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Sample GSM548865 Query DataSets for GSM548865
Status Public on Jun 02, 2010
Title [E-TABM-722] do100_Input_liver_none_cfa4_CRI01
Sample type SRA
 
Source name cf4
Organism Canis lupus familiaris
Characteristics developmentalstage: adult
organismpart: liver
sex: male
individual: cf4
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 gland 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://dx.doi.org/10.1016/j.ymeth.2009.03.001
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
 
Description do100_Input_liver_none_cfa4_CRI01.fq.gz
Factor Value [ORGANISMPART]: liver
Factor Value [ORGANISM]: Canis familiaris
Factor Value [IMMUNOPRECIPITATE]: input_DNA
Data processing none
 
Submission date Jun 01, 2010
Last update date May 15, 2019
Organization European Bioinformatics Institute
E-mail(s) miamexpress@ebi.ac.uk
Lab ArrayExpress
Street address Wellcome Trust Genome Campus
City Hinxton
State/province Cambridgeshire
ZIP/Postal code CB10 1SD
Country United Kingdom
 
Platform ID GPL10474
Series (1)
GSE22078 [E-TABM-722] Transcription factor binding evolution in five vertebrates
Relations
SRA ERX000513

Supplementary data files not provided
SRA Run SelectorHelp
Processed data not provided for this record
Raw data are available in SRA

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