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| Status |
Public on Jun 17, 2014 |
| Title |
48h_PH2 |
| Sample type |
SRA |
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| Source name |
liver, regeneration phase
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Fischer-344 (F-344)
protocol: partial hepatectomy
time: 48h
tissue: liver
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from different rat liver samples using the standard RNA extraction method with TRIzol (Invitrogen, Carlsbad, CA, USA). RNA concentration in each sample was determined with a NanoDrop-1000 spectrophotometer (Thermo Fisher Scientific Italy, Cinisello Balsamo, Italia) and quality assessed with the Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano cartridges (Agilent Technologies, Santa Clara, CA, USA).
small RNA-Seq were performed by next generation sequencing (NGS) with sequencing-by-synthesis technology. 1 μg of total RNA was used in a library preparation according to the Illumina TruSeq small RNA sample preparation protocol (Illumina, USA). Sized smallRNA libraries were gel purified and sequenced on HiSeq 1500 (Illumina) at a concentration of 10pM for 50 plus 7 additional cycles for indexes sequencing
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 1500 |
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| Description |
48h_post_PH
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| Data processing |
Basecalls was performed using CASAVA version 1.8
Adapter sequence was removed using cutadapt tools that is part of iMir
To predict piRNAs, iMir uses piRNABank (tranlib), while miRAnalyzer version 0.3 was used for the identification of known miRNAs and other sncRNA.
putative piRNAs were predicted by using NCBI BLAST (v 2.2.28+) using a cut-off of evalue <0.01 against homologous species human and mouse.
Differential expression analisys of piRNAs and putative piRNAs was done using DESEQ 1.14.0 package from R Bioconductor setting a p-value ≤ 0.05 and a fold-change ≤-1.5 and ≥1.5
Genome_build: Baylor 3.4/rn4
Supplementary_files_format_and_content: Tab-delimited text files represent piRNAs. They were generated using iMir.
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| Submission date |
Mar 11, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Judith Staerk |
| E-mail(s) |
judith.staerk@ncmm.uio.no
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| Organization name |
UiO (University of Oslo)
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| Department |
NCMM (Centre for Molecular Medicine Norway)
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| Lab |
STEM CELL GROUP
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| Street address |
NCMM - Forskningsparken, House 1, 3rd Floor - Gaustadalléen 21
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| City |
Oslo |
| State/province |
Oslo |
| ZIP/Postal code |
0349 |
| Country |
Norway |
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| Platform ID |
GPL18404 |
| Series (1) |
| GSE55783 |
Timed regulation of Piwi-interacting RNAs expression during rat liver regeneration |
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| Relations |
| BioSample |
SAMN02687642 |
| SRA |
SRX484303 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1346050_48h_PH2_piRNABank_unique.txt.gz |
4.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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