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| Status |
Public on Mar 12, 2024 |
| Title |
M. mulatta parathyroid gland cells; animal 4 |
| Sample type |
SRA |
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| Source name |
Dissociated primate parathyroid
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| Organism |
Macaca mulatta |
| Characteristics |
cell type: Parathyroid cells
tissue: Dissociated primate parathyroid
age: 23 years
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| Extracted molecule |
total RNA |
| Extraction protocol |
Freshly collected parathroid adenomas from human subjects were obtained with signed informed consent in compliace with the Declaration of Helsinki. Human tissue was dissociated with a gentleMACS on setting "mouse spleen program 1". The digestate was then passed through a 100 µm cell strainer, rinsed with 4 mL ice cold RBC lysis buffer (155mM NH4Cl, 10 mM KHCO3, 0.1 mM EDTA or BD Pharm Lyse solution from Becton Dickinson #555899), and pelleted by centrifugation at 200 x g for 3 minutes. Supernatant was discarded and cells were resuspended again in 5 mL RBC lysis buffer, pelleted, then resuspended in sterile PBS. Cells were counted, pelleted again, then resuspended at a concentration of 1E6 cells/mL in sterile PBS containing 0.1% BSA in preparation for downstream processing. Primate tise
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, parathyroids were dissociated with Collagenase B and agitation, then resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
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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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| Description |
10x Genomics Next GEM Single Cell 3' V3.1
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| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mmul_10 with transcriptome annotation v10.104; GRch38
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Jun 02, 2023 |
| Last update date |
Mar 12, 2024 |
| Contact name |
Diane S Krause |
| E-mail(s) |
diane.krause@yale.edu
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| Organization name |
Yale University
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| Department |
Laboratory Medicine
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| Street address |
10 Amistad St.
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| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06519 |
| Country |
USA |
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| Platform ID |
GPL27943 |
| Series (1) |
| GSE233962 |
Single-cell analysis reveals transcriptional dynamics in primary parathyroid tissue |
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| Relations |
| BioSample |
SAMN35565158 |
| SRA |
SRX20577110 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7439854_Mmul4-barcodes.tsv.gz |
51.5 Kb |
(ftp)(http) |
TSV |
| GSM7439854_Mmul4-features.tsv.gz |
289.8 Kb |
(ftp)(http) |
TSV |
| GSM7439854_Mmul4-matrix.mtx.gz |
63.0 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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