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| Status |
Public on Sep 06, 2023 |
| Title |
Macrophages, WT, replicate 1 |
| Sample type |
SRA |
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| Source name |
Hypodermis
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| Organism |
Mus musculus |
| Characteristics |
tissue: Hypodermis
cell type: Macrophages
genotype: Igf1-flox
age: 8-10 weeks old
treatment: No treatment
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Back skins from Igf1-flox and Csf1r-Cre x Igf1-flox female adult mice were harvested after shaving with an electric clipper. Subcutaneous fat was removed from hypodermis and hypodermal layers were physically isolated from the dermis with forceps. Hypodermis was minced with scissors and digested for 2H at 37°C in RPMI supplemented with 5% FCS and containing 0.25mg/mL of liberase T-Flex and 1ug/mL of DNAse I. Cells were isolated and immunostained with anti-CD45 and anti-CD64 antibodies as well as stained with Sytox-Red (SR) before being FACS sorted as live macrophages (SR–, CD45+, CD64+). Cells were lysed in cold lysis buffer (10 mM Tris–HCl (PH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P40, 0.01% Digitonin, 1mM DTT and 1U/μl RNase inhibitor) for 5 min on ice for nuclei isolation. Upon washing the nuclei extracts, targeted nuclei recovery was processed for single-cell ATAC-sequencing.
Library construction was performed in accordance with 10X Genomics protocol (Next GEM Single Cell Multiome ATAC + Gene expression (GEX) protocol, CGOOO338).
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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 software (v 2.1.0)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Mar 21, 2023 |
| Last update date |
Sep 06, 2023 |
| Contact name |
Keisuke Nagao |
| Organization name |
National Institutes of Health
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| Street address |
10 Center Dr, Bldg 10, 12N240B
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20852 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE227859 |
Single-cell epigenomic analysis of hypodermal macrophages from Csf1r-cre x Igf1-flox mice. |
| GSE228445 |
Dermal and hypodermal macrophages and dendritic cells |
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| Relations |
| BioSample |
SAMN33846562 |
| SRA |
SRX19743763 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7109886_WT1_fragments.tsv.gz |
1.2 Gb |
(ftp)(http) |
TSV |
| GSM7109886_WT1_peaks.bed.gz |
933.0 Kb |
(ftp)(http) |
BED |
| GSM7109886_WT1_singlecell.csv.gz |
5.8 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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