Developmental manganese exposure, but not concurrent lead, alters social processing selectively in male mice.
Paper
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The authors' code
Shell · 10 lines · 295 B · MIT
- # usage:
- # extractSJfromGTF.sh in.gtf > out.sj
- #
- # assumes transcript_id in the 12th field of GTF
- #
- awk '$3=="exon" {print $12,$1,$4,$5,$7}' $1 |\
- sort -k1,1V -k2,2V -k3,3n |\
- awk 'BEGIN {OFS="\t"} {if (t==$1) {print $2,e1+1,$3-1,$5}; e1=$4;t=$1 }' |\
- sort -k1,1V -k2,2n -k3,3n -k4,4 | uniq
extractSJfromGTF.sh at commit b1edc12, under MIT · at the source
Overview
- Centre for Behavioral Sciences and Mental Health, Istituto Superiore di Sanità, Rome, Italy
- Department of Physiology and Pharmacology “Vittorio Erspamer”, Sapienza Università di Roma, Rome, Italy
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
- Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania, Italy
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.
alexdobin/STAR
b1edc1208d91a53bf40ebae8669f71d50b994851, 25 January 2024Availability: 1 check, the latest on 27 September 2026: the link answers
- 27 September 2026: the link answers
331 files
- extras/
scripts/ , Shell, 10 linesextractSJfromGTF.sh - extras/
scripts/ , MATLAB, 45 linessjMotif.m - source/
AlignVsTranscript.h , C/C++, 9 lines - source/
BAMbinSortByCoordinate.c , C++, 81 linespp - source/
BAMbinSortByCoordinate.h , C/C++, 12 lines - source/
BAMbinSortUnmapped.cpp , C++, 91 lines - source/
BAMbinSortUnmapped.h , C/C++, 12 lines - source/
BAMfunctions.cpp , C++, 194 lines - source/
BAMfunctions.h , C/C++, 79 lines - source/
BAMoutput.cpp , C++, 186 lines - source/
BAMoutput.h , C/C++, 37 lines - source/
Chain.cpp , C++, 126 lines - source/
Chain.h , C/C++, 30 lines - source/
ChimericAlign.cpp , C++, 32 lines - source/
ChimericAlign.h , C/C++, 41 lines - source/
ChimericAlign_chimericBA , C++, 105 linesMoutput.cpp - source/
ChimericAlign_chimericJu , C++, 23 linesnctionOutput.cpp - source/
ChimericAlign_chimericSt , C++, 181 linesitching.cpp - source/
ChimericDetection.cpp , C++, 6 lines - source/
ChimericDetection.h , C/C++, 29 lines - source/
ChimericDetection_chimer , C++, 138 linesicDetectionMult.cpp - source/
ChimericSegment.cpp , C++, 32 lines - source/
ChimericSegment.h , C/C++, 23 lines - source/
ChimericTranscript.h , C/C++, 19 lines - source/
ClipCR4.cpp , C++, 109 lines - source/
ClipCR4.h , C/C++, 41 lines - source/
ClipMate.h , C/C++, 34 lines - source/
ClipMate_clip.cpp , C++, 78 lines - source/
ClipMate_clipChunk.cpp , C++, 62 lines - source/
ClipMate_initialize.cpp , C++, 32 lines - source/
ErrorWarning.cpp , C++, 37 lines - source/
ErrorWarning.h , C/C++, 9 lines - source/
GTF.cpp , C++, 171 lines - source/
GTF.h , C/C++, 36 lines - source/
GTF_superTranscript.cpp , C++, 257 lines - source/
GTF_transcriptGeneSJ.cpp , C++, 183 lines - source/
Genome.cpp , C++, 234 lines - source/
Genome.h , C/C++, 107 lines - source/
Genome_genomeGenerate.cp , C++, 438 linesp - source/
Genome_genomeLoad.cpp , C++, 521 lines - source/
Genome_genomeOutLoad.cpp , C++, 58 lines - source/
Genome_insertSequences.c , C++, 33 linespp - source/
Genome_transformGenome.c , C++, 324 linespp - source/
GlobalVariables.cpp , C++, 4 lines - source/
GlobalVariables.h , C/C++, 9 lines - source/
