Protocol for isolating viable human central nervous system T cells.

Code ↔ Paper

The paper beside its authors' code: matches between them have not been computed for this paper yet.

Paper

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The paper is loaded by your browser, with JavaScript: read it at doi.org or on Europe PMC.

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

Authors: Hendrik J. Engelenburg¹, Joost Smolders^1,2,3, Inge Huitinga^1,4,5, Jörg Hamann^1,6, Cheng-Chih Hsiao^1,5,6

ORCID iDs: Hendrik J. Engelenburg, Joost Smolders, Jörg Hamann

Neuroimmunology Research Group, Netherlands Institute for Neuroscience, Amsterdam 1105 BA, the Netherlands
Department of Immunology, MS Center ErasMS, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3015 GD, the Netherlands
Department of Neurology, MS Center ErasMS, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3015 GD, the Netherlands
Swammerdam Institute for Life Sciences, Center for Neuroscience, University of Amsterdam, Amsterdam 1098 XH, the Netherlands
Netherlands Brain Bank, Netherlands Institute for Neuroscience, Amsterdam 1105 BA, the Netherlands
Department of Experimental Immunology, Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam University Medical Center, Amsterdam 1105 AZ, the Netherlands

Institutions: Netherlands Institute for Neuroscience (Netherlands); Erasmus MC (Netherlands); Netherlands Brain Bank (Netherlands); University of Amsterdam (Netherlands); Amsterdam University Medical Centers (Netherlands); Amsterdam institute for Immunology and Infectious Diseases (Netherlands)

Journal: STAR protocols, volume 7, issue 2, article 104464

Dates: published online 25 March 2026; in print June 2026

Type: Research article · Language: English

License: CC BY

Identifiers: DOI 10.1016/j.xpro.2026.104464 · PMID 41886460 · PMCID PMC13052091 · OpenAlex W7140323373

Open access: gold, a free copy (OpenAlex)

Status: code verified (how the code is found and verified)

Categories: other (modality), human (organism), cellular / molecular (subfield)

Methods: Statistics, Smoothing, state filtering, decompositions

Keywords: Cell isolation, Flow Cytometry, Immunology, Neuroscience

MeSH: Cell Separation*, Central Nervous System*, T-Lymphocytes*, Brain, Centrifugation, Density Gradient, Flow Cytometry, Humans (* major topic)

Topic: Neuroinflammation and Neurodegeneration Mechanisms (Neurology, Neuroscience), according to OpenAlex

Funding: Universitair Medisch Centrum Utrecht; Nationaal MS fonds (OZ2018-003)

Citations: not cited yet (Europe PMC); 17 references in the paper

Research resources: Anti-human CD103–PE (1:50 dilution) RRID:AB_11150242, Anti-human CD3–PE-CF594 (1:500 dilution) RRID:AB_11153674, Anti-human CD69–BV650 (1:100 dilution) RRID:AB_2563158, Anti-human CD45RA–BV650 (1:500 dilution) RRID:AB_2563653, Anti-human CD8–BV510 (1:50 dilution) RRID:AB_2564624, Anti-human CD45–BB515 (1:100 dilution) RRID:AB_2869588, Anti-human CD4–R718 (1:100 dilution) RRID:AB_2869953, FcR Blocking Reagent RRID:AB_2892112, RRID:AB_396765, Anti-human CD11b–PE-Cy7 (1:200 dilution) RRID:AB_830643

Abstract

Brain-resident T cells act as sentinels, monitoring and supporting immune surveillance and homeostasis. Here, we present a rapid protocol for isolating viable T cells from post-mortem human brain tissue. We describe the process of extracting cells from multiple CNS compartments—including choroid plexus, leptomeninges, dura mater, cerebrospinal fluid, and parenchyma—as well as matched peripheral blood. We detail steps for achieving this through mechanical and enzymatic tissue dissociation, followed by density gradient centrifugation to isolate mononuclear cells for downstream applications.

For complete details on the use and execution of this protocol, please refer to Hsiao et al.1

Reproduced under the paper's license (CC BY), from the paper cited above.

