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| Status |
Public on Jan 01, 2019 |
| Title |
RNA sequencing (RNA-SEQ) of WT and LFS patient specific iPSC derived pre-osteoblasts |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: To understand molecular and cellular effects of sFRP2 overexpression in LFS patients
Methods: We performed RNA sequencing of 32 samples from WT, sFRP2OE, LFS, and sFRP2 knockdown MSCs or preosteoblasts in four differentiation time points and performed RNAsequencing.
Conclusion: molecular and cellular effects of sFRP2 overexpression in LFS patients
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| Overall design |
cDNA library preparation and sequencing were performed at Novogen (http://www.novogen.com/home). Briefly, RNA quality was determined with an Agilent Bioanalyzer (RNA integrity number [RIN] > 7.0 for all samples). mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, and double stranded cDNA synthesized using random hexamers, M-MuLV Reverse Transcriptase (RNase H), and DNA Polymerase I. NEBNext Adaptor with hairpin loop structure were ligated to the cDNA in preparation for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system (Beckman Coulter, Beverly, USA). Library of 150-200 bp fragments at an effective concentration of > 2nM were loaded onto an Illumina HiSeq 4000 for sequencing
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| Contributor(s) |
Kim HS, Yoo S, Zhu J |
| Citation(s) |
30385632 |
| Submission date |
Aug 16, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Seungyeul Yoo |
| Organization name |
Icahn School of Medicine at Mount Sinai
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| Department |
Genetics and Genomic Sciences
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| Lab |
Integrative Network Biology Group
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| Street address |
1425 Madison Avenue
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
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| Platforms (1) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (32)
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| GSM2743892 |
WT D7 pre-osteoblasts, 2 |
| GSM2743893 |
WT D14 pre-osteoblasts, 1 |
| GSM2743894 |
WT D14 pre-osteoblasts, 2 |
| GSM2743895 |
WT D17 pre-osteoblasts, 1 |
| GSM2743896 |
WT D17 pre-osteoblasts, 2 |
| GSM2743897 |
sFRP2OE D0 MSCs, 1 |
| GSM2743898 |
sFRP2OE D0 MSCs, 2 |
| GSM2743899 |
sFRP2OE D7 pre-osteoblasts, 1 |
| GSM2743900 |
sFRP2OE D7 pre-osteoblasts, 2 |
| GSM2743901 |
sFRP2OE D14 pre-osteoblasts, 1 |
| GSM2743902 |
sFRP2OE D14 pre-osteoblasts, 2 |
| GSM2743903 |
sFRP2OE D17 pre-osteoblasts, 1 |
| GSM2743904 |
sFRP2OE D17 pre-osteoblasts, 2 |
| GSM2743905 |
LFS D0 MSCs, 1 |
| GSM2743906 |
LFS D0 MSCs, 2 |
| GSM2743907 |
LFS D7 pre-osteoblasts, 1 |
| GSM2743908 |
LFS D7 pre-osteoblasts, 2 |
| GSM2743909 |
LFS D14 pre-osteoblasts, 1 |
| GSM2743910 |
LFS D14 pre-osteoblasts, 2 |
| GSM2743911 |
LFS D17 pre-osteoblasts, 1 |
| GSM2743912 |
LFS D17 pre-osteoblasts, 2 |
| GSM2743913 |
shSFRP2 D0 MSCs, 1 |
| GSM2743914 |
shSFRP2 D0 MSCs, 2 |
| GSM2743915 |
shSFRP2 D7 pre-osteoblasts, 1 |
| GSM2743916 |
shSFRP2 D7 pre-osteoblasts, 2 |
| GSM2743917 |
shSFRP2 D14 pre-osteoblasts, 1 |
| GSM2743918 |
shSFRP2 D14 pre-osteoblasts, 2 |
| GSM2743919 |
shSFRP2 D17 pre-osteoblasts, 1 |
| GSM2743920 |
shSFRP2 D17 pre-osteoblasts, 2 |
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| Relations |
| BioProject |
PRJNA398513 |
| SRA |
SRP115559 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE102732_RPKM_log2.txt.gz |
4.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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