NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE25840 Query DataSets for GSE25840
Status Public on May 19, 2011
Title Widespread RNA and DNA Sequence Differences in the Human Genome
Sample organism Homo sapiens
Experiment type Third-party reanalysis
Expression profiling by high throughput sequencing
Summary The transmission of information from DNA to RNA is a critical process. It is assumed that DNA is faithfully copied into RNA. However, when we compared RNA sequences from human B cells of 27 individuals to the corresponding DNA sequences from the same individuals, we uncovered more than 20,000 sites where the RNA sequences do not match that of the DNA. Validations using RNA sequences from another laboratory and re-sequencing of the DNA and RNA samples confirmed these findings. All 12 possible categories of discordances were found, with A-to-G and C-to-U being the most common. About 50% of the differences involved conversions between purines and pyrimidines. These differences were non-random as many sites were found in multiple individuals. The same differences were also found in primary skin cells in a separate set of 20 individuals. In addition, when these differences were found, they were seen in nearly all transcripts. Thus, these widespread RNA-DNA differences in the human genome provide a yet unexplored aspect of genome variation that affect gene expression and therefore phenotypic and disease manifestations.
 
Overall design identification of RNA and DNA differences

For alignment of the short reads sequences to the human transcriptome(Gencode NCBI36 version 3c), we used the program BOWTIE (version 0.12.7).

***This submission represents the RNA-seq component of the study
 
Contributor(s) Cheung VG, Li M, Li Y, Bruzel A, Richards A, Toung JM, Wang IX
Citation(s) 21596952
Submission date Dec 03, 2010
Last update date Mar 22, 2012
Contact name Mingyao Li
Organization name University of Pennsylvania
Department Biostatistics and Epidemiology
Street address 213 Blockley Hall, 423 Guardian Drive
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Relations
Reanalysis of GSM424320
Reanalysis of GSM424322
Reanalysis of GSM424323
Reanalysis of GSM424329
Reanalysis of GSM424330
Reanalysis of GSM424331
Reanalysis of GSM424332
Reanalysis of GSM424334
Reanalysis of GSM424336
Reanalysis of GSM424337
Reanalysis of GSM424338
Reanalysis of GSM424339
Reanalysis of GSM424340
Reanalysis of GSM424341
Reanalysis of GSM424342
Reanalysis of GSM424343
Reanalysis of GSM424344
Reanalysis of GSM424347
Reanalysis of GSM424349
Reanalysis of GSM424351
Reanalysis of GSM424352
Reanalysis of GSM424353
Reanalysis of GSM424354
Reanalysis of GSM424355
Reanalysis of GSM424356
Reanalysis of GSM424358
Reanalysis of GSM424359
BioProject PRJNA135757

