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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 15, 2016 |
| Title |
Heart, Control, rep1 |
| Sample type |
SRA |
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| Source name |
Heart, Control
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| Organism |
Danio rerio |
| Characteristics |
tissue: heart
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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.
Libraries of small RNAs for sequencing were prepared using the DGE-Small RNA Sample Kit, Alternative v1.5 Protocol (Illumina; San Diego, California) according to the protocol supplied with the reagents (Protocol Rev. A, published February 2009) and using 1ug of total RNA. One lane of each library was sequenced on the Genome Analyzer IIx (Illumina) using the 36 Cycle Sequencing Kit v5 and v4 flowcell and cluster reagents (Catalog FC-104-5020 and GD-300-1001)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
Pool of 50 resected ventrical samples, 2 weeks after surgery
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| Data processing |
Base calling was with Illumina GAP Pipeline Software v1.70
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 17) and non-coding RNA sequences (Rfam Version 10) 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.
Genome_build: miRBase17
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 |
Sep 19, 2013 |
| 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 |
GPL9319 |
| Series (2) |
| GSE51014 |
Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA-dependent repair pathways |
| GSE51018 |
Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA-dependent repair pathways |
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| Relations |
| BioSample |
SAMN02359215 |
| SRA |
SRX355598 |
| 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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