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Sample GSM7927736 Query DataSets for GSM7927736
Status Public on Feb 23, 2024
Title Jag1-3 [LN008]
Sample type SRA
 
Source name pancreas
Organism Mus musculus
Characteristics tissue: pancreas
cell type: pancreatic islets
genotype: RIP-Cre+, Rosa26-rtTA+, tetO_Jag1+
treatment: doxycycline supplementation: 8 weeks
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
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
 
Submission date Dec 01, 2023
Last update date Feb 23, 2024
Contact name Utpal Pajvani
E-mail(s) up2104@cumc.columbia.edu
Organization name Columbia University Medical Center
Street address 1150 St. Nicholas Avenue
City New York
State/province NY
ZIP/Postal code 10032
Country USA
 
Platform ID GPL24247
Series (1)
GSE249170 β-cell Jagged1 is sufficient but not necessary for islet Notch activity and insulin secretory defects.
Relations
BioSample SAMN38572385
SRA SRX22711509

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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