BioSample, `isPartOf@ExperimentalCondition`)
  255. link_ExperimentalCondition_BioSample
  256. #link_ExperimentalCondition_BioSample %>%
  257. # write_csv(paste(datatables_path, "link_ExperimentalCondition_Sample.csv", sep = "/"), na = "")
  259. # MiRNAExpression
  261. #all_counts <- load_prost_compressed_by_annotation("~/Documents/phenomir/prost_postprocess/prost_3/sample_all_compressed_by_annotation.tsv")
  262. #saveRDS(object = all_counts, file = "all_miRNA_counts.RDS")
  263. miRNAExpression <- readRDS(paste(data_path, "all_miRNA_counts.RDS", sep = "/")) %>%
  264. select(omy_miRNA, where(is.numeric)) %>%
  265. pivot_longer(-omy_miRNA) %>%
  266. mutate(name = str_remove(name, "_cutadapt")) %>%
  267. mutate(name = str_remove(name, "_final_trimming")) %>%
  268. separate(name, into = c("measuredIn@BioSample", "norm"), sep = "_nor") %>%
  269. left_join(bioSample, by = c("measuredIn@BioSample" = "bioSampleName")) %>%
  270. mutate(`measuredIn@BioSample` = BioSample) %>% select(-BioSample) %>%
  271. mutate(norm = if_else(!is.na(norm), "rawCount", "rpm")) %>%
  272. pivot_wider(names_from = norm, values_from = value) %>%
  273. left_join(select(miRNA, MiRNA, miRNAName), by = c("omy_miRNA"="miRNAName")) %>%
  274. dplyr::rename(`miRNA@MiRNA` = MiRNA) %>%
  275. mutate(MiRNAExpression = row_number()) %>%
  276. select(MiRNAExpression, `miRNA@MiRNA`, `measuredIn@BioSample`,
  277. rawCount, rpm)
  278. miRNAExpression
  279. miRNAExpression %>%
  280. write_csv(paste(datatables_path, "miRNAExpression.csv", sep = "/"), na = "")
  282. # DifferentialAnalysis
  284. differentialAnalysis <- list.files(path = paste(data_path, "miRDE", sep = "/"), pattern = "*.RDS", full.names = T) %>%
  285. purrr::map_dfr(function(x) {readRDS(x) %>% as_tibble(rownames = "concernsMiRNA@MiRNA") %>%
  286. mutate(filename = base::basename(x))}) %>%
  287. left_join(select(miRNA, MiRNA, miRNAName), by = c("concernsMiRNA@MiRNA" = "miRNAName")) %>%
  288. mutate(`concernsMiRNA@MiRNA` = MiRNA) %>%
  289. mutate(DifferentialAnalysis = row_number()) %>%
  290. select(DifferentialAnalysis, `concernsMiRNA@MiRNA`,
  291. baseMean, log2FoldChange, lfcSE, padj, filename) %>%
  292. mutate(link_ExperimentalCondition = case_when(
  293. filename == "ne2_geniteur_time_11sem_0sem.RDS"~ "PROJECT:nutriegg2 female broodstockCONTROL:early vitellogenesis stageTREATMENT:mid vitellogenesis stage",
  294. filename == "ne2_geniteur_time_16sem_11sem.RDS"~ "PROJECT:nutriegg2 female broodstockCONTROL:mid vitellogenesis stageTREATMENT:late vitellogenesis stage",
  295. filename == "ne2_reprog_mother_origin_MA_vs_C.RDS"~ "PROJECT:nutriegg2 maternal nutritional reprogramationCONTROL:fingerling mother fed commercial dietTREATMENT:fingerling mother fed vegetable+microalgae diet",
  296. filename == "ne2_reprog_mother_origin_V_vs_C.RDS"~ "PROJECT:nutriegg2 maternal nutritional reprogramationCONTROL:fingerling mother fed commercial dietTREATMENT:fingerling mother fed vegetable diet",
  297. filename == "ninaqua_fl_diet_PA_vs_CO.RDS"~ "PROJECT:ninaqua FLCONTROL:commercial diet (fish meal+fish oil)TREATMENT:vegetal+yeast+insect+transformed animal proteins diet",
  298. filename == "ninaqua_fl_diet_V1_vs_CO.RDS"~ "PROJECT:ninaqua FLCONTROL:commercial diet (fish meal+fish oil)TREATMENT:vegetal diet",
  299. filename == "ninaqua_fl_diet_V2_vs_CO.RDS"~ "PROJECT:ninaqua FLCONTROL:commercial diet (fish meal+fish oil)TREATMENT:vegetal+yeast+insect diet",
  300. filename == "ninaqua_fl_lignee_T_vs_S.RDS"~ "PROJECT:ninaqua FLCONTROL:selected genetic lineTREATMENT:control genetic line",
