An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex
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Cites methods from "An RNA-Sequencing Transcriptome and..."
...We mined our existing mouse astrocyte RNA sequencing (RNA-seq) datasets (Zhang et al., 2014) for potential surface markers that were enriched in astrocytes, not expressed by radial glial cells (a major cellular constituent of fetal human brain), and where antibodies to the human antigen already…...
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...We mined our existing mouse astrocyte RNA sequencing (RNA-seq) datasets (Zhang et al., 2014) for potential surface markers that were enriched in astrocytes, not expressed by radial glial cells (a major cellular constituent of fetal human brain), and where antibodies to the human antigen already existed....
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...RNA-seq data from mouse astrocytes were previously collected by FACS from transgenic lines (Zhang et al., 2014), we collected new mouse astrocyte samples using an identical procedure to our human astrocytes, including the use of the monoclonal HepaCAM antibody for immunopanning....
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...Digoxigenin (DIG)-labeled single-stranded antisense riboprobes were prepared, and fresh-frozen 12-mm-thick brain sections were processed as previously described (Zhang et al., 2014) (Supplemental Information)....
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1,388 citations
1,299 citations
Cites methods from "An RNA-Sequencing Transcriptome and..."
...We calculated percentile ranks for several canonical activation genes for our naïve and LPS-stimulated samples, as well as five published datasets (15, 17, 30, 33, 34); these datasets were generated using CD45 or Cx3cr1 rather than a specific microglia marker, such as Tmem119, and used enzymatic digestion or Percoll for dissociation and myelin depletion....
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...Given our interest in Tmem119 expression patterns and microglial maturity, we performed unsupervised hierarchical clustering of our microglial and published RNAseq datasets (30) to find other similarly behaved genes (SI Appendix, Table S3 and Dataset S1, “clusterID” column)....
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References
20,335 citations
"An RNA-Sequencing Transcriptome and..." refers methods in this paper
...…100 bp paired-end reads to the mouse reference genome [University of California, Santa Cruz (UCSC) Genome Browser version mm9] was performed using TopHat software (version 1.3.3; Trapnell et al., 2010), which invokes Bowtie (version 0.12.7) as an internal read mapper (Langmead et al., 2009)....
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13,337 citations
"An RNA-Sequencing Transcriptome and..." refers background or methods in this paper
...…100 bp paired-end reads to the mouse reference genome [University of California, Santa Cruz (UCSC) Genome Browser version mm9] was performed using TopHat software (version 1.3.3; Trapnell et al., 2010), which invokes Bowtie (version 0.12.7) as an internal read mapper (Langmead et al., 2009)....
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...After read mapping, transcripts were then assembled using Cufflinks software (version 1.3.0; Trapnell et al., 2010)....
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...We then recalculated expression levels with Cufflinks using the amended annotation file and extracted corresponding FPKM values for lncRNAs....
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...To correct for these biases, we adopted the widely accepted Cufflinks algorithm to estimate FPKM values....
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...…in lower falsenegative and false-positive discovery rates in addition to a greater linear range (Bainbridge et al., 2006; Cloonan et al., 2008; Marioni et al., 2008; Mortazavi et al., 2008; Nagalakshmi et al., 2008; Sultan et al., 2008; Wilhelm et al., 2008; Trapnell et al., 2010; Wu et al., 2010)....
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12,293 citations
"An RNA-Sequencing Transcriptome and..." refers background in this paper
...…in lower falsenegative and false-positive discovery rates in addition to a greater linear range (Bainbridge et al., 2006; Cloonan et al., 2008; Marioni et al., 2008; Mortazavi et al., 2008; Nagalakshmi et al., 2008; Sultan et al., 2008; Wilhelm et al., 2008; Trapnell et al., 2010; Wu et al., 2010)....
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...Transcript abundance is directly proportional to the number of sequencing reads that map to a specific transcript, resulting in lower falsenegative and false-positive discovery rates in addition to a greater linear range (Bainbridge et al., 2006; Cloonan et al., 2008; Marioni et al., 2008; Mortazavi et al., 2008; Nagalakshmi et al., 2008; Sultan et al., 2008; Wilhelm et al., 2008; Trapnell et al., 2010; Wu et al., 2010)....
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...Comparing these two technologies, RNA-Seq is believed to have increased sensitivity, improved linearity, and a vastly larger dynamic range (Marioni et al., 2008; Mortazavi et al., 2008; Wang et al., 2009)....
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11,528 citations
"An RNA-Sequencing Transcriptome and..." refers background in this paper
...Comparing these two technologies, RNA-Seq is believed to have increased sensitivity, improved linearity, and a vastly larger dynamic range (Marioni et al., 2008; Mortazavi et al., 2008; Wang et al., 2009)....
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4,911 citations
"An RNA-Sequencing Transcriptome and..." refers background in this paper
...However, the expression landscape of lncRNAs across different cell types has not been characterized in a complex organ such as the brain....
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...The eukaryotic genome is transcribed in a developmentally regulated manner to produce large numbers of lncRNA or large intervening noncoding RNAs (Guttman et al., 2009; Mercer et al., 2009), the function of which in gene regulation and cancer pathogenesis are increasingly being recognized....
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...DOI:10.1523/JNEUROSCI.1860-14.2014 Copyright © 2014 the authors 0270-6474/14/3411929-19$15.00/0 RNA sequencing (RNA-Seq) is a method that profiles the transcriptome by deep sequencing of isolated RNAs....
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...One possibility is the presence of distinct RNA granules containing Gdpd2 and Glast mRNAs within astrocytes....
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...Some lncRNAs are expressed in cell type-specific or enriched manners (Table 1)....
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