|
| Status |
Public on Nov 30, 2015 |
| Title |
HE_GFI1B:DAM |
| Sample type |
SRA |
| |
|
| Source name |
HE_GFI1B:DAM biological replicate 1
|
| Organism |
Mus musculus |
| Characteristics |
tissue: hemogenic endothelium
|
| Growth protocol |
FLK1+ cells were isolated from day 3.25 EBs from GFI1:DAM-, GFI1B:DAM or a DAM control AinV18 ES cell line. HE (TIE-2/c-KIT) comparment from all the samples were FACS isolated on day 2 after culture. EBs and Cultures grown as decribed in Lancrin et al, 2009 and Steanska et al, 2014
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA from each population was extracted and processed for sequencing as described in Vogel et al, 2007 and sequenced on a Illumina HiSeq 2500 platform
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
DamID-PIP
biological replicates 1 and 2
|
| Data processing |
DamID-seq reads were aligned to mouse genome mm9 using SHRiMP2 (default settings)
BayesPeak was applied to the GFI1:DamID, GFI1B:DAM and control DAM samples
Unique test sample peaks with no overlap with the control sample or overlapping peaks with a > 2 fold change (RPKM_test/RPKM_control) were carried forward
We then used Poisson model based scan statistics to identify peak-enriched-regions and pooled adjacent (<300bp) peak-enriched regions
Genome_build: mm9
Supplementary_files_format_and_content: excel file with geneID, gene symbol, biotype, read counts, readcounts Per KB, SS interval for peaks identified for GFI1:DAM and GFI1B:DAM
|
| |
|
| Submission date |
May 02, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Roshana S Thambyrajah |
| E-mail(s) |
Roshana.Thambyrajah@cruk.manchester.ac.uk
|
| Organization name |
CRUK Manchester
|
| Department |
Stem Cell Biology
|
| Street address |
Wilmslow Road
|
| City |
Manchester |
| ZIP/Postal code |
M20 4BX |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE57248 |
Gfi1 proteins regulate the emergence of HSCs and blood precursors in the AGM through recruitment of LSD1 [HTS] |
| GSE57251 |
Gfi1 proteins regulate the emergence of HSCs and blood precursors in the AGM through recruitment of LSD1 |
|
| Relations |
| BioSample |
SAMN02769534 |
| SRA |
SRX540196 |
