SRX152076
GSM945855: USC ChipSeq HCT-116 Input UCDavis

Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Digestive tract
Cell type
HCT 116
Primary Tissue
Colon
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
HCT-116
biomaterial_provider
ATCC
lab
USC
lab description
Farnham - University of Southern California
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
cell
HCT-116
cell organism
human
cell description
colorectal carcinoma (PMID: 7214343)
cell karyotype
cancer
cell lineage
endoderm
cell sex
M
treatment
None
treatment description
No special treatment or protocol applies
antibody
Input
antibody description
Control signal which may be subtracted from experimental raw signal before peaks are called.
control
UCDavis
control description
Input library was prepared at UC Davis.
control
UCDavis
control description
Input library was prepared at UC Davis.
controlid
wgEncodeEH000627
replicate
1

Sequenced DNA Library

library_name
GSM945855: USC_ChipSeq_HCT-116_Input_UCDavis
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
45288191
Reads aligned (%)
83.5
Duplicates removed (%)
5.3
Number of peaks
542 (qval < 1E-05)

hg19

Number of total reads
45288191
Reads aligned (%)
83.0
Duplicates removed (%)
6.1
Number of peaks
837 (qval < 1E-05)

Base call quality data from DBCLS SRA