  301. filename == "ninaqua_ss_diet_PA_vs_CO.RDS"~ "PROJECT:ninaqua SSCONTROL:commercial diet (fish meal+fish oil)TREATMENT:vegetal+yeast+insect+transformed animal proteins diet",
  302. filename == "ninaqua_ss_diet_V1_vs_CO.RDS"~ "PROJECT:ninaqua SSCONTROL:commercial diet (fish meal+fish oil)TREATMENT:vegetal diet",
  303. filename == "ninaqua_ss_diet_V2_vs_CO.RDS"~ "PROJECT:ninaqua SSCONTROL:commercial diet (fish meal+fish oil)TREATMENT:vegetal+yeast+insect diet",
  304. filename == "ninaqua_ss_lignee_T_vs_S.RDS"~ "PROJECT:ninaqua SSCONTROL:selected genetic lineTREATMENT:control genetic line",
  305. filename == "progrest_diet_HPR_vs_HP.RDS"~ "PROJECT:progrestCONTROL:challenged fish fed diet without carbohydrates at first feeding during 4 weeksTREATMENT:challenged fish fed diet without carbohydrate every other day at first feeding during 4 weeks",
  306. filename == "progrest_diet_LP_vs_HP.RDS"~ "PROJECT:progrestCONTROL:challenged fish fed diet without carbohydrates at first feeding during 4 weeksTREATMENT:challenged fish fed diet with carbohydrates at first feeding during 4 weeks",
  307. filename == "vim_treatment_IPNV_vs_Control.RDS"~ "PROJECT:VIMCONTROL:control fish not infectedTREATMENT:fish vaccinated twice against IPN virus",
  308. filename == "vim_treatment_VSHV_vs_Control.RDS"~ "PROJECT:VIMCONTROL:control fish not infectedTREATMENT:vaccinated fish infected with VSHV virus",
  310. filename == "eggpreserve_lc_J0_stripping_strippees_vs_non_strippees.RDS"~ "PROJECT:eggpreserveCONTROL:ovarian fluid-not stripped female-day of ovulationTREATMENT:ovarian fluid-stripped female-day of ovulation",
  311. filename == "eggpreserve_lc_non_strippees_time_J21_vs_J0.RDS"~ "PROJECT:eggpreserveCONTROL:ovarian fluid-not stripped female-day of ovulationTREATMENT:ovarian fluid-not stripped female-21 days after ovulation",
  312. filename == "eggpreserve_plasma_J0_stripping_strippees_vs_non_strippees.RDS"~ "PROJECT:eggpreserveCONTROL:plasma-not stripped female-day of ovulationTREATMENT:plasma-stripped female-day of ovulation",
  313. filename == "eggpreserve_plasma_J21_stripping_strippees_vs_non_strippees.RDS"~ "PROJECT:eggpreserveCONTROL:plasma-not stripped female-21 days after ovulationTREATMENT:plasma-stripped female-21 days after ovulation",
  314. filename == "eggpreserve_plasma_non_strippees_time_J21_vs_J0.RDS"~ "PROJECT:eggpreserveCONTROL:plasma-not stripped female-day of ovulationTREATMENT:plasma-not stripped female-21 days after ovulation",
  315. filename == "eggpreserve_plasma_strippees_time_J21_vs_J0.RDS"~ "PROJECT:eggpreserveCONTROL:plasma-stripped female-day of ovulationTREATMENT:plasma-stripped female-21 days after ovulation",
  317. filename == "sextiming_lifestage_male_immature_VS_male_premature.RDS"~ "PROJECT:SextimingCONTROL:immature-maleTREATMENT:preovulated or prespermiant-male",
  318. filename == "sextiming_lifestage_male_premature_VS_male_mature.RDS"~ "PROJECT:SextimingCONTROL:preovulated or prespermiant-maleTREATMENT:mature-male",
  319. filename == "sextiming_lifestage_female_immature_VS_female_premature.RDS"~ "PROJECT:SextimingCONTROL:immature-femaleTREATMENT:preovulated or prespermiant-female",
  320. filename == "sextiming_lifestage_female_premature_VS_female_mature.RDS"~ "PROJECT:SextimingCONTROL:preovulated or prespermiant-femaleTREATMENT:mature-female",
  321. filename == "sextiming_sex_female_immature_VS_male_immature.RDS"~ "PROJECT:SextimingCONTROL:immature-femaleTREATMENT:immature-male",
  322. filename == "sextiming_sex_female_premature_VS_male_premature.RDS"~ "PROJECT:SextimingCONTROL:preovulated or prespermiant-femaleTREATMENT:preovulated or prespermiant-male",
