GEO DataSets

(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) 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. Methods: Retinal mRNA profiles of 21-day-old wild-type (WT) and neural retina leucine zipper knockout (Nrl−/−) mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

6 Samples

Download data: BAM, TXT, XLS

(Submitter supplied) Purpose: The powdery mildew fungus, Blumeria graminis, is an obligate biotrophic pathogen of cereals and has significant impact on food security (Dean et al., 2012. Molecular Plant Pathology 13 (4): 414-430. DOI: 10.1111/j.1364-3703.2011.00783.x). Blumeria graminis f. sp. hordei (Bgh) is the causal agent of powdery mildew on barley (Hordeum vulgare L.). We sought to discover novel transcripts expressed following barley infection with blumeria.

Organism:

Hordeum vulgare; Blumeria hordei

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL29666

6 Samples

Download data: FASTA

(Submitter supplied) A critical task in high throughput sequencing is aligning millions of short reads to a reference genome. Alignment is especially complicated for RNA sequencing (RNA-Seq) because of RNA splicing. A number of RNA-Seq algorithms are available, and claim to align reads with high accuracy and efficiency while detecting splice junctions. RNA-Seq data is discrete in nature; therefore with reasonable gene models and comparative metrics RNA-Seq data can be simulated to sufficient accuracy to enable meaningful benchmarking of alignment algorithms. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

4 Samples

Download data: SAM, TXT

(Submitter supplied) Background: Though Illumina has largely dominated the RNA-Seq field, the simultaneous availability of Ion Torrent has left scientists wondering which platform is most effective for differential gene expression (DGE) analysis. Previous investigations of this question have typically used reference samples derived from cell lines and brain tissue, and do not involve biological variability. While these comparisons might inform studies of tissue-specific expression, marked by large-scale transcriptional differences, this is not the common use case. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17021 GPL18635

20 Samples

Download data: TXT

(Submitter supplied) We used the RNA-seq technology to do a genome-wide transcriptional analysis of A. pleuropneumoniae strain JL03 and investigated the transcriptome structure at a single-nucleotide resolution.The RNA-Seq based transcriptome map validated annotated genes and corrected annotations of open reading frames in the genome, and led to the identification of many functional elements (e.g. regions encoding novel proteins, non-coding sRNAs and operon structures).

Organism:

Actinobacillus pleuropneumoniae serovar 3 str. JL03

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20603

1 Sample

Download data: BED

(Submitter supplied) The advent of high-throughput RNA sequencing (RNA-seq) has led to the discovery of unprecedentedly immense transcriptomes encoded by eukaryotic genomes. However, the transcriptome maps are still incomplete partly because they were mostly reconstructed based on RNA-seq reads that lack their orientations (known as unstranded reads) and certain boundary information. Methods to expand the usability of unstranded RNA-seq data by predetermining the orientation of the reads and precisely determining the boundaries of assembled transcripts could significantly benefit the quality of the resulting transcriptome maps. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Third-party reanalysis

Platform:

GPL13112

2 Samples

Download data: GTF

(Submitter supplied) The advent of high-throughput RNA sequencing (RNA-seq) has led to the discovery of unprecedentedly immense transcriptomes encoded by eukaryotic genomes. However, the transcriptome maps are still incomplete partly because they were mostly reconstructed based on RNA-seq reads that lack their orientations (known as unstranded reads) and certain boundary information. Methods to expand the usability of unstranded RNA-seq data by predetermining the orientation of the reads and precisely determining the boundaries of assembled transcripts could significantly benefit the quality of the resulting transcriptome maps. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Third-party reanalysis

Download data: GTF, TXT, XLS

(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) Next-generation sequencing has been widely used for the genome-wide profiling of histone modifications, transcription factor binding and gene expression through chromatin immunoprecipitated DNA sequencing (ChIP-seq) and cDNA sequencing (RNA-seq). Here, we describe a versatile library construction method that can be applied to both ChIP-seq and RNA-seq on the widely used Illumina platforms. Standard methods for ChIP-seq library construction require nanograms of starting DNA, substantially limiting its application to rare cell types or limited clinical samples. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

