|
| Status |
Public on Nov 21, 2016 |
| Title |
SMART seq Tet2/3 DKO iNKT tetramer+TCRb+CD24-NK1.1- BR2 |
| Sample type |
SRA |
| |
|
| Source name |
Thymus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Thymus
cell type: Invariant NKT (iNKT) cells
genotype: Tet2/3 DKO
|
| Treatment protocol |
N/A
|
| Growth protocol |
iNKT cells were isolated from thymus of the desired genotypes after staining and FACS sorting of B220-, aGalCer tetramer+, TCRb+ cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the cell types of interest using the E.Z.N.A. HP Total RNA kit (Omega) according to the manufacturer’s instructions.
we performed SMARTseq as previously described (Picelli et al., 2014). In this case, the starting total RNA for each library was 10 ng. 9 cycles of preamplification were performed.Tagmentation was carried out by using the Illumina Nextera XT DNA sample preparation kit. 8 cycles were performed for amplification of adaptor- ligated fragments. 2 biological replicates per sample were used.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Tet2/3 DKO iNKT tetramer+TCRb+CD24-NK1.1- BR2
|
| Data processing |
The reads were mapped to the mm9 genome as well as UCSC transcriptome using Tophat
The read counts for each gene were quantified using HTSeq-count tool with parameters: -m union
Differential expression analysis was performed using edgeR (Robinson et al., 2010)
Genes with RPKM less than 1 in at least two replicates in each compared condition were filtered out before differential expression calling. Dispersion was estimated as tag-wise dispersion. Genes with FDR<0.05 and at least 1.5 fold difference in expression were identified as differentially expressed.
Genome_build: mm9
Supplementary_files_format_and_content: Estimated RPKM values (txt)
|
| |
|
| Submission date |
Aug 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sini Rautio |
| Organization name |
Aalto University
|
| Street address |
Konemiehentie 2
|
| City |
Espoo |
| ZIP/Postal code |
02100 |
| Country |
Finland |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE66834 |
TET proteins regulate lineage specification and TCR-mediated expansion of iNKT cells |
| GSE85674 |
TET proteins regulate lineage specification and TCR-mediated expansion of iNKT cells (SMART-Seq) |
|
| Relations |
| BioSample |
SAMN05578917 |
| SRA |
SRX2026233 |
