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| Status |
Public on Aug 20, 2017 |
| Title |
Day7 mock |
| Sample type |
SRA |
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| Source name |
mammary gland
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
tissue: mammary gland
age: lactating day 7
genotype: wild type
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| Extracted molecule |
total RNA |
| Extraction protocol |
mammary glands were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA 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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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rnor_5.0 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Aug 20, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Yanhong Wang |
| E-mail(s) |
7096871@163.com
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| Organization name |
Jiangsu Normal University
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| Street address |
shanghai road number101
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| City |
Xuzhou |
| ZIP/Postal code |
221116 |
| Country |
China |
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| Platform ID |
GPL14844 |
| Series (1) |
| GSE60539 |
Identify and characterize the circular RNAs expressed in lactating rat mammary glands |
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| Relations |
| BioSample |
SAMN03000029 |
| SRA |
SRX684275 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1481818_mock_day7.xlsx.gz |
202.5 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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