Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Variation in RNA expression in a panel of 30 breast cancer cell lines

ABSTRACT: RNA expression was measured using RNA sequencing in 30 different breast cancer cell lines, under untreated, exponentially growing conditions.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Homo sapiens

SUBMITTER: Katarzyna Jastrzebski

PROVIDER: E-MTAB-4801 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Integrative Modeling Identifies Key Determinants of Inhibitor Sensitivity in Breast Cancer Cell Lines.

Jastrzebski Katarzyna K Thijssen Bram B Kluin Roelof J C RJC de Lint Klaas K Majewski Ian J IJ Beijersbergen Roderick L RL Wessels Lodewyk F A LFA

Cancer research 20180529 15

Cancer cell lines differ greatly in their sensitivity to anticancer drugs as a result of different oncogenic drivers and drug resistance mechanisms operating in each cell line. Although many of these mechanisms have been discovered, it remains a challenge to understand how they interact to render an individual cell line sensitive or resistant to a particular drug. To better understand this variability, we profiled a panel of 30 breast cancer cell lines in the absence of drugs for their mutations ...[more]

PMID: 29844118

Similar Datasets

Characterization of two urea-utilizing pathways in coral reef ecosystems: implications for the significance of the urea cycle in facing global warming

Project description:Urea can serve as nitrogen source for coral holobionts and plays a cruscial role in coral calcification, although the degradation of urea by coral symbionts is not fully understood. In this study, we investigated the urea utilized pathway and the responses of the Symbiodiniaceae family to urea under high temperature conditions. Genome screening revealed that all Symbiodiniaceae species contain the urease (URE) and DUR2 subunit of urea amidolyase (UAD) system. However, only three speciesCladocopium goreaui, Cladopium c92, and Symbiodinium pilosum possess a complete UAD system, including both DUR1 and DUR2. Phylogentic analyses revealed that the UAD system in Symbiodiniaceae clusters more closely with symbiotic bacteria, indicating that horizontal gene transfer of UAD system has occured in coral symbionts. Physiology analysis showed that the symbiodiniacean species Cladocopium goreaui, which containing both URE and UAD, grew better under urea than ammonium conditions, as indicated by higher maximum specific growth rates. Furthermore, most genes of Symbiodiniaceae involved in urea utilization appeared to be stable under various conditions such as heat stress (HS), low light density, and nitrogen deficiency, wheras in ammonium and nitrate transporters were significantly regulated. These relatively stable molecular regulatory properties support sustained urea absorption by Symbiodiniaceae, as evidenced by an increase in δ15N2-urea absorption and the decreases in δ5N-NO3-, and δ15N-NH4+ from cultural environment to Symbiodiniaceae under HS conditions. Token together, this study reveals two distinct urea utilization systems in coral ecosystem and highlights the importance of the urea cycle in coral symbionts when facing fluctuating nitrogen environment in future warming ocean.

2024-09-27 | PXD056312 | Pride

RNA-seq of coding RNA of Staphylococcus aureus USA300 wild type strain before and after 30 min of exposure to 1.5 mM in RPMI HOCl stress during the log phase in RPMI media

Project description:Staphylococcus aureus USA300 wild type strain was cultivated in RPMI medium in 3 biological replicates and harvested at an OD500 of 0.5 before (as control) and at 30 min after exposure to 1.5 mM in RPMI HOCl stress. Cells were disrupted in 3 mM EDTA/ 200 mM NaCl lysis buffer with a Precellys24 ribolyzer followed by RNA isolation using the acid phenol extraction protocol as described. The RNA quality was approved by Trinean Xpose (Gentbrugge, Belgium) and the Agilent RNA Nano 6000 kit using an Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the rRNA. TruSeq Stranded mRNA Library Prep Kit from Illumina (San Diego, CA, USA) was applied to prepare the cDNA libraries. The cDNAs were sequenced paired end on an Illumina HiSeq 1500 (San Diego, CA, USA) using 70 and 75 bp read length and a minimum sequencing depth of 10 million reads per library. The paired end cDNA reads were mapped to the Staphylococcus aureus USA300 genome sequence (accession number FPR3757_CP255) using bowtie2 v2.2.7 (Langmead and Salzberg, 2012) with default settings for paired-end read mapping. All mapped sequence data were converted from SAM to BAM format with SAMtools v1.3 (Li et al., 2009) and imported to the software ReadXplorer v.2.2 (Hilker et al., 2016).

