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| Status |
Public on May 21, 2024 |
| Title |
M4 |
| Sample type |
SRA |
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| Source name |
Intestinal organoid
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| Organism |
Mus musculus |
| Characteristics |
cell type: Intestinal organoid
genotype: mg53-tg
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| Growth protocol |
Theorganoids were embedded in Matrigel (Corning, 356231), and cultured in IntestiCult OGM medium(STEM CELL, 06005).
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| Extracted molecule |
total RNA |
| Extraction protocol |
the intestine was cut into ~5 mm pieces and incubated with 5 mM EDTA-PBS at 4°C for 30 min. Following the incubation, the intestine was transferred to PBS and agitated vigorously. The supernatant was collected and filtered through 100-μm filter. The collection step was repeated 3 times. The combined cell suspension was filtered through 70-μm strainers and centrifuged at 300 x g for 5 min. The isolated crypts were embedded in Matrigel (Corning, 356231) at a density of approximately 100 crypts per μl and cultured in IntestiCult OGM medium (STEM CELL, 06005). For subculture and maintenance, the culture medium was replenished every two days, and the organoids were passaged at a 1:4 ratio every 5 days
Total RNA of each sample was extracted using TRIzol Reagent.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Quality control were processed by Cutadapt(V1.9.1), clean data were aligned to reference genome via software Hisat2 (v2.0.1), Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.Differential expression analysis used the DESeq2 Bioconductor package.
Assembly: mm10
Supplementary files format and content: excel file include fpkm for each sample
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| Submission date |
May 16, 2024 |
| Last update date |
May 21, 2024 |
| Contact name |
Yumeng Pei |
| E-mail(s) |
0623B01@zju.edu.cn
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| Organization name |
Zhejiang university
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| Street address |
Xihu district Zhuan Tang street
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| City |
hangzhou |
| State/province |
zhejiang |
| ZIP/Postal code |
310024 |
| Country |
China |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE267687 |
Overexpression of MG53 in mouse intestinal organoids |
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| Relations |
| BioSample |
SAMN41426524 |
| SRA |
SRX24584755 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8273158_M4.anno.fpkm.xls.gz |
1.7 Mb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
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