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| Status |
Public on Feb 23, 2024 |
| Title |
Control-1 [LN002] |
| Sample type |
SRA |
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| Source name |
pancreas
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| Organism |
Mus musculus |
| Characteristics |
tissue: pancreas
cell type: pancreatic islets
genotype: RIP-Cre+, Rosa26-rtTA+, tetO_Jag1-
treatment: doxycycline supplementation: 8 weeks
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| Extracted molecule |
total RNA |
| Extraction protocol |
Islets were islated from mice after doxyciline supplementatuoon in drinking water for 8 weeks, and RNA was harvested using Trizol reagent. For TruSeq Stranded mRNA LT Sample Prep Kit/TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E. Macrogen. For library construction, RNA is extracted from a sample. After performing quality control(QC), qualified samples proceed to library construction.
The sequencing library is prepared by random fragmentation of the DNA or cDNA sample, followed by 5’ and 3’ adapter ligation. Alternatively, “tagmentation” combines the fragmentation and ligation reactions into a single step that greatly increases the efficiency of the library preparation process. Adapter-ligated fragments are then PCR amplified and gel purified.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq. Adapters are not trimmed away from the reads.
Raw counts were pseudoaligned to the mouse transcriptome (GRCm38) by Kallisto and gene count tables generated
Differenrial gene expression analyses were performed with limma, implemented in the BioJupies application
Assembly: mm10, GCRm38
Supplementary files format and content: TetO-Jag1-Raw_count_table.txt
Supplementary files format and content: tetO-Jag1-DEGs.txt
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| Submission date |
Dec 01, 2023 |
| Last update date |
Feb 23, 2024 |
| Contact name |
Utpal Pajvani |
| E-mail(s) |
up2104@cumc.columbia.edu
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| Organization name |
Columbia University Medical Center
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| Street address |
1150 St. Nicholas Avenue
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE249170 |
β-cell Jagged1 is sufficient but not necessary for islet Notch activity and insulin secretory defects. |
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| Relations |
| BioSample |
SAMN38572390 |
| SRA |
SRX22711504 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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