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Sample GSM2077407 Query DataSets for GSM2077407
Status Public on Jun 02, 2016
Title Control for IP- chromatin only
Sample type SRA
Source name Erythroid cells
Organism Mus musculus
Characteristics strain: C57Bl6
tissue: Phenylhydrazine treated spleen
genes analysed: Genome-wide
antibody: input
Extracted molecule genomic DNA
Extraction protocol A single cell suspension was made by gently dissociating the spleen of a phenyhydrazine treated mouse and passing it through a 70um filter. Ter119 selection was performed by staining the cells with phycoerythrin conjugated anti-ter119 antibodies (BD biosciences)). The cells were subsequently washed and then incubated with MACS anti-phycoerythrin beads. Cells were then separated using an auto-MACS (miltenyi biotec).
Fragments double-crosslinked were immunoprecipitated with the antibody of interest (Med1). Libraries were prepared using the NEB Ultra library preparation kit according to manufacturer’s instructions. Samples were sequenced using 40 bp paired end reads on the NextSeq platform
The strategy was to isolate at a genome-wide level the DNA regions bound by Med1. Because the binding is assumed to be indirect, stronger croslinking conditions were used (double crosslinking FA and DSG).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Description DNA fragments from sonicated chromatin
Data processing Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Alignment to the genome (Bowtie) maintaining strict read order
Removal of PCR duplicates;
Combining data from multiple replicates (custom scripts)
Removal of ploidy regions
Genome_build: mm9
Supplementary_files_format_and_content: wig
Submission date Mar 01, 2016
Last update date May 15, 2019
Contact name Jim Hughes
Phone 1865222113
Organization name University of Oxford
Department MHU
Lab Genome Biology Group
Street address Weatherall Institute Of Molecular Me
City oxford
ZIP/Postal code OX3 9DS
Country United Kingdom
Platform ID GPL19057
Series (2)
GSE78804 Dissection of a super-enhancer in vivo (ChIP-seq)
GSE78835 Genetic dissection of the α-globin super-enhancer
BioSample SAMN04528817
SRA SRX1609550

Supplementary file Size Download File type/resource
GSM2077407_Input_Med1_ChIP_Ter119.wig.gz 236.3 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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