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Sample GSM2416953 Query DataSets for GSM2416953
Status Public on Sep 18, 2017
Title Control Rep1
Sample type SRA
 
Source name Whole Ear_control
Organism Mus musculus
Characteristics strain: C57Bl/6
tissue: Skin
genotype: WT
Extracted molecule total RNA
Extraction protocol Samples of murine skin were obtained and stored in RNAlater (Sigma) before processing following the manufacturer’s instructions. To extract whole tissue RNA, samples were homogenized using a bead homogenizer and processed using the Qiagen RNeasy kit following the manufacturer’s instructions. Following total RNA extraction, samples were treated with DNase (Turbo DNA-Free Kit, Thermo Scientific) following the manufacturer’s instructions before sequencing library preparation.
Library preparation was performed with 1 ug of total RNA, integrity was determined using an Agilent Bioanalyzer. Ribosomal RNA was removed by a hybridization method using Ribo-ZERO kits (Illumina-EpiCentre). mRNA was then fragmented in buffer containing 40 mM Tris Acetate (pH 8.2), 100 mM Potassium Acetate, and 30mM Magnesium Acetate and heated to 94°C for 150 seconds. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer’s instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina HiSeq-3000 using single reads extending 50 bases.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing RNA-sequencing reads were aligned to the Ensembl release 76 assembly with STAR version 2.0.4b. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3. Sequencing performance was assessed for total number of aligned reads, total number of uniquely aligned reads, genes and transcripts detected, ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including count values for each sample.
 
Submission date Dec 05, 2016
Last update date May 15, 2019
Contact name Landon Kyle Oetjen
E-mail(s) lkoetjen@wustl.edu
Organization name Washington University
Street address 660 S Euclid Avd
City St. Louis
State/province MO
ZIP/Postal code 63110
Country USA
 
Platform ID GPL21493
Series (1)
GSE90883 Sensory neurons co-opt classical immune signaling pathways to mediate chronic itch
Relations
BioSample SAMN06111408
SRA SRX2396147

Supplementary file Size Download File type/resource
GSM2416953_AAATGCA_gene_counts.txt.gz 2.7 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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