GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE90876 Query DataSets for GSE90876
Status Public on Feb 01, 2017
Title Transcriptomic Profiling of Developing Human Paraxial Mesoderm from 4.5-5 Weeks of Gestation Human Embryos
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Somites form during embryonic development and give rise to unique cell and tissue types, such as skeletal muscles and bones and cartilages of the vertebrae. Using somitogenesis stage human embryos, we performed the first ever transcriptomic profiling of human presomitic mesoderm as well as nascent and developed somites. Using this approach we uncovered novel regulators unique duing human somitogensis, and efficiently guided human pluripotent stem cells to differentiate to somite cells and downstream progeny. This work improves our understanding of human somite development and may enhance our ability to model and treat diseases affecting somite derivatives.
Overall design Human embryos of 4.5-5 weeks of gestation were obtained from electively aborted fetuses following informed consent and de-identification. After procurement, tissues were immediately washed in sterile PBS, placed in PBS supplemented with 5% fetal bovine serum, 1% Penicillin-Streptomycin and 2.5 µg/mL Amphotericin B, and shipped on ice. Within 48 hours, targeted tissues were micro-dissected from the embryos. Developed somites (SM Dev) included the two somite pairs at the forelimb bud level, nascent somites (SM) included the two somite pairs just anterior to the most caudal segmentation border that was visible, and presomitic mesoderm (PSM) included the tail region mesoderm posterior to SM. Duplicates were used for each sample type for RNA-seq.
Contributor(s) Xi H, Pyle AD
Citation(s) 28178531
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 AR064327 Reprogramming and Directed Differentiation of Skeletal Muscle Cells from hPSCs. UNIVERSITY OF CALIFORNIA LOS ANGELES April D Pyle
Submission date Dec 05, 2016
Last update date May 15, 2019
Contact name Haibin Xi
Organization name UCLA
Department MIMG
Lab April Pyle
Street address 615 Charles E Young Dr South, BSRB 257
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (6)
GSM2416865 PSM rep1
GSM2416866 PSM rep2
GSM2416867 SM rep1
BioProject PRJNA356265
SRA SRP094564

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
GSE90876_Cuffdiff_PSM_vs_SM.txt.gz 800.0 Kb (ftp)(http) TXT
GSE90876_Cuffdiff_SM_vs_SM_Dev.txt.gz 815.7 Kb (ftp)(http) TXT
GSE90876_RAW.tar 4.6 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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