Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

293_hORF3.1_drug_treatments_partIII

ABSTRACT: The human ORFeome collection version 3.1 was stably integrated into HEK293 (lentivirus based). The cells harboring the collection were harvested, collection specific DNA was amplified and sequenced to assess the collection representation.

INSTRUMENT(S): Illumina MiSeq

ORGANISM(S): Homo sapiens

SUBMITTER: Anthony Arnoldo

PROVIDER: E-MTAB-2498 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Codon and amino acid identity are major determinants of mRNA stability in humans

Project description:To investigate the effects of the coding sequence on mRNA decay, we globally analyzed the stability of endogenous mRNAs as well as those derived from the human ORFeome collection, which contains full-length coding sequences in the context of invariant UTRs.

2019-09-22 | GSE123165 | GEO

293_hORF3.1_drug_treatments

Project description:Identification of human ORFs conferring resistance to various drug treatments when overexpressed into HEK293-M2, assessed by microarrays

2014-05-15 | E-MTAB-2493 | biostudies-arrayexpress

Amplicon Sequencing of gRNAs from Druggable Genome CRISPR mutagenized Huh7.5.1 cells after live/dead selection with DENV2

Project description:Huh7.5.1 cells were stably transduced with lentiCas9-Blast (Addgene, #52962) and subsequently selected using Blasticidin. Then, Huh7.5.1 cells that constitutively express Cas9 were transduced with lentiGuide-Puro from the druggable genome library at MOI 0.3. Cells were then selected with puromycin, expanded, and then pooled together and cryofrozen in aliquots. Cells were thawed constituting over 1000× genome coverage worth of mutagenized library. The cells were infecting with DENV2_429557 and DENV-2_16681_Hap1-adapted at MOI of 0.1. Virus-resistant colonies were harvested. The uninfected reference used was the unselected starting population. The unselected and selected cells were both processed with QIAamp DNA columns to purify the gDNA. A first round of PCR was used to amplify the guide RNA sequences encoded in the gDNA, followed by a second round of PCR to add the barcodes/adapters for amplicon sequencing. 2% agarose gels and a QIAquick gel extraction kit were used to purify the amplicons. The amplicons were then subjected to next-generation sequencing on a HiSeq instrument lane (Illumina) via Novogene.

2024-12-29 | E-MTAB-14693 | biostudies-arrayexpress

Conformational plasticity of RAS Q61 family of neoepitopes results in distinct features for targeted recognition.

Project description:We utilize hydrogen deuterium exchange mass spectrometry (HDX-MS) to probe the solvation and conformational dynamics of HLA-A*01:01/hβ2m complexes that are emptied or loaded with NRAS Q61K peptide, as well as wild-type (Q61) and three additional, common neoepitopes (Q61H, Q61L, Q61R).

2023-11-30 | PXD044838 | Pride

Amplicon Sequencing of gRNAs from Brunello CRISPR mutagenized HT29-DKO cells after live/dead selection with PeV-A1 and PeV-A2

Project description:HT29-DKO cells were stably transduced with lentiCas9-Blast (Addgene, #52962) and subsequently selected using Blasticidin. Then, 300 million HT29-DKO cells that constitutively express Cas9 were transduced with lentiGuide-Puro from the Brunello library at MOI 0.3. Cells were then selected with puromycin, expanded to 3 billion cells, and then pooled together and cryofrozen in aliquots. One hundred million cells were thawed constituting over 1000× genome coverage worth of mutagenized library. The cells were infecting with PeV-A1 or PeV-A2 at an MOI of 0.1. Virus-resistant colonies were harvested. The uninfected reference used was the unselected starting population. The unselected and selected cells were both processed with QIAamp DNA columns to purify the gDNA. A first round of PCR was used to amplify the guide RNA sequences encoded in the gDNA, followed by a second round of PCR to add the barcodes/adapters for amplicon sequencing. 2% agarose gels and a QIAquick gel extraction kit were used to purify the amplicons. The amplicons were then subjected to next-generation sequencing on a HiSeq instrument lane (Illumina) via Novogene.

