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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 17, 2015 |
| Title |
cpo.kd.1 |
| Sample type |
SRA |
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| Source name |
Cavia porcellus_kidney
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| Organism |
Cavia porcellus |
| Characteristics |
strain (source): in-house colony
genotype/variation: wild type
age: adult
tissue: normal kidney
organ part: whole kidney
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNAeasy (Qiagen) purification kit according to the manufacturer’s instructions. RNA quality was assessed using an Agilent 2100 Bioanalyser.
Sequencing libraries were prepared using the mRNA-Seq Sample Prep Kit (Illumina, Inc.) in accordance with the manufacturer' instructions. Polyadenylated RNA was isolated using a poly-dT bead procedure, chemically fragmented and randomly primed for reverse transcription. After second-strand synthesis, the ends of the double-stranded complementary DNA were repaired. After 3'-end adenylation of these products, Illumina Paired-End Sequencing adapters were ligated to the blunt ends of the cDNA fragments. Ligated products were run on gels; 300-bp fragments were excised and then PCR-amplified (20 cycles). After column purification, qualities of the resulting libraries were assessed using Agilent 2100 Bioanalysers.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
biological replicate 1
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| Data processing |
The RNA-seq libraries were each sequenced (76 cycles) in at least one lane of the Illumina Genome Analyser IIx platform.
Samples were demultiplexed and the indexed adapter sequences were trimmed using the CASAVA v1.8.2 software (Illumina, Inc.).
The fluorophore intensity files were analyzed with the standard Illumina base-calling algorithms.
51-bp paired-end reads that passed the chastity filter threshold were mapped using TopHat4 2.0 with default parameter values, except for distance between mature pairs (r=200) and the number of allowable mismatches between read and genomic sequences (n=3) to ensure possible genetic heterogeneity between populations. The anchor size (i.e. the minimum aligned length spanning each of the two exons that define a splice junction) was set at 8 bp, and we allowed 1 mismatch on the anchor region. The transcript isoform abundance and averaged gene expression levels were calculated and FPKM normalized using Cufflinks.
Genome_build: Bos taurus Ensembl genome build 62,
Capra hircus de novo transcriptome assembly (PRJNA182763); see GSE43013_chi.rna.gtf.
Sus scrofa Ensembl genome build 62
Canis familiaris Ensembl genome build 62
Felis catus Ensembl genome build 62
Meles meles de novo transcriptome assembly (PRJNA182767)
Ursus americanus de novo transcriptome assembly (PRJNA182773)
Murina leucogaster de novo transcriptome assembly (PRJNA182766)
Tadarida brasiliensis de novo transcriptome assembly (PRJNA182772)
Petaurus breviceps de novo transcriptome assembly (PRJNA182769)
Erinaceus europaeus Ensembl genome build 62
Oryctolagus cuniculus Ensembl genome build 62
Equus caballus Ensembl genome build 62
Chlorocebus aethiops de novo transcriptome assembly (PRJNA182762)
Acomys cahirinus de novo transcriptome assembly (PRJNA182705)
Cavia porcellus Ensembl genome build 62
Mesocricetus auratus de novo transcriptome assembly (PRJNA182765)
Meriones unguiculatus de novo transcriptome assembly (PRJNA182768)
Mus musculus Ensembl genome build 62
Peromyscus leucopus de novo transcriptome assembly (PRJNA182770)
Rattus norvegicus Ensembl genome build 62
Tamias sibiricus de novo transcriptome assembly (PRJNA183188)
Suncus murinus de novo transcriptome assembly (PRJNA182771).
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.
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| Submission date |
Dec 19, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Alexey Fushan |
| E-mail(s) |
alexfushan@gmail.com
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| Organization name |
EWHA
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| Street address |
52, Ewhayeodae-gil
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| City |
Seoul |
| State/province |
Seodaemun-gu |
| ZIP/Postal code |
120-750 |
| Country |
South Korea |
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| Platform ID |
GPL16398 |
| Series (1) |
| GSE43013 |
Gene Expression Defines Natural Changes in Mammalian Lifespan |
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| Relations |
| SRA |
SRX211636 |
| BioSample |
SAMN01831913 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1055046_cpo.kd.1.txt.gz |
134.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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