Optimized PCR conditions and increased shRNA fold representation improve reproducibility of pooled shRNA screens (Q34369461)

1 August 2017

title

Optimized PCR conditions and increased shRNA fold representation improve reproducibility of pooled shRNA screens (English)

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1 August 2017

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Kaylene J Simpson

8

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author name string

Žaklina Strezoska

1

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1 August 2017

Abel Licon

2

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1 August 2017

Josh Haimes

3

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1 August 2017

Katie Jansen Spayd

4

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1 August 2017

Kruti M Patel

5

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1 August 2017

Kevin Sullivan

6

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1 August 2017

Katarzyna Jastrzebski

7

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1 August 2017

Devin Leake

9

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1 August 2017

Anja van Brabant Smith

10

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1 August 2017

Annaleen Vermeulen

11

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1 August 2017

language of work or name

English

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publication date

1 August 2012

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1 August 2017

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1 August 2017

volume

7

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1 August 2017

issue

8

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1 August 2017

page(s)

e42341

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Creative Commons Attribution 4.0 International

1 August 2017

copyright license

start time

1 August 2012

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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describes a project that uses

DESeq2

object named as

DESeq

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

A primer on using pooled shRNA libraries for functional genomic screens

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

High-throughput RNA interference screening using pooled shRNA libraries and next generation sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

Development of methods for quantitative comparison of pooled shRNAs by mass sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

Functional genomics reveal that the serine synthesis pathway is essential in breast cancer

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

A comprehensive platform for highly multiplexed mammalian functional genetic screens

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

Genome-wide functional screen identifies a compendium of genes affecting sensitivity to tamoxifen

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

FAS and NF-κB signalling modulate dependence of lung cancers on mutant EGFR.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

A genome-wide RNAi screen identifies multiple RSK-dependent regulators of cell migration

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

Differential expression analysis for sequence count data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

A genetic screen identifies the Triple T complex required for DNA damage signaling and ATM and ATR stability

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

Novel HIV-1 knockdown targets identified by an enriched kinases/phosphatases shRNA library using a long-term iterative screen in Jurkat T-cells

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

Decoding pooled RNAi screens by means of barcode tiling arrays

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

In vivo RNAi screening identifies regulators of actin dynamics as key determinants of lymphoma progression

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

A genome-wide short hairpin RNA screening of jurkat T-cells for human proteins contributing to productive HIV-1 replication

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

Rapid creation and quantitative monitoring of high coverage shRNA libraries

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

A large scale shRNA barcode screen identifies the circadian clock component ARNTL as putative regulator of the p53 tumor suppressor pathway

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

Design of 240,000 orthogonal 25mer DNA barcode probes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

Phosphatidylinositol 3-kinase hyperactivation results in lapatinib resistance that is reversed by the mTOR/phosphatidylinositol 3-kinase inhibitor NVP-BEZ235.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

Topoisomerase levels determine chemotherapy responsein vitroandin vivo

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

Systems analysis of quantitative shRNA-library screens identifies regulators of cell adhesion

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

The art and design of genetic screens: RNA interference.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

Twenty-five years of quantitative PCR for gene expression analysis.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

Cancer proliferation gene discovery through functional genomics.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

Profiling essential genes in human mammary cells by multiplex RNAi screening

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

An shRNA barcode screen provides insight into cancer cell vulnerability to MDM2 inhibitors

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

A genetic screen identifies PITX1 as a suppressor of RAS activity and tumorigenicity

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

A genetic screen for candidate tumor suppressors identifies REST

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

Bioconductor: open software development for computational biology and bioinformatics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

A large-scale RNAi screen in human cells identifies new components of the p53 pathway

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

More powerful procedures for multiple significance testing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

siRNA-mediated AMPKalpha1 subunit gene PRKAA1 silencing enhances methylmercury toxicity in HEK293 cells.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

High-throughput RNAi screening in cultured cells: a user's guide.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3411659

10.1371/JOURNAL.PONE.0042341

27 October 2018

Identifiers

DOI

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1 August 2017

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1 August 2017

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