run_metadata: 41181
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 |
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| 41181 | SRR3923681 | SRX1950215 | SRS1564976 | SRP078537 | PRJNA329141 | Expression profiling identifies Sertoli and Leydig cell genes as Fsh targets in adult zebrafish testis | GSE84436 | Transcriptome Analysis | Spermatogonial stem cells are quiescent undergo self renewal or differentiating divisions thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle stimulating hormone FSH through the production of Sertoli cell derived factors and by Leydig cell released androgens. Here we investigate the transcriptional events induced by Fsh in a steroid independent manner on the restart of zebrafish Danio rerio spermatogenesis ex vivo using testis from adult males where type A spermatogonia were enriched by estrogen treatment in vivo. Under these conditions RNA sequencing preferentially detected differentially expressed genes in somatic/Sertoli cells. Fsh stimulated spermatogonial proliferation was accompanied by modulating several signaling systems i.e. Tgf ß Hedgehog Wnt and Notch pathways. In silico protein protein interaction analysis indicated a role for Hedgehog family members potentially integrating signals from different pathways during fish spermatogenesis. Moreover Fsh had a marked impact on metabolic genes such as lactate and fatty acid metabolism or on Sertoli cell barrier components. Fish Leydig cells express the Fsh receptor and one of the most robust Fsh responsive genes was insulin like 3 insl3 a Leydig cell derived growth factor. Follow up work showed that recombinant zebrafish Insl3 mediated pro differentiation effects of Fsh on spermatogonia in an androgen independent manner. Our experimental approach allowed focusing on testicular somatic genes in zebrafish and showed that the activity of signaling systems known to be relevant in stem cell systems was modulated by Fsh providing promising leads for future work as exemplified by the studies on Insl3. Overall design: 12 samples in total were analyzed: 6 biological replicates from control testis samples and 6 biological replicates from Fsh treated testis samples all co incubated with trilostane. | pubmed:27566230 | Trilostane+Fsh 3 | GSM2236116 | source name:Testis|tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours | Trilostane+Fsh 3 | Image analysis and base calling were done by the Illumina pipeline CASAVA software v1.8 The read counts were extracted using the Python package HTSeq and normalized using the totally mapped reads per library Sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish genome Zv9 using STAR v2.3 standard parameters for single end reads Differential expression analysis was performed using the R/Bioconductor package NOISeq 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 | tissue:testis|age:Adult|genotype:Wild type|incubation:48 hours | GSM2236116 | GSM2236116: Trilostane+Fsh 3; Danio rerio; RNA Seq | GSM2236116 | 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:GSM2236116 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP078537 | Seq8_H9PG8ADXX_TCCGCGAA-CAGGACGT_L001_R1_001.fastq.gz | fastq | 547479650.0 | 10949593.0 | GSM2236116 r1 | 0:50 | A:132619117;C:134226431;G:118412018;T:157542627;N:4679457 | 50 | 132619117 | 134226431 | 118412018 | 157542627 | 4679457 | SRX1950215 | SRS1564976 | SRA440585 | GEO | Reproductive Biology, Biology, Utrecht University | 1 | 0.9055 | 0.32136 | 0.66793 | 0.60282 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Netherlands | 2016-07-14 | Adult | Adult | Gonad | Reproductive System |