|
| Status |
Public on Jan 18, 2017 |
| Title |
WT-48h |
| Sample type |
SRA |
| |
|
| Source name |
Macrophages
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Bone marrow-derived macrophages
strain: C57BL/6
genotype/variation: Wild type
treatment: Stimulated with yeast form Candida albicans for 48 hour
|
| Treatment protocol |
C. albicans were heat-inactivaed and add to BMDMs for 24 hours for stimulation at MOI=10
|
| Growth protocol |
Bone marrows cells were cultured for 6 days in DMEM supplemented with 10% FBS and 10% L929 cell supernatant as conditioned medium providing macrophage colony stimulating factor to generate
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell supernatant were remove, wasded with PBS twice and TRIZOl were added to extract the total cell mRNA
Sequencing libraries were generated using NEBNext UltraTM Directional RNA Library Prep Kit for Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
q3 in gene_exp. Diff
|
| Data processing |
The filtered reads were aligned to the mouse most recent genome reference mm10 by using TopHat (version 2.1.0)
the BAM files of each individual alignment were used to analyze genes differential expression by using Cufflinks (version 2.2.1)
Supplementary_files_format_and_content: diff files
|
| |
|
| Submission date |
Jun 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Xin Lin |
| Organization name |
Tsinghua University
|
| Street address |
Haidian Qu Tsinghua yuan
|
| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE83265 |
RNA-seq data for bone-marrow-derived macrophages from wildtype and JNK1 knockout mice stimulated with yeast form Candida albicans |
|
| Relations |
| BioSample |
SAMN05232074 |
| SRA |
SRX1838222 |
