|
| Status |
Public on Jul 05, 2013 |
| Title |
OX_input_DNA |
| Sample type |
SRA |
| |
|
| Source name |
YMC OX phase cells, input
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: CEN.PK a IFH1-FLAG::Nat
ymc phase: OX growth phase
chip antibody: None
|
| Treatment protocol |
OX and RC phase cells were collected and crosslinked for 15min at room temperature with 1% formaldehyde and quenched with 150mM glycine before being flash frozen.
|
| Growth protocol |
Yeast cells from the IFH1-FLAG strain were cultured in a fermentor under low glucose continuous growth conditions as described in Tu, et al. 2005 (PMID 16254148).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was sheared with the Bioruptor and precleared before immunoprecipitation with Flag antibody. The ChIP DNA was purified using MinElute PCR purification kit. ChIP-seq library construction was performed following the protocol at http://bioinfo.mbb.yale.edu/array/Solexa_LibraryPrep_20080229ge.pdf . Briefly, ends were repaired (End-it DNA End Repair Kit, Epicentre, Cat# ER0720), 'A' base was added to the 3' ends (Klenow (3'→5' exo-), NEB, Cat# M0212s), adaptors were ligated (LigaFast, Promega, Cat#M8221 and the adapter mix from Illumina), and PCR was performed (Phusion DNA polymerase, NEB, Cat# F-531 and Illumina primers), followed by size selection.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Input DNA.
|
| Data processing |
The fastq files were generated using CASAVA version 1.7.
4bp barcode was removed from the 40 bp reads.
Reads were aligned to the sacCer1 genome assembly using Bowtie-0.12.5 with parameters -m 1.
Data were processed by CisGenome. 2 sample ChIP analysis was performed using ChIP as the treated sample and Input as the control.
Peaks were called by CisGenome.
Genome_build: sacCer1
Supplementary_files_format_and_content: .bar files were generated from Cisgenome and converted to .wig files.
|
| |
|
| Submission date |
Jul 05, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Ling Cai |
| E-mail(s) |
ling.cai@utsouthwestern.edu
|
| Organization name |
UT Southwestern Medical Center at Dallas
|
| Street address |
5323 Harry Hines Boulevard
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL13272 |
| Series (1) |
| GSE39147 |
Genome-wide Ifh1p occupancy at the OX growth phase and RC quiescent phase of the yeast metabolic cycle |
|
| Relations |
| SRA |
SRX157919 |
| BioSample |
SAMN01085913 |
