|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on May 11, 2021 |
Title |
Sham-cJ-2 |
Sample type |
SRA |
|
|
Source name |
heart tissue
|
Organism |
Mus musculus |
Characteristics |
strain: Balb/cJ diet: Fat - 10 Kcal% surgery: sham
|
Extracted molecule |
total RNA |
Extraction protocol |
Qiagen RNeasy Mini Kit (Qiagen, cat# 74104) 2 ug of total RNA was then used in Illumina’s TruSeq Stranded mRNA Library kit (Cat# 20020594)
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
Hearts isolated 1 week after surgery 4439Rutgers_DESeq2_results_allgenes.xlsx
|
Data processing |
Illumina NextSeq 500 Alignement with the genome using STAR (Spliced Transcripts Alignment to a Reference) algorithm Read pairs that had both ends aligned were counted, and those with at least 25 bp overlapping bases in a fragment were assigned Gene annotations were obtained from Subread package. Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923-930, doi:10.1093/bioinformatics/btt656 (2014). Differential genes were detected by DESeq2 at 10%FDR (adjusted p-value). Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15, 550, doi:10.1186/s13059-014-0550-8 (2014). Genome_build: mm10
|
|
|
Submission date |
Jan 21, 2021 |
Last update date |
May 11, 2021 |
Contact name |
Maha Abdellatif |
E-mail(s) |
abdellma@njms.rutgers.edu
|
Phone |
9739721254
|
Organization name |
Rutgers-University
|
Department |
Cell Biology and Molecular Medicine
|
Street address |
185 S. Orange Ave.
|
City |
Newark |
State/province |
NJ |
ZIP/Postal code |
07103 |
Country |
USA |
|
|
Platform ID |
GPL19057 |
Series (1) |
GSE165236 |
The effect of transverse aortic constriction on gene expression in Balb/cJ versus Balb/cByJ(∆ACADS) mice hearts |
|
Relations |
BioSample |
SAMN17441408 |
SRA |
SRX9908658 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
|