ChIP-Atlas: SRX100421

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

source_name: PFSK-1
biomaterial_provider: ATCC
datatype: ChipSeq
datatype description: Chromatin IP Sequencing
cell description: neuroectodermal cell line derived from a cerebral brain tumor, (PMID: 1316433)
protocol description: a 25-cycle round of PCR and an additional 15-cycle round of PCR after gel size selection (Myers)
controlid: SL150,SL16,SL412
labexpid: SL150,SL16,SL412
replicate: 1,3,2
cell karyotype: cancer
cell lineage: ectoderm
cell sex: M
antibody: RevXlinkChromatin
treatment: None
treatment description: No special treatment or protocol applies
protocol: PCR2x
protocol description: 2-cycles of PCR (Myers)
controlid: SL150
labexpid: SL150
replicate: 1
replicate description: tier 1

Sequenced DNA Library

library_name: GSM803376: HudsonAlpha_ChipSeq_PFSK-1_RevXlinkChromatin_PCR2x
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: 56870897
Reads aligned (%): 63.9
Duplicates removed (%): 7.6
Number of peaks: 16226 (qval < 1E-05)

hg19

Number of total reads: 56870897
Reads aligned (%): 63.5
Duplicates removed (%): 8.3
Number of peaks: 15915 (qval < 1E-05)

Base call quality data from DBCLS SRA