 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 05, 2017 |
| Title |
set2d_60min_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Log Phase Yeast Cultures
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4742
genotype/variation: SET2 deletion
|
| Treatment protocol |
Cultures were collected and pelleted. Pellets were washed twice with ddH20 followed by resuspension in SD media and incubated at 30C. At 0, 30, 60, and120 minutes after the media shift, 1*10^8 cells were isolated, pelleted, and snap frozen for processing.
|
| Growth protocol |
Yeast cells were grown in YPD overnight to saturation. New YPD cultures were then innoculated to a final concentration of 2*10^6 cells and grown until the cultures reached a concentration of 1*10^7 cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using acid phenol, DNase treated, and cleaned up on Qiagen RNeasy columns.
Libraries were constructed using Illumina's TruSeq Stranded Total RNA Sample Preparation Kit with the yeast specific Ribo-Zero kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Ribo-depleted/Stranded
|
| Data processing |
Reads were first filtered for any adapter sequences using TagDust (v1.12) and an FDR of 0.001. For samples that had over 50 basepair reads, TagDust was used to trim 3' basepairs so all the reads were 50 bp
Bowtie (v1.1.2) was used to align reads to the sacCer3 genome. Alignment options included: -m 1, --seed=123.456, --nomaqround, and --best.
Alignments were filtered for properly mapped reads using samtools (v1.3.1).
Reads came off the sequencer with strand information reversed, and were corrected using the bedtools suite (v2.25.0).
To correct any PCR amplification artifacts, two identical reads were permitted per specific strand and alignment location, with all others being filtered.
Single base pair wiggle files were generated using the bedtools suite (v2.25.0).
Differentially expressed genes were identified using DESeq2 (v1.6.3) with default parameters. Genes with a p-value < 0.05, a minimum of log2(Fold Change) > 1 as identified by DESeq2, and an average RPKM > 1 across all replicates with a time point were considered differentially expressed.
Genome_build: sacCer3
Wig files are fixed step, with a step size of 1, wiggles containing the normalized read depth/signal at each base pair in the genome. The wigs contain either sense or antisense signal only, where sense or antisense is defined by annotated ORFs in sacCer3.
|
| |
|
| Submission date |
Oct 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Austin J Hepperla |
| E-mail(s) |
hepperla@unc.edu
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Genetics
|
| Street address |
7018B Mary Ellen Jones Building
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL17342 |
| Series (1) |
| GSE89265 |
H3K36 Methylation Regulates Nutrient Stress Response in S. cerevisiae by Enforcing Transcriptional Fidelity |
|
| Relations |
| BioSample |
SAMN05949363 |
| SRA |
SRX2279582 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2363364_yeast_SET2del_60min_Rep1_clean_filt_positionSorted_strandCorrected_dupsRemoved_sorted_antisenseStrand_normalized.wig.gz |
1.1 Mb |
(ftp)(http) |
WIG |
| GSM2363364_yeast_SET2del_60min_Rep1_clean_filt_positionSorted_strandCorrected_dupsRemoved_sorted_senseStrand_normalized.wig.gz |
4.5 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
