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Sample GSM2718569 Query DataSets for GSM2718569
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.
 
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.
 
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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