2023-09-30 | E-MTAB-13313 | biostudies-arrayexpress

RNA-seq of coding RNA of Staphylococcus aureus wild type strain before and after 30 min of exposure to 13 mM itaconic acid stress reveals adaption to the immunometabolite itaconate by inducing acid and oxidative stress responses

Project description:S. aureus COL was cultivated in RPMI medium in 3 biological replicates and harvested at an OD500 of 0.5 before (as control) and at 30 min after exposure to 13 mM itaconic acid stress. Cells were disrupted in 3 mM EDTA/ 200 mM NaCl lysis buffer with a Precellys24 ribolyzer followed by RNA isolation using the acid phenol extraction protocol as described. The RNA quality was approved by Trinean Xpose (Gentbrugge, Belgium) and the Agilent RNA Nano 6000 kit using an Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the rRNA. TruSeq Stranded mRNA Library Prep Kit from Illumina (San Diego, CA, USA) was applied to prepare the cDNA libraries. The cDNAs were sequenced paired end on an Illumina HiSeq 1500 (San Diego, CA, USA) using 70 and 75 bp read length and a minimum sequencing depth of 10 million reads per library.

2023-09-10 | E-MTAB-13287 | biostudies-arrayexpress

RNA-seq of coding RNA of Staphylococcus aureus COL wild type strain before and after 30 min of exposure to 176 μM neutrophil-derived oxidant hypothiocyanous acid (HOSCN) during exponential phase of an OD540 of 0.5 in LB medium

Project description:Staphylococcus aureus COL wild type strain was cultivated in LB medium in 3 biological replicates and harvested at an OD500 of 0.5 before (as control) and at 30 min after exposure to 1176 μM neutrophil-derived oxidant hypothiocyanous acid (HOSCN) stress. Cells were disrupted in 3 mM EDTA/ 200 mM NaCl lysis buffer with a Precellys24 ribolyzer followed by RNA isolation using the acid phenol extraction protocol as described. The RNA quality was approved by Trinean Xpose (Gentbrugge, Belgium) and the Agilent RNA Nano 6000 kit using an Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the rRNA. TruSeq Stranded mRNA Library Prep Kit from Illumina (San Diego, CA, USA) was applied to prepare the cDNA libraries. The cDNAs were sequenced paired end on an NextSeq 500 (San Diego, CA, USA) using 75 bp read length and a minimum sequencing depth of 8 million reads per library. The paired end cDNA reads were mapped to the Staphylococcus aureus COL genome sequence (accession number CP000046) using bowtie2 v2.2.7 (Langmead and Salzberg, 2012) with default settings for paired-end read mapping. All mapped sequence data were converted from SAM to BAM format with SAMtools v1.3 (Li et al., 2009) and imported to the software ReadXplorer v.2.2 (Hilker et al., 2016).

2023-09-30 | E-MTAB-13314 | biostudies-arrayexpress

Akkermanisa muciniphila response to oxygen exposure

Project description:The anaerobic gut microbe Akkermansia muciniphila ATCC BAA-835 lives in the mucus layer where it is exposed to oxygen. To investigate how it survives the changing oxygen concentrations, we exposed a exponentially growing culture to oxygen. The experiment was performed in parallel fermentor systems. To one system we added 0.2l/h oxygen after the culture reached an OD of 0.1, while the other remained anaerobic. Samples were taken just before addition of oxygen, about 1h after and when the cell reached stationary phase.

