|
| Status |
Public on Jan 23, 2018 |
| Title |
p3-016a |
| Sample type |
SRA |
| |
|
| Source name |
p3-016a
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: M
height (inches): 72
weight (lbs): 215
bmi: 29.1560571
time from injury (weeks): 129
smoker: No
injury type: ACL injury with Meniscus_tear
tissue: ACL tears remnants
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ACL remnants used in this study were harvested at the time of clinically indicated arthroscopic surgery from a discovery cohort of 28 patients, including 12 with an isolated injury pattern and 16 with a combined injury pattern in patients undergoing ACL reconstruction. RNA was extracted and purified as previously described31. Briefly, ACL remnant was thawed, replenished with 1 mL of Trizol reagent and homogenized with the use of a Polytron homogenizer (Brinkmann Instruments). Aliquot of the homogenized suspension was transferred to a microfuge tube and incubated at room temperature for 5 min to permit the complete dissociation of nucleoprotein complexes. After addition of 200 μL of chloroform, the sample was mixed vigorously and the contents were transferred to phase lock gel tube and centrifuged for 15 min at 4°C. The clear aqueous layer was transferred to a fresh tube and 1 volume of 70% ethyl alcohol was added to precipitate RNA. RNA was collected using RNeasy spin columns (Qiagen Inc.) according to the instruction manual. RNA was quantified by using a NanoDrop ND-100 spectrophotometer (NanoDrop) while quality was assessed with use of Agilent Bioanalyzer (Agilent).
Sigma SeqPlex
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Illumina bcl2fastq2
Demultiplexing with custom demultipler written in python
Technical replicate fastq files were combined and aligned with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45 and annotated with Ensembl Biomart
Genome_build: Ensembl GRCh38.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted text format
|
| |
|
| Submission date |
Jan 19, 2018 |
| Last update date |
Jan 24, 2018 |
| 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 |
GPL21290 |
| Series (1) |
| GSE109419 |
Presence of meniscus tear alters gene expression profile of anterior cruciate ligament tears |
|
| Relations |
| BioSample |
SAMN08379147 |
| SRA |
SRX3591750 |
