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| Status |
Public on Apr 29, 2014 |
| Title |
CTRL4 |
| Sample type |
SRA |
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| Source name |
Colon
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| Organism |
Homo sapiens |
| Characteristics |
location: Ascending colon
disease: patient matched uninvolved colon
Sex: Male
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| Extracted molecule |
total RNA |
| Extraction protocol |
Colon biopsy samples were stored in RNAlater at 4°C overnight and RNA extracted with TRIzol
Illumina TruSeq RNA Sample Prep Kit
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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 |
Fastq files were aligned to human genome (Hg19) using novocraft novoalign application version 2.08.02
SAM files were converted to binary BAM files using USeq SamTranscriptomeParser application version 8.2.6
Data normalization, differential gene expression and statistical analyses were performed using USeq OverDispersedDefinedRegionScanSeqs application version 8.2.6
Visualization tracks for the Integrated Genome Browser were created using Useq Sam2USeq application version 8.2.6
Genome_build: Hg19
Supplementary_files_format_and_content: Tab-delimited text file with false discovery rate (FDR), fold change (polyp/control), mean RPKM (reads per kilobase gene length per million reads) for each gene, and individual reads for each sample
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| Submission date |
Apr 30, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Don Delker |
| E-mail(s) |
don.delker@hsc.utah.edu
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| Organization name |
University of Utah
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| Department |
School of Medicine
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| Street address |
30 North 1900 East
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| City |
Salt Lake City |
| State/province |
Utah |
| ZIP/Postal code |
84132 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE46513 |
RNA-sequencing analysis of 5' capped RNAs identifies novel differentially expressed genes in sessile serrated colon polyps (SSPs) |
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| Relations |
| BioSample |
SAMN02087580 |
| SRA |
SRX272907 |
| 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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