|
| Status |
Public on Feb 10, 2014 |
| Title |
ICM3_miRNASeq |
| Sample type |
SRA |
| |
|
| Source name |
human left ventricle apex tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: left ventricle apex tissue
diagnosis: ischemic cardiomyopathy
lvad support: pre-LVAD
|
| Extracted molecule |
total RNA |
| Extraction protocol |
LV apex tissues were collected, incubated in RNAlater for 24 hours then frozen in -80℃; RNA were extracted using TriZol, RNA quality confirmed with Qbit (RIN>8)
RNA libraries were prepared using Illumina TrueSeq RNA Sample Prep Kits; small RNA libraries were prepared using Illumina TrueSeq Small RNA Sample Prep Kits
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Demultiplexing and basecalling performed using CASAVA version 1.6
(for miRNASeq) Sequencing data from samples pooled in the same flow cell lane were separated (demultiplexed) using CASAVA 1.6 software (Illumina). The sequence reads were analyzed using the miRanalyzer program, where the raw sequencing data were transformed and filtered to keep only sequences containing 17-26 bases. Filtered reads were then successively mapped (using Bowtie) to the miRBase22 v.16 mouse database (allowing up to two mismatches), to detect known miRNAs. Read counts are provided.
(for RNASeq) After demultiplexing the sequencing data, adapter sequences were removed and the individual libraries were converted to the FASTQ format. Sequence reads were mapped to the human genome (hg9) with TopHat, Sequence reads aligned to the human genome were imported into Partek Genomics Suite version 6.5 (Partek, St Louis, MO) for sequence read clustering, counting and annotation. The RefSeq and Ensemble transcript database was chosen as the annotation reference and subsequent data analyses were focused on sequence reads mapping to coding exons. The read counts of each known transcript were normalized to the length of the individual transcript and to the total mapped read counts in each sample and expressed as RPKM (reads per kilobase of exon per million mapped reads). Sequence reads mapped to different isoforms of individual genes were pooled together for subsequent comparative analyses.
Genome_build: hg9
Supplementary_files_format_and_content: normalized read counts of mRNA and raw read counts of miRNA for individual sample in txt file
|
| |
|
| Submission date |
Apr 19, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Kai-Chien Yang |
| Organization name |
Washington University in St Louis
|
| Department |
Developmental Biology
|
| Lab |
Nerbonne
|
| Street address |
660 South Euclid Avenue Box 8103
|
| City |
St Louis |
| State/province |
MO |
| ZIP/Postal code |
63110-1093 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE46224 |
Deep RNA Sequencing Reveals Dynamic Regulation of Myocardial Noncoding RNA in Failing Human Heart and Remodeling with Mechanical Circulatory Support |
|
| Relations |
| BioSample |
SAMN02053660 |
| SRA |
SRX268758 |
