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| Status |
Public on Feb 14, 2014 |
| Title |
SEQC_Thm_F_104_2 |
| Sample type |
SRA |
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| Source name |
Thymus
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Fisher 344
tissue: Thymus
Sex: F
developmental stage (week): 104
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| Growth protocol |
Male and female (unsynchronized) Fisher 344 rats obtained from NCTR's animal breeding colony were fed the NIH-31 diet (ad libitum) and housed under AAALAC- approved conditions with a 12-hr light/dark cycle (0600 - 1800). Rats were housed two per cage in standard polycarbonate cages with hardwood chip bedding maintained at 23 degrees C with a relative humidity of ~50%. Animals were sacrificed at 2, 5, 6, 8, 15, 21, 52, 78 and 104 weeks-of-age. Rats were treated according to the NCTR Institutional Animal Care and Use Committee guidelines.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Each whole organ was individually ground (mortar and pestle, under continuous liquid N2 chilling) into a fine powder prior to RNA extraction, with the exception of liver, spleen, and gastrocnemius muscle for which approximately 100 mg was ground. Ground organ tissue was stored at -80ºC. Total RNA was extracted from approximately 30 mg of ground tissue by using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol, including treatment with DNase.
RNA libraries were prepared for sequencing using an rRNA depletion protocol using the Ribo-Zero Nonmagnetic Kit (Epicentre) coupled with the Illumina TruSeq RNA-Seq library protocol using TruSeq RNA Sample Preparation Kit (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn4 whole genome using TopHat v2.0.4 with default parameters
Alignment results were then processed using Cufflinks v2.0.2 for gene and transcript quantification with default parameters. For samples with 2~3 technical replicates, average FPKM (Fragment Per Kilobase per Million mapped reads) values were used.
Genome_build: rn4
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample
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| Submission date |
Feb 14, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Leming Shi |
| E-mail(s) |
lemingshi@fudan.edu.cn
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| Phone |
+86-18616827008
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| Organization name |
Fudan University
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| Department |
School of Life Sciences
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| Lab |
Center for Pharmacogenomics
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| Street address |
2005 Songhu Road
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| City |
Shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
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| Platform ID |
GPL14844 |
| Series (2) |
| GSE47792 |
SEQC Project |
| GSE53960 |
A rat RNA-Seq transcriptomic Bodymap across eleven organs and four developmental stages |
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| Relations |
| BioSample |
SAMN02642692 |
| SRA |
SRX471637 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1328738_SEQC_Thm_F_104_2.txt.gz |
266.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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