Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MLLT3

Cell type

Cell type Class
Blood
Cell type
CD34+ cells
NA
NA

Attributes by original data submitter

Sample

source_name
FLAG MLL-AF9 ChIPseq
cell type
human CD34+
genotype
control untreated
antibody
Flag

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-Seq assay were performed essentially as previously described (Ptasinska et al., 2014). Antibody against Flag (Sigma, M2) was used for IP. Cells were first washed with PBS and then cross-linked with 0.83 mg/ml Di(N-succinimidyl) glutarate (DSG) (Sigma) for 45 minutes at room temperature with rotation. Cells were washed four times with PBS and further crosslinked in PBS with 1% formaldehyde (~0.34 M) for 10 minutes at room temperature. All crosslinking reactions were quenched by adding 4 volumes of PBS and 0.125 M glycine, cells were washed twice in PBS and incubated with Buffer A (10 mM HEPES pH 8.0, 10 mM EDTA, 0.5 mM EGTA, 0.25% Triton X-100, proteinase inhibitor cocktail (Roche UK, Burgess Hill, UK) and 0.1 mM PMSF), incubated for 10 min at 4°C with rotation, and centrifuged 5 min at 500 x g at 4 °C. The pellet was resuspended in 10 ml of ice–cold Buffer B (10 mM HEPES pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.01% Triton X-100, protease inhibitor cocktail and 0.1 mM PMSF), incubated for 10 min at 4 °C with rotation and centrifuged for 5 min at 500 x g at 4 °C. Cells were resuspended in 600 μl of ice-cold ChIP lysis buffer (25 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.25% SDS, protease inhibitor cocktail and 0.1 mM PMSF), incubated 10 min on ice and sonicated at 5 °C using a Bioruptor™ (Diagenode) to generate fragments an average length of 500 bp (10 min with 30 s “ON” and “OFF” cycles, power setting high). The lysates were centrifuged for 5 min at 16,000 x g at 4 °C and the supernatants were diluted with two volumes of ice-cold ChIP dilution buffer (25 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 7.5% glycerol, protease inhibitor cocktail and 0.1 mM PMSF). For each IP, 15 μl of Dynabeads® protein G (Dynal) were pre–incubated with 50 μg BSA and 1-2 μg antibody for 2 h at 4 °C with rotation. The blocked antibody-bound protein G mix was added to 20–25 μg chromatin in a total volume of 500 μl diluted ChIP lysis buffer and incubated for 2 h at 4°C with rotation. After magnetic separation the beads were washed once with 1 ml wash buffer 1 (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), twice with 1 ml wash buffer 2 (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), once with 1 ml LiCl buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na-deoxycholate) and twice with 1 ml TE/NaCl buffer (10 mM Tris-HCl pH 8.0, 50 mM NaCl, 1 mM EDTA). For each wash the beads were mixed with ice-cold washing buffers for 10 min at 4 °C. The immunoprecipitated DNA was eluted two times with 50 μl ChIP elution buffer (100 mM NaHCO3, 1% SDS) for 15 min at RT with shaking. At this step the input control (1% of the starting material) was included in the experimental procedure after first adjusting the final volume to 100 μl with ChIP elution buffer. The eluted DNA was incubated overnight at 65 °C in the presence of 50 μg proteinase K. The DNA was finally purified using Agencourt AMPure (Beckman Coulter) magnetic beads according to the manufacturer’s instructions, eluted with 50 μl x TE and analysed by qPCR using SYBR Green reagents. KAPA Hyper Prep Kit, Kapa biosystems

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
19048378
Reads aligned (%)
43.3
Duplicates removed (%)
46.8
Number of peaks
2640 (qval < 1E-05)

hg38

Number of total reads
19048378
Reads aligned (%)
45.3
Duplicates removed (%)
45.2
Number of peaks
3067 (qval < 1E-05)

Base call quality data from DBCLS SRA