Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CREB1

Cell type

Cell type Class
Prostate
Cell type
LNCAP
Primary Tissue
Prostate
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
LNCaP-abl siFoxA1
cell type
prostate cancer cells
passages
62-64
cell line
LNCaP-abl
chip antibody
CREB1 (Abcam ab31387)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For RNA, follow protocol in Rneasy Mini Kit. For Chip-seq, lysates were clarified from sonicated nuclei and CREB1-DNA complexes were isolated with corresponing antibody. For ChIP-seq libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part#15023092 ). Briefly, DNA was end-repaired, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, the DNA was size selected from an agarose gel and was PCR amplified with Illumina primers for 15 cycles. Libraries were sequenced on the Hi-seq 2500 following the manufacturer's protocols.For RNA-seq, follow instruction for TruSeq RNA Sample Preparation Kit v2 from Illumina(cat RS-122-2001).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
49662013
Reads aligned (%)
52.8
Duplicates removed (%)
46.1
Number of peaks
11481 (qval < 1E-05)

hg38

Number of total reads
49662013
Reads aligned (%)
54.9
Duplicates removed (%)
44.5
Number of peaks
11643 (qval < 1E-05)

Base call quality data from DBCLS SRA