Curated Sample Data


Genome
hg19
Antigen Class
Histone
Antigen
H3K4me1
Cell type Class
Adipocyte
Cell type
Capan-1

Cell type information


Primary Tissue
Pancreas
Tissue Diagnosis
Adenocarcinoma

Attributes by Original Data Submitter


source_name
H3K4me1.CAPAN1
cell line background
CAPAN1
cell type
original Pancreatic Ductal Adenocarcinoma (PDAC) cell line
chip antibody
Anti-H3K4me1
chip antibody vendor
Abcam

Metadata from Sequence Read Archive

Library Description


library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP lysates were generated from 2-5x10^6 cells for histone marks or 20-40x10^6 cells for transcription factors. Cells were fixed in 1% formaldehyde for 10min. Lysate was immunoprecipitated with 10ug of antibody. Antibodies were pre-bound overnight to 100ul of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (the preclearing step was omitted) and incubation was let to proceed overnight. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by QIAquick columns (Qiagen) and quantified using PicoGreen (Invitrogen). ChIP DNA was prepared for HiSeq 2000 Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, PCR with index primers and purification. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer’s instruction. Library preparation is carried out on SPRIworks Fragment Library System.

Platform Information


instrument_model
Illumina Genome Analyzer II

External Database Query

Logs in read processing pipeline


Number of total reads
38305555
Reads aligned (%)
96.8
Duplicates removed (%)
3.8
Number of peaks
35754 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA