Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Neural
Cell type
MEF derived photoreceptor like cells
NA
NA

Attributes by original data submitter

Sample

source_name
Reprogramming intermediate at d8
cell type
MEF derived photoreceptor intermediates
genotype
Strain (Nrl-GFP)

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Cells were harvested and frozen in culture media containing FBS and 5% DMSO. Cryopreserved cells were thawed in a 37oC water bath, pelleted, washed with cold PBS. Cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina) Tagmented DNA was purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter)

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
35257538
Reads aligned (%)
98.0
Duplicates removed (%)
18.2
Number of peaks
30237 (qval < 1E-05)

mm9

Number of total reads
35257538
Reads aligned (%)
97.9
Duplicates removed (%)
18.4
Number of peaks
30215 (qval < 1E-05)

Base call quality data from DBCLS SRA