|
| Status |
Public on May 11, 2016 |
| Title |
p20 LNR |
| Sample type |
SRA |
| |
|
| Source name |
sentinel lymph node
|
| Organism |
Homo sapiens |
| Characteristics |
sentinel ln tumor invasion: yes
illumina read 2 barcode: 5' - TGGTCA - 3'
custom read 1 barcode: 5' - ACGTNNNN - 3'
cell type isolated: CD8+ T cells
|
| Treatment protocol |
CD8+ T cells were selected from bulk samples using a positive selection kit. CD* T cells were incubated overnight in 10U/ml of IL-2 prior to emulsion RT-PCR sequencing
|
| Extracted molecule |
total RNA |
| Extraction protocol |
No extraction of RNA was performed, rather single cells were lysed within an emulsion droplet and RT-PCR was performed using TCR specific primers
PCR amplicons were generated using primers containing the Read1, Read2, and Bridge priming sites as well as Illumina indicies (Read 2 side) and custom indicies on the Read 1 side
amplicon sequencing following RT-PCR of a specific gene(s)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
total RNA via single cell analysis
TCR specific primers were used in single cell emulsion droplets to amplify only TCRs from single CD8 T cells lysed within the droplets
|
| Data processing |
Paired reads were joined following the reverse complementation of the Read 1 sequences to create a 500bp total length read with the C regions on the ends and the V regions in the center
Paired reads were then clipped from either end using the overlap sequence used to joined the alpha and beta TCR moelcules within the emulsion droplet during PCR amplification and overlap extension, generating an alpha and beta file with shared cluster IDs
Sequences were then processed using CompleteTCR to 1.) identify the V, J, and CDR3, 2.) to pair the reads using the cluster IDs, and 3.) compute frequency values for individual read pairs
Genome_build: IMGT TCR database
Supplementary_files_format_and_content: All processed files contain the identified TCR pairs and frequencies for each pair. The sample tissue as well as the patient ID are included in the file names for simplicity
|
| |
|
| Submission date |
May 11, 2016 |
| Last update date |
May 11, 2016 |
| Contact name |
Jill Slansky |
| E-mail(s) |
Jill.Slansky@ucdenver.edu
|
| Organization name |
Univ Colorado Som
|
| Street address |
12800 East 19th Ave
|
| City |
Aurora |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL15520 |
| Series (1) |
| GSE81313 |
Identification of shared TCR sequences from T cells in human breast cancer using emulsion RT-PCR |
|
| Relations |
| BioSample |
SAMN04978729 |
