|
| Status |
Public on Mar 17, 2020 |
| Title |
013_Ddc2-HA_WT_40min |
| Sample type |
SRA |
| |
|
| Source name |
Ddc2-HA
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype: WT
treatment: Untreated
cell-cycle phase: S-Phase 40min
antibody: Anti-HA_Santa Cruz_SC-7392
strain: W303-1208
|
| Treatment protocol |
Samples were either collected from G1 synchronised cultures or from cell released from alpha-factor arrest into S phase for 60 minutes in the presence of 200 mM HU (hydroxyurea).
|
| Growth protocol |
Cells were grown on YPD at 25°C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Standard protocol for preparation of yeast genomic DNA, chromatin immunoprecipitation and micrococcal nuclease digestion
NeoPrep Illumina system for automatic NGS library preparation using TruSeq Nano DNA Library Prep Kit for NeoPrep (Illumia)_Sequencer:HiSeq 4000 (1x51 nt)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Ip-HA of Wild type with Ddc2-HA 40' after release in S-Phase
ChIP-Seq, α-HA antibody
|
| Data processing |
Basecalls performed using HiSeq Control Software 1.5.15.1, RTA 1.13.48.0 and CASAVA version 1.8.2
Reads were aligned to the sacCer3 genome assembly using using Bowtie 2, version 2.1.0, allowing only perfect matches
bigwig files were generated with the tool "Bamcompare" from Deeptool2. Ramírez et al, (2016)
Genome_build: sacCer3
Supplementary_files_format_and_content: Bigwig files correspond to signal 1 bp step with ratio relative to Input (IP) or relative to G1 (ADNg)
|
| |
|
| Submission date |
Aug 29, 2019 |
| Last update date |
Mar 18, 2020 |
| Contact name |
romain forey |
| E-mail(s) |
romain.forey@epfl.ch
|
| Organization name |
IGH
|
| Street address |
142 avenue de la Cardonille
|
| City |
Montpellier |
| ZIP/Postal code |
34000 |
| Country |
France |
| |
|
| Platform ID |
GPL21656 |
| Series (2) |
| GSE136602 |
Mec1 is activated at the onset of normal S phase by low dNTP pools impeding DNA replication [sequencing] |
| GSE136605 |
Mec1 is activated at the onset of normal S phase by low dNTP pools impeding DNA replication |
|
| Relations |
| BioSample |
SAMN12655597 |
| SRA |
SRX6773263 |
