run_metadata: 63457
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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| 63457 | SRR13839918 | SRX10218308 | SRS8362894 | SRP309041 | PRJNA706190 | Bulk RNA seq comparing expression profiles between neural crest cells experiencing high and low levels of Wnt signaling | GSE168131 | Transcriptome Analysis | The purpose of this study was to obtain an unbiased list of wnt regulated genes in zebrafish neural crest. Overall design: NC cells were collected from 7xTCF:mCherry transgenic Wnt reporter zebrafish embryos. 3 samples each were collected for high and low levels of the transgene by FACS. | parent bioproject:PRJNA706402 | pubmed:34936864 | High Wnt NC cells 2 | GSM5129518 | tissue:FACS sorted NC cells|genotype:Tg7XTCF:nls mCherryia5 ;Tg 7.2sox10:EGFPir937|Stage:24 hpf|cell type:NC cell|wnt status:High Wnt | High Wnt NC cells 2 | reads were mapped using STAR Quantification of reads was performed using RSEM. TPMs were calculated for each sample and used for downstream analysis Differential expression was performed in R using edgeR in R Genome build: GRCz11 Supplementary files format and content: .txt file contains TPMs for each sample | FACS sorted NC cells | Embryos were dissociated using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed according to the Smart seq2 protocol. | genotype:Tg7XTCF:nls mCherryia5 ;Tg 7.2sox10:EGFPir937|Stage:24 hpf|cell type:NC cell|wnt status:High Wnt | GSM5129518 | GSM5129518: High Wnt NC cells 2; Danio rerio; RNA Seq | GSM5129518 | 1 | Embryos were dissociated using collagenase P and trypsin. Cells were then FACS sorted on an Aria II. Libraries were constructed according to the Smart seq2 protocol. | GEO Accession:GSM5129518 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP309041 | loader:fastq load.py | nR032-L4-G1-P011-CGTACT-READ1-Sequences.txt nR032-L4-G1-P011-CGTACT-READ2-Sequences.txt | fastq fastq | 3605408110.0 | 17848555.0 | GSM5129518 r1 | 0:101 1:101 | A:885541901;C:935723298;G:827921325;T:956154180;N:67406 | 101 | 101 | 885541901 | 935723298 | 827921325 | 956154180 | 67406 | SRX10218308 | SRS8362894 | SRA1202348 | GEO | Thomas F. Schilling, Developmental and Cell Biology, University of California Irvine | 2 | 0.94463 | 0.94671 | 0.0489 | 0.04859 | 0.75694 | 0.75564 | 0.51745 | 0.51843 | 101 | 101 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | United States | 2021-03-03 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures |