|
| Status |
Public on Nov 03, 2022 |
| Title |
HeLa_Mock_1 |
| Sample type |
SRA |
| |
|
| Source name |
HeLa
|
| Organisms |
Homo sapiens; Chlamydia trachomatis L2/434/Bu |
| Characteristics |
tissue: Mock-infected HeLa
treatment: Untreated
|
| Treatment protocol |
100 µM 2,2-bipyridyl was added to complete medium as described above; complete media was replaced with defined tryptophan-depleted media: DMEM-F12 w/o L-Trp + 10% dialyzed FBS + 2 mM L-Gln + 10 µg/mL gentamicin
|
| Growth protocol |
Cells were cultured in DMEM + 10% FBS + 2 mM L-Gln + 10 µg/mL gentamicin until treatments were applied
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was collected from cultured cells in Trizol, vortexed with zirconia beads, and phenol-chloroform extracted prior to isolation through a PureLink RNA Mini Kit with two on-column DNA digestion steps. To remove rRNA, 10 µg of total RNA was run in 5 µg parallel samples through the RiboMinus Transcriptome Isolation kit with 3 µL of pan-prokaryotic rRNA probe and 4 µL eukaryotic rRNA probe. Depleted RNA was subsequently concentrated in an RNA Clean and Concentrator Kit from Zymo.
TruSeq Stranded Total RNA library preparation kit (Illumina, San Diego, CA, USA) was used to generate RNA-sequencing libraries following manufacturer protocols with a starting amount of 100 ng rRNA-depleted RNA. Depletion of rRNA in the TruSeq kit was performed by the addition of 2.5 µL each of standard rRNA Removal Mix (RRM) or Prokaryotic RRM.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
sequencing files from a given replicate were concatenated (usegalaxy.org)
fastp: filter low quality reads, trim reads, cut adaptors (usegalaxy.org)
HISAT2: alignment to reference genome (usegalaxy.org)
htseq-count: count reads aligned to features (usegalaxy.org)
DESeq2: differential gene expression analysis (R)
Genome_build: Chlamydia trachomatis L2 434/Bu ASM6858v1; Homo sapiens GRCh38
Supplementary_files_format_and_content: Normalized count values for each feature output by DESeq2
|
| |
|
| Submission date |
Jun 27, 2021 |
| Last update date |
Nov 03, 2022 |
| Contact name |
Eduardo A Groisman |
| E-mail(s) |
eduardo.groisman@yale.edu
|
| Phone |
2037377943
|
| Organization name |
Yale School of Medicine
|
| Department |
Department of Microbial Pathogenesis
|
| Lab |
Groisman Laboratory
|
| Street address |
Boyer Center for Molecular Medicine, 295 Congress Ave
|
| City |
New Haven |
| State/province |
Connecticut |
| ZIP/Postal code |
06511 |
| Country |
USA |
| |
|
| Platform ID |
GPL30320 |
| Series (1) |
| GSE179003 |
Dual RNA-seq of chlamydial and host cell transcriptomes during nutritional stress |
|
| Relations |
| BioSample |
SAMN19906507 |
| SRA |
SRX11239236 |
