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| Status |
Public on Apr 05, 2024 |
| Title |
Amygdala, Rhesus Monkeys and Humans |
| Sample type |
SRA |
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| Source name |
Brain
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| Organisms |
Macaca mulatta; Homo sapiens |
| Characteristics |
tissue: Brain
tissue region: amygdala
amygdala region: mixed sample (ce, lat)
subject id: mixed sample (295, 355, 478, B33, B37, B48)
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single nuclei suspensions were made following minor modifications to 10x genomics demonstrated protocol: Nuclei Isolation from Cell Suspensions and Tissue for Single Cell RNA Sequencing. (CG000124 revE). Briefly, 1 ml of lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% Nonidet P40 substitute, in nuclease free water) was added to each sample, homogenized 20x, and incubated on ice for 5 minutes. Samples were centrifuged at 850 RCF for 5 minutes at 4C. The resulting pellet was rinsed 3 times by resuspending in 1.5% BSA in PBS and centrifuged at 850 RCF for 5 minutes at 4C. Finally, the pellet was resuspended in 250ul 1.5% BSA in PBS and passed through 40µm Flowmi Cell strainer (Bel-art, H13680-0040).
All barcoding and library preparation was performed by the UC Davis Genomics Core using the Single Cell Whole Transcriptome Kit (W01030, V1.3.1 Parse Biosciences) with strict adherence to manufacturer’s instructions
Libraries were prepared by the UC Davis Genomics Core and sequenced on a NovaSeq S4 300 150 bp pair-ended reads (PE150)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Alignment and count matrix generation was performed using the parse biosciences pipeline. Preprocessing, visualization and clustering was performed on the generated count matrix using scanpy (version 1.8.2) and anndata (version 0.7.8).
Sequenced reads from Human and Rhesus FASTQ files were aligned to the GRCH38 and RheMac10 genome assemblies. Rhesus reference genome was built using annotations created by the Comparative Annotation Toolkit (CAT). Human samples were annotated using the latest Ensembl annotation (Ensembl release 106).
Assembly: GRCH38 and RheMac10
Supplementary files format and content: .h5ad
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| Submission date |
Apr 01, 2024 |
| Last update date |
Apr 05, 2024 |
| Contact name |
Andrew Fox |
| E-mail(s) |
dfox@ucdavis.edu
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| Organization name |
University of California, Davis Davis, CA
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| Street address |
1 Shields Ave
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| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
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| Platform ID |
GPL32794 |
| Series (1) |
| GSE262905 |
Translational Insights from Cell-type variation across Amygdala Subnuclei in Rhesus Monkeys and Humans |
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| Relations |
| BioSample |
SAMN40706057 |
| SRA |
SRX24115126 |
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