GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM2084546

Query DataSets for GSM2084546

Status

Public on May 08, 2016

Title

TAC control 2

Sample type

SRA

Source name

Ventricle

Organism

Mus musculus

Characteristics

strain: FVBN
Sex: Male
surgery: TAC
treatment: LNA-control

Treatment protocol

FVBN male mice (12 week old) that underwent TAC/Sham surgery were injected subcutaneously a LNA-control or LNA-antimiR-34 for 6 weeks, as previously described (Bernardo PNAS 2012;109(43):17615-20).

Growth protocol

FVBN male mice (12 week old) that underwent Transverse Aortic Constriciton (TAC) surgery or Sham controls

Extracted molecule

total RNA

Extraction protocol

Ventricles were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
NGS library from total RNA were prepared (TruSeqTM Small RNA, Illumina) and samples were multiplexed (24 samples per lane) with adaptor primers and ran on 3 flow cell lanes on Illumina HiSeq2000 sequencing machine. RNA libraries were prepared for sequencing using standard Illumina protocols.

Library strategy

miRNA-Seq

Library source

transcriptomic

Library selection

size fractionation

Instrument model

Illumina HiSeq 2000

Data processing

Sequencing Control Software (SCS) and Consensus Assessment of Sequence and Variation (CASAVA) software programmes from Illumina were used to convert raw image data into intensity scores, base calls, quality scored alignments and additional formats for downstream analysis.
MiRNA-Seq reads were aligned to the mouse reference genome (mm10) using Partek Flow® ; version 3.0 (Partek Inc.) with default settings unless otherwise stated. After removing adaptor sequences, the bases of unaligned reads were trimmed for a minimum Phred quality score of 20 and minimum read length=17. Next, fastq files were aligned to the mm10 reference genome with Bowtie 1 (default parameters used except seed mismatch limit=0, seed length=22, alignments reported per read=10) and Bowtie 2 (default parameters except interval between seeds S,1,1.25, ambiguous characters function L,O.15, default reporting mode=false, max alignments reported per read=10). Read counts were then filtered for reads with minimum mapping quality of 20.
The trimmed, aligned and filtered reads were quantitated to known miRNAs using miRBase mature miRNA version 21.
Reads were normalized to reads per million (RPM) and calculated as follows: (Number of sequenced reads / Total reads) X 1,000,000. MiRNA reads containing less than 5 RPM in all groups were subsequently removed.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include miRNA RPM values for samples

Submission date

Mar 09, 2016

Last update date

May 15, 2019

Contact name

Jenny Ooi

Organization name

Baker IDI Heart & Diabetes Institute

Lab

Cardiac Hypertrophy

Street address

75 Commercial Road