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| Status |
Public on Dec 01, 2019 |
| Title |
WT_04_Muscle |
| Sample type |
SRA |
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| Source name |
Muscle
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| Organism |
Macaca mulatta |
| Characteristics |
tissue: Muscle
age: 75days
genotype/variation: wild type
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
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 |
Sample 6
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| Data processing |
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Macaca_mulatta.MMUL_1 (ftp://ftp.ensembl.org/pub/release-75/fasta/macaca_mulatta/dna/) whole genome using bowtie v0.12.2
Fragments per kilobase of transcript per million mapped fragments (FPKM) were calculated. Firstly align RNA seq reads to the genome by using Bowtie; Secondly TopHat uses Bowtie as an alignment ‘engine’ and breaks up reads; and then Cufflinks will assemble transcripts and computed the FPKM vlues(http://cufflinks.cbcb.umd.edu/),following protocol from Trapnellet al., Nature Protocol, 2012.
Genome_build: Macaca_mulatta.MMUL_1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Apr 22, 2014 |
| Last update date |
Dec 01, 2019 |
| Contact name |
lei shi |
| E-mail(s) |
shilei@mail.kiz.ac.cn
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| Organization name |
Kunming Institute of Zoology
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| Street address |
No.17 Longxin Road
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| City |
Kunming |
| State/province |
Yunnan |
| ZIP/Postal code |
650201 |
| Country |
China |
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| Platform ID |
GPL14954 |
| Series (1) |
| GSE56962 |
Transgenic rhesus monkeys carrying the human MCPH1 gene copies show human-like neoteny of brain development |
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| Relations |
| BioSample |
SAMN02731513 |
| SRA |
SRX523307 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1372352_wt1_Muscle_genes_fpkm.txt.gz |
832.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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