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Sample GSM548869

Query DataSets for GSM548869

Status

Public on Jun 03, 2010

Title

[E-TABM-722] do16_Input_liver_none_mmuC57BL6_CRI01_h0_t0

Sample type

SRA

Source name

mmu3

Organism

Mus musculus

Characteristics

strain: C57BL6/J
developmentalstage: adult
organismpart: liver
sex: male
individual: mmu3
chip antibody: none, input DNA

Extracted molecule

genomic DNA

Extraction protocol

hep prep | nucleic_acid_extraction | Hepatocytes were prepared by direct perfusion of the liver with buffered salt solution, followed by % formaldehyde. After 10 minutes, the tissue was removed and diced in 500 mM glycine buffer to neutralize the formaldehyde. After homogenization, the hepatocytes were rinsed with PBS.
liver_prep | immunoprecipitate | The animal livers were crosslinked with formaldehyde treatment and chromatin fragmented to an average of 300 bp by sonication. Chromatin from an mass equivalent of 1/4 mouse liver was used for each ChIP experiment. Solexa libraries were prepared following the instructions of Illumina (Sample preparation for genomic DNA - version 2.2) with the following modifications. The ChIP-enriched DNA and input DNA were not further fragmented. After end-repair and addition of an 'A' base to the 3' ends, the adapters were ligated to the ends of the DNA Fragments using 2 µl of fourtyfold diluted 'Adapter oligo mix' in a total reaction volume of 25 µl. Between these steps, the DNA was purified using the DNA Clean-and-Concentrator-5 kit (Zymo Research). Subsequently, the DNA was amplified by 18 cycles of PCR, purified with QIAquick PCR purification Kit, and eluted with 33.5 µl of 10 mM tris buffer at pH7.0. The PCR-product was sized fractionated on 2% agarose gel and a gel slice containing the 200-300 bp fragments was excised. The flowcells were prepared and processed according to the manufacturer's protocols, with single-end sequencing for 36 to 45 cycles.
input_seq | immunoprecipitate | The protocol describing how the input DNA was prepared can be found at http://0-dx-doi-org.brum.beds.ac.uk/10.1016/j.ymeth.2009.03.005

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina Genome Analyzer

Description

do16_Input_liver_none_mmuC57BL6_CRI01_h0_t0.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Mus musculus
Factor Value [IMMUNOPRECIPITATE]: input_DNA

Data processing

none

Submission date

Jun 01, 2010

Last update date

Jun 02, 2010

Organization

European Bioinformatics Institute

E-mail(s)

miamexpress@ebi.ac.uk

Lab

ArrayExpress