|
| Status |
Public on Aug 22, 2017 |
| Title |
bag101 overexpression 5 |
| Sample type |
SRA |
| |
|
| Source name |
wild type, overexp. bag101
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype: bag101 overexpression
|
| Growth protocol |
Growth at 29 C in EMM2 media.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hot phenol total RNA extraction
Library construction protocol not provided.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
BGI basecalling
Trimmomatic v0.32 (PE) used for adapter trimming with parameters: ILLUMINACLIP:./TruSeq3-PE-2.fa:2:30:10:8:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:0
Reads were aligned to the pombe genome with STAR v.2.3.0e with standard parameters except: MismatchNoverLmax=0.1, MismatchNmax=3, MatchNmin=18
Gene annotations in gtf format was downloaded from PomBase version 38 from October 2013
Gene count.txts based on the PomBase annotation were obtained from each STAR alignment file using htseq-count.txt with mode=union.
Genome_build: pombe.ASM294v2.21
Supplementary_files_format_and_content: Tab-delimited text files of raw ht-seq count.txt output
|
| |
|
| Submission date |
Sep 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Rasmus Hartmann-Petersen |
| Organization name |
University of Copenhagen
|
| Department |
Department of Biology
|
| Lab |
Section for Biomolecular Sciences
|
| Street address |
Ole Maaloes Vej 5
|
| City |
Copenhagen |
| ZIP/Postal code |
2200N |
| Country |
Denmark |
| |
|
| Platform ID |
GPL13988 |
| Series (1) |
| GSE86512 |
Bag101 overexpression in S. pombe |
|
| Relations |
| BioSample |
SAMN05736225 |
| SRA |
SRX2144124 |
