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| Status |
Public on Jun 06, 2023 |
| Title |
TEQUILA-seq: a versatile and low-cost method for targeted long-read RNA sequencing |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
Long-read RNA sequencing (RNA-seq) is a powerful technology for transcriptome analysis, but the relatively low throughput of current long-read sequencing platforms limits transcript coverage. We present TEQUILA-seq, a versatile, easy-to-implement, and low-cost method for targeted long-read RNA-seq. TEQUILA-seq can be broadly used for targeted sequencing of full-length transcripts in diverse biomedical research settings.
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| Overall design |
Targeted long-read sequencing on the Oxford nanopore platform was used to profile full-length transcript isoforms of preselected genes in poly(A)-selected RNA from human brain tissue (Clontech) and SH-SY5Y human neuroblastoma cells, each with three replicates. Targeted long-read sequencing was also used to examine full-length transcript isoforms of 468 actionable cancer genes in poly(A)-selected RNA extracted from 40 breast cancer cell lines (ATCC).
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| Web link |
https://www.nature.com/articles/s41467-023-40083-6
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| Contributor(s) |
Wang F, Xu Y, Wang R, Xing Y, Lin L |
| Citation(s) |
37553321 |
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| Submission date |
Sep 22, 2022 |
| Last update date |
Sep 05, 2023 |
| Contact name |
Yi Xing |
| E-mail(s) |
xingyi@email.chop.edu
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| Organization name |
The Children’s Hospital of Philadelphia
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| Department |
Executive Director, Department of Biomedical and Health Informatics
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| Street address |
9054 Colket Translational Research Bldg. 3501 Civic Center Blvd.
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platforms (2) |
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| Samples (123)
|
| GSM6597408 |
Brain-1 (xGenLockdown-seq) |
| GSM6597409 |
Brain-2 (xGenLockdown-seq) |
| GSM6597410 |
Brain-3 (xGenLockdown-seq) |
| GSM6597411 |
Brain-1 (TEQUILA-seq) |
| GSM6597412 |
Brain-2 (TEQUILA-seq) |
| GSM6597413 |
Brain-3 (TEQUILA-seq) |
| GSM6597414 |
SH-SY5Y-1 (direct RNA) |
| GSM6597415 |
SH-SY5Y-2 (direct RNA) |
| GSM6597416 |
SH-SY5Y-3 (direct RNA) |
| GSM6597417 |
SH-SY5Y-1 (1D cDNA) |
| GSM6597418 |
SH-SY5Y-2 (1D cDNA) |
| GSM6597419 |
SH-SY5Y-3 (1D cDNA) |
| GSM6597420 |
SH-SY5Y-1 (TEQUILA-seq_4h) |
| GSM6597421 |
SH-SY5Y-2 (TEQUILA-seq_4h) |
| GSM6597422 |
SH-SY5Y-3 (TEQUILA-seq_4h) |
| GSM6597423 |
SH-SY5Y-1 (TEQUILA-seq_8h) |
| GSM6597424 |
SH-SY5Y-2 (TEQUILA-seq_8h) |
| GSM6597425 |
SH-SY5Y-3 (TEQUILA-seq_8h) |
