|
| Status |
Public on Oct 06, 2018 |
| Title |
No stimulation 2 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow derived dendritic cells
|
| Organism |
Mus musculus |
| Characteristics |
phenotype: No stimulation
|
| Growth protocol |
the mice were 8-10 weeks old
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the RNeasy Mini Kit (Quiagen)
Total RNA was quantified using both the NanoDrop to assess sample contamination by proteins or carryover reagents from RNA isolation, and the Qubit fluorometer (Invitrogen). Samples were then qualified using the Bioanalyzer that analyzes the integrity of the total RNA by measuring the ratio between the 18S and 28S ribosomal peaks. Libraries were constructed using SMARTer Ultra Low Input RNA v3 kit (Clontech), indexed using Nextera indices (Illumina). Final libraries were again quantitated with the Qubit fluorometer and checked for size via the Fragment Analyzer. Libraries were diluted to 4nM and pooled in equal volumes for denaturation, hybridization, and sequencing on an Illumina NextSeq 500 (Illumina) with single end 75bp sequencing chemistry.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Wheeler-2-BC6_S4
|
| Data processing |
We used the STAR aligner to map the samples, and Qced them using Rseqc then used DEseq2 for DE to get the significantly differentially expressed genes between different treatment groups.
Genome_build: Gencode_vM8
Supplementary_files_format_and_content: Excel table includes the count values for each sample calculated by STAR.
|
| |
|
| Submission date |
Oct 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
vineela gangalapudi |
| E-mail(s) |
vineela.gangalapudi@cshs.org
|
| Organization name |
Cedars- sinai Medical center
|
| Department |
Biomedical sciences
|
| Lab |
Genomics Core
|
| Street address |
8723 Alden drive
|
| City |
Los Angeles |
| State/province |
CALIFORNIA |
| ZIP/Postal code |
90048 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE87670 |
Pathogen size alters C-type lectin receptor signaling in dendritic cells to influence CD4 T cell differentiation |
|
| Relations |
| BioSample |
SAMN05868060 |
| SRA |
SRX2214376 |
