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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 03, 2016 |
| Title |
KO.Derm.UV_1 |
| Sample type |
SRA |
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| Source name |
Skin, Dermis_KO_UV
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| Organism |
Mus musculus |
| Characteristics |
tissue: skin
tissue compartment: dermis
strain: C57BL/6J
genotype: PPARB KO
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol (Invitrogen). RNA quantities and quality were assessed using a NanoDrop ND-1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND-1000 spectrophotometer or an Agilent 2100 Bioanalyzer.
Small RNA libraries were prepared using 1 μg of total RNA according to the TruSeq Small RNA Sample Preparation Guide (Illumina, San Diego, CA). Libraries were sequenced HiSeq 2500 using v3 chemistry.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Sample_4s
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| Data processing |
Base calling was done with Illumina GAP Pipeline Software v1.82
Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX-Toolkit
Sequences were aligned to mouse mature microRNA sequences (from miRBase Version 19) and non-coding RNA sequences (Rfam Version 11) using MEGABLAST with a word size of 8 nucleotides. The criteria for counting a sequence match were if the % query was >=90% of the target sequence and if there were <= 2 mismatches over the alignment. The % query was calculated as (a/q) x p where a= alignment length, q= query length and p= percent identity over aligned region. The matches against miRBase were parsed and the top matches (based on % query) were selected. If a sequence had more than one top match against different database sequences, it was excluded from the subsequent analysis. Matches to Rfam were only taken into account for sequences not matching miRBase.
Supplementary_files_format_and_content: Raw count data for microRNAs were normalized to the relative size of each library using R/Bioconductor package DESeq, estimateSizeFactors function. Count data are provided in tab-delimited format
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| Submission date |
Apr 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Mark Ibberson |
| Organization name |
SIB Swiss Institute of Bioinformatics
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| Department |
Vital-IT
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| Street address |
Genopode building
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| City |
Lausanne |
| ZIP/Postal code |
CH-1015 |
| Country |
Switzerland |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE80430 |
Identification of a novel PPARβ/δ / miR-21-3p axis in UV-induced skin inflammation [human miRNA-seq] |
| GSE80431 |
Identification of a novel PPARβ/δ / miR-21-3p axis in UV-induced skin inflammation |
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| Relations |
| BioSample |
SAMN04869831 |
| SRA |
SRX1713041 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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