run_metadata: 36623
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 36623 | SRR658546 | SRX222290 | SRS389580 | SRP018379 | PRJNA188349 | Tmem88a Mediates GATA dependent Specification of Cardiomyocyte Progenitors by Restricting Canonical WNT Signaling | GSE44026 | Transcriptome Analysis | We sequenced mRNA from zebrafish wild type embryos gata5 morphants gata6 morphants and gata5/6 morphants at bud and 6 somite developmental stages to identify genes co operatively regulated by gata5 and gata6 during cardiomyocyte progenitor specification. Overall design: Samples were collected in duplicate with 40 embryos per sample. Single 36 base pair reads were sequenced on the Illumina Genome Analyzer IIx | pubmed:23903195 | Gata6 morphant 6 somites rep 2 | GSM1076995 | source name:Whole embryo|development stage:6 somites|genotype/variation:Gata6 morphant|tissue:whole embryo | Gata6 morphant 6 somites rep 2 | All data processing steps were performed in GobyWeb Dorff K. C. et al 2013 GobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data. Quantitative Methods q bio.QM; Genomics q bio.GN. in press arXiv:1211.6666. Alignments performed against Zv9.61 assembly. Genome build: Zv9 Supplementary files format and content: tab separated files include RPKM values for each Sample | Whole embryo | 40 embryos were collected per sample in Trizol Invitrogen and polyA mRNA was prepared for sequencing using the Illumina mRNA seq Sample Preparation Kit. RNA libraries were prepared for sequencing using standard Illumina protocols | developmental stage:6 somites|genotype/variation:Gata6 morphant|tissue:whole embryo | GSM1076995 | GSM1076995: Gata6 morphant 6 somites rep 2; Danio rerio; RNA Seq | GSM1076995 1 | 1 | GEO Accession:GSM1076995 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP018379 | 12hpf_G6_2.txt.gz | fastq | 1413551196.0 | 39265311.0 | GSM1076995 r1 | 0:36 | A:370616418;C:336932812;G:336785671;T:368764574;N:451721 | 36 | 370616418 | 336932812 | 336785671 | 368764574 | 451721 | SRX222290 | SRS389580 | SRA066053 | GEO | Weill Medical College of Cornell University | 1 | 0.92187 | 0.11635 | 0.72139 | 0.48206 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2013-02-02 | Segmentation | Embryo | Whole Organism | All anatomical structures |