  323. filename == "sextiming_sex_female_mature_VS_male_mature.RDS"~ "PROJECT:SextimingCONTROL:mature-femaleTREATMENT:mature-male",
  325. filename == "hypox_plasma_hypoxia_no_carbo_vs_carbo.RDS"~ "PROJECT:HypoxCONTROL:plasma-fish reared in hypoxia environment-fish fed with diet without carbohydrate during 4 weeksTREATMENT:plasma-fish reared in hypoxia environment-fish fed with diet rich in carbohydrate during 4 weeks",
  326. filename == "hypox_plasma_normoxia_no_carbo_vs_carbo.RDS"~ "PROJECT:HypoxCONTROL:plasma-fish reared in normoxia environment-fish fed with diet without carbohydrate during 4 weeksTREATMENT:plasma-fish reared in normoxia environment-fish fed with diet rich in carbohydrate during 4 weeks",
  327. filename == "hypox_plasma_carbo_hypoxia_vs_normoxia.RDS"~ "PROJECT:HypoxCONTROL:plasma-fish reared in hypoxia environment-fish fed with diet rich in carbohydrate during 4 weeksTREATMENT:plasma-fish reared in normoxia environment-fish fed with diet rich in carbohydrate during 4 weeks",
  328. filename == "hypox_plasma_no_carbo_hypoxia_vs_normoxia.RDS"~ "PROJECT:HypoxCONTROL:plasma-fish reared in hypoxia environment-fish fed with diet without carbohydrate during 4 weeksTREATMENT:plasma-fish reared in normoxia environment-fish fed with diet without carbohydrate during 4 weeks",
  329. filename == "hypox_mucus_hypoxia_no_carbo_vs_carbo.RDS"~ "PROJECT:HypoxCONTROL:mucus-fish reared in hypoxia environment-fish fed with diet without carbohydrate during 4 weeksTREATMENT:mucus-fish reared in hypoxia environment-fish fed with diet rich in carbohydrate during 4 weeks",
  330. filename == "hypox_mucus_normoxia_no_carbo_vs_carbo.RDS"~ "PROJECT:HypoxCONTROL:mucus-fish reared in normoxia environment-fish fed with diet without carbohydrate during 4 weeksTREATMENT:mucus-fish reared in normoxia environment-fish fed with diet rich in carbohydrate during 4 weeks",
  331. filename == "hypox_mucus_carbo_hypoxia_vs_normoxia.RDS"~ "PROJECT:HypoxCONTROL:mucus-fish reared in hypoxia environment-fish fed with diet rich in carbohydrate during 4 weeksTREATMENT:mucus-fish reared in normoxia environment-fish fed with diet rich in carbohydrate during 4 weeks",
  332. filename == "hypox_mucus_no_carbo_hypoxia_vs_normoxia.RDS"~ "PROJECT:HypoxCONTROL:mucus-fish reared in hypoxia environment-fish fed with diet without carbohydrate during 4 weeksTREATMENT:mucus-fish reared in normoxia environment-fish fed with diet without carbohydrate during 4 weeks",
  334. filename == "heatmeth_plasma_temperature_16_vs_12.RDS"~ "PROJECT:HeatMethCONTROL:plasma-male raised at 16°C for 8 months until they are spermiantTREATMENT:plasma-male raised at 12°C for 8 months until they are spermiant",
  335. filename == "heatmeth_seminal_fluid_temperature_16_vs_12.RDS"~ "PROJECT:HeatMethCONTROL:seminal fluid-male raised at 16°C for 8 months until they are spermiantTREATMENT:seminal fluid-male raised at 12°C for 8 months until they are spermiant",
  337. filename == "vim_controled_line_treatment_control_vs_VSHV.RDS"~ "PROJECT:VIM with controled genetic lineCONTROL:fish not infected control for VHSTREATMENT:fish infected with VSHV virus",
  338. filename == "vim_controled_line_treatment_control_vs_flavobacteria.RDS"~ "PROJECT:VIM with controled genetic lineCONTROL:fish not infected control for flavobacteriaTREATMENT:fish infected with flavobacteria",
  339. filename == "vim_controled_line_line_AP2_vs_A36.RDS"~ "PROJECT:VIM with controled genetic lineCONTROL:AP2strainTREATMENT:A36strain",
  340. filename == "vim_controled_line_line_AP2_vs_B57.RDS"~ "PROJECT:VIM with controled genetic lineCONTROL:AP2strainTREATMENT:B57strain",
