|
| Status |
Public on Oct 10, 2017 |
| Title |
Naive CD4_2 |
| Sample type |
SRA |
| |
|
| Source name |
helper T cell_Naive CD4
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: spleen
age: 12 weeks
genotype: wild type
cell type: helper T cell; CD4+ T cells
stimulated with: none (naïve)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Direct-zol RNA kits (ZYMO RESEARCH). NEBNext Ultra RNA Library Prep Kit for Illumina (NEB Biolabs) was used with 200 ng 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 1500 |
| |
|
| Description |
S06792
|
| 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 |
Oct 09, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Takayuki Imanishi |
| E-mail(s) |
takayuki.imanishi@riken.jp
|
| Organization name |
RIKEN Center for Integrative Medical Sciences (IMS)
|
| Street address |
1-7-22 Suehiro-cho, Tsurumi-ku
|
| City |
Yokohama |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE104725 |
Quantitative Transcriptome Analysis of T cells stimulated with STING ligands |
|
| Relations |
| BioSample |
SAMN07760022 |
| SRA |
SRX3260745 |
