|
| Status |
Public on Jun 07, 2019 |
| Title |
WB_ind2_naive_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
WB_ind2_naive
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: healthy individual
individual id: ind2
time post-infection (hours): 0
tissue/cell type: WB cells
replicate: 3
|
| Treatment protocol |
Salmonella strain used in this study was derived from the wild-type strain SL1344 containing GFP (pFPV25.1; Addgene). Cultures of Salmonella were grown in Luria-Bertani (LB) medium at 37°c for 16 hours and used for WB cells and PBMCs infection at MOI 25 for the exposed cells, and PBS was added to the naive samples. After 30 min of internalization, the cells were washed and suspended with media containing 50 ug/ml gentamicin to eliminate Salmonella that were not internalized. The cells were incubated for the time indicated in each experiment at 37°c in 5% CO2 in non-treated cell culture plates.
|
| Growth protocol |
Venous blood was drawn from the cubital vein of 4 volunteers and WB cells and PBMCS were isolated. The cells were counted, suspended in medium (RPMI 1640 with L- Glutamine supplemented with 10% heat inactivated fetal bovine serum and 1mM sodium pyruvate), divided to 3-4 replicates and plated on untreated plates.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At the indicated time points after infection the cells were washed with PBS, then suspended with RLT buffer (from RNeasy Mini Kit, Qiagen) + 1% β-mercaptoethanol and kept in -80°c until further extraction. RNA was then extracted with RNeasy Mini Kit (Qiagen).
RNA-seq libraries were prepared according to Cel-seq libraries protocol (Hashimshony, T. et al Genome Biology 2016) with a minor modification: the starting material was purified bulk RNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The cel-seq pipeline (https://github.com/yanailab/CEL-Seq-pipeline) was used for sample demultiplexing, alignment to the genome (GRCh38), and gene counting.
Data was normalized to a library size factor. Factors were calculated by dividing the total number of reads from each sample to the median of the total number of reads across all samples.
Data was transformed to log2 scale, and minimal expression threshold was set to 2.
The three replicates of each sample were averaged, except for 3 samples we excluded due to low coverage (<100K exonic reads), and therefore for 3 samples (TLR10#1 t=4h, TLR10#2 t=0 and WT#3 t=0), only 2 replicates were averaged.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalized number of reads mapped to exons (log2 scale) for each sample
|
| |
|
| Submission date |
Mar 20, 2019 |
| Last update date |
Jun 07, 2019 |
| Contact name |
Noa Bossel Ben-Moshe |
| Organization name |
Weizmann
|
| Street address |
Hertzl Street
|
| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE122084 |
Prediction of bacterial infection outcome using single cell RNA-seq analysis of human immune cells |
| GSE128627 |
Prediction of bacterial infection outcome using single cell RNA-seq analysis of human immune cells [WB/PBMCs bulk RNA-seq] |
|
| Relations |
| BioSample |
SAMN11178910 |
| SRA |
SRX5548683 |
