SRX100520
GSM803475: HudsonAlpha ChipSeq HCT-116 RevXlinkChromatin v041610.1

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
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
controlid
SL3457
labexpid
SL3457
cell
HCT-116
cell organism
human
cell description
colorectal carcinoma (PMID: 7214343)
cell karyotype
cancer
cell lineage
endoderm
cell sex
M
antibody
RevXlinkChromatin
treatment
None
treatment description
No special treatment or protocol applies
protocol
v041610.1
protocol description
2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers)
controlid
SL3457
labexpid
SL3457
replicate
1
replicate description
tier 1

Sequenced DNA Library

library_name
GSM803475: HudsonAlpha_ChipSeq_HCT-116_RevXlinkChromatin_v041610.1
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
35542451
Reads aligned (%)
93.5
Duplicates removed (%)
9.8
Number of peaks
356 (qval < 1E-05)

hg19

Number of total reads
35542451
Reads aligned (%)
93.0
Duplicates removed (%)
10.2
Number of peaks
557 (qval < 1E-05)

Base call quality data from DBCLS SRA