 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 02, 2018 |
| Title |
Uhrf1 KO mESC H3K9me3 |
| Sample type |
SRA |
| |
|
| Source name |
Uhrf1 KO E14 mESC
|
| Organism |
Mus musculus |
| Characteristics |
cell type: E14 mESC
status: Undifferentiated
genotype: Uhrf1 KO
antibody: anti-H3K9me3 (ab8898, abcam)
|
| Growth protocol |
ESCs were maintained in mES medium (DMEM supplemented with 15% FBS, 1% nonessential amino acids, 2 mM glutamine, 100 U/mL penicillin/streptomycin, 0.1 mM β-mercaptoethanol, and 1,000 U/mL ESGRO leukemia inhibitory factor) on 0.1% gelatin or MEF coated plates, incubated at 37°C and passaged every second or third day.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Histone-DNA and TF-DNA complexes were isolated with antibody
Illumina TrueSeq ChIP Sample Preparation Kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Gene expression in ESC
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
ChIP-seq reads were mapped to mm9 genome by Bowtie2 (v2.1.0) with options "--local -D 15 -R 3 -N 1 -L 20 -i S,1,0.50 -k 1".
For histone modifications, peak regions were identified by the rseg-diff program in RSEG software (v0.4.8) with parameters “-i 20 –v –mode 2” and the 50bp-deadzone correction file
Uhrf1 enriched and depleted regions were assigned when there was more than 2-fold difference between ChIP and input and less than a 0.05 adjusted p-value within 10k-bp sliding window. The p-value was estimated by Poisson distribution from the ChIP-seq read counts compared to the normalized input counts
Oct4, Nanog and Sox2 binding sites were identified by MACS peak caller (v1.4.2) with “-g mm” option.
Genome_build: mm9
Supplementary_files_format_and_content: Bed format file of ChIP peaks
|
| |
|
| Submission date |
May 01, 2018 |
| Last update date |
May 03, 2018 |
| Contact name |
Kun-Yong Kim |
| E-mail(s) |
kun-yong.kim@yale.edu
|
| Phone |
7344782979
|
| Organization name |
Yale University
|
| Department |
Genetics
|
| Street address |
10 Amistad Street
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06511 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE113913 |
Uhrf1 regulates active transcriptional marks at bivalent domains in pluripotent stem cells through Setd1a [ChIP-Seq] |
| GSE113915 |
Uhrf1 regulates active transcriptional marks at bivalent domains in pluripotent stem cells through Setd1a |
|
| Relations |
| BioSample |
SAMN09006903 |
| SRA |
SRX4017957 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3123500_NP95_H3K9me3_peaks.bed.gz |
51.0 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
