|
| Status |
Public on Mar 22, 2017 |
| Title |
KO1 |
| Sample type |
SRA |
| |
|
| Source name |
splenic dendritic cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: spleen
age: 10-week old
genotype: TBK1-DKO
cell type: dendritic cells (DCs)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fresh splenic dendritic cells were isolated from young WT and TBK1-DKO mice (8-week old) and used for total RNA isolation with Trizol (Invitrogen), and subjected to RNA-seq analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
RNA-Seq libraries were prepared and sequencing was performed by the MD Anderson Cancer Center Sequencing and Microarray Facility
The raw reads were aligned to the Mouse reference genome build mm10, using Tophat2 RNASeq alignment software.
HTseq software is used to summarize the gene expression counts from Tophat alignment data after sorting the BAM files.
The raw counts are normalized and differential expression analysis is performed between KO and WT samples using the DEseq2 package.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Gene-Level Read Count files
|
| |
|
| Submission date |
Feb 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Shao-cong Sun |
| E-mail(s) |
ssun@mdanderson.org
|
| Organization name |
MD Anderson Cancer Center
|
| Department |
Immunology
|
| Lab |
Dr. Sun's Lab
|
| Street address |
7455 Fannin St.
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE94543 |
Next Generation Sequencing analysis using splenic DCs freshly isolated from Wild Type and TBK1-DKO mice |
|
| Relations |
| BioSample |
SAMN06299369 |
| SRA |
SRX2539414 |
