|
| Status |
Public on Mar 05, 2023 |
| Title |
CDNRM RNA-seq replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
whole retina
|
| Organism |
Mus musculus |
| Characteristics |
tissue: whole retina
genotype: wild-type
treatment: none
|
| Growth protocol |
P0 mouse retinal explants were electroporated with plasmid library and cultured ex vivo for 8 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from retinas with TRIzol and treated with Turbo Dnase. cDNA was prepared using SuperScript III.
Sequence barcodes from reporter genes were amplified by PCR and purified with Monarch PCR cleanup kit. Custom Illumina adapters were added by PCR.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNA-seq performed on reporter gene barcode amplicons
|
| Data processing |
All raw reads were processed regardless of quality score. Reads with the expected in-line multiplexing barcode for each sample followed by the spacer sequence were identified using custom python scripts.
Demultiplexed reads were used to determine the read counts for each barcode. Read counts for each barcode were normalized by total reads in the sample (counts per million, cmp) and then dividing by the normlized DNA read counts to generate the activity scores, which are reported as log2 scores in the supplemental file. Data processing was performed using custom python scripts.
Assembly: mm10
Supplementary files format and content: Processed data are in the tab-delimited file cdnrm_mpra_library.txt. Column 1: synthetic cis-regulatory element name. Column 2: log2 activity scores (RNA/DNA)
Library strategy: Amplicon-seq
|
| |
|
| Submission date |
Feb 22, 2023 |
| Last update date |
Mar 05, 2023 |
| Contact name |
Michael Aaron White |
| E-mail(s) |
mawhite@wustl.edu
|
| Organization name |
Washington University in St. Louis School of Medicine
|
| Department |
Genetics
|
| Street address |
660 South Euclid Ave
|
| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63144 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE225867 |
Transcription factor interactions explain the context-dependent activity of CRX binding sites |
|
| Relations |
| BioSample |
SAMN33419329 |
| SRA |
SRX19477522 |
