|
| Status |
Public on Jan 01, 2020 |
| Title |
DNA sequencing for multiple rounds of the pMHC-yeast display selection for TCR6, TCR7 and FluTCR [other] |
| Organism |
synthetic construct |
| Experiment type |
Other
|
| Summary |
A peptide library was displayed on Db MHC class I allele expressed on yeast. TCRs of interest were used to select and enrich for cognate peptide-MHC.
|
| |
|
| Overall design |
A naive pMHC-yeast display library was selected with biotinylated TCRs of interest present on magnetic beads (Miltenyi) or fluorescently labelled streptavidin. After 4 rounds of TCR selection DNA was extracted using zymolase for all rounds of selected yeast, enriched for cognate pMHC, as well as the naive library. Isolated DNA/plasmid was amplified by PCR with appropriate barcodes and sequencing was performed using a Miseq.
|
| |
|
| Contributor(s) |
Davis MM, Saligrama N, Fernandes RA |
| Citation(s) |
31391585 |
| |
| Submission date |
Jun 26, 2019 |
| Last update date |
Apr 01, 2020 |
| Contact name |
Ricardo A Fernandes |
| E-mail(s) |
ralexandrelf@gmail.com
|
| Organization name |
Stanford University
|
| Department |
Molecular and Cellular Physiology
|
| Lab |
KC Garcia Beckman Bldg
|
| Street address |
279 Campus Drive
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94301 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL17769 |
Illumina MiSeq (synthetic construct) |
|
| Samples (2) |
|
| This SubSeries is part of SuperSeries: |
| GSE133364 |
RNA seq on SP specific CD8+ T cells, Ly49+ and Ly49-CD8+ T cells from MOG and MOG + SP immunized mice and DNA sequencing for multiple rounds of the pMHC-yeast display selection for TCR6, TCR7 and FluTCR |
|
| Relations |
| BioProject |
PRJNA551268 |
| SRA |
SRP212123 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE133363_Flu_10_round1.fasta.gz |
1.1 Mb |
(ftp)(http) |
FASTA |
| GSE133363_Flu_10_round2.fasta.gz |
4.7 Mb |
(ftp)(http) |
FASTA |
| GSE133363_Flu_10_round3.fasta.gz |
3.2 Mb |
(ftp)(http) |
FASTA |
| GSE133363_Flu_10_round4.fasta.gz |
2.7 Mb |
(ftp)(http) |
FASTA |
| GSE133363_Naive10mer-TCR7_20161202.fasta.gz |
11.9 Mb |
(ftp)(http) |
FASTA |
| GSE133363_Naive10mer_Flu_TCR6_20161214.fasta.gz |
7.1 Mb |
(ftp)(http) |
FASTA |
| GSE133363_Naive10mer_HA-enriched_TCR7_20161202.fasta.gz |
11.6 Mb |
(ftp)(http) |
FASTA |
| GSE133363_Naive10mer_Myc-enriched_Flu_TCR6_20161214.fasta.gz |
7.3 Mb |
(ftp)(http) |
FASTA |
| GSE133363_TCR6_615_10_round1.fasta.gz |
1.9 Mb |
(ftp)(http) |
FASTA |
| GSE133363_TCR6_615_10_round2.fasta.gz |
1.1 Mb |
(ftp)(http) |
FASTA |
| GSE133363_TCR6_615_10_round3.fasta.gz |
787.4 Kb |
(ftp)(http) |
FASTA |
| GSE133363_TCR6_615_10_round4.fasta.gz |
550.7 Kb |
(ftp)(http) |
FASTA |
| GSE133363_TCR7_716_round1.fasta.gz |
5.4 Mb |
(ftp)(http) |
FASTA |
| GSE133363_TCR7_716_round2.fasta.gz |
5.3 Mb |
(ftp)(http) |
FASTA |
| GSE133363_TCR7_716_round3.fasta.gz |
3.2 Mb |
(ftp)(http) |
FASTA |
| GSE133363_TCR7_716_round4.fasta.gz |
2.2 Mb |
(ftp)(http) |
FASTA |
| GSE133363_readme.xlsx |
13.7 Kb |
(ftp)(http) |
XLSX |
| GSE133363_uniques_stats-615-all-naive-rd1234-20171016.csv.gz |
1.9 Mb |
(ftp)(http) |
CSV |
| GSE133363_uniques_stats-716-naiverd1234-20171017.csv.gz |
767.7 Kb |
(ftp)(http) |
CSV |
| GSE133363_uniques_stats-Flu-all-naive-rd1234-20171016.csv.gz |
1.1 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
