Curated Sample Data


Genome
mm9
Antigen Class
TFs and others
Antigen
Stat1
Cell type Class
Blood
Cell type
HPC-7

Cell type information


NA
NA

Attributes by Original Data Submitter


source_name
HPC7 cells
cell line
HPC7
cell type
ES-derived multipotent hematopoietic progenitor cells
chip antibody
STAT1 (Cell Signaling, 9172)

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation (ChIP) assays on serum-starved and TPO stimulated HPC7 cells were performed as previously described (Wilson et al. 2010). Briefly, 10^8 cells were cross-linked in 1% formaldehyde for 10 min at room temperature. Cells were lysed in 10mM Tris pH 8.0, 10mM NaCl and 0.2% NP40 containing inhibitors (1g/mL leupeptin, 10mM NaBu and 50g/mL PMSF) for 10 min on ice and were collected by centrifugation at 2500 rpm for 5 min at 4ºC. The nuclei pellet was frozen until further use. Frozen nuclei were resuspended in 50mM Tris pH 8.0, 10mM EDTA, 1% SDS supplemented with inhibitors (1g/mL leupeptin, 10mM NaBu and 50g/mL PMSF) and sonicated in an equal volume of IP dilution buffer (20mM Tris pH 8.0, 2mM EDTA, 150mM NaCl, 1% Triton X-100, 0.01% SDS and protease inhibitors) in ice-water (Bioruptor, Diagenode) for 5 cycles (30s on, 30s off). Chromatin was pre-cleared with non-specific rabbit IgG (2 μg/μl, Sigma) for 1 hour and 100μL of protein G Dynabeads (Invitrogen) for 2 hours. The beads/IgG were removed by magnetic separation. Chromatin was immunoprecipitated at 4ºC overnight using antibodies against H3K27ac (Abcam, 4729), Rad21 (Abcam, 992), CTCF (Millipore, 07-729), STAT1 (Cell Signaling, 9172) or a control rabbit IgG (Invitrogen, 9172) and 100μl of protein G Dynabeads (Invitrogen) were added for additional 2 hours. Immunocomplexes were washed and eluted twice from the beads with 150μL elution buffer (100mM NaHCO3, 1% SDS). Cross-linking was reversed overnight with 0.3M NaCl and 2μL of RNase (10mg/ml) at 65ºC, and samples were further treated with Proteinase K (20mg/ml) for 2 hours at 42ºC. The ChIP DNA was purified using a PCR purification kit (Qiagen). Libraries were prepared according to Illumina's instructions accompanying the DNA and RNA Sample Kit. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on a HiSeq4000 sequencer.

Platform Information


instrument_model
Illumina HiSeq 4000

External Database Query

Logs in read processing pipeline


Number of total reads
30165569
Reads aligned (%)
88.3
Duplicates removed (%)
25.8
Number of peaks
1091 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA