data availability rna seq clean data Search Results


rna-seq data  (Helmholtz Zentrum fur Infektionsforschung GmbH)
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rna-seq data analysis  (BioMicro Systems Inc)
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rna-seq data gcell  (Genentech inc)
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c1 plate based scrna seq read count data  (fluidigm)
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bulk rna-seq data  (Epigenomics ag)
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Epigenomics ag bulk rna-seq data
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data analysis mirna-seq  (CloudSeq Biotech Inc)
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rna-seq expression data  (SusTech GmbH)
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SusTech GmbH rna-seq expression data
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scrna seq data  (10X Genomics)
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10X Genomics scrna seq data
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10x genomics snrna seq data  (10X Genomics)
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a Schematic view of the Microwell-seq3 workflow. Single nuclei are extracted from fresh or frozen tissues. DNA or RNA in nuclei is tagged with the first part of the cell barcode (BC#1) in multiple 96-well plates. Labeled nuclei and barcoded magnetic beads are pooled and evenly loaded into Microwell chips. Oligos are released from the beads and linear preamplification is performed in the chips. Preamplified DNA or RNA fragments are collected from the chips for final library preparation and sequencing. b Representative University of California Santa Cruz (UCSC) Genome Browser view of ATAC-seq and RNA-seq signal tracks (HEK293T cells) from Microwell-seq3, <t>10X</t> Genomics, VASA-seq and Smart-seq-total data. c Distribution of TSS enrichment scores from Microwell-seq3 and 10X Genomics ATAC-seq data in the indicated cell lines, reads (fragments) are down sampled to 2000 fragments per nucleus. The statistical test used is a two-sided Student’s t -test. d Number of the detected annotated genes in human and mouse cell lines (HEK293T, mouse NIH/3T3 and embryonic stem cells (mESCs)) in each method is plotted against the number of unique mapped reads per cell in different down-sampling thresholds. All the reads are remapped with the same pipeline after adapter filtering and trimming. Data of mESCs were generated by VASA-seq. e Comparison of mean ± standard deviation (SD) gene body coverage in protein-coding genes in cell lines across the different methods. Microwell-seq3, FLASH-seq and VASA-seq show even coverage across the length of the genes. Other methods show bias toward the 5′ and 3′ ends of transcripts, respectively. Reads in each method are trimmed to 500,000 per sample. f Proportions of the reads mapped to all annotated genes for each biotype in cell lines across the different methods. Microwell-seq3 detects proportionally higher levels of lncRNAs. Reads in each method are trimmed to 5000 per cell.
10x Genomics Snrna Seq Data, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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genomics scrna seq datasets  (10X Genomics)
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10X Genomics genomics scrna seq datasets
a Schematic view of the Microwell-seq3 workflow. Single nuclei are extracted from fresh or frozen tissues. DNA or RNA in nuclei is tagged with the first part of the cell barcode (BC#1) in multiple 96-well plates. Labeled nuclei and barcoded magnetic beads are pooled and evenly loaded into Microwell chips. Oligos are released from the beads and linear preamplification is performed in the chips. Preamplified DNA or RNA fragments are collected from the chips for final library preparation and sequencing. b Representative University of California Santa Cruz (UCSC) Genome Browser view of ATAC-seq and RNA-seq signal tracks (HEK293T cells) from Microwell-seq3, <t>10X</t> Genomics, VASA-seq and Smart-seq-total data. c Distribution of TSS enrichment scores from Microwell-seq3 and 10X Genomics ATAC-seq data in the indicated cell lines, reads (fragments) are down sampled to 2000 fragments per nucleus. The statistical test used is a two-sided Student’s t -test. d Number of the detected annotated genes in human and mouse cell lines (HEK293T, mouse NIH/3T3 and embryonic stem cells (mESCs)) in each method is plotted against the number of unique mapped reads per cell in different down-sampling thresholds. All the reads are remapped with the same pipeline after adapter filtering and trimming. Data of mESCs were generated by VASA-seq. e Comparison of mean ± standard deviation (SD) gene body coverage in protein-coding genes in cell lines across the different methods. Microwell-seq3, FLASH-seq and VASA-seq show even coverage across the length of the genes. Other methods show bias toward the 5′ and 3′ ends of transcripts, respectively. Reads in each method are trimmed to 500,000 per sample. f Proportions of the reads mapped to all annotated genes for each biotype in cell lines across the different methods. Microwell-seq3 detects proportionally higher levels of lncRNAs. Reads in each method are trimmed to 5000 per cell.
