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GSE95214
Rattus norvegicus
4 Downloadable Samples
Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
The gene expression profling between Control and 300 mg/kg PhIP treatment in ventral prostate lobe of male F344 rats
Publication Title
Early detection of prostate carcinogens by immunohistochemistry of HMGB2.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Cutaneous exposure to food antigen through impaired skin barrier has been shown to induce epicutaneous sensitization, and thereby cause IgE-mediated food allergy.
Publication Title
Skin inflammation exacerbates food allergy symptoms in epicutaneously sensitized mice.
Sample Metadata Fields
Sex, Specimen part
View Samples- Rattus norvegicus
- 6 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
HIV Tg rats exhibit pulmonary hypertension and pulmonary artery remodeling. In an effort to begin to understand cell signaling pathways which are altered in lungs from HIV transgenic rats, we used microarray analysis.
Publication Title
Human immunodeficiency virus transgenic rats exhibit pulmonary hypertension.
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
NK cells from NKDxIL15tg mice spleens and bone marrow were purified by FACS. NK cells from IL15tg mice spleens were purified by FACS.
Publication Title
Distal-less homeobox transcription factors regulate development and maturation of natural killer cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 5 Downloadable Samples
NextSeq 500
Description
Single cell RNA sequencing (scRNA-seq) technology has undergone rapid development in recent years and brings new challenges in data processing and analysis. This has led to an explosion of tailored analysis methods for scRNA-seq to address various biological questions. However, the current lack of gold-standard benchmarking datasets makes it difficult for researchers to evaluate the performance of the many methods available in a systematic manner. Here, we designed and generated a cross-platform benchmark dataset that has in-built truth in various forms and varying levels of biological noise. We used this dataset to compare different protocols and data analysis methods. We found that different protocols have different data quality and ERCC spike-in works independently to endogenous RNA. We found significant differences in the results from the methods compared and we associated the results with data characteristics to identify methods that perform well in different situations. Our dataset and analysis provide a valuable resource for algorithm selection in different biological settings. Overall design: our experiment utilized the 3 human lung adenocarcinoma cell lines H2228, H1975 and HCC827. The experiment included mixtures of RNA and single cells from these cell lines. For the single cell designs, the three cell lines were mixed equally and processed by 10X chromium, Drop-seq and CEL-seq2, referred to as sc_10X, sc_Drop-seq and sc_CEL-seq2 respectively in analysis that follows. For the mixture designs, we used plate-based protocols to mix and dilute samples in 2 different ways. 9 cell mixtures from the 3 cell lines were sorted in different combinations in the cell mixture experiment and data were generated by CEL-seq2, the material after pooling from 384 wells were subsampled in either 1/9 or 1/3 to simulate cells of different sizes, with different PCR product clean up ratios ranging from 0.7 to 0.9, referred to as cellmix1 to cellmix4. For the cell mixture experiment, we also sorted wells with 10 times more cells (90 cells) to provide a pseudo bulk reference for each mixture (referred to as cellmix5). Distinct RNA mixtures which were diluted down to create single cell equivalents (ranging from 3.75, 7.5, 15 to 30 pg per well) were generated using CEL-seq2 and SORT-seq (referred to as RNAmix_CEL-seq2 and RNAmix_Sort-seq. This is the 9 cell mixture dataset.
Publication Title
scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 3 Downloadable Samples
- NextSeq 500
Description
Single cell RNA sequencing (scRNA-seq) technology has undergone rapid development in recent years and brings new challenges in data processing and analysis. This has led to an explosion of tailored analysis methods for scRNA-seq to address various biological questions. However, the current lack of gold-standard benchmarking datasets makes it difficult for researchers to evaluate the performance of the many methods available in a systematic manner. Here, we designed and generated a cross-platform benchmark dataset that has in-built truth in various forms and varying levels of biological noise. We used this dataset to compare different protocols and data analysis methods. We found that different protocols have different data quality and ERCC spike-in works independently to endogenous RNA. We found significant differences in the results from the methods compared and we associated the results with data characteristics to identify methods that perform well in different situations. Our dataset and analysis provide a valuable resource for algorithm selection in different biological settings. Overall design: our experiment utilized the 5 human lung adenocarcinoma cell lines H2228, H1975, A549, H838 and HCC827. For the single cell designs, the five cell lines were mixed equally and processed by 10X chromium and CEL-seq2, referred to as sc_10X_5cl, and sc_CEL-seq2_5cl respectively in analysis that follows. For CEL-seq2, three plates were sorted and processed.
