Evidence map›Paper›PMID 42327118›Full record

ArticlebioRxiv : the preprint server for biology2026

Genomic in vitro transcription and Nanopore direct RNA sequencing of a human B-Lymphocyte cell line.

Talia Tzadikario, Stuart Akeson, Sally Dorer, Neda Ghohabi Esfahani, Andrew J Stein, Pooria Daneshvar Kakhaki, Urja Choudhary, Kshitij Amar, Miten Jain

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

9 authors.

Talia TzadikarioDepartment of Bioengineering, Northeastern University, Boston, MA, USA.ORCID 0009-0000-6795-0340
Stuart AkesonDepartment of Bioengineering, Northeastern University, Boston, MA, USA.ORCID 0009-0008-8008-2486
Sally DorerDepartment of Bioengineering, Northeastern University, Boston, MA, USA.
Neda Ghohabi EsfahaniDepartment of Bioengineering, Northeastern University, Boston, MA, USA.ORCID 0000-0003-0539-4603
Andrew J SteinDepartment of Bioengineering, Northeastern University, Boston, MA, USA.ORCID 0009-0001-6525-6512
Pooria Daneshvar KakhakiDepartment of Bioengineering, Northeastern University, Boston, MA, USA.ORCID 0009-0001-3030-836X
Urja ChoudharyDepartment of Bioengineering, Northeastern University, Boston, MA, USA.ORCID 0009-0007-8829-278X
Kshitij AmarDepartment of Bioengineering, Northeastern University, Boston, MA, USA.ORCID 0000-0002-8365-7942
Miten JainDepartment of Bioengineering, Northeastern University, Boston, MA, USA.ORCID 0000-0002-4571-3982

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Genomic DNA used as a template for in vitro transcription of RNA can serve as a true negative control for benchmarking RNA modification detection by Nanopore direct RNA sequencing (DRS) models. We generated DRS data for in vitro transcribed (IVT) RNA composed of canonical nucleotides using genomic DNA from a human cell line. We applied Dorado modification calling models to these data, and calculated 9-mer specific false-positive rates for eight RNA modifications as a comparison point for future development of RNA modification models.

Indexed as

Direct RNA SequencingGenomic in vitro transcriptionModification calling false positiveRNA Modification Negative Control Benchmarking

Identifiers

PMID42327118
PMCPMC13277973

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
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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 Socratic graph.