SRX190328
GSM1010872: HudsonAlpha ChipSeq HCT-116 RevXlinkChromatin v042211.1

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

GEO Accession
GSM1010872
antibody
RevXlinkChromatin
cell description
colorectal carcinoma (PMID: 7214343)
cell karyotype
cancer
cell lineage
endoderm
cell organism
human
cell sex
M
cell
HCT-116
controlid
SL12247,SL12246
datatype description
Chromatin IP Sequencing
datatype
ChipSeq
lab description
Myers - Hudson Alpha Institute for Biotechnology
lab
HudsonAlpha
labexpid
SL12247,SL12246
protocol description
Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)
protocol
v042211.1
replicate
1,2
treatment description
No special treatment or protocol applies
treatment
None

Sequenced DNA Library

library_name
GSM1010872: HudsonAlpha_ChipSeq_HCT-116_RevXlinkChromatin_v042211.1
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeHaibTfbs

Sequencing Platform

instrument_model
Illumina Genome Analyzer

Where can I get the processing logs?

Read processing pipeline log

hg38

Number of total reads
68496387
Reads aligned (%)
91.1
Duplicates removed (%)
14.2
Number of peaks
35694 (qval < 1E-05)

hg19

Number of total reads
68496387
Reads aligned (%)
90.8
Duplicates removed (%)
14.5
Number of peaks
35570 (qval < 1E-05)

Base call quality data from DBCLS SRA