|
| Status |
Public on Jun 01, 2020 |
| Title |
donor of TTYH2 editing stem |
| Sample type |
SRA |
| |
|
| Source name |
oligo chip
|
| Organism |
synthetic construct |
| Characteristics |
cell type: synthesized oligo
extraction: PCR from chip
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
nuclear fraction was extracted using Cell Biolabs kit (AKR-171), DNA was extracted using Zymo kit (D3020) and RNA was extracted using Trizol reagent.
gene specific primers with partial Illumina adapter were used to amplify each targets and then a second round of PCR was included to add barcodes.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
targeted mutagenesis
TTYH2donorECS_counts
|
| Data processing |
Library strategy: amplicon sequencing
genome with designed mutations was built using GMAP
alignment using GSNAP with parameter -m 12 -i 1000000
mutant isoforms with less than 50 reads were filtered out
RNA editing level were measured at target sits by calculating G in total reads
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including editing level, reads coverage of each isoform
|
| |
|
| Submission date |
Oct 15, 2019 |
| Last update date |
Jun 01, 2020 |
| Contact name |
Jin Li |
| E-mail(s) |
[email protected]
|
| Organization name |
Stanford University
|
| Department |
Genetics
|
| Street address |
M341, 300 Pasteur Dr.
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL27609 |
| Series (1) |
| GSE138860 |
CRISPR-mediated mutagenesis of RNA editing cis-regulatory elements |
|
| Relations |
| BioSample |
SAMN13031492 |
| SRA |
SRX6991995 |
