|
| Status |
Public on Feb 14, 2015 |
| Title |
DKOR_MEF1 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse embryo fibroblast
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Mouse embryo fibroblast
genotype: Bak−/− Bax−/− (C12 responsive)
|
| Growth protocol |
Cells were grown in a humidified 95/5% air/CO2 incubator at 37°C. The cells were passaged at 1:5–1:10 dilutions and the remaining cell suspension was seeded directly onto a 12-well tissue culture plate.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were grown to confluency in 12-well plates. Two wells of each cell line were used for library construction. Total RNA was isolated using Trizol reagent.
1 microgram of total RNA was used for library construction following standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava v1.8.0 software was used for basecalling.
Sequnced reads were mapped to mm9 whole genome using TopHat v2.0.9 with parameters -g 1 --no-novel-juncs --no-novel-indels
Gene level counts were measured using htseq-counts with parameters -m intersection-strict
Gene level counts were normalized across samples using DESeq package for R.
Differential expression between individual samples were measured using DESeq package for R, with padj < 0.01 as threshold.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for each sample
Supplementary_files_format_and_content: normalized_readcounts.txt: abundance measurements
Supplementary_files_format_and_content: raw_readcounts.txt: abundance measurements
Supplementary_files_format_and_content: WTvsDKOr_diffexp.txt: DESeq output
Supplementary_files_format_and_content: WTvsDKOnr_diffexp.txt: DESeq output
Supplementary_files_format_and_content: DKOrvsDKOnr_diffexp.txt: DESeq output
|
| |
|
| Submission date |
Feb 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Terry E Machen |
| E-mail(s) |
tmachen@berkeley.edu
|
| Phone |
510-642-2983
|
| Organization name |
Univ California-Berkeley
|
| Department |
Molec/Cell Bio
|
| Street address |
231 LSA
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720-3200 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE65935 |
Paraoxonase 2 Serves a Proapopotic Function in Mouse and Human Cells in Response to the Pseudomonas aeruginosa Quorum-Sensing Molecule N-(3-oxododecanoyl)-Homoserine Lactone. |
|
| Relations |
| BioSample |
SAMN03344770 |
| SRA |
SRX877990 |
