|
| Status |
Public on Aug 17, 2018 |
| Title |
Abf1 ChIP-exo 5.0 Replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
yeast
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
chip antibody: Abf1-TAP (Sigma i5006-100MG, Lot#SLBM2617V)
cell description: GRF88, MATa his4-38, S288C background
strain: BY4741
|
| Treatment protocol |
Cells were crosslinked with formaldehyde to a final concentration of 1.0%.
|
| Growth protocol |
Yeast cells were grown to an O.D600 of 0.8 - 1.0 at 25°C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with IgG antibody.
Libraries were prepared for sequencing using standard Illumina protocols with modifications; Reference paper:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
PSU11019
Abf1_ChIP-exo5.0_peaks.gff
|
| Data processing |
Library strategy: ChIP-exo
For paired end reads from NextSeq, basecalls were performed using Bcl2fastq version 2.16.
Reads were aligned to sacCer3 or GRch37(hg19) genome assembly using bwa mem version 0.7.9a for paired reads.
GeneTrack peak caller; https://github.com/ialbert/chipexo/tree/master/genetrack (-s 5 -e 10)
Genome_build: sacCer3
Genome_build: GRch37/hg19
Supplementary_files_format_and_content: gff, peak pair calls filtered for significance over background
|
| |
|
| Submission date |
Feb 15, 2018 |
| Last update date |
Aug 17, 2018 |
| Contact name |
Matthew John Rossi |
| E-mail(s) |
mjrossi2881@gmail.com
|
| Phone |
5709946197
|
| Organization name |
Penn State University
|
| Department |
Biochemistry & Molecular Biology
|
| Lab |
Pugh
|
| Street address |
453 N Frear Bldg
|
| City |
University Park |
| State/province |
Pennsylvania |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL19756 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN08550092 |
| SRA |
SRX3709362 |
