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| Status |
Public on May 08, 2020 |
| Title |
SCASC_3 |
| Sample type |
SRA |
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| Source name |
stem cells isolated from tissue
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| Organism |
Oryctolagus cuniculus |
| Characteristics |
tissue: subcutaneous adipose tissue
cell type: SCASC
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from expanded stem cells was isolated using Trizol (Invitrogen, Carlsbad, CA).
The WVU Genomics Core Facility used the Stranded mRNA kit from Kapa Biosystems Inc. (Wilmington, MA) following manufacturer’s recommended protocol when starting with 1 ug of total RNA. Upon completion of the libraries, a final QC check was initiated, which involved Qubit quantification and size estimation on the Agilent Bioanalyzer using a High Sensitivity DNA chip.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
We mapped the pair-end RNA-Seq reads to the reference genome of Oryctolagus cuniculus (OryCun2.0) using the Subread aligner (PMC3664803). The number of read counts corresponding to gene transcripts annotated by Ensembl (OryCun2.0.98) were summarized by the featureCounts function from the Rsubread package (PMC6486549). Gene expression levels were quantified by Reads Per Kilobase of transcript, per Million mapped reads (RPKM; PMID: 18516045) with in-house script. We applied Edger3 (PMC3378882) to call differentially expressed genes with the following criteria: FC > 2, FDR < 0.05, and an average expression (RPKM) higher than one in at least one condition.
Genome_build: OryCun2.0
Supplementary_files_format_and_content: XLS file, from left to right represent "Ensemb_gene_id", "Gene_sumbol", "log2FC (IPFSC/SCASC)", "FDR", "logCPM", "Pvalue", RPKMs for four SCASC samples, and RPKM for four IPFSC samples. Columns "log2FC (IPFSC/SCASC)", "FDR", "logCPM", and "Pvalue" are output from EdgeR 3.
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| Submission date |
Dec 26, 2019 |
| Last update date |
May 08, 2020 |
| Contact name |
Gangqing Hu |
| E-mail(s) |
michael.hu@hsc.wvu.edu
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| Organization name |
West Virginia University
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| Department |
MicroBiology, Immunology, and Cell Biology
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| Lab |
2072A, HSC North, Floor 2
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| Street address |
64 Medical Center Drive
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| City |
Morgantown |
| State/province |
West Virginia |
| ZIP/Postal code |
26506-9177 |
| Country |
USA |
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| Platform ID |
GPL21255 |
| Series (1) |
| GSE142626 |
Site-dependent lineage preference of adipose stem cells |
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| Relations |
| BioSample |
SAMN13683325 |
| SRA |
SRX7442980 |
| 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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