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| Status |
Public on Mar 27, 2018 |
| Title |
OG86 |
| Sample type |
SRA |
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| Source name |
THP1 AML cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: AML
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| Treatment protocol |
The Assay for Transposase Accessible Chromatin (ATACseq) protocol (Buenrostro et al., 2013) was performed using 50,000 THP1 cells cultured for 24 hours in the presence of DMSO or 250nM OG86 at a density of 3x105/ml.
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| Growth protocol |
THP1 cells were cultured in RPMI 1640 without supplemental growth factors.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell pellets were re-suspended in 50μl lysis buffer (10mM Tris-HCL pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630) and nuclei were pelleted by centrifugation for 10 minutes at 500 x g. Supernatant was discarded and the nuclei were re-suspended in 25μl reaction buffer containing 2μl of Tn5 transposase and 12.5ul TD buffer (Nextera Sample preparation kit from Illumina). The reaction was incubated for 30 minutes at 37ºC and 300rpm, and purified using the Qiagen MinElute Kit.
Library fragments were amplified using 1x NEBNext High-Fidelity PCR master mix and 1.25μM of custom PCR primers and conditions (Buenrostro et al., 2013). The PCR reaction was monitored to reduce GC and size bias by amplifying the full libraries for five cycles and taking an aliquot to run for 20 cycles using the same PCR cocktail and 0.6x SYBR Green. The remaining 45ul reaction was amplified for additional cycles as determined by qPCR. Libraries were finally purified using the Qiagen MinElute Kit. Libraries were size selected with AMPure beads (Beckman Coulter) for 200-800 base pair size range and quantified by Q-PCR using Kapa Library Quantification Kit (Kapa Biosystems).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Sequencing reads were quality checked using FASTQ (Andrews, 2010). Any adapter sequences present in the data were removed using Cutadapt (Martin, 2012). The cleaned and trimmed FASTQ files were mapped to the hg38 reference assembly using BWA (Li and Durbin, 2009) and processed using Samtools (Li et al, 2009). The data were cleaned for duplicates, low mapping quality reads (i.e. MAPQ<30), non-uniquely mapped reads, not properly paired reads and reads mapped to non-conventional chromosomes and mitochondrial DNA.
For analyses of reads surrounding MYB, GFI1 or LSD1 binding peaks, the region ±2.5kB surrounding the apex of the binding peak was divided into 50 100 base pair sub-regions. The number of reads mapped to each of the 100 regions was calculated.
Genome_build: hg38
Supplementary_files_format_and_content: ATACseq reads +/-2.5kB surrounding GFI1, MYB or LSD1 binding peaks in the presence of OG86 or DMSO vehicle control.
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| Submission date |
Dec 01, 2016 |
| 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 |
GPL18573 |
| Series (2) |
| GSE63222 |
Inhibitors of LSD1 target demethylase-independent activity to induce differentiation in acute myeloid leukemia |
| GSE90770 |
Inhibitors of LSD1 target demethylase-independent activity to induce differentiation in acute myeloid leukemia [ATAC-Seq] |
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| Relations |
| BioSample |
SAMN06094243 |
| SRA |
SRX2388748 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2412285_GFI1_binding_peaks_ATACseq_signal_OG86.txt.gz |
313.2 Kb |
(ftp)(http) |
TXT |
| GSM2412285_LSD1_binding_peaks_ATACseq_signal_OG86.txt.gz |
869.6 Kb |
(ftp)(http) |
TXT |
| GSM2412285_MYB_binding_peaks_ATACseq_signal_OG86.txt.gz |
2.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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