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Sample GSM7916668 Query DataSets for GSM7916668
Status Public on Apr 02, 2024
Title freshly isolated hepatocytes, replicate 3
Sample type SRA
 
Source name liver
Organism Mus musculus
Characteristics tissue: liver
cell line: C57BL/6J
cell type: Hepatocyte
genotype: WT
treatment: freshly isolated from tissue
Growth protocol Hepatocytes were isolated from 10 week-old adult mouse livers by two-step collagenase digestion (Seglen, 1979) and carefully separated from non-parenchymal cells and residual blood cells by repeated centrifugation. Isolated hepatocytes were cultuerd in the standard medium (Suzuki et al., 2000; Suzuki et al., 2002; Suzuki et al., 2008) with EGF (20 ng/mL). Cultured hepatocytes dedifferentiate into expandable progenitor-like cells. These dedifferentiated hepatocytes, termed dediHeps, can be maintaied in monolayer culture under the same culture condition. dediHeps can re-differentiate into mature hepatocytes by forming aggregates in each well of ultra-low attachment 96-well plates coated with poly 2-hydroxyethyl methacrylate and maintained in the medium used in a previous study (Yamamoto et al., 2018). In organoid culture, 3 × 104 dediHeps, adult intestinal crypts obtained from 10 weeks-old mice and fetal intestinal cells obtained from E13.5 mouse embryos were embedded in Matrigel (BD Biosciences, San Jose, CA) and cultured in the medium used in a previous study (Miura and Suzuki, 2017).
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from hepatocytes, dediHeps, dediHep aggregates, dediHep-derived organoids, FIPC-derived organoids, ISC-derived organoids, and CLiPs using an ISOGEN II (Nippon gene, Tokyo, Japan) or RNeasy mini kit (QIAGEN, Venlo, Netherlands), according to the manufacturer’s instructions.
Detailed protocol is described in "CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq (PMID: 27121950)".
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Hep_0h_4
Data processing Base-calling was performed with bcl2fastq program (v2.20).
The sequence reads were aligned to the mouse reference genome assembly (Ensemble GRCm38) using bowtie2 (v2.3.1).
Unique molecular identifier (UMI) count was calculated from raw read count data that were estimated from aligned data by using HTSeq (v0.6.0) as descrived in "CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq (PMID: 27121950)".
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files include UMI count values of all samples
 
Submission date Nov 24, 2023
Last update date Apr 02, 2024
Contact name Atsushi Suzuki
Organization name Kyushu University
Department Medical Institute of Bioregulation
Lab Division of Organogenesis and Regeneration
Street address 3-1-1 Maidashi, Higashi-ku
City Fukuoka
State/province Fukuoka
ZIP/Postal code 812-8582
Country Japan
 
Platform ID GPL24247
Series (1)
GSE248554 Hepatocytes differentiate into intestinal epithelial cells through a hybrid epithelial/mesenchymal cell state in culture II
Relations
BioSample SAMN38411958
SRA SRX22635343

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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