|
| Status |
Public on Dec 08, 2020 |
| Title |
OX40-1 |
| Sample type |
SRA |
| |
|
| Source name |
OX40, double-negative regulatory T cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype/variation: OX40-knockout
cell type: Primary lymphocyte
cell subtype: Double-negative regulatory T cells (DNT)
protocol: Converted from naïve CD4 T cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Double-negative regulatory T cells (DNT) were converted from naïve CD4 T by standard protocol which have been reported before [BLOOD, 1 MAY 2007 VOLUME 109, NUMBER 9].Then CD3+TCRαβ+NK-CD4-CD8- DNT were sorted by FACS Aria II, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
DNT converted from OX40 knockout mouse
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
|
| |
|
| Submission date |
Dec 11, 2017 |
| Last update date |
Dec 08, 2020 |
| Contact name |
Kai Liu |
| E-mail(s) |
lkfriendship@qq.com
|
| Phone |
86 18510763684
|
| Organization name |
Beijing Friendship Hospital, Capital Medical University
|
| Street address |
No. 95 Yong-an Road
|
| City |
Beijing |
| ZIP/Postal code |
100050 |
| Country |
China |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE107908 |
OX40 regulates double-negative regulatory T cells dependently of its effects on conversion and function |
|
| Relations |
| BioSample |
SAMN08159933 |
| SRA |
SRX3461206 |
