|
| Status |
Public on Oct 01, 2014 |
| Title |
Fhl1_myc |
| Sample type |
SRA |
| |
|
| Source name |
whole organism
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
antibody: Custom mouse monoclonal anti-myc
antibody: myc-tagged Fhl1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sample preparation and DNA analysis for ChIP-seq (Preti et al. 2010) were carried out as described.
Chromatin for MNase digestion was prepared essentially as described (Kent and Mellor 1995). Spheroplasts derived from 100-mL cultures were treated with either 0.5 U (underdigested) or 2 U (overdigested) of MNase (Sigma) for 45 min at 37°C. Samples were then decrosslinked and DNA was precipitated.
Purified and precipitated DNA was sequenced using the modified paired-end TruSeq protocol (Illumina) (Henikoff et al., 2011).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
strain info listed in Supplemental Table S1
|
| Data processing |
Raw reads were aligned to the sacCer2 genome assembly using Bowtie1 with options "--best --strata --chunkmbs 512 -Sam 20"
Data were filtered to retain only the mapped reads with at most 5 hits in the reference
Genome_build: sacCer2
Supplementary_files_format_and_content: Signal density in bigwig format
|
| |
|
| Submission date |
Sep 20, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jacques Rougemont |
| E-mail(s) |
jacques.rougemont@epfl.ch
|
| Organization name |
EPFL
|
| Department |
School of Life Sciences
|
| Lab |
Bioinformatics and Biostatistics Core Facility
|
| Street address |
Station 15
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17342 |
| Series (1) |
| GSE61596 |
Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription |
|
| Relations |
| BioSample |
SAMN03075073 |
| SRA |
SRX707473 |
