rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
44,DRR668250,DRX648352,DRS458865,DRP012880,PRJDB18466,Comparison of spinal cord regeneration capacity in zebrafish and medaka,PRJDB18466,Other,Unlike mammals  zebrafish have the remarkable ability to regenerate many tissues  including the spinal cord. Medaka  another model fish species  has a low regenerative ability in the spinal cord. Therefore  comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.,,pubmed:40278963,Zebrafish 2 weeks post spinal cord injury replicate 3,Zebrafish 2wpi 3,SAMD00799623,,sample name:Zebrafish 2wpi 3|biological replicate:3|biomaterial provider:Center of Medical Innovation and Translational Research  Osaka University|collection date:2023 04 25|dev stage:Adult|geo loc name:Japan|sex:not determined|strain:AB Zebrafish|tissue:Spinal cord,,,,,,,,,DNBSEQ G400 paired end sequencing of SAMD00799623,DRX648352,RNA seq of spinal cord in zebrafish at 2wpi injured 3,1,Total RNA was extracted using RNeasy Micro Kit Qiagen  74104 with DNase treatment RNase Free DNase Set  Qiagen  79254. Libraries were constructed from the amplified total RNA.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,DRP012880,DNBSEQ G400 paired end sequencing of SAMD00799623,,,,14782516800.0,73912584.0,DRR668250,0:100 1:100,A:4058090278;C:3335994894;G:3323563782;T:4062467903;N:2399943,100,100,,,4058090278,3335994894,3323563782,4062467903,2399943,DRX648352,DRS458865,DRA020617,Osaka University,Osaka University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2025-05-12,Adult,Adult,Spinal Cord,Nervous System
45,DRR668249,DRX648351,DRS458864,DRP012880,PRJDB18466,Comparison of spinal cord regeneration capacity in zebrafish and medaka,PRJDB18466,Other,Unlike mammals  zebrafish have the remarkable ability to regenerate many tissues  including the spinal cord. Medaka  another model fish species  has a low regenerative ability in the spinal cord. Therefore  comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.,,pubmed:40278963,Zebrafish 2 weeks post spinal cord injury replicate 2,Zebrafish 2wpi 2,SAMD00799622,,sample name:Zebrafish 2wpi 2|biological replicate:2|biomaterial provider:Center of Medical Innovation and Translational Research  Osaka University|collection date:2023 04 14|dev stage:Adult|geo loc name:Japan|sex:not determined|strain:AB Zebrafish|tissue:Spinal cord,,,,,,,,,DNBSEQ G400 paired end sequencing of SAMD00799622,DRX648351,RNA seq of spinal cord in zebrafish at 2wpi injured 2,1,Total RNA was extracted using RNeasy Micro Kit Qiagen  74104 with DNase treatment RNase Free DNase Set  Qiagen  79254. Libraries were constructed from the amplified total RNA.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,DRP012880,DNBSEQ G400 paired end sequencing of SAMD00799622,,,,13687641800.0,68438209.0,DRR668249,0:100 1:100,A:3759784620;C:3087398782;G:3083881581;T:3754378915;N:2197902,100,100,,,3759784620,3087398782,3083881581,3754378915,2197902,DRX648351,DRS458864,DRA020617,Osaka University,Osaka University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2025-05-12,Adult,Adult,Spinal Cord,Nervous System
46,DRR668248,DRX648350,DRS458863,DRP012880,PRJDB18466,Comparison of spinal cord regeneration capacity in zebrafish and medaka,PRJDB18466,Other,Unlike mammals  zebrafish have the remarkable ability to regenerate many tissues  including the spinal cord. Medaka  another model fish species  has a low regenerative ability in the spinal cord. Therefore  comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.,,pubmed:40278963,Zebrafish 2 weeks post spinal cord injury replicate 1,Zebrafish 2wpi 1,SAMD00799621,,sample name:Zebrafish 2wpi 1|biological replicate:1|biomaterial provider:Center of Medical Innovation and Translational Research  Osaka University|collection date:2023 04 14|dev stage:Adult|geo loc name:Japan|sex:not determined|strain:AB Zebrafish|tissue:Spinal cord,,,,,,,,,DNBSEQ G400 paired end sequencing of SAMD00799621,DRX648350,RNA seq of spinal cord in zebrafish at 2wpi injured 1,1,Total RNA was extracted using RNeasy Micro Kit Qiagen  74104 with DNase treatment RNase Free DNase Set  Qiagen  79254. Libraries were constructed from the amplified total RNA.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,DRP012880,DNBSEQ G400 paired end sequencing of SAMD00799621,,,,16376197200.0,81880986.0,DRR668248,0:100 1:100,A:4485868844;C:3700974430;G:3710833937;T:4475827800;N:2692189,100,100,,,4485868844,3700974430,3710833937,4475827800,2692189,DRX648350,DRS458863,DRA020617,Osaka University,Osaka University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2025-05-12,Adult,Adult,Spinal Cord,Nervous System
47,DRR668247,DRX648349,DRS458862,DRP012880,PRJDB18466,Comparison of spinal cord regeneration capacity in zebrafish and medaka,PRJDB18466,Other,Unlike mammals  zebrafish have the remarkable ability to regenerate many tissues  including the spinal cord. Medaka  another model fish species  has a low regenerative ability in the spinal cord. Therefore  comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.,,pubmed:40278963,Zebrafish Intact biological replicate 3,Zebrafish Control 3,SAMD00799620,,sample name:Zebrafish Control 3|biological replicate:3|biomaterial provider:Center of Medical Innovation and Translational Research  Osaka University|collection date:2023 04 21|dev stage:Adult|geo loc name:Japan|sex:not determined|strain:AB Zebrafish|tissue:Spinal cord,,,,,,,,,DNBSEQ G400 paired end sequencing of SAMD00799620,DRX648349,RNA seq of spinal cord in zebrafish at 0wpi control 3,1,Total RNA was extracted using RNeasy Micro Kit Qiagen  74104 with DNase treatment RNase Free DNase Set  Qiagen  79254. Libraries were constructed from the amplified total RNA.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,DRP012880,DNBSEQ G400 paired end sequencing of SAMD00799620,,,,13377538600.0,66887693.0,DRR668247,0:100 1:100,A:3725064764;C:2973653932;G:2980883214;T:3695767890;N:2168800,100,100,,,3725064764,2973653932,2980883214,3695767890,2168800,DRX648349,DRS458862,DRA020617,Osaka University,Osaka University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2025-05-12,Adult,Adult,Spinal Cord,Nervous System
48,DRR668246,DRX648348,DRS458861,DRP012880,PRJDB18466,Comparison of spinal cord regeneration capacity in zebrafish and medaka,PRJDB18466,Other,Unlike mammals  zebrafish have the remarkable ability to regenerate many tissues  including the spinal cord. Medaka  another model fish species  has a low regenerative ability in the spinal cord. Therefore  comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.,,pubmed:40278963,Zebrafish Intact biological replicate 2,Zebrafish Control 2,SAMD00799619,,sample name:Zebrafish Control 2|biological replicate:2|biomaterial provider:Center of Medical Innovation and Translational Research  Osaka University|collection date:2023 04 21|dev stage:Adult|geo loc name:Japan|sex:not determined|strain:AB Zebrafish|tissue:Spinal cord,,,,,,,,,DNBSEQ G400 paired end sequencing of SAMD00799619,DRX648348,RNA seq of spinal cord in zebrafish at 0wpi control 2,1,Total RNA was extracted using RNeasy Micro Kit Qiagen  74104 with DNase treatment RNase Free DNase Set  Qiagen  79254. Libraries were constructed from the amplified total RNA.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,DRP012880,DNBSEQ G400 paired end sequencing of SAMD00799619,,,,14971411400.0,74857057.0,DRR668246,0:100 1:100,A:4160326445;C:3329083037;G:3329123314;T:4150453700;N:2424904,100,100,,,4160326445,3329083037,3329123314,4150453700,2424904,DRX648348,DRS458861,DRA020617,Osaka University,Osaka University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2025-05-12,Adult,Adult,Spinal Cord,Nervous System
49,DRR668245,DRX648347,DRS458860,DRP012880,PRJDB18466,Comparison of spinal cord regeneration capacity in zebrafish and medaka,PRJDB18466,Other,Unlike mammals  zebrafish have the remarkable ability to regenerate many tissues  including the spinal cord. Medaka  another model fish species  has a low regenerative ability in the spinal cord. Therefore  comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.,,pubmed:40278963,Zebrafish Intact biological replicate 1,Zebrafish Control 1,SAMD00799618,,sample name:Zebrafish Control 1|biological replicate:1|biomaterial provider:Center of Medical Innovation and Translational Research  Osaka University|collection date:2024 05 04|dev stage:Adult|geo loc name:Japan|sex:not determined|strain:AB Zebrafish|tissue:Spinal cord,,,,,,,,,DNBSEQ G400 paired end sequencing of SAMD00799618,DRX648347,RNA seq of spinal cord in zebrafish at 0wpi control 1,1,Total RNA was extracted using RNeasy Micro Kit Qiagen  74104 with DNase treatment RNase Free DNase Set  Qiagen  79254. Libraries were constructed from the amplified total RNA.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,DRP012880,DNBSEQ G400 paired end sequencing of SAMD00799618,,,,13912523800.0,69562619.0,DRR668245,0:100 1:100,A:3888902049;C:3079617959;G:3075111814;T:3866655202;N:2236776,100,100,,,3888902049,3079617959,3075111814,3866655202,2236776,DRX648347,DRS458860,DRA020617,Osaka University,Osaka University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Japan,2025-05-12,Adult,Adult,Spinal Cord,Nervous System
40356,SRR3109810,SRX1538264,SRS1254843,SRP068656,PRJNA309293,RNA sequencing of adult zebrafish spinal cord,GSE77025,Transcriptome Analysis,The goal of this study is to determine gene expression changes in the adult zebrafish spinal cord at 2 weeks post complete transection. Overall design: 2 samples were analyzed in duplicates:  sham injured spinal cord and transected spinal cord at 2 xxx post injury,,pubmed:27811277,,transected spinal cord b,GSM2042684,,source name:spinal cord  transected  2 xxx post injury|age:6 month|tissue:spinal cord|tratment:2 weeks post transection injury,transected spinal cord b,Quality QC using Fastx Trimming of adapters and short sequences using Fastx Mapping using Bowtie2 Assembly using Cufflinks Quantification using Cuffdiff Genome build: zebrafish Zv9 genome Supplementary files format and content: gene exp.diff file includes gene expression data of injured spinal cord tissue relative to sham injured control tissue,spinal cord  transected  2 xxx post injury,Animals underwent complete cervical spinal cord transection  and spinal cord tissue was collected 2 xxx post injury.  Control animals were sham injured and spinal cord was collected at 2 wks post sham.,RNA was extracted with Trizol reagent  followed by clean up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. TruSeq libraries were constructed according to manufacturer's instructions,Adult  6 mpf wild type zebrafish were used for this study,age:6 month|tissue:spinal cord|tratment:2 weeks post transection injury,GSM2042684,GSM2042684: transected spinal cord b; Danio rerio; RNA Seq,GSM2042684,,1,RNA was extracted with Trizol reagent  followed by clean up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. TruSeq libraries were constructed according to manufacturer's instructions,GEO Accession:GSM2042684,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP068656,,,Sample_mm4b.bam,bam,1171337622.0,23961004.0,GSM2042684 r1,0:48.89,A:316224903;C:272433131;G:255385026;T:327251225;N:43337,48,,,,316224903,272433131,255385026,327251225,43337,SRX1538264,SRS1254843,SRA336740,GEO,"Ken Poss Lab, Cell Biology, Duke University Medical Center",1,0.95542,,0.0725,,0.68816,,0.45919,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-01-20,Adult,Adult,Spinal Cord,Nervous System
