|
| Status |
Public on Jul 01, 2014 |
| Title |
MPK1 deletion in KN99a background Mpk1_n |
| Sample type |
SRA |
| |
|
| Source name |
RNA isolated from cells growing in YPD+sorbitol at 30 degress
|
| Organism |
Cryptococcus neoformans |
| Characteristics |
biological replicate: second of three replicates
genotype: MPK1 deletion in KN99a background
|
| Treatment protocol |
none
|
| Growth protocol |
KN99a or deletion strains were grown in YPD + 1M sorbitiol at 30 degrees with shaking until OD600 = 1.0
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated from the cells using the Qiagen RNeasy Plant Mini Kit
Single-end libraries were generated using Illumina TruSeq RNA Sample Preparation Kit v2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequence reads were trimmed of adaptor sequences, low-quality reads and then aligned to C. neoformans genome (Broad H99, assembly 2) using TopHat version 2.0.0 using Bowtie, version 1.6
Transcript files were generated using Cufflinks version 2.02
Comparisons between the deletion strains and wild-type merged transcript files were done using CuffCompare at the gene level with the C. neoformans transcript file from the 2nd assembly of the H99 genome as a reference
Differentially expressed genes were identified using CuffDiff version 2.0.2
Genome_build: Broad C. neoformans H99 assembly 2 (2008)
Supplementary_files_format_and_content: transcript files generated by cufflinks (gtf format); fpkm values from merged transcript files generated by CuffCompare (tab-delimited) and gene experession differences generated by CuffDiff (tab-delimited).
|
| |
|
| Submission date |
Apr 30, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Maureen J Donlin |
| E-mail(s) |
[email protected]
|
| Phone |
314-977-8858
|
| Organization name |
Saint Louis University School of Medicine
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
1100 South Grand
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63104 |
| Country |
USA |
| |
|
| Platform ID |
GPL14571 |
| Series (1) |
| GSE57217 |
Cross talk between the cell wall integrity and cAMP/protein kinase A pathways in Cryptococcus neoformans |
|
| Relations |
| BioSample |
SAMN02741709 |
| SRA |
SRX530060 |