2024-03-16 | E-MTAB-13894 | biostudies-arrayexpress

Amplicon Sequencing of gRNAs from Brunello CRISPR mutagenized A549 and U87-MG cells after live/dead selection with EV-D68 IL

Project description:With the near eradication of poliovirus due to global vaccination campaigns, attention has shifted to other enteroviruses that can cause polio-like paralysis syndrome (now termed acute flaccid myelitis (AFM)). In particular, enterovirus D68 (EV-D68) is believed to be the main driver of epidemic outbreaks of AFM in recent years, yet not much is known about EV-D68 host interactions. EV-D68 is a respiratory virus but, in rare cases, can spread to the central nervous system to cause severe neuropathogenesis. We use genome-scale CRISPR screens to identify genes important for EV-D68 infection. A549 and U87-MG cells were stably transduced with lentiCas9-Blast (Addgene, #52962) and subsequently selected using Blasticidin. Then, 300 million cells that constitutively express Cas9 were transduced with lentiGuide-Puro from the Brunello library (MOI 0.3). Cells were then selected with puromycin, expanded to 3 billion cells, and then pooled together and cryofrozen in aliquots. One hundred million cells were thawed constituting over 1000× genome coverage worth of mutagenized library,expanded, and seeded for the screens. Each screen had over 500x genome coverage. The cells were infected with EV-D68 IL (BEI USA/2014/18952) (MOI 0.1). Virus-resistant colonies were harvested. The uninfected reference used was the unselected starting population. The unselected and selected cells were both processed with QIAamp DNA columns to purify the gDNA. A first round of PCR was used to amplify the guide RNA sequences encoded in the gDNA, followed by a second round of PCR to add the barcodes/adapters for amplicon sequencing. 2% agarose gels and a QIAquick gel extraction kit were used to purify the amplicons. The amplicons were then subjected to next-generation sequencing on a HiSeq instrument lane (Illumina) via Novogene.

2025-02-25 | E-MTAB-14765 | biostudies-arrayexpress

Project description:Candida albicans ORFeome

| PRJNA472959 | ENA

Comparative genomic hybridization of wild type yeast isolated from clinical samples and wine fermentations to investigate genetic variability in yeast from different ecological niches

Project description:Using microarrays targeting the complete ORFeome of Saccharomyces cerevisiae S288c, this study investigates the genetic variability present in wild type yeast from different ecological niches by comparative genome hybridization on array (aCGH). Genomic DNA of Saccharomyces strains isolated from clinical samples and strains from wine fermentations, either commercially available or isolated form spontaneous wine fermentations, was compared to genomic DNA of the sequenced laboratory strain S288c, using a common reference experimental design, with two dye-swap replicate hybridizations for each strain and six S288c self-self hybridizations for background noise estimation, in a total of 38 hybridizations.

2008-10-01 | E-MTAB-29 | biostudies-arrayexpress

DNA binding proteome changes in response to loss of glycosylation in Burkholderia Cenocepacia

Project description:Comparsion of DNA interacting proteome of BC muants to assess chnages in transcriptional proteins. Four strain comparsion between WT vs delta pglL vs delta ogc vs delta pglL complemented AmrAB::S7-pglL-his. LFQ based quantification

2019-11-01 | PXD014700 | Pride

The SaeR/S Gene Regulatory System is Essential for Innate Immune Evasion by Staphylococcus aureus

Project description:Methicillin-resistant Staphylococcus aureus (MRSA) is problematic both in hospitals and the community. Currently, we have limited understanding of mechanisms of innate immune evasion used by S. aureus. To that end, we created an isogenic deletion mutant in strain MW2 (USA400) of the saeR/S two-component gene regulatory system and studied its role in mouse models of pathogenesis and during human neutrophil interaction. In this study, we demonstrate saeR/S plays a distinct role in S. aureus pathogenesis and is vital for virulence of MW2 in a mouse model of sepsis. Moreover, deletion of saeR/S significantly impaired survival of MW2 in human blood and after neutrophil phagocytosis. Microarray analysis of genes influenced by saeR/S demonstrated SaeR/S of MW2 influences a wide variety of genes with diverse biological functions. These data shed new insight into how virulence is regulated in S. aureus and associates a specific staphylococcal gene-regulatory system with invasive staphylococcal disease. Wild type control vs mutant at two different growth phases

2010-05-14 | E-GEOD-15067 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data