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| Status |
Public on Oct 25, 2019 |
| Title |
RNA-seq and ATAC-seq to study dendritic cell heterogeneity |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The cDC2 subset is heterogeneous. We found the expression of T-bet delineates two distinct cDC2 subsets. Transcriptional profiling and analysis of chromatin accessibility in newly defined DC subsets identifies phenotypic specialisation and transcriptional regulators.
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| Overall design |
ATAC-seq in cDC1s, T-bet+ cDC2 and T-bet- cDC2s (duplicates). RNA-seq in cDC1s, T-bet+ cDC2 and T-bet- cDC2s (triplicates or duplicates).
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| Contributor(s) |
Brown C, Pritykin Y, Leslie C, Rudensky A |
| Citation(s) |
31668803 |
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https://www.cell.com/action/showPdf?pii=S0092-8674%2819%2931116-X
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| Submission date |
Apr 23, 2019 |
| Last update date |
Nov 13, 2019 |
| Contact name |
Yuri Pritykin |
| Organization name |
Princeton University
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| Street address |
245 Carl Icahn Lab, Lewis-Sigler Institute for Integrative Genomics
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| City |
Princeton |
| State/province |
NJ |
| ZIP/Postal code |
08540 |
| Country |
USA |
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| Platforms (1) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (22)
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| GSM3733703 |
RFP_pos_2: ATAC-seq in T-bet+ cDC2, rep2 |
| GSM3733704 |
RFP_neg_1: ATAC-seq in T-bet- cDC2, rep1 |
| GSM3733705 |
RFP_neg_2: ATAC-seq in T-bet- cDC2, rep2 |
| GSM3733706 |
Spleen_XCR1_1: RNA-seq in spleen cDC1, rep1 |
| GSM3733707 |
Spleen_XCR1_2: RNA-seq in spleen cDC1, rep2 |
| GSM3733708 |
Spleen_XCR1_3: RNA-seq in spleen cDC1, rep3 |
| GSM3733709 |
Spleen_RFP_pos_1: RNA-seq in spleen T-bet+ cDC2, rep1 |
| GSM3733710 |
Spleen_RFP_pos_2: RNA-seq in spleen T-bet+ cDC2, rep2 |
| GSM3733711 |
Spleen_RFP_pos_3: RNA-seq in spleen T-bet+ cDC2, rep3 |
| GSM3733712 |
Spleen_RFP_neg_1: RNA-seq in spleen T-bet- cDC2, rep1 |
| GSM3733713 |
Spleen_RFP_neg_2: RNA-seq in spleen T-bet- cDC2, rep2 |
| GSM3733714 |
Spleen_RFP_neg_3: RNA-seq in spleen T-bet- cDC2, rep3 |
| GSM3733715 |
MLN_XCR1_1: RNA-seq in MLN cDC1, rep1 |
| GSM3733716 |
MLN_XCR1_2: RNA-seq in MLN cDC1, rep2 |
| GSM3733717 |
MLN_XCR1_3: RNA-seq in MLN cDC1, rep3 |
| GSM3733718 |
MLN_RFP_pos_1: RNA-seq in MLN T-bet+ cDC2, rep1 |
| GSM3733719 |
MLN_RFP_pos_2: RNA-seq in MLN T-bet+ cDC2, rep2 |
| GSM3733720 |
MLN_RFP_neg_2: RNA-seq in MLN T-bet- cDC2, rep1 |
| GSM3733721 |
MLN_RFP_neg_3: RNA-seq in MLN T-bet- cDC2, rep2 |
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| Relations |
| BioProject |
PRJNA534273 |
| SRA |
SRP193486 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE130201_gene-counts.txt.gz |
641.5 Kb |
(ftp)(http) |
TXT |
| GSE130201_peaks-dendritic-counts.txt.gz |
802.8 Kb |
(ftp)(http) |
TXT |
| GSE130201_peaks-dendritic.bed.gz |
801.1 Kb |
(ftp)(http) |
BED |
| GSE130201_summits-dendritic-counts.txt.gz |
1.7 Mb |
(ftp)(http) |
TXT |
| GSE130201_summits-dendritic.bed.gz |
2.4 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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