GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM5908355

Query DataSets for GSM5908355

Status

Public on Mar 31, 2022

Title

Control 7-weeks Obese ZDF Intestine 1

Sample type

SRA

Source name

Obese ZDF

Organism

Rattus norvegicus

Characteristics

model: Obese ZDF
tissue: Intestine
gender: Male
treatment: Control 7-weeks

Treatment protocol

The porta hepatis was targeted for ultrasound stimulation using a 1.1 MHz single-element focused ultrasound system comprised of a signal generator (Model 33120A, Agilent Technologies Inc., Santa Clara, CA), a RF power amplifier (Model 350L, Electronics & Innovation Ltd., Rochester, NY) and a 1.1 MHz focused single-element ultrasound transducer (Model H102, Sonic Concepts Inc., Bothell, WA). The transducer was acoustically coupled to the animal through a 6-cm tall plastic standoff cone filled with degassed water. Prior to treatments, all rats were anesthetized at 2-4% isoflurane at 1 L/min O2. The Target porta hepatis was localized using a custom ultrasound imaging device (Vivid E9; GE Healthcare). Animals either received 3 minutes of ultrasonic stimulus (1.1 MHz, 200mV per pulse, 150 burst cycles, 500 µs burst period) or Sham stimulus where no energy was applied.

Growth protocol

n.a.

Extracted molecule

total RNA

Extraction protocol

Tissue were rapidly collected at the terminal time point and and treated with RNAlater tissue storage reagent. RNA extraction from tissues, assessment of RNA quality and RNA sequencing were performed at the Roswell Park Cancer Institute, Genomics Shared Resource, Buffalo, New York.
Sequencing RNA libraries were prepared using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) according to the manufacturer’s instructions for the RNA from all tissues except the pancreas and adipose. For these samples, TruSeq Stranded Total RNA Sample Preparation Kit was used.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

NextSeq 550

Data processing

Fastq files of the paired end reads were merged into two files for each sample, one for R1 and one for R2 using Unix commands.
Base quality control was checked using Fast QC v0.10.1 from Babraham Bioinformatics.
Sequencing reads were mapped to the annotated rat genome version, Rattus norvegicus Rnor 6.0.91, using STAR_2.5.3a aligner.
Transcript abundance estimates were generated from the sorted BAM files using RSEM.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: rsem_genes_read_counts.csv : comma-delimited text file that includes the table of raw read counts for every gene and every sample
Supplementary_files_format_and_content: rsem_isoforms_read_counts.csv : comma-delimited text file that includes the table of raw read counts for every transcript and every sample

Submission date

Feb 21, 2022

Last update date

Mar 31, 2022

Contact name

John Graf

Organization name

GE Global Research

Street address

One Research Circle

City

Niskayuna