| GSM6597426 |
SH-SY5Y-1 (TEQUILA-seq_48h) |
| GSM6597427 |
SH-SY5Y-2 (TEQUILA-seq_48h) |
| GSM6597428 |
SH-SY5Y-3 (TEQUILA-seq_48h) |
| GSM6597429 |
SH-SY5Y-1 (short-read) |
| GSM6597430 |
SH-SY5Y-2 (short-read) |
| GSM6597431 |
SH-SY5Y-3 (short-read) |
| GSM6597432 |
BRCA_1-1 (TEQUILA-seq) |
| GSM6597433 |
BRCA_1-2 (TEQUILA-seq) |
| GSM6597434 |
BRCA_2-1 (TEQUILA-seq) |
| GSM6597435 |
BRCA_2-2 (TEQUILA-seq) |
| GSM6597436 |
BRCA_3-1 (TEQUILA-seq) |
| GSM6597437 |
BRCA_3-2 (TEQUILA-seq) |
| GSM6597438 |
BRCA_4-1 (TEQUILA-seq) |
| GSM6597439 |
BRCA_4-2 (TEQUILA-seq) |
| GSM6597440 |
BRCA_5-1 (TEQUILA-seq) |
| GSM6597441 |
BRCA_5-2 (TEQUILA-seq) |
| GSM6597442 |
BRCA_6-1 (TEQUILA-seq) |
| GSM6597443 |
BRCA_6-2 (TEQUILA-seq) |
| GSM6597444 |
BRCA_7-1 (TEQUILA-seq) |
| GSM6597445 |
BRCA_7-2 (TEQUILA-seq) |
| GSM6597446 |
BRCA_8-1 (TEQUILA-seq) |
| GSM6597447 |
BRCA_8-2 (TEQUILA-seq) |
| GSM6597448 |
BRCA_9-1 (TEQUILA-seq) |
| GSM6597449 |
BRCA_9-2 (TEQUILA-seq) |
| GSM6597450 |
BRCA_10-1 (TEQUILA-seq) |
| GSM6597451 |
BRCA_10-2 (TEQUILA-seq) |
| GSM6597452 |
BRCA_11-1 (TEQUILA-seq) |
| GSM6597453 |
BRCA_11-2 (TEQUILA-seq) |
| GSM6597454 |
BRCA_12-1 (TEQUILA-seq) |
| GSM6597455 |
BRCA_12-2 (TEQUILA-seq) |
| GSM6597456 |
BRCA_13-1 (TEQUILA-seq) |
| GSM6597457 |
BRCA_13-2 (TEQUILA-seq) |
| GSM6597458 |
BRCA_14-1 (TEQUILA-seq) |
| GSM6597459 |
BRCA_14-2 (TEQUILA-seq) |
| GSM6597460 |
BRCA_15-1 (TEQUILA-seq) |
| GSM6597461 |
BRCA_15-2 (TEQUILA-seq) |
| GSM6597462 |
BRCA_16-1 (TEQUILA-seq) |
| GSM6597463 |
BRCA_16-2 (TEQUILA-seq) |
| GSM6597464 |
BRCA_17-1 (TEQUILA-seq) |
| GSM6597465 |
BRCA_17-2 (TEQUILA-seq) |
| GSM6597466 |
BRCA_18-1 (TEQUILA-seq) |
| GSM6597467 |
BRCA_18-2 (TEQUILA-seq) |
| GSM6597468 |
BRCA_19-1 (TEQUILA-seq) |
| GSM6597469 |
BRCA_19-2 (TEQUILA-seq) |
| GSM6597470 |
BRCA_20-1 (TEQUILA-seq) |
| GSM6597471 |
BRCA_20-2 (TEQUILA-seq) |
| GSM6597472 |
BRCA_21-1 (TEQUILA-seq) |
| GSM6597473 |
BRCA_21-2 (TEQUILA-seq) |
| GSM6597474 |
BRCA_22-1 (TEQUILA-seq) |
| GSM6597475 |
BRCA_22-2 (TEQUILA-seq) |
| GSM6597476 |
BRCA_23-1 (TEQUILA-seq) |
| GSM6597477 |
BRCA_23-2 (TEQUILA-seq) |
| GSM6597478 |
BRCA_24-1 (TEQUILA-seq) |
| GSM6597479 |
BRCA_24-2 (TEQUILA-seq) |
| GSM6597480 |
BRCA_25-1 (TEQUILA-seq) |
| GSM6597481 |
BRCA_25-2 (TEQUILA-seq) |
| GSM6597482 |
BRCA_26-1 (TEQUILA-seq) |
| GSM6597483 |
BRCA_26-2 (TEQUILA-seq) |
| GSM6597484 |
BRCA_27-1 (TEQUILA-seq) |
| GSM6597485 |
BRCA_27-2 (TEQUILA-seq) |
| GSM6597486 |
BRCA_28-1 (TEQUILA-seq) |
| GSM6597487 |
BRCA_28-2 (TEQUILA-seq) |
| GSM6597488 |
BRCA_29-1 (TEQUILA-seq) |
| GSM6597489 |
BRCA_29-2 (TEQUILA-seq) |
| GSM6597490 |
BRCA_30-1 (TEQUILA-seq) |
| GSM6597491 |
BRCA_30-2 (TEQUILA-seq) |
| GSM6597492 |
BRCA_31-1 (TEQUILA-seq) |
| GSM6597493 |
BRCA_31-2 (TEQUILA-seq) |
| GSM6597494 |
BRCA_32-1 (TEQUILA-seq) |
| GSM6597495 |
BRCA_32-2 (TEQUILA-seq) |
| GSM6597496 |
BRCA_33-1 (TEQUILA-seq) |
