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Sample GSM2309549

Query DataSets for GSM2309549

Status

Public on Sep 29, 2016

Title

Quad_Control_1

Sample type

SRA

Source name

Quadriceps muscle

Organism

Homo sapiens

Characteristics

source: biopsy
anonymized patient identifier: 26
anonymized center identifier: C
disease classification: None
tissue: Quadriceps muscle

Treatment protocol

Autopsy and biopsy samples were frozen at -80 until RNA extraction.

Growth protocol

Extracted molecule

total RNA

Extraction protocol

Frozen tissue samples were lysed using a homogenizer in Trizol. Chloroform was added and mixed, and the aqueous layer was added to isopropanol to precipitate RNA. The RNA was then cleaned up on RNeasy columns (Qiagen) with on column DNase treatment.
Strand-specific libraries (using dUTP incorporation during reverse transcription, and USER treatment prior to PCR) were prepared using standard protocols. RNA was first fragmented, and then ribosomal RNA was subtracted using ribo-zero beads from Epicentre Biotechnologies. Reverse transcription was performed using random primers, followed by 2nd strand cDNA synthesis, end repair, adenylation, and ligation of adapters. Products were run on agarose, size selected, and then subjected to 14-18 cycles of PCR.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

Used standard Hiseq 2000 software.
Reads were mapped using Hisat2.
Genome_build: hg19
Supplementary_files_format_and_content: [.txt] Alternative splicing events were quantitated using MISO software.

Submission date

Sep 13, 2016

Last update date

May 15, 2019

Contact name

Eric T Wang

Organization name

University of Florida

Street address

2033 Mowry Rd

City

Gainesville