|
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 |