Evidence map›Paper›PMID 39525967›Full record

ArticleBio-protocol2024

Accurate Measurement of Cell Number-Normalized Differential Gene Expression in Cells Treated With Retinoic Acid.

Nina Weichert-Leahey, Mark W Zimmerman, Alla Berezovskaya, A Thomas Look, Brian J Abraham

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bio-protocol, 2024. 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

5 authors.

Nina Weichert-LeaheyDepartment of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
Mark W ZimmermanDepartment of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
Alla BerezovskayaDepartment of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
A Thomas LookDepartment of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
Brian J AbrahamDepartment of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.

Funding

PATHOPHYSIOLOGY OF HUMAN BLOOD CELLST32HL007574 · NHLBI · CHILDREN'S HOSPITAL BOSTON · PI Daniel Evan Bauer · 1985 to 2026
$18.4M
Mechanisms and Vulnerabilities of Aberrant Transcriptional Enhancers in CancerR35CA210064 · NCI · DANA-FARBER CANCER INST · PI LOOK, A. THOMAS · 2016 to 2022
$7.3M
NCI NIH HHS R35 CA210064NHLBI NIH HHS T32 HL007574
6 · The paper itself

Abstract

Genome-wide gene expression analysis is a commonly used method to quantitatively examine the transcriptional signature of any tissue or cell state. Standard bulk cell RNA sequencing (RNA-seq) quantifies RNAs in the cells of the tissue type of interest through massive parallel sequencing of cDNA synthesized from the cellular RNA. The subsequent analysis of global RNA expression and normalization of RNA expression levels between two or more samples generally assumes that cells from all samples produce equivalent amounts of RNA per cell. This assumption may be invalid in cells where

Indexed as

DifferentiationGene regulationMYCNNeuroblastomaRetinoic acidRNA-sequencingSpiked-in RNATranscriptional amplification

Identifiers

PMID39525967
PMCPMC11543784

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Registered trials

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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.