|
| Status |
Public on Dec 18, 2019 |
| Title |
Sample_Patellar_Rat_3 |
| Sample type |
SRA |
| |
|
| Source name |
Patellar tendon
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
tissue: Patellar tendon
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified with a miRNeasy Micro Kit (Qiagen) supplemented with DNase I (Qiagen). RNA concentration was determined using a NanoDrop 2000 (Thermo Fisher). RNA was delivered to Weill Cornell Epigenomics Core Facility for RNA sequencing analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Rat tendons edgeR.txt
Rat tendons counts.txt
|
| Data processing |
Quality assessment and fold change calculations were performed in edgeR
Sequencing data was quality checked using FastQC, aligned to the reference genome (rn6) with the HiSAT2 software package
Differential expression based on counts per million mapped reads was performed using edgeR
Genome_build: rn6
Supplementary_files_format_and_content: edgeR
|
| |
|
| Submission date |
Oct 07, 2019 |
| Last update date |
Dec 18, 2019 |
| Contact name |
Christopher L Mendias |
| Organization name |
Hospital for Special Surgery
|
| Street address |
535 E 70th St
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (2) |
| GSE138540 |
Transcriptional analysis of tendons from rat |
| GSE138541 |
A tendon comparative transcriptional atlas |
|
| Relations |
| BioSample |
SAMN12989064 |
| SRA |
SRX6960060 |
