ChIP-Atlas: SRX4799479

Sample information curated by ChIP-Atlas

Antigen

Antigen Class: Unclassified
Antigen: Unclassified

Cell type

Cell type Class: Breast
Cell type: T-47D
Primary Tissue: Breast
Tissue Diagnosis: Adenocarcinoma Ductal

Attributes by original data submitter

Sample

source_name: T47D
cell type: ER+/PR+
target protein: ChIP-Pol_II
pre treatment: Untreated
pre treatment time: 0
treatment: Untreated
treatment time: 0
sequencing core: 4DGU
send for sequencing on: 8/24/2017
sequencing index: AGTGAG
illumina machine: Illumina NextSeq 500
application: ChIP-seq
read length: 75
sequencing type: SE
library type: Unknown

Sequenced DNA Library

library_strategy: ChIP-Seq
library_source: GENOMIC
library_selection: ChIP
library_construction_protocol: In Situ Hi-C was performed according previously described protocol (Rao et al., 2014) with some modifications (Le Dily et al., 2017). Paired-end libraries were generated with Truseq adaptors (Illumina) according previously published Hi-C protocols (Rao et al., 2014).

Sequencing Platform

instrument_model: NextSeq 500

Where can I get the processing logs?

Read processing pipeline log

hg38

Number of total reads: 37218913
Reads aligned (%): 98.3
Duplicates removed (%): 26.7
Number of peaks: 13746 (qval < 1E-05)

hg19

Number of total reads: 37218913
Reads aligned (%): 97.7
Duplicates removed (%): 27.8
Number of peaks: 13594 (qval < 1E-05)

Base call quality data from DBCLS SRA