|
| Status |
Public on Jun 26, 2019 |
| Title |
Adherent replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
Adherent
|
| Organism |
Crithidia fasciculata |
| Characteristics |
strain: CfC1
form: adherent haptomonad
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol.
1 microgram of total RNA was subjected to library synthesis using the TruSeq mRNA kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Cells were grown in brain heart infusion medium supplemented with 20 ug/ml hemin at 27 degrees C. 1 x 10^7 cells/ml in 20 ml were allowed to adhere for 2 h followed by media removal and 3 washes in media. 20 ml of media was then added back to the flask and adherent cells were allowed to grow for 24 h prior to RNA isolation.
|
| Data processing |
fastq files were aligned to the C. fasciculata transcriptome (version 28) and the Aedes aegypti Liverpool strain transcriptome (version AGWG AaegL5.1) using Kallisto, version 0.43.0
abundance data were read into the R/bioconductor environment using the TxImport package, version 1.0.2
transcripts with low/no read counts across all samples were eliminated, for analysis of Cf transcripts from infected mosquitoes, transcripts with low/no read counts in three of the cultured samples or any of the mosquito samples were eliminated
data was normalized using the calcNormFactors function from Limma (3.34.4), using the TMM method
for Ae. aegypti transcripts the SVA package ComBat function was used to correct for variation introduced by the batch experimental design
precision weights were applied to expression data using the Limma/VOOM function
differentially expressed genes (0.01 adjusted Pval and 2 fold change for C. fasciculata transcripts and 0.05 adjusted Pval and 1.5 fold change for Ae. aegypti transcripts) were identified using linear modeling and Bayesian statistics using the Limma package
|
| |
|
| Submission date |
Jun 12, 2019 |
| Last update date |
Jun 26, 2019 |
| Contact name |
Megan Povelones |
| E-mail(s) |
mlp29@psu.edu
|
| Organization name |
Penn State Brandywine
|
| Department |
Sciences
|
| Street address |
25 Yearsley Mill Road
|
| City |
Media |
| State/province |
PA |
| ZIP/Postal code |
19063 |
| Country |
USA |
| |
|
| Platform ID |
GPL26772 |
| Series (1) |
| GSE132641 |
Dramatic changes in gene expression in adherent C. fasciculata reveal potential mechanisms for insect-specific adhesion of kinetoplastid parasites |
|
| Relations |
| BioSample |
SAMN12042814 |
| SRA |
SRX6058746 |
