GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM4795796

Query DataSets for GSM4795796

Status

Public on Nov 08, 2020

Title

crypt cell: Input

Sample type

SRA

Source name

intestinal crypt

Organism

Mus musculus

Characteristics

strain: C57BL/6J
tissue: intestine
cell type: crypt

Extracted molecule

genomic DNA

Extraction protocol

The crypt cells were crosslinked with 1% formaldehyde for 10 min at 37℃, and the nuclei were extracted according to the manufacturer’s instructions (CST, 9004). The DNA was sheared to length of approximately 100-300 bp by sonicating the samples with 20 pulses. Samples were incubated on ice between each pulse. ChIP assays were then carried out with the manufacturer’s instructions, using anti-CREPT antibody.
The input and CREPT antibody enriched DNA were added by A at 3', and ligated by adaptors. The DNA were amplified by PCR.

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

BGISEQ-500

Description

contol sample

Data processing

Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then clean reads were obtained.
Clean reads were mapped to GCF_000001635.26_GRCm38.p6 genome sequence from NCBI using SOAPaligner/soap2.
Based on analysis model from BGISEQ (BGI genomics), perform Peak (ChIP Sequencing enrichment area) scan in the whole genome to obtain the position information of Peak on the genome and the sequence information of the Peak region.
Genome_build: GRCm38.p6 C57BL/6J
Supplementary_files_format_and_content: Peak results are stored in wiggle file format

Submission date

Sep 19, 2020

Last update date

Nov 08, 2020

Contact name

Liu Yang

E-mail(s)

[email protected]

Organization name

Tsinghua University

Street address

Qinghuayuan street