Genomics Scrna Seq Datasets, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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single cell rna seq scrna seq data  (10X Genomics)
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10X Genomics single cell rna seq scrna seq data
a Schematic view of the Microwell-seq3 workflow. Single nuclei are extracted from fresh or frozen tissues. DNA or RNA in nuclei is tagged with the first part of the cell barcode (BC#1) in multiple 96-well plates. Labeled nuclei and barcoded magnetic beads are pooled and evenly loaded into Microwell chips. Oligos are released from the beads and linear preamplification is performed in the chips. Preamplified DNA or RNA fragments are collected from the chips for final library preparation and sequencing. b Representative University of California Santa Cruz (UCSC) Genome Browser view of ATAC-seq and RNA-seq signal tracks (HEK293T cells) from Microwell-seq3, <t>10X</t> Genomics, VASA-seq and Smart-seq-total data. c Distribution of TSS enrichment scores from Microwell-seq3 and 10X Genomics ATAC-seq data in the indicated cell lines, reads (fragments) are down sampled to 2000 fragments per nucleus. The statistical test used is a two-sided Student’s t -test. d Number of the detected annotated genes in human and mouse cell lines (HEK293T, mouse NIH/3T3 and embryonic stem cells (mESCs)) in each method is plotted against the number of unique mapped reads per cell in different down-sampling thresholds. All the reads are remapped with the same pipeline after adapter filtering and trimming. Data of mESCs were generated by VASA-seq. e Comparison of mean ± standard deviation (SD) gene body coverage in protein-coding genes in cell lines across the different methods. Microwell-seq3, FLASH-seq and VASA-seq show even coverage across the length of the genes. Other methods show bias toward the 5′ and 3′ ends of transcripts, respectively. Reads in each method are trimmed to 500,000 per sample. f Proportions of the reads mapped to all annotated genes for each biotype in cell lines across the different methods. Microwell-seq3 detects proportionally higher levels of lncRNAs. Reads in each method are trimmed to 5000 per cell.
Single Cell Rna Seq Scrna Seq Data, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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rna seq data processing  (Azenta)
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Azenta rna seq data processing
a Schematic view of the Microwell-seq3 workflow. Single nuclei are extracted from fresh or frozen tissues. DNA or RNA in nuclei is tagged with the first part of the cell barcode (BC#1) in multiple 96-well plates. Labeled nuclei and barcoded magnetic beads are pooled and evenly loaded into Microwell chips. Oligos are released from the beads and linear preamplification is performed in the chips. Preamplified DNA or RNA fragments are collected from the chips for final library preparation and sequencing. b Representative University of California Santa Cruz (UCSC) Genome Browser view of ATAC-seq and RNA-seq signal tracks (HEK293T cells) from Microwell-seq3, <t>10X</t> Genomics, VASA-seq and Smart-seq-total data. c Distribution of TSS enrichment scores from Microwell-seq3 and 10X Genomics ATAC-seq data in the indicated cell lines, reads (fragments) are down sampled to 2000 fragments per nucleus. The statistical test used is a two-sided Student’s t -test. d Number of the detected annotated genes in human and mouse cell lines (HEK293T, mouse NIH/3T3 and embryonic stem cells (mESCs)) in each method is plotted against the number of unique mapped reads per cell in different down-sampling thresholds. All the reads are remapped with the same pipeline after adapter filtering and trimming. Data of mESCs were generated by VASA-seq. e Comparison of mean ± standard deviation (SD) gene body coverage in protein-coding genes in cell lines across the different methods. Microwell-seq3, FLASH-seq and VASA-seq show even coverage across the length of the genes. Other methods show bias toward the 5′ and 3′ ends of transcripts, respectively. Reads in each method are trimmed to 500,000 per sample. f Proportions of the reads mapped to all annotated genes for each biotype in cell lines across the different methods. Microwell-seq3 detects proportionally higher levels of lncRNAs. Reads in each method are trimmed to 5000 per cell.
Rna Seq Data Processing, supplied by Azenta, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results