InOutStreams.cpp , C++, 44 lines - source/
InOutStreams.h , C/C++, 23 lines - source/
IncludeDefine.h , C/C++, 255 lines - source/
OutSJ.cpp , C++, 123 lines - source/
OutSJ.h , C/C++, 59 lines - source/
PackedArray.cpp , C++, 43 lines - source/
PackedArray.h , C/C++, 34 lines - source/
ParameterInfo.h , C/C++, 112 lines - source/
Parameters.cpp , C++, 1,269 lines - source/
Parameters.h , C/C++, 374 lines - source/
ParametersChimeric.h , C/C++, 41 lines - source/
ParametersChimeric_initi , C++, 118 linesalize.cpp - source/
ParametersClip.h , C/C++, 37 lines - source/
ParametersClip_initializ , C++, 107 linese.cpp - source/
ParametersGenome.cpp , C++, 59 lines - source/
ParametersGenome.h , C/C++, 63 lines - source/
ParametersSolo.cpp , C++, 721 lines - source/
ParametersSolo.h , C/C++, 220 lines - source/
Parameters_closeReadsFil , C++, 12 lineses.cpp - source/
Parameters_openReadsFile , C++, 111 liness.cpp - source/
Parameters_readFilesInit , C++, 167 lines.cpp - source/
Parameters_readSAMheader , C++, 44 lines.cpp - source/
Parameters_samAttributes , C++, 263 lines.cpp - source/
Quantifications.cpp , C++, 37 lines - source/
Quantifications.h , C/C++, 22 lines - source/
ReadAlign.cpp , C++, 125 lines - source/
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ReadAlignChunk_processCh , C++, 302 linesunks.cpp - source/
ReadAlign_CIGAR.cpp , C++, 62 lines - source/
ReadAlign_alignBAM.cpp , C++, 614 lines - source/
ReadAlign_assignAlignToW , C++, 130 linesindow.cpp - source/
ReadAlign_calcCIGAR.cpp , C++, 58 lines - source/
ReadAlign_chimericDetect , C++, 57 linesion.cpp - source/
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ReadAlign_chimericDetect , C++, 74 linesionOldOutput.cpp - source/
ReadAlign_chimericDetect , C++, 39 linesionPEmerged.cpp - source/
ReadAlign_createExtendWi , C++, 85 linesndowsWithAlign.cpp - source/
ReadAlign_mapOneRead.cpp , C++, 118 lines - source/
ReadAlign_mapOneReadSpli , C++, 40 linesceGraph.cpp - source/
ReadAlign_mappedFilter.c , C++, 21 linespp - source/
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ReadAlign_oneRead.cpp , C++, 124 lines - source/
ReadAlign_outputAlignmen , C++, 325 linests.cpp - source/
ReadAlign_outputSpliceGr , C++, 164 linesaphSAM.cpp - source/
ReadAlign_outputTranscri , C++, 65 linesptCIGARp.cpp - source/
ReadAlign_outputTranscri , C++, 359 linesptSAM.cpp - source/
ReadAlign_outputTranscri , C++, 56 linesptSJ.cpp - source/
ReadAlign_outputVariatio , C++, 13 linesn.cpp - source/
ReadAlign_peOverlapMerge , C++, 368 linesMap.cpp - source/
ReadAlign_quantTranscrip , C++, 91 linestome.cpp - source/
ReadAlign_stitchPieces.c , C++, 350 linespp - source/
ReadAlign_stitchWindowSe , C++, 278 lineseds.cpp - source/
ReadAlign_storeAligns.cp , C++, 160 linesp - source/
ReadAlign_transformGenom , C++, 74 linese.cpp - source/
ReadAlign_waspMap.cpp , C++, 128 lines - source/
ReadAnnotations.h , C/C++, 47 lines - source/
STAR.cpp , C++, 313 lines - source/
SequenceFuns.cpp , C++, 445 lines - source/
SequenceFuns.h , C/C++, 32 lines - source/
SharedMemory.cpp , C++, 291 lines - source/
SharedMemory.h , C/C++, 182 lines - source/
SimpleGoodTuring/ , C/C++, 300 linessgt.h - source/
SjdbClass.h , C/C++, 17 lines - source/
Solo.cpp , C++, 91 lines - source/
