GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM3517126 Query DataSets for GSM3517126
Status Public on Dec 31, 2019
Title YN09_179_RheMac_NeuN
Sample type SRA
Source name brain
Organism Macaca mulatta
Characteristics tissue: brain
nuclei: NeuN
tissue preparation: Frozen Brain Tissue
region: Brodmann Area 46
sample id: YN09.179
gender: F
age: 28
humanized age: 86
hemisphere: R
pmi: 0.9
rin: 6.9
Extracted molecule total RNA
Extraction protocol nuclear extraction protocol: Tissue isolated from Brodmann Area 46 from 27 healthy humans, 11 healthy chimpanzee and 15 healthy rhesus macaque.700 mg of frozen postmortem brain was homogenized with lysis buffer using a dounce homogenizer. Brain lysate was placed on a sucrose solution to create a concentration gradient. Ultracentrifuge was used to separate nuclei and cytoplasmic fraction.
FANS protocol: Nuclei were resuspended in PBS plus RNase inhibitors and incubated with mouse Alexa488 conjugated anti-NeuN (1:200) (#MAB377X, Millipore, Billerica, MA) and rabbit Alexa555 conjugated anti-OLIG2 (1:75) (#AB9610-AF555, Millipore) antibodies with 0.5% BSA. Immuno-labeled nuclei were collected as NeuN-positive or OLIG2-positive populations by fluorescence-activated cell sorting (FACS).
total RNA extraction protocol: Total RNA were purified from each nuclei population using a ZR-Duet DNA/RNA MiniPrep (Plus) kit according to the manufacturer's instruction. 200 ng total RNA from each sample was treated for ribosomal RNA (rRNA) removal using the Low Input RiboMinus Eukaryote System v2 (#A15027, ThermoFisher) according to the manufacturer's instruction.
Total RNAs with an average RIN value of 7.5±0.16 were used for RNA-seq library preparation. 50 ng of total RNA after rRNA removal was subjected to fragmentation, first and second strand syntheses, and clean up by EpiNext beads (#P1063, EpiGentek, Farmingdale, NY). Second strand cDNA was adenylated, ligated and cleaned up twice by EpiNext beads. cDNA libraries were amplified by PCR, and cleaned up twice by EpiNext beads. cDNA library quality was quantified by a 2100 Bioanalyzer using an Agilent High Sensitivity DNA Kit (#5067-4626, Agilent, Santa Clara, CA). Barcoded libraries were pooled and underwent 75 bp single-end sequencing on an Illumina NextSeq 500.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description Protocol 1
Data processing Single-end reads were aligned with STAR 2.5.2b using options "“--outFilterMultimapNmax 10 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 3 --twopassMode Basic" to the reference sequence (hg19, PanTro5, RheMac8 from UCSC)
Crossmap and Liftover tools were used to translate non-human priamte coordinates into human coordinates. Human reference was used for gene annotation and counting (gencode v19). Uniquely mapped reads were quantified using HTSeq python suite using high-scored orthologs' protein coding genes by exons.
Genome_build: Human hg19, Chimpanzee PanTro5, Rhesus Macaque RheMac8
Supplementary_files_format_and_content: tab separated files with raw counts
Submission date Dec 17, 2018
Last update date Dec 31, 2019
Contact name Genevieve Konopka
Organization name UT Southwestern Medical Center
Department Neuroscience
Street address 5323 Harry Hines Blvd.
City Dallas
State/province TX
ZIP/Postal code 75390-9111
Country USA
Platform ID GPL21120
Series (1)
GSE123936 Accelerated evolution of oligodendrocytes in human brain
BioSample SAMN10602435
SRA SRX5139654

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap