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GEO help: Mouse over screen elements for information. |
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Status |
Public on Nov 20, 2014 |
Title |
40 dpp |
Sample type |
SRA |
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Source name |
40 dpp testis
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Organism |
Mus musculus |
Characteristics |
strain: C57BL6/J age: 40 dpp tissue: testis genetic background: C57BL/6
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Extracted molecule |
total RNA |
Extraction protocol |
RNA was harvested using Trizol reagent from testes or FACS-purified cells. 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 |
Directional
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Data processing |
Read sequences were mapped to the genome with Tophat software, and reads that were uniquely and perfectly mapped to the genome were used for following analysis.The unique reads extracted after mapping with Tophat were further mapped to the mRNAs of Ensemble genes with Bowtie software. Reads Per Kilobase of transcript per Million (RPKM) values were calculated for each gene by using (1) A = the number of reads perfectly mapped to either of mRNA variants in sense orientation, (2) B = the mean length of the mRNA variants, and (3) C = the number of unique reads extracted after mapping with Tophat (RPKM = A(103/B)(106/C)). Genome_build: mm9 Supplementary_files_format_and_content: [Gene ID] [Gene name] [6dpp RPKM] [10dpp RPKM] [15dpp RPKM] [18dpp RPKM] [22dpp RPKM] [28dpp RPKM] [40dpp RPKM]
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Submission date |
Nov 01, 2012 |
Last update date |
May 15, 2019 |
Contact name |
Toshiaki Watanabe |
E-mail(s) |
toshwatatoshiakiwatanabe@gmail.com
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Phone |
81-55-981-6796
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Organization name |
Yale University
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Street address |
10 Amistad
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City |
NewHaven |
State/province |
CT |
ZIP/Postal code |
06511 |
Country |
USA |
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Platform ID |
GPL13112 |
Series (2) |
GSE41979 |
Transcriptome analysis during mouse testis development |
GSE42004 |
Spermatogenesis |
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Relations |
SRA |
SRX202326 |
BioSample |
SAMN01797837 |
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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