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE25840_GSM424320_GM06985_gencode_spliced.bam 977.0 Mb (ftp)(http) BAM
GSE25840_GSM424320_GM06985_gencode_spliced.bam.bai.gz 686.9 Kb (ftp)(http) BAI
GSE25840_GSM424322_GM06994_gencode_spliced.bam 1.2 Gb (ftp)(http) BAM
GSE25840_GSM424322_GM06994_gencode_spliced.bam.bai.gz 728.7 Kb (ftp)(http) BAI
GSE25840_GSM424323_GM07000_gencode_spliced.bam 725.1 Mb (ftp)(http) BAM
GSE25840_GSM424323_GM07000_gencode_spliced.bam.bai.gz 671.8 Kb (ftp)(http) BAI
GSE25840_GSM424329_GM11829_gencode_spliced.bam 790.0 Mb (ftp)(http) BAM
GSE25840_GSM424329_GM11829_gencode_spliced.bam.bai.gz 681.7 Kb (ftp)(http) BAI
GSE25840_GSM424330_GM11830_gencode_spliced.bam 761.4 Mb (ftp)(http) BAM
GSE25840_GSM424330_GM11830_gencode_spliced.bam.bai.gz 690.4 Kb (ftp)(http) BAI
GSE25840_GSM424331_GM11831_gencode_spliced.bam 813.1 Mb (ftp)(http) BAM
GSE25840_GSM424331_GM11831_gencode_spliced.bam.bai.gz 696.2 Kb (ftp)(http) BAI
GSE25840_GSM424332_GM11832_gencode_spliced.bam 765.6 Mb (ftp)(http) BAM
GSE25840_GSM424332_GM11832_gencode_spliced.bam.bai.gz 696.1 Kb (ftp)(http) BAI
GSE25840_GSM424334_GM11881_gencode_spliced.bam 1.1 Gb (ftp)(http) BAM
GSE25840_GSM424334_GM11881_gencode_spliced.bam.bai.gz 689.8 Kb (ftp)(http) BAI
GSE25840_GSM424336_GM11992_gencode_spliced.bam 1.2 Gb (ftp)(http) BAM
GSE25840_GSM424336_GM11992_gencode_spliced.bam.bai.gz 717.8 Kb (ftp)(http) BAI
GSE25840_GSM424337_GM11993_gencode_spliced.bam 762.4 Mb (ftp)(http) BAM
GSE25840_GSM424337_GM11993_gencode_spliced.bam.bai.gz 674.9 Kb (ftp)(http) BAI
GSE25840_GSM424338_GM11994_gencode_spliced.bam 899.5 Mb (ftp)(http) BAM
GSE25840_GSM424338_GM11994_gencode_spliced.bam.bai.gz 689.1 Kb (ftp)(http) BAI
GSE25840_GSM424339_GM12003_gencode_spliced.bam 971.9 Mb (ftp)(http) BAM
GSE25840_GSM424339_GM12003_gencode_spliced.bam.bai.gz 672.4 Kb (ftp)(http) BAI
GSE25840_GSM424340_GM12004_gencode_spliced.bam 749.9 Mb (ftp)(http) BAM
GSE25840_GSM424340_GM12004_gencode_spliced.bam.bai.gz 640.0 Kb (ftp)(http) BAI
GSE25840_GSM424341_GM12005_gencode_spliced.bam 765.5 Mb (ftp)(http) BAM
GSE25840_GSM424341_GM12005_gencode_spliced.bam.bai.gz 619.9 Kb (ftp)(http) BAI
GSE25840_GSM424342_GM12006_gencode_spliced.bam 809.1 Mb (ftp)(http) BAM
GSE25840_GSM424342_GM12006_gencode_spliced.bam.bai.gz 638.4 Kb (ftp)(http) BAI
GSE25840_GSM424343_GM12043_gencode_spliced.bam 1.0 Gb (ftp)(http) BAM
GSE25840_GSM424343_GM12043_gencode_spliced.bam.bai.gz 690.8 Kb (ftp)(http) BAI
GSE25840_GSM424344_GM12044_gencode_spliced.bam 1.1 Gb (ftp)(http) BAM
GSE25840_GSM424344_GM12044_gencode_spliced.bam.bai.gz 671.3 Kb (ftp)(http) BAI
GSE25840_GSM424347_GM12144_gencode_spliced.bam 763.6 Mb (ftp)(http) BAM
GSE25840_GSM424347_GM12144_gencode_spliced.bam.bai.gz 635.0 Kb (ftp)(http) BAI
GSE25840_GSM424349_GM12155_gencode_spliced.bam 1.2 Gb (ftp)(http) BAM
GSE25840_GSM424349_GM12155_gencode_spliced.bam.bai.gz 683.3 Kb (ftp)(http) BAI
GSE25840_GSM424351_GM12716_gencode_spliced.bam 1.1 Gb (ftp)(http) BAM
GSE25840_GSM424351_GM12716_gencode_spliced.bam.bai.gz 672.9 Kb (ftp)(http) BAI
GSE25840_GSM424352_GM12717_gencode_spliced.bam 1.1 Gb (ftp)(http) BAM
GSE25840_GSM424352_GM12717_gencode_spliced.bam.bai.gz 708.8 Kb (ftp)(http) BAI
GSE25840_GSM424353_GM12750_gencode_spliced.bam 1.1 Gb (ftp)(http) BAM
GSE25840_GSM424353_GM12750_gencode_spliced.bam.bai.gz 694.4 Kb (ftp)(http) BAI
GSE25840_GSM424354_GM12762_gencode_spliced.bam 1.1 Gb (ftp)(http) BAM
GSE25840_GSM424354_GM12762_gencode_spliced.bam.bai.gz 709.1 Kb (ftp)(http) BAI
GSE25840_GSM424355_GM12813_gencode_spliced.bam 1.2 Gb (ftp)(http) BAM
GSE25840_GSM424355_GM12813_gencode_spliced.bam.bai.gz 714.6 Kb (ftp)(http) BAI
GSE25840_GSM424356_GM12814_gencode_spliced.bam 1.0 Gb (ftp)(http) BAM
GSE25840_GSM424356_GM12814_gencode_spliced.bam.bai.gz 688.0 Kb (ftp)(http) BAI
GSE25840_GSM424358_GM12872_gencode_spliced.bam 661.7 Mb (ftp)(http) BAM
GSE25840_GSM424358_GM12872_gencode_spliced.bam.bai.gz 599.7 Kb (ftp)(http) BAI
GSE25840_GSM424359_GM12874_gencode_spliced.bam 768.0 Mb (ftp)(http) BAM
GSE25840_GSM424359_GM12874_gencode_spliced.bam.bai.gz 598.5 Kb (ftp)(http) BAI
SRA Run SelectorHelp
Raw data not applicable for this record
Processed data is available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap