|
| Status |
Public on Mar 06, 2018 |
| Title |
Abf1 ChIP - Mixed Mnase |
| Sample type |
SRA |
| |
|
| Source name |
Saccharomyces cerevisiae
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
transcription factor: Abf1
mnase: Mix
antibody: Anti Flag (M2)
|
| Treatment protocol |
Cells were fixed with 1% formaldehyde for 15 minutes. Yeast cells were treated with zymolyase to generate spheroplasts prior to lysis and MNase treatment. Lysed spheroplasts or mESCs were treated with different amounts of MNase to digest chromatin into nucleosomes.
|
| Growth protocol |
Yeast cells were grown in YPD media at 30ºC with constant shaking to OD 0.6-0.8. Mouse R1 ESCs were grown on Gelatin and maintained in ESC medium.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
MNase digested chromatin was allowed to bind to antibodies for 2-4 hours. Paramagnetic protein G dynabeads were added for an additional hour and the beads were extensively washed. Bound chromatin was ligated to barcoded DNA adapters, and chromatin was reverse cross linked and pooled.
Barcoded chromatin was amplified with Illumina NGS - compatible primers and DNA libraries were paired end sequenced by Illumina NextSeq 500.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Base calling was performed with bcl2fastq (2.17).
Paired end reads were mapped to the yeast (sacCer3) and mouse (mm9) genomes using bowtie2 default parameters except for setting of maximal fragment size of 2,000 bp.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using genomeCoverageBed tool.
Genome_build: sacCer3, mm9
Supplementary_files_format_and_content: Genome coverage bigwig files were generated using bedGraphToBigWig tool. Peak table was generated from MACS output.
|
| |
|
| Submission date |
Jan 09, 2018 |
| Last update date |
Mar 06, 2018 |
| Contact name |
Nir Friedman |
| E-mail(s) |
nir@cs.huji.ac.il
|
| Organization name |
The Hebrew University of Jerusalem
|
| Street address |
Givat Ram
|
| City |
Jerusalem |
| ZIP/Postal code |
9190401 |
| Country |
Israel |
| |
|
| Platform ID |
GPL19756 |
| Series (1) |
| GSE108948 |
Fine Resolution Mapping of TF binding and Chromatin Interactions |
|
| Relations |
| BioSample |
SAMN08331851 |
| SRA |
SRX3544078 |
