GEO DataSets

(Submitter supplied) DNA was isolated from whole red blood cells from various lines and crosses of broiler chickens. DNA was genotyped using Axiom genome-wide chicken array and cel files were analyzed using Axiom Analysis Suite Software (version 3.0.1) with Gallus gallus 5.0 using the software's Best Practices for agricultural animals. The results were exported (Genotyping_Data-3-21-2018.vcf) for all genotype calls and text file of all SNPs with >= 97% call rate rate was also produced for filtering the VCF file (ALL_SNPSs_with_Call_Rate_97_Plus_3-21-2018).

Organism:

Gallus gallus

Type:

Genome variation profiling by SNP array

Platform:

GPL23815

96 Samples

Download data: CEL, VCF

(Submitter supplied) Genetic diversity in plants is remarkably high. Recent whole genome sequencing (WGS) of 67 rice accessions recovered 10,872 novel genes. Comparison of the genetic architecture among divergent populations or between crops and wild relatives is essential for obtaining functional components determining crucial traits. However, many major crops have gigabase-scale genomes, which are not well-suited to WGS. more...

Organism:

Oryza sativa; Triticum aestivum; Oryza sativa Japonica Group; Oryza sativa Indica Group

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

4 related Platforms

26 Samples

Download data: BED, TXT

(Submitter supplied) Here we compare the performance of these three approaches (inDrop, Drop-seq and 10x) using the same kind of sample with a unified data processing pipeline. We generated 2-3 replicates for each method using lymphoblastoid cell line GM12891. The average sequencing depth was around 50-60k reads per cell barcode. We also developed a versatile and rapid data processing workflow and applied it for all datasets. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

7 Samples

Download data: TXT

(Submitter supplied) We report here a new single-cell RNA-seq assay, Multiple Annealing and dC-Tailing based Quantitative single-cell RNA-seq (MATQ-seq), which provides the accuracy and sensitivity that enable the detection of transcriptional variations existing in single cells of the same type. We performed a systematic characterization of the technical noise using pool-and-split averaged single-cell samples and showed that the biological variations in single cells were observed with statistical significance.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

91 Samples

Download data: DAT, TXT

(Submitter supplied) Genetically engineered mice (GEM) are essential tools for understanding gene function and disease modeling. Due to historical reasons, gene targeting was at first done in embryonic stem cells (ESC) derived from the 129 family of inbred strains, leading to mixed background or congenic mice when crossed with C57BL/6 mice. Depending on the number of backcrosses and breeding strategies genomic segments from 129-derived ESC can be introgressed into the C57BL/6 genome at different levels, establishing a unique genetic makeup that needs characterization in order to obtain valid conclusions of experiments using GEM models. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

40 Samples

Download data: TXT

(Submitter supplied) Gene expression profiling via RNA-sequencing has become standard for measuring and analyzing the gene activity in bulk and at single cell level. Increasing sample sizes and cell counts provides substantial information about transcriptional architecture of samples. In addition to quantification of expression at cellular level, RNA-seq can be used for detecting of variants, including single nucleotide variants and small insertions/deletions and also large variants such as copy number variants. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

2 Samples

Download data: MTX, TSV

(Submitter supplied) This study presents a dynamic characterization of the sheep milk transcriptome aiming at achieving a better understanding of the sheep lactating mammary gland. Transcriptome sequencing (RNA-seq) was performed on total RNA extracted from milk somatic cells from ewes on days 10, 50, 120 and 150 after lambing. The experiment was performed in Spanish Churra and Assaf breeds, which differ in their milk production traits. more...

Organism:

Ovis aries

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15670

30 Samples

Download data: CSV

(Submitter supplied) Background: Whole transcriptome sequencing (RNA-seq) represents a powerful approach for whole transcriptome gene expression analysis. However, RNA-seq carries a few limitations, e.g., the requirement of a significant amount of input RNA and complications led by non-specific mapping of short reads. The Ion AmpliSeqTM Transcriptome Human Gene Expression Kit (AmpliSeq) was recently introduced by Life Technologies as a whole-transcriptome, targeted gene quantification kit to overcome these limitations of RNA-seq.To assess the performance of this new methodology, we performed a comprehensive comparison of AmpliSeq with RNA-seq using two well-established next-generation sequencing platforms (Illumina HiSeq and Ion Torrent Proton). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17303

6 Samples

Download data: TXT

(Submitter supplied) To address how genetic variation alters gene expression in complex cell mixtures, we developed Direct Nuclear Tagmentation and RNA-sequencing (DNTR-seq), which enables whole genome and mRNA sequencing jointly in single cells. DNTR-seq readily identified minor subclones within leukemia patients. In a large-scale DNA damage screen, DNTR-seq was used to detect regions under purifying selection, and identified genes where mRNA abundance was resistant to copy number alteration, suggesting strong genetic compensation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL18573

