run_metadata: 55474
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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| 55474 | SRR10434088 | SRX7130061 | SRS5639405 | SRP229597 | PRJNA589032 | mRNA profile of zebrafish periderm at 4 somite stage | GSE139808 | Transcriptome Analysis | In order to compare the transcriptome and tissue specific nucleosome free regions of zebrafish periderm cells at 4 somite stage we isolated the RNA from sorted GFP positive cells of Tgkrt4:GFP embryos and perform low input RNA seq. This study revealed periderm specific transcriptome at 4 somite stage. Moreover comparing with ATAC seq from the same tissue we confirmed the correlation between gene expression and nearby chromatin accessibility. Overall design: GFP positive embryos were harvested from three independent incross of Tgkrt4:GFP. Embryos were dissociated and sorted with FACS. For each batch 2000 GFP positive and 2000 GFP negative cells were collected and subjected to RNA seq. | parent bioproject:PRJNA589023 | pubmed:32031521 | GFP negative rep3 | GSM4146628 | source name:Tgkrt4:GFP embryos|age:4 somite stage|gfp:negative|tissue:non periderm | GFP negative rep3 | Sequencing reads were trimmed with Trimmomatic 0.35. Trimmed paired reads were pseudoaligned and quantified with kallisto v0.41; default parameters The output datasets from kallisto were normalized and compared using the sleuth program Genome build: danRer10 Supplementary files format and content: TPM.csv kallisto abundance.tsv | Tgkrt4:GFP embryos | FACS sort GFP positive and GFP negative cells | Total RNA was extracted from the sorted cells using the RNAqueous® Total RNA Isolation Kit Ambion Foster City CA and treated with Turbo DNase I Ambion Austin TX to remove residual genomic DNA. The treated RNA was then purified and concentrated using the RNA Clean & ConcentratorTM 5 Kit Zymo Research Irvine CA. 1 ug of RNA was subjected to first strand cDNA synthesis and cDNA amplification using the SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio Kusatsu Shiga Japan. Purified cDNA was quantified using Qubit and for each library 150 pg cDNA was used as input with the Nextera XT DNA Sample Preparation Kit Illumina San Diego CA following the manufacturer’s instructions. | age:4 somite stage|gfp:negative|tissue:non periderm | GSM4146628 | GSM4146628: GFP negative rep3; Danio rerio; RNA Seq | GSM4146628 | 1 | Total RNA was extracted from the sorted cells using the RNAqueous® Total RNA Isolation Kit Ambion Foster City CA and treated with Turbo DNase I Ambion Austin TX to remove residual genomic DNA. The treated RNA was then purified and concentrated using the RNA Clean & ConcentratorTM 5 Kit Zymo Research Irvine CA. 1 ug of RNA was subjected to first strand cDNA synthesis and cDNA amplification using the SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio Kusatsu Shiga Japan. Purified cDNA was quantified using Qubit and for each library 150 pg cDNA was used as input with the Nextera XT DNA Sample Preparation Kit Illumina San Diego CA following the manufacturer's instructions. | GEO Accession:GSM4146628 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP229597 | noGFP_3_1.fastq.gz noGFP_3_2.fastq.gz | fastq fastq | 7881357168.0 | 51851034.0 | GSM4146628 r1 | 0:76 1:76 | A:2071239433;C:1863550437;G:1882684630;T:2062940287;N:942381 | 76 | 76 | 2071239433 | 1863550437 | 1882684630 | 2062940287 | 942381 | SRX7130061 | SRS5639405 | SRA994593 | GEO | Anatomy and Cell Biology, University of Iowa | 2 | 0.91729 | 0.91789 | 0.07407 | 0.07433 | 0.73417 | 0.74251 | 0.46769 | 0.46379 | 76 | 76 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | nextera | sc | single_cell_plate | smartseq | United States | 2019-11-01 | Segmentation | Embryo | Embryo Imprecise | All anatomical structures |