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| Status |
Public on May 08, 2014 |
| Title |
rat1_DeepAC |
| Sample type |
SRA |
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| Source name |
deeper layers of articular cartilage
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
age: 10-week-old
tissue: deeper layers of articular cartilage (AC)
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Proximal tibia was removed, flash frozen in liquid nitrogen, cryosectioned and transferred to adhesive membrane. SFZ and deepAC were separately collected by LMD. Total RNA was extracted using Picopure RNA Isolation Kit. Amplified RNA (aRNA) was generated by linear amplification of mRNA using RiboAmp HS PLUS Kit. Illumina TruSeq RNA Sample Prep Kit v2 was used with 50ng of aRNA for the construction of sequencing libraries.
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 2000 |
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| Description |
PR0141_02
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| Data processing |
Illumina Casava1.8 software used for basecalling.
trimmed mean of M (TMM) values were calculated using protocol described by M.D. Robinson and A. Oshlack. (Genome Biol. 11 (2010) R25)
Genome_build: RefSeq Genes and Transcripts (2012.12.15; UCSC version rn4)
Supplementary_files_format_and_content: txt with TMM values for each Sample
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| Submission date |
May 07, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Yoshifumi Mori |
| E-mail(s) |
yoshimori-tky@umin.net
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| Organization name |
Tokyo University
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| Department |
Orthopaedic Surgery
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| Street address |
7-3-1, Hongo
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| City |
Bunkyo-ku, Tokyo |
| ZIP/Postal code |
113-8655 |
| Country |
Japan |
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| Platform ID |
GPL14844 |
| Series (1) |
| GSE57377 |
mRNA-seq analysis of superficial zone (SFZ) and deeper layers (deep AC) of articular cartilage of adult rats |
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| Relations |
| BioSample |
SAMN02766440 |
| SRA |
SRX534876 |
| 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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