4869 Samples

Download data: TSV, TXT

(Submitter supplied) Goal: To define the digital transcriptome of three breast cancer subtypes (TNBC, Non-TNBC, and HER2-positive) using RNA-sequencing technology. To elucidate differentially expressed known and novel transcripts, alternatively spliced genes and differential isoforms and lastly expressed variants in our dataset. Method: Dr. Suzanne Fuqua (Baylor College of Medicine) provided the human breast cancer tissue RNA samples. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

20 Samples

Download data: GTF, VCF

(Submitter supplied) This submission includes the sample data for a protocol covering differential expression analysis with TopHat and Cufflinks. The protocol also covers several accessory tools and utilities that aid in managing data, including CummeRbund, a tool for visualizing RNA-Seq analysis results. While the procedure assumes basic informatics skills, these tools assume little to no background with RNA-Seq analysis and are meant for novices and experts alike. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11203

6 Samples

Download data: BAM, DIFF, FPKM_TRACKING, GTF

(Submitter supplied) High eukaryotic genomes are populated with enhancers, but it has been a major challenge in defining specific enhancer-promoter relationship. Enhancers can also be divided into typical and super-enhancers, yet their functional distinctions remain to be understood. Here, we report a strategy to capture in situ Global RNA Interactions with DNA by deep sequencing (GRID-seq). By deducing general RNA background on chromatin, we unexpectedly detect a highly selective set of RNAs (including both lncRNAs and protein-coding pre-mRNAs) decorated on enhancers, particularly super-enhancers. more...

Organism:

Homo sapiens; Mus musculus; Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL16791 GPL17275

12 Samples

Download data: TXT

(Submitter supplied) We generated the first ultra-deep Nile grass rat RNA-seq data from 60 biopsy samples representing 22 major organs, providing a unique resource and spatial transcriptomic reference (e.g., tissue gene expression baseline) for using Nile grass rat as a model to study human diseases.

Organism:

Arvicanthis niloticus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32739

59 Samples

Download data: TXT

(Submitter supplied) RNA sequencing (RNA-seq) has been a widely used high-throughput method to characterize transcriptomic dynamics spatiotemporally. However, typical RNA-seq data analysis pipelines depend on either a sequenced genome or reference transcripts. This constriction makes the use of RNA-seq for species lacking both of sequenced genomes and reference transcripts challenging. To solve this problem, we developed CRSP, an RNA-seq pipeline integrating multiple comparative species strategy but not depending on a specific sequenced genome or reference transcripts. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

1 Sample

Download data: TXT

(Submitter supplied) We used RNA-seq data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine a biologically relevant allelic ratio cutoff, and define for the first time an entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

10 Samples

Download data: TXT

(Submitter supplied) Structural variants can lead to an alteration of gene expression which may be associated with disease worsening. In our study we attempted to describe expression changes associated with the presence of extensive genomic rearrangements in chronic lymphocytic leukemia.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

10 Samples

Download data: TXT

(Submitter supplied) Structural variants can lead to an alteration of gene expression which may be associated with disease worsening. In our study we attempted to describe expression changes associated with the presence of extensive genomic rearrangements in chronic lymphocytic leukemia.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; Genome variation profiling by genome tiling array

Platforms:

GPL11157 GPL16131

10 Samples

Download data: CEL, CYCHP, TXT

(Submitter supplied) Structural variants can lead to an alteration of gene expression which may be associated with disease worsening. In our study we attempted to describe expression changes associated with the presence of extensive genomic rearrangements in chronic lymphocytic leukemia. We used microarrays for establishing an algorithm for identification of unique expression profiles associated with extensive genomic rearrangements.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

10 Samples

Download data: CEL, CHP, TXT

(Submitter supplied) Next-generation sequencing (NGS) technology applications like RNA-sequencing (RNA-seq) have dramatically expanded the potential for novel genomics discoveries, but the proliferation of various platforms and protocols for RNA-seq has created a need for reference data sets to help gauge the performance characteristics of these disparate methods. Here we describe the results of the ABRF-NGS Study on RNA-seq, which leverages replicate experiments across multiple sites using two reference RNA standards tested with four protocols (polyA selected, ribo-depleted, size selected, and degraded RNA), and examined across five NGS platforms (Illumina’s HiSeqs, Life Technologies’ Personal Genome Machine and Proton, Roche 454 GS FLX, and Pacific Biosciences RS). more...

Organism:

synthetic construct; Homo sapiens

Type:

Expression profiling by high throughput sequencing

5 related Platforms

105 Samples

Download data

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL19057

142 Samples

Download data