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| Status |
Public on Dec 31, 2023 |
| Title |
EVD patient L04_mRNA |
| Sample type |
SRA |
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| Source name |
Human peripheral blood
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| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood
disease status: Ebola virus disease
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| Extracted molecule |
total RNA |
| Extraction protocol |
Whole blood was preserved in Trizol reagent (Ambion). RNA isolation was performed using the miRNeasy mini Kit (Qiagen Cat.No 217004)
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The library preparations were sequenced on an Illumina Hiseq 4000 platform and 150 bp paired-end reads were generated.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
L04
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| Data processing |
Basecalls performed using CASAVA version 1.8
Raw data were firstly processed through in-house perl scripts to obtain clean data by removing reads containing adapter, poly-N and with low quality. Indexes of the reference genome were built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
Cufflinks v2.1.1 was used to count the fragment numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and fragments count mapped to this gene.
Genome_build: human NCBI genome build 37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
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| Submission date |
Jun 21, 2016 |
| Last update date |
Dec 31, 2023 |
| Contact name |
xiong liu |
| E-mail(s) |
liuxiong714@163.com
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| Organization name |
State Key Laboratory of Pathogen and Biosecurity
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| Street address |
No.20，Dongdajie Street，Fengtai District
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100071 |
| Country |
China |
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| Platform ID |
GPL20301 |
| Series (2) |
| GSE83563 |
mRNA profiling of patients infected with Ebola virus compared with healthy adult |
| GSE83565 |
mRNA and miRNA profiling of patients infected with Ebola virus compared with healthy adult |
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| Relations |
| BioSample |
SAMN05277580 |
| SRA |
SRX1868506 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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