a Schematic view of the Microwell-seq3 workflow. Single nuclei are extracted from fresh or frozen tissues. DNA or RNA in nuclei is tagged with the first part of the cell barcode (BC#1) in multiple 96-well plates. Labeled nuclei and barcoded magnetic beads are pooled and evenly loaded into Microwell chips. Oligos are released from the beads and linear preamplification is performed in the chips. Preamplified DNA or RNA fragments are collected from the chips for final library preparation and sequencing. b Representative University of California Santa Cruz (UCSC) Genome Browser view of ATAC-seq and RNA-seq signal tracks (HEK293T cells) from Microwell-seq3, 10X Genomics, VASA-seq and Smart-seq-total data. c Distribution of TSS enrichment scores from Microwell-seq3 and 10X Genomics ATAC-seq data in the indicated cell lines, reads (fragments) are down sampled to 2000 fragments per nucleus. The statistical test used is a two-sided Student’s t -test. d Number of the detected annotated genes in human and mouse cell lines (HEK293T, mouse NIH/3T3 and embryonic stem cells (mESCs)) in each method is plotted against the number of unique mapped reads per cell in different down-sampling thresholds. All the reads are remapped with the same pipeline after adapter filtering and trimming. Data of mESCs were generated by VASA-seq. e Comparison of mean ± standard deviation (SD) gene body coverage in protein-coding genes in cell lines across the different methods. Microwell-seq3, FLASH-seq and VASA-seq show even coverage across the length of the genes. Other methods show bias toward the 5′ and 3′ ends of transcripts, respectively. Reads in each method are trimmed to 500,000 per sample. f Proportions of the reads mapped to all annotated genes for each biotype in cell lines across the different methods. Microwell-seq3 detects proportionally higher levels of lncRNAs. Reads in each method are trimmed to 5000 per cell.

Journal: Cell Discovery

Article Title: Fast and flexible profiling of chromatin accessibility and total RNA expression in single nuclei using Microwell-seq3

doi: 10.1038/s41421-023-00642-z

Figure Lengend Snippet: a Schematic view of the Microwell-seq3 workflow. Single nuclei are extracted from fresh or frozen tissues. DNA or RNA in nuclei is tagged with the first part of the cell barcode (BC#1) in multiple 96-well plates. Labeled nuclei and barcoded magnetic beads are pooled and evenly loaded into Microwell chips. Oligos are released from the beads and linear preamplification is performed in the chips. Preamplified DNA or RNA fragments are collected from the chips for final library preparation and sequencing. b Representative University of California Santa Cruz (UCSC) Genome Browser view of ATAC-seq and RNA-seq signal tracks (HEK293T cells) from Microwell-seq3, 10X Genomics, VASA-seq and Smart-seq-total data. c Distribution of TSS enrichment scores from Microwell-seq3 and 10X Genomics ATAC-seq data in the indicated cell lines, reads (fragments) are down sampled to 2000 fragments per nucleus. The statistical test used is a two-sided Student’s t -test. d Number of the detected annotated genes in human and mouse cell lines (HEK293T, mouse NIH/3T3 and embryonic stem cells (mESCs)) in each method is plotted against the number of unique mapped reads per cell in different down-sampling thresholds. All the reads are remapped with the same pipeline after adapter filtering and trimming. Data of mESCs were generated by VASA-seq. e Comparison of mean ± standard deviation (SD) gene body coverage in protein-coding genes in cell lines across the different methods. Microwell-seq3, FLASH-seq and VASA-seq show even coverage across the length of the genes. Other methods show bias toward the 5′ and 3′ ends of transcripts, respectively. Reads in each method are trimmed to 500,000 per sample. f Proportions of the reads mapped to all annotated genes for each biotype in cell lines across the different methods. Microwell-seq3 detects proportionally higher levels of lncRNAs. Reads in each method are trimmed to 5000 per cell.

Article Snippet: As for the comparison with 10X Genomics snRNA-seq data, only cells that had been sequenced to at least 1000 reads in coding and intronic regions were used to down-sampling.

Techniques: Labeling, Magnetic Beads, Sequencing, RNA Sequencing, Sampling, Generated, Comparison, Standard Deviation