|
| Status |
Public on Jul 19, 2021 |
| Title |
YTH1-4h_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
RH::TIR1::YTH1-AID strain Toxoplasma gondii
|
| Organism |
Toxoplasma gondii |
| Characteristics |
strain: RH::TIR1::YTH1-AID
treatment: 500uM IAA treatment, 4h
|
| Treatment protocol |
treatment with 500 uM 3-indole acetic acid (IAA) for 0, 4 16h
|
| Growth protocol |
parasites innoculated at MOI 10:1, grown in confluent human foreskin fibroblasts in DMEM+10%FBS (no antibiotic) for 36h prior to harvest
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
infected monolayer was scraped & syringe lysed. Parasites washed 3x with PBS. Pellet resuspended in TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols
paired end 2x150bp RNAseq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
YTH1_4h.gtf
YTH1_4h2
|
| Data processing |
trim with TrimGalore!
map to Toxoplasma genome (v45 from toxodb) with HISAT2
get feature counts with htseq-count
differential expression with DESeq2
transcriptome assembly with StringTie
Genome_build: Toxoplasma gondii (ME49) v45 from toxodb.org
Supplementary_files_format_and_content: tab delimited file with gene counts
|
| |
|
| Submission date |
Jun 16, 2021 |
| Last update date |
Jul 19, 2021 |
| Contact name |
Michael James Holmes |
| E-mail(s) |
[email protected]
|
| Organization name |
Indiana University School of Medicine
|
| Department |
Pharmacology & Toxicology
|
| Street address |
635 Barnhill Drive
|
| City |
Indianapolis |
| State/province |
IN |
| ZIP/Postal code |
46202 |
| Country |
USA |
| |
|
| Platform ID |
GPL26742 |
| Series (1) |
| GSE178355 |
Depletion of m6A writers and readers impair 3'-end formation in Toxoplasma |
|
| Relations |
| BioSample |
SAMN19732591 |
| SRA |
SRX11169563 |
