run_metadata: 41339
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 41339 | SRR4243172 | SRX2164187 | SRS1692132 | SRP089896 | PRJNA343041 | Antagonistic regulation of spermatogonial differentiation in zebrafish Danio rerio by Igf3 and Amh | GSE86944 | Transcriptome Analysis | Fsh mediated regulation of zebrafish spermatogenesis includes modulating the expression of testicular growth factors. Here we study if and how two Sertoli cell derived Fsh responsive growth factors anti Müllerian hormone Amh; inhibiting steroidogenesis and germ cell differentiation and insulin like growth factor 3 Igf3; stimulating germ cell differentiation cooperate in regulating spermatogonial development. In dose response and time course experiments with primary testis tissue cultures Fsh upregulated igf3 transcript levels and down regulated amh transcript levels; igf3 transcript levels were more rapidly up regulated and responded to lower Fsh concentrations than were required to decrease amh mRNA levels. Quantification of immunoreactive Amh and Igf3 on testis sections showed that Fsh increased slightly Igf3 staining but decreased clearly Amh staining. Studying the direct interaction of the two growth factors showed that Amh compromised Igf3 stimulated proliferation of type A both undifferentiated [Aund] and differentiating [Adiff] spermatogonia. Also the proliferation of those Sertoli cells associated with Aund spermatogonia was reduced by Amh. To gain more insight into how Amh inhibits germ cell development we examined Amh induced changes in testicular gene expression by RNA sequencing. The majority 69% of the differentially expressed genes was down regulated by Amh including several stimulators of spermatogenesis such as igf3 and steroidogenesis related genes. At the same time Amh increased the expression of inhibitory signals such as inha and id3 or facilitated prostaglandin E2 PGE2 signaling. Evaluating one of the potentially inhibitory signals we indeed found in tissue culture experiments that PGE2 promoted the accumulation of Aund at the expense of Adiff and B spermatogonia. Our data suggest that an important aspect of Fsh bioactivity in stimulating spermatogenesis is implemented by restricting the different inhibitory effects of Amh and by counterbalancing them with stimulatory signals such as Igf3 Overall design: 10 samples in total were analyzed: 5 biological replicates from control testis samples and 5 biological replicates from Amh treated testis samples all co incubated with 11KT | pubmed:28645700 | 11KT+Amh 4 | GSM2310626 | tissue:Testis|age:Adult|genotype:Wild type|incubation:3 days|treatment:Amh | 11KT+Amh 4 | 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|incubation:3 days|treatment:Amh | GSM2310626 | GSM2310626: 11KT+Amh 4; Danio rerio; RNA Seq | GSM2310626 | 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:GSM2310626 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP089896 | IL-14-08-15_CGTACG_L001_R1_001.fastq.gz | fastq | 1020609348.0 | 20011948.0 | GSM2310626 r1 | 0:51 | A:280659283;C:233389387;G:227016796;T:279291132;N:252750 | 51 | 280659283 | 233389387 | 227016796 | 279291132 | 252750 | SRX2164187 | SRS1692132 | SRA471529 | GEO | Reproductive Biology, Biology, Utrecht University | 1 | 0.91619 | 0.10708 | 0.66125 | 0.51479 | 51 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Netherlands | 2016-09-14 | Adult | Adult | Gonad | Reproductive System |