RNA sequencing of LINC02015 knockdown in human aortic smooth muscle cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE188964 | GEO | 2021/11/18
REPOSITORIES: GEO
Similar Datasets
Project description:Fibroblast-like synoviocytes (FLS) were cultured from synovial tissues from 19 RA patients. RNA was isolated using the Fast Track 2.0 kit (Invitrogen, Carlsbad, California)from the FLS cultures. Fluorescent cDNA probes were prepared from 1 ug experimental mRNA by oligo dT-primed polymerization using Superscript II reverse transcriptase in the presence of Cy5 labeled dCTP. A common reference mRNA sample (CRE) that consists of a mixture of mRNAs isolated from 11 different cell-lines, was labeled with Cy3. The Cy5 and Cy3 labeled cDNAs were pooled and hybridized to a 24,000 cDNA microarray. Set of arrays that are part of repeated experiments Keywords: Biological Replicate
2006-01-19 | GSE4061 | GEO
Project description:Peripheral blood mononuclear cells were collected from the patients. RNA-seq and analysis was performed on the collected samples. Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions(Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined using 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). High-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) is used to construct sequencing library
2024-05-09 | GSE249812 | GEO
Project description:Fibroblast-like synoviocytes (FLS) were cultured from synovial tissues from 19 RA patients. RNA was isolated using the Fast Track 2.0 kit (Invitrogen, Carlsbad, California)from the FLS cultures. Fluorescent cDNA probes were prepared from 1 ug experimental mRNA by oligo dT-primed polymerization using Superscript II reverse transcriptase in the presence of Cy5 labeled dCTP. A common reference mRNA sample (CRE) that consists of a mixture of mRNAs isolated from 11 different cell-lines, was labeled with Cy3. The Cy5 and Cy3 labeled cDNAs were pooled and hybridized to a 24,000 cDNA microarray. Set of arrays that are part of repeated experiments Biological Replicate Using regression correlation
2006-01-18 | E-GEOD-4061 | biostudies-arrayexpress
Project description:RAW 264.7 murine osteoclastic cells were cultured with recombinant cytokines (RANKL and M-CSF) in culture medium with normal sodium (NS; Na=140 mmol/l) and low sodium and reduced sodium (Na=120 mmol.l) while maintaining normal ostmolality with the addition of mannitol. After 24 hours, total RNA was extracted using PureLink kit (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions, and purified using the Rneasy Mini Kit (Invitrogen). 5 µg RNA from each sample was converted into biotin-labeled cDNA and hybridized to GeneChip Mouse Genome 430 2.0 arrays containing 45,101 probe sets corresponding to known genes and expressed sequence tags. Total RNA was extracted using PureLink kit (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions, and purified using the Rneasy Mini Kit (Invitrogen). 5 µg RNA from each sample was converted into biotin-labeled cDNA and hybridized to GeneChip Mouse Genome 430 2.0 arrays containing 45,101 probe sets corresponding to known genes and expressed sequence tags.
2022-08-09 | GSE128152 | GEO
Project description:Gene expression microarray was performed using early log phase culture at 37 degree and 200 rpm followed by RNA extraction from M.tb H37Rv, HigB KO M.tb H37Rv and complemented Hig B KO M.tb H37Rv For gene expression profiling, total RNA was isolated from wild type H37Rv, higB KO mutant strain and complemented strains. The bacterial pellets for M.tb H37Rv wild type, M.tb H37Rv HigB KO mutant strain and complemented strain were resuspended in 1.0 ml TRIzol (Invitrogen Corporation, Carlsbad, CA); mRNA was extracted as per standard protocols and cleaned using RNAeasy columns (Qiagen GmbH, Hilden, Germany). Extracted mRNA (1 μg) was treated with DNase I using the Ambion DNA-free kit (Invitrogen Corporation, Carlsbad, CA) to remove genomic DNA contamination and quantified using Nanodrop 2000c spectrophotometer (Thermo Scientific, USA). The purity and integrity of RNA samples were assessed Agilent 2100 Bio analyzer (Agilent TechnologiesInc., USA). Further, 25ng of RNA was amplified and labeled using Low input Quick Amp WT Labeling kit (Agilent Technologies, USA). The labeled cRNA was purified using RNAeasy columns (Qiagen, USA) and total yields were quantified using Nanodrop 2000c spectrophotometer.
2021-11-30 | GSE179403 | GEO
Project description:Purpose: The present study aimed to investigate the anthocyanin components and identify relevant regulatory genes in purple wheat grain by carrying out transcriptome analyses. Methods: The seeds of purple grain wheat and white grain wheat were collected 30 days after flowering, and three biological replicates were set. Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000. Then synthesizing the fragmented RNA into cDNA through the action of reverse transcriptase, and finally obtaining acDNA library. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol. Results: A total of 10440 diferentially expressed genes were signifcantly enriched by RNA sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed signifcantly enriched flavonoid biosynthesis and anthocyanin biosynthesis in CW_S versus W_S. And the ANS and UFGT genes were predicted as core genes in anthocyanin biosynthesis. Conclusions: Our study represents the detailed analysis of wheat grain transcriptomes, with biologic replicates, generated by RNA-seq technology. Through this study, we speculated that ANS and UFGT genes are the core genes of anthocyanin biosynthesis.The significant differences of these genes affect the synthesis of anthocyanins in wheat grains, and thus affect the grain color of wheat.
