title: rno5
organism: Rattus norvegicus
description: Protocols: Samples were prepared by direct perfusion of the tissue 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 cells were rinsed with PBS. The animal tissues 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 was 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 ul of fortyfold diluted 'Adapter oligo mix' in a total reaction volume of 25 ul. 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 ul 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.
attributes.tag: ENA first public
attributes.value: 2011-07-29
attributes.tag: ENA last update
attributes.value: 2018-03-08
attributes.tag: External Id
attributes.value: SAMEA787405
attributes.tag: INSDC center alias
attributes.value: CRUK-CRI
attributes.tag: INSDC center name
attributes.value: CRUK-CRI
attributes.tag: INSDC first public
attributes.value: 2011-07-29T17:00:38Z
attributes.tag: INSDC last update
attributes.value: 2018-03-08T15:27:40Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-424_complete:rno5
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: common name
attributes.value: Norway rat
attributes.tag: developmental stage
attributes.value: adult
attributes.tag: organism part
attributes.value: liver
attributes.tag: sample name
attributes.value: E-MTAB-424_complete:rno5
attributes.tag: sex
attributes.value: male