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Series GSE49417 Query DataSets for GSE49417
Status Public on Nov 20, 2014
Title The conserved organization of the human and mouse transcriptomes
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary We characterized by RNA-seq the transcriptional profiles of a large and heterogeneous collection of mouse tissues, augmenting the mouse transcriptome with thousands of novel transcript candidates. Comparison with transcriptome profiles obtained in human cell lines reveals substantial conservation of transcriptional programs, and uncovers a distinct class of genes with levels of expression across cell types and species, that have been constrained early in vertebrate evolution. This core set of genes capture a substantial and constant fraction of the transcriptional output of mammalian cells, and participates in basic functional and structural housekeeping processes common to all cell types. Perturbation of these constrained genes is associated with significant phenotypes including embryonic lethality and cancer. Evolutionary constraint in gene expression levels is not reflected in the conservation of the genomic sequences, but it is associated with strong and conserved epigenetic marking, as well as to a characteristic post-transcriptional regulatory program in which sub-cellular localization and alternative splicing play comparatively large roles.
Overall design Comparison of human and mouse transcriptome profiles has uncovered a distinct class of genes (6600- one third of all expressed genes in both human and mouse) whose variation in expression levels have been constrained irrespective of cell types and species that they are express in. Such constraint appears to have been developed early in vertebrate evolution since it seen in multiple other species. This constraint is not associated with the conservation of the genomic sequences found in each species. Finally, this core set of genes helps in interpreting how non-human organisms like the mouse can better be used as models for human disease and why perturbation of these constrained genes is associated with significant phenotypes including embryonic lethality and cancer.
Contributor(s) Pervouchine DD, Djebali S, Breschi A, Davis CA, Barja PP, Dobin A, Tanzer A, Lagarde J, Zaleski C, See L, Fastuca M, Drenkow J, Wang H, Bussotti G, Pei B, Balasubramanian S, Monlong J, Harmanci A, Gerstein M, Beer MA, Notredame C, Guigo R, Gingeras TR
Citation(s) 25409824
Submission date Jul 31, 2013
Last update date Feb 26, 2020
Contact name ENCODE DCC
Organization name ENCODE DCC
Street address 300 Pasteur Dr
City Stanford
State/province CA
ZIP/Postal code 94305-5120
Country USA
Platforms (4)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (64)
GSM758559 CSHL_RnaSeq_GM12878_cell_longPolyA (superseded by GSE86658)
GSM758561 CSHL_RnaSeq_AG04450_cell_longPolyA (superseded by GSE78585)
GSM758562 CSHL_RnaSeq_BJ_cell_longPolyA (superseded by GSE90221)
BioProject PRJNA267840

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
GSE49417_RAW.tar 93.0 Gb (http)(custom) TAR (of BAM, BEDRNAELEMENTS, BIGWIG, GFF, GTF, PDF)
SRA Run SelectorHelp
Raw data provided as supplementary file
Processed data provided as supplementary file

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