 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 06, 2025 |
| Title |
qs4, 360mpi, wt433 |
| Sample type |
SRA |
| |
|
| Source name |
whole organism
|
| Organism |
Dictyostelium discoideum |
| Characteristics |
tissue: whole organism
cell line: qs4
infection: infected
genotype: wt433
treatment: 360mpi
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
All cells were collected into RNAlater (Qiagen). Subsequent total RNA extractions from each sample were performed with RNeasy plus Mini kits (Qiagen).
Illumina stranded mRNA-seq libraries were prepared and sequenced as 151 bp paired-end reads at University of Minnesota Genome Center (UMGC).
Libraries were barcoded, pooled, and sequenced across three lanes to minimize lane (batch) effects.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Quality control of sequencing reads was performed using fastp v.0.23.1 (Chen et al. 2018). Reference data were obtained from DictyBase (Chisholm et al. 2006; Fey et al. 2009) on January 16, 2023, and included a reference genome (FASTA), a gene annotation file (GTF), and a Gene Ontology (GO) annotation file. The reference genome was indexed and reads were aligned to the indexed reference using STAR v.2.7.5c (Dobin et al. 2013). To process the alignments and check the quality, only reads mapped in proper pairs were included and sorted by read query using SAMtools v.1.3.1 (Danecek et al. 2021). Read groups were added using SAMtools and subsequently counted using htseq-count v.0.11.2 (Anders et al. 2015). The count table was generated with the -s reverse flag and reads were required to have a minimum alignment quality score of 20.
Assembly: DictyBase (downloaded January 16, 2023)
Supplementary files format and content: Tab-delimited file of raw counts per gene for each sample
|
| |
|
| Submission date |
Sep 07, 2024 |
| Last update date |
Jan 06, 2025 |
| Contact name |
Suegene Noh |
| E-mail(s) |
[email protected]
|
| Organization name |
Colby College
|
| Department |
Biology
|
| Street address |
5717 Mayflower Hill
|
| City |
Waterville |
| State/province |
ME |
| ZIP/Postal code |
04901 |
| Country |
USA |
| |
|
| Platform ID |
GPL26668 |
| Series (1) |
| GSE276651 |
Time series of host responses to symbiotic T6SS disruption in an amoeba-bacteria symbiosis |
|
| Relations |
| BioSample |
SAMN43533746 |
| SRA |
SRX26012976 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8503665_qs4_360mpi_wt433_S12.star.count.txt.gz |
59.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
