|
| Status |
Public on Sep 01, 2023 |
| Title |
Library5 DNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
DH5alpha
|
| Organism |
Escherichia coli |
| Characteristics |
cell line: DH5alpha
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 |
genomic DNA |
| Extraction protocol |
RNA was extracted from retinas with TRIzol and treated with Turbo Dnase. cDNA was prepared using SuperScript IV.
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 |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
DNA-seq on reporter gene barcode amplicons from plasmid DNA library
|
| 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 with custom python scripts.
To obtain barcode read counts, reads were matched to barcoded reporter gene sequences using custom python scripts. Only exact barcoded matches were counted. FASTA files with reporter gene sequences for each library are included as supplementary files.
Assembly: mm10
Supplementary files format and content: Each sample has its own tab-delimited file. Column 1: Barcode sequence. Column 2: cis-regulatory element name. Column 3: Barcode counts.
|
| |
|
| Submission date |
Aug 21, 2023 |
| Last update date |
Sep 01, 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 |
GPL21222 |
| Series (1) |
| GSE241353 |
Active learning of enhancer and silencer regulatory grammar in photoreceptors |
|
| Relations |
| BioSample |
SAMN37096596 |
| SRA |
SRX21437485 |
