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| Status |
Public on May 22, 2018 |
| Title |
552-14 |
| Sample type |
SRA |
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| Source name |
Hippocampus
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| Organism |
Sus scrofa |
| Characteristics |
group: coNEC
Sex: Male
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| Extracted molecule |
total RNA |
| Extraction protocol |
Intact frozen left hippocampi were homogenized by cryogenic tissue pulveriser in liquid nitrogen and total RNA was isolated with RNeasy Lipid Tissue Mini Kit (Qiagen, Copenhagen, Denmark).
Sequencing libraries were constructed using NEBNext UltraTM RNA library Prep Kit for Illumina (New England BioLabs, Ipswich, MA, USA), following the manufacturer’s recommendations. After amplification, products were purified with a AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Raw reads were trimmed to produce clean reads, including removal of the adapter sequence and low-quality reads containning more than 50% bases with Q-value < 10, and more than 10% N bases, as detected by the FASTX tool kit (v0.0.13).
Clean reads were aligned to the porcine genome (Sscrofa10.2) using Tophat v2.1.1.
The bam files aligned by Tophat were assembled to the porcine annotated gene/transcript information by Cufflinks v2.2.1.
The assemblies of all the samples created by Cufflinks were merged together using Cuffmerge.
The bam files were mapped to the merged transcripts, and the expression level of each transcript was estimated using Fragments Per Kilobases per Million reads (FPKM) values by Cuffdiff.
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: Tab delimited files list the results of gene-level differential expression testing between two groups.
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| Submission date |
May 21, 2018 |
| Last update date |
May 22, 2018 |
| Contact name |
Xiaoyu Pan |
| E-mail(s) |
panxiaoyu1988@gmail.com
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| Organization name |
University of Copenhagen
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| Street address |
Dyrlægevej 68
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| City |
Copenhagen |
| ZIP/Postal code |
1870 |
| Country |
Denmark |
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| Platform ID |
GPL22475 |
| Series (1) |
| GSE114705 |
Intestinal necrotizing enterocolitis triggers hippocampal gene expression and neuronal differentiation in preterm neonates |
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| Relations |
| BioSample |
SAMN09232412 |
| SRA |
SRX4107941 |
| 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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