|
| 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 |
| E-mail(s) |
jim.hughes@imm.ox.ac.uk
|
| 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 |
|
| Relations |
| BioSample |
SAMN04528817 |
| SRA |
SRX1609550 |
