|
| Status |
Public on Mar 08, 2023 |
| Title |
siRPL18-1-ATAC-48h |
| Sample type |
SRA |
| |
|
| Source name |
E14
|
| Organism |
Mus musculus |
| Characteristics |
cell type: E14
sirna: siRPL18
|
| Treatment protocol |
DharmaFECT (Horizon) was used for transfection of siRNA according to the manufacturer’s instructions. cells were harvested for experiments after 3 days of knockdown.
|
| Growth protocol |
E14 mouse embryonic stem cells (mESCs) were cultured with mouse ESC medium (DMEM high glucose supplemented with 15% defined FBS (Hyclone), 2mM L-glutamine (Gibco), 1X PenStrep (Gibco), 100μM MEM non-essential amino acids (Gibco), 100μM β-mercaptoethanol (Gibco) and 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore)). All the EC and ESC cell lines used in this study were cultured on gelatin-coated tissue culture plates and all the cell lines were cultured at 37°C with 5% CO 2 .
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chormatin was using Illumina tagment DNA TDE1 Enzyme and Buffer kit as per manufacturer's instructions.
Library was prepared using Nextera DNA library preparation kit as per manufacturer's instructions.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
ATAC-seq
|
| Data processing |
Libraries were mapped to mm9 genome using STAR with the options –alignIntronMax and –AlignEndsType set to 1 and EndToEnd respectively.
peaks were called using MACS2 and bigiwg files were produced by deeptools
Assembly: mm9
Supplementary files format and content: narrowPeaks indicating the highly accessible region of the libraries on the Genome
Supplementary files format and content: bigwig file, indicating the enrichment of the libraries on the Genome
|
| |
|
| Submission date |
Oct 06, 2022 |
| Last update date |
Mar 08, 2023 |
| Contact name |
Yingying Zeng |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute of Molecular and Cell Biology
|
| Lab |
Epigenetics and Cell Fates Laboratory
|
| Street address |
61 Biopolis Drive
|
| City |
Singapore |
| State/province |
--- Select a state --- |
| ZIP/Postal code |
138673 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE167177 |
ATAC-seq for E14 cells knockdown with siRNA or shRNA |
| GSE167182 |
E14 cells knockdown with siRNA or shRNA |
|
| Relations |
| BioSample |
SAMN31182946 |
| SRA |
SRX17813793 |
