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Sample GSM785842 Query DataSets for GSM785842
Status Public on Feb 25, 2021
Title 4_H3K4me3_ChIP_Seq_Day1_mES_s_1_sequence
Sample type SRA
 
Source name Mouse ES
Organism Mus musculus
Characteristics strain: AINV15
cell type: Esrrb_Rescue Clone
time point: Day1
fraction: Chromatin IP
antibody: H3K4me3
antibody vendor: Abcam
antibody catalog#: ab 8580
antibody lot#: 1016899
Treatment protocol Esrrb_R rescue clone was grown in +Dox (1ug/ml) media_Day0; Dox withdrawal was performed for 5 days performing H3K4me3 and H3K27me3 ChIP-Seq at the respective days: Day0 ( Esrrb expressed) and days 1,3 and 5 ( Esrrb non expressed)
Growth protocol Esrrb_R rescue clone was grown under under typical ES conditions; D-MEM–High Glucose (Dulbecco’s modified Eagle’s medium-1X-High Glucose) (Gibco®, Invitrogen), 15% FBS (Fetal bovine serum) (Hyclone, Thermo Scientific), 100 mM MEM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 1 mM L-glutamine, Penicillin/Streptomycin (Gibco, Invitrogen) and 103 U ml-1 LIF (Chemicon, Millipore) on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for one passage off of MEFs, on gelatinized tissue-culture plates.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes or Esrrb (TF)-complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
 
Description Chromatin IP against H3K4me3. Abcam (ab 8580). Lot #1016899
Data processing Alignment: Sequence reads were obtained and mapped to the Mouse July, 2007 (NCBI37/mm9) genome using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
 
Submission date Aug 24, 2011
Last update date Feb 25, 2021
Contact name Ana Sevilla
E-mail(s) anasevilla@ub.edu
Phone +34 675348398
Organization name Universidad de Barcelona
Department Departamento de Biologia Celular, Fisiologia e Inmunologia
Lab 4 Floor.
Street address Avda Diagonal 643. Edificio Malagef 4rd Floor, Faculty of Biology
City Barcelona
State/province Barcelona
ZIP/Postal code 08028
Country Spain
 
Platform ID GPL9185
Series (2)
GSE31640 An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feedback Interactions [ChIP-seq]
GSE31842 An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feed Forward Loop Interactions.
Relations
SRA SRX093169
BioSample SAMN00714097

Supplementary file Size Download File type/resource
GSM785842_4_H3K4me3_ChIP_Seq_Day1_mES.wig.gz 24.5 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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