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| Status |
Public on Sep 01, 2015 |
| Title |
chimp lv 1 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Pan troglodytes |
| Characteristics |
tissue: Liver
Sex: Male
age: 18 weeks
protocol: dUTP stranded protocol
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using a miRNeasy Mini kit.
Libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit v2 according to the manufacturer’s protocol. Poly (A)-positive RNA was purified from 250-500 mg of total RNA using streptavidin-coated magnetic beads (AMPure XP) and subsequently fragmented to ~300 bp. cDNA was synthesized using reverse transcriptase (SuperScript II, Invitrogen) and random primers. The strand-specific RNA-Seq library preparation was based on the incorporation of dUTP in place of dTTP in the second strand of the cDNA. Double-stranded DNA was further used for library preparation. Such dsDNA was subjected to A-tailing and ligation of the barcoded Truseq adapters. Library amplification was performed by PCR on the size selected fragments using the primer cocktail supplied in the kit. Final libraries were analyzed using Agilent DNA 1000 chip to estimate the quantity and check size distribution, and they were quantified by qPCR using the KAPA Library Quantification Kit (KapaBiosystems). Sequencing was done with a Illumina HiSeq 2000 sequencer in a paired-end design according to the manufacturer’s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
dUTP stranded protocol, paired-end reads
Strand-specific and paired-end RNA-seq
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor and low-quality sequences using Condetri with the following settings (-hq=30 –lq=10). Adapters were trimmed from filtered reads if at least 5 nucleotides of the adaptor sequence matched the end of each read. In all experiments, reads below 50 nucleotides or with only one member of the pair were not considered.
We aligned the reads to the correspondent reference species genome with Tophat (v. 2.0.8) with parameters –N 3, -a 5 and –m 1, and including the correspondent parameters for paired-end and strand-specific reads whenever necessary. Multiple mapping to several locations in the genome was allowed unless otherwise stated.
Genome_build: hg19, panTro4, rheMac2 (Mmul_051212), mm10
Supplementary_files_format_and_content: Cufflinks output (isoforms.fpkm_tracking) containing abundance measurements and transcript assembly coordinates
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| Submission date |
May 26, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jorge Ruiz-Orera |
| E-mail(s) |
jorruior@gmail.com
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| Organization name |
Max Delbruck Center for Molecular Medicine
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| Street address |
Robert-Rössle-Straße 10
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| City |
Berlin |
| State/province |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
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| Platform ID |
GPL16809 |
| Series (1) |
| GSE69241 |
Analysis of human, chimpanzee, macaque and mouse tissue transcriptomes using Next Generation Sequencing |
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| Relations |
| BioSample |
SAMN03734999 |
| SRA |
SRX1038918 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1695918_ptr_lv1.cuff.gz |
4.2 Mb |
(ftp)(http) |
CUFF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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