|
| Status |
Public on Nov 08, 2023 |
| Title |
Spec-seq_r90w_1m |
| Sample type |
SRA |
| |
|
| Source name |
synthetic construct
|
| Organism |
synthetic construct |
| Characteristics |
peptide: CRX R90W HD
emsa band: bound
molecule type: synthetic DNA
|
| Extracted molecule |
other |
| Extraction protocol |
After EMSA, Spec-seq libraries from both bound and unbound bands were eluted from the excised Tris-glycine gel.
Sequencing adapters and primers were added to both ends of the Spec-seq library using two-step PCR.
|
| |
|
| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
r90w_1_RBE.txt
|
| Data processing |
Reads with any mismatch in the Spec-seq library conserved regions were discarded prior to quantification.
The ratio of individual sequence in bound and unbound reads was calculated as a measurement of relative binding affinity compared to the consensus sequence.
The relative binding energy was then derived from the natural logarithm of the relative binding affinity and represented in kcal/mol units.
Supplementary files format and content: Text files with normalized read counts in bound and unbound fraction and the derived relative binding affinity and relative binding energy.
Library strategy: Spec-seq (amplicon based sequencing)
|
| |
|
| Submission date |
Jan 24, 2023 |
| Last update date |
Nov 08, 2023 |
| Contact name |
Yiqiao Zheng |
| E-mail(s) |
yiqiao.zheng@wustl.edu
|
| Phone |
314-747-4351
|
| Organization name |
Washington University in St Louis
|
| Department |
Department of Ophthalmology & Visual Sciences
|
| Lab |
Shiming Chen, Ph.D.
|
| Street address |
517 South Euclid Avenue
|
| City |
Saint Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL17769 |
| Series (2) |
| GSE223658 |
Missense mutations in CRX homeodomain cause dominant retinopathies through two distinct mechanisms [Spec-seq] |
| GSE223659 |
Missense mutations in CRX homeodomain cause dominant retinopathies through two distinct mechanisms |
|
| Relations |
| BioSample |
SAMN32901358 |
| SRA |
SRX19162834 |
