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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 08, 2022 |
| Title |
βTG miR-503 |
| Sample type |
SRA |
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| Source name |
Islet
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: islet
age: postnatal day 70
genotype: Beta cell specific miR-503 transgenic
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| Extracted molecule |
total RNA |
| Extraction protocol |
Islets were isolated and digested at 37°C for 5 min by 0.08 % trypsin containing 0.006 % EDTA to generate islet single cell, cell suspension was centrifuged and resuspended in cold PBS buffer with 0.4% of BSA at the concentration of ~1000/μl, which then was loaded onto the 10X Chromium Controller using Chromium Single Cell 3’ v2 reagents.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
single cell total RNA
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| Data processing |
Illumina NovaSeq PE150 was used for sequencing and Illumina Casava1.7 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The quality control of our sequenced reads is as follows: the first and last base mass of reads less than 3 will be removed. A group of 4 bases is taken as a group, if the average base mass of the group is less than 15, the sequence of this base group is removed.
The trimmed data was then mapped to mm10 whole genome using STAR_2.5.1b software and calibrated using the GTF annotation file to distinguish exon region, intron region and intergene regionreads. The discrimination rule was: reads were denoted as an exon region at least 50% sequence were matched, reads that were aligned to non-exons and intersected with the intron region were denoted as an intron region, otherwise were denoted as intergenomic regions.
Principal component analysis (PCA) was used to reduce the dimensionality of data sets, and transferred to t-Stochastic Neighbor Embedding (t-SNE) by Cell Ranger 2.1.0 software.
Cell clustering and significant analysis of differentially expressed genes were accomplished by cell ranger 2.1.0 software.
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger matrix
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| Submission date |
Aug 06, 2020 |
| Last update date |
Jul 08, 2022 |
| Contact name |
Yuncai Zhou |
| E-mail(s) |
zyc2012st@126.com
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| Phone |
18360861855
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| Organization name |
Nanjing medical university
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| Street address |
No. 818 Tianyuan East Road, Jiangning District
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| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210000 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE155798 |
Insulin secretory granules release exosomal miR-503 to promote insulin resistance and β-cell senescence. |
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| Relations |
| BioSample |
SAMN15747799 |
| SRA |
SRX8898498 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4712313_BetaTG_miR-503_filtered_barcodes.tsv.gz |
17.2 Kb |
(ftp)(http) |
TSV |
| GSM4712313_BetaTG_miR-503_filtered_genes.tsv.gz |
212.8 Kb |
(ftp)(http) |
TSV |
| GSM4712313_BetaTG_miR-503_filtered_matrix.mtx.gz |
40.6 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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