40357,SRR3109809,SRX1538263,SRS1254842,SRP068656,PRJNA309293,RNA sequencing of adult zebrafish spinal cord,GSE77025,Transcriptome Analysis,The goal of this study is to determine gene expression changes in the adult zebrafish spinal cord at 2 weeks post complete transection. Overall design: 2 samples were analyzed in duplicates:  sham injured spinal cord and transected spinal cord at 2 xxx post injury,,pubmed:27811277,,transected spinal cord a,GSM2042683,,source name:spinal cord  transected  2 xxx post injury|age:6 month|tissue:spinal cord|tratment:2 weeks post transection injury,transected spinal cord a,Quality QC using Fastx Trimming of adapters and short sequences using Fastx Mapping using Bowtie2 Assembly using Cufflinks Quantification using Cuffdiff Genome build: zebrafish Zv9 genome Supplementary files format and content: gene exp.diff file includes gene expression data of injured spinal cord tissue relative to sham injured control tissue,spinal cord  transected  2 xxx post injury,Animals underwent complete cervical spinal cord transection  and spinal cord tissue was collected 2 xxx post injury.  Control animals were sham injured and spinal cord was collected at 2 wks post sham.,RNA was extracted with Trizol reagent  followed by clean up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. TruSeq libraries were constructed according to manufacturer's instructions,Adult  6 mpf wild type zebrafish were used for this study,age:6 month|tissue:spinal cord|tratment:2 weeks post transection injury,GSM2042683,GSM2042683: transected spinal cord a; Danio rerio; RNA Seq,GSM2042683,,1,RNA was extracted with Trizol reagent  followed by clean up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. TruSeq libraries were constructed according to manufacturer's instructions,GEO Accession:GSM2042683,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP068656,,,Sample_mm4a.bam,bam,906559320.0,18557265.0,GSM2042683 r1,,,,,,,,,,,,SRX1538263,SRS1254842,SRA336740,GEO,"Ken Poss Lab, Cell Biology, Duke University Medical Center",1,0.9696,,0.06993,,0.68913,,0.4662,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-01-20,Adult,Adult,Spinal Cord,Nervous System
40358,SRR3109808,SRX1538262,SRS1254844,SRP068656,PRJNA309293,RNA sequencing of adult zebrafish spinal cord,GSE77025,Transcriptome Analysis,The goal of this study is to determine gene expression changes in the adult zebrafish spinal cord at 2 weeks post complete transection. Overall design: 2 samples were analyzed in duplicates:  sham injured spinal cord and transected spinal cord at 2 xxx post injury,,pubmed:27811277,,sham spinal cord b,GSM2042682,,source name:spinal cord  sham control  2 wks post sham|age:6 month|tissue:spinal cord|tratment:2 wks post sham injury,sham spinal cord b,Quality QC using Fastx Trimming of adapters and short sequences using Fastx Mapping using Bowtie2 Assembly using Cufflinks Quantification using Cuffdiff Genome build: zebrafish Zv9 genome Supplementary files format and content: gene exp.diff file includes gene expression data of injured spinal cord tissue relative to sham injured control tissue,spinal cord  sham control  2 wks post sham,Animals underwent complete cervical spinal cord transection  and spinal cord tissue was collected 2 xxx post injury.  Control animals were sham injured and spinal cord was collected at 2 wks post sham.,RNA was extracted with Trizol reagent  followed by clean up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. TruSeq libraries were constructed according to manufacturer's instructions,Adult  6 mpf wild type zebrafish were used for this study,age:6 month|tissue:spinal cord|tratment:2 wks post sham injury,GSM2042682,GSM2042682: sham spinal cord b; Danio rerio; RNA Seq,GSM2042682,,1,RNA was extracted with Trizol reagent  followed by clean up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. TruSeq libraries were constructed according to manufacturer's instructions,GEO Accession:GSM2042682,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP068656,,,Sample_mm2b.bam,bam,976598317.0,19979953.0,GSM2042682 r1,0:48.88,A:269123614;C:222873099;G:208746430;T:275819417;N:35757,48,,,,269123614,222873099,208746430,275819417,35757,SRX1538262,SRS1254844,SRA336740,GEO,"Ken Poss Lab, Cell Biology, Duke University Medical Center",1,0.95785,,0.09352,,0.71433,,0.48637,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-01-20,Adult,Adult,Spinal Cord,Nervous System
40359,SRR3109807,SRX1538261,SRS1254845,SRP068656,PRJNA309293,RNA sequencing of adult zebrafish spinal cord,GSE77025,Transcriptome Analysis,The goal of this study is to determine gene expression changes in the adult zebrafish spinal cord at 2 weeks post complete transection. Overall design: 2 samples were analyzed in duplicates:  sham injured spinal cord and transected spinal cord at 2 xxx post injury,,pubmed:27811277,,sham spinal cord a,GSM2042681,,source name:spinal cord  sham control  2 wks post sham|age:6 month|tissue:spinal cord|tratment:2 wks post sham injury,sham spinal cord a,Quality QC using Fastx Trimming of adapters and short sequences using Fastx Mapping using Bowtie2 Assembly using Cufflinks Quantification using Cuffdiff Genome build: zebrafish Zv9 genome Supplementary files format and content: gene exp.diff file includes gene expression data of injured spinal cord tissue relative to sham injured control tissue,spinal cord  sham control  2 wks post sham,Animals underwent complete cervical spinal cord transection  and spinal cord tissue was collected 2 xxx post injury.  Control animals were sham injured and spinal cord was collected at 2 wks post sham.,RNA was extracted with Trizol reagent  followed by clean up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. TruSeq libraries were constructed according to manufacturer's instructions,Adult  6 mpf wild type zebrafish were used for this study,age:6 month|tissue:spinal cord|tratment:2 wks post sham injury,GSM2042681,GSM2042681: sham spinal cord a; Danio rerio; RNA Seq,GSM2042681,,1,RNA was extracted with Trizol reagent  followed by clean up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. TruSeq libraries were constructed according to manufacturer's instructions,GEO Accession:GSM2042681,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP068656,,,Sample_mm2a.bam,bam,1576837523.0,32234481.0,GSM2042681 r1,0:48.92,A:437851706;C:356136709;G:337965564;T:444822016;N:61528,48,,,,437851706,356136709,337965564,444822016,61528,SRX1538261,SRS1254845,SRA336740,GEO,"Ken Poss Lab, Cell Biology, Duke University Medical Center",1,0.95904,,0.09551,,0.71486,,0.48699,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2016-01-20,Adult,Adult,Spinal Cord,Nervous System
42545,SRR5805915,SRX2985081,SRS2337741,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OL5,GSM2694027,,tissue:adult spinal cord|cell type:oligodendrocyte,OL5,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte,GSM2694027,GSM2694027: OL5; Danio rerio; RNA Seq,GSM2694027,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694027,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13381_Track-36588_R1.fastq.gz,fastq,367232608.0,4832008.0,GSM2694027 r1,0:76,A:108020448;C:77176838;G:77161902;T:104867470;N:5950,76,,,,108020448,77176838,77161902,104867470,5950,SRX2985081,SRS2337741,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.90504,,0.10694,,0.81897,,0.34015,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42546,SRR5805916,SRX2985081,SRS2337741,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OL5,GSM2694027,,tissue:adult spinal cord|cell type:oligodendrocyte,OL5,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte,GSM2694027,GSM2694027: OL5; Danio rerio; RNA Seq,GSM2694027,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694027,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13381_Track-36601_R1.fastq.gz,fastq,1112803020.0,14642145.0,GSM2694027 r2,0:76,A:327618064;C:233631080;G:233528495;T:318005605;N:19776,76,,,,327618064,233631080,233528495,318005605,19776,SRX2985081,SRS2337741,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.90398,,0.10742,,0.81895,,0.3387,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42547,SRR5805917,SRX2985081,SRS2337741,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OL5,GSM2694027,,tissue:adult spinal cord|cell type:oligodendrocyte,OL5,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte,GSM2694027,GSM2694027: OL5; Danio rerio; RNA Seq,GSM2694027,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694027,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13381_Track-36721_R1.fastq.gz,fastq,1366015412.0,17973887.0,GSM2694027 r3,0:76,A:404748086;C:283771453;G:285083287;T:392327918;N:84668,76,,,,404748086,283771453,285083287,392327918,84668,SRX2985081,SRS2337741,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.90185,,0.11132,,0.82154,,0.34006,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42548,SRR5805912,SRX2985080,SRS2337740,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OL4,GSM2694026,,tissue:adult spinal cord|cell type:oligodendrocyte,OL4,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte,GSM2694026,GSM2694026: OL4; Danio rerio; RNA Seq,GSM2694026,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694026,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13380_Track-36587_R1.fastq.gz,fastq,360675556.0,4745731.0,GSM2694026 r1,0:76,A:106025824;C:75705006;G:76148954;T:102789747;N:6025,76,,,,106025824,75705006,76148954,102789747,6025,SRX2985080,SRS2337740,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.86855,,0.08794,,0.82112,,0.32375,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42549,SRR5805913,SRX2985080,SRS2337740,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OL4,GSM2694026,,tissue:adult spinal cord|cell type:oligodendrocyte,OL4,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte,GSM2694026,GSM2694026: OL4; Danio rerio; RNA Seq,GSM2694026,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694026,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13380_Track-36600_R1.fastq.gz,fastq,1098926332.0,14459557.0,GSM2694026 r2,0:76,A:323251709;C:230498299;G:231757231;T:313399836;N:19257,76,,,,323251709,230498299,231757231,313399836,19257,SRX2985080,SRS2337740,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.90618,,0.09414,,0.82215,,0.32432,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42550,SRR5805914,SRX2985080,SRS2337740,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OL4,GSM2694026,,tissue:adult spinal cord|cell type:oligodendrocyte,OL4,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte,GSM2694026,GSM2694026: OL4; Danio rerio; RNA Seq,GSM2694026,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694026,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13380_Track-36720_R1.fastq.gz,fastq,1193782464.0,15707664.0,GSM2694026 r3,0:76,A:353125594;C:247908840;G:250316138;T:342359001;N:72891,76,,,,353125594,247908840,250316138,342359001,72891,SRX2985080,SRS2337740,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.90544,,0.09556,,0.82233,,0.32116,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42551,SRR5805909,SRX2985079,SRS2337739,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OL3,GSM2694025,,tissue:adult spinal cord|cell type:oligodendrocyte,OL3,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte,GSM2694025,GSM2694025: OL3; Danio rerio; RNA Seq,GSM2694025,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694025,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13379_Track-36586_R1.fastq.gz,fastq,312102360.0,4106610.0,GSM2694025 r1,0:76,A:91621229;C:65883338;G:65770808;T:88821893;N:5092,76,,,,91621229,65883338,65770808,88821893,5092,SRX2985079,SRS2337739,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.86402,,0.09444,,0.82181,,0.33279,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42552,SRR5805910,SRX2985079,SRS2337739,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OL3,GSM2694025,,tissue:adult spinal cord|cell type:oligodendrocyte,OL3,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte,GSM2694025,GSM2694025: OL3; Danio rerio; RNA Seq,GSM2694025,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694025,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13379_Track-36599_R1.fastq.gz,fastq,994629328.0,13087228.0,GSM2694025 r2,0:76,A:292173588;C:209769693;G:209444134;T:283224496;N:17417,76,,,,292173588,209769693,209444134,283224496,17417,SRX2985079,SRS2337739,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.90872,,0.10051,,0.82233,,0.32123,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42553,SRR5805911,SRX2985079,SRS2337739,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OL3,GSM2694025,,tissue:adult spinal cord|cell type:oligodendrocyte,OL3,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte,GSM2694025,GSM2694025: OL3; Danio rerio; RNA Seq,GSM2694025,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694025,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13379_Track-36719_R1.fastq.gz,fastq,1183535688.0,15572838.0,GSM2694025 