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| Status |
Public on Oct 03, 2020 |
| Title |
ChBR.GLU.rna |
| Sample type |
SRA |
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| Source name |
brain
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| Organism |
Pan troglodytes |
| Characteristics |
cell type: glutamatergic neurons
brain area: dorsolateral prefrontal cortex
Sex: Male
age (years): 28
genotype: wild type
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| Extracted molecule |
total RNA |
| Extraction protocol |
The dorsolateral prefrontal cortex (DLPFC) tissue specimens were sampled from frozen brains of macaque and chimpanzee subjects, in a region corresponding to human BA9.
Nuclei of glutamatergic or MGE-derived GABAergic neurons were isolated by flow cytometry, using antibodies against neuronal nuclei (anti-NeuN) and MGE-derived GABAergic neurons (anti-SOX6).
Total RNA was isolated from sorted nuclei, using PicoPure Kit (Thermo Fisher Scientific).
RNA-seq libraries were constructed using SMARTer Stranded Total Pico-Input RNA-seq kit (Clontech) and 10 ng RNA from each sample.
Sequencing was performed on an Illumina HiSeq 2500 instrument, using a paired-end 50 (PE50) protocol to an average of ∼50 million read pairs per sample.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
RNA isolated from FANS-sorted nuclei
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| Data processing |
RNA-seq FASTQ files were pre-processed using tools: Scythe, Sickle, and seqtk (trimming 3 bp from the 5′ end of Read 1, in accordance with the SMARTer RNA-seq library kit protocol).
Reads were quantifiied using a transcript- quantification software tool Salmon (version 0.9.1), and aggregated by gene using the R package "tximport" (version 1.6.0)
Differential expression analysis was performed using DESeq2, with the settings: abs(fold change) > 2, FDR < 0.05
Genome_build: hg38, panTro5, rheMac8
Supplementary_files_format_and_content: diiferential expression comparison tables
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| Submission date |
Oct 02, 2020 |
| Last update date |
Oct 06, 2020 |
| Contact name |
Stella Dracheva |
| E-mail(s) |
stella.dracheva@mssm.edu
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| Organization name |
Icahn School of Medicine at Mount Sinai
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| Department |
Dept. of Psychiatry
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| Street address |
James J. Peters VA Medical Center,130 W Kingsbridge Rd
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| City |
Bronx |
| State/province |
New York |
| ZIP/Postal code |
10468 |
| Country |
USA |
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| Platform ID |
GPL19148 |
| Series (2) |
| GSE158932 |
Evolution of regulatory signatures in primate cortical neurons at cell-type resolution [RNA-Seq] |
| GSE158934 |
Evolution of regulatory signatures in primate cortical neurons at cell-type resolution |
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| Relations |
| BioSample |
SAMN16351624 |
| SRA |
SRX9235507 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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