  342. filename == "bien_etre_condition_enriched_vs_non_enriched.RDS"~ "PROJECT:bien_etreCONTROL:fish reared in enriched environment during 185 daysTREATMENT:fish reared in non enriched environment during 185 days",
  344. filename == "qualipostov_plasma_color_pigmented_vs_depigmented.RDS" ~ "PROJECT:QualipostovCONTROL:plasma-female fed adlibitum 5 months before ovulation-sampling days of ovulation-pigmentedTREATMENT:plasma-female fed adlibitum 5 months before ovulation-sampling days of ovulation-depigmented",
  345. filename == "qualipostov_plasma_diet_adlibitum_vs_restricted.RDS" ~ "PROJECT:QualipostovCONTROL:plasma-female fed adlibitum 5 months before ovulation-sampling days of ovulation-pigmentedTREATMENT:plasma-female fed at 80% of adlibitum (restricted) 5 months before ovulation-sampling days of ovulation-pigmented",
  346. filename == "qualipostov_ovarian_fluid_diet_adlibitum_vs_restricted.RDS" ~ "PROJECT:QualipostovCONTROL:ovarian fluid-female fed adlibitum 5 months before ovulation-sampling days of ovulation-pigmentedTREATMENT:ovarian fluid-female fed at 80% of adlibitum (restricted) 5 months before ovulation-sampling days of ovulation-pigmented",
  347. filename == "qualipostov_plasma_date_9weeks_vs_18weeks.RDS" ~ "PROJECT:QualipostovCONTROL:plasma-female fed adlibitum 5 months before ovulation-sampling days of ovulation-pigmentedTREATMENT:plasma-female fed adlibitum 5 months before ovulation-sampling 9 weeks after ovulation-pigmented",
  348. filename == "qualipostov_plasma_date_ovulation_vs_9weeks.RDS" ~ "PROJECT:QualipostovCONTROL:plasma-female fed adlibitum 5 months before ovulation-sampling 9 weeks after ovulation-pigmentedTREATMENT:plasma-female fed adlibitum 5 months before ovulation-sampling 18 weeks after ovulation-pigmented",
  349. filename == "qualipostov_ovarian_fluid_color_pigmented_vs_depigmented.RDS" ~ "PROJECT:QualipostovCONTROL:ovarian fluid-female fed adlibitum 5 months before ovulation-sampling days of ovulation-pigmentedTREATMENT:ovarian fluid-female fed adlibitum 5 months before ovulation-sampling days of ovulation-depigmented",
  352. filename == "vdr_feeding_previtello.RDS" ~ "PROJECT:NutriEgg_VDRCONTROL:commercial diet-previtellogenesis-classical feeding rateTREATMENT:commercial diet-previtellogenesis-restricted feeding rate",
  353. filename == "vdr_feeding_earlyvitello.RDS" ~ "PROJECT:NutriEgg_VDRCONTROL:commercial diet-early vitellogenesis stage-classical feeding rateTREATMENT:commercial diet-early vitellogenesis stage-restricted feeding rate",
  354. filename == "vdr_feeding_midvitello.RDS" ~ "PROJECT:NutriEgg_VDRCONTROL:commercial diet-mid vitellogenesis stage-classical feeding rateTREATMENT:commercial diet-mid vitellogenesis stage-restricted feeding rate",
  355. filename == "vdr_feeding_latevitello.RDS" ~ "PROJECT:NutriEgg_VDRCONTROL:commercial diet-late vitellogenesis stage-classical feeding rateTREATMENT:commercial diet-late vitellogenesis stage-restricted feeding rate",
  356. filename == "vdr_feeding_postvitello.RDS" ~ "PROJECT:NutriEgg_VDRCONTROL:commercial diet-ovulation-classical feeding rateTREATMENT:commercial diet-ovulation-restricted feeding rate",
  357. filename == "vdr_diet_previtello.RDS" ~ "PROJECT:NutriEgg_VDRCONTROL:commercial diet-previtellogenesis-classical feeding rateTREATMENT:vegetable+microalgae diet-previtellogenesis-classical feeding rate",
  358. filename == "vdr_diet_earlyvitello.RDS" ~ "PROJECT:NutriEgg_VDRCONTROL:commercial diet-early vitellogenesis stage-classical feeding rateTREATMENT:vegetable+microalgae diet-early vitellogenesis stage-classical feeding rate",
