|
| Status |
Public on Feb 20, 2013 |
| Title |
Kdm2b_Kdm2bKD |
| Sample type |
SRA |
| |
|
| Source name |
Kdm2b knockdown mouse ES cells
|
| Organism |
Mus musculus |
| Characteristics |
chip antibody: Flag
antibody manufacturer: Sigma
antibody catalog number: F7425
antibody lot number: N/A
strain: inbred 129
cell line: E14
cell type: embryonbic stem cells
genotype: Kdm2b knockdown
|
| Treatment protocol |
Around 1x10^5 ES cells/well in 24-well plates are infected with lentiviral vectors at 10 MOI. 48 hours after transduction, puromycin (2ug/ml) is added to the medium for selecting transduced cells.
|
| Growth protocol |
E14 mESCs are cultured on the 0.1% gelatin coated plates in the DMEM medium (Sigma) supplemented with 100U/ml penicillin/streptomycin, 15% fetal bovine serum (Sigma), 1x nonessential amino acid, 1x sodium pyruvate, 1x GlutaMax, 1x beta-mercaptoethanol (Invitrogen) and 1000 units/ml leukemia inhibitory factor (ESGRO, EMD Millipore).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (NEB) following manufacture's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Kdm2b ChIP-seq was done by Flag antibody because we knocked in a Flag tag upstream of Kdm2b gene.
|
| Data processing |
Basecalls were performed using CASAVA version v.1.8.2
Sequenced reads were de-multiplexed, trimmed and mapped to mm8 whole genome using bowtie v0.12.7
Peak calling were performed using MACS 1.4.1, meanwhile, wiggle files were generated
Genome_build: mm8
Supplementary_files_format_and_content: wiggle files (scores represent tag numbers per 10 million reads)
|
| |
|
| Submission date |
Oct 03, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Li Shen |
| Organization name |
HHMI/Boston Children's Hospital/Harvard Medical School
|
| Street address |
200 Longwood Ave
|
| City |
Boston |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE41314 |
Kdm2b maintains murine embryonic stem cell status by recruiting PRC1 complex to CpG islands of lineage genes [ChIP-Seq] |
| GSE41316 |
Kdm2b maintains murine embryonic stem cell status by recruiting PRC1 complex to CpG islands of developmental genes |
|
| Relations |
| SRA |
SRX191071 |
| BioSample |
SAMN01757981 |
| Named Annotation |
GSM1014547_Kdm2b_Kdm2bKD.wig.gz |