Solo.h , C/C++, 30 lines - source/
SoloBarcode.cpp , C++, 152 lines - source/
SoloBarcode.h , C/C++, 38 lines - source/
SoloBarcode_extractBarco , C++, 34 linesde.cpp - source/
SoloCommon.h , C/C++, 80 lines - source/
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SoloFeatureTypes.h , C/C++, 12 lines - source/
SoloFeature_addBAMtags.c , C++, 26 linespp - source/
SoloFeature_cellFilterin , C++, 131 linesg.cpp - source/
SoloFeature_collapseUMI_ , C++, 172 linesGraph.cpp - source/
SoloFeature_collapseUMIa , C++, 658 linesll.cpp - source/
SoloFeature_countCBgeneU , C++, 112 linesMI.cpp - source/
SoloFeature_countSmartSe , C++, 159 linesq.cpp - source/
SoloFeature_countVelocyt , C++, 166 lineso.cpp - source/
SoloFeature_emptyDrops_C , C++, 231 linesR.cpp - source/
SoloFeature_loadRawMatri , C++, 141 linesx.cpp - source/
SoloFeature_outputResult , C++, 241 liness.cpp - source/
SoloFeature_processRecor , C++, 87 linesds.cpp - source/
SoloFeature_quantTranscr , C++, 327 linesipt.cpp - source/
SoloFeature_redistribute , C++, 80 linesReadsByCB.cpp - source/
SoloFeature_statsOutput. , C++, 123 linescpp - source/
SoloFeature_sumThreads.c , C++, 101 linespp - source/
SoloFilteredCells.h , C/C++, 33 lines - source/
SoloRead.cpp , C++, 22 lines - source/
SoloRead.h , C/C++, 23 lines - source/
SoloReadBarcode.cpp , C++, 51 lines - source/
SoloReadBarcode.h , C/C++, 46 lines - source/
SoloReadBarcodeStats.h , C/C++, 27 lines - source/
SoloReadBarcode_getCBand , C++, 429 linesUMI.cpp - source/
SoloReadFeature.cpp , C++, 63 lines - source/
SoloReadFeature.h , C/C++, 50 lines - source/
SoloReadFeatureStats.h , C/C++, 49 lines - source/
SoloReadFeature_inputRec , C++, 172 linesords.cpp - source/
SoloReadFeature_record.c , C++, 276 linespp - source/
SoloRead_record.cpp , C++, 15 lines - source/
SpliceGraph.cpp , C++, 33 lines - source/
SpliceGraph.h , C/C++, 58 lines - source/
SpliceGraph_findSuperTr. , C++, 186 linescpp - source/
SpliceGraph_swScoreSplic , C++, 249 linesed.cpp - source/
SpliceGraph_swTraceBack. , C++, 19 linescpp - source/
Stats.cpp , C++, 156 lines - source/
Stats.h , C/C++, 41 lines - source/
SuffixArrayFuns.cpp , C++, 410 lines - source/
SuffixArrayFuns.h , C/C++, 18 lines - source/
SuperTranscriptome.cpp , C++, 92 lines - source/
SuperTranscriptome.h , C/C++, 42 lines - source/
ThreadControl.cpp , C++, 7 lines - source/
ThreadControl.h , C/C++, 29 lines - source/
TimeFunctions.cpp , C++, 20 lines - source/
TimeFunctions.h , C/C++, 9 lines - source/
Transcript.cpp , C++, 59 lines - source/
Transcript.h , C/C++, 83 lines - source/
Transcript_alignScore.cp , C++, 60 linesp - source/
Transcript_convertGenome , C++, 161 linesCigar.cpp - source/
Transcript_generateCigar , C++, 63 linesP.cpp - source/
Transcript_transformGeno , C++, 167 linesme.cpp - source/
Transcript_variationAdju , C++, 74 linesst.cpp - source/
Transcript_variationOutp , C++, 6 linesut.cpp - source/
Transcriptome.cpp , C++, 190 lines - source/
Transcriptome.h , C/C++, 63 lines - source/
Transcriptome_alignExonO , C++, 278 linesverlap.cpp - source/
Transcriptome_classifyAl , C++, 267 linesign.cpp - source/
Transcriptome_geneCounts , C++, 63 linesAddAlign.cpp - source/
Transcriptome_geneFullAl , C++, 56 linesignOverlap.cpp - source/