  359. filename == "vdr_diet_midvitello.RDS" ~ "PROJECT:NutriEgg_VDRCONTROL:commercial diet-mid vitellogenesis stage-classical feeding rateTREATMENT:vegetable+microalgae diet-mid vitellogenesis stage-classical feeding rate",
  360. filename == "vdr_diet_latevitello.RDS" ~ "PROJECT:NutriEgg_VDRCONTROL:commercial diet-late vitellogenesis stage-classical feeding rateTREATMENT:vegetable+microalgae diet-late vitellogenesis stage-classical feeding rate",
  361. filename == "vdr_diet_postvitello.RDS" ~ "PROJECT:NutriEgg_VDRCONTROL:commercial diet-ovulation-classical feeding rateTREATMENT:vegetable+microalgae diet-ovulation-classical feeding rate"
  362. )) %>%
  363. tidyr::extract(link_ExperimentalCondition, into = c("projectName","control_description", "treatment_description"),
  364. regex = "PROJECT:(.+)CONTROL:(.+)TREATMENT:(.+)") %>%
  365. left_join(select(project, Project, projectName), by = "projectName") %>%
  366. select(-projectName) %>%
  367. dplyr::rename(`analysisOf@Project` = Project) %>%
  368. left_join(select(experimentalCondition, ExperimentalCondition, description, `conditionOf@Project`),
  369. by = c("control_description" = "description", "analysisOf@Project" = "conditionOf@Project")) %>%
  370. dplyr::rename(`controlCondition@ExperimentalCondition` = ExperimentalCondition) %>%
  371. left_join(select(experimentalCondition, ExperimentalCondition, description, `conditionOf@Project`),
  372. by = c("treatment_description" = "description", "analysisOf@Project" = "conditionOf@Project")) %>%
  373. dplyr::rename(`treatmentCondition@ExperimentalCondition` = ExperimentalCondition) %>%
  374. select(DifferentialAnalysis, `concernsMiRNA@MiRNA`, `analysisOf@Project`,
  375. `controlCondition@ExperimentalCondition`, `treatmentCondition@ExperimentalCondition`,
  376. baseMean, log2FoldChange, lfcSE, padj, filename)
  378. ## askoRCondition
  379. askoRCondition <- read_excel(paste(data_path, "biosample_attributes_extended.xlsx", sep = "/")) %>%
  380. select(projectName, description) %>%
  381. distinct %>%
  382. left_join(experimentalCondition, by = c("projectName" = "conditionOf@Project", "description")) %>%
  383. mutate(AskoRCondition = paste(projectName, "-", description)) %>%
  384. dplyr::rename(`sameConditionAs@ExperimentalCondition` = ExperimentalCondition) %>%
  385. dplyr::rename(`conditionOf@Project` = projectName) %>%
  386. select(AskoRCondition, `conditionOf@Project`, description ,`sameConditionAs@ExperimentalCondition`)
  388. link_AskoRCondition_BioSample <- read_excel(paste(data_path, "biosample_attributes_extended.xlsx", sep = "/")) %>%
  389. select(projectName, description, sample_name) %>%
  390. left_join(bioSample, by = c("sample_name" = "bioSampleName")) %>%
  391. left_join(askoRCondition, by = c("projectName"="conditionOf@Project", "description")) %>%
  392. select(BioSample, AskoRCondition) %>% dplyr::rename(`isPartOf@AskoRCondition` = AskoRCondition)
  394. ## askoRContext
  395. askoRContext <- differentialAnalysis %>%
  396. select(`controlCondition@ExperimentalCondition`, `treatmentCondition@ExperimentalCondition`) %>%
  397. pivot_longer(everything()) %>%
  398. select(value) %>%
  399. distinct() %>%
  400. left_join(subsetsOfExperimentalCondition,
  401. by = c("value" = "isASubsetOf@ExperimentalCondition")) %>%
  402. mutate(`has@Condition` = if_else(is.na(ExperimentalCondition), value, ExperimentalCondition)) %>%
  403. left_join(experimentalCondition, by = c("value" = "ExperimentalCondition")) %>%
  404. mutate(AskoRContext = paste(`conditionOf@Project`, "-", description)) %>%
  405. select(value, AskoRContext, `has@Condition`) %>%
  406. left_join(askoRCondition, by = c("has@Condition" = "sameConditionAs@ExperimentalCondition")) %>%
