 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 25, 2019 |
| Title |
Dissection of c-AMP Response Element Architecture by Using Genomic and Episomal Massively Parallel Reporter Assays |
| Organisms |
Escherichia coli; Homo sapiens |
| Experiment type |
Other
|
| Summary |
We designed and assayed synthetic regulatory elements varying c-amp response element number, affinity, distance to the promoter, spacing between multiple CREs, and surrounding sequence content. Using 5 massively-parallel reporter assays, we measured the expression of 17,406 unique sequences when placed upstream of a minimal promoter using next-generation sequencing of barcodes associated with synthesized elements. We then determine how the varied c-amp response element architectures influence expression when these variants are assayed in an episomal and genomic context across a range of forskolin concentrations, an inducer of c-amp response element activity. Included here are all sequences designed and analyzed in the assay. Assay results from certain library designs were not insightful and not included in the main text but are additionally included here in the barcode-mapping and MPRA sequencing datasets.
|
| |
|
| Overall design |
We associated barcodes to variants using next-generation sequencing, then analyzed variant expression using barcode next-generation sequencing on amplified cDNA and DNA samples per assay condition.
|
| Web link |
https://doi.org/10.1016/j.cels.2020.05.011
|
| |
|
| Contributor(s) |
Davis JE, Insigne KD, Jones EM, Hastings QA, Boldridge WB, Kosuri S |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Sep 24, 2019 |
| Last update date |
Jun 29, 2020 |
| Contact name |
Jessica Elizabeth Davis |
| E-mail(s) |
jessdavis@g.ucla.edu
|
| Phone |
9492285639
|
| Organization name |
UCLA
|
| Department |
CHEMISTRY AND BIOCHEMISTRY
|
| Lab |
Kosuri
|
| Street address |
607 Charles E Young Dr E
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platforms (3) |
| GPL16085 |
Illumina MiSeq (Escherichia coli) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
|
| Samples (55)
|
| GSM4094373 |
20170320 MPRA DNA barcode reads |
| GSM4094374 |
20170320 MPRA RNA barcode reads, 0 forksolin, replicate A |
| GSM4094375 |
20170320 MPRA RNA barcode reads, 0 forksolin, replicate B |
| GSM4094376 |
20170320 MPRA RNA barcode reads, 25 forksolin, replicate A |
| GSM4094377 |
20170320 MPRA RNA barcode reads, 25 forksolin, replicate B |
| GSM4094378 |
20170631 MPRA DNA barcode reads |
| GSM4094379 |
20170631 MPRA RNA barcode reads, 0 forksolin, replicate A |
| GSM4094380 |
20170631 MPRA RNA barcode reads, 0 forksolin, replicate B |
| GSM4094381 |
20170631 MPRA RNA barcode reads, 16 forksolin, replicate A |
| GSM4094382 |
20170631 MPRA RNA barcode reads, 16 forksolin, replicate B |
| GSM4094383 |
20170631 MPRA RNA barcode reads, 1 forksolin, replicate A |
| GSM4094384 |
20170631 MPRA RNA barcode reads, 1 forksolin, replicate B |
| GSM4094385 |
20170631 MPRA RNA barcode reads, 25 forksolin, replicate A |
| GSM4094386 |
20170631 MPRA RNA barcode reads, 25 forksolin, replicate B |
| GSM4094387 |
20170631 MPRA RNA barcode reads, 2 forksolin, replicate A |
| GSM4094388 |
20170631 MPRA RNA barcode reads, 2 forksolin, replicate B |
| GSM4094389 |
