 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 15, 2024 |
| Title |
S3: 106 Day, T21, Female |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Lung
genotype: Trisomy 21
|
| Treatment protocol |
Lungs were received as fresh whole lobes and processed either immediately for single cell suspension or fixed in 4% PFA for immunohistochemical analyses
|
| Extracted molecule |
total RNA |
| Extraction protocol |
From each lung, 400 mg of tissue was weighed out and placed on a clean glass petri dish containing chilled HBSS and minced (1-2 mm sized pieces) using a sterile razor blade. Lung was then further dissociated with the Miltenyi gentleMACs dissociator (Cat: 130-093-235) using the manufacturer-set dissociator program. Cell solution was then passed through prepared 70um cell strainer. C tube was then rinsed with 3mL HBSS and passed through strainer, and strainer was rinsed further with an additional 2mL HBSS. Strained cell suspension was then centrifuged at 500G for 5 minutes followed by decanting. Cell pellet was then incubated in Red Blood Cell Lysis Buffer (3 minutes at room temperature), diluted with HBSS (4 HBSS:1 RBC), and centrifuged at 500G for 5 minutes followed by decanting. Cell pellet was subsequently resuspended in 2mL 1% BSA and centrifuged at 500G for 5 minutes followed by decanting (this step was repeated a second time). Cells were then resuspended in 1%FBS DMEM/F12 at a concentration of 1000 cells/μL for single cell RNA library preparation with all subsequent cells frozen down in 90% FBS/10% DMSO solution.
Single cell capture and library production was performed on the Chromium 10X Genomics system with version 3 chemistry according to the manufacturer’s instructions.
Sequencing was performed on an Illumina NovaSeq, with read alignment to GRCh38.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10X Genomics
|
| Data processing |
All single cell sequencing data analysis was performed using Seurat v3.2.
Filtered data were log transformed, scaled, integrated using reverse Principal Component Analysis (rPCA), clustered and represented by Uniform Manifold Approximation and Projection (UMAP) dimensionality reduction.
Assembly: GRCh38
Supplementary files format and content: barcodes, features and matrix files
|
| |
|
| Submission date |
Jul 17, 2024 |
| Last update date |
Aug 15, 2024 |
| Contact name |
Soumyaroop Bhattacharya |
| E-mail(s) |
soumyaroop_bhattacharya@urmc.rochester.edu
|
| Phone |
5852764683
|
| Organization name |
University of Rochester
|
| Department |
Pediatrics
|
| Street address |
601 Elmwood Ave Box 703
|
| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14642 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN42563238 |
| SRA |
SRX25363534 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8403165_3442_barcodes.tsv.gz |
21.8 Kb |
(ftp)(http) |
TSV |
| GSM8403165_3442_features.tsv.gz |
325.6 Kb |
(ftp)(http) |
TSV |
| GSM8403165_3442_matrix.mtx.gz |
39.0 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
