|
| Status |
Public on Aug 30, 2018 |
| Title |
Endothelium WT rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Endothelium of embryonic dorsal aorta
|
| Organism |
Mus musculus |
| Characteristics |
tissue: embryonic dorsal aorta
genotype: WT
developmental stage: E11.5
cell type: Endothelium (Ter119- VE-Cadherin+ c-Kit- CD41- CD45-)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
E11.5 AGM was manually dissected and prepared as single cell suspensions using a Collagenase I-based digestion, then hematopoietic clusters (Ter119- VE-Cadherin+ c-Kit+) were FACS-sorted into lysis buffer (1:20 Rnase inhibitor, 0.2% Triton X-100).
RNA-Seq libraries prepared using Smart-seq2 protocol (Picelli et al., Nature Protocols 2014)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Paired end reads mapped to mm9 mouse reference genome using STAR v2.4.2a, with lane replicates pooled into a single BAM file for each sample
Read counts for genes determined using the featureCounts program from the Subread package v1.4.5.
Counts were normalised and analysed for differential expression using R and the package DESEQ2 v1.12.4. P values were corrected for multiple testing using the Benjamini & Hochberg method, and differentially expressed genes were identified as those with p<0.05 and adjusted p value (FDR) < 0.1.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file containing raw counts for each sample
|
| |
|
| Submission date |
Oct 19, 2017 |
| Last update date |
May 28, 2020 |
| Contact name |
Marella de Bruijn |
| E-mail(s) |
marella.debruijn@imm.ox.ac.uk
|
| Organization name |
University of Oxford
|
| Department |
Radcliffe Department of Medicine
|
| Lab |
de Bruijn Lab
|
| Street address |
MRC MHU, WIMM, John Radcliffe Hospital
|
| City |
Oxford |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE105267 |
Expression data of endothelium and hematopoietic cluster cells in the wild type and Steel mutant E11.5 AGM and vitelline and umbilical arteries |
|
| Relations |
| BioSample |
SAMN07815162 |
| SRA |
SRX3302826 |
