SRX190253
GSM1010797: HudsonAlpha ChipSeq PFSK-1 RevXlinkChromatin v041610.1

Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Neural
Cell type
PFSK-1
Primary Tissue
Brain
Tissue Diagnosis
Medulloblastoma

Attributes by original data submitter

Sample

GEO Accession
GSM1010797
antibody
RevXlinkChromatin
cell description
neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433)
cell karyotype
cancer
cell lineage
ectoderm
cell organism
human
cell sex
M
cell
PFSK-1
controlid
SL2339
datatype description
Chromatin IP Sequencing
datatype
ChipSeq
lab description
Myers - Hudson Alpha Institute for Biotechnology
lab
HudsonAlpha
labexpid
SL2339
protocol description
2x10^7 cells, fragmentation by bioruptor, one 15-cycle round of PCR (Myers)
protocol
v041610.1
replicate
1
treatment description
No special treatment or protocol applies
treatment
None

Sequenced DNA Library

library_name
GSM1010797: HudsonAlpha_ChipSeq_PFSK-1_RevXlinkChromatin_v041610.1
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
27734812
Reads aligned (%)
68.2
Duplicates removed (%)
9.6
Number of peaks
480 (qval < 1E-05)

hg19

Number of total reads
27734812
Reads aligned (%)
67.9
Duplicates removed (%)
10.0
Number of peaks
624 (qval < 1E-05)

Base call quality data from DBCLS SRA