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| Status |
Public on Mar 10, 2018 |
| Title |
Lung_cDC_CD11c_cre+_MyD88 fx_0h |
| Sample type |
SRA |
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| Source name |
Lung cDC CD11c cre+ MyD88 fx/fx-0h
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| Organism |
Mus musculus |
| Characteristics |
background: C57BL/6
gender: male
tissue: Lung
cell type: Sorted cDC
timepoint: 0h
treatment: none
genotype: MyD88 fx/fx; Itgax-cre+/Tg
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| Treatment protocol |
Mice were either untreated or sensitized oropharyngeally with 100 ug ovalbumin (OVA)/ 1250 ng standard flagellin (stFLA) for 6 hours in vivo. After this time, lungs were isolated and digested with collagenease, DNase, hyaluronidase, and Liberase TM to generate a single cell suspension. Cells were stained for flow cytometry and sorted for autofluorescence-, CD11c+, I-A(b) hi, CD88-, Ly6C- cells to include cDCs but not alveolar macrophages, moDCs, or inflammatory DCs.
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| Growth protocol |
None
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from 25,000 sorted cells were lysed in cold lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40) for 5 min.
The ATAC-seq tagmentation reaction was performed as previously described (Buenrostro, 2013) with the following modifications. Nuclei were incubated with 2.5 μl of Tn5 Transposase in 25 μl of reaction buffer. Purified DNA fragments were amplified with 9 cycles of PCR, and PCR products were purified by using AMPure XP beads (1:3 ratio of sample to beads, Beckman Coulter). The libraries were sequenced on NextSeq 500 (Illumina) in 50 bp paired-end format. The data was highly reproducible since the number of peaks observed was almost completely the same between biological replicates with similar read depth
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Sorted cDC
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| Data processing |
Library strategy: ATAC-seq
Raw reads were first cleaned for adapter sequences using Trim Galore with default parameters;
Cleaned reads were aligned to mm9 using Bowtie with the parameters -m1, -v2 and –X1500; duplicates were removed using Picard;
Two biology replicates for each condition were merged into one sample;
we adjusted the read start sites to represent the center of the transposon binding event; all reads aligning to the + strand were offset by +4 bp, and all reads aligning to the – strand were offset −5 bp;
PeaKDEck (Version 1.1)was used to call all reported ATAC-seq peaks;with a window size of 300 bp and probabilityValue –sig0.0001.
Genome_build: mm9
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| Submission date |
Mar 10, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Seddon Thomas |
| E-mail(s) |
sythomas@gmail.com
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| Organization name |
NIEHS
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| Street address |
111 T. W. Alexander Dr.,
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| City |
RTP |
| State/province |
North Carolina |
| ZIP/Postal code |
27709 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE79062 |
ATAC-seq of sorted lung cDCs (conventional dendritic cells) from cell-specific MyD88 KO at 0h and 6h in vivo sensitization with OVA/standard flagellin |
| GSE79615 |
MYD88-dependent dendritic and epithelial cell crosstalk in the lung orchestrates immune responses to inhaled allergens |
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| Relations |
| BioSample |
SAMN04544418 |
| SRA |
SRX1623680 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2084788_CD11c_h0_combine_Sorted_dedup_peak.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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