run_metadata: 70256
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 70256 | SRR19638124 | SRX15688336 | SRS13384743 | SRP379896 | PRJNA848804 | RNA seq of endothelial cells from 28 hpf sf3b1 mutant and sibling zebrafish with Stat3 overexpression | GSE206019 | Transcriptome Analysis | The purpose of the experiment was to define the gene expression and splicing alterations occurring when wildtype or consitutively active Stat3 are expressed in embryonic zebrafish endothelial cells with low levels of splicing factor 3b subunit 1 Sf3b1. Results provide insight the interplay of Sf3b1 and Stat3 in hematopoietic development. Overall design: mRNA profiling of kdrl positive endothelial cells isolated from 28 hpf wildtype sf3b1 mutant and sibling zebrafish with wildtype or constitutively active Stat3 overexpression using the Novogene 6000 platform. A total of 15 samples were sequenced. | parent bioproject:PRJNA848802 | pubmed:36516770 | wt WTstat3 1 | GSM6238960 | tissue:endothelial cells|time:28 hpf | wt WTstat3 1 | basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. FeatureCounts was used to calculate reads per gene. Assembly: GRcz10 Supplementary files format and content: tab delimited text file includes feature count values for each sample | endothelial cells | kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000 | time:28 hpf | GSM6238960 | GSM6238960: wt WTstat3 1; Danio rerio; RNA Seq | GSM6238960 r1 | GSM6238960 | 1 | kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Poly A RNA was selected by oligo dT primer with low input library generation by Novogene. Libraries were made following the low input library prep and sequenced on a Novoseq 6000 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP379896 | loader:fastq load.py | Exp1_1_S151_L008_R1_001.fastq.gz Exp1_1_S151_L008_R2_001.fastq.gz | fastq fastq | 12110767458.0 | 40101879.0 | GSM6238960 r1 | 0:151 1:151 | A:2374851845;C:3648786741;G:3800016692;T:2285963576;N:1148604 | 151 | 151 | 2374851845 | 3648786741 | 3800016692 | 2285963576 | 1148604 | SRX15688336 | SRS13384743 | SRA1436901 | Albert Einstein College of Medicine | Albert Einstein College of Medicine | 2 | 0.95385 | 0.95362 | 0.24549 | 0.20304 | 0.83063 | 0.83524 | 0.62301 | 0.83616 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2022-06-13 | Pharyngula | Embryo | Endothelium | Cardiovascular System |