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| Status |
Public on May 26, 2021 |
| Title |
FENDRR_Cro Male |
| Sample type |
SRA |
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| Source name |
Lung tissue
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| Organism |
Mus musculus |
| Characteristics |
transfection: FENDRR
treatment: asbestos
tissue: Lung tissue
gender: male
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from mouse lung tissues by using Tri reagent
Libraries were prepared with the Illumina mRNA Library Preparation kit. mRNA is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
LKS_07
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| Data processing |
The qualified libraries are fed into Illumina sequencers after pooling according to its effective concentration and expected data volume
Paired-end reads were directionally mapped to the genomic loci of mousse genome (GRCm38.p6) by TopHat2.
Cufflinks/Cuffdiff analysis was run to identify the dysregulated RNAs
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Gene expression file generated by cuffdiff analysis
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| Submission date |
May 25, 2021 |
| Last update date |
May 26, 2021 |
| Contact name |
CHAOQUN HUANG |
| E-mail(s) |
chaoqh@okstate.edu
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| Phone |
405-744-3410
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| Organization name |
Oklahoma State University
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| Department |
Physiological Sciences
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| Lab |
Lundberg-Kienlen Lung Biology and Toxicology Laboratory
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| Street address |
264 McElroy Hall
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| City |
Stillwater |
| State/province |
OK |
| ZIP/Postal code |
74078 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE175496 |
Long noncoding RNA FENDRR inhibits lung fibroblast proliferation via a reduction of beta-catenin |
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| Relations |
| BioSample |
SAMN19328023 |
| Supplementary data files not provided |
| Raw data are available in SRA |
| Processed data are available on Series record |
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