|
| Status |
Public on Sep 08, 2022 |
| Title |
Patient 10022 undam |
| Sample type |
SRA |
| |
|
| Source name |
knee cartilage
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: knee cartilage
patient id: 10022
age: 54 years
Sex: male
pathology: undamaged
treatment: placebo
treatment time: 7days
rna library size: 7765164.89465712
rna library complexity: 11939
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from knee cartilage of consented subjects and quality-controlled in the experiment. RNA quality was evaluated with Agilent 2100 Bioanalyzer System using Eukaryote Total RNA Pico chips.
The sequencing libraries were prepared following the Pico Input Mammalian protocol of the Clontech SMARTer Stranded Total RNA-Seq Kit v2. When possible, 250 pg of RNA per sample were used as input for the sequencing library preparation. In the case of limited amount of material, the highest possible amount of the sample was used for the sequencing library preparation Libraries were clustered in a high-output flow cell using HiSeq PE (paired-end) Cluster Kit v4 on a cBot (Illumina).
After cluster generation, the flow cell was loaded onto HiSeq 2500 for sequencing using HiSeq SBS kit v4 (Illumina). DNA was sequenced from both ends (paired-end) with a read length of 76 bp.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
norm_counts.txt
raw_counts.txt
10022_undam
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to ENSEBML Human Genome 76 reference transcriptome (http://ftp.ensembl.org/pub/grch37/release-76/) using the BOWTIE2 aligner (Langmead 2012).
Gene counts were calculated using HTseq (Anders 2015) and summerized as counts based GRh38 Refseq genes.
Normalization on library size was performed using calcNormFactors.DGEList from edgeR.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw_counts.txt, norm_counts.txt
|
| |
|
| Submission date |
Oct 20, 2021 |
| Last update date |
Sep 08, 2022 |
| Contact name |
Yunyu Zhang |
| E-mail(s) |
[email protected]
|
| Organization name |
Novartis Institute for Biomedical Research
|
| Street address |
22 Windsor Ave
|
| City |
Cambrdige |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL27467 |
| Series (1) |
| GSE186220 |
Human OA cartilages treated with ANGPTL3 mimetic LNA043 and placebo |
|
| Relations |
| BioSample |
SAMN22445664 |
