Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25501200_1.fastq.gz | Fastqsanger.gz | |||
| SRR25501200_2.fastq.gz | Fastqsanger.gz | |||
| SRR25501201_1.fastq.gz | Fastqsanger.gz | |||
| SRR25501201_2.fastq.gz | Fastqsanger.gz | |||
| SRR25501202_1.fastq.gz | Fastqsanger.gz |
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Project description:Trachinops noarlungae (Yellowhead Hulafish), xxxx, sequence data
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Project description:Trachinops noarlungae (Yellowhead Hulafish) genome, xxxx, haplotype 1
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Project description:Trachinops noarlungae (Yellowhead Hulafish) genome, xxxx, haplotype 2
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Project description:The purpose of this study was to compare the transcriptome of NIPBL patient derived iPSCs and patient-derived cardiomyocytes to healthy unaffected individuals Methods: iPSC transcriptome profiles of three CdLS patient iPSCs harboring mutations in the NIPBL gene and cardiomyocytes derived from patient-iPSCS were generated by deep sequencing, in triplicate, using Illumina XXXXXX. 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. Results: Using an optimized data analysis workflow, we mapped about 15 million sequence reads per sample to the human genome and identified XXXX transcripts in CdLS-iPSCs and XXXXXX transcripts in control-iPSCs with XXXX workflow. Conclusion: Our data is the represents the first human developmental model for studying CdLS through pluripotent stem cells and lineage commited subtypes (cardiomyocytes). This data highlights NIPBLs role in regulating transcriptional regulation and has significant consequences on DNA nucleosome involvement as it relates to global gene expression. This work provides preliminary evidence that NIPBL is required for normal epigenetic and DNA landscape establishment during embryonic cardiomyocyte generation.
2018-02-22 | GSE102873 | GEO
Project description:The study aims to assess gene expression in plaque samples collected from twin pairs that are both concordant and discordant with respect to dental Caries diagnosis. File Naming Conventions are as follows: Patient ID : 4 digit identifier Diagnosis : Caries Negative(CN) or Caries Positive(CP) Type of Twin: Monozygotic(MZ)or Dizygotic(DZ) Pair to xxxx: 4 digit twin identifier maps to the Patient ID E.g: 2126_CP_MZ_PairTo_2125_fastqc - 2126 is a caries positive patient and pairs to monozygotic twin pair 2125. Plaque samples from twin pairs that are both concordant and discordant with respect to dental Caries diagnosis are enriched for bacterial messenger RNA to study the gene expression differences in the samples.
2011-09-26 | GSE31439 | GEO
Project description:In this study, we investigated somatic mutations in T cells in patients with various hematological disorders. To analyze immune cell phenotypes with somatic mutations, we performed scRNA+TCRab sequencing from 9 patients with chronic GVHD and clonal expansions of CD4+ or CD8+ T cells based on T cell receptor sequencing. CD45+ PBMCs (lymphocytes and monocytes) were sorted with BD Influx cell sorter and subjected to sequencing with Chromium VDJ and Gene Expression platform (v1.1, 10X Genomics). Sequencing was performed with Novaseq 6000 (Illumina). The immune cell phenotypes were compared to healthy controls processed in the same laboratory (accession number E-MTAB-11170). Due to data privacy concerns, the raw sequencing data is in the European Genome-Phenome Archive (EGA) under accession code [xxxx] and can be requested through the EGA Data Access Committee.
2024-04-10 | E-MTAB-13419 | biostudies-arrayexpress
Project description:The study aims to assess gene expression in plaque samples collected from twin pairs that are both concordant and discordant with respect to dental Caries diagnosis. File Naming Conventions are as follows: Patient ID : 4 digit identifier Diagnosis : Caries Negative(CN) or Caries Positive(CP) Type of Twin: Monozygotic(MZ)or Dizygotic(DZ) Pair to xxxx: 4 digit twin identifier maps to the Patient ID E.g: 2126_CP_MZ_PairTo_2125_fastqc - 2126 is a caries positive patient and pairs to monozygotic twin pair 2125. Plaque samples from twin pairs that are both concordant and discordant with respect to dental Caries diagnosis are enriched for bacterial messenger RNA to study the gene expression differences in the samples. RNA was extracted from RNAprotect (Qiagen, In c.) treated dental plaque scrapings from 38 patients. Amplified cDNA was created and rRNA sequence was removed by subtractive hybridization. Individual patient samples were run on a single lane of an Illumina Genome Analyzer.
2011-09-26 | E-GEOD-31439 | biostudies-arrayexpress
Project description:Purpose: The goals of this study are to use hepatic transcriptome profiling (RNA-seq) to examine the role of liquid sugar consumption in the progression of NAFLD. Methods: Hepatic mRNA profiles of 12-week chow (n=4), high fat Western diet (n=5), and high fat Western diet + fructose/sucore in the drinking water (n=5) fed mice were generated by deep sequencing 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. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: We mapped about 100 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts in the livers of mice. RNA-seq data confirmed stable expression of X known liver specific genes. Approximately 10% of the transcripts showed differential expression between the XXX, with a fold change ≥1.5 and p value <0.05. Altered expression of XX genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several pathways that may contribute to NAFLD progression. RNA-seq data had a linear relationship with qRT–PCR: a goodness of fit (R2) of xxxx. Conclusions:
2018-05-16 | GSE89296 | GEO