|
| Status |
Public on Jan 30, 2023 |
| Title |
AV_MPRA_V2 |
| Sample type |
SRA |
| |
|
| Source name |
ventricle
|
| Organism |
Mus musculus |
| Characteristics |
tissue: ventricle
cell type: cardiomyocytes
genotype: WT
treatment: AAV9 library
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol and purified with RNA Clean and Concentrator kit from Zymo; AAV genome was released by incubating with Proteinase K solution and then used as template for MPRA library construction.
DNA/RNA were reversed transcripted with UMI-primer which recognized the cloning sites of the specific enhancers. The P5 and P7 adapters were added through two cycles of touch-down PCR.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
AV_enhancers_400bp_MPRA_vCMs_RNA_rep2
|
| Data processing |
Cutadapt 2.5 was used to remove primer sequences within each read.
MPRA pair-end reads were aligned to mm10 using Bowtie2 2.3.4.3 (--end-to-end) with default parameters.
A custom script was used to determine DNA and RNA read counts for each enhancer.
PCR duplicates were removed by UMI. Read counts were then normalized to sequencing depth (FPM).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include reads count values for each sample.
Library strategy: MPRA
|
| |
|
| Submission date |
Oct 07, 2022 |
| Last update date |
Feb 01, 2023 |
| Contact name |
Xiaoran Zhang |
| E-mail(s) |
xiaoran.zhang@childrens.harvard.edu
|
| Phone |
8574259855
|
| Organization name |
Boston Children's Hospital
|
| Department |
Cardiology
|
| Lab |
Pu lab
|
| Street address |
14 Perkins Square, Apt 11
|
| City |
Jamaica Plain |
| State/province |
MA |
| ZIP/Postal code |
02130 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE215033 |
Chamber selective enhancers identified in vivo by AAV-MPRA |
| GSE215065 |
Regulation of mouse chamber selective enhancers |
|
| Relations |
| BioSample |
SAMN31208440 |
| SRA |
SRX17828080 |