Publication Title
scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data.
Sample Metadata Fields
Subject
View Samples- Homo sapiens
- 1 Downloadable Sample
- NextSeq 500
Description
Single cell RNA sequencing (scRNA-seq) technology has undergone rapid development in recent years and brings new challenges in data processing and analysis. This has led to an explosion of tailored analysis methods for scRNA-seq to address various biological questions. However, the current lack of gold-standard benchmarking datasets makes it difficult for researchers to evaluate the performance of the many methods available in a systematic manner. Here, we designed and generated a cross-platform benchmark dataset that has in-built truth in various forms and varying levels of biological noise. We used this dataset to compare different protocols and data analysis methods. We found that different protocols have different data quality and ERCC spike-in works independently to endogenous RNA. We found significant differences in the results from the methods compared and we associated the results with data characteristics to identify methods that perform well in different situations. Our dataset and analysis provide a valuable resource for algorithm selection in different biological settings. Overall design: our experiment utilized the 3 human lung adenocarcinoma cell lines H2228, H1975 and HCC827. The experiment included mixtures of RNA and single cells from these cell lines. For the single cell designs, the three cell lines were mixed equally and processed by 10X chromium, Drop-seq and CEL-seq2, referred to as sc_10X, sc_Drop-seq and sc_CEL-seq2 respectively in analysis that follows. For the mixture designs, we used plate-based protocols to mix and dilute samples in 2 different ways. 9 cell mixtures from the 3 cell lines were sorted in different combinations in the cell mixture experiment and data were generated by CEL-seq2, the material after pooling from 384 wells were subsampled in either 1/9 or 1/3 to simulate cells of different sizes, with different PCR product clean up ratios ranging from 0.7 to 0.9, referred to as cellmix1 to cellmix4. For the cell mixture experiment, we also sorted wells with 10 times more cells (90 cells) to provide a pseudo bulk reference for each mixture (referred to as cellmix5). Distinct RNA mixtures which were diluted down to create single cell equivalents (ranging from 3.75, 7.5, 15 to 30 pg per well) were generated using CEL-seq2 and SORT-seq (referred to as RNAmix_CEL-seq2 and RNAmix_Sort-seq. This is the RNAmix_CEL-seq2 dataset.
Publication Title
scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 1 Downloadable Sample
- NextSeq 500
Description
Single cell RNA sequencing (scRNA-seq) technology has undergone rapid development in recent years and brings new challenges in data processing and analysis. This has led to an explosion of tailored analysis methods for scRNA-seq to address various biological questions. However, the current lack of gold-standard benchmarking datasets makes it difficult for researchers to evaluate the performance of the many methods available in a systematic manner. Here, we designed and generated a cross-platform benchmark dataset that has in-built truth in various forms and varying levels of biological noise. We used this dataset to compare different protocols and data analysis methods. We found that different protocols have different data quality and ERCC spike-in works independently to endogenous RNA. We found significant differences in the results from the methods compared and we associated the results with data characteristics to identify methods that perform well in different situations. Our dataset and analysis provide a valuable resource for algorithm selection in different biological settings. Overall design: our experiment utilized the 3 human lung adenocarcinoma cell lines H2228, H1975 and HCC827. The experiment included mixtures of RNA and single cells from these cell lines. For the single cell designs, the three cell lines were mixed equally and processed by 10X chromium, Drop-seq and CEL-seq2, referred to as sc_10X, sc_Drop-seq and sc_CEL-seq2 respectively in analysis that follows. For the mixture designs, we used plate-based protocols to mix and dilute samples in 2 different ways. 9 cell mixtures from the 3 cell lines were sorted in different combinations in the cell mixture experiment and data were generated by CEL-seq2, the material after pooling from 384 wells were subsampled in either 1/9 or 1/3 to simulate cells of different sizes, with different PCR product clean up ratios ranging from 0.7 to 0.9, referred to as cellmix1 to cellmix4. For the cell mixture experiment, we also sorted wells with 10 times more cells (90 cells) to provide a pseudo bulk reference for each mixture (referred to as cellmix5). Distinct RNA mixtures which were diluted down to create single cell equivalents (ranging from 3.75, 7.5, 15 to 30 pg per well) were generated using CEL-seq2 and SORT-seq (referred to as RNAmix_CEL-seq2 and RNAmix_Sort-seq. This is the RNAmix_CEL-seq2 dataset.
