|
| Status |
Public on May 30, 2019 |
| Title |
CTCF ChIP seq in SEM cells |
| Sample type |
SRA |
| |
|
| Source name |
CTCF
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Leukemia cell line (SEM)
treatment: N/A
cell type: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation
chip antibody: CTCF (Millipore 07-729)
|
| Treatment protocol |
Where indicated, cells were treated with EPZ-5676 or DMSO for 7 days
|
| Growth protocol |
Cells were continuously grown in IMDM with 10% FBS, split when they reached a density of 1-2x10e6 cells/ml down to 5x10e5 cells/ml
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were washed with PBS and fixed in either 1% FA for 10 minutes (histones) or 2mM DSG for 30 minutes and 1% FA for 30 minutes (transcription factors). Cells were sonicated to give fragments of 100-300bp followed by IP. For ChIP-rx fixed SEM cells were mixed at a 4:1 ratio with fixed Drosophila S2 cells prior to sonication.
DNA libraries were made using the NEBnext ultra DNA library preparation kit for Illumina (Cat no. E7370).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ChIP seq performed using CTCF antibody in SEM cells
CTCF_peaks.bed
|
| Data processing |
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Peak calling using Homer v4.7
Genome_build: hg19
Supplementary_files_format_and_content: bed file reporting called peaks
|
| |
|
| Submission date |
Jul 30, 2018 |
| Last update date |
May 30, 2019 |
| Contact name |
Thomas A Milne |
| E-mail(s) |
thomas.milne@imm.ox.ac.uk
|
| Organization name |
University of Oxford
|
| Department |
MRC Weatherall Institute of Molecular Medicine
|
| Street address |
John Radcliffe Hospital, Headington
|
| City |
Oxford |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE117864 |
DOT1L inhibition reveals a distinct subset of enhancers dependent on H3K79 methylation (ChIP-seq) |
| GSE117865 |
DOT1L inhibition reveals a distinct class of enhancers dependent upon H3K79 methylation |
|
| Relations |
| BioSample |
SAMN09739228 |
| SRA |
SRX4484978 |
