|
| Status |
Public on May 30, 2019 |
| Title |
H3K4me3 ChIP seq in THP1 cells |
| Sample type |
SRA |
| |
|
| Source name |
Leukemia cell line (THP1)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: THP1
treatment: N/A
cell type: Paediatric monocytic cell line derived from AML M5 with t(9;11)(q21;q23) translocation
chip antibody: Diagenode cat no. pAB-003-050
|
| Treatment protocol |
Where indicated, cells were treated with EPZ-5676 or DMSO for 7 days
|
| Growth protocol |
Cells were continuously grown in IMDM (SEM) or RPMI (THP1) 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 H3K4me3 antibody in THP1 cells
THP1_H3K4me3_peaks.bed.gz
|
| 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
Genome_build: hg19
Peak calling using Homer v4.7
|
| |
|
| Submission date |
Mar 20, 2019 |
| 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 |
SAMN11179204 |
| SRA |
SRX5548868 |
