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| Status |
Public on Jan 01, 2019 |
| Title |
MoM_14B |
| Sample type |
SRA |
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| Source name |
Periacetabular synovial tissue
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| Organism |
Homo sapiens |
| Characteristics |
tha status: Revision
cell type: Fibroblast
tissue: hip capsular tissue
status: metal
exposure: cobalt chromium exposed tissue
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were immediately snap-frozen in liquid nitrogen and stored at -80C until mRNA isolation. Frozen biopsy samples were pulverized into powder using a cold mortar and pestle. Crushed samples were then placed into Qiazol reagent and homogenized using the TissueLyser LT (Qiagen, Hilden, Germany). Genomic RNA extractions were performed using the miRNeasy mini kit (Qiagen, Venlo, Netherlands) according to the manufacturer's protocol.The Mayo Clinic Gene Expression Core (Advanced Genomics Technology Center, Mayo Clinic, Rochester, MN) provided RNA integrity (RIN) scores for prioritization of samples best suited to RNA-seq data acquisition
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 2.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample
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| Submission date |
Aug 31, 2018 |
| Last update date |
Jan 01, 2019 |
| Contact name |
Asha Nair |
| E-mail(s) |
nair.asha@mayo.edu
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| Organization name |
Mayo Clinic
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| Street address |
200 1ST ST SW
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| City |
Rochester |
| ZIP/Postal code |
55901 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE119331 |
Molecular Pathology of adverse local tissue reaction caused by metal-on-metal implants |
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| Relations |
| BioSample |
SAMN09941303 |
| SRA |
SRX4629673 |
| 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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