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| Status |
Public on Apr 15, 2020 |
| Title |
WT_5_sorted |
| Sample type |
SRA |
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| Source name |
Ear skin Keratinocytes
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6 mixed 129/SV
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| Extracted molecule |
total RNA |
| Extraction protocol |
Ear skin or ear tumors were dissected and prepared for FACS as described. Subsequently, total RNA from sorted cells was extracted using RNeasy Micro Kit (Quiagen, 74004).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Ctrls_3
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| Data processing |
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR v2.5.4b, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Mus musculus, Ensembl, GRCm38.p5
Supplementary_files_format_and_content: tad-delimited, raw counts
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| Submission date |
Mar 27, 2020 |
| Last update date |
Apr 16, 2020 |
| Contact name |
giancarlo russo |
| E-mail(s) |
giancarlo.russo@fgcz.ethz.ch
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| Organization name |
ETH/University of Zurich
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| Department |
Functional Genomics Center Zurich
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| Street address |
winterthurerstrasse 190
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| City |
Zurich |
| State/province |
Schweiz |
| ZIP/Postal code |
8057 |
| Country |
Switzerland |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE147642 |
Oncogenic ALKF1174L drives tumorigenesis in cutaneous squamous cell carcinoma |
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| Relations |
| BioSample |
SAMN14469238 |
| SRA |
SRX8012871 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4437175_WT_5_sorted.txt.gz |
120.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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