|
| Status |
Public on Jul 08, 2017 |
| Title |
Forsubtelomere_YXY919_IP_Arp5_WT_replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
INO80-FRB, MOT1-13myc
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: MJE7 Background
antibody: Anti Arp5 antibody from Abcam (ab12099).
|
| Treatment protocol |
Cells were crosslinked with 1% formaldehyde.
|
| Growth protocol |
Log phase cells were crosslinked with 1% formaldehyde for 45 minutes.
Yeast cells were grown in YPD to exponential phase at OD600 around 0.8-1.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell were lysed with glass beads in lysis buffer and chromatin were extensively washed. chromatin was sonicated for 4 minutes with 30s on and 1 min off on a Biodisruptor. The supernatant from sonicated lysates were precleared with Protein A beads and ChIP was performed as described using commercial antibodies
Cell were lysed with glass beads in lysis buffer and chromatin were extensively washed. chromatin was sonicated for 4 minutes with 30s on and 1 min off on a Biodisruptor. The supernatant from sonicated lysates were precleared with Protein A/G 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 |
in YPD
Sample 110
|
| Data processing |
For yeast ChIP-seq
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 |
Jun 08, 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 |
SAMN07204607 |
| SRA |
SRX2894825 |