  407. dplyr::rename(`sameContextAs@ExperimentalCondition` = value) %>%
  408. dplyr::rename(`has@AskoRCondition` = AskoRCondition) %>%
  409. select(AskoRContext, `has@AskoRCondition`, `sameContextAs@ExperimentalCondition`)
  411. ## askoRContrast
  412. askoRContrast <- differentialAnalysis %>%
  413. select(`controlCondition@ExperimentalCondition`, `treatmentCondition@ExperimentalCondition`) %>%
  414. distinct() %>%
  415. left_join(askoRContext %>% select(`sameContextAs@ExperimentalCondition`, AskoRContext),
  416. by = c("controlCondition@ExperimentalCondition" = "sameContextAs@ExperimentalCondition")) %>%
  417. dplyr::rename(`context1_of@AskoRContext` = AskoRContext) %>%
  418. distinct() %>%
  419. left_join(askoRContext %>% select(`sameContextAs@ExperimentalCondition`, AskoRContext),
  420. by = c("treatmentCondition@ExperimentalCondition" = "sameContextAs@ExperimentalCondition")) %>%
  421. dplyr::rename(`context2_of@AskoRContext` = AskoRContext) %>%
  422. distinct() %>%
  423. mutate(AskoRContrast = paste0(`context1_of@AskoRContext`, "VS", `context2_of@AskoRContext`)) %>%
  424. select(AskoRContrast, `context1_of@AskoRContext`, `context2_of@AskoRContext`,
  425. `controlCondition@ExperimentalCondition`,`treatmentCondition@ExperimentalCondition`)
  427. ## askoRTest
  428. askoRTest <- differentialAnalysis %>% left_join(askoRContrast) %>%
  429. dplyr::rename(`fromContrast@AskoRContrast` = AskoRContrast) %>%
  430. dplyr::rename(`sameAnalysisAs@DifferentialAnalysis` = DifferentialAnalysis) %>%
  431. mutate(AskoRTest = row_number()) %>%
  432. mutate(FC = (log2FoldChange/abs(log2FoldChange))*2**(abs(log2FoldChange))) %>%
  433. mutate(logFC = log2FoldChange) %>%
  434. mutate(pvalue = padj) %>%
  435. mutate(expression = case_when(
  436. pvalue > 0.05 ~ paste0(`context1_of@AskoRContext`, "=", `context2_of@AskoRContext`),
  437. FC > 0 ~ paste0(`context1_of@AskoRContext`, ">", `context2_of@AskoRContext`),
  438. FC < 0 ~ paste0(`context1_of@AskoRContext`, "<", `context2_of@AskoRContext`)
  439. )) %>%
  440. mutate(significance = (pvalue <= 0.05) * (log2FoldChange)/(abs(log2FoldChange))) %>%
  441. mutate(significance = if_else(is.na(pvalue) | pvalue == 1, 0, significance)) %>%
  442. select(AskoRTest, `concernsMiRNA@MiRNA`, `fromContrast@AskoRContrast`, logFC, FC, pvalue, expression, significance, `sameAnalysisAs@DifferentialAnalysis`)
  444. askoRContrast <- askoRContrast %>% select(AskoRContrast, `context1_of@AskoRContext`, `context2_of@AskoRContext`)
  446. # askoRContrast %>%
  447. # pivot_longer(cols = c(`context1_of@AskoRContext`, `context2_of@AskoRContext`)) %>%
  448. # mutate(name = if_else(name == "context1_of@AskoRContext", "+", "-")) %>%
  449. # pivot_wider(names_from = value, values_from = name) %>%
  450. # write_csv(paste(datatables_path, "askoRContrastMatrix.csv", sep = "/"), na = "")
  452. askoRCondition %>% select(-`sameConditionAs@ExperimentalCondition`) %>% write_csv(paste(datatables_path, "askoRCondition.csv", sep = "/"), na = "")
  453. link_AskoRCondition_BioSample %>% write_csv(paste(datatables_path, "link_AskoRCondition_BioSample.csv", sep = "/"), na = "")
  454. askoRContext %>% select(-`sameContextAs@ExperimentalCondition`) %>% write_csv(paste(datatables_path, "askoRContext.csv", sep = "/"), na = "")
  455. askoRContrast %>% write_csv(paste(datatables_path, "askoRContrast.csv", sep = "/"), na = "")
  456. askoRTest %>% select(-`sameAnalysisAs@DifferentialAnalysis`) %>% mutate(significance = as.character(significance)) %>% write_csv(paste(datatables_path, "askoRTest.csv", sep = "/"), na = "")

