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Sample GSM2438706 Query DataSets for GSM2438706
Status Public on Feb 01, 2017
Title 28_CTTGTA_L005_R1_001
Sample type SRA
 
Source name Brain
Organism Nothobranchius korthausae
Characteristics strain: "Aquarienstamm"
tissue: Brain
age: lifespan class 2
Extracted molecule total RNA
Extraction protocol The organs of the fishes were dissected and transferred into 2 ml tubes with 1 ml cooled QIAzol (Qiagen, Hilden, Germany) and one 5 mm stainless steel bead (Qiagen) was added. Homogenization was performed using a TissueLyzer II (Qiagen) at 30 Hz for 3x 1 min. After incubation for 5 min at room temperature 200 µl chloroform was added. The tube was shaken for 15 s and incubated for 3 min at room temperature. Phase separation was achieved by centrifugation at 12,000x g for 20 min at 4°C. The aqueous phase was transferred into a fresh cup and 10 µg of Glycogen (Invitrogen, Darmstadt, Germany), 0.16x volume NaAc (2 M; pH 4.0) and 1.1x volume isopropanol were added, mixed thoroughly and incubated for 10 min at room temperature. The RNA was precipitated by a centrifugation step with 12,000 x g at 4°C for 20 min. The supernatant was removed and the pellet was washed with 80% Ethanol twice and air dried for 10 min. The RNA was resuspended in 20 µl DEPC-treated water by pipetting up and down, followed by incubation at 65°C for 5 min. The RNA was quantified with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at -80°C until use.
Sequencing procedure was done using Illumina methodology [Bentley et al, 2008]. Around 1 µg of total RNA was used for library preparation (Illumina, TruSeq™ small RNA Sample Prep Kit) using the manufacturer’s description.
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2500
 
Data processing bcl2fastq v1.8.4 used for Basecalling
Sequenced reads were trimmed for adaptor sequence and low-quality sequence ends and filtered by sequence size (<15) using PRINSEQ v0.20.3
Reads were mapped with the aligner segemehl with the -H 1 parameter enabled to the Nothobranchius furzeri genome published by Reichwald et al Cell 2015
Reads were counted using rnacounter with parameters -s -m raw
Genome_build: nfurzeri_genebuild_v1
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each Sample
 
Submission date Dec 22, 2016
Last update date May 15, 2019
Contact name Marco Groth
E-mail(s) [email protected]
Organization name Leibniz Institute on Aging - FLI
Department Core Facility - Next Generation Sequencing
Street address Beutenbergstraße 11
City Jena
ZIP/Postal code 07747
Country Germany
 
Platform ID GPL22848
Series (2)
GSE92854 small RNA-seq of three tissues (brain, liver, skin) of Nothobranchius furzeri (at different ages), embryonic samples of N. furzeri and 6 other killifish species
GSE104321 small RNA-seq of three tissues (brain, liver, skin) of Nothobranchius furzeri (at different ages) and Brain samples of 6 other killifish species
Relations
BioSample SAMN06179842
SRA SRX3289208
SRA SRX2442846

Supplementary file Size Download File type/resource
GSM2438706_28_CTTGTA_L005_R1_001.count.txt.gz 4.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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