|
| Status |
Public on Oct 31, 2023 |
| Title |
WT, YPD, RNA-seq biol rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Cell pellet
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
tissue: Cell pellet
cell line: YEF4734A
cell type: Yeast cell
genotype: WT
treatment: YPD
|
| Treatment protocol |
Switching media from YPGal to YPD
|
| Growth protocol |
Cells were cultured in YPGal medium at 30°C and 230 rpm before H3-shutoff experiment. The H3 inducible shut-off strain (i.e., “DGS200.1” or “H3i”) from the YEF473A strain by knocking out the HHT1 gene (encoding H3), and replacing the native promoter of the HHT2 gene (the other H3-encoding gene) with an inducible Gal1 promoter.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by MagMax96 total RNA isolation kit (AM1830, Invitrogen) for the first and second replicates. Trizol reagent (15596026, Invitrogen) was used in extraction with glass beads for the third replicate.
Librarires of the first and second replicates were prepared using the Illumina TruSeq Stranded mRNA Library Prep. For the third replicate, the TruSeq Stranded mRNA LT sample prep kit was used for library construction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
WT_YPD_1
|
| Data processing |
FastQC
Reads were align to Saccer3 genome using the Hisat2
Sorting and indexing using Samtools
Duplication was removed by Picard tools
Raw read counts were normalized by DEseq2
Assembly: Saccer3
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
|
| |
|
| Submission date |
May 17, 2023 |
| Last update date |
Oct 31, 2023 |
| Contact name |
Peerapat Khamwachirapithak |
| Organization name |
Mahidol University
|
| Street address |
Rachthevi
|
| City |
Bangkok |
| ZIP/Postal code |
10400 |
| Country |
Thailand |
| |
|
| Platform ID |
GPL19756 |
| Series (2) |
| GSE232684 |
Investigation of Rap1 binding occupancy in global H3-depletion condition [RNA-seq] |
| GSE232685 |
Investigation of Rap1 binding occupancy in global H3-depletion condition |
|
| Relations |
| BioSample |
SAMN35130830 |
| SRA |
SRX20389125 |
