 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 04, 2024 |
| Title |
CHO_multiome_S2_ATAC |
| Sample type |
SRA |
| |
|
| Source name |
Ovaries
|
| Organism |
Cricetulus griseus |
| Characteristics |
tissue: Ovaries
cell line: Humira431
cell type: Nuclei
library: ATAC
treatment (glutamine_adaption): no
passage: Passage 36
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
To isolate the nuclei, the cells were transferred to a 1.5 ml Eppendorf tube and centrifuged at 200 g for 5 mins. The supernatant was discarded and 1 ml of 1x PBS was added. The cells were then centrifuged for 5 minutes at 200 g and the supernatant discarded. Cells were treated for 10 minutes on ice in 125 µl buffer (10 mM HEPES (pH 7.9), 10 mM KCl, 1.5 mM MgCl2, 0.34 M sucrose, 10% glycerol, 1mM DTT) supplemented with 0.1 % Triton X-100 and a freshly added cOmplete mini tablet (Roche). Afterwards, the samples were centrifuged at 1300 g for 5 minutes and the supernatant was discarded. To freeze the nuclei, the samples were resuspended in 1 ml buffer containing 700 µl glycerol and slowly cooled down to -80°C. Prior to library preparation, samples were thawed on ice, filled up with buffer to a total volume of 1.5 ml, and centrifuged for 3 min at 1300 g. Next, the supernatant was discarded without fully exposing the pellet. Samples were subsequently resuspended in 1 ml of buffer, centrifuged for 3 minutes at 1300 g and 4°C. The supernatant was discarded, and the nuclei were resuspended in 100 µl buffer and stored on ice. Subsequently, they were processed with the 10X Multiome Gene Expression + ATAC kit.
Approximately 10,000 nuclei per sample were loaded into the Chromium Controller system, and libraries were subsequently prepared using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kit (10X Genomics), following the manufacturer’s instructions. Libraries were sequenced on a NovaSeq 6000 device (Illumina) using paired-end (50 + 100 bp) settings for 150 cycles for the scRNA-seq, and paired-end (50+100 bp) for 150 cycles for the scATAC-seq.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Alignment of the raw fastq-data with cellranger-arc-2.0.2 to reference genome.
QC and data filtering with cellranger-arc-2.0.2.
Sample combination with cellranger-arc-2.0.2.
QC with Signac v1.12.
Clustering and visualization with Seurat v.4.0.5. & Signac v.1.12
Assembly: Cricetulus_griseus CHOK1GS_HDv1.108
Supplementary files format and content: RData objects containing the Signac object and the GRanges ATAC peak objects
|
| |
|
| Submission date |
Jul 23, 2024 |
| Last update date |
Nov 04, 2024 |
| Contact name |
Elias Böhl |
| E-mail(s) |
[email protected]
|
| Organization name |
German Cancer Research Center (DKFZ)
|
| Department |
Divison of Epigenetics
|
| Street address |
Im Neuenheimer Feld 580
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL27425 |
| Series (2) |
| GSE272869 |
Analysis of population heterogeneity in CHO cells by genome-wide DNA methylation analysis and by multi-modal single-cell sequencing [multiome] |
| GSE273685 |
Analysis of population heterogeneity in CHO cells by genome-wide DNA methylation analysis and by multi-modal single-cell sequencing |
|
| Relations |
| BioSample |
SAMN42763091 |
| SRA |
SRX25423545 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
