U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SRX10681912: 293T_CD19_Increasing_PCR_cDNA
1 OXFORD_NANOPORE (MinION) run: 10.2M spots, 9.9G bases, 8.3Gb downloads

Design: SQK-PCS109
Submitted by: Children's Hospital of Philadelphia
Study: Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts
show Abstracthide Abstract
Resistance to CD19-directed immunotherapies in lymphoblastic leukemia has been attributed, among other things, to several aberrant CD19 pre-mRNA splicing events, including recently reported excision of a cryptic intron embedded within CD19 exon 2. While exitrons are known to exist in hundreds of human transcripts, we discovered, using reporter assays and direct long-read RNA sequencing (dRNA-seq), that the CD19 exitron is an artifact of reverse transcription. Extending our analysis to publicly available datasets, we identified dozens of questionable exitrons (dubbed falsitrons) that appear only in cDNA-seq, but never in dRNA-seq. Our results highlight the importance of dRNA-seq for transcript isoform validation.
Sample: Cells transfected with the CD19 minigene report
SAMN18872785 • SRS8775276 • All experiments • All runs
Organism: Homo sapiens
Library:
Name: 293T_CD19_Increasing_PCR_cDNA
Instrument: MinION
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: Oligo-dT
Layout: SINGLE
Runs: 1 run, 10.2M spots, 9.9G bases, 8.3Gb
Run# of Spots# of BasesSizePublished
SRR1432697310,245,2469.9G8.3Gb2021-06-08

ID:
14198114

Supplemental Content

Search details

See more...

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...