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Status |
Public on Aug 10, 2023 |
Title |
D8-1-H |
Sample type |
SRA |
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Source name |
liver
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Organism |
Rattus norvegicus |
Characteristics |
tissue: liver Sex: male treatment: DEN time: 8 week
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Extracted molecule |
total RNA |
Extraction protocol |
Each sample was placed in a sterile Petri dish on ice. Fat, fibrous and necrotic areas were removed, and the tissue was subsequently minced to smaller pieces of less than 3 mm. Samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with collagenase Ⅱ (Worthington) for 60 min at 37°C, with agitation. Subsequently, the sample was filtered using a 70-mm nylon mesh (Miltenyi #130-095-823). 10 ml of this cell suspension was counted by Trypan Blue to determine the concentration of live cells. The sample was then centrifuged at 300g and 4℃ for 5 min, and the supernatant was discarded. The cell pellet was resuspended in 1 ml freezing media (Gibco) for long term cryopreservation in liquid nitrogen. Throughout the dissociation procedure, cells were maintained on ice whenever possible, and the entire procedure was completed in less than 1 hr. Cryopreserved single-cell suspensions were promptly thawed and prepared as outlined by the 10x Genomics Single Cell 30 v3 Reagent Kit user guide.
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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
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Data processing |
Basecalls performed using CASAVA version 1.8 Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria: MT% < 30%; Cell Gene Number < Median Gene Number * 2; Cell Gene Number > 200. PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples. Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis. Assembly: Rnor_6.0 (Ensembl release 93) Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes
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Submission date |
Nov 22, 2022 |
Last update date |
Aug 10, 2023 |
Contact name |
qiudong zhao |
E-mail(s) |
zhaoqd@gmail.com
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Organization name |
Shanghai Eastern Hepatobiliary Surgery Hospital
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Department |
Tumor Immunology and Gene Therapy Center
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Street address |
225 Changhai Road
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City |
Shanghai |
ZIP/Postal code |
200438 |
Country |
China |
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Platform ID |
GPL25947 |
Series (1) |
GSE218561 |
GPNMB+Gal-3+ Hepatic Parenchymal Cells Promote Immunosuppressive Microenvironment Formation and Hepatocellular Carcinogenesis |
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Relations |
BioSample |
SAMN31840335 |
SRA |
SRX18352317 |
Supplementary file |
Size |
Download |
File type/resource |
GSM6752543_D8-1-H.barcodes.tsv.gz |
35.3 Kb |
(ftp)(http) |
TSV |
GSM6752543_D8-1-H.genes.tsv.gz |
201.2 Kb |
(ftp)(http) |
TSV |
GSM6752543_D8-1-H.matrix.mtx.gz |
46.5 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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