|
| Status |
Public on Sep 08, 2018 |
| Title |
Henle-407 infected with Shigella, 20 mM formate |
| Sample type |
SRA |
| |
|
| Source name |
Sf Formate
|
| Organisms |
Homo sapiens; Shigella flexneri 2a str. 2457T |
| Characteristics |
host cell line: Henle-407 cells
host cell type: epithelial cell
treatment: Shigella infection with 20 mM formate
|
| Treatment protocol |
20 mM formate was added to tissue culture medium after Shigella invasion for 2 hours
|
| Growth protocol |
Shigella flexneri 2457T was grown in LB with DOC, then added to Henle-407 cells at an MOI of 20. After 60 minute incubation, Henle-407 cells were washed with PBS, and MEM+gentamycin was added to kill extracellular bacteria. Cells were incubated wih or without 20 mM formate for 2 hours prior to RNA extraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNABee was applied directly to infected cells for lysis, total RNA was extracted and DNAse treated.
RNA libraries were prepared for sequencing using standard Illumina protocols by the University of Texas at Austin GSAF, and RiboZero Gold was used to remove rRNA. Sequencing was performed twice, and reads were combined.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
7_Sf_f_A_S7
|
| Data processing |
CLC Workbench version 9.5.1 used for mapping and analysis
Reads were pooled by sample
Mapping was performed to inter-genic regions and both strands, using a mismatch cost of 2, insertion cost of 3, deletion cost of 3, length fraction of 0.8, similarity fraction of 0.8
We restricted the maximum number of hits per read to 1
RPKM was used for differential expression
Genome_build: S. flexneri 2457T genome (GenBank accession no. AE014073.1) and the pCP301 plasmid (GenBank accession no. AF386526.1)
Supplementary_files_format_and_content: .xlsx files contain Shigella reads that mapped to mock treatment, which were dropped from analysis, and differential gene expression between Shigella and Shigella with formate
|
| |
|
| Submission date |
Sep 06, 2018 |
| Last update date |
Sep 10, 2018 |
| Contact name |
Ben James Koestler |
| Organization name |
Western Michigan University
|
| Department |
Biological Sciences
|
| Lab |
Koestler
|
| Street address |
1903 West Michigan Avenue, 3119 Wood Hall
|
| City |
Kalamazoo |
| State/province |
MI |
| ZIP/Postal code |
49008 |
| Country |
USA |
| |
|
| Platform ID |
GPL25540 |
| Series (1) |
| GSE119622 |
S. flexneri transcriptome in Henle-407 cells |
|
| Relations |
| BioSample |
SAMN09988111 |
| SRA |
SRX4652718 |