Transcriptome_geneFullAl , C++, 43 linesignOverlap_ExonOverIntro n.cpp - source/
Transcriptome_quantAlign , C++, 114 lines.cpp - source/
Variation.cpp , C++, 157 lines - source/
Variation.h , C/C++, 53 lines - source/
bamRemoveDuplicates.cpp , C++, 271 lines - source/
bamRemoveDuplicates.h , C/C++, 10 lines - source/
bamSortByCoordinate.cpp , C++, 97 lines - source/
bamSortByCoordinate.h , C/C++, 11 lines - source/
bam_cat.c , C, 143 lines - source/
bam_cat.h , C/C++, 8 lines - source/
binarySearch2.cpp , C++, 43 lines - source/
binarySearch2.h , C/C++, 7 lines - source/
blocksOverlap.cpp , C++, 41 lines - source/
blocksOverlap.h , C/C++, 10 lines - source/
extendAlign.cpp , C++, 93 lines - source/
extendAlign.h , C/C++, 6 lines - source/
funCompareUintAndSuffixe , C++, 40 liness.cpp - source/
funCompareUintAndSuffixe , C/C++, 11 liness.h - source/
funCompareUintAndSuffixe , C++, 33 linessMemcmp.cpp - source/
funCompareUintAndSuffixe , C/C++, 10 linessMemcmp.h - source/
funPrimaryAlignMark.cpp , C++, 43 lines - source/
funPrimaryAlignMark.h , C/C++, 5 lines - source/
genomeGenerate.h , C/C++, 4 lines - source/
genomeParametersWrite.cp , C++, 45 linesp - source/
genomeParametersWrite.h , C/C++, 9 lines - source/
genomeSAindex.cpp , C++, 217 lines - source/
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genomeScanFastaFiles.cpp , C++, 92 lines - source/
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insertSeqSA.h , C/C++, 11 lines - source/
mapThreadsSpawn.cpp , C++, 33 lines - source/
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opal/ , C++, 1,568 linesopal.cpp - source/
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opal/ , C/C++, 5,590 linessimde_avx2.h - source/
outputSJ.cpp , C++, 163 lines - source/
outputSJ.h , C/C++, 4 lines - source/
readBarcodeLoad.h , C/C++, 9 lines - source/
readLoad.cpp , C++, 100 lines - source/
readLoad.h , C/C++, 12 lines - source/
samHeaders.cpp , C++, 108 lines - source/
samHeaders.h , C/C++, 10 lines - source/
serviceFuns.cpp , C++, 351 lines - source/
signalFromBAM.cpp , C++, 209 lines - source/
signalFromBAM.h , C/C++, 13 lines - source/
sjAlignSplit.cpp , C++, 15 lines - source/
sjAlignSplit.h , C/C++, 9 lines - source/
sjdbBuildIndex.cpp , C++, 333 lines - source/
sjdbBuildIndex.h , C/C++, 10 lines - source/
sjdbInsertJunctions.cpp , C++, 102 lines - source/
sjdbInsertJunctions.h , C/C++, 10 lines - source/
sjdbLoadFromFiles.cpp , C++, 27 lines - source/
sjdbLoadFromFiles.h , C/C++, 10 lines - source/
sjdbLoadFromStream.cpp , C++, 29 lines - source/
sjdbLoadFromStream.h , C/C++, 8 lines - source/
sjdbPrepare.cpp , C++, 225 lines - source/
sjdbPrepare.h , C/C++, 10 lines - source/
soloInputFeatureUMI.cpp , C++, 44 lines - source/
soloInputFeatureUMI.h , C/C++, 13 lines - source/
sortSuffixesBucket.h , C/C++, 3 lines - source/
stitchAlignToTranscript. , C++, 415 linescpp - source/
stitchAlignToTranscript. , C/C++, 7 linesh - source/
stitchGapIndel.cpp , C++, 59 lines - source/
stitchWindowAligns.cpp , C++, 355 lines - source/
stitchWindowAligns.h , C/C++, 12 lines - source/
streamFuns.cpp , C++, 149 lines - source/
streamFuns.h , C/C++, 17 lines - source/
stringSubstituteAll.cpp , C++, 10 lines - source/
stringSubstituteAll.h , C/C++, 8 lines - source/
sysRemoveDir.cpp , C++, 28 lines - source/
