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Next Generation Sequencing Facilitates Quantitative Analysis of transcriptomes in ARP-1 cells treated with DMSO and carfilzomib (Cfz)

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of transcriptomes in ARP-1 cells treated with DMSO and carfilzomib (Cfz)

PROVIDER: PRJNA600307 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10861685.fastq.gz	Fastqsanger.gz
	SRR10861686.fastq.gz	Fastqsanger.gz
	SRR10861687.fastq.gz	Fastqsanger.gz
	SRR10861688.fastq.gz	Fastqsanger.gz
	SRR10861689.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of transcriptomes in ARP-1 cells treated with DMSO and carfilzomib (Cfz)

Project description:The goals of NGS-derived retinal transcriptome profiling (RNA-seq) is to identify the signaling pathways in multiple myeloma (MM) cells affected by Cfz treatment. We treated ARP-1 MM cells with DMSO or 6nM Cfz for 16 hours (each group has 3 replicates) and extracted the total RNA using RNeasy Mini Kit (Qiagen). 5-10 µg RNA samples were sent to BGI genomics for RNA-seq followed by data analysis.

2020-05-07 | GSE143406 | GEO

Comparison of the gene expression profiles of carfilzomib-resistant derivatives versus parental human myeloma cell lines

Project description:KMS-11 and KMS-34 cells were exposed to stepwise increasing concentrations of carfilzomib over a period of 18 weeks: cells adapted to growth in 4 nM carfilzomib by 4 weeks, in 6 nM in another 6 weeks and in 12 nM after a further 8 weeks. The resulting cell cultures, denoted KMS-11/Cfz and KMS-34/Cfz, respectively, retained resistance to carfilzomib even when tested after removal of selective pressure for approximately 8 weeks. KMS-11/Cfz and KMS-34/Cfz cells were profiled for gene expression after 1 week of growth in the absence of carfilzomib together with parental KMS-11 and KMS-34 cells which had not been selected in the drug (triplicate samples).

2015-07-09 | E-GEOD-69078 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of transcriptomes in MM.1S cells treated with DMSO, All-trans retinoic acid (ATRA), carfilzomib (Cfz), and their combinations

Project description:ATRA is important for sensitizing MM cells to Cfz. To determine what signalling pathways are affected by ATRA+Cfz in MM cells, MM.1S MM cell line was pulsed with Cfz and then cultured with DMSO or 10µM ATRA for 12 h. Total RNAs of 2 x 106 MM.1S cells for each sample were extracted by RNeasy Mini Kit (Qiagen). 5-10 µg RNA samples were sent to Cancer Genomics Center at The University of Texas (Houston, TX) for genearray followed by data analysis. We use gene experssion profiling data to determine differential expression of genes in MM cells in culture with DMSO, ATRA, Cfz or ATRA+Cfz.

2021-12-31 | GSE178340 | GEO

Effect of Carfilzomib and/or Spautin on proteome ubiquitination

Project description:Jurkat cells were treated with either Carfilzomib (CFZ) or DMSO for 1h before Spautin-1 or DMSO as a control were added for 4 h. As an additional condition, Cells were treated only with CFZ for 1h before being harvested. This experiment should show the potential alterations of protein ubiquitination caused by the respective compounds and the effect of CFZ on the ubiquitome after 1 and 5h.

2025-05-31 | PXD062845 | Pride

Expression data from DMSO- and ATRA-treated human multiple myeloma (MM) cells

Project description:All-trans retinoic acid (ATRA) is important for sensitizing MM cells to carfilzomib (Cfz). To determine what signalling pathways are affected by ATRA in Cfz-treated MM cells, MM.1S MM cell line was pulsed with Cfz and then cultured with DMSO or 10µM ATRA for 12 h. Total RNAs of 2 x 106 MM.1S cells were extracted by RNeasy Mini Kit (Qiagen). 5-10 µg RNA samples were sent to Gene Expression and Genotyping Facility at Case Western Reserve University (Cleveland, OH) for genearray followed by data analysis. We use microarray data to determine differential expression of genes in Cfz-treated MM cells in culture with DMSO and ATRA.

