|
| Status |
Public on Oct 26, 2012 |
| Title |
Suz12_WT |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic Stem Cell
|
| Organism |
Mus musculus |
| Characteristics |
background mouse strain: 129SvJae/C57BL/6
chip antibody: Suz12
antibody vendor/catalog: Cell Signaling, 3737
genotype/variation: WT
|
| Growth protocol |
V6.5 ESCs (derived from the F1 hybrid of 129SvJae/C57BL/6) were maintained in DMEM (Dulbecco's modified Eagle's medium) supplemented with 15% fetal calf serum, 0.1 mM β-mercaptoethanol, 2 mM L-glutamine, 0.1 mM nonessential amino acid, 1000 U/ml recombinant leukemia inhibitory factor (LIF; Millipore), and 30 U/ml Penicillin/Streptomycin (the ESC medium) either with or without a feeder layer. For feeder-free culture, V6.5 ESCs and their derivatives were grown on plates coated with gelatin (Millipore).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Following Illumina True-Seq DNA Sample Preparation V2 protocol and Illumina True-Seq RNA Sample Preparation V2 protocol
Using ChIP-Seq DNA Sample Prep Kit Part # 11257047. Step 1: Perform End Repair of ChIP enriched DNA using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. Step 2: Add ?A? Bases to the 3' End of the DNA Fragments from step 1 using Klenow buffer and Klenow exo. Step 3: Ligate Adapters to DNA Fragments from step 3 using DNA ligase. Step 4: Size (300-400bp) Select the Library by 2% agarose gel with TAE buffer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The densities of RNA-seq reads (in reads per kilo-bases per million reads, RPKM) were normalized to the library size and the number of sites in 20bp sliding windows along the genome.
|
| |
|
| Submission date |
Jul 19, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Yixian Zheng |
| E-mail(s) |
zheng@ciwemb.edu
|
| Organization name |
Carnegie Institution for Science
|
| Department |
Embryology
|
| Lab |
Yixian Zheng
|
| Street address |
3520 San Martin Drive
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21218 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE39513 |
Regulation of pluripotency and self-renewal of ES cells through epigenetic-threshold modulation and mRNA pruning |
|
| Relations |
| SRA |
SRX172570 |
| BioSample |
SAMN01096322 |
