|
| Status |
Public on Nov 21, 2023 |
| Title |
YKR011C_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
MAT⍺ can1::HphMX lyp1::STE3pr-LEU2 his3Δ1 leu2Δ0 ura3Δ0 met15Δ0 FPT1-TAP-His3MX6
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
cell line: NKI5623
genotype: MATalpha can1::HphMX lyp1::STE3pr-LEU2 his3{delta}1 leu2{delta}0 ura3{delta}0 met15{delta}0 FPT1-TAP-His3MX6
chip antibody: TAP Tag (CAB1001)
|
| Growth protocol |
Cells were grown to mid-log phase in YEPD at 30°C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Exponentially growing cells were cross-linked with 1% formaldehyde for 15 minutes and chromatin lysated were prepared. Pulldown of cross-linked proteins was done using a TAP antibody.
Sequencing libraries were made using the KAPA Hyper Prep Kit (KAPA Biosystems). Libraries were amplified by PCR and size selection (200-450 bp) was performed using AMPure XP beads (Beckman Coultier). DNA concentration was measured using a Qubit dsDNA HS Assay Kit (Invitrogen) and size-distribution of DNA fragments was visualized using an Agilent 2100 Bioanalyzer. Purified DNA was sequenced (single read, 65 bp) on a HiSeq2500 platform (Illumina).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
YKR011C_pooled.bw
|
| Data processing |
Reads were mapped to the sacCer3 reference genome downloaded from UCSC using the BWA-MEM program version 0.7.17-r1188 using the option ‘-M’. No filtering for mapping quality was performed. Coverage tracks were created using the GenomicRanges and rtracklayer R/Bioconductor packages. Specifically, unduplicated reads were extended 200 basepairs from their 5’ end and inversely weighted by the number of (multi-)mapping positions. Coverage was scaled to integrate to 1x genome size (reads per genomic content, RPGC). R version 4.2.1 and Bioconductor release 3.15 were used.
Assembly: SacCer3
Supplementary files format and content: Peak file with quantitative data (bigwig)
|
| |
|
| Submission date |
Mar 15, 2023 |
| Last update date |
Nov 21, 2023 |
| Contact name |
Fred van Leeuwen |
| E-mail(s) |
fred.v.leeuwen@nki.nl
|
| Organization name |
Netherlands Cancer Institute
|
| Department |
Gene Regulation
|
| Street address |
Plesmanlaan 121
|
| City |
Amsterdam |
| ZIP/Postal code |
1066CX |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL17342 |
| Series (2) |
| GSE227423 |
Genome-wide profiling of Fpt1, Rpb2, Rpo31 and Rpl13a in glucose [ChIP-seq] |
| GSE227470 |
A regulator of RNA Polymerase III at tRNA genes revealed by locus-specific proteome decoding |
|
| Relations |
| BioSample |
SAMN33770937 |
| SRA |
SRX19682555 |
