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| Status |
Public on Feb 03, 2014 |
| Title |
P3 |
| Sample type |
SRA |
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| Source name |
papilloma
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| Organism |
Mus musculus |
| Characteristics |
tissue: skin
background strain: FVB/N
disease state: papilloma
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| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen miRNeasy mini kit
NEBNext Small RNA Library Prep Set for SOLiD
Libraries were size selected on acrylamide gels (Library size: 110 to 150 nt)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
AB SOLiD System 3.0 |
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| Data processing |
Reads were first filtered to remove SOLiD adaptors, SOLiD barcodes and rRNAs reads.
Alignment was performed within Lifescope 2.5.1 software smallRNAs pipeline using default parameters.
Annotation process has been performed within home made pipeline. Alignment bam files with primary alignments (lowest MAPQV) were annotated with .GFF files with genomic coordinates of smallRNAs such as miRNAs (mirbase release 18), tRNAs (UCSC tracks), yRNAs, snoRNAs and piRNAs (fRNAdb) and ensembl ncRNAs tracks (release 69).
Processed data file submitted is a matrix file containning counts for each sample without normalization.
Genome_build: mm9
Supplementary_files_format_and_content: Tabular text-file with feature name, feature type, feature description, feature genomic coordinates and counts associated within each samples, ordered by expression decreasing
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| Submission date |
Nov 12, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin Lebrigand |
| Organization name |
IPMC/CNRS
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| Lab |
Functional Genomics Platform of Nice-Sophia-Antipolis, France.
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| Street address |
660 route des lucioles
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| City |
Valbonne - Sophia-Antipolis |
| ZIP/Postal code |
06560 |
| Country |
France |
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| Platform ID |
GPL9318 |
| Series (1) |
| GSE52299 |
Small RNA next generation sequencing of mice skin biopsies from acetone-treated healthy skins and DMBA/PMA-treated hyperplastic skins, papillomas and cutaneous Squamous Cell Carcinomas |
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| Relations |
| SRA |
SRX376797 |
| BioSample |
SAMN02401804 |
| 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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