|
| Status |
Public on Jan 27, 2014 |
| Title |
W. dermatitidis in pH2.5 minimal media replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
W. dermatitidis cells, pH 2.5
|
| Organism |
Exophiala dermatitidis |
| Characteristics |
strain: ATCC 34100
stress: pH 2.5
|
| Growth protocol |
W. dermatitidis cells were cultured in defined minimal medium adjusted at pH6 and pH2.5, respectively, with shaking at 25 oC for 24 hours
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RiboPureYM-Yeast Kit (Invitrogen)
dUTP second strand marking method (Parkhomchuck 2009 NAR 37:e123) with modifications previously described (Cuomo 2012 Genome Research 22: 2478-2488)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
pH 2.5 replicate 2
|
| Data processing |
Base caller: GAPipeline RTA1.12.4.2 Sequencer Application 1.4.8
Aligner: Trinity (version r2013-02-25) alignReads.pl (parameters --aligner bowtie (version 1) and --SS_lib_type RF)
Estimate counts: Trinity run_RSEM.pl (RSEM version 1.2.3) on properly mapped paired reads (parameters --paired --no_group_by_component --SS_lib_type RF)
Normalized counts: Trinity summarize_RSEM_fpkm.pl on RSEM output
Differential expression: edgeR (version 3.2.4) with TMM normalization
Genome_build: AFPA01000000
Supplementary_files_format_and_content: Wangiella_pH_GEOsubmission_processeddata.txt reports FPKM counts, and FC/FDR from Edge R.
|
| |
|
| Submission date |
Oct 24, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Christina A Cuomo |
| E-mail(s) |
[email protected]
|
| Organization name |
Broad Institute
|
| Street address |
7 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL17834 |
| Series (1) |
| GSE51646 |
Comparative genomic and transcriptomic analysis of Wangiella dermatitidis, a major cause of phaeohyphomycosis and a model black yeast human pathogen |
|
| Relations |
| SRA |
SRX103202 |
| BioSample |
SAMN02383527 |
