{"database": "metadata", "table": "run_metadata", "rows": [[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", null, "pubmed:28959189", null, "OL3", "GSM2694025", null, "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", null, "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\u00b4 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 \u00b5L 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 \u00b5L pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 \u00b5L of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 \u00b5L HBSS. postwards the cell suspension was allowed to sit for 5\u2019 at on ice  before it was applied to a 20 \u00b5m OPCs  Miltenyi Biotec  # 130 101 812 or a 35 \u00b5m OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5\u2019 at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 \u00b5l Vybrant\u2122 DyeCycle\u2122 Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30\u00b4 at 28 \u00b0C 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\u2122 DyeCycle\u2122 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\u2122 DyeCycle\u2122 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.", null, "cell type:oligodendrocyte", "GSM2694025", "GSM2694025: OL3; Danio rerio; RNA Seq", "GSM2694025", null, "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\u00b4 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 \u00b5L 0.25% Trypsin Sigma; T4549 / 1mM EDTA and triturated using a 200 \u00b5L pipette during the whole incubation time avoiding the formation of air bubbles. Then  tissue digestion was stopped by adding 100 \u00b5L of 20% fetal calf serum Sigma; F0804 in 2 mM CaCl2 and 300 \u00b5L HBSS. postwards the cell suspension was allowed to sit for 5\u2019 at on ice  before it was applied to a 20 \u00b5m OPCs  Miltenyi Biotec  # 130 101 812 or a 35 \u00b5m OL  Corning  # 352235 cell strainer  respectively. post washing with 9 ml of HBSS  the cells were pelleted by centrifugation for 5\u2019 at RT at 300g. The supernatant was removed  cells were resuspended in 1 ml HBSS including 1 \u00b5l Vybrant\u2122 DyeCycle\u2122 Violet Stain Molecular Probes  Invitrogen  V35003 and incubated for 30\u00b4 at 28 \u00b0C 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\u2122 DyeCycle\u2122 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\u2122 DyeCycle\u2122 Violet Stain were gated because this proved to be an ideal selection to separate the small zebrafish CNS cells from remaining cellular and myelin debris. For the RNAseq experiment  the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit   HV from Clontech was used to reverse transcribe the RNA and amplify full length cDNA according to the user manual. Therefore  2000 cells from five biological replicates of both lines Tgolig2:eGFP and Tgmbp:GFP where directly FACsorted in 5ul reaction buffer containing RNAse Inhibitor. post amplification of cDNA using 12 cycles  the cDNA was sheared to 200bp fragment length with 8 micro TUBE strip in the ultrasonicator Covaris LE220  followed by a library prep using NEBNext Ultra DNA Library Prep Kit for Illumina NEB.", "GEO Accession:GSM2694025", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP111129", null, null, "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, null, null, null, 349531521, 247172348, 248019907, 338738175, 73737, "SRX2985079", "SRS2337739", "SRA584085", "GEO", "Reimer Lab, CRT Dresden, TU Dresden", 1, 0.90617, null, 0.10315, null, 0.82329, null, 0.33103, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2017-07-05", "Adult", "Adult", "Spinal Cord", "Nervous System"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["42553"], "units": {}, "query_ms": 12.658282999836956}