create_datatables_askoR.R at commit 6475dca, no license · at the source

Overview

Authors: Mariana Roza de Abreu1, Emilie Cardona1,2, Camille Lagarde1, Leo Milhade3, Goro Yoshizaki4, Violette Thermes1, Julien Bobe1
ORCID iDs: Julien Bobe
  1. INRAE, LPGP, Rennes, 35000 France
  2. INRAE, Univ. Pau & Pays Adour, E2S UPPA, NUMEA, Saint-Pée-Sur-Nivelle, 64310 France
  3. IRISA, INRIA, CNRS, Université de Rennes 1, Rennes, 35000 France
  4. Tokyo University of Marine Science and Technology, Tokyo, Japan
Institutions: Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (France); Laboratoire de Physiologie et Génomique des Poissons (France); Université de Pau et des Pays de l'Adour (France); Nutrition Metabolism Aquaculture (France); Centre National de la Recherche Scientifique (France); Institut national de recherche en sciences et technologies du numérique (France); Institut de Recherche en Informatique et Systèmes Aléatoires (France); Université Rennes 1 (France); Université de Rennes (France); Tokyo University of Marine Science and Technology (Japan)
Journal: BMC biology, volume 24, issue 1, article 166
Dates: received 5 December 2025; accepted 14 May 2026; published online 21 May 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1186/s12915-026-02643-2 · PMID 42168984 · PMCID PMC13374286 · OpenAlex W7161976911
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: other (organism), cellular / molecular (subfield)
Methods: Statistics, Smoothing, state filtering, decompositions, Machine learning, Preprocessing
Keywords: Biomarker, Egg quality, MiR-139, MiR-202, MiR-457a, MiR-135c, Iteroparity
MeSH: Brain*, Circulating MicroRNA*, MicroRNAs*, Oncorhynchus mykiss*, Ovum*, Reproduction*, Animals, Female, Ovary (* major topic)
Topic: Reproductive biology and impacts on aquatic species (Physiology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: European Regional Development Fund (817923); Agence Nationale de la Recherche (ANR-16-CE20-0001); Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
Citations: not cited yet (Europe PMC); 43 references in the paper

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repository

Its files are read in the Code ↔ Paper reader above, with 3 matches between paragraphs and lines of code.

