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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 13, 2019 |
| Title |
X721_08_H |
| Sample type |
SRA |
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| Source name |
basal
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| Organism |
Mus musculus |
| Characteristics |
strain: FVB/N
tissue: Skin
age: post natal day 4
genotype: Wild type
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| Extracted molecule |
total RNA |
| Extraction protocol |
Primary keratinocytes were isolated and processed for FACS. After sorting, cells were pelleted by centrifugation and re-suspended in Trizol (Invitrogen) followed by chloroform extraction. The aqueous phase was applied to RNeasy minElute column (Qiagen) and the RNA was purified according to manufacturer instructions.
10 ng of purified RNA were processed with Nugen Ovation RNA-Seq System (NuGen) for mouse, to make strand specific RNA-Seq libraries.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
RNAseq: Strand specific RNA-Seq libraries were pooled and paired-end sequenced on an Illumina Hiseq 2000 sequencing system. The generated sequence reads were mapped to the mouse genome (mm10) using Galaxy software. Sequences were aligned to the reference genome using TopHat (Trapnell et al., 2009) and differential expression analysis was done using Cufflinks (Trapnell et al., 2012).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each tissue source, basal wt vs basal bt and suprabasal wt vs suprabasal bt
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| Submission date |
May 13, 2019 |
| Last update date |
Aug 13, 2019 |
| Contact name |
Maria Eriksson |
| E-mail(s) |
Maria.Eriksson.2@ki.se
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| Phone |
+46852481066
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| Organization name |
Karolinska Institutet
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| Department |
BioNut
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| Street address |
Karolinska Institutet, Biosciences and Nutrition, NEO Halsovagen 7
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| City |
Huddinge |
| ZIP/Postal code |
14157 |
| Country |
Sweden |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE131104 |
Accumulation of progerin affects the symmetry of cell division and is associated with impaired Wnt signaling and the mislocalization of nuclear envelope proteins [RNA-Seq] |
| GSE131311 |
Accumulation of progerin affects the symmetry of cell division and is associated with impaired Wnt signaling and the mislocalization of nuclear envelope proteins |
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| Relations |
| BioSample |
SAMN11634974 |
| SRA |
SRX5824694 |
| 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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