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Homo sapiens
27 Downloadable Samples
IlluminaHiSeq2000
Description
Advantages of RNA-Seq over array based platforms are quantitative gene expression and discovery of expressed single nucleotide variants (eSNVs) and fusion transcripts from a single platform, but the sensitivity for each of these characteristics is unknown. We measured gene expression in a set of manually degraded RNAs, nine pairs of matched fresh-frozen, and FFPE RNA isolated from breast tumor with the hybridization based, NanoString nCounter, (226 gene panel) and with whole transcriptome RNA-Seq using RiboZeroGold ScriptSeq V2 library preparation kits. We performed correlation analyses of gene expression between samples and across platforms. We then specifically assessed whole transcriptome expression of lincRNA and discovery of eSNVs and fusion transcripts in the FFPE RNA-Seq data. For gene expression in the manually degraded samples, we observed Pearson correlation of >0.94 and >0.80 with NanoString and ScriptSeq protocols respectively. Gene expression data for matched fresh-frozen and FFPE samples yielded mean Pearson correlations of 0.874 and 0.783 for NanoString (226 genes) and ScriptSeq whole transcriptome protocols respectively. Specifically for lincRNAs, we observed superb Pearson correlation (0.988) between matched fresh-frozen and FFPE pairs. FFPE samples across NanoString and RNA-Seq platforms gave a mean Pearson correlation of 0.838. In FFPE libraries, we detected 53.4% of high confidence SNVs and 24% of high confidence fusion transcripts. Sensitivity of fusion transcript detection was not overcome by an increase in depth of sequencing up to 3-fold (increase from ~56 to ~159 million reads). Both NanoString and ScriptSeq RNA-Seq technologies yield reliable gene expression data for degraded and FFPE material. The high degree of correlation between NanoString and RNA-Seq platforms suggests discovery based whole transciptome studies from FFPE material will produce reliable expression data. The RiboZeroGold ScriptSeq protocol performed particularly well for lincRNA expression from FFPE libraries but detection of eSNV and fusion transcripts was less sensitive. Overall design: We performed RNASeq on RNA from nine matched pairs of fresh-frozen and FFPE tissues from breast cancer patients. The goal was to test the RiboZeroGold ScriptSeq complete low input library preparation kit for degraded RNA samples.
Publication Title
Gene expression, single nucleotide variant and fusion transcript discovery in archival material from breast tumors.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 32 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
The goal of our study is to build an integrated transcriptome landscape model for HER2 positive breast tumors and identify the crucial signaling pathways associated with HER2 tumors. Genomic features include, 685 genes that were differentially expressed only in HER2-positive tumors, 102 genes that were alternatively spliced in a pattern that is unique to HER2-positive tumors, and 303 genes that expressed single nucleotide sequence variants (eSNVs) that were unique to HER2-positive tumors. Network analysis was performed to integrate the genomic features into a transcriptome landscape model that identified 12 highly interconnected cellular processes that appear to be critical to the establishment and maintenance of HER2-positive tumors. We observed that integrin signaling was linked to lapatinib sensitivity in vitro and strongly associated with risk of relapse in the NCCTG N9831 adjuvant trastuzumab clinical trial dataset. Overall design: We analyzed RNA-seq data from a survey panel consisting of 8 benign breast lesions, 8 ER+, 8 triple negative, and 8 HER2-positive primary breast tumors to identify genomic features that were uniquely associated with HER2-positive tumors
Publication Title
An integrated model of the transcriptome of HER2-positive breast cancer.
Sample Metadata Fields
Specimen part, Subject
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Goal of this study was to determine changes in transcription profile in mock versus G3P treated plants. Arabidopsis (Col-0 ecotype) plants were infiltrated with petiole exudate, with or without G3P, and distal leaves were sampled 24 h post treatments.
