Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Antiviral and anti-inflammatory properties of novel anti-HIV candidate ABX464 promotes specifics RNA splicing while preserving cellular RNA integrity.

ABSTRACT: Purpose: To ensure that ABX464 acted specifically on HIV splicing and did not significantly or globally affect the splicing events of human genes, we used an assembly approach of HIV (YU2 strain) putative transcripts and human long non-coding sequences from paired-reads (2x75bp) captured on a NimbleGen SeqCap® EZ Developer Library (Roche/NimbleGen). Methods: Cells were infected with 80 ng of p24/106 cells of the YU-2 strain for 4 to 6 hours and then rinsed with PBS before medium renewal, followed by high-throughput RNAseq from custom SeqCap EZ capture libraries. Each raw dataset of the samples contained between 5 and 30 million paired-end reads (75 bp), with an average of approximately 12 million raw reads per sample. Results: The raw reads were then cleaned and assembled per library to generate contigs, giving an average of 930 contigs per sample for further analyses. Conclusions: Our results show that high-throughput analyses coupled with bioinformatics-specific tools offers a comprehensive and more accurate view of mRNA splicing within a cell.

ORGANISM(S): Homo sapiens

PROVIDER: GSE120109 | GEO | 2018/12/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Specific modulation of HIV RNA splicing and upregulation of anti-inflammatory miR-124 by the new drug candidate ABX464

Project description:Purpose: To ensure that ABX464 acted specifically on HIV splicing and did not significantly or globally affect the splicing events of human genes, we used a high-throughput RNAseq approach. Many genome-wide expression studies of HIV infection are based on analyses of total peripheral blood mononuclear cells (PBMCs), which consist of over a dozen cell subsets, including T cells, B cells, NK cells and monocytes Methods: The CD4 T cells were uninfected or infected with the YU2 strain and were untreated or treated for 6 days with ABX464, followed by high-throughput RNAseq. Each raw dataset of the samples contained between 44 and 105 million single-end reads (50 bp), with an average of approximately 60 million raw reads per sample Results: Approximately 98% of the total raw reads were mapped to the human genome sequence (GRCh38), giving an average of 60 million human reads per sample for further analyses. The reads that were correctly mapped (approximately 98% of total input reads) to the gene and transcript locations (GTF annotation file) Conclusions: The MDS of our gene expression data showed, without any outliers, that the different donors segregated well and distributed into the DMSO (untreated) and ABX464 treatments that were infected or uninfected. The displayed variance was donor-dependent (clustered by donor) but treatment-independent (no data structure related to the different treatments), which suggests that the ABX464 molecule did not induce a major difference in CD4 T cell gene expression.

2018-06-22 | GSE116073 | GEO

RNA-Seq analysis facilitates quantitative analysis to identify DEGs in lung cancer cell lines regulated by S100A7A introduction in comparison with Cl1-0 control and S100A7A knockdown in comparison with CL1-5 control.

Project description:Methods: The cDNA libraries from 3 pooled samples of cultured cells for each group were sequenced to generate RNA profiles using Illumina Miseq platform Results: The sequencing runs yielded a total of 95.01 M reads with an average length of 73-74 bp. The high-throughput sequencing performed for liver samples with different treatments showed similar numbers of yielded reads ranged from 5.57 to 5.74 M and the same average length. The Strand NGS software (version 2.1) was used using default parameters for pre-alignment and post-alignment quality control analysis and 100% of the raw reads remained in the dataset. Of these, 19.02 M reads (84%) were mapped into contigs of the rat genome (rn5) and identified 31457 transcripts in liver samples.

2017-01-31 | GSE86344 | GEO

RNA-Seq analysis facilitates quantitative analysis to identify genes in hepatic tissue of partially hepatectomized rats regulated by ASCs-miR27b introduction in comparison with ASCs-siRNC or saline controls

Project description:Methods: The cDNA libraries from 3 pooled samples of liver tissues for each group were sequenced to generate RNA profiles using Illumina Miseq platform Results: The sequencing runs yielded a total of 22.67 M reads with an average length of 100 bp. The high-throughput sequencing performed for liver samples with different treatments showed similar numbers of yielded reads ranged from 5.57 to 5.74 M and the same average length. The Strand NGS software (version 2.1) was used using default parameters for pre-alignment and post-alignment quality control analysis and 100% of the raw reads remained in the dataset. Of these, 19.02 M reads (84%) were mapped into contigs of the rat genome (rn5) and identified 31457 transcripts in liver samples.

