|
| Status |
Public on Feb 17, 2022 |
| Title |
Gm12878_benchmark_run1 |
| Sample type |
SRA |
| |
|
| Source name |
GM12878
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GM12878
library: benchmark
molecule: GFP mRNA
|
| Treatment protocol |
Cells were electroporated by using NEON transfection system and recovered in culture medium for 24 hours.
|
| Growth protocol |
37C with 5% CO2 supplementation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified by using Maxi RNeasy (QIAGEN) from homogenized cells. Then GFP mRNA was isolated by using biotinilated primers and magnetic beads followd by cDNA synthesis.
Libraries were initially amplified from cDNA or plasmid, and then secondarily amplified and added P5 and P7 tag sequences.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Library strategy: MPRA
Sequences were processed through MPRAduo pipeline (https://github.com/tewhey-lab/MPRAduo).
Supplementary_files_format_and_content: Processed data files contain raw count tables for barcode tag.
|
| |
|
| Submission date |
Feb 04, 2022 |
| Last update date |
Feb 17, 2022 |
| Contact name |
Kousuke Mouri |
| E-mail(s) |
kousuke.mouri@jax.org
|
| Organization name |
The Jackson Laboratory
|
| Street address |
600 Main Street
|
| City |
Bar Harbor |
| State/province |
ME |
| ZIP/Postal code |
04609 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE196171 |
Whole genome functional characterization of RE1 silencers using a modified massively parallel reporter assay |
|
| Relations |
| BioSample |
SAMN25655153 |
| SRA |
SRX14046725 |
