Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21981008_1.fastq.gz | Fastqsanger.gz | |||
| SRR21981008_2.fastq.gz | Fastqsanger.gz | |||
| SRR21981009_1.fastq.gz | Fastqsanger.gz | |||
| SRR21981009_2.fastq.gz | Fastqsanger.gz | |||
| SRR21981010_1.fastq.gz | Fastqsanger.gz |
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Project description:Chem-seq analysis was conducted to reveal genome-wide localization of a cell penetrating peptide, SVS-1. A549 cells treated with 15 mM of biotin-PEG-GG-SVS-1 for 1 hour were passaged once to remove dead cell debris. After 24 hours incubation from the passage, the treated cells were fixed with formaldehyde to crosslink SVS-1 and chromatin, and total chromatin was subjected to fragmentation by sonication. Chromatin bound by the biotin-PEG-GG-SVS-1 was isolated with avidin-conjugated resin, followed by DNA purification. The input DNAs were also purified and employed as controls for the peak callings. The purified DNAs were subjected to library preparation for deep sequencing by the illumina platform. Sequencing was run by the NextSeq with paired end sequencing (2x76), 100 million clusters /sample.
2018-11-07 | GSE122241 | GEO
Project description:We have developed a microfluidics-based in vitro model of the human gut allowing co-culture of human and microbial cells and subsequent multi-omic assessment of the effect of the co-culture on the host transcriptome. We compare the transcriptional changes induced in the human epithelial cell line, Caco-2 after co-culture with Lactobacillus rhamnosus GG or a consortium of Lactobacillus rhamnosus GG and Bacteroides caccae.
2016-05-05 | GSE79383 | GEO
Project description:A new high-density oligonucleotide array of the human transcriptome (GG-H array) has been developed for high-throughput and cost-effective analyses in clinical studies. This array allows comprehensive examination of gene expression and genome-wide identification of alternative splicing, as well as detection of coding SNPs and non-coding transcripts. The GG-H array was validated using samples from multiple independent preparations of human liver and muscle, and compared with results obtained from mRNA sequencing analysis. The GG-H array is highly reproducible in estimating gene and exon abundance, and is sensitive in detecting expression changes and alternative splicing. This array has been implemented in a multi-center clinical program and has generated high quality, reproducible data. When current cost, as well as sample and time requirements for sequencing are considered in the context of a required throughput of hundreds of samples per week for a clinical trial, the array provides a high-throughput and cost effective platform for clinical genomic studies.
2011-01-27 | GSE26109 | GEO
Project description:A new high-density oligonucleotide array of the human transcriptome (GG-H array) has been developed for high-throughput and cost-effective analyses in clinical studies. This array allows comprehensive examination of gene expression and genome-wide identification of alternative splicing, as well as detection of coding SNPs and non-coding transcripts. The GG-H array was validated using samples from multiple independent preparations of human liver and muscle, and compared with results obtained from mRNA sequencing analysis. The GG-H array is highly reproducible in estimating gene and exon abundance, and is sensitive in detecting expression changes and alternative splicing. This array has been implemented in a multi-center clinical program and has generated high quality, reproducible data. When current cost, as well as sample and time requirements for sequencing are considered in the context of a required throughput of hundreds of samples per week for a clinical trial, the array provides a high-throughput and cost effective platform for clinical genomic studies.