INRAE-LPGP/phenomir

License: none: the authors keep all their rights
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Commit: 6475dca11d0e4e79a6595dc454230906b575468a, 10 April 2023
Languages: R (39), JavaScript (12), Python (1), Shell (1)
Size: 268 files, 53 scripts
Software Heritage: not archived
Found in: “Data availability”
Holds: README, environment (prost/environment.yml), 18 notebooks
Not found: license file, CITATION.cff, tests, continuous integration, documentation
Tools: tidyverse (35 files), DESeq2 (19 files), ggplot2 (16 files), ggpubr (2 files), Nextflow (1 file), pheatmap (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers
  • 28 September 2026: the link answers
54 files
At the source: github.com/INRAE-LPGP/phenomir

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 53 scripts, each with its path and the digest of its content;
  • 3 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

Datasets cited

Code and data availability statement

The paper has a code and data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

Read it in the paper: doi.org/10.1186/s12915-026-02643-2.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 2, 28 September 2026

  • Funding: added European Commission: 817923; Agence Nationale de la Recherche: ANR-16-CE20-0001; Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement

Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 7 authors, 7 keywords, 9 MeSH terms, 40 references.

Cite

This paper

Roza de Abreu, M., Cardona, E., Lagarde, C., Milhade, L., Yoshizaki, G., Thermes, V., & Bobe, J. (2026). Circulating microRNAs reveal egg-brain crosstalk and a brain-predominant microRNA linked to the onset of the next reproductive cycle in iteroparous salmonids. BMC biology, 24(1), 166. https://doi.org/10.1186/s12915-026-02643-2

BibTeX

@article{rozadeabreu2026circulating,
author = {Roza de Abreu, Mariana and Cardona, Emilie and Lagarde, Camille and Milhade, Leo and Yoshizaki, Goro and Thermes, Violette and Bobe, Julien},
title = {{Circulating microRNAs reveal egg-brain crosstalk and a brain-predominant microRNA linked to the onset of the next reproductive cycle in iteroparous salmonids}},
journal = {BMC biology},
year = {2026},
month = may,
volume = {24},
number = {1},
pages = {166},
publisher = {BMC},
issn = {1741-7007},
doi = {10.1186/s12915-026-02643-2},
url = {https://doi.org/10.1186/s12915-026-02643-2},
pmid = {42168984},
pmcid = {PMC13374286}
}

RIS

TY - JOUR
AU - Roza de Abreu, Mariana
AU - Cardona, Emilie
AU - Lagarde, Camille
AU - Milhade, Leo
AU - Yoshizaki, Goro
AU - Thermes, Violette
AU - Bobe, Julien
TI - Circulating microRNAs reveal egg-brain crosstalk and a brain-predominant microRNA linked to the onset of the next reproductive cycle in iteroparous salmonids
T2 - BMC biology
J2 - BMC Biol
PY - 2026
DA - 2026/05/21
VL - 24
IS - 1
SP - 166
SN - 1741-7007
PB - BMC
DO - 10.1186/s12915-026-02643-2
UR - https://doi.org/10.1186/s12915-026-02643-2
LA - en
ER -

CSL-JSON

{
"id": "10.1186/s12915-026-02643-2",
"type": "article-journal",
"title": "Circulating microRNAs reveal egg-brain crosstalk and a brain-predominant microRNA linked to the onset of the next reproductive cycle in iteroparous salmonids",
"container-title": "BMC biology",
"author": [
{
"family": "Roza de Abreu",
"given": "Mariana"
},
{
"family": "Cardona",
"given": "Emilie"
},
{
"family": "Lagarde",
"given": "Camille"
},
{
"family": "Milhade",
"given": "Leo"
},
{
"family": "Yoshizaki",
"given": "Goro"
},
{
"family": "Thermes",
"given": "Violette"
},
{
"family": "Bobe",
"given": "Julien"
}
],
"container-title-short": "BMC Biol",
"volume": "24",
"issue": "1",
"page": "166",
"DOI": "10.1186/s12915-026-02643-2",
"PMID": "42168984",
"PMCID": "PMC13374286",
"ISSN": "1741-7007",
"publisher": "BMC",
"URL": "https://doi.org/10.1186/s12915-026-02643-2",
"language": "en",
"issued": {
"date-parts": [
[
2026,
5,
21
]
]
}
}

The tracing map gets a citation of its own once an author has validated it and it has a DOI.

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