|
| Status |
Public on Sep 18, 2019 |
| Title |
Massively Parallel Reporter Assay for pluripotency factors in mESCs |
| Organisms |
Escherichia coli; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
A massively parallel reporter assay, MPRA, was conducted in mouse embryonic stem cells (mESC). Synthetic cis-regulatory elements comprised of binding sites for pluripotency transcription factors and genomic sequences with comparable binding sites configurations were used in the assay. Transcripts of dsRed were amplified via PCR from the end of the transcript to sequence 3' UTR barcodes.
|
| |
|
| Overall design |
MPRA from RW.4 mESCs transfected with either Synthetic (SYN) element library or a Genomic ('GEN' or 'g') WT/MUT sequence library. Each unique sequence or element of interest is tagged with 8 unique 9bp barcodes (provided in the description field in each sample record). Each library also includes a basal control (basal promoter only) tagged with 112 unique 9bp barcodes. The original DNA plasmids that were used for transfections were sequenced to use for normalizating plasmid copy number for final expresson calculations. Tested SYN element and gWT/gMUT sequence names are included in processed data files.
These data are part of SRA submission SUB4287756 (SRP153192) and BioProject PRJNA480686.
|
| |
|
| Contributor(s) |
King DM, Maricque BB, Cohen BA |
| Citation(s) |
32043966 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 GM092910 |
PROMOTERS |
WASHINGTON UNIVERSITY |
Barak A Cohen |
|
| BioProject |
PRJNA480686 |
| |
| Submission date |
Sep 20, 2018 |
| Last update date |
Mar 30, 2020 |
| Contact name |
Dana M King |
| E-mail(s) |
d.king@wustl.edu
|
| Organization name |
Washington University
|
| Department |
Department of Genetics
|
| Lab |
Cohen
|
| Street address |
4523 CLAYTON AVE, CB 8510
|
| City |
St. Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL21222 |
Illumina NextSeq 500 (Escherichia coli) |
|
| Samples (8)
|
|
| Relations |
| SRA |
SRP153192 |
Less...
More...