run_metadata: 70235
This data as json
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| 70235 | SRR19638156 | SRX15688387 | SRS13384794 | SRP379921 | PRJNA848797 | RNA seq of endothelial cells from 28 hpf sf3b1 mutant and sibling zebrafish | GSE206017 | Transcriptome Analysis | The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of splicing factor 3b subunit 1 Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in hematopoietic development. Overall design: mRNA profiling of kdrl positive endothelial cells isolated from 28 hpf sf3b1 mutant and sibling zebrafish using Illumina HiSeq4000. Four sibling control samples and Four mutant samples were sequenced. | parent bioproject:PRJNA848802 | pubmed:36516770 | Sib3 | GSM6238952 | tissue:endothelial cells|time:28 hpf | Sib3 | 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 DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM Cufflinks version 2.2.1 was used. Assembly: GRcz10 Supplementary files format and content: tab delimited text file includes raw counts for each sample | endothelial cells | kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech. | time:28 hpf | GSM6238952 | GSM6238952: Sib3; Danio rerio; RNA Seq | GSM6238952 r1 | GSM6238952 | 1 | kdrl positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP379921 | SIB3_FCH5WC7BBXX_L2_CHKPEI85216020030_1.fq.gz SIB3_FCH5WC7BBXX_L2_CHKPEI85216020030_2.fq.gz | fastq fastq | 6297899800.0 | 31489499.0 | GSM6238952 r1 | 0:100 1:100 | A:1299893326;C:1802214016;G:1871542594;T:1323664459;N:585405 | 100 | 100 | 1299893326 | 1802214016 | 1871542594 | 1323664459 | 585405 | SRX15688387 | SRS13384794 | SRA1436858 | Albert Einstein College of Medicine | Albert Einstein College of Medicine | 2 | 0.86882 | 0.879 | 0.13327 | 0.13465 | 0.76976 | 0.77273 | 0.73674 | 0.61341 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | rrna_depletion | smarter | bulk | unknown | unknown | United States | 2022-06-13 | Pharyngula | Embryo | Endothelium | Cardiovascular System |