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Comparison of the gene expression profiles of carfilzomib-resistant derivatives versus parental human myeloma cell lines

2015-07-09 | GSE69078 | GEO

Electroacupuncture at PC6 Acupoint Adjusts Genome-Wide Gene Expressions and Alters Carfilzomib-Induced Cardiotoxicity in Mice

Project description:Carfilzomib (CFZ) is a proteasome inhibitor commonly used in the treatment of multiple myeloma, but its clinical application is limited due to its cardiotoxicity. The Neiguan acupoint (PC6) stimulation has been reported to effectively improve cardiac function, but its regulatory mechanism remains unclear. The aim of this study was to investigate the effect and underlying mechanism of electroacupuncture (EA) against CFZ-induced cardiotoxicity in C57BL/6 mice. According to our results, EA treatment significantly reversed CFZ-induced ejection fraction and fractional shortening reduction, which showed great potential effect for heart protection. By using RNA-sequencing, we compared the transcriptome profile of heart samples from DMSO control, CFZ injection, and EA treatment mice, and nearly 40,000,000 valid sequence reads aligned with 20,000 genes from six libraries were obtained. A total of 770 differentially expressed genes (DEGs) were identified in the CFZ (vs. Control) group, including 65 up-regulated and 705 down-regulated genes. Meanwhile, 329 DEGs were obtained in the EA (vs. CFZ) group, including 251 up-regulated and 78 down-regulated genes. Our results shed new insights into the regulatory mechanism of EA at PC6 against CFZ-induced cardiotoxicity, which could further provide theoretical basis for clinical EA therapy.

2025-09-01 | GSE243878 | GEO

Comparative expression analysis of carfilzomib-resistant and parental LP-1 human multiple myeloma cells

Project description:LP-1 cells were exposed to stepwise increasing concentrations of carfilzomib over a period of 18 weeks: cells adapted to growth in 4 nM carfilzomib by 4 weeks, in 6 nM in another 6 weeks and in 12 nM after a further 8 weeks. The resulting cell culture, denoted LP-1/Cfz, retained resistance to carfilzomib even when tested after removal of selective pressure for approximately 8 weeks.

2016-09-13 | GSE78069 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of transcriptomes in MM.1S cells treated with DMSO, All-trans retinoic acid (ATRA), carfilzomib (Cfz), and their combinations

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of transcriptomes in MM.1S cells treated with DMSO, All-trans retinoic acid (ATRA), carfilzomib (Cfz), and their combinations

| PRJNA738516 | ENA

Differential protein expression between Carfilzomib-sensitive (AMO1) and resistant (AMO1-CFZ) multiple myeloma cells

Project description:Carfilzomib-sensitive (AMO1) and resistant (AMO1-CFZ) MM cells were grown in RPMI-1640 medium supplemented with 10 % FBS and 0.68 mM L-glutamine, in a humidified incubator at 5% CO2 and 37 °C. The AMO1-CFZ medium was additionally added 90 nM CFZ, while the CFZ sensitive AMO1 cells were added vehicle (0.009 % DMSO) only. AMO1-CFZ was either harvested directly or grown for 1 week in CFZ free medium (vehicle only) prior to harvest. AMO1 and carfilzomib-resistant AMO1-CFZ cells were resuspended in 100 µl 1% sodium deoxycholate, 100 mM Tris-HCl pH 8.5, 10 mM tris(2-carboxyethyl)phosphine (TCEP), 40 mM chloroacetamide (CAA), heated at 90 °C for 45 min and sonicated for 10 cycles (30 s ON/30 s OFF) using a Bioruptor pico sonicator. After centrifugation at 16000 × g for 10 min, 50 µg soluble protein from each sample was added 100 µl 0.1M ammonium bicarbonate, 0.5 µg trypsin and digested overnight at 37°C. Peptides were desalted using C18 spin columns, dried in a speedvac centrifuge and resuspended in 0.1% formic acid prior to MS analysis. Label-free quantitatative (LFQ) LC-MS/MS was performed on a timsTOF Pro (Bruker Daltonics) connected to a nanoElute (Bruker Daltonics) HPLC. Peptides were separated over a Bruker PepSep C18 (75 µm × 15 cm) column with running buffers A (0.1 % formic acid) and B (0.1 % formic acid in acetonitrile) using a 100 min gradient from 2 % B to 40 % B. The timsTof instrument was operated in the DDA PASEF mode with 10 PASEF scans per acquisition cycle and accumulation and ramp times of 100 ms each. The ‘target value’ was set to 20000 and dynamic exclusion was activated and set to 0.4 min. The quadrupole isolation width was set to 2 Th for m/z < 700 and 3 Th for m/z > 800.

2024-06-07 | PXD045439 | Pride

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