|
Status |
Public on Oct 12, 2018 |
Title |
human_rnaseq_glia_AI |
Sample type |
SRA |
|
|
Source name |
nuclear RNA from specific cell types obtained via the INSPECTION method
|
Organism |
Homo sapiens |
Characteristics |
gender: female age: 89 brain region: cerebellum cell type: glia target molecule: nuclear rna
|
Extracted molecule |
total RNA |
Extraction protocol |
Cell-type specific nuclei were isolated from post-mortem cerebellar tissue using the INSPECTION method. Isolated nuclei were resuspended in Buffer PKD (INSPECTION) for RNA purification using the QNeasy FFPE kit. Standard protocols were followed except with the following modifications: after Proteinase K digestion, RNA was spun at max speed for 15 minutes. The supernatant was removed and incubated at 65oC for 30 minutes, 70oC for 30 minutes, and 80oC for 15 minutes. An on-column DNase digestion was performed in place of the in-solution DNAase digestion. RNA quality was determined using Agilent 2100 Bioanalyzer. Purified RNA was converted to cDNA and amplified using the Nugen Ovation RNA-seq System V2. Amplified cDNA was fragmented, end-repared, adpater ligated, fragment enriched, and sequenced on an Illumina HiSeq 2500 or NextSeq 500 instrument.
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
Data was mapped to the Homo sapiens reference genome (hg38). Analysis for RNA-seq datasets were performed as described in Xu et al., 2017 RNA-seq: Reads were aligned to the mm10 genome using STAR v2.4.2a (--outFilterMismatchNmax 999 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 35 --outFilterMismatchNoverLmax 0.05) RNA-seq: Gene expression levels were estimated using featureCounts v1.5.2 (-C) RNA-seq: Visualization tracks were generated using igvtools v2.3.32. Genome_build: hg38 Supplementary_files_format_and_content: Tab delimited txt format; Table of raw counts for all samples generated using species-specific annotations, mouse-rat-human ortholog annotations, or mouse-human ortholog annotations.
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|
|
Submission date |
Jul 26, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Xiao Xu |
E-mail(s) |
xxu@rockefeller.edu
|
Organization name |
The Rockefeller University
|
Department |
Laboratory of Molecular Biology
|
Lab |
Nathaniel Heintz
|
Street address |
1230 York Ave
|
City |
New York |
State/province |
NY |
ZIP/Postal code |
10065 |
Country |
USA |
|
|
Platform ID |
GPL18573 |
Series (2) |
GSE101913 |
Species and Cell-Type Properties of Classically Defined Human and Rodent Neurons and Glia [Human RNA-Seq] |
GSE101918 |
Species and Cell-Type Properties of Classically Defined Human and Rodent Neurons and Glia |
|
Relations |
BioSample |
SAMN07417088 |
SRA |
SRX3038847 |