|
| Status |
Public on Aug 31, 2018 |
| Title |
Donor 1 T cells |
| Sample type |
SRA |
| |
|
| Source name |
T cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Total T cells
exprssion pattern: Unsorted total T cells
donor: Donor 1
|
| Treatment protocol |
PBMC were acquired from peripheral blood,cells were surfaced stained with CD3, then intracellularly stained with Granzyme B, perforin and granulysin. Subsets of cytotoxic CD3 postiive cells were sorted.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated according to the MARIS protocol (Hrvatin, S et al. MARIS: method for analyzing RNA following intracellular sorting. 2014 PLoS One Vol 9, e89459)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
donor 1 Unsorted T cells
Donor 1 normalized counts GEO.csv
|
| Data processing |
Sequenced reads were aligned to the human reference genome (build hg19 UCSC) using TopHat and Bowtie2.
Raw counts were calculated with HTseq using the hg19 Ensembl annotation.
Genome_build: hg19
Supplementary_files_format_and_content: comma-separated values file containing raw counts of mapped reads
|
| |
|
| Submission date |
Jun 12, 2018 |
| Last update date |
Aug 31, 2018 |
| Contact name |
Samuel Jackson Balin |
| E-mail(s) |
sbalin@mednet.ucla.edu
|
| Phone |
3108256911
|
| Organization name |
UCLA
|
| Street address |
10833 Le Conte Ave, Div of Dermatology, 52-121 CHS
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-3075 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE115686 |
Human antimicrobial cytotoxic T lymphocytes, defined by NK receptors and antimicrobial proteins, kill intracellular bacteria |
|
| Relations |
| BioSample |
SAMN09401610 |
| SRA |
SRX4198448 |