2011-01-27 | GSE26072 | GEO
Project description:An M307 G/A point mutation of FUT1 gene has been considered as a usful marker to select the piglets that are sensitive(GG/AG genotype) or resistant(AA) to Escherichia coli F18 in foreign pig breeds. However,it is not suitable to Chinese native breeds. Duodenal tissues were collected from 3 full-sib pairs of Sutai pigs (a new hybrid between the Duroc and Taihu breeds) at the age of 28-day differing in adhesion phenotype to find the differential miRNAs that can provide the basis for analyzing the different mechanisms of E.coli F18 resistance between foreign and Chinese native breeds,as well as for breeding for disease resistance in Chinese native breeds in the future. piglets at the age of 28-day sensitive(GG genotype) to Escherichia coli F18 vs resistant(AA) ones.Biological replicates:3 full-sib pairs of Sutai pigs(3 pairs for GG/AA genotype of FUT1 gene).One GG sample (512 piglet) was sequenced twice to verify the result. 2385 piglet and 2383 piglet were a pair of full-sib with AA and GG genotype at M307 positionof FUT1 gene, respectively. Unfortunately, the sequencing of 2385 was a failure and was excluded. 2385 piglet has an AA genotype of the FUT1 gene
2014-09-21 | E-GEOD-32257 | biostudies-arrayexpress
Project description:A new high-density oligonucleotide array of the human transcriptome (GG-H array) has been developed for high-throughput and cost-effective analyses in clinical studies. This array allows comprehensive examination of gene expression and genome-wide identification of alternative splicing, as well as detection of coding SNPs and non-coding transcripts. The GG-H array was validated using samples from multiple independent preparations of human liver and muscle, and compared with results obtained from mRNA sequencing analysis. The GG-H array is highly reproducible in estimating gene and exon abundance, and is sensitive in detecting expression changes and alternative splicing. This array has been implemented in a multi-center clinical program and has generated high quality, reproducible data. When current cost, as well as sample and time requirements for sequencing are considered in the context of a required throughput of hundreds of samples per week for a clinical trial, the array provides a high-throughput and cost effective platform for clinical genomic studies. Examination exon/gene expression of liver and muscle in quadraplicates using both the array technology and RNA-Seq
2011-01-27 | E-GEOD-26109 | biostudies-arrayexpress
Project description:A new high-density oligonucleotide array of the human transcriptome (GG-H array) has been developed for high-throughput and cost-effective analyses in clinical studies. This array allows comprehensive examination of gene expression and genome-wide identification of alternative splicing, as well as detection of coding SNPs and non-coding transcripts. The GG-H array was validated using samples from multiple independent preparations of human liver and muscle, and compared with results obtained from mRNA sequencing analysis. The GG-H array is highly reproducible in estimating gene and exon abundance, and is sensitive in detecting expression changes and alternative splicing. This array has been implemented in a multi-center clinical program and has generated high quality, reproducible data. When current cost, as well as sample and time requirements for sequencing are considered in the context of a required throughput of hundreds of samples per week for a clinical trial, the array provides a high-throughput and cost effective platform for clinical genomic studies. Examination exon/gene expression of liver and muscle in quadraplicate using both the array technology and RNA-Seq
2011-01-27 | E-GEOD-26072 | biostudies-arrayexpress
Project description:Primary outcome(s): Analysis of the diversity and composition of the gut microbiome by 16S rRNA sequencing
Study Design: Observational Study Model : Others, Time Perspective : Prospective, Enrollment : 60, Biospecimen Retention : Collect & Archive- Sample with DNA, Biospecimen Description : Blood, Stool
| 26030 | ecrin-mdr-crc
Project description:Transcriptional profiling of probiotic Lactobacillus rhamnosus strain GG mid-exponential pH-controlled bioreactor cultures before and after exposure to bovine bile (0.2% ox gall). Keywords: bile, stress response Cell samples from four biological replicates were harvested right before (time point 0 min) and 10, 30 and 120 min after bile treatment. Each sample was compared to a common reference sample (time point 0 min, mid-exponential growth phase Lactobacillus rhamnosus GG cultures). A total of 12 hybridizations were performed using balanced dye-swap design. Dyes were balanced between compared sample pairs and between biological replicates.
2011-01-01 | E-GEOD-22536 | biostudies-arrayexpress
Project description:Purpose: Utilized Next-generation sequencing (NGS) to profile transcriptional differences between two populations, carriers (CC) of rs10846744 SNP associated with cardiovascular disease (CVD) and non-carriers (GG) who are disease free. Methods: Total RNA was isolated from three subjects homozygous for the rs10846744 reference (GG) allele and three subjects homozygous for the rs10846744 risk (CC) allele and then subjected to full transcriptome sequencing using the Perkin Elmer next gen sequencing platform (Perkin Elmer, Branford, CT). Bioinformatics was performed using Perkin Elmer GeneSifter software program. The data was adjusted by selecting total map reads, quality reads >20, log transformation, and using Benjamini Hochberg to correct for multiple testing. RNA targets of interest were validated by qRT–PCR using TaqMan assays and western blotting using standard methodologies. Results: Using Perkin Elmer's Genesifter Analysis Edition Software, we mapped about 100 million sequence reads per sample to the human genome (build 37.2), normalized the raw read count by total mapped million reads and identified 937 upregulated and 587 downregulated transcripts in the EBV (Epstein Barr Virus)-transformed B lymphocyte cells isolated from 3 carriers of the risk (CC) allele and 3 non-carriers of the (GG) reference allele with BWA workflow. RNA-seq data confirmed differential expression of LAG3 and this was validated with qRT–PCR. Conclusions: Our study represents the first detailed analysis of differential LAG3 expression, contributing to CVD, with biologic replicates, generated by RNA-seq technology.
2016-10-20 | GSE87891 | GEO