run_metadata: 48932
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 48932 | SRR7468683 | SRX4338461 | SRS3499379 | SRP151935 | PRJNA479503 | Endocrine and local signaling interact to regulate spermatogenesis in zebrafish: Follicle stimulating hormone retinoic acid and androgens | GSE116611 | Transcriptome Analysis | post an acclimatization period with increasing temperature from 27 to 35°C; 1°C increment/day adult zebrafish males were exposed to 35°C for 14 days and injected with the cytostatic agent busulfan single intraperitoneal injection post 7 days at xxx°C; 40 mg/Kg. Then fish were placed back to normal water temperature and testis samples collected at different time points. Morphological analysis of testicular samples showed maximum germ cell depletion 10 days post busulfan injection i.e. 10 dpi and the recovery of endogenous spermatogenesis 14 dpi. Total RNA was isolated from 1 testes of untreated adult control zebrafish 2 germ cell depleted and 3 testis tissue at the beginning of the recovery period and selected samples were used for library preparation Overall design: 15 samples in total were analyzed: 5 biological replicates from control testis samples 5 biological replicates from depleted testis samples and 5 biological replicates from recovering testis samples | pubmed:31597660;pubmed:33589679 | Testis Control 5 | GSM3243767 | source name:Testis|age:Adult|genotype:Wild type|tissue:Testis | Testis Control 5 | Image analysis and base calling were done by the Illumina pipeline. Quality control of the obtained reads was performed using FastQC suite v0.10.1; default parameters Reads were aligned to the zebrafish genome using TopHat v2.0.5 standard parameters for single end reads Data were filtered using SAMtools v0.1.18 The read counts were extracted using the Python package HTSeq Differential expression analysis was performed using the R/Bioconductor package DESeq Genome build: Zv9 Supplementary files format and content: Tab delimited text files include gene ID and raw counts for each sample | Testis | Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer’s protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer’s instructions | age:Adult|genotype:Wild type|tissue:Testis | GSM3243767 | GSM3243767: Testis Control 5; Danio rerio; RNA Seq | GSM3243767 | 1 | Total RNA was isolated from testis tissue using the miRNeasy Mini Kit Qiagen according to the manufacturer's protocol. RNA integrity was checked with an Agilent Bio analyzer 2100 total RNA Nano series II chip Agilent Illumina RNAseq libraries were prepared from 2 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina Inc. according to the manufacturer's instructions | GEO Accession:GSM3243767 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP151935 | ZFG-14-10_5_CAGATC_L002_R1_001_HBGRYADXX.fastq.gz | fastq | 1788601008.0 | 35070608.0 | GSM3243767 r2 | 0:51 | A:447675880;C:422557474;G:398397059;T:519829628;N:140967 | 51 | 447675880 | 422557474 | 398397059 | 519829628 | 140967 | SRX4338461 | SRS3499379 | SRA732862 | GEO | Reproductive Biology, Biology, Utrecht University | 1 | 0.92324 | 0.10891 | 0.63954 | 0.4884 | 51 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Netherlands | 2018-07-03 | Adult | Adult | Gonad | Reproductive System |