r3,0:76,A:349531521;C:247172348;G:248019907;T:338738175;N:73737,76,,,,349531521,247172348,248019907,338738175,73737,SRX2985079,SRS2337739,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.90617,,0.10315,,0.82329,,0.33103,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42554,SRR5805906,SRX2985078,SRS2337738,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OL2,GSM2694024,,tissue:adult spinal cord|cell type:oligodendrocyte,OL2,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte,GSM2694024,GSM2694024: OL2; Danio rerio; RNA Seq,GSM2694024,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694024,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13378_Track-36585_R1.fastq.gz,fastq,405537748.0,5336023.0,GSM2694024 r1,0:76,A:118435711;C:85437254;G:85942337;T:115715820;N:6626,76,,,,118435711,85437254,85942337,115715820,6626,SRX2985078,SRS2337738,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.8695,,0.09795,,0.82189,,0.33413,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42555,SRR5805907,SRX2985078,SRS2337738,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OL2,GSM2694024,,tissue:adult spinal cord|cell type:oligodendrocyte,OL2,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte,GSM2694024,GSM2694024: OL2; Danio rerio; RNA Seq,GSM2694024,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694024,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13378_Track-36598_R1.fastq.gz,fastq,1228952756.0,16170431.0,GSM2694024 r2,0:76,A:359305067;C:258652975;G:260090708;T:350882129;N:21877,76,,,,359305067,258652975,260090708,350882129,21877,SRX2985078,SRS2337738,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.90938,,0.10251,,0.82031,,0.32861,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42556,SRR5805908,SRX2985078,SRS2337738,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OL2,GSM2694024,,tissue:adult spinal cord|cell type:oligodendrocyte,OL2,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte,GSM2694024,GSM2694024: OL2; Danio rerio; RNA Seq,GSM2694024,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694024,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13378_Track-36718_R1.fastq.gz,fastq,1468733440.0,19325440.0,GSM2694024 r3,0:76,A:431919690;C:306294778;G:309065028;T:421362107;N:91837,76,,,,431919690,306294778,309065028,421362107,91837,SRX2985078,SRS2337738,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.90756,,0.10615,,0.81949,,0.33644,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42557,SRR5805903,SRX2985077,SRS2337737,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OL1,GSM2694023,,tissue:adult spinal cord|cell type:oligodendrocyte,OL1,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte,GSM2694023,GSM2694023: OL1; Danio rerio; RNA Seq,GSM2694023,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694023,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13377_Track-36584_R1.fastq.gz,fastq,466135360.0,6133360.0,GSM2694023 r1,0:76,A:135755208;C:99052881;G:99001624;T:132317853;N:7794,76,,,,135755208,99052881,99001624,132317853,7794,SRX2985077,SRS2337737,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.87348,,0.07763,,0.81844,,0.31419,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42558,SRR5805904,SRX2985077,SRS2337737,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OL1,GSM2694023,,tissue:adult spinal cord|cell type:oligodendrocyte,OL1,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte,GSM2694023,GSM2694023: OL1; Danio rerio; RNA Seq,GSM2694023,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694023,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13377_Track-36597_R1.fastq.gz,fastq,1411330868.0,18570143.0,GSM2694023 r2,0:76,A:411208825;C:299646339;G:299445590;T:401005116;N:24998,76,,,,411208825,299646339,299445590,401005116,24998,SRX2985077,SRS2337737,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.91442,,0.08129,,0.81868,,0.31098,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42559,SRR5805905,SRX2985077,SRS2337737,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OL1,GSM2694023,,tissue:adult spinal cord|cell type:oligodendrocyte,OL1,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte,GSM2694023,GSM2694023: OL1; Danio rerio; RNA Seq,GSM2694023,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694023,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13377_Track-36717_R1.fastq.gz,fastq,1694230988.0,22292513.0,GSM2694023 r3,0:76,A:496435234;C:356390144;G:357718951;T:483580476;N:106183,76,,,,496435234,356390144,357718951,483580476,106183,SRX2985077,SRS2337737,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.91116,,0.0827,,0.81854,,0.31198,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42560,SRR5805900,SRX2985076,SRS2337736,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OPC5,GSM2694022,,tissue:adult spinal cord|cell type:oligodendrocyte precursor cell,OPC5,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte precursor cell,GSM2694022,GSM2694022: OPC5; Danio rerio; RNA Seq,GSM2694022,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694022,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13376_Track-36583_R1.fastq.gz,fastq,280153404.0,3686229.0,GSM2694022 r1,0:76,A:81451669;C:59566227;G:59669362;T:79461530;N:4616,76,,,,81451669,59566227,59669362,79461530,4616,SRX2985076,SRS2337736,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.87692,,0.11958,,0.78683,,0.37449,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42561,SRR5805901,SRX2985076,SRS2337736,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OPC5,GSM2694022,,tissue:adult spinal cord|cell type:oligodendrocyte precursor cell,OPC5,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte precursor cell,GSM2694022,GSM2694022: OPC5; Danio rerio; RNA Seq,GSM2694022,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694022,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13376_Track-36596_R1.fastq.gz,fastq,905919164.0,11919989.0,GSM2694022 r2,0:76,A:263683260;C:192386277;G:192756447;T:257077269;N:15911,76,,,,263683260,192386277,192756447,257077269,15911,SRX2985076,SRS2337736,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.91322,,0.12482,,0.78695,,0.38581,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42562,SRR5805902,SRX2985076,SRS2337736,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OPC5,GSM2694022,,tissue:adult spinal cord|cell type:oligodendrocyte precursor cell,OPC5,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte precursor cell,GSM2694022,GSM2694022: OPC5; Danio rerio; RNA Seq,GSM2694022,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694022,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13376_Track-36716_R1.fastq.gz,fastq,1102695932.0,14509157.0,GSM2694022 r3,0:76,A:322423795;C:232167818;G:233489197;T:314545918;N:69204,76,,,,322423795,232167818,233489197,314545918,69204,SRX2985076,SRS2337736,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.91113,,0.12832,,0.78902,,0.38324,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42563,SRR5805897,SRX2985075,SRS2337735,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OPC4,GSM2694021,,tissue:adult spinal cord|cell type:oligodendrocyte precursor cell,OPC4,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte precursor cell,GSM2694021,GSM2694021: OPC4; Danio rerio; RNA Seq,GSM2694021,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694021,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13375_Track-36582_R1.fastq.gz,fastq,281755636.0,3707311.0,GSM2694021 r1,0:76,A:82997556;C:58935470;G:59188963;T:80628803;N:4844,76,,,,82997556,58935470,59188963,80628803,4844,SRX2985075,SRS2337735,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.87083,,0.12585,,0.79042,,0.35633,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42564,SRR5805898,SRX2985075,SRS2337735,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OPC4,GSM2694021,,tissue:adult spinal cord|cell type:oligodendrocyte precursor cell,OPC4,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte precursor cell,GSM2694021,GSM2694021: OPC4; Danio rerio; RNA Seq,GSM2694021,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694021,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13375_Track-36595_R1.fastq.gz,fastq,856872336.0,11274636.0,GSM2694021 r2,0:76,A:252638777;C:179079271;G:179782360;T:245356644;N:15284,76,,,,252638777,179079271,179782360,245356644,15284,SRX2985075,SRS2337735,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.91479,,0.1324,,0.78959,,0.36277,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42565,SRR5805899,SRX2985075,SRS2337735,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OPC4,GSM2694021,,tissue:adult spinal cord|cell type:oligodendrocyte precursor cell,OPC4,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte precursor cell,GSM2694021,GSM2694021: OPC4; Danio rerio; RNA Seq,GSM2694021,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694021,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13375_Track-36715_R1.fastq.gz,fastq,1067787080.0,14049830.0,GSM2694021 r3,0:76,A:316592408;C:220986701;G:222738880;T:307403458;N:65633,76,,,,316592408,220986701,222738880,307403458,65633,SRX2985075,SRS2337735,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.91223,,0.13673,,0.78957,,0.36042,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42566,SRR5805894,SRX2985074,SRS2337734,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OPC3,GSM2694020,,tissue:adult spinal cord|cell type:oligodendrocyte precursor cell,OPC3,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte precursor cell,GSM2694020,GSM2694020: OPC3; Danio rerio; RNA Seq,GSM2694020,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694020,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13374_Track-36581_R1.fastq.gz,fastq,258394604.0,3399929.0,GSM2694020 r1,0:76,A:75988348;C:54232048;G:54304534;T:73865549;N:4125,76,,,,75988348,54232048,54304534,73865549,4125,SRX2985074,SRS2337734,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.86675,,0.10485,,0.79166,,0.35524,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42567,SRR5805895,SRX2985074,SRS2337734,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OPC3,GSM2694020,,tissue:adult spinal cord|cell type:oligodendrocyte precursor cell,OPC3,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte precursor cell,GSM2694020,GSM2694020: OPC3; Danio rerio; RNA Seq,GSM2694020,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694020,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13374_Track-36594_R1.fastq.gz,fastq,802809356.0,10563281.0,GSM2694020 r2,0:76,A:236297052;C:168384708;G:168556277;T:229557436;N:13883,76,,,,236297052,168384708,168556277,229557436,13883,SRX2985074,SRS2337734,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.90891,,0.11028,,0.79115,,0.35162,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42568,SRR5805896,SRX2985074,SRS2337734,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OPC3,GSM2694020,,tissue:adult spinal cord|cell type:oligodendrocyte precursor cell,OPC3,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte precursor cell,GSM2694020,GSM2694020: OPC3; Danio rerio; RNA Seq,GSM2694020,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694020,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13374_Track-36714_R1.fastq.gz,fastq,996263860.0,13108735.0,GSM2694020 r3,0:76,A:294853084;C:206867581;G:208047523;T:286432957;N:62715,76,,,,294853084,206867581,208047523,286432957,62715,SRX2985074,SRS2337734,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.90671,,0.1148,,0.78993,,0.36115,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42569,SRR5805891,SRX2985073,SRS2337733,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OPC2,GSM2694019,,tissue:adult spinal cord|cell type:oligodendrocyte precursor cell,OPC2,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte precursor cell,GSM2694019,GSM2694019: OPC2; Danio rerio; RNA Seq,GSM2694019,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694019,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13373_Track-36580_R1.fastq.gz,fastq,290268624.0,3819324.0,GSM2694019 r1,0:76,A:83225179;C:62931491;G:62628688;T:81478215;N:5051,76,,,,83225179,62931491,62628688,81478215,5051,SRX2985073,SRS2337733,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.84469,,0.11786,,0.78742,,0.38555,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42570,SRR5805892,SRX2985073,SRS2337733,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OPC2,GSM2694019,,tissue:adult