sysRemoveDir.h , C/C++, 8 lines - source/
systemFunctions.cpp , C++, 27 lines - source/
systemFunctions.h , C/C++, 6 lines - source/
twoPassRunPass1.cpp , C++, 97 lines - source/
twoPassRunPass1.h , C/C++, 11 lines - LICENSE, License, 21 lines
- README.md, Text, 115 lines
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;
- 329 scripts, each with its path and the digest of its content;
- no match between paragraphs and code yet;
- 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
- geo:GSE303190, at NCBI GEO; found in “Data and code availability”
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:
- it points to a dataset: NCBI GEO GSE303190
- it says that the data are available on request
- it says that the code is available on request
Read it in the paper: doi.org/10.1016/j.isci.2026.116123.
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
- Authors: added Anna Maria Tartaglione (0000-0002-9761-8098); Laura Ricceri (0000-0001-9850-2284); removed Anna Maria Tartaglione; Laura Ricceri
Version 1, 27 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 11 authors, 4 keywords, 3 funders, 100 references.
Cite
This paper
Tartaglione, A. M., Dinckol, O., Macchioni, G., Meccia, E., Privitera, G. F., Fuentes, B., Parlanti, E., Pino, A., Pulvirenti, A., Ricceri, L., & Calamandrei, G. (2026). Developmental manganese exposure, but not concurrent lead, alters social processing selectively in male mice. iScience, 29(6), 116123. https://
BibTeX
@article{tartaglione2026
author = {Tartaglione, Anna Maria and Dinckol, Oyku and Macchioni, Giorgia and Meccia, Ettore and Privitera, Grete Francesca and Fuentes, Byron and Parlanti, Eleonora and Pino, Anna and Pulvirenti, Alfredo and Ricceri, Laura and Calamandrei, Gemma},
title = {{Developmental manganese exposure, but not concurrent lead, alters social processing selectively in male mice}},
journal = {iScience},
year = {2026},
month = jun,
volume = {29},
number = {6},
pages = {116123},
publisher = {Elsevier},
issn = {2589-0042},
doi = {10.1016/
url = {https://
pmid = {42305584},
pmcid = {PMC13265901}
}
RIS
TY - JOUR
AU - Tartaglione, Anna Maria
AU - Dinckol, Oyku
AU - Macchioni, Giorgia
AU - Meccia, Ettore
AU - Privitera, Grete Francesca
AU - Fuentes, Byron
AU - Parlanti, Eleonora
AU - Pino, Anna
AU - Pulvirenti, Alfredo
AU - Ricceri, Laura
AU - Calamandrei, Gemma
TI - Developmental manganese exposure, but not concurrent lead, alters social processing selectively in male mice
T2 - iScience
J2 - iScience
PY - 2026
DA - 2026/
VL - 29
IS - 6
SP - 116123
SN - 2589-0042
PB - Elsevier
DO - 10.1016/
UR - https://
LA - en
ER -
CSL-JSON
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{
"family": "Tartaglione",
"given": "Anna Maria"
},
{
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"family": "Pino",
"given": "Anna"
},
{
"family": "Pulvirenti",
"given": "Alfredo"
},
{
"family": "Ricceri",
"given": "Laura"
},
{
"family": "Calamandrei",
"given": "Gemma"
}
],
"container-title-short":
"volume": "29",
"issue": "6",
"page": "116123",
"DOI": "10.1016/
"PMID": "42305584",
"PMCID": "PMC13265901",
"ISSN": "2589-0042",
"publisher": "Elsevier",
"URL": "https://
"language": "en",
"issued": {
"date-parts": [
[
2026,
6,
4
]
]
}
}
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