|
| Status |
Public on Dec 24, 2021 |
| Title |
cDNA_rtf2_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Schizosaccharomyces pombe
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain number: BAY175
genotype: rtf2{delta}::NAT, ade6-704, leu1-32, ura4-d18
|
| Growth protocol |
Cells were grown to mid log phase in YE media at 30C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolated from whole cells were used to isolate mRNA using poly-dT beads
cDNA libraries were constructed using mRNA following the Nanopore Direct cDNA Sequencing Protocol
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
MinION |
| |
|
| Description |
derived from mRNA
|
| Data processing |
Library strategy: Nanopore Direct cDNA-Sequencing
pychopper is used for processing and filtering for full length reads
processed reads are mapped to the reference genome using minimap2
mapped reads are then processed by stringtie in long read mode to evaluate the transcripts and produce a GFF annotation file
standard parameters were used as set in the nanopore pipeline used to produce the results (https://github.com/nanoporetech/pipeline-nanopore-ref-isoforms)
Genome_build: Schizosaccharomyces pombe reference sequence (http://www.pombase.org/downloads/genome-datasets)
Supplementary_files_format_and_content: files ending in .coverage.csv contain read counts for each position along the genome
Supplementary_files_format_and_content: files ending in .tracking.csv contain all transcripts identified by stringtie with associated transcript type allocation and their respective expression levels in FPKM and TPM
|
| |
|
| Submission date |
Dec 21, 2021 |
| Last update date |
Dec 25, 2021 |
| Contact name |
Alice Budden |
| Organization name |
University of Sussex
|
| Department |
GDSC
|
| Lab |
Tony Carr
|
| Street address |
Science Park Road
|
| City |
Brighton |
| ZIP/Postal code |
BN1 9QG |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL31123 |
| Series (2) |
| GSE192343 |
Rtf2 is Important for Replication Fork Barrier Activity of RTS1 via Splicing of Rtf1 [cDNA-Seq] |
| GSE192344 |
Rtf2 is Important for Replication Fork Barrier Activity of RTS1 via Splicing of Rtf1 |
|
| Relations |
| BioSample |
SAMN24256918 |
| SRA |
SRX13464223 |
