Experiment Detail
| Title | Illumina HiSeq 2000 paired end sequencing; RNA-Seq analysis of human intact and damaged osteoarthrtitic cartilage following total knee replacement. |
| Design Description | RNA-Seq analysis of human intact and damaged osteoarthrtitic cartilage following total knee replacement. |
| Organism | Homo sapiens |
Library Description
| Name | Patient_6_DMC |
| Strategy | RNA-Seq |
| Source | TRANSCRIPTOMIC |
| Selection | RANDOM |
| Layout | PAIRED |
| Orientation | |
| Nominal Length | 270 |
| Nominal Sdev | 250 |
| Construction Protocol | Cartilage was obtained under Ethics Committee approval with written informed consent from 8 patients with symptomatic OA at total knee replacement (n=8, age range 65-79 years, mean age 70.3). Cartilage from paired osteochondral samples were isolated from the intact PLC (posterior lateral condyle) and the damaged DMC (distal medial condyle) for RNA-seq analysis. Strand specific RNA-seq libraries were generated from 0.5-1 g RNA using the TruSeq Stranded mRNA assay (Illumina, Inc.) using the manufacturers Stranded mRNA Sample Preparation Kit and 101bp paired-end reads were generated with each sample yielding at least 39 million total reads. Total RNA was extracted from 200-400 mg of cartilage using TRIzol (Life-technologies) reagent and homogenisation (Braun Mikrodismembrator) following freezing in liquid nitrogen. The RNA was purified using RNeasy Qiagen clean-up columns (Qiagen) and for sequencing had a RIN score of >6 (2200 TapeStation, Agilent Technologies). |
Platform
| Platform | ILLUMINA |
| Instrument Model | Illumina HiSeq 2000 |
Processing
| Base Calls | |
|---|---|
| Sequence Space | |
| Base Caller | |
Spot Information
| Number of Reads per Spots | 0 |
| Spot Length | 202 |
Read Spec
| Read Index 0 | |
|---|---|
| Read Label | |
| Read Class | Application Read |
| Read Type | Forward |
| Base Coord | 1 |
| Read Index 1 | |
| Read Label | |
| Read Class | Application Read |
| Read Type | Reverse |
| Base Coord | 102 |
Navigation
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Submission | ERA553598 |
 FTP
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Study | ERP013914 | ||
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Sample | ERS1034564 | ||
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Run | ERR1223337 |
FASTQ
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SRA
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