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| Status |
Public on Dec 15, 2022 |
| Title |
Islets MUT1_1118 |
| Sample type |
SRA |
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| Source name |
Islets
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Islets
age: 8 weeks old
genotype: Ngn3-Cre; Ctnna1 flox/flox
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| Extracted molecule |
total RNA |
| Extraction protocol |
Islet were isolated, disrupted and lyzed in RLT buffer. RNA was harvested using RNeasy kit (Quiagen).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Illumina bcl2fastq v2.18.0.12 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR 2.6.0.a with default parameters
The HTSeq software (v.0.6.0) was applied to generate the count matrix, with default parameters. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using EdgeR 3.28.1.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Dec 13, 2021 |
| Last update date |
Dec 15, 2022 |
| Contact name |
Wenyong Chen |
| Organization name |
City of Hope
|
| Department |
Cancer Biology
|
| Street address |
1500 E. Duarte Road
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| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE190788 |
Investigating the role of cell adhesion molecule alpha-catenin during islet development |
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| Relations |
| BioSample |
SAMN24006320 |
| SRA |
SRX13397598 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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