|
| Status |
Public on May 15, 2024 |
| Title |
Wt, INPUT, Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
MATa his4-912δ lys2-128δ leu2Δ1 trp1Δ63 RPB3-3XFLAG::KANMX
|
| Organisms |
Saccharomyces cerevisiae; Kluyveromyces lactis |
| Characteristics |
cell line: KY4302/KL02
treatment: None
time (min): NA
|
| Treatment protocol |
Yeast cultures were grown to OD600 = 1-1.2 at 30°C. At the time of harvest, cells were fixed with 1% v/v formaldehyde for 20 min at room temperature after 30 min of treatment with 1:1000 v/v vehicle (DMSO) or auxin (final concentration of 500 μM in DMSO) if necessary. Fixation was quenched for 5 min with a 37.5 mL of 3M glycine and 20 mM Tris solution, the culture pelleted at 4,000 rpm at 4°C, and pellets were washed twice in TBS before snap freezing in liquid nitrogen.
|
| Growth protocol |
S. cerevisiae and S. pombe were grown in YPD standard rich growth medium supplemented with 400 μM tryptophan at 30°C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was fragmented using a Bioruptor® (Diagenode B01060010) with 25 cycles of 30 sec on and 30 sec off at 4°C.
Libraries were built using the NEBNext® Ultra™ II DNA Library Prep Kit (Illumina #E7645S/L) with 1.5 ng of immunoprecipitated or input DNA
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Fastq files were demultiplexed and aligned to a hybrid K. lactis - S. cerevisiae genome using bowtie2
The resultant sam files were converted to bam and duplicates removed with Picard
Samtools counts of spike-in and sample and bam reads generated counts for Spike-in normalization factors using the inverse counts per-million method
Bam files were normalized and converted to bigwig using deeptools
Assembly: S. cerevisiae: Ensembl R64-3-1/K.lactis: ASM251v1 Hybrid Genome
Supplementary files format and content: spike-in normalized bigwig for IPs or unnormalized bigwigs for inputs
|
| |
|
| Submission date |
Feb 08, 2024 |
| Last update date |
May 15, 2024 |
| Contact name |
Karen Arndt |
| E-mail(s) |
arndt@pitt.edu
|
| Organization name |
University of Pittsburgh
|
| Department |
Biological Sciences
|
| Lab |
A316 Langley Hall
|
| Street address |
4249 Fifth Ave
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15260 |
| Country |
USA |
| |
|
| Platform ID |
GPL34174 |
| Series (1) |
| GSE255361 |
Dynamic Roles for the Paf1 Complex in Regulating Transcription Elongation and Co-Transcriptional Processes [ChIP-seq] |
|
| Relations |
| BioSample |
SAMN39888914 |
| SRA |
SRX23576100 |
