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Sample GSM1377857 Query DataSets for GSM1377857
Status Public on Nov 30, 2015
Sample type SRA
Source name HE_GFI1: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
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
BioSample SAMN02769533
SRA SRX540195

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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