spinal cord|cell type:oligodendrocyte precursor cell,OPC2,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte precursor cell,GSM2694019,GSM2694019: OPC2; Danio rerio; RNA Seq,GSM2694019,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694019,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13373_Track-36593_R1.fastq.gz,fastq,872053640.0,11474390.0,GSM2694019 r2,0:76,A:250248044;C:188809860;G:187959005;T:245021560;N:15171,76,,,,250248044,188809860,187959005,245021560,15171,SRX2985073,SRS2337733,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.87823,,0.12293,,0.78699,,0.38395,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42571,SRR5805893,SRX2985073,SRS2337733,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OPC2,GSM2694019,,tissue:adult spinal cord|cell type:oligodendrocyte precursor cell,OPC2,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte precursor cell,GSM2694019,GSM2694019: OPC2; Danio rerio; RNA Seq,GSM2694019,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694019,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13373_Track-36713_R1.fastq.gz,fastq,1035504180.0,13625055.0,GSM2694019 r3,0:76,A:298790829;C:222016282;G:222262419;T:292369013;N:65637,76,,,,298790829,222016282,222262419,292369013,65637,SRX2985073,SRS2337733,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.88262,,0.12859,,0.78707,,0.36444,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42572,SRR5805888,SRX2985072,SRS2337732,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OPC1,GSM2694018,,tissue:adult spinal cord|cell type:oligodendrocyte precursor cell,OPC1,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte precursor cell,GSM2694018,GSM2694018: OPC1; Danio rerio; RNA Seq,GSM2694018,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694018,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13372_Track-36579_R1.fastq.gz,fastq,275307568.0,3622468.0,GSM2694018 r1,0:76,A:80768745;C:57628302;G:57760609;T:79145252;N:4660,76,,,,80768745,57628302,57760609,79145252,4660,SRX2985072,SRS2337732,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.87887,,0.12197,,0.79807,,0.35871,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42573,SRR5805889,SRX2985072,SRS2337732,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OPC1,GSM2694018,,tissue:adult spinal cord|cell type:oligodendrocyte precursor cell,OPC1,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte precursor cell,GSM2694018,GSM2694018: OPC1; Danio rerio; RNA Seq,GSM2694018,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694018,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13372_Track-36592_R1.fastq.gz,fastq,844153204.0,11107279.0,GSM2694018 r2,0:76,A:247798416;C:176560506;G:176978398;T:242800972;N:14912,76,,,,247798416,176560506,176978398,242800972,14912,SRX2985072,SRS2337732,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.912,,0.12665,,0.79742,,0.36358,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
42574,SRR5805890,SRX2985072,SRS2337732,SRP111129,PRJNA393181,Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro,GSE100821,Transcriptome Analysis,Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded  and therefore vulnerable  axons. Demyelination is the result of a primary insult and secondary injury  leading to conduction blocks and long term degeneration of the axons  which subsequently can lead to the loss of their neuron. In response to SCI  dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore  researchers strive to control OPC responses  and utilize small molecule screening approaches in order to identify mechanisms of OPC activation  proliferation  migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations  5 biological replicates per population,,pubmed:28959189,,OPC1,GSM2694018,,tissue:adult spinal cord|cell type:oligodendrocyte precursor cell,OPC1,basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments  were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID  Chromosom  Exon Start Coordinates  Exon End Coordinates  Gene Length; Counts from the 2 Conditions and their 5 replicates,adult spinal cord,,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,,cell type:oligodendrocyte precursor cell,GSM2694018,GSM2694018: OPC1; Danio rerio; RNA Seq,GSM2694018,,1,Spinal cord dissection  tissue dissociation and nuclear labelling:  Adult zebrafish were terminally anesthetized  their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS  Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature  the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice  before it was applied to a 20 µm OPCs  Miltenyi Biotec  # 130 101 812 or a 35 µm OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30´ at 28 °C to stain cellular nuclei.  FACsorting of myelin rich spinal cord tissue:  Cell suspensions were sorted directly into 96 well plates  filled with culture media only  or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection  all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.,GEO Accession:GSM2694018,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP111129,,,L13372_Track-36712_R1.fastq.gz,fastq,990996528.0,13039428.0,GSM2694018 r3,0:76,A:292539296;C:205334965;G:206678725;T:286381798;N:61744,76,,,,292539296,205334965,206678725,286381798,61744,SRX2985072,SRS2337732,SRA584085,GEO,"Reimer Lab, CRT Dresden, TU Dresden",1,0.90825,,0.1314,,0.80004,,0.3635,,76,,B,,usable mapping rate,illumina,hiseq_era,full_length,random_priming,nebnext,bulk,unknown,unknown,,Germany,2017-07-05,Adult,Adult,Spinal Cord,Nervous System
66008,SRR15783460,SRX12076342,SRS10057008,SRP336073,PRJNA761449,Myostatin is a negative regulator of adult neurogenesis in zebrafish,GSE183644,Transcriptome Analysis,Intrinsic and extrinsic inhibition of axonal and neuronal regeneration obstruct spinal cord SC repair in mammals. In contrast  adult zebrafish achieve functional recovery post SC damage. While studies of innate SC regeneration have focused on axon regrowth as a primary repair mechanism  how local neurogenesis impacts functional recovery is unknown. We uncovered dynamic expression of myostatin b mstnb in a niche of dorsal ependymal progenitors post complete SC transection in zebrafish. Genetic loss of function in mstnb impaired functional recovery  although glial and axonal bridging across the lesion were unaffected. Using a series of transgenic reporter lines  we quantified the numbers of stem  progenitor  and neuronal cells in the absence of mstnb. We found neural stem cell proliferation was reduced  while newborn neurons were increased in mstnb null tissues  suggesting mstnb is a negative regulator of neurogenesis. Molecularly  neuron differentiation genes were upregulated  while the neural stem cell maintenance gene fgf1b was downregulated in mstnb mutants. Finally  we show that human FGF1 treatment rescued neuronal gene expression in mstnb mutants. These studies uncover unanticipated neurogenic functions for mstnb in adult zebrafish  and establish the importance of local neurogenesis for functional SC repair. Overall design: Gene expression profiling of mstn mutants and wildtype at control and one xxx post injury.,,pubmed:36417881,,SC  mstnb mutant   Uninjured   replicate 2,GSM5566279,,source name:Spinal cord|tissue:Spinal cord|experiment:Uninjured|time:Control|genotype:mstnb mutant  / ,SC  mstnb mutant   Uninjured   replicate 2,Quality QC and trimming of adapters and short sequences were performed using Fastx. Sequencing reads were mapped to the zebrafish genome Zv11 using Bowtie2  then assembled and quantified using the Cufflinks and Cuffdiff algorithms. Genes with log2fold enrichment between  1 and 1 or adjusted p value ≥ 0.01 were considered insignificant. Genome build: Zv11 Supplementary files format and content: Processed data is store csv format files. All files contain FPKM expression values of all the genes in different replicates and experimental condition. Supplementary files format and content: Additionally  log2 Fold change is calculate between conditions as indicated in the file name.,Spinal cord,Zebrafish were anaesthetized using MS 222. Fine scissors were used to make a small incision that transects the SC 4 mm caudal to the brainstem region. Complete transection was visually confirmed at the time of surgery. Injured animals were also assessed at 2 or 3 dpi to confirm loss of swim capacity post surgery. For sham injuries  animals were anaesthetized  and fine scissors were used to transect skin and muscle tissues without xxx SCI.,Two mm SC sections  including the lesion site plus additional rostral and caudal tissue proximal to the lesion  were collected from mstnb mutants and wild type siblings at 1 wpi. Uninjured mstnb mutants and wild type SCs were also  collected. Total RNA was prepared using NucleoSpin RNA Plus XS Clontech  cat# 740990 TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp paired end reading strategy.,Adult zebrafish  were maintained at the Washington University Zebrafish Core Facility. All animal experiments were performed in compliance with institutional animal protocols. Male and female animals between 3 month and 9 month of 2 cm in length were used. Experimental fish and control siblings of similar size and equal sex distribution were used for all experiments. SC transection surgeries and regeneration analyses were performed in a blinded manner  and 2 to 4 independent experiments were repeated using different clutches of animals.,tissue:Spinal cord|experiment:Uninjured|time:Control|genotype:mstnb mutant  / ,GSM5566279,GSM5566279: SC  mstnb mutant   Uninjured   replicate 2; Danio rerio; RNA Seq,GSM5566279,,1,Two mm SC sections  including the lesion site plus additional rostral and caudal tissue proximal to the lesion  were collected from mstnb mutants and wild type siblings at 1 wpi. Uninjured mstnb mutants and wild type SCs were also  collected. Total RNA was prepared using NucleoSpin RNA Plus XS Clontech  cat# 740990 TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp paired end reading strategy.,GEO Accession:GSM5566279,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP336073,,loader:fastq load.py,b9-mstnb-mut-uninj-2.ACTTCTCGTA-AGTCCAGCGT.ACTTCTCGTA-AGTCCAGCGT_S16_L003_R1_001.fastq.gz b9-mstnb-mut-uninj-2.ACTTCTCGTA-AGTCCAGCGT.ACTTCTCGTA-AGTCCAGCGT_S16_L003_R2_001.fastq.gz,fastq fastq,18561707616.0,61462608.0,GSM5566279 r1,0:151 1:151,A:5376008692;C:3846947319;G:4240142329;T:5098398439;N:210837,151,151,,,5376008692,3846947319,4240142329,5098398439,210837,SRX12076342,SRS10057008,SRA1289934,GEO,"Developmental Biology, Washington University in St. Louis",2,0.90875,0.91227,0.22236,0.22895,0.71729,0.72571,0.53799,0.53913,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2021-09-07,Adult,Adult,Spinal Cord,Nervous System
