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Status |
Public on Dec 01, 2019 |
Title |
TG_02_Brain |
Sample type |
SRA |
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Source name |
Brain
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Organism |
Macaca mulatta |
Characteristics |
tissue: Brain age: 75days genotype/variation: MCPH1 transgenic
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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 1
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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 |
SAMN02731507 |
SRA |
SRX523302 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1372347_transgenic_Brain_genes_fpkm.txt.gz |
849.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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