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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 05, 2024 |
| Title |
HET, replicate 2, 10X multiome scATAC |
| Sample type |
SRA |
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| Source name |
Spleen
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| Organism |
Mus musculus |
| Characteristics |
tissue: Spleen
strain: C57BL/6
age: 8-10 weeks
genotype: Smarca4+/-
cell type: Germinal Center B Cells
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
GC B cells were isolated from mice spleens at day 10 post-immunization using the Germinal Center B Cell (PNA) MicroBead Kit (Miltenyi Biotec,130-110-479). To improve the quality of single cell ATAC libraries, pre-enriched cells were stained with Zombie Green (BioLegend) and sorted by FACS. Cells were washed in PBS containing 0.04% BSA 2 times. Determine the cell concentration using a Countess II FL Automated Cell counter and viable cell number was counted by the trypan blue dye exclusion method, before proceeding to nuclei isolation. Pellet 100,000~200,000 cells at 300 rcf for 5 min at 4 °C, remove all supernatant and resuspend in lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP-40, 0.01% Digitonin, 1% BSA, 1 mM DTT and 1 U/µl RNase inhibitor). Incubate for 5 min on ice. After a total of 3 washes, nuclei were resuspended in diluted nuclei buffer (10x Genomics) and nuclei concentration was determined.
Proceed immediately to Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide (CG000338). Briefly, 10,000 nuclei/sample were loaded on the Chromium Controller. The 10X libraries were then prepared following the manufacturer’s instruction (Next GEM Single Cell Multiome)
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10x Genomics
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| Data processing |
Demultiplexing, barcoded processing, gene counting were done using the Cell Ranger ARC software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
Analyses were performed in R (version 4.2.1) using various R packages. FASTQ files were processed using cellranger-arc count (10x genomics). This pipeline aligns reads to the mm10 mouse reference genome, performs barcode error correction, PCR duplicate marking, peak calling, and ATAC and gene expression molecule counting to produce expression and fragment count matrices. The gene expression matrices and ATAC fragments were loaded into R and processed with Signac (version 1.9.0, https://github.com/timoast/signac) and Seurat (version 4.3.0, https://github.com/satijalab/seurat) for downstream analyses.
Assembly: mm10
Supplementary files format and content: Tab-separated matrix files and fragments files
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| Submission date |
Aug 02, 2023 |
| Last update date |
Feb 05, 2024 |
| Contact name |
Michael Green |
| E-mail(s) |
mgreen5@mdanderson.org
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| Phone |
713-745-4244
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| Organization name |
The University of Texas MD Anderson Cancer Center
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| Department |
Department of Lymphoma/Myeloma
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| Street address |
7455 Fannin Street
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| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77054 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE239937 |
Smarca4 (Brg1) is a haploinsufficient B-cell tumor suppressor that fine-tunes centrocyte cell fate decisions [scMultiome] |
| GSE254908 |
Smarca4 (Brg1) is a haploinsufficient B-cell tumor suppressor that fine-tunes centrocyte cell fate decisions |
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| Relations |
| BioSample |
SAMN36812318 |
| SRA |
SRX21229363 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7677869_Brg1_HET_M6_atac_fragments.tsv.gz |
1017.2 Mb |
(ftp)(http) |
TSV |
| GSM7677869_Brg1_HET_M6_atac_fragments.tsv.gz.tbi.gz |
772.9 Kb |
(ftp)(http) |
TBI |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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