metadata: run_metadata: 40 rows where experiment.library_layout = "SINGLE", technology = "unknown" and tissue

40 rows where experiment.library_layout = "SINGLE", technology = "unknown" and tissue_curation = "Spinal Cord"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.title	sample.alias	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.study_ref	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.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
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
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");;