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| Status |
Public on Mar 27, 2018 |
| Title |
H3K4Me2_DMSO |
| Sample type |
SRA |
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| Source name |
THP1 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: acute myeloid leukemia (AML)
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| Treatment protocol |
THP1 AML cells were treated with 250nM OG86 or DMSO vehicle for 24 hours in semi-solid culture.
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| Growth protocol |
THP1 cells were cultured in methylcellulose (H4320, Stem Cell Technologies, Vancouver, BC) without supplemental growth factors.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed using a HighCell# ChIP kit (Diagenode, Liege, Belgium) according to the manufacturer’s instructions. Prior to ChIPseq, DNA was purified with an iPure kit (Diagenode), according to manufacturer’s instructions.
To prepare samples for sequencing on the Illumina HiSeq 2500 (Illumina, San Diego, CA), a Microplex Library Preparation Kit (Diagenode) was used to generate libraries from 1ng ChIP DNA. Libraries were then size selected (200-800 base pairs) by adding 0.55x volume of AMPure beads (Beckman Coulter, Pasadena, CA) to the sample, followed by 0.3x volume of AMPure beads to the supernatant. The supernatant was then discarded and the beads washed with 70% ethanol before drying and elution of the size selected library. Library quantitation was performed by Q-PCR using a Kapa Library Quantification Kit (Kapa Biosystems, Woburn, MA). Next, 15pM of the library was used for on board cluster generation in the Rapid Mode of a HiSeq 2500 (Illumina) and then paired end 75 or 101 base pair sequencing was performed using a TruSeq Rapid SBS Kit (Illumina).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Reads were aligned to human genome hg19 using SMALT (www.sanger.ac.uk/resources/software/smalt) using default settings. The numbers of uniquely mapped reads were: 75-100 million for the monomethyl- and dimethyl-H3K4 samples and 40-60 million for the trimethyl-H3K4 samples. Reads were mapped relative to annotated genes (ENSEMBL v66) using the annmap database, R and Bioconductor (Gentleman et al., 2004; Yates et al., 2007).
For analysis of histone methylation marks, for each gene the gene body (i.e. from the transcription start site (TSS) to the end of the gene) was divided into ten sub-regions of equal length. The region upstream of the gene was divided into two regions: from 10kb to 2.5kb upstream, and from 2.5kb upstream to the TSS. The region downstream of the gene was similarly divided. Therefore each gene consists of 14 regions covering upstream sequences, the gene body and downstream sequences. The number of reads mapped to each of the 14 regions for each gene was calculated, as were values for reads per kilobase.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files 1 to 6. For analysis of histone methylation marks, for each gene the gene body (i.e. from the transcription start site (TSS) to the end of the gene) was divided into ten sub-regions of equal length. The region upstream of the gene was divided into two regions: from 10kb to 2.5kb upstream, and from 2.5kb upstream to the TSS. The region downstream of the gene was similarly divided. Therefore each gene consists of 14 regions covering upstream sequences, the gene body and downstream sequences. The number of reads mapped to each of the 14 regions for each gene was calculated, as were values for reads per kilobase.
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| Submission date |
Nov 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Tim C Somervaille |
| E-mail(s) |
tim.somervaille@cruk.manchester.ac.uk
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| Organization name |
Cancer Research UK Manchester Institute
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| Lab |
Leukaemia Biology Laboratory
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| Street address |
Wilmslow Road
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| City |
Manchester |
| State/province |
Lancashire |
| ZIP/Postal code |
M20 4BX |
| Country |
United Kingdom |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE63218 |
Inhibitors of LSD1 target demethylase-independent activity to induce differentiation in acute myeloid leukemia [ChIP-Seq: histone modifications] |
| GSE63222 |
Inhibitors of LSD1 target demethylase-independent activity to induce differentiation in acute myeloid leukemia |
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| Relations |
| BioSample |
SAMN03177313 |
| SRA |
SRX758162 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1543978_Processed_data_file3_H3K4Me2_DMSO.txt.gz |
1.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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