|
| Status |
Public on Oct 29, 2018 |
| Title |
Naive_3 |
| Sample type |
SRA |
| |
|
| Source name |
Naive
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: 10BiT IL-21-tRFP
time point: day 18 p.i. with LCMV Cl13
cell type: CD4 T cell
cell subset: Naive (CD44lo)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Splenic CD4 T cells from 10Bit IL-21-tRFP mice on day 18 p.i. with LCMV Cl13 were sorted for each of the three groups (naive, Tfh IL21+ IL10-, Tfh IL21+ IL10+) directly into lysis buffer (Picelli et al., Nature Protocols 2014). About 500 cells were used per sample
Libraries were constructed using Smart-seq2 protocol (Picelli et al, Nature Protocols 2014)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
genes.read_group_tracking
|
| Data processing |
Reads were aligned to the mouse reference genome (mm9) using Tophat (version 2.1.1)
Expression values for each gene were quantified and differential gene expression analysis was carried out using Cuffdiff (Cufflinks version 2.2.2)
Genome_build: mm9
Supplementary_files_format_and_content: genes.read_group_tracking contains the FPKM values for each gene in each replicate
|
| |
|
| Submission date |
Feb 22, 2018 |
| Last update date |
Oct 29, 2018 |
| Contact name |
Weiguo Cui |
| E-mail(s) |
wcui04@gmail.com
|
| Phone |
312-503-0332
|
| Organization name |
Northwestern University
|
| Department |
Pathology
|
| Lab |
Cui
|
| Street address |
303 E Chicago Ave
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60654 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE111025 |
RNA-seq of Tfh IL21+ single producers and Tfh IL21+ IL10+ double producers |
| GSE111027 |
Single-cell RNA sequencing unveils a unique IL-10-producing T follicular helper subset that sustains humoral immunity during chronic viral infection |
|
| Relations |
| BioSample |
SAMN08581625 |
| SRA |
SRX3734981 |
