 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 12, 2014 |
| Title |
FVB_F_7wk_mRNA_2 |
| Sample type |
SRA |
| |
|
| Source name |
Heart
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB/NJ
tissue: Whole-heart tissue
age (weeks): 7
Sex: F
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Hearts were removed and ventricular apexes were flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Polyadenylated RNA was isolated using oligo(dT) binding, followed by chemical fragmentation and preparation of non-strand-specific, single-end RNA-Seq libraries, as per the Supplement of Matkovich SJ, Hu Y, Eschenbacher WH, Dorn LE, Dorn GW, II. Direct and indirect involvement of microRNA-499 in clinical and experimental cardiomyopathy. Circ Res. 2012;111:521-31.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| 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.
Sequence reads were mapped to the transcriptome, defined by the UCSC genes.gtf, for the mm10 genome and associated bowtie2 index provided by Illumina iGenomes, using tophat v2.0.10 .
htseq-count (authored by Simon Anders) was used to assign tophat-aligned reads to gene entries in the UCSC mm10 genes.gtf.
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.
basecalling quality score phred33 and phred64 (9 week samples only)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include htseq-count values for each gene
|
| |
|
| Submission date |
Mar 11, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Scot J Matkovich |
| E-mail(s) |
[email protected]
|
| Organization name |
Eli Lilly and Company
|
| Street address |
Lilly Corporate Center
|
| City |
Indianapolis |
| State/province |
IN |
| ZIP/Postal code |
46285 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE55790 |
Next Generation Sequencing of Wild-Type FVB/NJ Mouse Cardiac Polyadenylated RNA |
| GSE55792 |
Next Generation Sequencing of Wild-Type C57BL/6J and FVB/NJ Mouse Cardiac Polyadenylated RNA and Small RNA |
|
| Relations |
| Reanalyzed by |
GSE80797 |
| BioSample |
SAMN02687806 |
| SRA |
SRX484403 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1346128_FVB_F_7wk_mRNA_2_HTSeq-count.txt.gz |
90.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
