SAMEA2155660

ERS323162

Released on 2013 / 07 / 05 17:00:43 UTC
Updated on 2019 / 07 / 24 12:14:42 UTC

Attributes

Type Value
INSDC center alias The Babraham Institute
INSDC center name The Babraham Institute
INSDC first public 2013-07-05T17:00:43Z
INSDC last update 2018-03-08T16:37:00Z
INSDC status public
Organism Mus musculus
SRA accession ERS323162
alias E-MTAB-1754:ES (E14)
broker name ArrayExpress
cell type embryonic stem cell
description Protocols: ES, TS, XEN, and EpiSC stem cell lines were cultured under standard conditions (see Supporting Information in the publication). Cell lines used were: ES, lines J1, E14, KH2, and PGK12.1 (a kind gift of Prof. N. Brockdorff, University of Oxford, U.K.); EpiSC, lines #5 and #9 (both a kind gift of Dr. P. Tesar, Case Western Reserve University, OH) and line PRG (a kind gift of Dr. P. Rugg-Gunn, The Babraham Institute, Cambridge, U.K.); TS, lines Rs26, GFP, and B6 (kind gifts of Dr. J. Rossant, Hospital for Sick Children, Toronto, Canada and Dr. A. Erlebacher, NY University School of Medicine, New York, USA); and XEN, lines IM8A1 (Dr. J. Rossant), #16, and E4 (Dr. P. Rugg-Gunn). DNA was extracted using a standard phenol choroform procedure. MeDIP-Seq was carried out as described previously [21]. Briefly, purified genomic DNA was sonicated to yield 150-600 bp fragments, and adaptors for paired-end sequencing (Illumina, San Diego, CA, USA, http://www.illumina.com) were ligated using NEB Next DNA Sample Prep Reagent Set 1 (New England Biolabs Hitchin, UK, http://www.neb.com). Immunoprecipitations (IPs) were carried out in triplicate using 500 ng DNA per sample, 1.25ug anti-5-methylcytosine (anti-5mC) antibody (Eurogentec, Southhampton, UK, http://www.eurogentec.com), and 10 ul Dynabeads coupled with M-280 sheep anti-mouse IgG (Invitrogen, Carlsbad, CA, http://www.invitrogen.com). The three IPs were pooled and amplified for 12 cycles with adapter specific primers, run on a 1% agarose gel, and fragments ranging between 300 and 500 bp in size were cut out and purified using the Gel Elution Kit (Qiagen, Crawley, UK, http://www.qiagen.com) before cluster generation and sequencing.
karyotype XY
organism Mus musculus
specimen with known storage state fresh specimen
synonym E-MTAB-1754:ES (E14)
title ES (E14)

Relationships

Source Type Target
SAMEG163038 has member SAMEA2155660

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