Evidence map›Paper›PMID 37291427›Full record

ArticleNature biotechnology2024

High-throughput RNA isoform sequencing using programmed cDNA concatenation.

Aziz M Al'Khafaji, Jonathan T Smith, Kiran V Garimella, Mehrtash Babadi, Victoria Popic, Moshe Sade-Feldman, Michael Gatzen, Siranush Sarkizova, Marc A Schwartz, Emily M Blaum and 9 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature biotechnology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 132 papers.

0numbers the graph read from it
0cells of the map it votes in
132citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

132 citing papers in PubMed.

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72 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

19 authors.

Aziz M Al'Khafaji *Broad Institute of MIT and Harvard, Cambridge, MA, USA. aalkhafa@broadinstitute.org.ORCID http://orcid.org/0000-0002-4677-5667
Jonathan T Smith *Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-4279-8220
Kiran V Garimella *Broad Institute of MIT and Harvard, Cambridge, MA, USA. kiran@broadinstitute.org.
Mehrtash Babadi *Broad Institute of MIT and Harvard, Cambridge, MA, USA. mehrtash@broadinstitute.org.
Victoria Popic *Broad Institute of MIT and Harvard, Cambridge, MA, USA. vpopic@broadinstitute.org.ORCID http://orcid.org/0000-0003-3181-5432
Moshe Sade-FeldmanBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-0022-0287
Michael GatzenBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-5390-0705
Siranush SarkizovaBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Marc A SchwartzBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Emily M BlaumBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-8656-8216
Allyson DayBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Maura CostelloBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Tera BowersBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Stacey GabrielBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Eric BanksBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Anthony A PhilippakisBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Genevieve M BolandDivision of Surgical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
Paul C BlaineyBroad Institute of MIT and Harvard, Cambridge, MA, USA. pblainey@broadinstitute.org.ORCID http://orcid.org/0000-0002-4889-8783
Nir HacohenBroad Institute of MIT and Harvard, Cambridge, MA, USA. nhacohen@broadinstitute.org.ORCID http://orcid.org/0000-0002-2349-2656

Funding

Virology CoreU19AI082630 · NIAID · MASSACHUSETTS GENERAL HOSPITAL · PI GEORG Michael LAUER · 2009 to 2026
$48.1M
Center for Cell CircuitsP50HG006193 · NHGRI · BROAD INSTITUTE, INC. · PI REGEV, AVIV · 2011 to 2015
$15.6M
Center for Cell CircuitsRM1HG006193 · NHGRI · BROAD INSTITUTE, INC. · PI BLAINEY, PAUL CLARK, HACOHEN, NIR · 2016 to 2020
$14.9M
Targeting Dysregulated RNA Splicing in Neurodegenerative DiseasesRM1NS133601 · NINDS · MASSACHUSETTS GENERAL HOSPITAL · PI Paul Clark Blainey, Clotilde Lagier-Tourenne · 2023 to 2026
$7.4M
NHGRI NIH HHS P50 HG006193NHGRI NIH HHS RM1 HG006193NIAID NIH HHS U19 AI082630NINDS NIH HHS RM1 NS133601
6 · The paper itself

Abstract

Full-length RNA-sequencing methods using long-read technologies can capture complete transcript isoforms, but their throughput is limited. We introduce multiplexed arrays isoform sequencing (MAS-ISO-seq), a technique for programmably concatenating complementary DNAs (cDNAs) into molecules optimal for long-read sequencing, increasing the throughput >15-fold to nearly 40 million cDNA reads per run on the Sequel IIe sequencer. When applied to single-cell RNA sequencing of tumor-infiltrating T cells, MAS-ISO-seq demonstrated a 12- to 32-fold increase in the discovery of differentially spliced genes.

Indexed as

High-Throughput Nucleotide SequencingRNA IsoformsDNA, ComplementaryGene Expression ProfilingProtein IsoformsRNASequence Analysis, RNATranscriptomeDNA, ComplementaryProtein IsoformsRNARNA Isoforms

Identifiers

PMID37291427
PMCPMC12236355

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.