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Hypoxic transcriptomic signature of A549 cells (Agilent microarrays)

ABSTRACT: To assess the transcriptomic response of the LUAD cell line A549 to hypoxia, cells were exposed to 1% (Hx) or 21% O2 (Nx) during 24 hours. Two independent experiments were carried out.

ORGANISM(S): Homo sapiens

PROVIDER: GSE117041 | GEO | 2019/09/04

REPOSITORIES: GEO

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Hypoxic transcriptomic signature of A549 cells (RNA-Seq)

Project description:To assess the transcriptomic response of the LUAD cell line A549 to hypoxia, cells were exposed to 1% (Hx) or 21% O2 (Nx) during 24 hours. Two µg of total RNAs were depleted from ribosomal RNA with the Ribozero kit (epicenter), libraries were generated with the NEBNext Small RNA Library Prep Set for SOLiD and sequenced on SOLiD 5500XL (Life Technologies) with single-end 50bp reads. Reads were aligned to the human genome release hg19 with the LifeScope software v2.5.1 (Life Technologies) using whole transcriptome pipeline for RNA‐seq libraries with default parameters.

2019-09-04 | GSE117048 | GEO

Impact of NLUCAT1 deletion on A549 cells in normoxic and hypoxic conditions

Project description:Three independent parental or NLUCAT1 CRISPR/Cas9-deleted A549 clones were cultured in normoxia (Nx) or exposed to hypoxia (Hx) at 1% O2 for 24 hours.

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Hypoxic transcriptomic signature of A549 cells (Agilent microarrays)

Project description:Hypoxic transcriptomic signature of A549 cells (Agilent microarrays)

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RNA-seq profiling of parental and NLUCAT1-deleted A549 cells under hypoxia

Project description:Parental or NLUCAT1 CRISPR/Cas9-deleted A549 clones (WT A549 Hx, n = 1 clone; DEL A549 Hx, n = 1 clone) were exposed to hypoxia (Hx) at 1% O2 for 24 hours. Libraries were generated from 500 ng of total RNAs using TruSeq Stranded Total RNA kit with Ribo-Zero (Illumina) and sequenced on a NextSeq500 sequencer (Illumina) with 2x75bp paired-end chemistry. Reads were aligned to the human genome release hg19 using STAR v2.4.0a with default parameters.

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Hypoxic transcriptomic signature of A549 cells (RNA-Seq)

Project description:Hypoxic transcriptomic signature of A549 cells (RNA-Seq)

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Profile of mRNAs associated with Ago (Argonaute) 1 in normoxic and hypoxic endothelial cells

Project description:Messenger RNAs that are bound to Ago1 is to be transcriptionally or translational suppressed. Therefore the changes in Ago1-associated transcripts indicate the changes of suppression of these genes. We used microarrays to detail changes of mRNA transcripts that are associated with Ago1 in endothelial cells under normoxia and hypoxia conditions. Human umbilical vein endothelial cells pooled from 8 different sources were subjected to normoxia (21% oxygen, Nx) or hypoxia (2% hypoxia, Hx) for 24 hr. Ago1 was immunoprecipitated with mouse anti-human Ago1 using a lysis buffer containing 0.1% NP-40. The associated RNA was extracted and hybridized on Affymetrix Human Gene 1.0 ST arrays.

2013-06-30 | E-GEOD-43165 | biostudies-arrayexpress

RNA-seq of human adipose-derived mesenchymal stem cells cultured in hypoxia against normoxia controls, and human tympanic membrane keratinocytes

Project description:Human adipose-derived mesenchymal stem cells were cultured either in hypoxia (Hx; <0.1% oxygen) or standard culture conditions (normoxia, Nx) over 48 hours in serum-free medium. Human tympanic membrane keratinocytes were cultured in standard culture conditions over 48 hours in serum-free medium.

2022-03-31 | E-MTAB-9979 | biostudies-arrayexpress

Genome-wide effect of conditioned media supernatant (CMS) derived from human endometrial stromal cells treated by long-acting progestin-only contraceptives (LAPCs) on Human endometrial endothelial cells

Project description:Analysis of differential gene expression in Human endometrial endothelial cells (HEECs) incubated with CMS derived from human endoemtrial stromal cells (HESCs) treated by LAPCs. We tested the hypothesis that paracrine factors sectreted from HESCs treated LAPCs, etonogestrol (ETO) or medorxyprogesterone acetate (M) influence several common genes associated with survival in HEECs. Thefore, whole genome analyses were performed in HEECs treated with HESC derived CMS obtained from vehicle (estrodial (E) as control) or progesterone (P) or ETO or M incubations under hypoxia (HX) and normoxia (NX). Results provide important information of several common and unique gene expression profiles in cultured HEECs treated with HESC CMS from P or ETO or M incubations. Among M and ETO responsive genes, up- or down-regulated survival related common genes were determined and used further confirmation and in vitro functional analyses. Total RNA (n=3) obtained from cultured HEECs incubated 6h with vehicle- or P4- or ETO- or MPA- treated NX or HX conditioned HESC-derived CMS.

2014-03-08 | E-GEOD-55691 | biostudies-arrayexpress

Circ101093 regulated proteins in Lung carcinoma (LUAD) cells.

Project description:Circ101093 was knocked down in A549 LUAD cell lines, and overexpressed in H1975 LUAD cell lines. Then, downregulated proteins in A549 cell lines and upregulated proteins in H1975 cell lines were analyzed.

2022-05-20 | PXD025491 | Pride

Extended analysis of benchmark datasets for Agilent two-color microarrays.

Project description:BackgroundAs part of its broad and ambitious mission, the MicroArray Quality Control (MAQC) project reported the results of experiments using External RNA Controls (ERCs) on five microarray platforms. For most platforms, several different methods of data processing were considered. However, there was no similar consideration of different methods for processing the data from the Agilent two-color platform. While this omission is understandable given the scale of the project, it can create the false impression that there is consensus about the best way to process Agilent two-color data. It is also important to consider whether ERCs are representative of all the probes on a microarray.ResultsA comparison of different methods of processing Agilent two-color data shows substantial differences among methods for low-intensity genes. The sensitivity and specificity for detecting differentially expressed genes varies substantially for different methods. Analysis also reveals that the ERCs in the MAQC data only span the upper half of the intensity range, and therefore cannot be representative of all genes on the microarray.ConclusionAlthough ERCs demonstrate good agreement between observed and expected log-ratios on the Agilent two-color platform, such an analysis is incomplete. Simple loess normalization outperformed data processing with Agilent's Feature Extraction software for accurate identification of differentially expressed genes. Results from studies using ERCs should not be over-generalized when ERCs are not representative of all probes on a microarray.

| S-EPMC2174956 | biostudies-literature

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