|
| Status |
Public on Jun 17, 2024 |
| Title |
h- 972 cells, wild type, minimal medium w/o nitrogen 4 hrs, rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
h- 972
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
cell line: h- 972
genotype: WT
treatment: Minimal medium without nitrogen after 4 hours
|
| Treatment protocol |
Cells were centrifuged and washed three times in MM-N with thiamine, and cultured in MM-N at 25ºC. 2x10 8 cells were harvested at 4 hours
|
| Growth protocol |
Wild type, igo1∆ and cells repressing pab1+ from the nmt41+ promoter were grown to mid-exponential phase in supplemented yeast extract medium (YES) and minimal medium with thiamine.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were washed with cold DEPC-H2O and snap freeze. RNA extraction was carried out by disrupting the cells with cells with glass beads in TRIzol® Reagent (Invitrogen) and following the manufacturer’s instructions.
Library preparation using the Illumina TruSeq Stranded Total RNA and subsequent NGS sequencing was performed by Macrogen.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
wt_2_4
norm_counts_Deseq2_DE_wt_igo1pab1_N4.txt
h- 972 cells, wild type, minimal medium without nitrogen 4 hours, bio rep 2
|
| Data processing |
Sequencing quality was check with FastQC (v 0.11.8, Babraham Bioinformatics).
Adaptors were trimmed using Trimmomatic (v 0.38) (Bolger et al. 2014) .
Alignment was performed with HISAT2 v 2.1.0 (CCB in John Hopkins University) (Kim et al. 2015)
Read counts were obtained with featureCounts (Subread package v 1.6.3, Walter+Eliza Hall Bioinformatics) (Liao et al.2014) .
Assembly: ASM294v2
Supplementary files format and content: tab-delimited text files include normalized counts after Deseq2 analysisis
|
| |
|
| Submission date |
Jun 14, 2024 |
| Last update date |
Jun 17, 2024 |
| Contact name |
Sergio Moreno |
| E-mail(s) |
smo@usal.es, ibfg_smp@usal.es
|
| Organization name |
Institute of Functional Biology and Genomics (IBFG) (CSIC)
|
| Department |
IBFG
|
| Lab |
https://ibfg.usal-csic.es/sergio-moreno.html
|
| Street address |
Zacarias Gonzalez 2
|
| City |
Salamanca |
| State/province |
Salamanca |
| ZIP/Postal code |
37007 |
| Country |
Spain |
| |
|
| Platform ID |
GPL28961 |
| Series (1) |
| GSE269854 |
The Greatwall-Endosulfine-PP2A/B55 pathway controls entry into quiescence by promoting translation of Elongator-tuneable transcripts |
|
| Relations |
| BioSample |
SAMN41834022 |
| SRA |
SRX24925768 |
