|
| Status |
Public on Sep 21, 2023 |
| Title |
Patient_P1608_Pre_Treatment_ATAC-seq |
| Sample type |
SRA |
| |
|
| Source name |
Primary CD138+ MM cells
|
| Organism |
Homo sapiens |
| Characteristics |
patient number: P1608
time point: Pre
cell type: Primary CD138+ MM cells
library preparation: 10X Genomics Single Cell ATACseq v1 Chemistry
|
| Growth protocol |
Primary CD138+ MM cells were obtained from the BM aspirates of MM patients at the time of diagnostic procedure, using positive selection with CD138 microbeads (Miltenyi Biotech, Auburn, CA) and accordingly to manufacturer’s instructions. CD138+ fractions were subsequently analyzed by flow cytometry in order to confirm the sample’s purity. HEK293T cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% FBS, 100 U/mL penicillin and 100 g/mL streptomycin. All of the listed cells above were cultured at 37°C and 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For single-cell library preparation for ATAC-seq the desired number of nuclei were targeted and processed according to 10X Genomics Reagent Kits User Guide (CG000168). The Nuclei Isolation was performed ad indicated in the nuclei Isolation protocol for Single Cell ATAC Sequencing (10x Genomics). Based on the starting number of cells and desired final nuclei concentration primary MM cells were washed, lysed and re-suspended in appropriate volume of chilled Diluted Nuclei Buffer. The resulting nuclei were then immediately used to generate scATAC-seq libraries. ScATAC-seq libraries were prepared according to 10X Genomics Reagent Kits User Guide. Briefly, the desired number of nuclei were combined with ATAC Buffer and master mix to form transposed Nuclei. Single-cell GEMs were then generated, amplified and subjected to bead clean-ups. Indexed sequencing libraries were constructed using Chromium i7 Sample Index and the barcode sequencing libraries subjected to a final bead clean-up prior to quantification.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
All raw FASTQs reads were aligned against the human reference genome GRCh38 with default parameters using cellranger-atac count.
Assembly: Pre-generated human reference GRCh38
Supplementary files format and content: Filtered peak barcode matrix in hdf5 format and a BED-like tabular file where each line represents a unique ATAC-seq fragment captured by the assay from CellRanger-atac count.
|
| |
|
| Submission date |
Feb 13, 2023 |
| Last update date |
Sep 21, 2023 |
| Contact name |
Nizar Bahlis |
| E-mail(s) |
nbahlis@ucalgary.ca
|
| Phone |
403-220-2801
|
| Organization name |
University of Calgary
|
| Department |
Divisions of Hematology and Oncology
|
| Street address |
3330 Hospital Dr NW HMRB328
|
| City |
Calgary |
| State/province |
Alberta |
| ZIP/Postal code |
T2N4N1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE199268 |
scATACseq Datasets Supporting Integrated Epigenetic and Transcriptional Single-Cell Analysis of t(11;14) Multiple Myeloma and Its BCL2 Dependency |
| GSE199373 |
Integrated Epigenetic and Transcriptional Single-Cell Analysis of t(11;14) Multiple Myeloma and Its BCL2 Dependency |
|
| Relations |
| BioSample |
SAMN33271157 |
| SRA |
SRX19353461 |
