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59 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "unknown" and tissue_curation = "Spinal Cord"

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experiment.platform 3

devstage_curation_coarse 3

devstage_curation 3

experiment.library_selection 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Spinal Cord · 59 ✖

technology 1

  • unknown · 59 ✖

experiment.library_strategy 1

experiment.library_source 1

  • TRANSCRIPTOMIC · 59 ✖
Link 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 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 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 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 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 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 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 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 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 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 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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 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 R…   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 R… 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
55972 55972 SRR10895875 SRX7564604 SRS6001805 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 009   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Spinal cord|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103178 L01 9 CL100103178 L01 9       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103178_L01_567_1.fq.gz CL100103178_L01_567_2.fq.gz fastq fastq 7926659000.0 79266590.0 CL100103178 L01 567 1.fq.gz 0:100 1:100 A:2177233520;C:1750763335;G:1793690428;T:2195598681;N:9373036 100 100     2177233520 1750763335 1793690428 2195598681 9373036 SRX7564604 SRS6001805 SRA1026516 BGI|BGI-Research BGI 1 0.90731   0.11069   0.70548   0.53521   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Spinal Cord Nervous System
55973 55973 SRR10895876 SRX7564603 SRS6001805 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 009   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Spinal cord|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103178 L01 8 CL100103178 L01 8       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103178_L01_563_1.fq.gz CL100103178_L01_563_2.fq.gz fastq fastq 9981278800.0 99812788.0 CL100103178 L01 563 1.fq.gz 0:100 1:100 A:2753622693;C:2192952746;G:2243702494;T:2779006876;N:11993991 100 100     2753622693 2192952746 2243702494 2779006876 11993991 SRX7564603 SRS6001805 SRA1026516 BGI|BGI-Research BGI 1 0.90715   0.11372   0.71467   0.5089   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Spinal Cord Nervous System
55974 55974 SRR10895877 SRX7564602 SRS6001805 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 009   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Spinal cord|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103178 L01 7 CL100103178 L01 7       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103178_L01_562_1.fq.gz CL100103178_L01_562_2.fq.gz fastq fastq 8857552800.0 88575528.0 CL100103178 L01 562 1.fq.gz 0:100 1:100 A:2418167382;C:1969456035;G:2015821568;T:2442764114;N:11343701 100 100     2418167382 1969456035 2015821568 2442764114 11343701 SRX7564602 SRS6001805 SRA1026516 BGI|BGI-Research BGI 1 0.90895   0.10978   0.71336   0.50272   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Spinal Cord Nervous System
55975 55975 SRR10895878 SRX7564601 SRS6001805 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 009   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Spinal cord|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103178 L01 6 CL100103178 L01 6       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103178_L01_564_1.fq.gz CL100103178_L01_564_2.fq.gz fastq fastq 7468499200.0 74684992.0 CL100103178 L01 564 1.fq.gz 0:100 1:100 A:2052720985;C:1649448011;G:1690698471;T:2068073830;N:7557903 100 100     2052720985 1649448011 1690698471 2068073830 7557903 SRX7564601 SRS6001805 SRA1026516 BGI|BGI-Research BGI 1 0.90905   0.10883   0.69578   0.54193   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Spinal Cord Nervous System
55976 55976 SRR10895881 SRX7564598 SRS6001805 SRP241982 PRJNA599026 Project of basal ray finned fishes PRJNA599026 Other The project is to study the oldest fish lineages in the ray finned fishes. Although they belong to fish their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates we provides insights into the molecular basis of terrestrial adaptation of basal ray finned fishes.   pubmed:33545088;pubmed:12470943     Zebrafish 009   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:Adult|sex:not determined|tissue:Spinal cord|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio : adult CL100103178 L01 5 CL100103178 L01 5       RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED BGISEQ BGISEQ-500   SRP241982     CL100103178_L01_561_1.fq.gz CL100103178_L01_561_2.fq.gz fastq fastq 9173572800.0 91735728.0 CL100103178 L01 561 1.fq.gz 0:100 1:100 A:2527132650;C:2020739240;G:2066720461;T:2548747865;N:10232584 100 100     2527132650 2020739240 2066720461 2548747865 10232584 SRX7564598 SRS6001805 SRA1026516 BGI|BGI-Research BGI 1 0.91539   0.11063   0.71427   0.48162   100   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2020-01-15 Adult Adult Spinal Cord Nervous System
66008 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 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 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 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 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 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 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 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 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 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 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 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 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 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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;