|
| Status |
Public on Jan 21, 2023 |
| Title |
Late Infection biological rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
excised fungus from infected mosquito
|
| Organism |
Coelomomyces lativittatus |
| Characteristics |
tissue: excised fungus from infected mosquito
|
| Growth protocol |
Developmental stages of the mosquito larvae were monitored and tissues selected at appropriate timepoint
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Trizol extraction of RNA from tissue was performed on each tissue sample
Library was constructed with NEBNext Ultra Directional RNA Library Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
LateInf.rB
|
| Data processing |
Mosquito transcripts were removed from the transcriptome data using BBMap against a mosquito (Accession: GBTE00000000) reference transcriptome.
To create a Coelomomyces lattivatus reference, we used CD-HIT-EST to cluster transcripts at 90% sequence identity from three C. lattivatus draft annotations (Accessions: JADGJU010000000, JADGJV010000000 and JADHYY010000000).
We then used kallisto v. 0.48.0 to quantify read counts against this combined reference.
data were loaded into R with tximport and hypothesis testing applied with DEseq2
Assembly: JADGJU010000000, JADGJV010000000 and JADHYY010000000
Supplementary files format and content: kallisto.counts.csv - comma delimited file containg raw counts from kallisto
Supplementary files format and content: kallisto.TPM.csv - comma delimited file with normalized expression, Transcripts Per Million (TPM) compted by kallisto
|
| |
|
| Submission date |
Jan 05, 2023 |
| Last update date |
Jan 21, 2023 |
| Contact name |
Jason E Stajich |
| E-mail(s) |
jason.stajich@ucr.edu
|
| Organization name |
University of California, Riverside
|
| Department |
Microbiology & Plant Pathology
|
| Street address |
900 University Ave
|
| City |
Riverside |
| State/province |
CA - California |
| ZIP/Postal code |
92521 |
| Country |
USA |
| |
|
| Platform ID |
GPL33004 |
| Series (1) |
| GSE222209 |
Genomic resources enable study of the blastoclad fungus, Coelomomyces lativittatus, an obligate parasite of mosquitoes and microcrustaceans, during infection and sporulation |
|
| Relations |
| BioSample |
SAMN32598940 |
| SRA |
SRX18941397 |
