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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 22, 2024 |
| Title |
liver CD45+ cells, pex2 KO, Rep1 |
| Sample type |
SRA |
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| Source name |
liver
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| Organism |
Mus musculus |
| Characteristics |
tissue: liver
cell type: CD45+ cells
genotype: pex2-/- (KO)
age: postnatal day 0
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| Extracted molecule |
total RNA |
| Extraction protocol |
Postnatal day-0 mice from three genotypes (Pex2-/-, Pex2Het, and WT) were euthanized by decapitation, their livers were excised and passed through a 70 μm cell strainer (Falcon Cat#352350) into 1x HBSS (Gibco Cat#14025-092)using a 1 mL syringe plunger. Liver cell suspensions were then centrifuged at 20 xg for 5 min to remove hepatocytes. The supernatant was isolated and cells were treated with Ammonium-Chloride-Potassium (ACK) Lysing Buffer to lyse red blood cells, and then washed. The final cell suspension was resuspended in 1x PBS 0.5% BSA, cell counts were determined and surface-stained using a 1:50 dilution of FITC- and ef450-conjugated anti-CD45 antibodies (BioLegend Cat#103108 and ThermoFisher eBioscence Cat#48-0451-82), and staining with a fixable viability dye (ThermoFisher eBioscience Cat#65-0865). Viable CD45+ cells were sorted by Fluorescence-activated cell sorting (FACs) on a BD FACs ARIA II cell sorter.
Sorted CD45+ cells were processed and fixed according to the 10X Genomics Flex Assay protocol using the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10X Genomics Cat#PN-1000414). Fixed cells were counted and stored at -80oC and shipped on dry ice to the Princess Margaret Genomics Centre, Toronto Ontario, Canada for the generation of barcoded libraries using the Chromium Fixed RNA Kit, Mouse Transcriptome (10X Genomics Cat#PN-1000495) and Dual Index Kit TS Set A 96 rxns (10X Genomics Cat#PN-1000251) prior to sequencing.
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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 |
Instrument model used (Illumina NovaSeq X Plus) was not available in drop down menu
10X Genomics
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| Data processing |
Demultiplexing,barcode processing, gene counting and aggregation were made using the cell ranger multi pipeline in Cell Ranger software v.7.0.0.
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files
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| Submission date |
Nov 24, 2023 |
| Last update date |
May 22, 2024 |
| Contact name |
Francesca Di Cara |
| Organization name |
Dalhousie University
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| Street address |
5850/5980 University Avenue
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| City |
Halifax |
| State/province |
Nova Scotia |
| ZIP/Postal code |
B3K 6R8 |
| Country |
Canada |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE248598 |
Deficiency in peroxisomes underlies failures in neonatal hepatic immune cell hematopoiesis and antigen presentation in a severe Zellweger disease model |
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| Relations |
| BioSample |
SAMN38414909 |
| SRA |
SRX22637442 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7917815_Pex2KO_barcodes.tsv.gz |
43.6 Kb |
(ftp)(http) |
TSV |
| GSM7917815_Pex2KO_features.tsv.gz |
157.9 Kb |
(ftp)(http) |
TSV |
| GSM7917815_Pex2KO_matrix.mtx.gz |
116.7 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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