|
| Status |
Public on Oct 27, 2011 |
| Title |
H3K4me3_LKOJarid1b |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
chip or dip: ChIP
cell type: LKO Jarid1b ESCs
chip/dip antibody: H3K4me3 [Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb]
chip/dip antibody vendor: Cell Signaling
chip/dip antibody lot#: 2
chip/dip antibody catalog#: 9751
|
| Treatment protocol |
Cells were transduced with LKO scramble or Jarid1b
|
| Growth protocol |
E14TG2a.4 feeder independent ES cells were cultured on 0.1% gelatin-coated plates in Glasgow medium (Sigma) supplemented with glutamine (Gibco), non-essential amino acids (Gibco), sodium pyruvate (Gibco), 50 µM Ã-mercaptoethanol, and 15% foetal bovine serum (HyClone) in the presence of LIF. Recombinant lentiviruses encoding Jarid1b shRNA were produced by standard methods employing co-transfection of PLKO.1 shRNA and packaging vectors in 293FT cells. ESCs were transduced with lentiviral particles for >16 h, and selected with 2 µg/µl Puromycin (Invitrogen) 48 h after transduction.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was adaptor-ligated and amplified using a kit from Illumina (IP-102-1001). The amplified DNA from hme/me-DIP or ChIP-seq experiments was analyzed by Solexa/Illumina high-throughput sequencing. The tags were mapped to the mouse genome (assembly mm9) with the Bowtie alignment tool26. To avoid any PCR bias we allowed only one count (match) per chromosomal position thus eliminating spurious spikes. Peak detection and binding analysis were performed using the MACS program at an FDR cut-off value <0.2. IgG was used for normalization
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Alignment: Sequence reads were obtained and mapped to the mouse (mm9) genomes using the the BOWTIE tool with parameters: -t --best -k 1 -y -p 4 --solexa1.3-quals --chunkmbs 512 -n 2 -l 28 -e 120 .
|
| |
|
| Submission date |
Sep 07, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Sandra Ursula Schmitz |
| E-mail(s) |
sandra.schmitz@bric.ku.dk
|
| Organization name |
Biotech Research and Innovation Centre
|
| Street address |
Ole Maaløes Vej 5
|
| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL9185 |
| Series (2) |
| GSE31966 |
Jarid1b targets genes regulating development and is involved in neural differentiation [ChIP-seq] |
| GSE31968 |
Jarid1b targets genes regulating development and is involved in neural differentiation |
|
| Relations |
| Reanalyzed by |
GSE63286 |
| SRA |
SRX096138 |
| BioSample |
SAMN00715913 |
