|
| Status |
Public on Jun 08, 2016 |
| Title |
qsp1∆ Saturated Experiment 2 RNA-Seq replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Yeast
|
| Organism |
Cryptococcus neoformans |
| Characteristics |
strain: Kn99alpha(wild-type) with qsp1(del)
media: YPAD
cell density: Saturated
|
| Growth protocol |
50 ODs of cells from overnight YPAD cultures were washed once in water and resuspended in 20 mLs DMEM, transferred to 150mm tissue culture dishes, and incubated for 24 hours at 37ºC, 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA was isolated using trizol to isolate total RNA and oligotex mRNA mini kit to isolate mRNA. ChIP DNA was isolated from antibody incubation by SDS/proteinase K followed by purification using MN Nucleospin Gel Cleanup columns
cDNA libraries were prepared from DNase-treated mRNA using NEBNext Ultra Directional RNA Library Prep Kit. ChIP DNA libraries were prepared using End-It DNA End Repair Kit followed by A-tailing using Klenow fragment (NEB), ligation to Illumina adaptors using Rapid T4 DNA Ligase (Enzymatics), PCR amplification for 15 cycles, and size selection between 200-350bp
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
RNA-Seq data were aligned using Tophat. Indexed, sorted bam files were created and then rpkm values were calculated for pairwise comparisons between wild-type and knockout mutant samples.
Genome_build: Sequence and feature files for C. neoformans var grubii H99 were obtained from the Broad institute, Cambridge, MA as current as January 20th, 2011.
Supplementary_files_format_and_content: Peak lists and locations for ChIP-seq samples and RPKM lists and ratios for each gene for RNA-seq samples.
|
| |
|
| Submission date |
Oct 27, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Christina M. Homer |
| E-mail(s) |
[email protected]
|
| Organization name |
UCSF
|
| Department |
Biochemistry & Biophysics
|
| Lab |
Madhani Lab
|
| Street address |
600 16th St
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL21073 |
| Series (1) |
| GSE73203 |
Convergent evolution of peptide-based quorum sensing required for virulence in a eukaryotic pathogen |
|
| Relations |
| BioSample |
SAMN04217066 |
| SRA |
SRX1386854 |
