SRX190310
GSM1010854: HudsonAlpha ChipSeq MCF-7 RevXlinkChromatin v042211.1

Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

GEO Accession
GSM1010854
antibody
RevXlinkChromatin
cell description
mammary gland, adenocarcinoma. (PMID: 4357757), newly promoted to tier 2: not in 2011 analysis
cell karyotype
cancer
cell lineage
ectoderm
cell organism
human
cell sex
F
cell
MCF-7
controlid
SL16758,SL16757,SL13504,SL16756
datatype description
Chromatin IP Sequencing
datatype
ChipSeq
lab description
Myers - Hudson Alpha Institute for Biotechnology
lab
HudsonAlpha
labexpid
SL16758,SL16757,SL13504,SL16756
protocol description
Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)
protocol
v042211.1
replicate
1,3,2,4
treatment description
No special treatment or protocol applies
treatment
None

Sequenced DNA Library

library_name
GSM1010854: HudsonAlpha_ChipSeq_MCF-7_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
127089379
Reads aligned (%)
94.2
Duplicates removed (%)
5.7
Number of peaks
6439 (qval < 1E-05)

hg19

Number of total reads
127089379
Reads aligned (%)
93.6
Duplicates removed (%)
6.8
Number of peaks
5923 (qval < 1E-05)

Base call quality data from DBCLS SRA