ChIP-Atlas: SRX190019

Sample information curated by ChIP-Atlas

Antigen

Antigen Class: Input control
Antigen: Input control

Cell type

Cell type Class: Digestive tract
Cell type: Caco-2
Primary Tissue: Colon
Tissue Diagnosis: Adenocarcinoma

Attributes by original data submitter

Sample

source_name: Caco-2
biomaterial_provider: ATCC
lab: UW
lab description: Stamatoyannopoulous - University of Washington
datatype: ChipSeq
datatype description: Chromatin IP Sequencing
cell: Caco-2
cell organism: human
cell description: colorectal adenocarcinoma. (PMID: 1939345)
cell karyotype: cancer
cell lineage: endoderm
cell sex: M
antibody: Input
antibody description: Control signal which may be subtracted from experimental raw signal before peaks are called.
treatment: None
treatment description: No special treatment or protocol applies
control: std
control description: Standard input signal for most experiments.
controlid: wgEncodeEH000454
labexpid: DS13597
labversion: Bowtie 0.12.5
replicate: 1

Sequenced DNA Library

library_name: GSM945236: UW_ChipSeq_Caco-2_Input
library_strategy: ChIP-Seq
library_source: GENOMIC
library_selection: ChIP

Sequencing Platform

instrument_model: Illumina Genome Analyzer

Where can I get the processing logs?

Read processing pipeline log

hg38

Number of total reads: 17312913
Reads aligned (%): 98.1
Duplicates removed (%): 1.7
Number of peaks: 365 (qval < 1E-05)

hg19

Number of total reads: 17312913
Reads aligned (%): 97.3
Duplicates removed (%): 3.0
Number of peaks: 688 (qval < 1E-05)

Base call quality data from DBCLS SRA