GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM887878 Query DataSets for GSM887878
Status Public on Mar 07, 2012
Title splenDC_H3K9me2_G9a_KO
Sample type SRA
Source name DC
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: Splenic dendritic cells
genotype: G9a f/f; Vav-cre
passages: Ex-vivo isolated
chip antibody: H3K9me2
vendor: Abcam (ab1220)
lot: GR38973
Treatment protocol Primary MEFs were immortalized at passage 2. At passage 5, MEFs were treated witheither 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, G9af/f, G9a;Vav-cre 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 HiSeq 2000
Description chromatin IP against H3K9me2 in G9a f/f; Vav-cre splenic DCs
Data processing Raw data processed using onboard SCS/RTA, alignments performed using Bowtie keeping only unique reads with 2 or fewer mismatches in 36bp. Alignments summed in 100bp windows for wig files
Submission date Mar 06, 2012
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 GPL13112
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 SRX128096
BioSample SAMN00809342

Supplementary file Size Download File type/resource
GSM887878_Uwe_splenDC_H3K9me2_G9a_KO_110529_2011_06_04.bowtie.bam.wig.gz 82.6 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