|
| Status |
Public on Oct 11, 2017 |
| Title |
Quantitative profiling of BATF family proteins/JUNB/IRF hetero-trimers using Spec-seq |
| Organism |
synthetic construct |
| Experiment type |
Other
|
| Summary |
Spec-seq directly mesaures specificity by sequencing. We run an EMSA experiment on TF of interest with a library of DNA targets. Then we extract and sequence the bound and unbound portion of the DNA separately. Finally we count the occurences of each varient in the library and calculate the ratio and the relative binding energy.
|
| |
|
| Overall design |
15 independent Spec-seq experiments
|
| |
|
| Contributor(s) |
Chang YK, Stormo GD |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Aug 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Gary D. Stormo |
| E-mail(s) |
stormo@genetics.wustl.edu
|
| Phone |
(314) 362-2722
|
| Organization name |
Washington University School of Medicine
|
| Department |
Genetics
|
| Lab |
Stormo
|
| Street address |
4515 McKinley Ave. Room 4208.
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL17769 |
Illumina MiSeq (synthetic construct) |
|
| Samples (30)
|
|
| Relations |
| BioProject |
PRJNA397060 |
| SRA |
SRP114778 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE102219_BATF-IRF4-Specseq_processed.txt.gz |
4.7 Kb |
(ftp)(http) |
TXT |
| GSE102219_BATF-IRF8-Specseq_processed.txt.gz |
9.4 Kb |
(ftp)(http) |
TXT |
| GSE102219_BATF-JUNB-IRF4_processed.txt.gz |
17.9 Kb |
(ftp)(http) |
TXT |
| GSE102219_BATF-JUNB-IRF8_processed.txt.gz |
18.1 Kb |
(ftp)(http) |
TXT |
| GSE102219_BATF-JUNB_processed.txt.gz |
18.6 Kb |
(ftp)(http) |
TXT |
| GSE102219_BATF2-IRF4-Specseq_processed.txt.gz |
10.1 Kb |
(ftp)(http) |
TXT |
| GSE102219_BATF2-IRF8-Specseq_processed.txt.gz |
10.0 Kb |
(ftp)(http) |
TXT |
| GSE102219_BATF2-JUNB-IRF4_processed.txt.gz |
19.0 Kb |
(ftp)(http) |
TXT |
| GSE102219_BATF2-JUNB-IRF8_processed.txt.gz |
19.0 Kb |
(ftp)(http) |
TXT |
| GSE102219_BATF2-JUNB_processed.txt.gz |
19.0 Kb |
(ftp)(http) |
TXT |
| GSE102219_BATF3-IRF4-Specseq_processed.txt.gz |
10.0 Kb |
(ftp)(http) |
TXT |
| GSE102219_BATF3-IRF8-Specseq_processed.txt.gz |
9.8 Kb |
(ftp)(http) |
TXT |
| GSE102219_BATF3-JUNB-IRF4_processed.txt.gz |
19.1 Kb |
(ftp)(http) |
TXT |
| GSE102219_BATF3-JUNB-IRF8_processed.txt.gz |
19.1 Kb |
(ftp)(http) |
TXT |
| GSE102219_BATF3-JUNB_processed.txt.gz |
19.0 Kb |
(ftp)(http) |
TXT |
| GSE102219_Processed_data_description.txt.gz |
407 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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