|
| Status |
Public on Apr 25, 2017 |
| Title |
RC2-wt grown in 2%YPD replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
RC2 RM-wt_whole cell
|
| Organism |
Cryptococcus neoformans |
| Characteristics |
strain: RC2
genotype/variation: wild type
growth condition: rich media; 2% glucose
seq_index: TCAACTG
|
| Growth protocol |
Comparable number of wt or sir2mutant yeast cells (background strain H99 or RC2) were grown in yeast extract peptone with 2% or 0.05% glucose for 16 hours at 37degCelsius with agitation at 150rpm
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using a QIAGEN RNeasy kit per manufacturer's instructions
The library preparation protocol was oligo-d(T)-priming based Clontech SMARTer Ultra Low RNA Kit for Illumina® Sequencing from Clontech (a Takara Bio Company, hereafter labeled as “ClonTech”). A starting amount of 10 ng RNAs was processed in ClonTech assays, amplified cDNA was sheared using a Covaris E210 instrument. cDNA was then end repaired, A tailed, and standard Illumina adapters were ligated on. Libraries were then amplified with primers to incorporate a unique index to each sample. In pooling of multiple libraries for running on 2 lanes of 50bp single reads, equal amount of library mass was determined by Qubit reading and Bioanalyzer for the 24 RNA libraries. Lastly, pooled libraries were amplified with Illumina® TruSeq™ Cluster kits and sequenced with Illumina® sequencing primers on Illumina® HiSeq2500™ next-generation sequencing system as a high output single read 50 cycle run.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
bf03-6
|
| Data processing |
Illumina Casava1.8+ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Cryptococcus_neoformans reference build Ensembl_R23 with STAR version 2.0.4b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. All gene-level and transcript counts were then imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size. Genes or transcripts not expressed in any sample were excluded from further analysis.
Genome_build: Cryptococcus_neoformans reference build Ensembl_R23
http://www.ncbi.nlm.nih.gov/assembly/GCF_000149245.1
Supplementary_files_format_and_content:
tab-delimited text files include read count values for each or all samples.
gene_counts_*.txt: abundance measurements at gene level
transcript_counts_all.txt: abundance measurements at transcript level
|
| |
|
| Submission date |
Oct 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jinsheng Yu |
| E-mail(s) |
[email protected]
|
| Organization name |
Washington University School of Medicine
|
| Department |
Genetics
|
| Lab |
GTAC Lab
|
| Street address |
660 S. Euclid Ave.
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL19081 |
| Series (1) |
| GSE74298 |
C. neoformans gene expression by SIR2 deletion in strains H99 and RC2 subjected to glucose starvation |
|
| Relations |
| BioSample |
SAMN04210103 |
| SRA |
SRX1370634 |
