|
| Status |
Public on Oct 23, 2015 |
| Title |
gDNA eGFP(+) |
| Sample type |
SRA |
| |
|
| Source name |
Designed oligonucleotides
|
| Organism |
synthetic construct |
| Characteristics |
functional assay: splicing activity
cell line: H1299
master plasmid: pEF1-mRFP-oligos-eGFP
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
none provided by the submitter
Illumina adaptors ligation
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
oligos_measurements_processed_data.tab
|
| Data processing |
Single-end reads in the length of 50 or 200nt were trimmed to 45nt containing the common priming site and the unique 25nt of the oligo’s variable region.
Trimmed reads were mapped to the synthetic library sequences using Novoalign aligner
The number of reads for each designed oligo was counted in each sample.
Genome_build: Synthetic library oligonucleotides
Supplementary_files_format_and_content: Tab delimited file that holds the synthetic oligo id number, sequence, cap-independnet translation activity, promoter activitiy and cDNA/gDNA ratio
|
| |
|
| Submission date |
Oct 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Shira Weingarten-Gabbay |
| Organization name |
The Broad Institute
|
| Street address |
75 Ames St
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL17769 |
| Series (1) |
| GSE74277 |
Systematic discovery of cap-independent translation sequences in human and viral genomes |
|
| Relations |
| BioSample |
SAMN04208865 |
| SRA |
SRX1366403 |
