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Sample GSM1131777 Query DataSets for GSM1131777
Status Public on Jan 01, 2015
Title naiveT-H3K4me3_ChIPseq
Sample type SRA
Source name spleen
Organism Mus musculus
Characteristics cell type: CD4+
chip antibody: H3K4me3 (07-473, Millipore), lot# DAM1798683
genetic background: C57bl/6
Treatment protocol For purification of activated cells, naïve CD4+ T cells were prepared as described. Plates were coated with goat-anti-hamster antibodies followed by anti-CD3e (2C11) and the naïve T cells plated in complete RPMI including anti-CD28. 72 hours later cells were harvested, fixed with formaldehyde and frozen.
Growth protocol CD4+ T cells were isolated from spleens from C57bl/6 mice by magnetic bead selection.Cells were treated with biotinylated antibodies allowing a negative selection on the Automacs separation system (Miltenyi Biotech). Cells were fixed in formahdehyde and frozen. Purity of CD4 T cells was greater than 90%.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated cells and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions. 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 (minus exo) 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, ChIP DNA was PCR-amplified with Illumina primers with the respective indexes for 18 cycles and library fragments (ChIP) (insert plus adaptor and PCR primer sequences) were size- selected from a 8% polyacrylamide gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on a HiSeq 2000 (Illumina) following the manufacturer's protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Data processing For ChIP-Seq (single end reads), reads were aligned to the mm9 genome using Bowtie (v0.12.7), keeping only reads that mapped to a single, unique location. Aligned read files were analyzed with HOMER (
Genome_build: mm9
Supplementary_files_format_and_content: Processed files include bedgraph files (Chipseq fragment density files which were analyzed using the UCSC Genome Browser) and a bed file (peak position file used for motif analysis using HOMER)
Submission date Apr 30, 2013
Last update date May 15, 2019
Contact name Carol Katayama
Phone 858-534-5961
Fax 858-534-0980
Organization name UC San Diego
Department BIO/CMM
Lab Hedrick
Street address 9500 Gilman Dr.
City La Jolla
State/province CA
ZIP/Postal code 92024
Country USA
Platform ID GPL13112
Series (1)
GSE46525 ICOS coreceptor signaling inactivates the transcription factor FOXO1 to promote Tfh cell differentiation
BioSample SAMN02087667
SRA SRX272971

Supplementary file Size Download File type/resource
GSM1131777_naiveT.me3.ucsc.bedGraph.gz 45.5 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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