 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 05, 2023 |
| Title |
YBP2, 4C, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
w303a
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: w303a
chip antibody: NA
condition: NA
genotype: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1
treatment: methionine depletion
|
| Growth protocol |
Yeast strains were grown in 200 mL synthetic media without methionine to OD660 = 0.3.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Standard 4C protocol was used for the preparation of 4C samples
4C-seq libraries were prepared with NEBNext Ultra II DNA Library Prep Kit.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
150 bp paired-end reads were merged and aligned to S. cerevisiae genome (sacCer3) and analyzed with pipe4C.Bigwig file was generated by pipe4C, peak calling was performed with PeakC.
Assembly: sacCer3
Supplementary files format and content: bigwig
|
| |
|
| Submission date |
Sep 05, 2023 |
| Last update date |
Sep 07, 2023 |
| Contact name |
Lu Bai |
| E-mail(s) |
lub15@psu.edu
|
| Organization name |
Penn State University
|
| Department |
BMB
|
| Lab |
Bai
|
| Street address |
406 SOUTH FREAR, UNIVERSITY PARK
|
| City |
UNIVERSITY PARK |
| State/province |
PENNSYLVANIA |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL31112 |
| Series (2) |
| GSE242394 |
DNA Methylation-Based High-Resolution Mapping of Long-Distance Chromosomal Interactions in Nucleosome-Depleted Regions (4C) |
| GSE242400 |
DNA Methylation-Based High-Resolution Mapping of Long-Distance Chromosomal Interactions in Nucleosome-Depleted Regions |
|
| Relations |
| BioSample |
SAMN37286215 |
| SRA |
SRX21638529 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7762055_4C_YBP2_2.bigwig |
340.9 Kb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
