GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM610766 Query DataSets for GSM610766
Status Public on Mar 02, 2012
Title G9a_minus_minus_L2K_PolII_total
Sample type SRA
Source name MEF
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: Fibroblasts from day 13.5 embryos immortalized with SV40-LTA
genotype: G9a -/-, ERT2-Cre
passages: Passaged 12-15 times
chip antibody: Pol II
vendor: Abcam (ab5408)
lot: 722997
treatment: treated with transfection reagent only
Treatment protocol Primary MEFs were immortalized at passage 2. At passage 5, MEFs were treated with either EtOH as a vehicle control or Tamoxifen to induce deletion of G9a. MEFs were either left untreated, treated with Lipofectamine 200, the tranfection reagent or tranfected with PolyIC.
Growth protocol MEFs were grown in 10 cm plates with DMEM medium containing 15% FBS, Pen/Strep, Glutamine, NEAA and 2-mercaptoethanol. After immortalization with SV40-LTA, MEFs were grown in 15 cm plates with the same medium except FBS was 10%. DC were isolated from WT C57Bl/6 or IFNaR1 -/- mice that subcutaneously injected with B16-Flt3L cells. 2 weeks later splenic DCs were enriched for the CD11c+ population using CD11c MACS beads. ChIP was carried out directly on ex vivo isolated cells.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA 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 (3' to 5' 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 15 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 II
Description chromatin IP against Pol II in G9a -/- MEFs treated with transfection reagent only
Data processing Raw data processed using onboard SCS/RTA 2.6, alignments performed using Bowtie keeping only unique reads with 2 or fewer mismatches in 36bp. Alignments summed in 100bp windows for wig files and integrated profiles.
Submission date Oct 19, 2010
Last update date May 15, 2019
Contact name Terry Fang
Phone 212-327-8265
Fax 212-327-8258
Organization name Rockefeller University
Street address 1230 York Ave
City New York
State/province NY
ZIP/Postal code 10065
Country USA
Platform ID GPL9250
Series (2)
GSE22102 Histone H3 lysine 9 di-methylation as an epigenetic signature of the interferon response (sequencing)
GSE24826 Histone H3 lysine 9 di-methylation as an epigenetic signature of the interferon response
SRA SRX029285
BioSample SAMN00116693

Supplementary file Size Download File type/resource
GSM610766_G9a_minus_minus_L2K_PolII_total_fastq_prefilter_bowtie.sam.bed.wig.gz 21.9 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap