|
| Status |
Public on Jun 22, 2017 |
| Title |
+vitC allo-iTregs 1 |
| Sample type |
SRA |
| |
|
| Source name |
+vitC allo-iTregs
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: Foxp3 RFP reporter
age: 6-10 weeks
tissue: secondary lymphoid organs (spleen and peripherla LNs)
cell type: in vitro induced alloantigen specific regulatory T cells
cell subtype: FACS sorted allo-iTregs (CD4+CD90.2+Foxp3RFP+)
treated with: vitamin C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from purified APCs with RNAeasy Plus mini kit (Qiagen).
Purification of poly‑A containing mRNA was done using poly‑T oligo attached magnetic beads (Illumina). Following the purification, the mRNA was used for library preparation using Script Seq v2 Library preparation kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
EN02
|
| Data processing |
library quality assessment using FastQC
alignment vs. reference genome using Tophat2 (V1.20) with default parametrization
read count quantification using htseq-count (http://www.huber.embl.de/users/anders/HTSeq) and subsequent RPKM normalization
Detection of differentially expressed genes using DeSEQ2 with raw count data and default parametrization
Genome_build: mus musculus GRCm38
Supplementary_files_format_and_content: htseqcounts*.tab files: CSV format with raw read counts per gene; htseqcounts*.rpkm files: CSV format with RPKM normalized read counts per gene; DESeq2_genes_diffexp*.csv: CSV files with differentially expressed genes
|
| |
|
| Submission date |
Mar 23, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Beckstette |
| Organization name |
Helmholtz Centre for Infection Research
|
| Department |
Molecular Infection Biology
|
| Lab |
Experimental Immunology
|
| Street address |
Inhoffenstrase 7
|
| City |
Braunschweig |
| State/province |
Lower Saxony |
| ZIP/Postal code |
38124 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE96960 |
Alloantigen-Induced Regulatory T Cells Generated in Presence of Vitamin C Display Enhanced Stability of Foxp3 Expression and Promote Skin Allograft Acceptance |
|
| Relations |
| BioSample |
SAMN06629869 |
| SRA |
SRX2663653 |
