|
| Status |
Public on Mar 27, 2018 |
| Title |
MLL4 DMSO |
| Sample type |
SRA |
| |
|
| Source name |
THP1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: AML
antibody: MLL4 (kindly provided by Dr Kai Ge; Wang et al., 2016)
treatment: DMSO
|
| Treatment protocol |
THP1 AML cells were treated with 250nM OG86 or DMSO vehicle for 24 hours in RPMI with 10% fetal bovine serum.
|
| Growth protocol |
THP1 AML cells were treated with 250nM OG86 or DMSO vehicle for 24 hours in RPMI with 10% fetal bovine serum.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIPs for acetyl-H3K9 (ab4441), acetyl-H3K27 (ab4729) (both from Abcam) RCOR1 (07-455 from Merck Millipore), SPI1 (2258 from Cell Signaling) and MLL4 (kindly provided by Dr Kai Ge; Wang et al., 2016) were performed using 50-100 million cells and the protocol of Lee et al. (2006).
ChIP DNA samples were prepared for sequencing using the Microplex Library Preparation Kit (Diagenode) and 1ng ChIP DNA. Libraries were size selected with AMPure beads (Beckman Coulter) for 200-800 base pair size range and quantified by Q-PCR using a KAPA Library Quantification Kit. ChIPseq data were generated using the NextSeq platform from Illumina with 2x75bp Mid Output.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were aligned to human genome hg38 using BWA-MEM (version 0.7.13) (http://bio-bwa.sourceforge.net/, using 16 threads and with -M set to flag shorter split hits as secondary) or Bowtie2 (version 2.2.1) (http://bowtie-bio.sourceforge.net/bowtie2/) using default settings. Reads were then filtered using Samtools (version 0.1.9) (Li et al., 2009) keeping only reads with alignment quality score >= 20. The number of uniquely mapped reads per sample was 50-100 million.
Reads were mapped relative to annotated genes (ENSEMBL v66) using the Annmap database, R and Bioconductor (Gentleman et al., 2004; Yates et al., 2007). MACS2 (Model-based Analysis of ChIP-seq, version 2.1.0) software was used to call peaks (Zhang et al., 2008).
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files; browser-ready peak histograms for ChIP seq
|
| |
|
| Submission date |
Mar 20, 2018 |
| Last update date |
Mar 27, 2018 |
| Contact name |
Tim C Somervaille |
| E-mail(s) |
tim.somervaille@cruk.manchester.ac.uk
|
| Organization name |
Cancer Research UK Manchester Institute
|
| Lab |
Leukaemia Biology Laboratory
|
| Street address |
Wilmslow Road
|
| City |
Manchester |
| State/province |
Lancashire |
| ZIP/Postal code |
M20 4BX |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE63222 |
Inhibitors of LSD1 target demethylase-independent activity to induce differentiation in acute myeloid leukemia |
| GSE112074 |
Inhibitors of LSD1 target demethylase-independent activity to induce differentiation in acute myeloid leukemia [anti-H3K9 ac, anti-H3K27, RCOR1, SPI1, and MLL4 ChIP-Seq] |
|
| Relations |
| BioSample |
SAMN08743023 |
| SRA |
SRX3824043 |