2015-10-01 | GSE69783 | GEO

Alternative splicing changes are associated with pre-birth adaptation during mouse lung development

Project description:Analysis of gene expression and alternative splicing changes in mouse lungs at different developmental time-points (E15.5, E18.5, P5, P8) was performed through RNAseq. We performed 101 nt paired-end RNAseq using HiSeq 4000 on triplicate samples. We obtained an average of 59.8 million reads per sample. The sequence reads that passed quality filters were analyzed at the transcript and at the alternative splicing events level using using D For gene expression analysis, the ~56.8 M raw reads generated per sample were uniquely mapped to the mm10 assembly and annotated to the Gencode vM14 transcriptome using TopHat2, with Bowtie2. Gene expression levels were quantified with HTSeq-count (version 0.10.0). After applying quality filters, we obtained 16,152 expressed genes for downstream analysis. For AS event-level analysis, raw reads were mapped to previously annotated AS events for the mouse reference assembly (mm10 vastdb.mm2.23.06.20) from VastDB (VastDB v2 released). Abundance of AS events in Percent spliced in (PSI) values was estimated using VAST-TOOLS. We found that most of the AS changes during alveologenesis occur at the perinatal period in genes associated with blood vessel and epithelial cell development. In particular, we found that Vegfa undergoes AS in lungs at the transition from embryonic to post-natal life, starting at the end of the embryonic period. Our results suggest provide a framework for understanding how AS changes impact on lung development during the critical period of transition to the postnatal life.

2022-08-25 | GSE175403 | GEO

Platelet Transcriptome Profiling in HIV and ABCC4 as a Biomarker of Platelet Activity

Project description:The purpose of this study was to perform an unbiased RNA expression profile in platelets from HIV subjects under ART and healthy controls to identify a gene signature for the HIV hyperactive phenotype. Methods: Rna-Sequencing was performed in leukocyte-depleted platelet RNA from 6 HIV subjects and 3 healthy controls. qRT–PCR validation was performed to validate our candidate transcripts. Results: Across the 9 platelet samples, there was an average of 28.3 million mapped reads per sample with an average unique mapping rate of 91.6 %. Using a cut-off of normalized counts ≥1 across the 9 samples, we found 11988 expressed transcripts. Conclusions: Our study represents a detailed analysis of platelet transcriptome generated by RNA-seq technology in HIV patients under ART. Further experiments identified the mechanism of our transcript target in mediating platelet activity and platelet cell effector function.

2018-06-10 | GSE99737 | GEO

Exome sequencing in classic Hairy cell leukaemia reveals widespread variation in acquired somatic mutations between individual tumours apart from the signature BRAF V(600)E lesion

Project description:Whole exome sequencing of 5 HCLc tumor-germline pairs. Genomic DNA from HCLc tumor cells and T-cells for germline was used. Whole exome enrichment was performed with either Agilent SureSelect (50Mb, samples S3G/T, S5G/T, S9G/T) or Roche Nimblegen (44.1Mb, samples S4G/T and S6G/T). The resulting exome libraries were sequenced on the Illumina HiSeq platform with paired-end 100bp reads to an average depth of 120-134x. Bam files were generated using NovoalignMPI (v3.0) to align the raw fastq files to the reference genome sequence (hg19) and picard tools (v1.34) to flag duplicate reads (optical or pcr), unmapped reads, reads mapping to more than one location, and reads failing vendor QC.

2016-02-01 | E-MTAB-4313 | biostudies-arrayexpress

Transcription-dependent control of stem cell self-renewal and differentiation by the splicing factor U2AF1

Project description:Purpose: Here we describe the modulation of a gene expression program involved in cell fate. Methods: We depleted U2AF1 in human induced pluripotent stem cells (hiPSCs) to the level found in differentiated cells using an inducible shRNA system, followed by high-throughput RNAseq, revealing a gene expression program involved in cell fate determination. Results: Approximately 85% of the total raw reads were mapped to the human genome sequence (GRCh37), giving an average of 200 million human reads per sample for total RNA and 15 million human reads per sample for small RNA libraries. Conclusions: Our results show that transcriptional control of gene expression in hiPSCs can be set by the CSF U2AF1, establishing a direct link between transcription and AS during cell fate determination.

2018-12-03 | GSE119700 | GEO

Whole-genome transcriptomic analysis from stem internodes in Sorghum bicolor variety ICSV12012

Project description:We report transcriptome profiling of middle internode tissues from four development stages and three soil moisture readings representing progressive drought stress in sweet sorghum. Sequencing of 14 libraries (two biological replicates for each stage). Each replicate yielded an average of 86 million reads per sample for developmental stages and drought stressed samples yielded an average of 74 million reads per sample .

2023-12-31 | GSE178993 | GEO

Whole-genome transcriptomic analysis in Sorghum bicolor variety M35-1

Project description:We report transcriptome profiling of middle internode tissues from four development stages and three soil moisture readings representing progressive drought stress in grain sorghum. Sequencing of 14 libraries (two biological replicates for each stage). Each replicate yielded an average of 86 million reads per sample for developmental stages and drought stressed samples yielded an average of 74 million reads per sample .

2023-12-31 | GSE178603 | GEO

Whole-genome transcriptomic analysis in Sorghum bicolor variety CSV24SS

2023-12-31 | GSE155194 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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