|
| Status |
Public on Feb 24, 2018 |
| Title |
Nrd1-AA dSet2 BrdU-seq +Rap rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Nrd1-AA dSet2 BrdU-seq +Rap
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: Nrd1-AA dSet2
treatment: +Rap
chip antibody: BrdU antibody (BD PharMingen, 555627)
|
| Growth protocol |
Cells grown at 30°C to an OD600= 0.4 were synchronized in G1-phase with α-factor (20 ng/ml, Sigma) for 3h in total. After two washes with distilled water, cells were released into S-phase at 18°C. Depending on the experiment, cells were released or not in YEPD medium containing BrdU (100 μg/ml, Sigma) and treated or not with rapamycin. Cells were then collected at t=70min 18°C after G1-release and treated with 0.1% Sodium Azide (Sigma).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
BrdU immunoprecipitation was mainly performed as described in (Soudet et al., 2014) with the following modifications. Genomic DNA was sonicated into 300-400 bp fragments and denatured. 5 μg BrdU antibody (BD PharMingen, 555627) coupled to 75μl of Dynabeads Protein G (Invitrogen) were added to 5μg of denatured BrdU-containing genomic DNA in BrdU IP buffer (PBS + 0.0625% Triton X-100). After 1 hour incubation at room temperature on a wheel, beads were washed twice with BrdU IP buffer and eluted in Tris-HCl 10mM (pH 8.0), EDTA 1mM, 1% SDS. Eluates were cleared of SDS using the NucleoSpin Gel and PCR Clean-up (Macherey-Nagel).
iDeal library preparation kit was used for library construction.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
BrdUseq_Nrd1dSet2_PlusRap_merged_final.bigWig
|
| Data processing |
Library strategy: BrdU-Seq
fastq files were processed through the mapping function of HTS EPFL station.PCR duplicates were discarded from the analysis.
bigwig were generated using HTS EPFL station. Strands were merged by 125bp for BrdU-seq.
Genome_build: saccer3
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
Feb 23, 2018 |
| Last update date |
Feb 25, 2018 |
| Contact name |
Julien Soudet |
| E-mail(s) |
julien.soudet@unige.ch
|
| Organization name |
Université de Genève
|
| Department |
BICEL
|
| Street address |
30 quai Ansermet
|
| City |
Geneva |
| ZIP/Postal code |
1204 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL21656 |
| Series (1) |
| GSE111058 |
Pervasive transcription-dependent chromatin remodeling influences the replication initiation program |
|
| Relations |
| BioSample |
SAMN08595495 |
| SRA |
SRX3738773 |
