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| Status |
Public on Jul 18, 2022 |
| Title |
WT_Injured_3 |
| Sample type |
SRA |
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| Source name |
Cells from knee joints
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: Wildtype
tissue: Knee joints
age: 16 weeks
condition: Injured
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| Treatment protocol |
10-week-old C57BL/6 mice and Trem2 KO mice (purchased from Jackson Laboratory, Bar Harbor, ME, USA) were subjected to anterior cruciate ligament injury using a non-invasive single dynamic tibial compressive overload model.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Control and T1DM mice were euthanized at 16 weeks old. Knee joints were collected, dissected and cut at the edges of the joint region with small traces of soft tissue to preserve the articular integrity. Joints were then homogenized in Qiazol (79306, Qiagen, Valencia, CA, USA) using a PRO tissue homogenizer (Bio-Gen PRO 200, PRO Scientific Inc.). Total RNA was purified using RNeasy Mini Kit (QIAGEN Inc., Germantown, MD, USA) according to the manufacturer’s protocol and the RNA integrity was assessed using a bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Poly(A)+-enriched cDNA libraries were generated using the Illumina TruSeq RNA Library Prep kit v2 (Illumina Inc., Hayward, CA, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Sequence reads were aligned against Mus musculus reference genome (mm10) using STAR. After read alignment, the number of read counts per gene locus was summarized with ‘featureCounts’ from Rsubread package using mm10 gene annotation. Read counts were subsequently normalized using TMM normalization from edgeR.
Assembly: mm10 (GRCm38)
Supplementary files format and content: normCounts.txt: Tab-delimited text file includes TMM normalized CPM values for each Sample.
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| Submission date |
Apr 14, 2022 |
| Last update date |
Jul 18, 2022 |
| Contact name |
Stephen Patrick Wilson |
| E-mail(s) |
wilson265@llnl.gov
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| Organization name |
LLNL
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| Department |
BBTD
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| Street address |
7000 East Ave
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| City |
Livermore |
| State/province |
CA |
| ZIP/Postal code |
94550 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE200842 |
Transcriptomic analysis of injured and uninjured knee joints from Trem2 KO mice [bulk RNA-seq] |
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| Relations |
| BioSample |
SAMN27590456 |
| SRA |
SRX14862191 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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