66009,SRR15783459,SRX12076340,SRS10057005,SRP336073,PRJNA761449,Myostatin is a negative regulator of adult neurogenesis in zebrafish,GSE183644,Transcriptome Analysis,Intrinsic and extrinsic inhibition of axonal and neuronal regeneration obstruct spinal cord SC repair in mammals. In contrast  adult zebrafish achieve functional recovery post SC damage. While studies of innate SC regeneration have focused on axon regrowth as a primary repair mechanism  how local neurogenesis impacts functional recovery is unknown. We uncovered dynamic expression of myostatin b mstnb in a niche of dorsal ependymal progenitors post complete SC transection in zebrafish. Genetic loss of function in mstnb impaired functional recovery  although glial and axonal bridging across the lesion were unaffected. Using a series of transgenic reporter lines  we quantified the numbers of stem  progenitor  and neuronal cells in the absence of mstnb. We found neural stem cell proliferation was reduced  while newborn neurons were increased in mstnb null tissues  suggesting mstnb is a negative regulator of neurogenesis. Molecularly  neuron differentiation genes were upregulated  while the neural stem cell maintenance gene fgf1b was downregulated in mstnb mutants. Finally  we show that human FGF1 treatment rescued neuronal gene expression in mstnb mutants. These studies uncover unanticipated neurogenic functions for mstnb in adult zebrafish  and establish the importance of local neurogenesis for functional SC repair. Overall design: Gene expression profiling of mstn mutants and wildtype at control and one xxx post injury.,,pubmed:36417881,,SC  mstnb mutant   Uninjured   replicate 1,GSM5566278,,source name:Spinal cord|tissue:Spinal cord|experiment:Uninjured|time:Control|genotype:mstnb mutant  / ,SC  mstnb mutant   Uninjured   replicate 1,Quality QC and trimming of adapters and short sequences were performed using Fastx. Sequencing reads were mapped to the zebrafish genome Zv11 using Bowtie2  then assembled and quantified using the Cufflinks and Cuffdiff algorithms. Genes with log2fold enrichment between  1 and 1 or adjusted p value ≥ 0.01 were considered insignificant. Genome build: Zv11 Supplementary files format and content: Processed data is store csv format files. All files contain FPKM expression values of all the genes in different replicates and experimental condition. Supplementary files format and content: Additionally  log2 Fold change is calculate between conditions as indicated in the file name.,Spinal cord,Zebrafish were anaesthetized using MS 222. Fine scissors were used to make a small incision that transects the SC 4 mm caudal to the brainstem region. Complete transection was visually confirmed at the time of surgery. Injured animals were also assessed at 2 or 3 dpi to confirm loss of swim capacity post surgery. For sham injuries  animals were anaesthetized  and fine scissors were used to transect skin and muscle tissues without xxx SCI.,Two mm SC sections  including the lesion site plus additional rostral and caudal tissue proximal to the lesion  were collected from mstnb mutants and wild type siblings at 1 wpi. Uninjured mstnb mutants and wild type SCs were also  collected. Total RNA was prepared using NucleoSpin RNA Plus XS Clontech  cat# 740990 TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp paired end reading strategy.,Adult zebrafish  were maintained at the Washington University Zebrafish Core Facility. All animal experiments were performed in compliance with institutional animal protocols. Male and female animals between 3 month and 9 month of 2 cm in length were used. Experimental fish and control siblings of similar size and equal sex distribution were used for all experiments. SC transection surgeries and regeneration analyses were performed in a blinded manner  and 2 to 4 independent experiments were repeated using different clutches of animals.,tissue:Spinal cord|experiment:Uninjured|time:Control|genotype:mstnb mutant  / ,GSM5566278,GSM5566278: SC  mstnb mutant   Uninjured   replicate 1; Danio rerio; RNA Seq,GSM5566278,,1,Two mm SC sections  including the lesion site plus additional rostral and caudal tissue proximal to the lesion  were collected from mstnb mutants and wild type siblings at 1 wpi. Uninjured mstnb mutants and wild type SCs were also  collected. Total RNA was prepared using NucleoSpin RNA Plus XS Clontech  cat# 740990 TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp paired end reading strategy.,GEO Accession:GSM5566278,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP336073,,loader:fastq load.py,b8-mstnb-mut-uninj-1.TCTGGATAAG-GAAGGAGCCT.TCTGGATAAG-GAAGGAGCCT_S80_L003_R1_001.fastq.gz b8-mstnb-mut-uninj-1.TCTGGATAAG-GAAGGAGCCT.TCTGGATAAG-GAAGGAGCCT_S80_L003_R2_001.fastq.gz,fastq fastq,19751058512.0,65400856.0,GSM5566278 r1,0:151 1:151,A:5608025200;C:4101762755;G:4708073935;T:5332976769;N:219853,151,151,,,5608025200,4101762755,4708073935,5332976769,219853,SRX12076340,SRS10057005,SRA1289934,GEO,"Developmental Biology, Washington University in St. Louis",2,0.93136,0.93887,0.10405,0.10774,0.75282,0.76416,0.57913,0.54405,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2021-09-07,Adult,Adult,Spinal Cord,Nervous System
66010,SRR15783458,SRX12076338,SRS10057004,SRP336073,PRJNA761449,Myostatin is a negative regulator of adult neurogenesis in zebrafish,GSE183644,Transcriptome Analysis,Intrinsic and extrinsic inhibition of axonal and neuronal regeneration obstruct spinal cord SC repair in mammals. In contrast  adult zebrafish achieve functional recovery post SC damage. While studies of innate SC regeneration have focused on axon regrowth as a primary repair mechanism  how local neurogenesis impacts functional recovery is unknown. We uncovered dynamic expression of myostatin b mstnb in a niche of dorsal ependymal progenitors post complete SC transection in zebrafish. Genetic loss of function in mstnb impaired functional recovery  although glial and axonal bridging across the lesion were unaffected. Using a series of transgenic reporter lines  we quantified the numbers of stem  progenitor  and neuronal cells in the absence of mstnb. We found neural stem cell proliferation was reduced  while newborn neurons were increased in mstnb null tissues  suggesting mstnb is a negative regulator of neurogenesis. Molecularly  neuron differentiation genes were upregulated  while the neural stem cell maintenance gene fgf1b was downregulated in mstnb mutants. Finally  we show that human FGF1 treatment rescued neuronal gene expression in mstnb mutants. These studies uncover unanticipated neurogenic functions for mstnb in adult zebrafish  and establish the importance of local neurogenesis for functional SC repair. Overall design: Gene expression profiling of mstn mutants and wildtype at control and one xxx post injury.,,pubmed:36417881,,SC  mstnb wildtype   Uninjured   replicate 2,GSM5566277,,source name:Spinal cord|tissue:Spinal cord|experiment:Uninjured|time:Control|genotype:wildtype,SC  mstnb wildtype   Uninjured   replicate 2,Quality QC and trimming of adapters and short sequences were performed using Fastx. Sequencing reads were mapped to the zebrafish genome Zv11 using Bowtie2  then assembled and quantified using the Cufflinks and Cuffdiff algorithms. Genes with log2fold enrichment between  1 and 1 or adjusted p value ≥ 0.01 were considered insignificant. Genome build: Zv11 Supplementary files format and content: Processed data is store csv format files. All files contain FPKM expression values of all the genes in different replicates and experimental condition. Supplementary files format and content: Additionally  log2 Fold change is calculate between conditions as indicated in the file name.,Spinal cord,Zebrafish were anaesthetized using MS 222. Fine scissors were used to make a small incision that transects the SC 4 mm caudal to the brainstem region. Complete transection was visually confirmed at the time of surgery. Injured animals were also assessed at 2 or 3 dpi to confirm loss of swim capacity post surgery. For sham injuries  animals were anaesthetized  and fine scissors were used to transect skin and muscle tissues without xxx SCI.,Two mm SC sections  including the lesion site plus additional rostral and caudal tissue proximal to the lesion  were collected from mstnb mutants and wild type siblings at 1 wpi. Uninjured mstnb mutants and wild type SCs were also  collected. Total RNA was prepared using NucleoSpin RNA Plus XS Clontech  cat# 740990 TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp paired end reading strategy.,Adult zebrafish  were maintained at the Washington University Zebrafish Core Facility. All animal experiments were performed in compliance with institutional animal protocols. Male and female animals between 3 month and 9 month of 2 cm in length were used. Experimental fish and control siblings of similar size and equal sex distribution were used for all experiments. SC transection surgeries and regeneration analyses were performed in a blinded manner  and 2 to 4 independent experiments were repeated using different clutches of animals.,tissue:Spinal cord|experiment:Uninjured|time:Control|genotype:wildtype,GSM5566277,GSM5566277: SC  mstnb wildtype   Uninjured   replicate 2; Danio rerio; RNA Seq,GSM5566277,,1,Two mm SC sections  including the lesion site plus additional rostral and caudal tissue proximal to the lesion  were collected from mstnb mutants and wild type siblings at 1 wpi. Uninjured mstnb mutants and wild type SCs were also  collected. Total RNA was prepared using NucleoSpin RNA Plus XS Clontech  cat# 740990 TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp paired end reading strategy.,GEO Accession:GSM5566277,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP336073,,loader:fastq load.py,b7-mstnb-wt-uninj-2.AAGCGGATTA-TTCAGATCCA.AAGCGGATTA-TTCAGATCCA_S5_L003_R1_001.fastq.gz b7-mstnb-wt-uninj-2.AAGCGGATTA-TTCAGATCCA.AAGCGGATTA-TTCAGATCCA_S5_L003_R2_001.fastq.gz,fastq fastq,16361235956.0,54176278.0,GSM5566277 r1,0:151 1:151,A:4710356079;C:3362427190;G:3849175583;T:4439093873;N:183231,151,151,,,4710356079,3362427190,3849175583,4439093873,183231,SRX12076338,SRS10057004,SRA1289934,GEO,"Developmental Biology, Washington University in St. Louis",2,0.91784,0.92473,0.16572,0.16836,0.72255,0.7349,0.54847,0.54107,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2021-09-07,Adult,Adult,Spinal Cord,Nervous System
66011,SRR15783457,SRX12076336,SRS10057001,SRP336073,PRJNA761449,Myostatin is a negative regulator of adult neurogenesis in zebrafish,GSE183644,Transcriptome Analysis,Intrinsic and extrinsic inhibition of axonal and neuronal regeneration obstruct spinal cord SC repair in mammals. In contrast  adult zebrafish achieve functional recovery post SC damage. While studies of innate SC regeneration have focused on axon regrowth as a primary repair mechanism  how local neurogenesis impacts functional recovery is unknown. We uncovered dynamic expression of myostatin b mstnb in a niche of dorsal ependymal progenitors post complete SC transection in zebrafish. Genetic loss of function in mstnb impaired functional recovery  although glial and axonal bridging across the lesion were unaffected. Using a series of transgenic reporter lines  we quantified the numbers of stem  progenitor  and neuronal cells in the absence of mstnb. We found neural stem cell proliferation was reduced  while newborn neurons were increased in mstnb null tissues  suggesting mstnb is a negative regulator of neurogenesis. Molecularly  neuron differentiation genes were upregulated  while the neural stem cell maintenance gene fgf1b was downregulated in mstnb mutants. Finally  we show that human FGF1 treatment rescued neuronal gene expression in mstnb mutants. These studies uncover unanticipated neurogenic functions for mstnb in adult zebrafish  and establish the importance of local neurogenesis for functional SC repair. Overall design: Gene expression profiling of mstn mutants and wildtype at control and one xxx post injury.,,pubmed:36417881,,SC  mstnb wildtype   Uninjured   replicate 1,GSM5566276,,source name:Spinal cord|tissue:Spinal cord|experiment:Uninjured|time:Control|genotype:wildtype,SC  mstnb wildtype   Uninjured   replicate 1,Quality QC and trimming of adapters and short sequences were performed using Fastx. Sequencing reads were mapped to the zebrafish genome Zv11 using Bowtie2  then assembled and quantified using the Cufflinks and Cuffdiff algorithms. Genes with log2fold enrichment between  1 and 1 or adjusted p value ≥ 0.01 were considered insignificant. Genome build: Zv11 Supplementary files format and content: Processed data is store csv format files. All files contain FPKM expression values of all the genes in different replicates and experimental condition. Supplementary files format and content: Additionally  log2 Fold change is calculate between conditions as indicated in the file name.,Spinal cord,Zebrafish were anaesthetized using MS 222. Fine scissors were used to make a small incision that transects the SC 4 mm caudal to the brainstem region. Complete transection was visually confirmed at the time of surgery. Injured animals were also assessed at 2 or 3 dpi to confirm loss of swim capacity post surgery. For sham injuries  animals were anaesthetized  and fine scissors were used to transect skin and muscle tissues without xxx SCI.,Two mm SC sections  including the lesion site plus additional rostral and caudal tissue proximal to the lesion  were collected from mstnb mutants and wild type siblings at 1 wpi. Uninjured mstnb mutants and wild type SCs were also  collected. Total RNA was prepared using NucleoSpin RNA Plus XS Clontech  cat# 740990 TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp paired end reading strategy.,Adult zebrafish  were maintained at the Washington University Zebrafish Core Facility. All animal experiments were performed in compliance with institutional animal protocols. Male and female animals between 3 month and 9 month of 2 cm in length were used. Experimental fish and control siblings of similar size and equal sex distribution were used for all experiments. SC transection surgeries and regeneration analyses were performed in a blinded manner  and 2 to 4 independent experiments were repeated using different clutches of animals.,tissue:Spinal cord|experiment:Uninjured|time:Control|genotype:wildtype,GSM5566276,GSM5566276: SC  mstnb wildtype   Uninjured   replicate 1; Danio rerio; RNA Seq,GSM5566276,,1,Two mm SC sections  including the lesion site plus additional rostral and caudal tissue proximal to the lesion  were collected from mstnb mutants and wild type siblings at 1 wpi. Uninjured mstnb mutants and wild type SCs were also  collected. Total RNA was prepared using NucleoSpin RNA Plus XS Clontech  cat# 740990 TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp paired end reading strategy.,GEO Accession:GSM5566276,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP336073,,loader:fastq load.py,b6-mstnb-wt-uninj-1.GTCGGTTCAC-ATCCTCGAGT.GTCGGTTCAC-ATCCTCGAGT_S72_L003_R1_001.fastq.gz b6-mstnb-wt-uninj-1.GTCGGTTCAC-ATCCTCGAGT.GTCGGTTCAC-ATCCTCGAGT_S72_L003_R2_001.fastq.gz,fastq fastq,20288059208.0,67179004.0,GSM5566276 r1,0:151 1:151,A:6194227425;C:3762932453;G:4520501753;T:5810174695;N:222882,151,151,,,6194227425,3762932453,4520501753,5810174695,222882,SRX12076336,SRS10057001,SRA1289934,GEO,"Developmental Biology, Washington University in St. Louis",2,0.85748,0.88273,0.16029,0.16517,0.74862,0.76213,0.53814,0.52267,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2021-09-07,Adult,Adult,Spinal Cord,Nervous System
