|
| Status |
Public on Sep 16, 2022 |
| Title |
Ascl1-mutAscl1-Myod1, 72h ATAC |
| Sample type |
SRA |
| |
|
| Source name |
Skin
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Skin
cell type: Mouse Embryonic fibroblasts
strain: R26-M2rtTA
age: E14.5
treatment: Doxycyline
|
| Growth protocol |
DMEM (High Glucose), 10% fetal bovine serum,1x Sodium Pyruvate, 1 mM HEPES, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library preparation was performed according to the manufacter’s instructions (Single Cell Multiome ATAC + Gene Expression, 10x Genomics). Briefly, nuclei were isolated from MEFs, resuspended in a transposition master mix and incubated at 60°C for 60 min. Transposed nuclei were added to the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The transposed genomic DNA was barcoded during transposition and contains Illumina R1, R2 and P5 primer sequences as well as a 10x Barcode. Both transposed DNA and retrotranscribed cDNA were pre-amplified via PCR. ATAC-seq libraries were generated by a final PCR during which a P7 primer sequence and an i7 sample index are added. Gene expression libraries were generated through further amplification of the cDNA by PCR followed by enzymatic fragmentation and final PCR amplification adding both P5 and P7 Illumina primer sequences as well as i5 and i7 indexes. Library quality was validated using the Agilent High Sensitivity DNA Kit.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic single cell |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics scMultiome
|
| Data processing |
scRNA-seq & scATAC-seq data was processed using the cellranger-arc software (v2.0.0)
CellRanger arc was run with the cellranger-arc count command using standard parameters and the mouse GRCm38 genome.
To build the reference genome index for mouse, GRCm38 was used and the sequences and custom annotations of the syunthetic transcription factors were appended to the genome fasta and annotation files
The samples processed with cellranger-arc were aggregated using the cellranger-arc aggr command with the –normalize = none parameter
Assembly: GRCm38
Supplementary files format and content: ATAC Peaks in .bed format
Supplementary files format and content: Annotated ATAC peaks in .tsv format
Supplementary files format and content: Raw and filtered CellRanger output in .h5 format. Note: this data contains both the ATAC and scRNAseq data
Supplementary files format and content: Processed RNA and ATAC-seq data in .h5ad format
|
| |
|
| Submission date |
Aug 23, 2022 |
| Last update date |
Sep 16, 2022 |
| Contact name |
Bob Hersbach |
| E-mail(s) |
bob.hersbach@helmholtz-muenchen.de
|
| Organization name |
Helmholtz Zentrum Munich
|
| Department |
Institute of Stem Cell Research
|
| Street address |
Großhaderner Str. 9
|
| City |
Planegg-Martinsried |
| ZIP/Postal code |
82152 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE211863 |
Probing cell identity hierarchies by fate titration and collision during direct reprogramming [scRNA-seq & scATAC-seq] |
| GSE211864 |
Probing cell identity hierarchies by fate titration and collision during direct reprogramming |
|
| Relations |
| BioSample |
SAMN30466093 |
| SRA |
SRX17182563 |
