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| Status |
Public on Nov 07, 2024 |
| Title |
WKM Ctrl replicate 1 |
| Sample type |
SRA |
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| Source name |
Whole Kidney Marrow
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| Organism |
Danio rerio |
| Characteristics |
tissue: Whole Kidney Marrow
cell type: Whole Kidney Marrow
genotype: wild type
treatment: Heart cryoinjury
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| Treatment protocol |
Heart cryoinjury or untreated
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| Growth protocol |
Standard zebrafish husbandry protocol.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Heart ventricles were placed in the ice-cold PBS buffer with 1% BSA. After several washes removing blood cells, ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer (0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum) for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum, and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re-suspended in HBSS with 0.05% BSA. The cell suspension (2 ml) was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. After spinning down at 200 g for 5 min at 4°C, the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly, kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re-suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer (0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum) at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar (Bel-Art Products), and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. After spinning down at 300 g for 5 min, pellets were washed one more time with PBS plus 0.05% BSA. After centrifuging at 300 g for 5 min, the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer.
Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3, and Chromium Single Cell B Chip Kit.
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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 |
Demultiplexing, alignment, filtering, and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command.
Sample integration (batch correction), expression value normalization, clustering, cell type annotation and so on were done scater and scran. For more details and the cell type annotation information, see https://github.com/abcwcm/CZI_MI_mouseZebrafish
Assembly: GRCz11
Supplementary files format and content: CellRanger produced filtered feature-barcode matrix in H5 format.
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| Submission date |
Mar 12, 2023 |
| Last update date |
Nov 07, 2024 |
| Contact name |
Paul Zumbo |
| Organization name |
Weill Cornell Medicine
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| Department |
Applied Bioinformatics Core
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| Lab |
Applied Bioinformatics Core
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| Street address |
1300 York Ave
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| City |
New York |
| ZIP/Postal code |
10021 |
| Country |
USA |
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| Platform ID |
GPL24995 |
| Series (2) |
| GSE227190 |
Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish] |
| GSE227191 |
Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish |
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| Relations |
| BioSample |
SAMN33731562 |
| SRA |
SRX19646194 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7092958_Ctrl-WKM-1_filtered_feature_bc_matrix.h5 |
10.7 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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