| GSM6597497 |
BRCA_33-2 (TEQUILA-seq) |
| GSM6597498 |
BRCA_34-1 (TEQUILA-seq) |
| GSM6597499 |
BRCA_34-2 (TEQUILA-seq) |
| GSM6597500 |
BRCA_35-1 (TEQUILA-seq) |
| GSM6597501 |
BRCA_35-2 (TEQUILA-seq) |
| GSM6597502 |
BRCA_36-1 (TEQUILA-seq) |
| GSM6597503 |
BRCA_36-2 (TEQUILA-seq) |
| GSM6597504 |
BRCA_37-1 (TEQUILA-seq) |
| GSM6597505 |
BRCA_37-2 (TEQUILA-seq) |
| GSM6597506 |
BRCA_38-1 (TEQUILA-seq) |
| GSM6597507 |
BRCA_38-2 (TEQUILA-seq) |
| GSM6597508 |
BRCA_39-1 (TEQUILA-seq) |
| GSM6597509 |
BRCA_39-2 (TEQUILA-seq) |
| GSM6597510 |
BRCA_40-1 (TEQUILA-seq) |
| GSM6597511 |
BRCA_40-2 (TEQUILA-seq) |
| GSM6597512 |
HCC1806 (1D cDNA) |
| GSM6597513 |
MDA-MB-157 (1D cDNA) |
| GSM6597514 |
AU-565 (1D cDNA) |
| GSM6597515 |
MCF7 (1D cDNA) |
| GSM7245756 |
HCC1806 (TEQUILA-seq) |
| GSM7245757 |
MDA-MB-157 (TEQUILA-seq) |
| GSM7245758 |
AU-565 (TEQUILA-seq) |
| GSM7245759 |
MCF7 (TEQUILA-seq) |
| GSM7245760 |
HCC1806 (TEQUILA-seq, blocking oligos(+), multiplex(-)) |
| GSM7245761 |
MDA-MB-157 (TEQUILA-seq, blocking oligos(+), multiplex(-)) |
| GSM7245762 |
AU-565 (TEQUILA-seq, blocking oligos(+), multiplex(-)) |
| GSM7245763 |
MCF7 (TEQUILA-seq, blocking oligos(+), multiplex(-)) |
| GSM7245764 |
HCC1806 (TEQUILA-seq, blocking oligos(+), multiplex(+)) |
| GSM7245765 |
MDA-MB-157 (TEQUILA-seq, blocking oligos(+), multiplex(+)) |
| GSM7245766 |
AU-565 (TEQUILA-seq, blocking oligos(+), multiplex(+)) |
| GSM7245767 |
MCF7 (TEQUILA-seq, blocking oligos(+), multiplex(+)) |
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| Relations |
| BioProject |
PRJNA883409 |
| SRA |
SRP398751 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE213984_BRCA_1D_cDNA_N2_R0_abundance.esp.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
| GSE213984_BRCA_1D_cDNA_N2_R0_updated.gtf.gz |
6.1 Mb |
(ftp)(http) |
GTF |
| GSE213984_BRCA_TEQUILA-seq_N2_R0_abundance.esp.txt.gz |
9.1 Mb |
(ftp)(http) |
TXT |
| GSE213984_BRCA_TEQUILA-seq_N2_R0_updated.gtf.gz |
9.9 Mb |
(ftp)(http) |
GTF |
| GSE213984_BRCA_TEQUILA-seq_refinement_N2_R0_abundance.esp.txt.gz |
1.3 Mb |
(ftp)(http) |
TXT |
| GSE213984_BRCA_TEQUILA-seq_refinement_N2_R0_updated.gtf.gz |
4.0 Mb |
(ftp)(http) |
GTF |
| GSE213984_Brain_hg19_N2_R0_abundance.esp.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
| GSE213984_Brain_hg19_N2_R0_updated.gtf.gz |
4.5 Mb |
(ftp)(http) |
GTF |
| GSE213984_SH-SY5Y_SE.MATS.JC.txt.gz |
4.5 Mb |
(ftp)(http) |
TXT |
| GSE213984_SH-SY5Y_SIRV_N2_R0_abundance.esp.txt.gz |
4.7 Kb |
(ftp)(http) |
TXT |
| GSE213984_SH-SY5Y_SIRV_N2_R0_updated.gtf.gz |
5.5 Kb |
(ftp)(http) |
GTF |
| GSE213984_SH-SY5Y_hg19_N2_R0_abundance.esp.txt.gz |
1.7 Mb |
(ftp)(http) |
TXT |
| GSE213984_SH-SY5Y_hg19_N2_R0_updated.gtf.gz |
4.9 Mb |
(ftp)(http) |
GTF |
| GSE213984_Target_gene_panel.txt.gz |
1.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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