Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Liver
Cell type
Liver
MeSH Description
A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.

Attributes by original data submitter

Sample

source_name
M1L/shRen organoid
strain
C57BL/6
cell type
Mouse PDA liver metastasis (M1L)
peturbation
Transduced with miR-E/shRen retrovirus
antibody
Ipt genomic DNA

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were prepared from ~1 millon single cell dissociated of organoid cultures, or ~5 million of monolayer cultures. Sonicated nuclei with Bioruptor were further proceeded to ChIP assay with apporiate antibodies. Libraries were prepared according to Illumina's instructions of TruSeq ChIP Sample Prep kit.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
32744567
Reads aligned (%)
98.0
Duplicates removed (%)
20.6
Number of peaks
432 (qval < 1E-05)

mm9

Number of total reads
32744567
Reads aligned (%)
97.6
Duplicates removed (%)
20.6
Number of peaks
520 (qval < 1E-05)

Base call quality data from DBCLS SRA