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| Status |
Public on Sep 06, 2023 |
| Title |
dendritic cells, hypodermis, replicate 2 |
| Sample type |
SRA |
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| Source name |
Hypodermis
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| Organism |
Mus musculus |
| Characteristics |
tissue: Hypodermis
cell type: Dendritic cells
strain: C57BL/6
age: 8-10 weeks
Sex: Female
treatment: No treatment
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| Extracted molecule |
total RNA |
| Extraction protocol |
Back skins from C57BL/6 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. Dermis was isolated from epidermis after 45min of an enzymatic treatment with 0.15% Trypsin/0.75mM EDTA. Isolated dermis and hypodermis were each 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 from each layer and stained with antibodies as well as with propidium iodide (PI) before being FACS sorted as dendritic cells (PI–, singlet, CD45+, CD11b+, Ly6c-lo, MHCII-hi, CD64–), CCR2+ macrophages (PI–, singlet, CD45+, CD11b+, Ly6c-lo, CD11c-mid/lo, CD64+, CCR2+) and CCR2– macrophages (PI–, singlet, CD45+, CD11b+, Ly6c-lo, CD11c-mid/lo, CD64+, CCR2–). Cells were then washed, counted and used for RNA-sequencing. RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's instructions.
Libraries were prepared using the SMART-Seq Ultra Low Input RNA kit with Nextera XT library prep protocol according to the manufacturer’s instructions (Illumina, San Diego, CA, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Hypodermal dendritic cells #2
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| Data processing |
The FASTQ files with 125bp paired-end reads were processed using Trimmomatic (v0.30) to remove adaptors and low-quality bases. The trimmed FASTQ data were aligned to mouse genome (GRCm38) with STAR (v2.4.2a) using GENCODE mouse gtf file version 4 (Ensembl 78). About 90% of ~42 million reads per sample were mapped to mouse genome uniquely for a total of 97% mapping rate. The STAR software was also used to generate the gene read counts. Statistical analysis was performed in R computing environment (https://www.r-project.org). The gene read count data from STAR for all samples were normalized with the R Package limma (v3.34.9).
Assembly: GRCm38
Supplementary files format and content: Excel files containing raw read counts.
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| Submission date |
Mar 20, 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 |
GPL17021 |
| Series (2) |
| GSE227758 |
Transcriptomic profile of dermal and hypodermal CCR2+ macrophages, CCR2- macrophages and dendritic cells from C57BL/6 mice |
| GSE228445 |
Dermal and hypodermal macrophages and dendritic cells |
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| Relations |
| BioSample |
SAMN33830286 |
| SRA |
SRX19731242 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7107654_Hypodermal_DC_2.xlsx |
1.3 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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