20170631 MPRA RNA barcode reads, 32 forksolin, replicate A |
| GSM4094390 |
20170631 MPRA RNA barcode reads, 32 forksolin, replicate B |
| GSM4094391 |
20170631 MPRA RNA barcode reads, 4 forksolin, replicate A |
| GSM4094392 |
20170631 MPRA RNA barcode reads, 4 forksolin, replicate B |
| GSM4094393 |
20170631 MPRA RNA barcode reads, 64 forksolin, replicate A |
| GSM4094394 |
20170631 MPRA RNA barcode reads, 64 forksolin, replicate B |
| GSM4094395 |
20170631 MPRA RNA barcode reads, 8 forksolin, replicate A |
| GSM4094396 |
20170631 MPRA RNA barcode reads, 8 forksolin, replicate B |
| GSM4094397 |
20170921 MPRA DNA barcode reads |
| GSM4094398 |
20170921 MPRA RNA barcode reads, 0 forksolin, replicate A |
| GSM4094399 |
20170921 MPRA RNA barcode reads, 0 forksolin, replicate B |
| GSM4094400 |
20170921 MPRA RNA barcode reads, 2^0 forksolin, replicate A |
| GSM4094401 |
20170921 MPRA RNA barcode reads, 2^0 forksolin, replicate B |
| GSM4094402 |
20170921 MPRA RNA barcode reads, 2^-1 forksolin, replicate A |
| GSM4094403 |
20170921 MPRA RNA barcode reads, 2^-1 forksolin, replicate B |
| GSM4094404 |
20170921 MPRA RNA barcode reads, 2^-2 forksolin, replicate A |
| GSM4094405 |
20170921 MPRA RNA barcode reads, 2^2 forksolin, replicate A |
| GSM4094406 |
20170921 MPRA RNA barcode reads, 2^-2 forksolin, replicate B |
| GSM4094407 |
20170921 MPRA RNA barcode reads, 2^2 forksolin, replicate B |
| GSM4094408 |
20170921 MPRA RNA barcode reads, 2^-3 forksolin, replicate A |
| GSM4094409 |
20170921 MPRA RNA barcode reads, 2^-3 forksolin, replicate B |
| GSM4094410 |
20170921 MPRA RNA barcode reads, 2^-4 forksolin, replicate A |
| GSM4094411 |
20170921 MPRA RNA barcode reads, 2^-4 forksolin, replicate B |
| GSM4094412 |
20170921 MPRA RNA barcode reads, 2^-5 forksolin, replicate A |
| GSM4094413 |
20170921 MPRA RNA barcode reads, 2^-5 forksolin, replicate B |
| GSM4094414 |
20171129 MPRA DNA barcode reads, biological replicate 1, technical replicate 1 |
| GSM4094415 |
20171129 MPRA DNA barcode reads, biological replicate 1, technical replicate 2 |
| GSM4094416 |
20171129 MPRA DNA barcode reads, biological replicate 2, technical replicate 1 |
| GSM4094417 |
20171129 MPRA DNA barcode reads, biological replicate 2, technical replicate 2 |
| GSM4094418 |
20171129 MPRA RNA barcode reads, 8 forskolin, biological replicate 1 |
| GSM4094419 |
20171129 MPRA RNA barcode reads, 8 forskolin, biological replicate 2 |
| GSM4094420 |
20190712 MPRA DNA barcode reads |
| GSM4094421 |
20190712 MPRA RNA barcode reads, 0 forskolin, replicate A |
| GSM4094422 |
20190712 MPRA RNA barcode reads, 0 forskolin, replicate B |
| GSM4094423 |
20190712 MPRA RNA barcode reads, 4 forskolin, replicate A |
| GSM4094424 |
20190712 MPRA RNA barcode reads, 4 forskolin, replicate B |
| GSM4094425 |
20161206 merged barcode mapping reads |
| GSM4094426 |
20160930 merged barcode mapping reads |
| GSM4094427 |
20190705 merged barcode mapping reads follow-up library |
|
| Relations |
| BioProject |
PRJNA573901 |
| SRA |
SRP223087 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE137922_RAW.tar |
3.1 Gb |
(http)(custom) |
TAR (of TXT) |
| GSE137922_barcode_statistics_followup.txt.gz |
48.8 Mb |
(ftp)(http) |
TXT |
| GSE137922_uniqueSP2345.txt.gz |
45.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...