Publication Title
scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 1 Downloadable Sample
- NextSeq 500
Description
Single cell RNA sequencing (scRNA-seq) technology has undergone rapid development in recent years and brings new challenges in data processing and analysis. This has led to an explosion of tailored analysis methods for scRNA-seq to address various biological questions. However, the current lack of gold-standard benchmarking datasets makes it difficult for researchers to evaluate the performance of the many methods available in a systematic manner. Here, we designed and generated a cross-platform benchmark dataset that has in-built truth in various forms and varying levels of biological noise. We used this dataset to compare different protocols and data analysis methods. We found that different protocols have different data quality and ERCC spike-in works independently to endogenous RNA. We found significant differences in the results from the methods compared and we associated the results with data characteristics to identify methods that perform well in different situations. Our dataset and analysis provide a valuable resource for algorithm selection in different biological settings. Overall design: our experiment utilized the 3 human lung adenocarcinoma cell lines H2228, H1975 and HCC827. The experiment included mixtures of RNA and single cells from these cell lines. For the single cell designs, the three cell lines were mixed equally and processed by 10X chromium, Drop-seq and CEL-seq2, referred to as sc_10X, sc_Drop-seq and sc_CEL-seq2 respectively in analysis that follows. For the mixture designs, we used plate-based protocols to mix and dilute samples in 2 different ways. 9 cell mixtures from the 3 cell lines were sorted in different combinations in the cell mixture experiment and data were generated by CEL-seq2, the material after pooling from 384 wells were subsampled in either 1/9 or 1/3 to simulate cells of different sizes, with different PCR product clean up ratios ranging from 0.7 to 0.9, referred to as cellmix1 to cellmix4. For the cell mixture experiment, we also sorted wells with 10 times more cells (90 cells) to provide a pseudo bulk reference for each mixture (referred to as cellmix5). Distinct RNA mixtures which were diluted down to create single cell equivalents (ranging from 3.75, 7.5, 15 to 30 pg per well) were generated using CEL-seq2 and SORT-seq (referred to as RNAmix_CEL-seq2 and RNAmix_Sort-seq.
Publication Title
scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 44 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Renal cell carcinoma (RCC) is among the ten most common malignancies. By far, the most common histology is clear cell (ccRCC). The Cancer Genome Atlas and other large scale sequencing studies of ccRCC have been integral to the current understanding of molecular events underlying RCC and its biology. However, these data sets have focused on primary RCC which often demonstrates indolent behavior. In contrast, metastatic disease is the major cause of mortality associated with ccRCC. However, data sets examining metastatic tumor are sparse. We therefore undertook an integrative analysis of gene expression and DNA methylome profiling of metastatic ccRCC in addition to primary RCC and normal kidney. Integrative analysis of the methylome and transcriptome identified over 30 RCC specific genes whose mRNA expression inversely correlated with promoter methylation including several known targets of hypoxia inducible factors (HIFs). Notably, genes encoding several metabolism-related proteins were identified as differentially regulated via methylation. Collectively, our data provide novel insight into biology of aggressive RCC. Furthermore, they demonstrate a clear role for epigenetics in the promotion of HIF signaling and invasive phenotypes in renal cancer.
Publication Title
Integrative Epigenetic and Gene Expression Analysis of Renal Tumor Progression to Metastasis.
Sample Metadata Fields
Specimen part
View Samples