66012,SRR15783456,SRX12076334,SRS10057000,SRP336073,PRJNA761449,Myostatin is a negative regulator of adult neurogenesis in zebrafish,GSE183644,Transcriptome Analysis,Intrinsic and extrinsic inhibition of axonal and neuronal regeneration obstruct spinal cord SC repair in mammals. In contrast  adult zebrafish achieve functional recovery post SC damage. While studies of innate SC regeneration have focused on axon regrowth as a primary repair mechanism  how local neurogenesis impacts functional recovery is unknown. We uncovered dynamic expression of myostatin b mstnb in a niche of dorsal ependymal progenitors post complete SC transection in zebrafish. Genetic loss of function in mstnb impaired functional recovery  although glial and axonal bridging across the lesion were unaffected. Using a series of transgenic reporter lines  we quantified the numbers of stem  progenitor  and neuronal cells in the absence of mstnb. We found neural stem cell proliferation was reduced  while newborn neurons were increased in mstnb null tissues  suggesting mstnb is a negative regulator of neurogenesis. Molecularly  neuron differentiation genes were upregulated  while the neural stem cell maintenance gene fgf1b was downregulated in mstnb mutants. Finally  we show that human FGF1 treatment rescued neuronal gene expression in mstnb mutants. These studies uncover unanticipated neurogenic functions for mstnb in adult zebrafish  and establish the importance of local neurogenesis for functional SC repair. Overall design: Gene expression profiling of mstn mutants and wildtype at control and one xxx post injury.,,pubmed:36417881,,SC  mstnb mutant   1 wpi   replicate 2,GSM5566275,,source name:Spinal cord|tissue:Spinal cord|experiment:Spinal cord SC injury|time:1 xxx post injury|genotype:mstnb mutant  / ,SC  mstnb mutant   1 wpi   replicate 2,Quality QC and trimming of adapters and short sequences were performed using Fastx. Sequencing reads were mapped to the zebrafish genome Zv11 using Bowtie2  then assembled and quantified using the Cufflinks and Cuffdiff algorithms. Genes with log2fold enrichment between  1 and 1 or adjusted p value ≥ 0.01 were considered insignificant. Genome build: Zv11 Supplementary files format and content: Processed data is store csv format files. All files contain FPKM expression values of all the genes in different replicates and experimental condition. Supplementary files format and content: Additionally  log2 Fold change is calculate between conditions as indicated in the file name.,Spinal cord,Zebrafish were anaesthetized using MS 222. Fine scissors were used to make a small incision that transects the SC 4 mm caudal to the brainstem region. Complete transection was visually confirmed at the time of surgery. Injured animals were also assessed at 2 or 3 dpi to confirm loss of swim capacity post surgery. For sham injuries  animals were anaesthetized  and fine scissors were used to transect skin and muscle tissues without xxx SCI.,Two mm SC sections  including the lesion site plus additional rostral and caudal tissue proximal to the lesion  were collected from mstnb mutants and wild type siblings at 1 wpi. Uninjured mstnb mutants and wild type SCs were also  collected. Total RNA was prepared using NucleoSpin RNA Plus XS Clontech  cat# 740990 TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp paired end reading strategy.,Adult zebrafish  were maintained at the Washington University Zebrafish Core Facility. All animal experiments were performed in compliance with institutional animal protocols. Male and female animals between 3 month and 9 month of 2 cm in length were used. Experimental fish and control siblings of similar size and equal sex distribution were used for all experiments. SC transection surgeries and regeneration analyses were performed in a blinded manner  and 2 to 4 independent experiments were repeated using different clutches of animals.,tissue:Spinal cord|experiment:Spinal cord SC injury|time:1 xxx post injury|genotype:mstnb mutant  / ,GSM5566275,GSM5566275: SC  mstnb mutant   1 wpi   replicate 2; Danio rerio; RNA Seq,GSM5566275,,1,Two mm SC sections  including the lesion site plus additional rostral and caudal tissue proximal to the lesion  were collected from mstnb mutants and wild type siblings at 1 wpi. Uninjured mstnb mutants and wild type SCs were also  collected. Total RNA was prepared using NucleoSpin RNA Plus XS Clontech  cat# 740990 TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp paired end reading strategy.,GEO Accession:GSM5566275,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP336073,,loader:fastq load.py,b5-mstnb-mut-1wpi-2.TCATACTGTC-GACGGTAACA.TCATACTGTC-GACGGTAACA_S76_L003_R1_001.fastq.gz b5-mstnb-mut-1wpi-2.TCATACTGTC-GACGGTAACA.TCATACTGTC-GACGGTAACA_S76_L003_R2_001.fastq.gz,fastq fastq,14646143226.0,48497163.0,GSM5566275 r1,0:151 1:151,A:4126803891;C:3109100967;G:3456339137;T:3953737070;N:162161,151,151,,,4126803891,3109100967,3456339137,3953737070,162161,SRX12076334,SRS10057000,SRA1289934,GEO,"Developmental Biology, Washington University in St. Louis",2,0.91954,0.92658,0.15759,0.16283,0.70767,0.71843,0.53151,0.52744,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2021-09-07,Adult,Adult,Spinal Cord,Nervous System
66013,SRR15783455,SRX12076332,SRS10056999,SRP336073,PRJNA761449,Myostatin is a negative regulator of adult neurogenesis in zebrafish,GSE183644,Transcriptome Analysis,Intrinsic and extrinsic inhibition of axonal and neuronal regeneration obstruct spinal cord SC repair in mammals. In contrast  adult zebrafish achieve functional recovery post SC damage. While studies of innate SC regeneration have focused on axon regrowth as a primary repair mechanism  how local neurogenesis impacts functional recovery is unknown. We uncovered dynamic expression of myostatin b mstnb in a niche of dorsal ependymal progenitors post complete SC transection in zebrafish. Genetic loss of function in mstnb impaired functional recovery  although glial and axonal bridging across the lesion were unaffected. Using a series of transgenic reporter lines  we quantified the numbers of stem  progenitor  and neuronal cells in the absence of mstnb. We found neural stem cell proliferation was reduced  while newborn neurons were increased in mstnb null tissues  suggesting mstnb is a negative regulator of neurogenesis. Molecularly  neuron differentiation genes were upregulated  while the neural stem cell maintenance gene fgf1b was downregulated in mstnb mutants. Finally  we show that human FGF1 treatment rescued neuronal gene expression in mstnb mutants. These studies uncover unanticipated neurogenic functions for mstnb in adult zebrafish  and establish the importance of local neurogenesis for functional SC repair. Overall design: Gene expression profiling of mstn mutants and wildtype at control and one xxx post injury.,,pubmed:36417881,,SC  mstnb mutant   1 wpi   replicate 1,GSM5566274,,source name:Spinal cord|tissue:Spinal cord|experiment:Spinal cord SC injury|time:1 xxx post injury|genotype:mstnb mutant  / ,SC  mstnb mutant   1 wpi   replicate 1,Quality QC and trimming of adapters and short sequences were performed using Fastx. Sequencing reads were mapped to the zebrafish genome Zv11 using Bowtie2  then assembled and quantified using the Cufflinks and Cuffdiff algorithms. Genes with log2fold enrichment between  1 and 1 or adjusted p value ≥ 0.01 were considered insignificant. Genome build: Zv11 Supplementary files format and content: Processed data is store csv format files. All files contain FPKM expression values of all the genes in different replicates and experimental condition. Supplementary files format and content: Additionally  log2 Fold change is calculate between conditions as indicated in the file name.,Spinal cord,Zebrafish were anaesthetized using MS 222. Fine scissors were used to make a small incision that transects the SC 4 mm caudal to the brainstem region. Complete transection was visually confirmed at the time of surgery. Injured animals were also assessed at 2 or 3 dpi to confirm loss of swim capacity post surgery. For sham injuries  animals were anaesthetized  and fine scissors were used to transect skin and muscle tissues without xxx SCI.,Two mm SC sections  including the lesion site plus additional rostral and caudal tissue proximal to the lesion  were collected from mstnb mutants and wild type siblings at 1 wpi. Uninjured mstnb mutants and wild type SCs were also  collected. Total RNA was prepared using NucleoSpin RNA Plus XS Clontech  cat# 740990 TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp paired end reading strategy.,Adult zebrafish  were maintained at the Washington University Zebrafish Core Facility. All animal experiments were performed in compliance with institutional animal protocols. Male and female animals between 3 month and 9 month of 2 cm in length were used. Experimental fish and control siblings of similar size and equal sex distribution were used for all experiments. SC transection surgeries and regeneration analyses were performed in a blinded manner  and 2 to 4 independent experiments were repeated using different clutches of animals.,tissue:Spinal cord|experiment:Spinal cord SC injury|time:1 xxx post injury|genotype:mstnb mutant  / ,GSM5566274,GSM5566274: SC  mstnb mutant   1 wpi   replicate 1; Danio rerio; RNA Seq,GSM5566274,,1,Two mm SC sections  including the lesion site plus additional rostral and caudal tissue proximal to the lesion  were collected from mstnb mutants and wild type siblings at 1 wpi. Uninjured mstnb mutants and wild type SCs were also  collected. Total RNA was prepared using NucleoSpin RNA Plus XS Clontech  cat# 740990 TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp paired end reading strategy.,GEO Accession:GSM5566274,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP336073,,loader:fastq load.py,b4-mstnb-mut-1wpi-1.CGACTTATGC-CTCTCCAACG.CGACTTATGC-CTCTCCAACG_S55_L003_R1_001.fastq.gz b4-mstnb-mut-1wpi-1.CGACTTATGC-CTCTCCAACG.CGACTTATGC-CTCTCCAACG_S55_L003_R2_001.fastq.gz,fastq fastq,14196618642.0,47008671.0,GSM5566274 r1,0:151 1:151,A:3947758941;C:3098646858;G:3422183464;T:3727869800;N:159579,151,151,,,3947758941,3098646858,3422183464,3727869800,159579,SRX12076332,SRS10056999,SRA1289934,GEO,"Developmental Biology, Washington University in St. Louis",2,0.92795,0.9335,0.13646,0.14167,0.71104,0.72062,0.45975,0.53033,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2021-09-07,Adult,Adult,Spinal Cord,Nervous System
