|
| Status |
Public on Jul 24, 2013 |
| Title |
ECM5_4hrs_DMSO_RapExpt_ChIP |
| Sample type |
SRA |
| |
|
| Source name |
S. cerevisiae Ecm5-13Myc strain
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
yeast strain: Ecm5-13Myc
treatment: DMSO
hours treatment: 4
antibody: anti-Myc (9E10 monoclonal)
|
| Treatment protocol |
An aliquot of each yeast culture was taken for the 0 hour (T0) ChIP/Input samples. Each culture was then divided into two separate cultures: one of these was treated with rapamycin dissolved in DMSO (final rapamycin concentration 50 nM), while the other cultures was treated with DMSO as a control. Samples were taken 0.5 and 4 hours after treatment for ChIP/Inputs.
|
| Growth protocol |
Saturated overnight cultures of strains (Snt2-Myc, Ecm5-Myc, or BY4741) were diluted in YPD and grown to mid-log phase (OD600=0.4)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were crosslinked by adding formaldehyde (final conc 1%) at room temp for 20 minutes, and then quenched with glycine (final conc 125 mM). ChIPs were performed as described (Aparicio et al. 2005 Curr Protoc Mol Biol). Briefly cells were lysed using glass beads, and chromatin was sheared to 150-500 bp. Chromatin was isolated and used for ChIP with the anti-Myc 9E10 antibody (Millipore #05-419) according to standard procedures.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA Sample Preparation Kit (cat # FC-121-2001). After adapter ligation DNA was PCR amplified with Illumina primers for 21 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
ChIP-seq reads were aligned at 51bp to the SacCer2 genome assembly using Bowtie: only unique reads with no more than 2 mismatches were kept
Aligned BAM files were converted to Wig files using IGVtools
Genome_build: sacCer2
|
| |
|
| Submission date |
Dec 18, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
David Allis |
| Organization name |
The Rockefeller University
|
| Department |
Laboratory of Chromatin Biology and Epigenetics
|
| Lab |
Allis Laboratory
|
| Street address |
1230 York Ave Box 78
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL13821 |
| Series (2) |
| GSE43001 |
The yeast Snt2 protein helps coordinate the transcriptional response to hydrogen-peroxide mediated oxidative stress (rapamycin or DMSO) |
| GSE43002 |
The yeast Snt2 protein helps coordinate the transcriptional response to hydrogen-peroxide mediated oxidative stress |
|
| Relations |
| SRA |
SRX211422 |
| BioSample |
SAMN01831695 |