Repository

Its files are read in the Code ↔ Paper reader above.

alexdobin/STAR

License: MIT

State: the link answers, verified on 28 October 2026

Evidence: files inventoried

Commit: b1edc1208d91a53bf40ebae8669f71d50b994851, 25 January 2024

Languages: C++ (160), C/C++ (133), C (34), Shell (1), MATLAB (1)

Size: 389 files, 329 scripts

Software Heritage: not archived

Found in: the text, “Key resources table”

Holds: README, license file, environment (extras/docker/Dockerfile), continuous integration, documentation

Not found: CITATION.cff, tests

Availability: 2 checks, the latest on 28 October 2026: the link answers

28 October 2026: the link answers
27 September 2026: the link answers

331 files

extras/scripts/extractSJfromGTF.sh, Shell, 10 lines
extras/scripts/sjMotif.m, MATLAB, 45 lines
source/AlignVsTranscript.h, C/C++, 9 lines
source/BAMbinSortByCoordinate.cpp, C++, 81 lines
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_chimericBAMoutput.cpp, C++, 105 lines
source/ChimericAlign_chimericJunctionOutput.cpp, C++, 23 lines
source/ChimericAlign_chimericStitching.cpp, C++, 181 lines
source/ChimericDetection.cpp, C++, 6 lines
source/ChimericDetection.h, C/C++, 29 lines
source/ChimericDetection_chimericDetectionMult.cpp, C++, 138 lines
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.cpp, C++, 438 lines
source/Genome_genomeLoad.cpp, C++, 521 lines
source/Genome_genomeOutLoad.cpp, C++, 58 lines
source/Genome_insertSequences.cpp, C++, 33 lines
source/Genome_transformGenome.cpp, C++, 324 lines
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_initialize.cpp, C++, 118 lines
source/ParametersClip.h, C/C++, 37 lines
source/ParametersClip_initialize.cpp, C++, 107 lines
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_closeReadsFiles.cpp, C++, 12 lines
source/Parameters_openReadsFiles.cpp, C++, 111 lines
source/Parameters_readFilesInit.cpp, C++, 167 lines
source/Parameters_readSAMheader.cpp, C++, 44 lines
source/Parameters_samAttributes.cpp, C++, 263 lines
source/Quantifications.cpp, C++, 37 lines
source/Quantifications.h, C/C++, 22 lines
source/ReadAlign.cpp, C++, 125 lines
source/ReadAlign.h, C/C++, 239 lines
source/ReadAlignChunk.cpp, C++, 170 lines
source/ReadAlignChunk.h, C/C++, 49 lines
source/ReadAlignChunk_mapChunk.cpp, C++, 128 lines
source/ReadAlignChunk_processChunks.cpp, C++, 302 lines
source/ReadAlign_CIGAR.cpp, C++, 62 lines
source/ReadAlign_alignBAM.cpp, C++, 614 lines
source/ReadAlign_assignAlignToWindow.cpp, C++, 130 lines
source/ReadAlign_calcCIGAR.cpp, C++, 58 lines
source/ReadAlign_chimericDetection.cpp, C++, 57 lines
source/ReadAlign_chimericDetectionOld.cpp, C++, 312 lines
source/ReadAlign_chimericDetectionOldOutput.cpp, C++, 74 lines
source/ReadAlign_chimericDetectionPEmerged.cpp, C++, 39 lines
source/ReadAlign_createExtendWindowsWithAlign.cpp, C++, 85 lines
source/ReadAlign_mapOneRead.cpp, C++, 118 lines
source/ReadAlign_mapOneReadSpliceGraph.cpp, C++, 40 lines
source/ReadAlign_mappedFilter.cpp, C++, 21 lines
source/ReadAlign_maxMappableLength2strands.cpp, C++, 115 lines
source/ReadAlign_multMapSelect.cpp, C++, 95 lines
source/ReadAlign_oneRead.cpp, C++, 124 lines
source/ReadAlign_outputAlignments.cpp, C++, 325 lines
source/ReadAlign_outputSpliceGraphSAM.cpp, C++, 164 lines
source/ReadAlign_outputTranscriptCIGARp.cpp, C++, 65 lines
source/ReadAlign_outputTranscriptSAM.cpp, C++, 359 lines
source/ReadAlign_outputTranscriptSJ.cpp, C++, 56 lines
source/ReadAlign_outputVariation.cpp, C++, 13 lines
source/ReadAlign_peOverlapMergeMap.cpp, C++, 368 lines
source/ReadAlign_quantTranscriptome.cpp, C++, 91 lines
source/ReadAlign_stitchPieces.cpp, C++, 350 lines