66014,SRR15783454,SRX12076330,SRS10056998,SRP336073,PRJNA761449,Myostatin is a negative regulator of adult neurogenesis in zebrafish,GSE183644,Transcriptome Analysis,Intrinsic and extrinsic inhibition of axonal and neuronal regeneration obstruct spinal cord SC repair in mammals. In contrast  adult zebrafish achieve functional recovery post SC damage. While studies of innate SC regeneration have focused on axon regrowth as a primary repair mechanism  how local neurogenesis impacts functional recovery is unknown. We uncovered dynamic expression of myostatin b mstnb in a niche of dorsal ependymal progenitors post complete SC transection in zebrafish. Genetic loss of function in mstnb impaired functional recovery  although glial and axonal bridging across the lesion were unaffected. Using a series of transgenic reporter lines  we quantified the numbers of stem  progenitor  and neuronal cells in the absence of mstnb. We found neural stem cell proliferation was reduced  while newborn neurons were increased in mstnb null tissues  suggesting mstnb is a negative regulator of neurogenesis. Molecularly  neuron differentiation genes were upregulated  while the neural stem cell maintenance gene fgf1b was downregulated in mstnb mutants. Finally  we show that human FGF1 treatment rescued neuronal gene expression in mstnb mutants. These studies uncover unanticipated neurogenic functions for mstnb in adult zebrafish  and establish the importance of local neurogenesis for functional SC repair. Overall design: Gene expression profiling of mstn mutants and wildtype at control and one xxx post injury.,,pubmed:36417881,,SC  mstnb wildtype   1 wpi   replicate 2,GSM5566273,,source name:Spinal cord|tissue:Spinal cord|experiment:Spinal cord SC injury|time:1 xxx post injury|genotype:wildtype,SC  mstnb wildtype   1 wpi   replicate 2,Quality QC and trimming of adapters and short sequences were performed using Fastx. Sequencing reads were mapped to the zebrafish genome Zv11 using Bowtie2  then assembled and quantified using the Cufflinks and Cuffdiff algorithms. Genes with log2fold enrichment between  1 and 1 or adjusted p value ≥ 0.01 were considered insignificant. Genome build: Zv11 Supplementary files format and content: Processed data is store csv format files. All files contain FPKM expression values of all the genes in different replicates and experimental condition. Supplementary files format and content: Additionally  log2 Fold change is calculate between conditions as indicated in the file name.,Spinal cord,Zebrafish were anaesthetized using MS 222. Fine scissors were used to make a small incision that transects the SC 4 mm caudal to the brainstem region. Complete transection was visually confirmed at the time of surgery. Injured animals were also assessed at 2 or 3 dpi to confirm loss of swim capacity post surgery. For sham injuries  animals were anaesthetized  and fine scissors were used to transect skin and muscle tissues without xxx SCI.,Two mm SC sections  including the lesion site plus additional rostral and caudal tissue proximal to the lesion  were collected from mstnb mutants and wild type siblings at 1 wpi. Uninjured mstnb mutants and wild type SCs were also  collected. Total RNA was prepared using NucleoSpin RNA Plus XS Clontech  cat# 740990 TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp paired end reading strategy.,Adult zebrafish  were maintained at the Washington University Zebrafish Core Facility. All animal experiments were performed in compliance with institutional animal protocols. Male and female animals between 3 month and 9 month of 2 cm in length were used. Experimental fish and control siblings of similar size and equal sex distribution were used for all experiments. SC transection surgeries and regeneration analyses were performed in a blinded manner  and 2 to 4 independent experiments were repeated using different clutches of animals.,tissue:Spinal cord|experiment:Spinal cord SC injury|time:1 xxx post injury|genotype:wildtype,GSM5566273,GSM5566273: SC  mstnb wildtype   1 wpi   replicate 2; Danio rerio; RNA Seq,GSM5566273,,1,Two mm SC sections  including the lesion site plus additional rostral and caudal tissue proximal to the lesion  were collected from mstnb mutants and wild type siblings at 1 wpi. Uninjured mstnb mutants and wild type SCs were also  collected. Total RNA was prepared using NucleoSpin RNA Plus XS Clontech  cat# 740990 TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp paired end reading strategy.,GEO Accession:GSM5566273,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP336073,,loader:fastq load.py,b3-mstnb-wt-1wpi-3.CGAATGGTAA-GCCGTTGAAG.CGAATGGTAA-GCCGTTGAAG_S53_L003_R1_001.fastq.gz b3-mstnb-wt-1wpi-3.CGAATGGTAA-GCCGTTGAAG.CGAATGGTAA-GCCGTTGAAG_S53_L003_R2_001.fastq.gz,fastq fastq,14482193466.0,47954283.0,GSM5566273 r1,0:151 1:151,A:4100543408;C:3089308480;G:3430244810;T:3861934913;N:161855,151,151,,,4100543408,3089308480,3430244810,3861934913,161855,SRX12076330,SRS10056998,SRA1289934,GEO,"Developmental Biology, Washington University in St. Louis",2,0.91623,0.92213,0.16999,0.17638,0.71098,0.72216,0.52445,0.52788,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2021-09-07,Adult,Adult,Spinal Cord,Nervous System
66015,SRR15783453,SRX12076328,SRS10056997,SRP336073,PRJNA761449,Myostatin is a negative regulator of adult neurogenesis in zebrafish,GSE183644,Transcriptome Analysis,Intrinsic and extrinsic inhibition of axonal and neuronal regeneration obstruct spinal cord SC repair in mammals. In contrast  adult zebrafish achieve functional recovery post SC damage. While studies of innate SC regeneration have focused on axon regrowth as a primary repair mechanism  how local neurogenesis impacts functional recovery is unknown. We uncovered dynamic expression of myostatin b mstnb in a niche of dorsal ependymal progenitors post complete SC transection in zebrafish. Genetic loss of function in mstnb impaired functional recovery  although glial and axonal bridging across the lesion were unaffected. Using a series of transgenic reporter lines  we quantified the numbers of stem  progenitor  and neuronal cells in the absence of mstnb. We found neural stem cell proliferation was reduced  while newborn neurons were increased in mstnb null tissues  suggesting mstnb is a negative regulator of neurogenesis. Molecularly  neuron differentiation genes were upregulated  while the neural stem cell maintenance gene fgf1b was downregulated in mstnb mutants. Finally  we show that human FGF1 treatment rescued neuronal gene expression in mstnb mutants. These studies uncover unanticipated neurogenic functions for mstnb in adult zebrafish  and establish the importance of local neurogenesis for functional SC repair. Overall design: Gene expression profiling of mstn mutants and wildtype at control and one xxx post injury.,,pubmed:36417881,,SC  mstnb wildtype   1 wpi   replicate 1,GSM5566272,,source name:Spinal cord|tissue:Spinal cord|experiment:Spinal cord SC injury|time:1 xxx post injury|genotype:wildtype,SC  mstnb wildtype   1 wpi   replicate 1,Quality QC and trimming of adapters and short sequences were performed using Fastx. Sequencing reads were mapped to the zebrafish genome Zv11 using Bowtie2  then assembled and quantified using the Cufflinks and Cuffdiff algorithms. Genes with log2fold enrichment between  1 and 1 or adjusted p value ≥ 0.01 were considered insignificant. Genome build: Zv11 Supplementary files format and content: Processed data is store csv format files. All files contain FPKM expression values of all the genes in different replicates and experimental condition. Supplementary files format and content: Additionally  log2 Fold change is calculate between conditions as indicated in the file name.,Spinal cord,Zebrafish were anaesthetized using MS 222. Fine scissors were used to make a small incision that transects the SC 4 mm caudal to the brainstem region. Complete transection was visually confirmed at the time of surgery. Injured animals were also assessed at 2 or 3 dpi to confirm loss of swim capacity post surgery. For sham injuries  animals were anaesthetized  and fine scissors were used to transect skin and muscle tissues without xxx SCI.,Two mm SC sections  including the lesion site plus additional rostral and caudal tissue proximal to the lesion  were collected from mstnb mutants and wild type siblings at 1 wpi. Uninjured mstnb mutants and wild type SCs were also  collected. Total RNA was prepared using NucleoSpin RNA Plus XS Clontech  cat# 740990 TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp paired end reading strategy.,Adult zebrafish  were maintained at the Washington University Zebrafish Core Facility. All animal experiments were performed in compliance with institutional animal protocols. Male and female animals between 3 month and 9 month of 2 cm in length were used. Experimental fish and control siblings of similar size and equal sex distribution were used for all experiments. SC transection surgeries and regeneration analyses were performed in a blinded manner  and 2 to 4 independent experiments were repeated using different clutches of animals.,tissue:Spinal cord|experiment:Spinal cord SC injury|time:1 xxx post injury|genotype:wildtype,GSM5566272,GSM5566272: SC  mstnb wildtype   1 wpi   replicate 1; Danio rerio; RNA Seq,GSM5566272,,1,Two mm SC sections  including the lesion site plus additional rostral and caudal tissue proximal to the lesion  were collected from mstnb mutants and wild type siblings at 1 wpi. Uninjured mstnb mutants and wild type SCs were also  collected. Total RNA was prepared using NucleoSpin RNA Plus XS Clontech  cat# 740990 TruSeq libraries were prepared and sequenced on Illumina HiSeq 3000 using 50 bp paired end reading strategy.,GEO Accession:GSM5566272,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP336073,,loader:fastq load.py,b1-mstnb-wt-1wpi-1.TGCACTAGGC-ACCAGAAGTA.TGCACTAGGC-ACCAGAAGTA_S83_L003_R1_001.fastq.gz b1-mstnb-wt-1wpi-1.TGCACTAGGC-ACCAGAAGTA.TGCACTAGGC-ACCAGAAGTA_S83_L003_R2_001.fastq.gz,fastq fastq,13011457090.0,43084295.0,GSM5566272 r1,0:151 1:151,A:3677087058;C:2775903100;G:3064396339;T:3493922901;N:147692,151,151,,,3677087058,2775903100,3064396339,3493922901,147692,SRX12076328,SRS10056997,SRA1289934,GEO,"Developmental Biology, Washington University in St. Louis",2,0.92358,0.92964,0.1313,0.13299,0.71745,0.72772,0.52678,0.52632,151,151,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2021-09-07,Adult,Adult,Spinal Cord,Nervous System
68047,SRR17568714,SRX13737925,SRS11618582,SRP354594,PRJNA796379,RNA sequencing of zebrafish spinal cord tissue at 1 xxx post injury,GSE193502,Transcriptome Analysis,To identify regulators of spinal cord regeneration  we  performed RNA sequencing of zebrafish spinal cord at 1 week post sham injury and post transection. Overall design: Spinal cord RNA profiles 1week post spinal cord transection and in sham injured controls.,parent bioproject:PRJNA796373,pubmed:37567873,,spinal cord  1 week post transection 3 RNA seq,GSM5811629,,source name:spinal cord  1 week post transection|treatment:injured|tissue:spinal cord|geo loc name:missing|collection date:missing,spinal cord  1 week post transection 3 RNA seq,Reads were trimed by trim galore and them aligned to the zebrafish genome danRer10 using Tophat2 v 2.2.1 Mapped reads were filtered by samtools v 1.3.1and counted by htseq count v 0.6.0 Differential analyses were performed by Bioconductor package DESeq2 v 1.26.0 Supplementary files format and content: text file contain raw counts for genes exported by htseq counts v 0.6.0,spinal cord  1 week post transection,,Sham injured and injured 2 mm rostral and caudal to the lesion site spinal cords were dissected and RNA was harvested using Trizol reagent. Genomic DNA was removed using RNA Clean and Concentrator Kit Zymo Research.  Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using Hiseq4000 50bp  SR  1 lane,,treatment:injured|tissue:spinal cord,GSM5811629,GSM5811629: spinal cord  1 week post transection 3 RNA seq; Danio rerio; RNA Seq,GSM5811629 r1,GSM5811629,1,Sham injured and injured 2 mm rostral and caudal to the lesion site spinal cords were dissected and RNA was harvested using Trizol reagent. Genomic DNA was removed using RNA Clean and Concentrator Kit Zymo Research.  Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using Hiseq4000 50bp  SR  1 lane,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP354594,,loader:fastq load.py,5010-R-S6_S6_L001_R1_001.fastq.gz,fastq,3115530585.0,61088835.0,GSM5811629 r1,0:51,A:767862089;C:747817723;G:714538287;T:885123149;N:189337,51,,,,767862089,747817723,714538287,885123149,189337,SRX13737925,SRS11618582,SRA1355593,"Cell biology, Duke University","Poss, Cell Biology, Duke University",1,0.9171,,0.12443,,0.68527,,0.48166,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2022-01-11,Larval,Larval,Spinal Cord,Nervous System
