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| Status |
Public on Dec 29, 2023 |
| Title |
BL6_macrophage |
| Sample type |
SRA |
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| Source name |
Peritoneal cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: Peritoneal cells
strain: C57BL/6
age: 6-8 weeks old
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Peritoneal cells were isolated from both BL/6 and BALB/c mice after IL-4 treatment.Nuclei isolation for snRNA-seq and snATAC-seq was optimized and performed following the demonstrated protocol CG000365 from 10x Genomics.
The libraries were prepared following the 10x Genomics user guide CG000338 for Single Cell Multiome ATAC + Gene Expression Reagent Bundle (PN-1000285,10xGenomics). Only the ATAC Library Construction is performed by Sample Index Plate N, Set A (3000427, 10xGenomics).
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| Library strategy |
ATAC-seq |
| Library source |
genomic single cell |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10x Genomics
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| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger ATAC 2.0.0 software using the default parameters. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Integration of scATAC-seq samples,clustering of cells, and visualization of chromatin accessibility and pseudobulk coverage tracks was performed with Seurat (version 3.0) and its extension Signac (version 0.15;https://github.com/timoast/signac).
Assembly: mm10
Supplementary files format and content: fragments.and peaks files
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| Submission date |
Nov 16, 2023 |
| Last update date |
Dec 29, 2023 |
| Contact name |
Mingming Zhao |
| E-mail(s) |
mingming.zhao@nih.gov
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| Organization name |
national institutes of health
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| Street address |
9000 Rockville Pike
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| City |
Bethesda |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE248035 |
Genetic variation in IL-4 activated tissue resident macrophages alters the epigenetic state to determine strain specific synergistic responses to LPS [scATAC-seq] |
| GSE248038 |
Genetic variation in IL-4 activated tissue resident macrophages alters the epigenetic state to determine strain specific synergistic responses to LPS |
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| Relations |
| BioSample |
SAMN38285650 |
| SRA |
SRX22550200 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7904994_BL6_fragments.tsv.gz |
1.3 Gb |
(ftp)(http) |
TSV |
| GSM7904994_BL6_peaks.bed.gz |
1.0 Mb |
(ftp)(http) |
BED |
| GSM7904994_BL6_singlecell.csv.gz |
5.3 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
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