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Next Generation Sequencing Facilitates Quantitative Analysis of HaCaT and OSM-treated HaCaT Transcriptomes

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of HaCaT and OSM-treated HaCaT Transcriptomes

PROVIDER: PRJNA634341 | ENA |

REPOSITORIES: ENA

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Next Generation Sequencing Facilitates Quantitative Analysis of HaCaT and OSM-treated HaCaT Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling (RNA-seq) between HaCaT cell and OSM-treated HaCaT cells Methods: mRNA profiles of HaCaT cells and OSM-treated HaCaT cells were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.

2021-03-18 | GSE150994 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Primary Keratinocytes and OSM-treated Primary Keratinocytes Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling (RNA-seq) between Primary Keratinocytes and OSM-treated Primary Keratinocytes Methods: mRNA profiles of Primary Keratinocytes and OSM-treated Primary Keratinocytes were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.

2021-03-18 | GSE151174 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Primary Keratinocytes and OSM-treated Primary Keratinocytes Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Primary Keratinocytes and OSM-treated Primary Keratinocytes Transcriptomes

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Next Generation Sequencing Facilitates Quantitative Analysis of WT MRSA USA300 Infected HEKn and HaCaT Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Method: HaCaTs and primary keratinocytes were infected with WT USA300 S. aureus (MOI 100:1) for 1 hour before cell lysates were prepared. Poly-A pull-down was used to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and to proceed to library preparation by using Illumina TruSeq RNA prep kit. Libraries were then sequenced using Illumina HiSeq2500 at Columbia Genome Center. The samples were multiplexed in each lane, which yields targeted number of singleend/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane. The raw read files were not available for submission because they have been deleted by the core facility. Results: Using an optimized data analysis workflow, we identified 15,780 transcripts in the skin of both HEKn and HaCaT cells. Expression values were analyzed using Ingenuity Pathway Analysis (IPA). Conclusions: Our study represents the first detailed analysis of HEKn and HaCaT transcriptomes, with biologic replicates, generated by RNA-seq technology after WT MRSA USA300 infection. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2017-02-21 | GSE95080 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of UVB(20mJ/cm2 and 40mJ/cm2) exposed and untreated HaCaT keratinocytes Transcriptomes

Project description:Purpose: To compare the transcriptomes of UVB (20mJ/cm2 and 40mJ/cm2) exposed and untreated HaCaT keratinocytes by RNA-Seq analysis, trying to find differences in gene expression between UVB exposed and untreated of keratinocytes and then elucidate the candidate genes that may play important roles in the differentiation of UVB-induced damage in keratinocytes. Methods: HaCaT keratinocytes were subjected to 20mJ/cm2 and 40mJ/cm2 UVB irradiation. Results: To better understand the effects of UVB (20 mJ/cm2), mRNA-sequecing (n=3) were completed by Novogene Inc. A total 891 differentially expressed genes (DEGs) were identified between UV group and control group with 604 down-regulated and 287 up-regulated. A total of 4036 differentially expressed genes (DEGs) which compared with untreated group were identified by RNA-Seq, which provided abundant data for further analysis.

2019-10-12 | GSE138800 | GEO

Next-generation sequencing facilitates quantitative analysis of wild-type and Nrl(-/-) retinal transcriptomes.

Project description: Not available

| S-EPMC3233386 | biostudies-literature

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and SMAD4 Y95 Mutation Transcriptomes

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2018-10-22 | GSE121188 | GEO

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2021-02-27 | GSE164382 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Normal Human Kidney Transcriptomes

Project description:Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived normal human kidney transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis The kidney tissue was immediately placed and stored in RNAlater® (Ambion), according to the manufacturer’s instruction. The tissue was manually microdissected under microscope in RNAlater® pool for glomerular and tubular compartment. Dissected tissue was homogenized and RNA was prepared using RNAeasy mini columns (Qiagen, Valencia, CA, US), according to the manufacturer’s instructions. RNA quality and quantity were determined using the Laboratory-on-Chip Total RNA PicoKit Agilent BioAnalyzer. Only samples without evidence of degradation were further used (RNA Integrity Number >6).

2014-08-06 | E-GEOD-60119 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of UVB(20mJ/cm2 and 40mJ/cm2) exposed and untreated HaCaT keratinocytes Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of UVB(20mJ/cm2 and 40mJ/cm2) exposed and untreated HaCaT keratinocytes Transcriptomes

| PRJNA577153 | ENA

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