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Sample GSM2942664 Query DataSets for GSM2942664
Status Public on Jan 23, 2018
Title p3-038a
Sample type SRA
 
Source name p3-038a
Organism Homo sapiens
Characteristics Sex: F
height (inches): 67
weight (lbs): 200
bmi: 31.32100691
time from injury (weeks): 44
smoker: Yes
injury type: ACL injury only
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 SAMN08379134
SRA SRX3591763

Supplementary file Size Download File type/resource
GSM2942664_p3-038a.AAACCTT.gene_counts.txt.gz 3.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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