|
| Status |
Public on Aug 05, 2014 |
| Title |
RNA-seq wt 3 |
| Sample type |
SRA |
| |
|
| Source name |
Haemogenic Endothelium
|
| Organism |
Mus musculus |
| Characteristics |
cell line: BryGFP
strain: 129
|
| Growth protocol |
ES cell–derived haemogenic endothelium cells were routinely generated by isolating FLK1+ cells from d3.25 embryonic eody differentiations. FLK1+ cells where maintained on gelatin coated plates in liquid blast medium (IMDM supplemented with 10% FCS, P/S, 2mM L-Glutamine, 20μg/ml transferrin, 0.45mM MTG, 25μg/ml AA, 15% D4T conditioned medium, 5ng/ml VEGF and 10ng/ml IL6). After 2 days of liquid blast culture haemogenic endothelial cells where isolated according to the cKIT+ TIE2+ CD41- phenotype.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from snap frozen samples with the RNeasy Plus Mini Kit (Qiagen) and ribosomes depleted with the Ribozero Gold Kit (Epicentre) according to manufacturers instructions.
RNA-seq libraries were generated with the SOLiD Total RNA-Seq Kit (Life Technologies, 4445374).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| Description |
FACS: cKIT+ TIE2+ CD41-
|
| Data processing |
Sequencing reads were aligned to mm9 genome using SHRiMP2 with default settings. Reads aligning to multiple loci were discarded.
Reads were aligned to ENSEMBL (v66) annotated genes using the annmap database and Bioconductor package and only exonic reads were selected.
The Bioconductor package edgeR (FDR < 0.05; exact test method) was used to call differentially expressed genes between Runx1ko (iDamko, Ainv18ko ) and Runx1wt Bry-GFP or Runx1wt iDam HE samples
Common genes, which displayed same directional change, between the Runx1ko – Bry-GFP and Runx1ko – iDam comparisons were chosen for subsequent analysis
Genome_build: mm9
|
| |
|
| Submission date |
Feb 24, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
michael lie-a-ling |
| E-mail(s) |
Michael.Lie-A-Ling@ics.manchester.ac.uk
|
| Organization name |
Cancer Research UK Manchester Institute
|
| Department |
Stem Cell Biology
|
| Street address |
The University of Manchester | Wilmslow Road
|
| City |
manchester |
| ZIP/Postal code |
M204BX |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL15907 |
| Series (2) |
| GSE55310 |
RUNX1 positively regulates a cell adhesion and migration program in murine hemogenic endothelium prior to blood emergence (RNA-seq) |
| GSE55335 |
RUNX1 positively regulates a cell adhesion and migration program in murine hemogenic endothelium prior to blood emergence |
|
| Relations |
| BioSample |
SAMN02664702 |
| SRA |
SRX475930 |
