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| Status |
Public on Aug 02, 2023 |
| Title |
Exp 1 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Sus scrofa domesticus |
| Characteristics |
breed: Yorkshire
tissue: Liver
treatment: Parenteral Nutrition
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| Extracted molecule |
total RNA |
| Extraction protocol |
Liver sections were flash frozen in liquid nitrogen and stored a -80C. RNA was harvested using the Trizol method.
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene, Inc.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
mRNA-Seq was performed by Novogene Co. (Sacramento, CA, USA). RNA integrity was assessed with the RNA Nano 6000 Assay kit (Agilent Technologies, CA, USA). All samples had RIN> 4 and passed the established quality thresholds. mRNA was purified using poly-T oligo-attached magnetic beads and library quality was assessed using the Agilent Bioanalyzer 2100 system. RNA-Seq was performed on the Illumina NovaSeq 6000 platform with 150bp paired-end reads. Raw data were cleaned with removal of low-quality reads and then mapped to the Sscrofa11.1 pig genome using Hisat2 v2.0.5. Read counts were then calculated by featureCounts software (v 2.0.3). Differentially expressed genes (DEGs) were identified by using the DESeq2 (v 1.26.0) R package (adjusted p value <=0.05). A principal components analysis was performed and two outliers were excluded from the experimental group.
Assembly: GCF_000003025.6
Supplementary files format and content: Processed data are provided as a tab-delimited text file including read counts for all genes across all samples, including FPKM values
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| Submission date |
Jun 05, 2023 |
| Last update date |
Aug 02, 2023 |
| Contact name |
Scott C Fligor |
| Organization name |
Boston Children's Hospital
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| Department |
Surgery
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| Street address |
300 Longwood Ave
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL29562 |
| Series (1) |
| GSE234108 |
Transcriptomic analysis of early IFALD in preterm piglets receiving parenteral nutrition |
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| Relations |
| BioSample |
SAMN35632667 |
| SRA |
SRX20598167 |
| 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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