{"database": "metadata", "table": "run_metadata", "rows": [[68620, "SRR18053116", "SRX14205156", "SRS12027297", "SRP360188", "PRJNA807685", "Zebrafish establish female germ cell identity by advancing cell proliferation and meiosis", "GSE196899", "Transcriptome Analysis", "In this study  we utilize the RNA seq of germ cell to uncover the early germ cell development. To obtain fish with defined sex  we crossed domesticated zebrafish with the Nadia strain that has a female dominant W segment. These fish were placed on a ziwi:GFP background to facilitate sorting of fluorescent germ cells for transcriptomic analysis. We analyzed the transcriptomes of germ cells at 10 dpf to 14 dpf dpf  when sex dimorphic changes started to appear. Overall design: Germ cells mRNA of 10  12  and 14 dpf in W hybrid ZW*Tupfel long fin and Z hybrid ZZ*Tupfel long fin", null, null, null, "WGC 12d 4", "GSM5904409", null, "source name:Germ cells|strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:12 dpf", "WGC 12d 4", "Sequencing was performed on an Illumina NextSeq500  platform in a 75 base paired end mode.Illumina NextSeq Control software and RTA  used for basecalling. sequenced reads were trimmed and mapped to GRCz11 by STAR v2.7.7a expected count  TPM and FPKM were calculated by RSEM v1.3.1 Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene id  transcript id  expected count  TPM and FPKM for each sample", "Germ cells", null, "Gonads were dissected  Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara  Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification.  In SMART seq HT  full length cDNA was synthesized in one step  and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter  cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara  Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina  FC 131 1096.", null, "strain:Nadia/Tupfel long fin hybrid|tissue:Germ cells|age:12 dpf", "GSM5904409", "GSM5904409: WGC 12d 4; Danio rerio; RNA Seq", "GSM5904409 r1", "GSM5904409", "1", "Gonads were dissected  Germ cells were sorted by FACS. and directly into lysis buffer provided with the SMART seq HT Kit Takara  Cat. 634438. The SMART seq HT Kit was then used for reverse transcription and cDNA amplification.  In SMART seq HT  full length cDNA was synthesized in one step  and then amplified by 12 cycles of PCR. post purification with the AMPure XP kit Beckman Coulter  cDNAs were analyzed by a bioanalyzer for their qualities. cDNA libraries were generated using the SMART seq HT Kit Takara  Cat. 634438. Final libraries were prepared using Nextera XT DNA Library Prep Kit Illumina  FC 131 1096.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP360188", null, "loader:fastq load.py", "WGC-12d-4_S4_R1_001.fastq.gz WGC-12d-4_S4_R2_001.fastq.gz", "fastq fastq", 6359260156.0, 45475594.0, "GSM5904409 r1", "0:69.91 1:69.93", "A:1809337849;C:1356748319;G:1393608207;T:1796993266;N:2572515", 69, 69, null, null, 1809337849, 1356748319, 1393608207, 1796993266, 2572515, "SRX14205156", "SRS12027297", "SRA1374254", "Institute of Molecular Biology, Academia Sinica", "Institute of Molecular Biology, Academia Sinica", 2, 0.90486, 0.90498, 0.10907, 0.10859, 0.66531, 0.66667, 0.49946, 0.50298, 75, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "nextera", "bulk", "unknown", "unknown", null, "Taiwan", "2022-02-16", "Larval", "Larval", "Gonad", "Reproductive 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": ["68620"], "units": {}, "query_ms": 8.884847004082985}