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Sample GSM2808727 Query DataSets for GSM2808727
Status Public on Dec 27, 2018
Title sampleWT-2A
Sample type SRA
 
Source name single FLK1+mesoderm
Organism Mus musculus
Characteristics cell type: ES cell-derived embryoid bodies
strain: C57Bl/6 X Sv129
ebs stage: day 3.75
samples: WT2
antibody: anti DEDAF (AB3637,) Millipore
Extracted molecule genomic DNA
Extraction protocol Complexes were eluted from beads in a thermomixer at 65 degres for 15 min and the eluates and reserved inputs were reverse cross-linked overnight at 65C. The samples were then treated with RNaseA, proteinase K and phenol/chloroform purified.
ChIP samples were submitted to library preparation using NEBNext Ultra DNA Library prep kit for Illumina (NEB 7370) and multiplexing barcodes (NEB E7500) following Illumina’s instructions.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model NextSeq 550
 
Data processing Base calling performed on illumina 1.9 platform
Chip-seq reads were aligned to the mm9 genome using Bowtie v1.1.2b with the following parameters: -q -p 8 --chunkmbs 10000 -n 2 -m 2
Peaks were called using Macs2 v2.0.10 with the following parameters -B -q 0.05
Genome_build: mm9
Supplementary_files_format_and_content: narrowPeak file were generated using Macs2 narrowPeak -q 0.05
Supplementary_files_format_and_content: The bed file is the intersection of the 2 narrowPeak files and was generated with bedtools intersect
 
Submission date Oct 11, 2017
Last update date May 15, 2019
Contact name Hedia Chagraoui
E-mail(s) hedia.chagraoui@imm.ox.ac.uk
Phone 00441865222309
Organization name Weatherall Institute of Molecular Medicine
Department Molecular Hematology Unit
Lab PORCHER/VYAS lab
Street address john radcliffe hospital headley way headington
City Oxford
ZIP/Postal code OX3 9DS
Country United Kingdom
 
Platform ID GPL21626
Series (2)
GSE104841 SCL establishes a global repressive environment and cooperates with Polycomb RYBP-PRC1 to suppress alternative lineages in blood-fated cells [RYBP ChIP-seq]
GSE104883 SCL establishes a global repressive environment and cooperates with Polycomb RYBP-PRC1 to suppress alternative lineages in blood-fated cells
Relations
BioSample SAMN07775327
SRA SRX3272101

Supplementary file Size Download File type/resource
GSM2808727_sampleWT_2_broad_peaks.broadPeak.gz 447.2 Kb (ftp)(http) BROADPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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