source/ReadAlign_stitchWindowSeeds.cpp, C++, 278 lines
source/ReadAlign_storeAligns.cpp, C++, 160 lines
source/ReadAlign_transformGenome.cpp, C++, 74 lines
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/sgt.h, C/C++, 300 lines
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_extractBarcode.cpp, C++, 34 lines
source/SoloCommon.h, C/C++, 80 lines
source/SoloFeature.cpp, C++, 65 lines
source/SoloFeature.h, C/C++, 110 lines
source/SoloFeatureTypes.h, C/C++, 12 lines
source/SoloFeature_addBAMtags.cpp, C++, 26 lines
source/SoloFeature_cellFiltering.cpp, C++, 131 lines
source/SoloFeature_collapseUMI_Graph.cpp, C++, 172 lines
source/SoloFeature_collapseUMIall.cpp, C++, 658 lines
source/SoloFeature_countCBgeneUMI.cpp, C++, 112 lines
source/SoloFeature_countSmartSeq.cpp, C++, 159 lines
source/SoloFeature_countVelocyto.cpp, C++, 166 lines
source/SoloFeature_emptyDrops_CR.cpp, C++, 231 lines
source/SoloFeature_loadRawMatrix.cpp, C++, 141 lines
source/SoloFeature_outputResults.cpp, C++, 241 lines
source/SoloFeature_processRecords.cpp, C++, 87 lines
source/SoloFeature_quantTranscript.cpp, C++, 327 lines
source/SoloFeature_redistributeReadsByCB.cpp, C++, 80 lines
source/SoloFeature_statsOutput.cpp, C++, 123 lines
source/SoloFeature_sumThreads.cpp, C++, 101 lines
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_getCBandUMI.cpp, C++, 429 lines
source/SoloReadFeature.cpp, C++, 63 lines
source/SoloReadFeature.h, C/C++, 50 lines
source/SoloReadFeatureStats.h, C/C++, 49 lines
source/SoloReadFeature_inputRecords.cpp, C++, 172 lines
source/SoloReadFeature_record.cpp, C++, 276 lines
source/SoloRead_record.cpp, C++, 15 lines
source/SpliceGraph.cpp, C++, 33 lines
source/SpliceGraph.h, C/C++, 58 lines
source/SpliceGraph_findSuperTr.cpp, C++, 186 lines
source/SpliceGraph_swScoreSpliced.cpp, C++, 249 lines
source/SpliceGraph_swTraceBack.cpp, C++, 19 lines
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.cpp, C++, 60 lines
source/Transcript_convertGenomeCigar.cpp, C++, 161 lines
source/Transcript_generateCigarP.cpp, C++, 63 lines
source/Transcript_transformGenome.cpp, C++, 167 lines
source/Transcript_variationAdjust.cpp, C++, 74 lines
source/Transcript_variationOutput.cpp, C++, 6 lines
source/Transcriptome.cpp, C++, 190 lines
source/Transcriptome.h, C/C++, 63 lines
source/Transcriptome_alignExonOverlap.cpp, C++, 278 lines
source/Transcriptome_classifyAlign.cpp, C++, 267 lines
source/Transcriptome_geneCountsAddAlign.cpp, C++, 63 lines
source/Transcriptome_geneFullAlignOverlap.cpp, C++, 56 lines
source/Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp, C++, 43 lines
source/Transcriptome_quantAlign.cpp, C++, 114 lines
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/funCompareUintAndSuffixes.cpp, C++, 40 lines
source/funCompareUintAndSuffixes.h, C/C++, 11 lines
source/funCompareUintAndSuffixesMemcmp.cpp, C++, 33 lines
source/funCompareUintAndSuffixesMemcmp.h, C/C++, 10 lines
source/funPrimaryAlignMark.cpp, C++, 43 lines
source/funPrimaryAlignMark.h, C/C++, 5 lines
source/genomeGenerate.h, C/C++, 4 lines
source/genomeParametersWrite.cpp, C++, 45 lines
source/genomeParametersWrite.h, C/C++, 9 lines
source/genomeSAindex.cpp, C++, 217 lines
source/genomeSAindex.h, C/C++, 11 lines
source/genomeScanFastaFiles.cpp, C++, 92 lines
source/genomeScanFastaFiles.h, C/C++, 10 lines
source/htslib/bgzf.c, C, 1,085 lines
source/htslib/bgzip.c, C, 283 lines
source/htslib/config.h, C/C++, 3 lines
source/htslib/cram/cram.h, C/C++, 66 lines
source/htslib/cram/cram_codecs.c, C, 1,764 lines
source/htslib/cram/cram_codecs.h, C/C++, 155 lines
source/htslib/cram/cram_decode.c, C, 2,138 lines
source/htslib/cram/cram_decode.h, C/C++, 112 lines