68048,SRR17568715,SRX13737924,SRS11618581,SRP354594,PRJNA796379,RNA sequencing of zebrafish spinal cord tissue at 1 xxx post injury,GSE193502,Transcriptome Analysis,To identify regulators of spinal cord regeneration  we  performed RNA sequencing of zebrafish spinal cord at 1 week post sham injury and post transection. Overall design: Spinal cord RNA profiles 1week post spinal cord transection and in sham injured controls.,parent bioproject:PRJNA796373,pubmed:37567873,,spinal cord  1 week post transection 2 RNA seq,GSM5811628,,source name:spinal cord  1 week post transection|treatment:injured|tissue:spinal cord|geo loc name:missing|collection date:missing,spinal cord  1 week post transection 2 RNA seq,Reads were trimed by trim galore and them aligned to the zebrafish genome danRer10 using Tophat2 v 2.2.1 Mapped reads were filtered by samtools v 1.3.1and counted by htseq count v 0.6.0 Differential analyses were performed by Bioconductor package DESeq2 v 1.26.0 Supplementary files format and content: text file contain raw counts for genes exported by htseq counts v 0.6.0,spinal cord  1 week post transection,,Sham injured and injured 2 mm rostral and caudal to the lesion site spinal cords were dissected and RNA was harvested using Trizol reagent. Genomic DNA was removed using RNA Clean and Concentrator Kit Zymo Research.  Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using Hiseq4000 50bp  SR  1 lane,,treatment:injured|tissue:spinal cord,GSM5811628,GSM5811628: spinal cord  1 week post transection 2 RNA seq; Danio rerio; RNA Seq,GSM5811628 r1,GSM5811628,1,Sham injured and injured 2 mm rostral and caudal to the lesion site spinal cords were dissected and RNA was harvested using Trizol reagent. Genomic DNA was removed using RNA Clean and Concentrator Kit Zymo Research.  Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using Hiseq4000 50bp  SR  1 lane,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP354594,,loader:fastq load.py,5010-R-S5_S5_L001_R1_001.fastq.gz,fastq,2766582873.0,54246723.0,GSM5811628 r1,0:51,A:680143141;C:661759820;G:636420820;T:788093710;N:165382,51,,,,680143141,661759820,636420820,788093710,165382,SRX13737924,SRS11618581,SRA1355593,"Cell biology, Duke University","Poss, Cell Biology, Duke University",1,0.91556,,0.12145,,0.67874,,0.48519,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2022-01-11,Larval,Larval,Spinal Cord,Nervous System
68049,SRR17568716,SRX13737923,SRS11618580,SRP354594,PRJNA796379,RNA sequencing of zebrafish spinal cord tissue at 1 xxx post injury,GSE193502,Transcriptome Analysis,To identify regulators of spinal cord regeneration  we  performed RNA sequencing of zebrafish spinal cord at 1 week post sham injury and post transection. Overall design: Spinal cord RNA profiles 1week post spinal cord transection and in sham injured controls.,parent bioproject:PRJNA796373,pubmed:37567873,,spinal cord  1 week post transection 1 RNA seq,GSM5811627,,source name:spinal cord  1 week post transection|treatment:injured|tissue:spinal cord|geo loc name:missing|collection date:missing,spinal cord  1 week post transection 1 RNA seq,Reads were trimed by trim galore and them aligned to the zebrafish genome danRer10 using Tophat2 v 2.2.1 Mapped reads were filtered by samtools v 1.3.1and counted by htseq count v 0.6.0 Differential analyses were performed by Bioconductor package DESeq2 v 1.26.0 Supplementary files format and content: text file contain raw counts for genes exported by htseq counts v 0.6.0,spinal cord  1 week post transection,,Sham injured and injured 2 mm rostral and caudal to the lesion site spinal cords were dissected and RNA was harvested using Trizol reagent. Genomic DNA was removed using RNA Clean and Concentrator Kit Zymo Research.  Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using Hiseq4000 50bp  SR  1 lane,,treatment:injured|tissue:spinal cord,GSM5811627,GSM5811627: spinal cord  1 week post transection 1 RNA seq; Danio rerio; RNA Seq,GSM5811627 r1,GSM5811627,1,Sham injured and injured 2 mm rostral and caudal to the lesion site spinal cords were dissected and RNA was harvested using Trizol reagent. Genomic DNA was removed using RNA Clean and Concentrator Kit Zymo Research.  Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using Hiseq4000 50bp  SR  1 lane,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP354594,,loader:fastq load.py,5010-R-S4_S4_L001_R1_001.fastq.gz,fastq,2295404022.0,45007922.0,GSM5811627 r1,0:51,A:562239638;C:552545662;G:529838068;T:650650889;N:129765,51,,,,562239638,552545662,529838068,650650889,129765,SRX13737923,SRS11618580,SRA1355593,"Cell biology, Duke University","Poss, Cell Biology, Duke University",1,0.91584,,0.12184,,0.6817,,0.4858,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2022-01-11,Larval,Larval,Spinal Cord,Nervous System
68050,SRR17568717,SRX13737922,SRS11618579,SRP354594,PRJNA796379,RNA sequencing of zebrafish spinal cord tissue at 1 xxx post injury,GSE193502,Transcriptome Analysis,To identify regulators of spinal cord regeneration  we  performed RNA sequencing of zebrafish spinal cord at 1 week post sham injury and post transection. Overall design: Spinal cord RNA profiles 1week post spinal cord transection and in sham injured controls.,parent bioproject:PRJNA796373,pubmed:37567873,,spinal cord  sham 3 RNA seq,GSM5811626,,source name:spinal cord  sham|treatment:uninjured|tissue:spinal cord|geo loc name:missing|collection date:missing,spinal cord  sham 3 RNA seq,Reads were trimed by trim galore and them aligned to the zebrafish genome danRer10 using Tophat2 v 2.2.1 Mapped reads were filtered by samtools v 1.3.1and counted by htseq count v 0.6.0 Differential analyses were performed by Bioconductor package DESeq2 v 1.26.0 Supplementary files format and content: text file contain raw counts for genes exported by htseq counts v 0.6.0,spinal cord  sham,,Sham injured and injured 2 mm rostral and caudal to the lesion site spinal cords were dissected and RNA was harvested using Trizol reagent. Genomic DNA was removed using RNA Clean and Concentrator Kit Zymo Research.  Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using Hiseq4000 50bp  SR  1 lane,,treatment:uninjured|tissue:spinal cord,GSM5811626,GSM5811626: spinal cord  sham 3 RNA seq; Danio rerio; RNA Seq,GSM5811626 r1,GSM5811626,1,Sham injured and injured 2 mm rostral and caudal to the lesion site spinal cords were dissected and RNA was harvested using Trizol reagent. Genomic DNA was removed using RNA Clean and Concentrator Kit Zymo Research.  Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using Hiseq4000 50bp  SR  1 lane,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP354594,,loader:fastq load.py,5010-R-S3_S3_L001_R1_001.fastq.gz,fastq,2083979646.0,40862346.0,GSM5811626 r1,0:51,A:511949359;C:497119626;G:483019281;T:591758053;N:133327,51,,,,511949359,497119626,483019281,591758053,133327,SRX13737922,SRS11618579,SRA1355593,"Cell biology, Duke University","Poss, Cell Biology, Duke University",1,0.91688,,0.12011,,0.67359,,0.48254,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2022-01-11,Undetermined,Undetermined,Spinal Cord,Nervous System
68051,SRR17568718,SRX13737921,SRS11618578,SRP354594,PRJNA796379,RNA sequencing of zebrafish spinal cord tissue at 1 xxx post injury,GSE193502,Transcriptome Analysis,To identify regulators of spinal cord regeneration  we  performed RNA sequencing of zebrafish spinal cord at 1 week post sham injury and post transection. Overall design: Spinal cord RNA profiles 1week post spinal cord transection and in sham injured controls.,parent bioproject:PRJNA796373,pubmed:37567873,,spinal cord  sham 2 RNA seq,GSM5811625,,source name:spinal cord  sham|treatment:uninjured|tissue:spinal cord|geo loc name:missing|collection date:missing,spinal cord  sham 2 RNA seq,Reads were trimed by trim galore and them aligned to the zebrafish genome danRer10 using Tophat2 v 2.2.1 Mapped reads were filtered by samtools v 1.3.1and counted by htseq count v 0.6.0 Differential analyses were performed by Bioconductor package DESeq2 v 1.26.0 Supplementary files format and content: text file contain raw counts for genes exported by htseq counts v 0.6.0,spinal cord  sham,,Sham injured and injured 2 mm rostral and caudal to the lesion site spinal cords were dissected and RNA was harvested using Trizol reagent. Genomic DNA was removed using RNA Clean and Concentrator Kit Zymo Research.  Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using Hiseq4000 50bp  SR  1 lane,,treatment:uninjured|tissue:spinal cord,GSM5811625,GSM5811625: spinal cord  sham 2 RNA seq; Danio rerio; RNA Seq,GSM5811625 r1,GSM5811625,1,Sham injured and injured 2 mm rostral and caudal to the lesion site spinal cords were dissected and RNA was harvested using Trizol reagent. Genomic DNA was removed using RNA Clean and Concentrator Kit Zymo Research.  Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using Hiseq4000 50bp  SR  1 lane,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP354594,,loader:fastq load.py,5010-R-S2_S2_L001_R1_001.fastq.gz,fastq,3052752186.0,59857886.0,GSM5811625 r1,0:51,A:774368739;C:715482304;G:690800657;T:871933843;N:166643,51,,,,774368739,715482304,690800657,871933843,166643,SRX13737921,SRS11618578,SRA1355593,"Cell biology, Duke University","Poss, Cell Biology, Duke University",1,0.90922,,0.14399,,0.70067,,0.49521,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2022-01-11,Undetermined,Undetermined,Spinal Cord,Nervous System
68052,SRR17568719,SRX13737920,SRS11618577,SRP354594,PRJNA796379,RNA sequencing of zebrafish spinal cord tissue at 1 xxx post injury,GSE193502,Transcriptome Analysis,To identify regulators of spinal cord regeneration  we  performed RNA sequencing of zebrafish spinal cord at 1 week post sham injury and post transection. Overall design: Spinal cord RNA profiles 1week post spinal cord transection and in sham injured controls.,parent bioproject:PRJNA796373,pubmed:37567873,,spinal cord  sham 1 RNA seq,GSM5811624,,source name:spinal cord  sham|treatment:uninjured|tissue:spinal cord|geo loc name:missing|collection date:missing,spinal cord  sham 1 RNA seq,Reads were trimed by trim galore and them aligned to the zebrafish genome danRer10 using Tophat2 v 2.2.1 Mapped reads were filtered by samtools v 1.3.1and counted by htseq count v 0.6.0 Differential analyses were performed by Bioconductor package DESeq2 v 1.26.0 Supplementary files format and content: text file contain raw counts for genes exported by htseq counts v 0.6.0,spinal cord  sham,,Sham injured and injured 2 mm rostral and caudal to the lesion site spinal cords were dissected and RNA was harvested using Trizol reagent. Genomic DNA was removed using RNA Clean and Concentrator Kit Zymo Research.  Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using Hiseq4000 50bp  SR  1 lane,,treatment:uninjured|tissue:spinal cord,GSM5811624,GSM5811624: spinal cord  sham 1 RNA seq; Danio rerio; RNA Seq,GSM5811624 r1,GSM5811624,1,Sham injured and injured 2 mm rostral and caudal to the lesion site spinal cords were dissected and RNA was harvested using Trizol reagent. Genomic DNA was removed using RNA Clean and Concentrator Kit Zymo Research.  Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using Hiseq4000 50bp  SR  1 lane,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP354594,,loader:fastq load.py,5010-R-S1_S1_L001_R1_001.fastq.gz,fastq,2701690014.0,52974314.0,GSM5811624 r1,0:51,A:690988139;C:631021472;G:606713558;T:772805073;N:161772,51,,,,690988139,631021472,606713558,772805073,161772,SRX13737920,SRS11618577,SRA1355593,"Cell biology, Duke University","Poss, Cell Biology, Duke University",1,0.90707,,0.14694,,0.69897,,0.48056,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2022-01-11,Undetermined,Undetermined,Spinal Cord,Nervous System