2023-04-24 | GSE198515 | GEO
Project description:Total RNA was extracted from CD69-overexpressing NB4 cells and matched control NB4 cells using TRIzol (Thermo Fisher, Cat#15596018). RNA quantity and purity were evaluated using NanoDrop ND-1000, and RNA integrity was confirmed on an Agilent Bioanalyzer 2100, with samples meeting the criteria of concentration >50 ng/µL, total RNA >1 µg, and RIN >7.0. Polyadenylated mRNA was enriched using Dynabeads Oligo(dT) (Thermo Fisher, Cat#25-61005) with two rounds of purification. Fragmentation was performed using the NEBNext Magnesium RNA Fragmentation Module (NEB, Cat#E6150S) at 94°C for 5–7 minutes. First-strand cDNA was synthesized with SuperScript II (Invitrogen, Cat#1896649), and second-strand synthesis used DNA Polymerase I (NEB, Cat#M0209) and RNase H (NEB, Cat#M0297) incorporating dUTP (Thermo Fisher, Cat#R0133) to generate strand-specific libraries. Libraries were end-repaired, A-tailed, ligated to adapters, and size-selected (~300 bp ± 50 bp), followed by UDG treatment and PCR amplification. Sequencing was performed on an Illumina NovaSeq 6000 (PE150). Resulting FASTQ files and processed gene expression matrices are included in this submission.
2026-03-31 | GSE313879 | GEO
Project description:36 cases of UCB and 29 adjacent normal bladder tissues (22 pairs) were derived from patients diagnosed with UCB and received radial cystectomy at Sun Yat-sen University Cancer Center (SYSUCC, Guangzhou, China).Total RNA was isolated using TRIzol® Reagent (Ambion). The RNA concentration and quality were determined with NanoDrop, Qubit and agarose gel analysis. The Dynabeads® mRNA Purification Kit (Ambion) was used to enrich the mRNAs, which were used as templates for RNA-BisSeq library construction. For RNA-BisSeq, bisulfite-treated mRNAs were first subjected to reverse transcription with ACT hexamers and Superscript II Reverse Transcriptase (Invitrogen), and the following processes were carried out with KAPA mRNA Stranded mRNA-Seq Kit (KAPA) according to the manufacturer’s instructions. The libraries were sequenced on the Illumina HiSeq X-Ten platform at Novogene (Tianjin, CA) with paired-end 150 bp read length. The m5C sites were called using meRanCall from meRanTK (FDR < 0.01). The differential m5C sites were detected and the hypermethylated m5C in UCB samples correlates with oncogene mRNA overexpression in UCBs.
2019-07-02 | GSE133622 | GEO
Project description:Human fibroblast monolayers plated at a density of 3 x 104 cells/cm2 in 850 cm2 roller bottles were infected at confluency (day 5 post-seeding) with purified virions of human cytomegalovirus (CMV) strain AD169varATCC (AD) or the AD169 US27/US28 deletion mutant virus RV101 (RV) at a multiplicity of infection of 10. After virus adsorption for 1h at 37C with 5% CO2, the inoculum was removed and the cells were washed twice with culture medium prior to the addition of fresh medium. At 50, 72 and 98 hpi, infected monolayers were harvested, snap-frozen and stored at -80:C until the time course was completed. Uninfected confluent HF cultures were used as reference. mRNA was extracted using the FastTrack. 2.0 mRNA Isolation Kit (Invitrogen, Carlsbad, CA). Only RNA preparations reaching OD260/280 ratio values of 2.0 were used. Labeled cDNA populations were synthesized from 2 microg of mRNA per sample by reverse transcription and simultaneous incorporation of Cy3- (reference sample, green) or Cy5- (infected samples, red) dUTP using an oligo-dT20 primer and the Superscript II Reverse Transcriptase. Reference and sample cDNA populations were mixed and applied on the arrays. Hybridizations were performed at 650C for 16 to 18 h in a custom slide chamber with humidity maintained by a small reservoir of 3x SSC. The arrays were then washed, scanned with a Gene Pix 4000A Scanner, gridded and flagged with Gene Pix Pro 4.0 software before submission to the SMD. Groups of assays that are related as part of a time series. Keywords: time_series_design
2005-08-25 | GSE3194 | GEO
Project description:Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. Total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with NimbleGen one-color DNA labeling kit; 3) Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit; 4) Array scanning using the Axon GenePix 4000B microarray scanner (Molecular Devices Corporation). Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. The 2 gene level files were imported into Agilent GeneSpring GX software (version 11.5.1). Genes that have values greater than or equal to lower cut-off: 100.0 in that at least 1 out of 2 samples (“All Targets Value”) were chosen for data analysis.
2022-07-20 | GSE208583 | GEO