|
| Status |
Public on Jan 30, 2018 |
| Title |
LPS RNA-seq rep2 |
| Sample type |
SRA |
| |
|
| Source name |
LPS RNA-seq
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Detroit 562 cells
treatment: LPS
batch: 3
|
| Treatment protocol |
Detroit 562 cells were treated with LPS at 1μg/mL for 100 minutes, TNFα at 10ng/mL for 70 minutes, Pam2CSK4 at 1μg/mL for 80 minutes, Poly I:C at 10μg/mL for 110 minutes or M tri-DAP at 20 μg/mL for 110 minutes. For each experiment, a “no treatment” control consisting of a change of culture medium was processed along with the treated samples.
|
| Growth protocol |
Detroit 562 cells were purchased from ATCC and cultured in RPMI medium (Gibco) supplemented with 10% fetal bovine serum performance (Gibco), 100U/ml penicillin, 100ug/ml streptomycin (Gibco) and 1mM sodium pyruvate (Gibco).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using the RNeasy Plus Universal kit (Qiagen) and loaded on a NanoRNA Bioanalyzer chip (Agilent) for qualification and quantification.
Libraries for RNA-seq were prepared with the TruSeq Stranded mRNA Library Prep kit (Illumina) according to the manufacturer’s instructions. Samples were sequenced on an Illumina NextSeq-High 1x76bp
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
mapping of the reads to hg19 with TopHat
Differential gene expression analysis with CuffDiff, using the Ensemble gtf file GRCh37.73 and running the treated condition against the non-treated condition (for the same batch) bam file (cuffdiff-2.2.0 -u -o xxx GRCh37.73_+chrm.gtf no_treatment.bam treatment.bam)
Calculate the average Log2 (Fold change) for each condition: mean of the Log2 (Fold change) of both duplicates for each condition
Genome_build: hg19
Supplementary_files_format_and_content: For each replicate, the 'gene_exp.diff' output file from cuffdiff against non-treated sample is given
|
| |
|
| Submission date |
Dec 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Lisa Borghini |
| E-mail(s) |
[email protected]
|
| Organization name |
GIS
|
| Department |
Infectious Diseases
|
| Lab |
Martin Hibberd
|
| Street address |
60 Biopolis Street, Genome, #02-01
|
| City |
Singapore |
| State/province |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL21697 |
| Series (2) |
| GSE91019 |
Gene expression response to 5 microbial stimuli in Detroit562 cells [RNA-seq] |
| GSE91020 |
Variation of genome-wide NF-kappa B RELA binding sites in response to different microbial stimuli |
|
| Relations |
| BioSample |
SAMN06118954 |
| SRA |
SRX2404233 |
