Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Bcl6

Cell type

Cell type Class
Blood
Cell type
Th9
NA
NA

Attributes by original data submitter

Sample

source_name
Th9 cells, 72h, BCL6 ChIP
strain/background
C57BL/6
tissue
spleen
cell type
Th9
time
72h
chip antibody
BCL6 (Santa Cruz, N-3, sc-858)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-Seq, chromatin was prepared from cells cross-linked with 1% formaldehyde at 37oC for 15 min. Chromatin was fragmented by sonication and the ChIP DNA was blunt-ended, ligated to the Solexa adaptor and amplified using adaptor primers for 17 cycles. Fragments around 200bp were isolated from agarose gel and purified DNA was used directly for cluster generation and sequencing following the manufacturer protocols. For RNA-Seq, total RNA was extracted from 5x10^6 cells per sample using RNeasy Mini kit (QIAGEN) and the quality and concentration were determined by Nanodrop ND-1000 spectrophotometer. Double-stranded cDNA was synthesized using random hexamer primers, SuperScript II, DNA polymerase I, and T4 DNA polymerase (all from Invitrogen) and fragmented using Bioraptor. After repairing ends, adaptor (Illumina) was added using T4 DNA ligase (New England Biolabs), and 220-400 bp fragments were isolated using 2% E-Gel (Invitrogen) and amplified for 17 cycles using PE 1.0 and PE 2.0 primers (Illumina) and Phusion High Fidelity PCR Master Mix (New England Biolabs).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
15467608
Reads aligned (%)
77.7
Duplicates removed (%)
75.3
Number of peaks
204 (qval < 1E-05)

mm9

Number of total reads
15467608
Reads aligned (%)
77.6
Duplicates removed (%)
75.5
Number of peaks
209 (qval < 1E-05)

Base call quality data from DBCLS SRA