{"database": "metadata", "table": "run_metadata", "rows": [[68250, "SRR17691952", "SRX13855137", "SRS11731662", "SRP356155", "PRJNA799333", "RNA seq dataset of different neuronal cell types and progenitors in the developing zebrafish retina at 42 hpf", "GSE194158", "Transcriptome Analysis", "This dataset was acquired to identify the gene expression profile of developing retinal cell types at 42 hpf: retinal ganglion cells  photoreceptors  inhibitory neurons amacrine cells and horizontal cells and progenitor cells. Overall design: Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP  Tgcrx:gap CFP  Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates  25 retinas were pooled.", null, null, null, "Progenitors rep1", "GSM5829831", null, "tissue:Retina|age:42 hpf|expression of reporter genes:ath5  crx  ptf1a ", "Progenitors rep1", "Basecalling performed using bcl2fastq version 2.19.1 Read alignment performed using GSNAP version 2018 07 04 gsnap  d GRCz11   gunzip  A sam  t 6   use sarray=1   input buffer size=500000   output buffer size=500000  B 5  N 0  n 1  s EnsemblGene 95.ss.GRCz11.iit   read group platform=illumina\u00a0 Read counting performed using featureCounts version 1.6.3\u00a0 featureCounts  a annotation/danio rerio/GRCz11/EnsemblGene 95.GRCz11.TR.gtf  s 0  Q 1  T 8 Genome build: Danio rerio GRCz10 Supplementary files format and content: Matrix table .xlsx with normalised gene counts for every gene and every sample Supplementary files format and content: Matrix table .txt with raw gene counts for every gene and every sample", "Retina", "MS 222 0.01% prior to dissection of the retinas.", "Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP  Tgcrx:gap CFP  Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates  25 retinas were pooled.   During dissection  retinas were maintained at 4\u00b0C in a volume of 100 \u00b5l in PBS. Prior to dissociation  the volume was adjusted to 500 \u00b5l. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes.   500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads.", "Embryos were incubated at 28\u00baC until 24 hpf  then at 21\u00baC until 30 hpf and finally at 28\u00baC until 42 hpf.", "age:42 hpf|expression of reporter genes:ath5  crx  ptf1a ", "GSM5829831", "GSM5829831: Progenitors rep1; Danio rerio; RNA Seq", "GSM5829831 r1", "GSM5829831", "1", "Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP  Tgcrx:gap CFP  Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates  25 retinas were pooled.   During dissection  retinas were maintained at 4\u00b0C in a volume of 100 \u00b5l in PBS. Prior to dissociation  the volume was adjusted to 500 \u00b5l. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes.   500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP356155", null, "loader:fastq load.py", "L39832_Track-77359_R1.fastq.gz", "fastq", 2184577820.0, 28744445.0, "GSM5829831 r1", "0:76", "A:627633686;C:452127477;G:463833090;T:640750578;N:232989", 76, null, null, null, 627633686, 452127477, 463833090, 640750578, 232989, "SRX13855137", "SRS11731662", "SRA1360146", "Max Planck Institute of Molecular Cell Biology and Genetics", "Max Planck Institute of Molecular Cell Biology and Genetics", 1, 0.89216, null, 0.07417, null, 0.80225, null, 0.52375, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2022-01-21", "Pharyngula", "Embryo", "Eye", "Sensory 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": ["68250"], "units": {}, "query_ms": 5.9411390029708855}