23 Samples

Download data: TXT, WIG

(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) Sickle cell transcriptome was analyzed using whole blood clinical specimens on the Affymetrix Human Exon 1.0 ST arrays and Illumina’s deep sequencing technologies. Data analysis indicated a strong concordance (R=0.64) between exon array and RNA-seq in both gene level and exon level expression of transcripts. The magnitude of fold changes in the expression levels for the differentially expressed genes (p<0.05) was found to be higher in RNA-seq than microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

10 Samples

Download data: CEL

(Submitter supplied) To quantify gene expression differences in olfactory epithelium between the mouse (Mus musculus) and the Nile rat (Arvicanthis niloticus), paired-end RNA sequencing (RNA-seq) was used to profile olfactory epithelium transcriptomes of six Nile rats and six mice (C57BL/6J) (one male and one female at the age of 8, 12, and 16 weeks for each species).

Organism:

Mus musculus; Arvicanthis niloticus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL32219

12 Samples

Download data: TXT

(Submitter supplied) Tumor heterogeneity and its drivers impair tumor progression and cancer therapy. Single-cell RNA sequencing has been used to investigate the heterogeneity of tumor ecosystems. However, most methods of scRNA-seq amplify the termini of polyadenylated transcripts, making it challenging to perform total RNA analysis and somatic mutation analysis during tumor processing. Additionally, frozen tumor samples constitute a vast and valuable material bank for cancer research. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25526 GPL28330 GPL30440

12 Samples

Download data: H5AD, MTX, TSV

(Submitter supplied) We developed a Transcriptomic Analysis Pipeline (TAP) as a flexible workflow for comprehensive transcriptome analysis from any species with a reference genome. We tested TAP in a case study to compare polyA+ and rRNA-depletion RNA-seq library protocols using Drosophila melanogaster following different thermal stress temperatures. TAP provides a flexible and complete pipeline to enable researchers to extract more biologically relevant interpretations by integrated and interactive transcriptome analysis.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13304 GPL25244

30 Samples

Download data: CSV

(Submitter supplied) Profiling of gene expression in sparse populations of genetically defined neurons is essential for dissecting the molecular mechanisms that control the development and plasticity of neural circuits. However, current transcriptomic approaches are ill suited for detailed mechanistic studies in sparse neuronal populations, as they either are technically complex and relatively expensive (e.g., single-cell RNA sequencing [RNA-seq]) or require large amounts of input material (e.g., traditional bulk RNA-seq). more...

Organism:

Macaca fascicularis; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL22523

80 Samples

Download data: CSV

(Submitter supplied) In this work, we applied a6A to label and sequence cellular mRNA in an immunoprecipitation-free and mutation-based manner, termed a6A-seq. a6A-seq was utilized to study the change of cellular gene expression profile under a methionine-free stressed condition. Compared with regular RNA-seq, a6A-seq could more sensitively detect the level change of newly synthesized mRNAs.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL20795

8 Samples

Download data: TXT

(Submitter supplied) The functional complexity of nucleus accumbens (NAc) has been extensively characterized in recent years. However, the molecular and cellular heterogeneity beyond the established D1 and D2 medium spiny neuron (MSN) subtypes, which likely underlie its diverse functions, are not well understand. Here, we present the cell taxonomy of mouse NAc generated from single-cell transcriptomic profiling, which not only reveals a rich cellular heterogeneity within both NAc MSN and interneuron populations, but also identified tight correlation between the transcriptional feature and spatial distribution of NAc neuron subtypes, supporting the notion that functional heterogeneity of NAc sub-regions can arises from differential distribution of molecularly distinct neuronal populations. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

11 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) RNA-sequencing data across a large number of tissues in mouse, rat, dog, and monkey to evaluate baseline expression levels and establish a preclinical gene expression body atlas

Organism:

Mus musculus; Macaca fascicularis; Rattus norvegicus; Canis lupus familiaris

Type:

Expression profiling by high throughput sequencing

4 related Platforms

761 Samples

Download data: XLSX