|
| Status |
Public on Jan 30, 2015 |
| Title |
P3-007A |
| Sample type |
SRA |
| |
|
| Source name |
Anterior cruciate liagment
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Anterior cruciate liagment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol-chloroform method followed by purification using Minispin columns (Qiagen)(45). Total RNA concentrations were obtained using NanoDrop spectrophotometer (NanoDrop Technologies) and quality was determined by Agilent 2100 Bioanalyzer (Agilent Technologies).
Library preparation was performed with 10 ng of total RNA. All samples were DNAseq treated to remove residual DNA and ds-cDNA was prepared using the SeqPlex RNA kit (Sigma-Aldrich) per manufacturer’s protocol. cDNA was then blunt ended, an A base added to the 3’ ends, and then Illumina sequencing adapters were ligated to the ends. Ligated fragments were then amplified for 12 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina HiSeq-2500 using single reads extending 50 bases, targeting 30M read per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalling with Casava version 1.8.2
Raw reads were aligned to Ensembl GRch38.76 and adapters were trimmed with STAR version 2.0.4b
Gene counts of uniquely aligned unambigously mapped readsto Ensembl gene ID's were extracted with Subread:featureCounts version 1.4.5 from the aligned BAM files.
Genome_build: Ensembl GRch38.76
Supplementary_files_format_and_content: Text delimitted file containing raw counts of uniquely aligned unambiguous reads to Ensembl Gene IDs
|
| |
|
| Submission date |
Jan 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Muhammad Farooq Rai |
| Organization name |
Washington University School of Medicine
|
| Department |
Orthopaedic Surgery
|
| Lab |
Linda Sandell
|
| Street address |
660 S. Euclid Ave.
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE65469 |
RNA-seq and Microarray in Transcriptome Profiling of Anterior Cruciate Ligament Tears: Implications for Prognostic Biomarkers Discovery |
|
| Relations |
| BioSample |
SAMN03322686 |
| SRA |
SRX860937 |