Publication Title
Glycerol-3-phosphate is a critical mobile inducer of systemic immunity in plants.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 28 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The white adipose tissue (WAT) rapidly loses mass when mice are fed a diet containing trans-10, cis-12 conjugated linoleic acid (t10c12 CLA). A microarray analysis of WAT due to CLA feeding was performed to better define the processes and genes involved. WAT weight decreased by ca. 80% over 17 days of feeding a 0.5% t10c12 CLA diet. The lipid volume decreased by 90% and the number of adipocytes and total cells were reduced by15% and 47%, respectively. Microarray profiling of replicated pools of control and treated mice (n=140) at seven time points over the 17day feeding indicated between 2798 to 4318 genes showed mRNA changes of 2-fold or more. Transcript levels for genes of glucose and fatty acid import or biosynthesis were significantly reduced. A prolific inflammation response was indicated by the 2 to100-fold induction of many cytokine transcripts, including those for IL-6, IL1?, TNF ligands, and CXC family members
Publication Title
Trans-10, cis-12 conjugated linoleic acid causes inflammation and delipidation of white adipose tissue in mice: a microarray and histological analysis.
Sample Metadata Fields
Age
View Samples- Mus musculus
- 88 Downloadable Samples
- Illumina HiSeq 2500
Description
Cg.5XFAD females (MMRRC Stock No #34848-JAX) were bred to males from BXD strains. The resulting F1 progeny were monitored throughout their lifepan to evaluate the effect of genetic background on cognitive and pathological traits. Samples here come from various AD-BXD lines at either 6 or 14 months of age. An earlier dataset of similar design (plus Non-transgenic littermates) was deposited as GSE101144. Ntg littermates of mice sampled here will be deposited as a separate GEO series. Overall design: 88 AD samples. For final by-strain analysis, samples were averaged into strain/age/genotype/sex groups (For example, all D2 6mo 5XFAD males were averaged for final by-strain analysis)
Publication Title
Identification of Pre-symptomatic Gene Signatures That Predict Resilience to Cognitive Decline in the Genetically Diverse AD-BXD Model.
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Subject
View Samples- Mus musculus
- 108 Downloadable Samples
- Illumina HiSeq 2500
Description
Female C57BL/6J mice hemizygous for the 5XFAD transgene (MMRRC Stock No #34848-JAX) were bred to males from BXD strains, which do not carry the 5XFAD transgene. The resulting F1 progeny were monitored throughout their lifespan to evaluate the effect of genetic background on cognitive and pathological traits. All of the mice were fear conditioned and sacrificed within 30 minutes of testing. On the sample records, the characteristics: age field provides the age at which fear conditioning, sacrifice, and tissue collection occurred. Samples here come from various AD-BXD lines and their non-transgenic (Ntg) littermate counterparts at either 6 or 14 months of age. Overall design: 133 samples, 64 Ntg and 69 AD. For final by-strain analysis, samples were averaged into strain/age/genotype/sex groups (For example, all D2 6mo 5XFAD males were averaged for final by-strain analysis)
Publication Title
Harnessing Genetic Complexity to Enhance Translatability of Alzheimer's Disease Mouse Models: A Path toward Precision Medicine.
Sample Metadata Fields
Sex, Age, Specimen part, Subject
View Samples
SRP066231- Mus musculus
- 77 Downloadable Samples
- Illumina HiSeq 2500
Description
High temporal resolution RNAseq timecourse of mouse ES differentiation Investigations of transcriptional responses during developmental transitions typically use time courses with intervals that are not commensurate with the timescales of known biological processes. Moreover, such experiments typically focus on protein-coding transcripts, ignoring the important impact of long noncoding RNAs. We evaluated coding and noncoding expression dynamics at unprecedented temporal resolution (6-hourly) in differentiating mouse embryonic stem cells and report the effects of increased temporal resolution on the characterization of the underlying molecular processes. Overall design: Biological duplicate 120 hours of undirected mouse ES cell differentiation sampled 6 hourly Biological duplicate, low passage number (P18) W9.5 ESCs were cultured and differentiated as described previously [PMID:18562676; 17286599]. Cultures were harvested every six hours from the induction of differentiation to 120 hours post differentiation induction. Total RNA from cultures was purified using Trizol (Life Technologies) and DNase treatment was performed by RQ1 DNase (Promega) according to the manufacturer’s instructions. RNA integrity was measured on a Bioanalyzer RNA Nano chip (Agilent). RNA-Seq library preparation and sequencing of Poly-A-NGS libraries generated from 500 ng total RNA using SureSelect Strand Specific RNA Library Preparation Kit (Agilent) according to the manufacturer’s instructions. Paired-end libraries were sequenced to the first 100 bp on a HiSeq 2500 (Illumina) on High Output Mode. Library sequencing quality was determined using FastQC (Babraham Bioinformatics) and FastQ Screen (Babraham Bioinformatics). Illumina adaptor sequence and low quality read trimming (read pair removed if < 20 base pairs) was performed using Trim Galore! (Babraham Bioinformatics: www.bioinformatics.babraham.ac.uk/). Tophat2 [PMID:23618408] was used to align reads to the December 2011 release of the mouse reference genome (mm10) as outlined by Anders et al.[PMID:23975260]. Read counts data corresponding to GENCODE vM2 transcript annotations were generated using HTSeq[PMID:25260700]. All analyses were performed in the R Statistical Environment [PMID:18000755]. Briefly, counts data were background corrected and normalized for library size using edgeR [PMID:19910308], then transformed using voom[PMID:24485249] for differential expression analysis using LIMMA[PMID: 16646809].
