|
| Status |
Public on Jul 08, 2017 |
| Title |
YXY1006_DMSO_IP_Nc2β |
| Sample type |
SRA |
| |
|
| Source name |
INO80-FRB, Nc2β-13myc, bar1∆
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
cell type: yeast cells
strain: MJE7 Background
antibody: Anti Myc antibody from Abcam (ab32)
|
| Treatment protocol |
Cells were synchronized in G1 with a-factor in YPD (3hours treatment) and treat with DMSO for 2 hours, harvested at O.D of 0.8-1.0 and crosslinked with 1% formaldehyde
|
| Growth protocol |
Overnight incubated yeast cells were diluted in YPD and grow to exponential phase.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were lysed with glass beads in lysis buffer, chromatin was collected by centrifugation, resuspended in lysis buffer and subjected to sonification. The supernatant from sonicated lysates were precleared with Protein A beads and ChIP was performed as described using commercial antibodies
Libraries were prepared with a KAPA LTP kit following the manufacturer’s protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
YPD + DMSO
|
| Data processing |
Fastq files were used to map reads to yeast genome(saccer3) with or Bowtie 0.12.9
Mapped reads were counted and shuffled to similar reads.
Shuffled reads were used to calculate the p value and log2 ratio of Ip vs Input
log2 ratio of Ip vs input at significant windows were used to plot with metagene profiles or center with TSS or TTS
genome_build: = sacCer3
|
| |
|
| Submission date |
Mar 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Siavash K Kurdistani |
| E-mail(s) |
Skurdistani@mednet.ucla.edu
|
| Organization name |
UCLA
|
| Department |
Biological Chemistry
|
| Lab |
Kurdistani
|
| Street address |
615 Charles E Young Dr South
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL21656 |
| Series (1) |
| GSE95633 |
MINC Regulates Pervasive Transcription in Yeast and Mammals |
|
| Relations |
| BioSample |
SAMN06469716 |
| SRA |
SRX2609713 |
