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GEO help: Mouse over screen elements for information. |
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Status |
Public on Apr 02, 2024 |
Title |
freshly isolated hepatocytes, replicate 3 |
Sample type |
SRA |
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Source name |
liver
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Organism |
Mus musculus |
Characteristics |
tissue: liver cell line: C57BL/6J cell type: Hepatocyte genotype: WT treatment: freshly isolated from tissue
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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).
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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)".
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
Hep_0h_4
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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
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Submission date |
Nov 24, 2023 |
Last update date |
Apr 02, 2024 |
Contact name |
Atsushi Suzuki |
Organization name |
Kyushu University
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Department |
Medical Institute of Bioregulation
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Lab |
Division of Organogenesis and Regeneration
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Street address |
3-1-1 Maidashi, Higashi-ku
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City |
Fukuoka |
State/province |
Fukuoka |
ZIP/Postal code |
812-8582 |
Country |
Japan |
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Platform ID |
GPL24247 |
Series (1) |
GSE248554 |
Hepatocytes differentiate into intestinal epithelial cells through a hybrid epithelial/mesenchymal cell state in culture II |
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Relations |
BioSample |
SAMN38411958 |
SRA |
SRX22635343 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
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