2016-09-30 | E-MTAB-5111 | biostudies-arrayexpress

RNA-Seq analysis of KLF3 knockout E14.5 TER119+ (erythroid) murine fetal liver cells

Project description:The aim of this study was to analyze the transcriptome of TER119+ fetal liver cells in the absence of the transcription factor KLF3 at murine embryonic day E14.5 Three wildtype (WT; Klf3+/+) and three knockout (KO; Klf3-/-) samples

2014-02-23 | E-GEOD-50554 | biostudies-arrayexpress

A serum microRNA panel as potential biomarkers for hepatocellular carcinoma related with hepatitis B virus

Project description:Background: The identification of new high sensitivity and specificity markers for HCC are essential. We aimed to identify serum microRNAs for diagnosing hepatitis B virus (HBV) â??related HCC. Methods: Serum microRNA expression was investigated with four cohorts including 667 participants (261 HCC patients ,233 cirrhosi patients and 173 healthy controls), recruited between August 2010 and June 2013. First, An initial screening of miRNA expression by Illumina sequencing was performed using serum samples pooled from HCC patients and controls,respectively. Quantitative reverse-transcriptase polymerase chain reaction assay was then applied to evaluate the expression of selected microRNAs. A logistic regression model was constructed using a training cohort (n=357) and then validated using a cohort(n=241). The area under the receiver operating characteristic curve (AUC) was used to evaluate diagnostic accuracy. Results: , We identified 8 miRNAs(hsa-miR-206, hsa-miR-141-3p, hsa-miR-433-3p, hsa-miR-1228-5p, hsa-miR-199a-5p, hsa-miR-122-5p, hsa-miR-192-5p and hsa-miR-26a-5p.) formed a miRNA panel that provided a high diagnostic accuracy of HCC (AUC=0.887 and 0.879 for training and validation data set, respectively). The microRNA panel can also differentiate HCC from healthy (AUC =0.894) and cirrhosis (AUC = 0.892), respectively. Conclusions:We found a serum microRNAs panel that has considerable clinical value in diagnosing HCC. 9 serum samples pooled from 3 healthy control donors and 3 HCC patients, 3 cirrhosi patients treated at The First Affiliated Hospital of Soochow University were subjected to Illumina HiSeq 2000 deep sequencing to identify the miRNAs that were significantly differentially expressed.

2015-12-20 | E-GEOD-59418 | biostudies-arrayexpress

Tet1 and Tet2 mediate epigenetic regulation of developmental genes by protecting DNA methylation canyons against hypermethylation [RNA-Seq]

Project description:This study uses whole-transcriptome sequencing to characterize the transcriptomes of mouse embryonic fibroblasts (MEF's). Two conditions were analyzed, MEF cells with intact TET1/TET2 enzymes (WT) and MEF cells with TET1/TET2 knocked out (DKO). Our results identify sets of differentially expressed genes which are correlated with TET1/TET2 induced methylation changes of the corresponding genes. Whole transcriptome analysis of M. musculus MEF cells. Two conditions were sequenced and analyzed, the first is wild type (WT), the second corresponds to knock-out of TET1 and TET2 enzymes.

2015-12-07 | E-GEOD-58609 | biostudies-arrayexpress

Liver transcriptome profile associated with feed efficiency in Nellore Cattle (Bos indicus)

Project description:8 animals of high feed efficiency and 8 animals of low feed efficiency, selected by the measure of residual intake and body weight gain at the end of a feeding trial, had their liver samples collected by biopsy and sequenced in a Illumina HiSeq2500 plataform

2015-03-16 | E-MTAB-3376 | biostudies-arrayexpress

Circadian 30-h time-course RNA-seq study of SW480 and SW620 cells

Project description:A 30-h time-course RNA-seq study was performed to analyse the different circadian phenotypes of SW480 and SW620 cells, a cell line from a primary tumour and a metastatic cell line from the same patient. Samples were taken every 3 h for a period of 30 h resulting in 11 time-points for each cell line.

2019-10-16 | E-MTAB-7779 | 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