 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 01, 2017 |
| Title |
JG35_5_ATCACG_L001_R1_001 |
| Sample type |
SRA |
| |
|
| Source name |
Skin
|
| Organism |
Nothobranchius furzeri |
| Characteristics |
strain: grz
tissue: Skin
age: 5 weeks
|
| 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) |
dnaseq@leibniz-fli.de
|
| 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 |
GPL19871 |
| 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 |
SAMN06179900 |
| SRA |
SRX3289083 |
| SRA |
SRX2442709 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2438581_JG35_5_ATCACG_L001_R1_001.count.txt.gz |
4.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
