|
Status |
Public on Dec 03, 2017 |
Title |
RNA-seq_sham_d4_rep1 |
Sample type |
SRA |
|
|
Source name |
Mouse left ventricle, sham day 4.
|
Organism |
Mus musculus |
Characteristics |
tissue: Heart
|
Growth protocol |
Heart tissues were harvested at indicated time. Left ventricles were dissected and immediately frozen in liquid nitrogen.
|
Extracted molecule |
total RNA |
Extraction protocol |
For RNA-seq analysis using the Illumina NextSeq500, 0.1-2 ug of total RNA was processed for library generation using the NuGEN Ovation RNA-seq library prep kit following the manufacturer’s protocol.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
RNA-seq_read_count.txt RNA-seq_RPKM.txt
|
Data processing |
Sequencing reads were aligned to human genome assembly hg19 by TopHat. The number of reads aligned to RefSeq annotated genes' exons were counted and further normalized to be of unit RPKM (number of reads per kilo base pair per million total reads). Differential gene expression analyses were performed using DEseq. Genome_build: hg19 Supplementary_files_format_and_content: text file of gene read count values Supplementary_files_format_and_content: text file of gene RPKM values
|
|
|
Submission date |
Jul 27, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Jian Xu |
E-mail(s) |
Jian.Xu@stjude.org
|
Phone |
9015955208
|
Organization name |
St. Jude Children's Research Hospital
|
Department |
Pathology
|
Street address |
262 Danny Thomas Place, MS 345
|
City |
Memphis |
State/province |
Tennessee |
ZIP/Postal code |
38105 |
Country |
USA |
|
|
Platform ID |
GPL19057 |
Series (1) |
GSE101977 |
RNA-seq transcriptonal profiling in mouse hearts under pressure overload |
|
Relations |
BioSample |
SAMN07419971 |
SRA |
SRX3044463 |