|
| Status |
Public on Oct 06, 2020 |
| Title |
CGAGGCTGTTAAAG_Lane2_Ctrl_Th1_1 |
| Sample type |
SRA |
| |
|
| Source name |
murine spleen
|
| Organism |
Mus musculus |
| Characteristics |
celltype: CD4 T cell
genotype: SMARTA Cd4-CreERT2+ CXCR5+/+ CD45.1/2
strain: C57BL/6
|
| Treatment protocol |
mice were treated with tamoxifen to induce the CreERT2-mediated knockout of Bcl6 or CXCR5 in CD4 T cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
secondary lymphoid organs were removed, single cell suspensions and antibody stainings for flow cytometry and cell sorting were prepared on ice. Cells were sorted directly into lysis buffer and immediately spun down and frozen on dry ice. RNA was isolated using magnetic beads
Libraries were constructed using a bulk adjusted mcSCRB-seq protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Lane2_UMI.txt
|
| Data processing |
Fastq reads were processed with the zUMIs pipeline (Parekh et al., 2017)
cDNA reads were aligned to the Mouse (mm10) Genome with STAR 2.6.0a
Quantification was done with ENSEMBL gene models (GRCm38.75)
Genome_build: Mouse: mm10, Ensembl 75
Supplementary_files_format_and_content: sample (columns) and gene (rows) -wise UMI expression table
|
| |
|
| Submission date |
Dec 17, 2019 |
| Last update date |
Oct 06, 2020 |
| Contact name |
Dirk Baumjohann |
| E-mail(s) |
dirk.baumjohann@uni-bonn.de
|
| Organization name |
University Hospital Bonn
|
| Department |
Medical Clinic III
|
| Lab |
Baumjohann Lab
|
| Street address |
Venusberg-Campus 1
|
| City |
Bonn |
| State/province |
NRW |
| ZIP/Postal code |
53127 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE142229 |
Continued Bcl6 expression prevents the transdifferentiation of established Tfh cells into Th1 cells during acute viral infection |
|
| Relations |
| BioSample |
SAMN13616421 |
| SRA |
SRX7400822 |
