run_metadata: 42573

This data as json

rowid	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	tech_variant	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
42573	SRR5805889	SRX2985072	SRS2337732	SRP111129	PRJNA393181	Primary spinal OPC culture system from adult zebrafish to study oligodendrocyte differentiation in vitro	GSE100821	Transcriptome Analysis	Endogenous oligodendrocyte progenitor cells OPCs are a promising target to improve functional recovery post spinal cord injury SCI by remyelinating denuded and therefore vulnerable axons. Demyelination is the result of a primary insult and secondary injury leading to conduction blocks and long term degeneration of the axons which subsequently can lead to the loss of their neuron. In response to SCI dormant OPCs can be activated and subsequently start to proliferate and differentiate into mature myelinating oligodendrocytes OLs. Therefore researchers strive to control OPC responses and utilize small molecule screening approaches in order to identify mechanisms of OPC activation proliferation migration and differentiation. Overall design: DEG analysis of primary OPC and OL populations 5 biological replicates per population		pubmed:28959189		OPC1	GSM2694018		tissue:adult spinal cord\|cell type:oligodendrocyte precursor cell	OPC1	basecalling: bcl2fastq 2.17.1.14 alignment: Libraries were mapped to GRCz10 with GSNAP v 2016 09 23; splice site were supported by using Ensembl version 81 fragment count: fragments were counted with featureCounts v1.5.2 based on Ensembl version 81 Genome build: GRCz10 Supplementary files format and content: tab delimited file from featureCounts bfx684.GRCz10.e81.txt.gz; columns are in the following order: Ensembl Gene ID Chromosom Exon Start Coordinates Exon End Coordinates Gene Length; Counts from the 2 Conditions and their 5 replicates	adult spinal cord		Spinal cord dissection tissue dissociation and nuclear labelling: Adult zebrafish were terminally anesthetized their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice before it was applied to a 20 µm OPCs Miltenyi Biotec # 130 101 812 or a 35 µm OL Corning # 352235 cell strainer respectively. post washing with 9 ml of HBSS the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes Invitrogen V35003 and incubated for 30´ at 28 °C to stain cellular nuclei. FACsorting of myelin rich spinal cord tissue: Cell suspensions were sorted directly into 96 well plates filled with culture media only or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore 2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220 followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.		cell type:oligodendrocyte precursor cell	GSM2694018	GSM2694018: OPC1; Danio rerio; RNA Seq	GSM2694018		1	Spinal cord dissection tissue dissociation and nuclear labelling: Adult zebrafish were terminally anesthetized their spinal cords exposed and the spinal cord tissue was carefully removed. Up to 5 spinal cords were dissected at once and placed in 1ml of Hanks´ Buffered Salt Solution HBSS Gibco. For the dissociation of spinal cords into a single cell suspension at room temperature the tissue was incubated for 3 min with 100 µL 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 µL pipette during the whole incubation time avoiding the formation of air bubbles. Then tissue digestion was stopped by adding 100 µL of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 µL HBSS. postwards the cell suspension was allowed to sit for 5’ at on ice before it was applied to a 20 µm OPCs Miltenyi Biotec # 130 101 812 or a 35 µm OL Corning # 352235 cell strainer respectively. post washing with 9 ml of HBSS the cells were pelleted by centrifugation for 5’ at RT at 300g. The supernatant was removed cells were resuspended in 1 ml HBSS including 1 µl Vybrant™ DyeCycle™ Violet Stain Molecular Probes Invitrogen V35003 and incubated for 30´ at 28 °C to stain cellular nuclei. FACsorting of myelin rich spinal cord tissue: Cell suspensions were sorted directly into 96 well plates filled with culture media only or pre seeded with MN using a BD FACSAria sorter. For the detection of GFP a 488 nm excitation laser and a 530/30 bandpass filter were used. DsRed was detected with a 582/15 bandpass filter post excitation with a 561 nm laser. Vybrant™ DyeCycle™ Violet Stain was detected post 405 nm excitation and a 450/40 bandpass filter. Cellular events were defined by forward and side scatter profile and by the dsRed or GFP signal of the corresponding transgenic line. From this selection all events that showed incorporation of the Vybrant™ DyeCycle™ Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore 2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220 followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.	GEO Accession:GSM2694018	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP111129			L13372_Track-36592_R1.fastq.gz	fastq	844153204.0	11107279.0	GSM2694018 r2	0:76	A:247798416;C:176560506;G:176978398;T:242800972;N:14912	76				247798416	176560506	176978398	242800972	14912	SRX2985072	SRS2337732	SRA584085	GEO	Reimer Lab, CRT Dresden, TU Dresden	1	0.912		0.12665		0.79742		0.36358		76		B		usable mapping rate	illumina	hiseq_era	full_length	random_priming	nebnext	bulk	unknown	unknown		Germany	2017-07-05	Adult	Adult	Spinal Cord	Nervous System