Evidence map›Paper›PMID 34709619›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2022

Using Genome Scale Mutant Libraries to Identify Essential Genes.

Kevin S Myers, Piyush Behari Lal, Daniel R Noguera, Timothy J Donohue

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Review
  2. Article
  3. Review
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

4 authors.

Kevin S MyersWisconsin Energy Institute and Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.
Piyush Behari LalWisconsin Energy Institute and Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.
Daniel R NogueraWisconsin Energy Institute and Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.
Timothy J DonohueWisconsin Energy Institute and Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA. tdonohue@bact.wisc.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Identification of essential genes is key to understanding the required processes and gene products of organisms under one or more conditions. Transposon sequencing (Tn-seq) has been used to predict essential genes or ones that conditionally impact fitness in a wide variety of organisms. Here, we describe the generation of genome-scale mutant libraries and the analysis of Tn-seq data to identify essential genes from cultures grown in a single condition as well as those that are conditionally important by analyzing the behavior of these mutant libraries in different growth environments. While we illustrate the approach using data derived from Tn-seq analysis of the α-proteobacteria Rhodobacter sphaeroides and Zymomonas mobilis, the protocols and systems we describe should be generally applicable to a variety of organisms.

Indexed as

Genomic LibraryDNA Transposable ElementsGenes, EssentialGenome, BacterialHigh-Throughput Nucleotide SequencingMutagenesis, InsertionalSequence AnalysisDNA Transposable ElementsBacteriaComputational biologyConditional fitnessEssential genesGene disruptionGenomicsMicrobial lifestylesSequencingTransposon

Identifiers

PMID34709619

What OpenQuestion holds

Textmetadata
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.