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Sample GSM7040829 Query DataSets for GSM7040829
Status Public on Sep 21, 2023
Title Patient_P1675_Post_Treatment_ATAC-seq
Sample type SRA
 
Source name Primary CD138+ MM cells
Organism Homo sapiens
Characteristics patient number: P1675
time point: Post
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 SAMN33271156
SRA SRX19353462

Supplementary file Size Download File type/resource
GSM7040829_P1675_Post_filtered_peak_bc_matrix.h5 81.1 Mb (ftp)(http) H5
GSM7040829_P1675_Post_peaks.bed.gz 891.8 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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