run_metadata: 61504
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 61504 | SRR12780055 | SRX9249643 | SRS7482117 | SRP286526 | PRJNA667677 | Bipartite histone H3 recognition by the PZP domain of PHF14 facilitates zygotic genome activation in zebrafish | GSE159087 | Transcriptome Analysis | Standard and Phf14 MOs were injected into 1 cell stage embryos and when developed into sphere stage 4.7 hpf embryos were lysed for mRNA extraction for high through put sequencing based on BGISEQ in order to compare gene expression test at the whole genome level. Overall design: mRNA profiles of standard std MO 4.7h versus phf14 MO injected phf tMO 4.7h zebrash embryos at 4.7 hpf. | std MO 4.7h | GSM4819004 | tissue:embryos|strain:Tuebingen|genotype/variation:standard MO injected|developmental stage:4.7 hpf|tissue/cell type:whole embryos | std MO 4.7h | Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to zv9 whole genome using SOAPaligner/soap2 Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from mortazavi et al. nature method 2008. Genome build: zv9 Supplementary files format and content: Excel files include RPKM values and read counts for each gene in the two samples | embryos | Embryos were injected with 5 ng standard or Phf14 morpholinos at xxx cell stage | Zebrafish embryos mRNA were extracted using Qiagen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols | Embryos were cultured in the holfretor water. | strain:Tuebingen|genotype/variation:standard MO injected|developmental stage:4.7 hpf|tissue/cell type:whole embryos | GSM4819004 | GSM4819004: std MO 4.7h; Danio rerio; RNA Seq | GSM4819004 | 1 | Zebrafish embryos mRNA were extracted using Qiagen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols | GEO Accession:GSM4819004 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | BGISEQ | BGISEQ-500 | SRP286526 | std_MO_4.7h.fq.gz | fastq | 1169210150.0 | 23384203.0 | GSM4819004 r1 | 0:50 | A:311848924;C:271805947;G:268541126;T:317014153;N:0 | 50 | 311848924 | 271805947 | 268541126 | 317014153 | 0 | SRX9249643 | SRS7482117 | SRA1139165 | GEO | Haitao Li, School of medicine, Tsinghua University | 1 | 0.94838 | 0.07833 | 0.74192 | 0.48213 | 50 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | China | 2020-10-06 | Blastula | Embryo | Embryo Imprecise | All anatomical structures |