source/htslib/cram/cram_encode.c, C, 2,630 lines
source/htslib/cram/cram_encode.h, C/C++, 105 lines
source/htslib/cram/cram_index.c, C, 503 lines
source/htslib/cram/cram_index.h, C/C++, 98 lines
source/htslib/cram/cram_io.c, C, 3,652 lines
source/htslib/cram/cram_io.h, C/C++, 532 lines
source/htslib/cram/cram_samtools.c, C, 144 lines
source/htslib/cram/cram_samtools.h, C/C++, 97 lines
source/htslib/cram/cram_stats.c, C, 357 lines
source/htslib/cram/cram_stats.h, C/C++, 59 lines
source/htslib/cram/cram_structs.h, C/C++, 752 lines
source/htslib/cram/files.c, C, 76 lines
source/htslib/cram/mFILE.c, C, 634 lines
source/htslib/cram/mFILE.h, C/C++, 88 lines
source/htslib/cram/md5.c, C, 295 lines
source/htslib/cram/md5.h, C/C++, 54 lines
source/htslib/cram/misc.h, C/C++, 110 lines
source/htslib/cram/open_trace_file.c, C, 386 lines
source/htslib/cram/open_trace_file.h, C/C++, 115 lines
source/htslib/cram/os.h, C/C++, 306 lines
source/htslib/cram/pooled_alloc.c, C, 170 lines
source/htslib/cram/pooled_alloc.h, C/C++, 56 lines
source/htslib/cram/sam_header.c, C, 1,222 lines
source/htslib/cram/sam_header.h, C/C++, 452 lines
source/htslib/cram/string_alloc.c, C, 153 lines
source/htslib/cram/string_alloc.h, C/C++, 69 lines
source/htslib/cram/thread_pool.c, C, 713 lines
source/htslib/cram/thread_pool.h, C/C++, 197 lines
source/htslib/cram/vlen.c, C, 432 lines
source/htslib/cram/vlen.h, C/C++, 48 lines
source/htslib/cram/zfio.c, C, 185 lines
source/htslib/cram/zfio.h, C/C++, 54 lines
source/htslib/faidx.c, C, 421 lines
source/htslib/hfile.c, C, 526 lines
source/htslib/hfile_internal.h, C/C++, 75 lines
source/htslib/hfile_net.c, C, 99 lines
source/htslib/hts.c, C, 1,326 lines
source/htslib/htslib/bgzf.h, C/C++, 313 lines
source/htslib/htslib/faidx.h, C/C++, 112 lines
source/htslib/htslib/hfile.h, C/C++, 204 lines
source/htslib/htslib/hts.h, C/C++, 305 lines
source/htslib/htslib/hts_defs.h, C/C++, 47 lines
source/htslib/htslib/kfunc.h, C/C++, 49 lines
source/htslib/htslib/khash.h, C/C++, 617 lines
source/htslib/htslib/khash_str2int.h, C/C++, 98 lines
source/htslib/htslib/klist.h, C/C++, 121 lines
source/htslib/htslib/knetfile.h, C/C++, 75 lines
source/htslib/htslib/kseq.h, C/C++, 253 lines
source/htslib/htslib/ksort.h, C/C++, 285 lines
source/htslib/htslib/kstdint.h, C/C++, 64 lines
source/htslib/htslib/kstring.h, C/C++, 270 lines
source/htslib/htslib/sam.h, C/C++, 401 lines
source/htslib/htslib/synced_bcf_reader.h, C/C++, 255 lines
source/htslib/htslib/tbx.h, C/C++, 52 lines
source/htslib/htslib/vcf.h, C/C++, 824 lines
source/htslib/htslib/vcf_sweep.h, C/C++, 15 lines
source/htslib/htslib/vcfutils.h, C/C++, 94 lines
source/htslib/kfunc.c, C, 254 lines
source/htslib/knetfile.c, C, 622 lines
source/htslib/kstring.c, C, 229 lines
source/htslib/sam.c, C, 1,797 lines
source/htslib/synced_bcf_reader.c, C, 1,183 lines
source/htslib/tabix.c, C, 374 lines
source/htslib/tbx.c, C, 290 lines
source/htslib/vcf.c, C, 2,967 lines
source/htslib/vcf_sweep.c, C, 158 lines
source/htslib/vcfutils.c, C, 642 lines
source/insertSeqSA.cpp, C++, 319 lines
source/insertSeqSA.h, C/C++, 11 lines
source/mapThreadsSpawn.cpp, C++, 33 lines
source/mapThreadsSpawn.h, C/C++, 7 lines
source/opal/opal.cpp, C++, 1,568 lines
source/opal/opal.h, C/C++, 171 lines
source/opal/simde_avx2.h, C/C++, 5,590 lines
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.cpp, C++, 415 lines
source/stitchAlignToTranscript.h, C/C++, 7 lines
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
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source/twoPassRunPass1.cpp, C++, 97 lines
source/twoPassRunPass1.h, C/C++, 11 lines
LICENSE, License, 21 lines
README.md, Text, 115 lines

