|
| Status |
Public on Jan 01, 2013 |
| Title |
Set3-9myc yeast ChIP Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
set3Δ_Set3-9myc yeast ChIP
|
| Organism |
Candida albicans |
| Characteristics |
genotype/variation: set3-delta
morphological phase: yeast phase
chip antibody: anti-myc (EZ-View anti-c-myc Affininty Gel)
chip antibody vendor: Sigma
chip antibody cat. #: E6654
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cultures were crosslinked by the addition of formaldehyde at a final concentration of 1% for 15 minutes at room temperature. Crosslinking was quenched by the addition of 125mM glycine for 5 minutes. Cells were washed twice with ice-cold TBS and pellets were frozen in liquid N2. Pellets corresponding to 80 OD600 cells were resuspended in 480 μl ice-cold ChIP lysis buffer (50 mM HEPES/KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, protease inhibitors). After addition of around 500μl glass beads (425–600 mm, Sigma), cells were broken at 6 m/s for 60 seconds 8 times on a FastPrep instrument (MP Biomedicals). Samples were cooled on ice for five minutes between cycles. The bottom of the tubes was punctured with a 27 3/4G needle and lysates were collected by centrifugation at 1500g for 1 min at 4C into a fresh tube. The lysates were diluted to 2.4 ml with ChIP lysis buffer. 300 μl aliquots were sonicated 15 times with 30s ON/30s OFF cycles at high setting on a Bioruptor (Diagenode). After sonication the aliquots were combined and centrifuged once at 14000g for 5 min at 4C. Supernatants were collected and used as input chromatin lysates. Set3-9myc and Hos2-9myc ChIPs were performed using EZ-View anti-myc coupled agarose beads (Sigma). After overnight incubation at 4C washing and DNA purification was performed exactly as described in (Hernday AD, Noble SM, Mitrovich QM, Johnson AD (2010) Methods Enzymol 470: 737-758.)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Sample 4
|
| Data processing |
Basecalls performed using CASAVA version 1.4
Multiplexing adaptor sequences were removed.
Reads were mapped onto the chromosomal Assembly 21 of the C. albicans genome with Bowtie, allowing only for uniquely mapping reads.
The RPKM values of all ORFs (using their default chromosomal coordinates) of Assembly 21 were calculated with Cufflinks (Trapnell C, Nat Biotechnology, 2010).
Genome_build: Assembly 21 of the C. albicans genome
Supplementary_files_format_and_content: txt file containing RPKM values for all ORFs in all samples
|
| |
|
| Submission date |
Jun 03, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Denes Hnisz |
| E-mail(s) |
[email protected], [email protected]
|
| Organization name |
Max F Perutz Laboratories
|
| Department |
Medical Biochemistry
|
| Lab |
Kuchler
|
| Street address |
Dr Bohr-gasse
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL15149 |
| Series (2) |
| GSE38425 |
Histone deacetylation at coding sequences adjusts transcription kinetics during Candida albicans morphogenesis [ChIP-seq] |
| GSE38427 |
Histone deacetylation at coding sequences adjusts transcription kinetics during Candida albicans morphogenesis. |
|
| Relations |
| SRA |
SRX151311 |
| BioSample |
SAMN01036578 |
