Curated Sample Data


Genome
mm9
Antigen Class
Unclassified
Antigen
Unclassified
Cell type Class
Blood
Cell type
HPC-7

Cell type information


NA
NA

Attributes by Original Data Submitter


source_name
HPC7 cells
tissue
HPC7 cells
genotype/variation
empty vector

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were sorted for GFP expression one week after viral transduction and expanded for ChIP-sequencing. Cells were fixed in 1% formaldehyde for 10 minutes at room temperature. To terminate cross linking 0.125M glycine was added for 5 minutes, washed with PBS and lysed (10mM Tris, 10mM NaCl, 0.2% NP-40) on ice for 10 minutes. Pelleted nuclei were then lysed in nucleus lysis buffer (50mM Tris, 10mM EDTA, 150mM NaCl, 1% Triton-X100, 0.01% SDS) and DNA sonicated to yield an average fragmentation size of 200bp. Sonicated chromatin was pre-cleared with rabbit IgG and immunoprecipitated with antibody and protein G beads. Immunoprecipitated chromatin was eluted using Elution Buffer (100mM NaHCO3, 1%SDS) and reverse cross linked by incubation with RNAse A and 0.3M NaCl, followed by incubation with Proteinase K. Purified DNA was re-suspended in 20ul nuclease-free water for sequencing. ChIP-sequencing libraries were prepared using the Truseq ChIP library preparation kit from Illumina (Snai1 ChIP) or a variation of Illumina's standard protocol by BGI (H3K4me1 and H3K4me2).

Platform Information


instrument_model
NextSeq 500

External Database Query

Logs in read processing pipeline


Number of total reads
11915671
Reads aligned (%)
94.8
Duplicates removed (%)
8.6
Number of peaks
111 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA