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| Status |
Public on Aug 23, 2017 |
| Title |
S_Pombe.WT.RM |
| Sample type |
SRA |
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| Source name |
rich media, wild type
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| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype: wild type
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| Extracted molecule |
total RNA |
| Extraction protocol |
Library construction protocol is explained in Hoque et al (2014) Methods Mol Biol.
Specific protocol was used to amplify the 3'Ends of polyA+ RNA
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
The details of the method was described previously (Hoque, et al., 2014). Briefly, the 3'-adapter sequence was first removed (using fastx_clipper -a TGGAATT). Reads were mapped to yeast genomes (S. cerevisiae: EF4, Ensembl v16; S. pombe: ASM294v2, Ensembl v17) using Bowtie2 (local mode). 5' four random nucleotides were removed before mapping using "-5 4" parameter in bowtie2. Reads with a mapping quality score (MAPQ) ≥10 were selected for further analysis. Reads with ≥2 non-genomic As after alignment were called polyA site supporting (PASS) reads.
All PASS reads mapped to the 3’-most exons of a gene were used to calculate the expression level of the gene, shown as the reads per million total PASS reads (RPM) value.
Genome_build: Two yeast genomes (S. cerevisiae: EF4, Ensembl v16; S. pombe: ASM294v2, Ensembl v17)
Supplementary_files_format_and_content: tab delimited file containing information of Chr., Strand, pA coordinates, read number of pAs in different samples
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| Submission date |
Feb 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Bin Tian |
| E-mail(s) |
[email protected]
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| Phone |
9739723615
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| Organization name |
Rutgers University
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| Department |
Department of Microbiology, Biochemistry and Molecular Genetics
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| Street address |
205 South Orange Ave., CC-F1230
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| City |
Newark |
| State/province |
NEW JERSEY |
| ZIP/Postal code |
07103 |
| Country |
USA |
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| Platform ID |
GPL17225 |
| Series (1) |
| GSE95139 |
Comparative Analysis of Alternative Polyadenylation in S. cerevisiae and S. pombe |
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| Relations |
| BioSample |
SAMN06352090 |
| SRA |
SRX2580015 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2496938_S_Pombe.WT.RM.pA.read_counts.txt.gz |
451.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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