ChIP-Atlas: SRX1836022

Sample information curated by ChIP-Atlas

Antigen

Antigen Class: DNase-seq
Antigen: DNase-Seq

Cell type

Cell type Class: Embryo
Cell type: Embryonic brains
NA: NA

Attributes by original data submitter

Sample

tissue: hindbrain
age: 14.5 day
donor ID: ENCDO956IXV
dev stage: embryonic
sample type: tissue
sex: pooled male and female
health state: healthy
lab: John Stamatoyannopoulos, UW

Sequenced DNA Library

library_strategy: DNase-Hypersensitivity
library_source: GENOMIC
library_selection: DNase
library_construction_protocol: document: https://www.encodeproject.org/documents/926174f5-d14c-4e77-bc52-5517b56daac0/@@download/attachment/Culturedcells_SOP_nuclei_DNase_crosslink_RNA_V1.pdf See ENCODE portal

Sequencing Platform

instrument_model: Illumina HiSeq 2500

Where can I get the processing logs?

Read processing pipeline log

mm10

Number of total reads: 231224526
Reads aligned (%): 80.1
Duplicates removed (%): 66.6
Number of peaks: 38623 (qval < 1E-05)

mm9

Number of total reads: 231224526
Reads aligned (%): 80.0
Duplicates removed (%): 66.9
Number of peaks: 40479 (qval < 1E-05)

Base call quality data from DBCLS SRA