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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 06, 2018 |
| Title |
lung from control group, rep3 |
| Sample type |
SRA |
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| Source name |
lung from mock-infected mouse
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| Organism |
Mus musculus |
| Characteristics |
strain: BALB/c
tissue: lung
age: 6-week old
genotype: wild type
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| Extracted molecule |
total RNA |
| Extraction protocol |
The mouse lungs were homogenized in TRIzol (Invitrogen, CA, US) using the MagNA Lyser system (Roche) according to the manufacturer’s instructions. RNA was further purified using the miRNeasy minikit (Qiagen) based on the manufacturer’s instructions. The purity of the RNA samples was verified spectroscopically, and RNA quality was assessed using Agilent Bioanalyzer 2100 (Cui et al., 2014). Only samples with an RNA integrity number greater than 8 were used. rRNA was depleted from 1 mg of total RNA using RiboZero (Illumina).
cDNA libraries were prepared from the remaining RNA, without poly (A) selection, using the TruSeq Stranded RNA LT kit (Illumina) following the TruSeq stranded total RNA sample preparation guide provided by the vendor (RS-122-9007DOC). The libraries underwent cluster generation using TruSeq PE Cluster Kit v3-cBot-HS and 100 cycles of paired-end sequencing using TruSeq SBS Kit v3-HS (Illumina) and an Illumina HiSeq 2000 sequencer 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 |
M-3
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| Data processing |
Illumina Casava1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Cufflinks v2.1.1 was used to count the read numbers mapped to each gene
To identify most differentially expressed genes, we ranked genes according to their size and sequencing coverage normalized FPKM (fragments per kilo base of exon per million). The log2 fold changes of gene FPKM between two group were tested statistically to determine whether an individual gene expression was altered significantly or not.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.
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| Submission date |
Jun 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jiao Hu |
| E-mail(s) |
hujiao@yzu.edu.cn
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| Organization name |
Yangzhou University
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| Street address |
48 Wenhui Road
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| City |
Yangzhou |
| ZIP/Postal code |
225009 |
| Country |
China |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE100522 |
RNA-seq data of lungs from mouse infected with different H5N1 Avian Influenza Viruses |
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| Relations |
| BioSample |
SAMN07280730 |
| SRA |
SRX2959486 |
| 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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