|
| Status |
Public on Dec 18, 2018 |
| Title |
RNAseq_RISP_Chimera_KO3 |
| Sample type |
SRA |
| |
|
| Source name |
CD4+ YFP-Foxp3+ CD25+ Cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6NJ
age: 8-12-Week-Old
genotype: RISP KO
cell type: CD4+ YFP-Foxp3+ CD25+ Cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
NEB kit
Cells were lysed with RLT Buffer from the Qiagen RNeasy Plus Mini kit (Qiagen). Cell lysates were stored at -80°C until RNA was extracted. RNA isolations were performed using Qiagen RNeasy Plus Micro/Mini kit (Qiagen) (Extended Data Fig. 5) or the AllPrep DNA/RNA Micro Kit (Qiagen) (Figure 3 and 4) following the manufacturer’s protocol with an additional on-column DNase treatment using the RNase-Free DNase Set (Qiagen). RNA quality and quantity were measured using Agilent 4200 Tapestation using the high-sensitivity RNA ScreenTape System. (Agilent Technologies).
mRNA libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA, Inc) +Nextera XT DNA sample preparation kit (Illumina Inc) (Extended Data Fig. 5) or the NEBNext Ultra I RNA Library Prep Kit for Illumina with poly (A) mRNA selection (NEB Inc) (Figure 3,4).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
htseq.all.counts_TREG-RISP-Chimera-KO-vs-WT.txt
|
| Data processing |
Basecalls performed using bcl2fastq
RNA-seq reads were aligned to the mm10 genome assembly using Tophat
Reads were counted on the exons of mm10 genes using htseq
Differential gene expression analysis was performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file including raw counts values for each sample
|
| |
|
| Submission date |
Sep 25, 2018 |
| Last update date |
Dec 18, 2018 |
| Contact name |
Benjamin D. Singer |
| E-mail(s) |
benjamin-singer@northwestern.edu
|
| Organization name |
Northwestern University Feinberg School of Medicine
|
| Street address |
303 E. Superior St., Simpson Querrey 5th floor
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE120449 |
Mitochondrial complex III is essential for regulatory T cell suppressive function. [gene expression/RNA-seq] |
| GSE120452 |
Mitochondrial complex III is essential for regulatory T cell suppressive function |
|
| Relations |
| BioSample |
SAMN10127799 |
| SRA |
SRX4740147 |
