|
| Status |
Public on Sep 09, 2020 |
| Title |
UR-2_sRNA |
| Sample type |
SRA |
| |
|
| Source name |
S. pombe cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype: h- ED972 wild-type (wt)
phenotype: Unstable 16 mM Caffeine Resistant Isolate
treatment: no treatment
|
| Growth protocol |
Cells were grown in liquid yeast extract plus supplements (YES) media at 32C to a concentration of 5x10^6-1x10^7 cells/mL
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected and processed using the mirVana miRNA Isolation kit (Invitrogen). Resulting sRNA was treated with TURBO DNase (Invitrogen) and used for library construction.
Libraries were prepared using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) according to manufacturer’s instructions. Libraries were pooled and sequenced on an Illumina NextSeq 500/550 platform by 50 bp single-end sequencing.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Total Small RNA
|
| Data processing |
ChIP-Seq: Raw reads were de-multiplexed and trimmed using Trimmomatic (v0.35) to remove adapter contamination and regions of poor sequencing quality. Trimmed reads were aligned to the S. pombe reference genome (972h-, ASM294v2.20) using Bowtie2 (v2.3.3). Resulting bam files were processed using Samtools (v1.3.1) and picard-tools (v2.1.0) for sorting, removing duplicates and indexing. Ratios IP/input were calculated using BamCompare (deepTools v2.0) in SES mode for normalisation.
sRNA-Seq: Raw reads were de-multiplexed. Raw reads were trimmed using Cutadapt (v1.17) to remove adapters and filter out reads <19 nt and >25 nt. Filtered fastq files were then processed using SCRAM and coverage files (.csv) at defined locations (cen1L, hba1 locus, ncRNA394 locus) were obtained.
Genome_build: ASM294v2.20
Supplementary_files_format_and_content: ChIP-Seq: bigWig files of ratio IP/input. sRNA-Seq: csv files indicating coverage over specific genomic locations (cen1L / hba1locus / ncRNA394 locus).
|
| |
|
| Submission date |
Oct 04, 2019 |
| Last update date |
Mar 03, 2021 |
| Contact name |
Sito Torres-Garcia |
| E-mail(s) |
j.torres@ed.ac.uk
|
| Organization name |
Wellcome Centre for Cell Biology. University of Edinburgh
|
| Lab |
Allshire Lab
|
| Street address |
6.4 Michael Swann Building. Max Born Crescent
|
| City |
Edinburgh |
| ZIP/Postal code |
EH9 3BF |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL20584 |
| Series (1) |
| GSE138436 |
Epigenetic gene silencing by heterochromatin primes fungal resistance |
|
| Relations |
| BioSample |
SAMN12912273 |
| SRA |
SRX6950754 |
