|
| Status |
Public on Nov 30, 2021 |
| Title |
unstimulated_2 |
| Sample type |
SRA |
| |
|
| Source name |
CD11c+ BMDC
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
treatment: NA
|
| Treatment protocol |
BMDCs were stimulated with LPS or cocultured with Th0 cells in the presence or absence of soluble anti-CD3. BMDCs were then sorted by Moflo on the basis of CD45.2+ CD90.2- CD11c+.
|
| Growth protocol |
Bone marrow progenitors were cultured with GMCSF for 7 days with media being replenished every 2 days. WT Th0 cells were differentiated on anti-CD3/anti-CD28 coated plates in the presence of IL-2 for 5 days then rested for 2 days in uncoated plates supplemented with low dose IL-2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA prep for mRNA-sequencing was performed using the miRNeasy (Qiagen) and treated with DNase I (Qiagen), according to the manufacturer's instructions. Quantities of extracted RNA were determined using NanoDrop2000 for cDNA synthesis or Agilent Bioanalyzer 2100 before RNA-Seq Library preparation.
RNA-seq libraries were prepared with the Illumina TruSeq RNA Sample Preparation kit (Illumina) according to the manufacturer’s protocol. Libraries were validated on an Agilent Bioanalyzer 2100.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
CD11c+ BMDCs, unstimulated, replicate-2
2-DC-NO-LPS
|
| Data processing |
Alignment of RNA-seq reads on Mouse reference genome mm10 was performed on CLC Genomics Workbench 7 (Qiagen).
The expression of the genes in all samples was calculated as Reads Per Kilobase of transcript per Million mapped reads (RPKM).
Genome_build: mm10
Supplementary_files_format_and_content: .txt, raw counts matrix that contains all gene names and counts for each sample
|
| |
|
| Submission date |
Sep 22, 2021 |
| Last update date |
Nov 30, 2021 |
| Contact name |
Chandrashekhar Pasare |
| E-mail(s) |
Chandrashekhar.pasare@cchmc.org
|
| Organization name |
Cincinnati Children's Hospital Medical Center
|
| Department |
Immunology
|
| Lab |
Chandrashekhar Pasare
|
| Street address |
250 Albert Sabin Way
|
| City |
Cincinnati |
| State/province |
Ohio |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE184607 |
Effector Memory CD4 T cells engage the innate immune system through CD40 and TNFR to trigger cytokine storm and autoimmune pathology I |
|
| Relations |
| BioSample |
SAMN21554812 |
| SRA |
SRX12299032 |
