|
| Status |
Public on Jul 01, 2024 |
| Title |
HEPG2_ctrl_r2 |
| Sample type |
SRA |
| |
|
| Source name |
HEPG2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEPG2
cell type: liver cancer
genotype: WT
treatment: NA
|
| Growth protocol |
All the cell lines were maintained in DMEM with 10% FBS and antibiotics under humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol and 10 ug total RNA was used for downstream Dnase treatment and reverse transcription
Targeted PCR was perforem with Phusion to add illumina sequencing adaptors
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
RORC RNA switch DMS reactivity
|
| Data processing |
Reads from multiple lanes were merged and collapsed using fastq2collapse.pl (CTK package)
UMIs were then extracted using `umi_tools extract` with --extract-method string --bc-pattern=NNNNNNNNNNN flags
cutadapt (v3.5) was used to remove the constant sequences
bwa (v0.7.17-r1188) was used to align the reads to the reference.
Aligned reads were then sorted and deduplicated using UMICollapse (with -k 1 --algo adj --merge avgqua flags)
Mutations were then counted at each position for As and Cs (common SNPs were filtered)
Assembly: hg38
Supplementary files format and content: DMS signal at each position
Library strategy: DMS-MaPseq
|
| |
|
| Submission date |
Apr 28, 2024 |
| Last update date |
Jul 01, 2024 |
| Contact name |
Hani Goodarzi |
| Organization name |
UCSF
|
| Department |
Biochemistry and Biophysics
|
| Street address |
600 16th St, GH S312D
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE266051 |
DMS-MaPseq of RORC reporters and endogeneous RORC locus |
| GSE266070 |
RORC RNA Switch Mechanisms |
|
| Relations |
| BioSample |
SAMN41105974 |
| SRA |
SRX24387142 |
