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Sample GSM4751780 Query DataSets for GSM4751780
Status Public on Aug 28, 2020
Title miRNA sequencing of iBAT 2
Sample type SRA
Source name Mouse whole adipose tissue depot
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: iBAT
Treatment protocol No treatment applied to adipose tissue depots
Growth protocol For miRNAseq, total RNA was extracted from fat pads of 13-week old C57BL/6J male mice housed at room temperature and from inguinal fat pads of 13-week old mice housed at 4° C for 1 week prior to sacrifice. For mRNAseq, iBAT and eWAT tissue was dissected from 15-week old C57BL/6J male mice and immediately flash frozen in liquid nitrogen
Extracted molecule total RNA
Extraction protocol RNA was extracted from tissues and cells using a TRIzol (Invitrogen)/chloroform extraction, followed by purification with RNeasy mini kits (Qiagen). To retain small RNAs during RNA purification, 1.5X volumes of 100% ethanol was used to precipitate RNA prior to column loading and RW1 buffer was substituted with RWT (Qiagen).
For miRNA, The TruSeq Small RNA Library Prep Kit (Illumina) was used to prepare libraries for sequencing, which was performed by LC Sciences. For mRNA, the library was prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit, and sequencing was performed on an Illumina NextSeq 500 sequencer.
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2500
Data processing Raw counts per transcript were determined by pseudo alignment tool Kallisto (version: 0.45.0) to mouse index GRCm38 (version: 10)
Per gene abundance measurements were calculated for each sample in R (version: 3.6.1) using package TxImport (version: 1.14.2)
Normalized abundance and log2FoldChange measurements were calculated using DESeq2 output, method "apelgm" (version: 1.26.0)
Genome_build: mm10
Supplementary_files_format_and_content: DEseq normalized counts of miRNA seq.csv
Supplementary_files_format_and_content: DEseq normalized counts of mRNA seq.csv
Submission date Aug 28, 2020
Last update date Aug 29, 2020
Contact name Sean O'Connor
Organization name Rockefeller University
Department Laboratory of Molecular Metabolism
Lab Paul Cohen
Street address 1230 York Ave
City New York
State/province NY
ZIP/Postal code 10065
Country USA
Platform ID GPL17021
Series (1)
GSE142677 AGO HITS-CLIP Reveals Distinct Patterns of miRNA Regulation of Visceral and Brown Adipose Tissue Identity
BioSample SAMN15931901
SRA SRX9029677

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

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