|
| Status |
Public on Jan 22, 2015 |
| Title |
The Ino80 complex prevents invasion of euchromatin into silent chromatin |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Purpose: We want to know whether Ino80C contribute to chromatin silencing at both euchromatin and heterochromatin
Methods: All yeast cells were collected in exponential phase. Total RNA was extracted with phenol, digested with DNase and further purified by Trizol. Libraries of mRNA were prepared with Illumina TruSeq RNA Sample Prep Kits v2 or stranded RNA Sample Prep Kits. Libraries were sequenced on Illumina HiSeq 2000. ChIP DNA were purified through chromatin immunoprecipitation using an Arp5, H3K79me3 and H3K4me3 antibody. Libraries were prepared with a KAPA LTP kit and sequenced using the Illumina HiSeq 2000 platform.
Conclusion: Our ChIP-Seq and mRNA-Seq data show that Ino80C contributes to silent chromatin in both euchromatin an heterochromatin
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| |
|
| Overall design |
mRNA profiles of WT_CY337 and ino80Δ, WT_BY4741, sir3Δ, arp5Δ, ies6Δ, ies2Δ sir3Δ-arp5Δwere generated by deep sequencing, using Illumina HiSeq 2000. WT_BY4741, sir3Δ, arp5Δ, ies6Δ, ies2Δ were duplicates. Enrichment of Arp5, H3K79me3 and H3K4Me3 on chromatin were generated by ChIP-Seq
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| |
|
| Contributor(s) |
Xue Y, Carey M, Kurdistani S, Peterson C |
| Citation(s) |
25691465 |
| Submission date |
Nov 01, 2013 |
| 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 |
| |
|
| Platforms (1) |
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
|
| Samples (27)
|
|
| Relations |
| BioProject |
PRJNA226082 |
| SRA |
SRP032457 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE52000_Arp5vsInput_sig_log2ratio.bed.gz |
905.5 Kb |
(ftp)(http) |
BED |
| GSE52000_BY4741_K4Me3vsInput_log2ratio.bed.gz |
2.6 Mb |
(ftp)(http) |
BED |
| GSE52000_BY4741_K4Me3vsInput_sig_log2ratio.bed.gz |
728.4 Kb |
(ftp)(http) |
BED |
| GSE52000_BY4741_K79Me3vsInput_log2ratio.bed.gz |
2.6 Mb |
(ftp)(http) |
BED |
| GSE52000_BY4741_K79Me3vsInput_sig_log2ratio.bed.gz |
990.8 Kb |
(ftp)(http) |
BED |
| GSE52000_K79me3_arp5vsBY4741_log2ratio.bed.gz |
2.5 Mb |
(ftp)(http) |
BED |
| GSE52000_README_processed_data_files.txt |
1.6 Kb |
(ftp)(http) |
TXT |
| GSE52000_arp5_K4Me3vsInput_log2ratio.bed.gz |
2.6 Mb |
(ftp)(http) |
BED |
| GSE52000_arp5_K79Me3vsInput_log2ratio.bed.gz |
2.6 Mb |
(ftp)(http) |
BED |
| GSE52000_mRNA_FPKM.txt.gz |
306.8 Kb |
(ftp)(http) |
TXT |
| GSE52000_mRNA_arp5delveBY4741_metagene.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
| GSE52000_mRNA_arp5vsBY4741_metagene_antisense.txt.gz |
227.1 Kb |
(ftp)(http) |
TXT |
| GSE52000_mRNA_arp5vsBY4741_metagene_sense.txt.gz |
289.0 Kb |
(ftp)(http) |
TXT |
| GSE52000_mRNA_ies2delveBY4741_metagene.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
| GSE52000_mRNA_ies6delveBY4741_metagene.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
| GSE52000_mRNA_ies6vsBY4741_metagene_antisense.txt.gz |
223.3 Kb |
(ftp)(http) |
TXT |
| GSE52000_mRNA_ies6vsBY4741_metagene_sense.txt.gz |
289.4 Kb |
(ftp)(http) |
TXT |
| GSE52000_mRNA_ino80delvsCY337_metagene.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
| GSE52000_mRNA_ino80vsBY4741_metagene_antisense.txt.gz |
240.7 Kb |
(ftp)(http) |
TXT |
| GSE52000_mRNA_ino80vsBY4741_metagene_sense.txt.gz |
293.4 Kb |
(ftp)(http) |
TXT |
| GSE52000_mRNA_sir3delveBY4741_metagene.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
| GSE52000_mRNA_sir3vsBY4741_metagene_antisense.txt.gz |
198.9 Kb |
(ftp)(http) |
TXT |
| GSE52000_mRNA_sir3vsBY4741_metagene_sense.txt.gz |
282.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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