SRX5006970
GSM3473049: Z138 SMARCA4 KD; Homo sapiens; ATAC-seq

Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Blood
Cell type
Z-138
Primary Tissue
Blood
Tissue Diagnosis
Lymphoma Mantle Cell

Attributes by original data submitter

Sample

source_name
Mantle Cell Lymphoma
tissue
Mantle Cell Lymphoma
cell line
Z-138
genotype
SMARCA4 shRNA knockdown

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Cell were washed in ice cold PBS then lysed in lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP40) Nextera DNA library prep kit

Sequencing Platform

instrument_model
NextSeq 500

Where can I get the processing logs?

Read processing pipeline log

hg38

Number of total reads
60035888
Reads aligned (%)
76.0
Duplicates removed (%)
64.7
Number of peaks
12558 (qval < 1E-05)

hg19

Number of total reads
60035888
Reads aligned (%)
75.7
Duplicates removed (%)
64.8
Number of peaks
12450 (qval < 1E-05)

Base call quality data from DBCLS SRA