At the source: github.com/alexdobin/STAR

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

No dataset and no data link were found in the paper.

Data and code availability

The dataset generated during this study is available at GEO: GSE307577.

Reproduced under the paper's license (CC BY), from the paper cited above.

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 1, 30 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 5 authors, 4 keywords, 7 MeSH terms, 2 funders, 16 references, 10 RRIDs.

Cite

This paper

Engelenburg, H. J., Smolders, J., Huitinga, I., Hamann, J., & Hsiao, C.-C. (2026). Protocol for isolating viable human central nervous system T cells. STAR protocols, 7(2), 104464. https://doi.org/10.1016/j.xpro.2026.104464

BibTeX

@article{engelenburg2026protocol, author = {Engelenburg, Hendrik J. and Smolders, Joost and Huitinga, Inge and Hamann, Jörg and Hsiao, Cheng-Chih}, title = {{Protocol for isolating viable human central nervous system T cells}}, journal = {STAR protocols}, year = {2026}, month = mar, volume = {7}, number = {2}, pages = {104464}, publisher = {Elsevier}, issn = {2666-1667}, doi = {10.1016/j.xpro.2026.104464}, url = {https://doi.org/10.1016/j.xpro.2026.104464}, pmid = {41886460}, pmcid = {PMC13052091} }

RIS

TY - JOUR AU - Engelenburg, Hendrik J. AU - Smolders, Joost AU - Huitinga, Inge AU - Hamann, Jörg AU - Hsiao, Cheng-Chih TI - Protocol for isolating viable human central nervous system T cells T2 - STAR protocols J2 - STAR Protoc PY - 2026 DA - 2026/03/25 VL - 7 IS - 2 SP - 104464 SN - 2666-1667 PB - Elsevier DO - 10.1016/j.xpro.2026.104464 UR - https://doi.org/10.1016/j.xpro.2026.104464 LA - en ER -

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{ "id": "10.1016/j.xpro.2026.104464", "type": "article-journal", "title": "Protocol for isolating viable human central nervous system T cells", "container-title": "STAR protocols", "author": [ { "family": "Engelenburg", "given": "Hendrik J." }, { "family": "Smolders", "given": "Joost" }, { "family": "Huitinga", "given": "Inge" }, { "family": "Hamann", "given": "Jörg" }, { "family": "Hsiao", "given": "Cheng-Chih" } ], "container-title-short": "STAR Protoc", "volume": "7", "issue": "2", "page": "104464", "DOI": "10.1016/j.xpro.2026.104464", "PMID": "41886460", "PMCID": "PMC13052091", "ISSN": "2666-1667", "publisher": "Elsevier", "URL": "https://doi.org/10.1016/j.xpro.2026.104464", "language": "en", "issued": { "date-parts": [ [ 2026, 3, 25 ] ] } }

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