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| Status |
Public on Mar 12, 2014 |
| Title |
FVB_F_8wk_smallRNA_1 |
| Sample type |
SRA |
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| Source name |
Heart
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| Organism |
Mus musculus |
| Characteristics |
strain: FVB/NJ
tissue: Whole-heart tissue
age (weeks): 8
Sex: F
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| Extracted molecule |
total RNA |
| Extraction protocol |
Hearts were removed and ventricular apexes were flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Illumina TruSeq small RNA preparation kits (version C) were used for all library construction. 3' and 5' adapters capable of recognizing non-mRNA species were sequentially ligated to 1 microgram of total cardiac RNA, followed by reverse transcription, limited PCR amplification to add indexes, and size-selection.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina Casava1.6 and Casava1.8 software was used for basecalling; all 50 nt reads use phred33 quality scores, while all 42 nt reads use phred64 quality scores.
Indexes have been removed from the supplied raw data files. However, raw reads still contain Illumina sequencing adapters 3' to the termination of small RNAs. Thus, pre-processing of raw reads needs to involve sequence removal including, and 3' to, the Illumina adapter sequence.
The E-miR software package (Buermans et al 2010, see below) was used to map trimmed sequencing reads to the mouse genome and quantitate mapped reads. Mouse noncoding RNA and miR-3p/5p annotation was current as of 3/7/14.
Buermans HP, Ariyurek Y, van Ommen G, den Dunnen JT, t Hoen PA. New methods for next generation sequencing based microRNA expression profiling. BMC Genomics. 2010;11:716. PubMed PMID: 21171994; PubMed Central PMCID: PMC3022920.
We have not further normalized or manipulated the count data, preferring that each user perform sample (library) depth normalization using software such as DESeq or edgeR.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include microRNA names, Ensembl transcript information, chromosomal location, and counts.
basecalling quality score phred33 and phred64 (9 week samples only)
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| Submission date |
Mar 11, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Scot J Matkovich |
| E-mail(s) |
[email protected]
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| Organization name |
Eli Lilly and Company
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| Street address |
Lilly Corporate Center
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| City |
Indianapolis |
| State/province |
IN |
| ZIP/Postal code |
46285 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE55791 |
Next Generation Sequencing of Wild-Type FVB/NJ Mouse Cardiac Small RNA |
| GSE55792 |
Next Generation Sequencing of Wild-Type C57BL/6J and FVB/NJ Mouse Cardiac Polyadenylated RNA and Small RNA |
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| Relations |
| BioSample |
SAMN02687868 |
| SRA |
SRX484444 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1346169_FVB_F_8wk_smallRNA_1_count.txt.gz |
22.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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