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| Status |
Public on May 19, 2023 |
| Title |
BMI0040, Control, scRNAseq |
| Sample type |
SRA |
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| Source name |
PBMC
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| Organism |
Homo sapiens |
| Characteristics |
tissue: PBMC
disease state: Control
age: 31
Sex: Male
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Thawed PBMCs were washed with PBS/0.04% BSA. Cells were counted and 100,000-1,000,000 cells were added to a 2 mL-microcentrifuge tube. Cells were centrifuged at 300xg for 5min at 4°C. The supernatant carefully completely removed, and 0.1X lysis buffer (1x: 10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, nuclease-free H2O, 0.1% v/v NP-40, 0.1% v/v Tween-20, 0.01% v/v digitonin) was added. After 3 min incubation on ice, 1 ml of chilled wash buffer was added. The nuclei were pelted at 500 xg for 5 min at 4°C and resuspended in a chilled diluted nuclei buffer (10X Genomics) for scATAC-seq. Nuclei were counted and the concentration was adjusted to run the assay.
ScRNAseq was performed as described (10x Genomics, Pleasanton, CA), following the Single Cell 3’ Reagents Kits V3.1 User Guidelines. Cells were filtered, counted on a Countess instrument, and resuspended at a concentration of 1,000 cells/μl. The number of cells loaded on the chip was determined based on the 10X Genomics protocol. The 10X chip (Chromium Single Cell 3’ Chip kit G PN-200177) was loaded to target 5,000-10,000 cells final. Reverse transcription was performed in the emulsion and cDNA was amplified following the Chromium protocol. Quality control and quantification of the amplified cDNA were assessed on a Bioanalyzer (High-Sensitivity DNA Bioanalyzer kit) and the library was constructed. Each library was tagged with a different index for multiplexing (Chromium i7 Multiplex Single Index Plate T Set A, PN-2000240) and quality controlled by Bioanalyzer prior to sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| Description |
BMI0040
MRSA-MSSA-CTRL-all-combine-20210908.Rdata
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| Data processing |
Reads of scRNAseq experiments were aligned to hg38 using Cell Ranger v3.1.0 and the filtered feature-by-barcode count matrices were then processed using Seurat v4.0 [PMID: 34062119].
Assembly: hg38
Supplementary files format and content: RDS file contains the integrated data of all samples
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| Submission date |
Dec 06, 2022 |
| Last update date |
May 19, 2023 |
| Contact name |
Elena Zaslavsky |
| E-mail(s) |
elena.zaslavsky@mssm.edu
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| Organization name |
Icahn School of Medicine at Mount Sinai
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| Street address |
1 Gustave L. Levy Pl
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
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| Platform ID |
GPL30173 |
| Series (2) |
| GSE220189 |
Mapping disease-associated regulatory circuits by cell type from single-cell multiomics data (S. aureus scRNA-seq) |
| GSE220190 |
Mapping disease-associated regulatory circuits by cell type from single-cell multiomics data |
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| Relations |
| BioSample |
SAMN32074397 |
| SRA |
SRX18511853 |
| 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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