run_metadata: 75634
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 75634 | SRR24746217 | SRX20523362 | SRS17832949 | SRP439774 | PRJNA976671 | RNA seq of RNAs immunoprecipitated with eIF4E1c and eiF4E1c in early zebrafish embryos | GSE233570 | Other | To investigate the mRNAs that are bound by eIF4E1b and eIF4E1c we performed RNA immunoprecipitation RIP experiments using anti GFP beads and transgenic embryos expressing GFP eIF4E1b or GFP eIF4E1c at the 8 cell stage. Overall design: We performed differential expression gene analyses of eIF4E1b n = 3 biological replicates versus eIF4E1c n = 2 biological replciates RIP and input samples. | pubmed:38177902 | eIF4E1c input biol rep 2 | GSM7430667 | source name:Whole embryo lysate|tissue:Whole embryo lysate|cell type:8 cell stage|genotype:tgactb2:3xflag sfGFP eIF4E1c|geo loc name:missing|collection date:missing | eIF4E1c input biol rep 2 | RNA seq reads were trimmed using trim galore v0.5.0 and reads mapping to abundant sequences Dr mitochondrial chromosome SILVA Dr ribosomal RNA phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts with parameter s 0 for unstranded analysis subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts | Whole embryo lysate | RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro | tissue:Whole embryo lysate|cell type:8 cell stage|genotype:tgactb2:3xflag sfGFP eIF4E1c | GSM7430667 | GSM7430667: eIF4E1c input biol rep 2; Danio rerio; RIP Seq | GSM7430667 r1 | GSM7430667 | 1 | RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro | RIP-Seq | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP439774 | loader:fastq load.py | e1c-RIP_input_2_1.fastq.gz e1c-RIP_input_2_2.fastq.gz | fastq fastq | 3698444058.0 | 18309129.0 | GSM7430667 r1 | 0:101 1:101 | A:882466312;C:908503385;G:987657378;T:919768451;N:48532 | 101 | 101 | 882466312 | 908503385 | 987657378 | 919768451 | 48532 | SRX20523362 | SRS17832949 | SRA1645065 | IMP | IMP | 2 | 0.89236 | 0.88681 | 0.06986 | 0.07322 | 0.76897 | 0.77037 | 0.53302 | 0.53232 | 101 | 101 | B | B | biological fallback assumption | illumina | novaseq_era | full_length | rrna_depletion | ribozero | bulk | unknown | unknown | Austria | 2023-05-26 | Cleavage | Embryo | Whole Organism | All anatomical structures |