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GEO help: Mouse over screen elements for information. |
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Status |
Public on Jun 16, 2016 |
Title |
mRNA-seq WT3 |
Sample type |
SRA |
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Source name |
mouse skin squamous tumours
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Organism |
Mus musculus |
Characteristics |
tumour stage: skin papilloma strain: C57BL/6 age: 1 month
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Extracted molecule |
total RNA |
Extraction protocol |
1 cm2 pieces of skin papilloma were snap-frozen in liquid N2 and then transferred to lysis buffer. RNAs were prepared for Ribo-seq as in Ingolia, N. T., Brar, G. A., Rouskin, S., McGeachy, A. M. & Weissman, J. S. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc 7, 1534-1550, doi:10.1038/nprot.2012.086 (2012). For mRNA-seq standard Illumina library preparation protocols were used.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina Genome Analyzer II |
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Data processing |
For Ribo-seq analysis, Adapters were removed, and Ribo-seq reads were initially aligned to a collection of rRNA sequences to filter rRNA reads in the libraries; and non-rRNA reads with at least 23 nt length were kept. To obtain only high-confidence assignments of ribosome footprints to transcripts, the reads were aligned to the mouse reference genome (GRCm38/UCSC mm10) with Tophat2 (version: 2.1; options: ‘--read-mismatch 1 --max-multihits 1 –GTF’) guided by ENSEMBL gene models to account for splice sites, allowing one mismatch per read and unique alignments only. For RNA-seq analysis, the reads were aligned to the mouse reference genome (GRCm38/UCSC mm10) with Tophat2 (version: 2.1; options: ‘--read-mismatch 1 --max-multihits 1 –GTF’) guided by ENSEMBL gene models allowing one mismatch per read and unique alignments only. Genome_build: GRCm38/UCSC mm10 Supplementary_files_format_and_content: Processed data files were generated with bedtools genomeCoveragBed showing counts per genomic position.
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Submission date |
Aug 14, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Sabine Dietmann |
Organization name |
Washington University School of Medicine
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Street address |
4565 McKinley Avenue
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City |
St Louis |
State/province |
MO |
ZIP/Postal code |
63110 |
Country |
USA |
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Platform ID |
GPL9250 |
Series (2) |
GSE72066 |
Ribosome Profiling of mouse skin squamous tumours |
GSE72067 |
Stem cell function and sensitivity to genotoxic stress is controlled by protein translation rates |
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Relations |
BioSample |
SAMN03992965 |
SRA |
SRX1149711 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1854039_in.vivo.tumour.wt.5.bedGraph.gz |
6.3 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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