|
| Status |
Public on Nov 16, 2023 |
| Title |
Mutagenesis MPRA in iPSC-CMs day 24 DNA-Rep-2 |
| Sample type |
SRA |
| |
|
| Source name |
WTC-11
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: WTC-11
cell type: iPSC-derived cardiomyocytes
genotype: WT
treatment: Transduced with lentiMPRA lentivirus
|
| Treatment protocol |
iPSC-CMs were transfected with the mutagenesis lentiMPRA library at day 17 of iPSC-CM differentiation, and cells were collected 7 days later.
|
| Growth protocol |
iPSC-CMs were maintained in RPMI supplemented with B27 supplement in humidified atmosphere with 5% CO2 at 37C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Both DNA and RNA were extracted from transfected iPSC-CMs using Quick-DNA/RNA Miniprep Kit (Zymo #D7001). Purified genomic DNA and RNA were stored at -80C.
RNA was transcribed into cDNA with a specific primer using the PrimeScript™ RT reagent Kit with gDNA Eraser (Takara #RR047A). Amplicons containing 15 bp barcodes were amplified from gDNA and cDNA.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Mutagenesis_MPRA_DNA_2
|
| Data processing |
Cutadapt 2.5 was used to remove primer sequences within each read.
Sequence reads were mapped to library variants based on the barcode by a custom Python script.
Read counts were then normalized to sequencing depth (FPM).
Assembly: hg19
Supplementary files format and content: *.txt: Tab-delimited text files include reads count values for each Sample.
Library strategy: Amplicon-seq
|
| |
|
| Submission date |
Jul 15, 2022 |
| Last update date |
Nov 16, 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 |
GPL18573 |
| Series (2) |
| GSE208284 |
Functional analysis of human cardiac enhancers by tiling mutagenesis |
| GSE208286 |
Analysis of human iPSC-derived cardiomyocytes |
|
| Relations |
| BioSample |
SAMN29767380 |
| SRA |
SRX16292946 |