Publication Title
High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci.
Sample Metadata Fields
Specimen part, Cell line, Subject, Time
View Samples- Homo sapiens
- 58 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
In addition to being causally linked to the formation of multiple tumor types, tobacco use has been associated with decreased anticancer treatment efficacy and reduced survival time. A detailed understanding of the cellular mechanisms that are affected by tobacco smoke should facilitate the development of improved preventive and therapeutic strategies. We have investigated the effects of a tobacco smoke (TS) extract on the transcriptome of MSK-Leuk1 cells, a cellular model of oral leukoplakia. Using Affymetrix HGU133 Plus 2 arrays, 411 differentially expressed probesets were identified. The observed transcriptome changes were grouped according to functional information, and translated into molecular interaction network maps and signaling pathways. Pathways related to cellular proliferation, inflammation, apoptosis and tissue injury appeared to be perturbed. Analysis of networks connecting the affected genes identified specific molecular interactions, hubs and key transcription regulators affected by TS. Thus TS was found to induce several EGFR ligands forming an EGFR-centered molecular interaction network, as well as several AhR-dependent genes, including the xenobiotic metabolizing enzymes CYP1A1 and CYP1B1. Notably, the latter findings in vitro are consistent with our parallel finding that levels of CYP1A1 and CYP1B1 were increased in oral mucosa of smokers. Collectively, these results offer insights into the mechanisms underlying the procarcinogenic effects of TS and raise the possibility that inhibitors of EGFR or AhR signaling will prevent or delay the development of tobacco smoke-related tumors. Moreover, the inductive effects of TS on xenobiotic metabolizing enzymes may help explain reduced efficacy of chemotherapy, and suggest targets for chemopreventive agents in smokers.
Publication Title
Effects of tobacco smoke on gene expression and cellular pathways in a cellular model of oral leukoplakia.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
Appropriate bone mass is maintained by the actions of the main cells in the bone, osteoclasts and osteoblasts. The Stat3 transcription factor is known to have an effect on maintaining bone mass, but it is not known whether its key actions are in osteoblasts, osteoclasts, or both. Preliminary data indicated that Stat3 plays a role in osteoclast differentiation, but the mechanisms of this role are not yet understood.
Publication Title
The loss of STAT3 in mature osteoclasts has detrimental effects on bone structure.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 77 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
40 current smokers and 40 age- and gender- matched never smokers underwent buccal biopsies.The study had four objectives: (a) to define the effects of smoking on the transcriptome of oral epithelial cells; (b) to determine if any of the effects of tobacco smoke on the transcriptome are gender-dependent; (c) to compare the effects of tobacco smoke exposure on the transcriptome in oral v. bronchial epithelium and (d) to identify agents with the potential to suppress the effects of tobacco smoke on the transcriptome.
Publication Title
Effects of cigarette smoke on the human oral mucosal transcriptome.
Sample Metadata Fields
Sex, Specimen part
View Samples