|
| Status |
Public on Jul 25, 2023 |
| Title |
PMY2649_A |
| Sample type |
SRA |
| |
|
| Source name |
Bt22
|
| Organism |
Cryptococcus neoformans |
| Characteristics |
cell line: Bt22
cell type: yeast
treatment: amoeba
|
| Growth protocol |
Samples were grown overnight in liquid YPD on a rollerdrum and were added to V8 petri dishes. V8 cultures were grown at 30◦C for 60 hours. Amoeba cultures were collected and suspended at a concentration of 1 × 106 cells/mL. 450 μL of amoeba culture was added to the center of the Cryptococcus lawn with slight agitation to aid in the spread of the culture. Plates were allowed to dry on the benchtop for 30 minutes before being incubated at 25◦C for 48 hours. A consistent area of 30 cm2 was cut from the plates and then scraped to collect cells. Collected cells were resuspended in 1 mL of PBS and were placed in dry ice for 10 minutes. Samples were then lyophilized for 12 - 18 hours.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Whole RNA was extracted using the RNAeasy Plant Mini Kit (Qiagen 74904).
Libraries were prepared and sequenced by the using the Illumina NextSeq 500 High Output Kit producing 150-base pair paired end read.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Bt1a
|
| Data processing |
Reads were aligned using the CNA3 of H99 C. neoformans var. grubii (accession GCA_000149245.3) from the Ensemble Fungi database. Reads were aligned using Kallisto.
Analysis of RNA sequences was performed using Deseq2 in R. Briefly, transcript abundance was normalized using a built in median of ratios method. Samples were normalized based on condition (amobea or control). GO term analysis was performed using the fungidb GeneByLocusTag tool. Correlation of gene expression with BZP4 was performed using the normalized count output from Deseq2.
Assembly: GCA_000149245.3
Supplementary files format and content: tab delimited files containing read counts and TPK values for each gene
|
| |
|
| Submission date |
Jul 24, 2023 |
| Last update date |
Jul 25, 2023 |
| Contact name |
Paul Magwene |
| E-mail(s) |
paul.magwene@duke.edu
|
| Organization name |
Duke University
|
| Department |
Biology
|
| Lab |
Magwene
|
| Street address |
124 Science dr.
|
| City |
Durham |
| State/province |
North Carolina |
| ZIP/Postal code |
27701 |
| Country |
USA |
| |
|
| Platform ID |
GPL27451 |
| Series (1) |
| GSE238170 |
Amoeba Predation of Cryptococcus: A Quantitative and Population Genomic Evaluation of the Accidental Pathogen Hypothesis |
|
| Relations |
| BioSample |
SAMN36698832 |
| SRA |
SRX21144758 |
