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| Status |
Public on Jan 07, 2014 |
| Title |
chimpanzee(12y)_CBC |
| Sample type |
SRA |
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| Source name |
chimpanzee_12y_Cerebellar cortex
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| Organism |
Pan troglodytes |
| Characteristics |
age: postnatal 12 years
tissue: Cerebellar cortex
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA). Oligo(dT) selection was performed twice using Oligotex mRNA Midi Kit (Qiagen). After selection, 100 ng mRNA was first fragmented by addition of 5 X fragmentation buffer (200 mM Tris acetate, pH 8.2, 500 mM potassium acetate, and 150 mM magnesium acetate) with heating at 94 °C for 2 min 30 s in a thermo-cycler. The fragments were then transferred to ice and run over a Sephadex-G50 column (USA Scientific) to remove the fragmentation ions.
Sequencing libraries were prepared according to the paired-end non-strand-specific sample preparation protocol of Illumina(http://www.illumina.com)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
s_12
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| Data processing |
Image files were preprocessed by illumina software, which generates qseq files
qseq files were converted into fastq files by perl scripts, and only the ones passing illumina quality controls were retained
Reads were mapped onto reference genome panTro2 and rheMac2 by Tophat(1.0.1.0)
mapped reads with more than three mismatches, multiple location mapping filtered out using perl script
sequencing information for each exonic genome sites were extracted by SAMtools (0.1.18)
Processed data files contain the counts of 'A' and 'G' base nucleotides with high sequencing quality (Phred quality score supplied by Illumina sequencing platform >20) for each predicted editing site (DARNED sites) used for analysis of each sample.
Genome_build: Pan_troglodytes-2.1 (http://www.ncbi.nlm.nih.gov/assembly/GCF_000001515.3/) for Pan troglodytes,
Genome_build: Mmul_051212 (http://www.ncbi.nlm.nih.gov/assembly/GCF_000002255.2/) for Macaca mulatta
Supplementary_files_format_and_content: Tab delimited file, counts of 'G' and 'A' base nucleotides for each DARNED sites used;
Supplementary_files_format_and_content: first column: the genomic coordinates
Supplementary_files_format_and_content: second column: counts of 'A' base nucleotides with high sequencing quality
Supplementary_files_format_and_content: third column: counts of 'G' base nucleotides with high sequencing quality
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| Submission date |
Mar 18, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
zs li |
| E-mail(s) |
zsl.picb@gmail.com
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| Phone |
+8621-54920470
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| Organization name |
Partner Institute of Computational Biology
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| Street address |
No. 320, Yueyang Road
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| City |
Shang Hai |
| ZIP/Postal code |
200031 |
| Country |
China |
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| Platform ID |
GPL9378 |
| Series (1) |
| GSE45244 |
Evolutionary and ontogenetic changes in RNA editing in human, chimpanzee and macaque brains |
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| Relations |
| SRA |
SRX251943 |
| BioSample |
SAMN01983912 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1099736_s_12.txt.gz |
1.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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