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Sample GSM3348109 Query DataSets for GSM3348109
Status Public on Feb 24, 2020
Title Sox9eGFP Low Female HFD Rep #3
Sample type SRA
 
Source name Intestine
Organism Mus musculus
Characteristics tissue: small intestine
strain: C57BL/6J
gender: female
diet: HFD
Extracted molecule total RNA
Extraction protocol Libraries were prepared according to the TriLink CleanTag Small RNA Library Preparation Kit protocol
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2500
 
Description Sox9-EGFP Low sorted intestine crypt cells from high fat diet sample
Sox9_HFD_RPMMM_mirs_over_50.csv
BC242_chow_Low_AGTCAA_L002_R1
Data processing Small RNA-seq samples were processed using miRquant2.0 (https://github.com/Sethupathy-Lab/miRquant) using default settings
RNA-seq samples were aligned using STAR, quantified using Salmon, and normalized counts were determined using DESeq2
Genome_build: mm9 and dm3 for mouse and fruit fly small RNA-seq, mm10 for mouse RNA-seq
Supplementary_files_format_and_content: RPMMM and normalized counts files are comma separated value matrices containing the Reads Per Million miRs Mapped (RPMMM) or DESeq2 normalized counts for each of the samples, respectively.
 
Submission date Aug 20, 2018
Last update date Feb 24, 2020
Contact name Praveen Sethupathy
Organization name Cornell University
Lab Dr. Sethupathy Lab
Street address Cornell University College of Veterinary Medicine, Box 17
City Ithica
State/province NY
ZIP/Postal code 14853
Country USA
 
Platform ID GPL17021
Series (1)
GSE118814 MicroRNA-7 regulates the plasticity of the enteroendocrine lineage
Relations
BioSample SAMN09866523
SRA SRX4580918

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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