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| Status |
Public on Nov 24, 2021 |
| Title |
CON CT16-1 (RNA-seq) |
| Sample type |
SRA |
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| Source name |
Islet
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Pancreatic islets
age: 20 weeks
time: CT16
treatment: Control
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from freshly picked mouse islets or transfected INS-1 832/13 cells using the RNeasy mini kit (Qiagen, Hilden, Germany). RNA size and quality were assessed using the Tape Station Bionalyzer (Agilent, Santa Clara, CA), and concentration was determined by Qubit fluorometry. RNA libraries were prepared using 100 ng of total RNA.
RNA libraries were prepared using polyA selection method (Illumina, San Diego, CA) according to manufacturer's instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
RNAseq_CountMatrix_CON_CD_CDtRF.xlsx
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| Data processing |
Illumina's RTA version 2.7.7. for basecalling
RNA-sequencing reads were first mapped to the mm10 or rn6 build of the mouse and rat reference genome, respectively, using HISAT v2.1.0 with default settings. FeatureCounts v2.0.0 from the Subread package was used to count mapped gene-level reads. Gene count matrices were uploaded into the edgeR v3.28.1 package and normalized to counts per million (CPM) reads using the default Trimmed Mean of M-values (TMM) method.
Genome_build: mm10, rn6
Supplementary_files_format_and_content: counts
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| Submission date |
Aug 27, 2021 |
| Last update date |
Nov 24, 2021 |
| Contact name |
Matthew R Brown |
| E-mail(s) |
brownm@broadinstitute.org
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| Organization name |
Broad Institute
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| Street address |
75 Ames St
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE182931 |
Time-restricted feeding prevents deleterious metabolic effects of circadian disruption through epigenetic control of β-cell function [RNAseq] |
| GSE182938 |
Time-restricted feeding prevents deleterious metabolic effects of circadian disruption through epigenetic control of β-cell function |
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| Relations |
| BioSample |
SAMN21023632 |
| SRA |
SRX11951748 |
| 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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