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| Status |
Public on May 24, 2023 |
| Title |
cDC1_WT 3 |
| Sample type |
SRA |
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| Source name |
Spleen
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| Organism |
Mus musculus |
| Characteristics |
cell type: splenic cDC3
genotype: naive WT
strain: C57BL/6
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| Treatment protocol |
No treatment
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| Growth protocol |
Spleens were digested, and denritic cells were enriched with anti-CD11c MicroBeads prior to sorting. Splenic cDC1 (CD11c+CD8α+CD24+TCRβ−CD49b−B220−) were sorted from naïve WT and Flcn∆DC mice.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed in 50 μl ATAC-seq lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630 detergent) on ice for 10 min. Resulting nuclei were pelleted at 500g for 10 min at 4 °C. Supernatant was carefully removed with a pipette and discarded. The pellet was resuspended in 50 μl transposase reaction mix (25 μl 2 × TD buffer, 22.5 μl nuclease-free water, 2.5 μl transposase) and incubated for 30 min at 37 °C. After the reaction, the DNA was cleaned up using the Qiagen MinElute kit
The barcoding reaction was run using the NEBNext HiFi kit on the basis of the manufacturer’s instructions and amplified for five cycles
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
1894342
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| Data processing |
Adapter sequences were removed using cutadapt v.1.9
and aligned them to the mouse genome mm10 (NCBIM37_um from Sanger; ftp://ftp-mouse.sanger.ac.uk/ref/NCBIM38_um.fa) using the Burrows–Wheeler algorithm32 (version 0.5.9-r26-dev, default parameter)
duplicated reads were then marked with Picard (version 1.65 (1160)) and only non-duplicated reads were kept, using samtools (parameter ‘-q 1 -F 1024’ version 0.1.18 (r982:295))
After adjustment using the Tn5 shift (by which reads were offset by +4 bp for the sense strand and −5 bp for the antisense strand), we separated reads into nucleosome-free, mononucleosome, dinucleosome and trinucleosome by fragment size
performed peak-calling for nucleosome-free reads using MACS2 (version 2.1.0.20150603, default parameters with ‘–extsize 200 –nomodel’, merged by bedtools if within 100 bp) for individual samples
Assembly: mm10
Supplementary files format and content: Consensus peaks and fragment counts for all samples
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| Submission date |
Jul 31, 2022 |
| Last update date |
May 24, 2023 |
| Contact name |
Hongbo Chi |
| E-mail(s) |
hongbo.chi@stjude.org
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| Organization name |
St Jude Children's Research Hospital
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| Department |
Immunology
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| Street address |
262 Danny Thomas Place
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| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE210151 |
SLC38A2 and glutamine signaling in cDC1 dictate anti-tumor immunity [ATAC-Seq] |
| GSE210155 |
SLC38A2 and glutamine signaling in cDC1 dictate anti-tumor immunity |
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| Relations |
| BioSample |
SAMN30072356 |
| SRA |
SRX16744439 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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