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Sample GSM6752543 Query DataSets for GSM6752543
Status Public on Aug 10, 2023
Title D8-1-H
Sample type SRA
 
Source name liver
Organism Rattus norvegicus
Characteristics tissue: liver
Sex: male
treatment: DEN
time: 8 week
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.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 10x Genomics
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
 
Submission date Nov 22, 2022
Last update date Aug 10, 2023
Contact name qiudong zhao
E-mail(s) zhaoqd@gmail.com
Organization name Shanghai Eastern Hepatobiliary Surgery Hospital
Department Tumor Immunology and Gene Therapy Center
Street address 225 Changhai Road
City Shanghai
ZIP/Postal code 200438
Country China
 
Platform ID GPL25947
Series (1)
GSE218561 GPNMB+Gal-3+ Hepatic Parenchymal Cells Promote Immunosuppressive Microenvironment Formation and Hepatocellular Carcinogenesis
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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