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| Status |
Public on Jan 19, 2021 |
| Title |
Uncovering the Gene Regulatory Networks Underlying Macrophage Polarization Through Comparative Analysis of Bulk and Single-Cell Data |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Gene regulatory networks (GRNs) provide a powerful framework for studying cellular differentiation. However, it is less clear how GRNs encode cellular responses to everyday microenvironmental cues. Macrophages can be polarized and potentially repolarized based on environmental signaling. In order to identify the GRNs that drive macrophage polarization and the heterogeneous single-cell subpopulations that are present in the process, we used a high-resolution time course of bulk and single-cell RNA-seq and ATAC-seq assays of HL-60-derived macrophages polarized towards M1 or M2 over 24 hours. We identified transient M1 and M2 markers, including the main transcription factors that underlie polarization, and subpopulations of naive, transitional, and terminally polarized macrophages. We built bulk and single-cell polarization GRNs to compare the recovered interactions and found that each technology recovered only a subset of known interactions. Our data provide a resource to study the GRN of cellular maturation in response to microenvironmental stimuli in a variety of contexts in homeostasis and disease.
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| Overall design |
We used a high-resolution time course of bulk and single-cell RNA-seq and ATAC-seq assays of HL-60-derived macrophages polarized towards M1 or M2 over 24 hours.
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| Contributor(s) |
Carvalho K, Mortazavi SA |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Jan 09, 2021 |
| Last update date |
Jan 22, 2021 |
| Contact name |
Ali Mortazavi |
| Organization name |
UC Irvine
|
| Street address |
2300E Biological Sciences III
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (80)
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| Relations |
| BioProject |
PRJNA690953 |
| SRA |
SRP301086 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE164498_HL60_bATACseq_IDRoutput.bed.gz |
143.2 Kb |
(ftp)(http) |
BED |
| GSE164498_M1_12hrs_bATACseq_IDRoutput.bed.gz |
662.4 Kb |
(ftp)(http) |
BED |
| GSE164498_M1_24hrs_bATACseq_IDRoutput.bed.gz |
597.6 Kb |
(ftp)(http) |
BED |
| GSE164498_M1_3hrs_bATACseq_IDRoutput.bed.gz |
653.7 Kb |
(ftp)(http) |
BED |
| GSE164498_M1_6hrs_bATACseq_IDRoutput.bed.gz |
622.1 Kb |
(ftp)(http) |
BED |
| GSE164498_M2_12hrs_bATACseq_IDRoutput.bed.gz |
515.6 Kb |
(ftp)(http) |
BED |
| GSE164498_M2_24hrs_bATACseq_IDRoutput.bed.gz |
729.4 Kb |
(ftp)(http) |
BED |
| GSE164498_M2_3hrs_bATACseq_IDRoutput.bed.gz |
556.0 Kb |
(ftp)(http) |
BED |
| GSE164498_M2_6hrs_bATACseq_IDRoutput.bed.gz |
499.3 Kb |
(ftp)(http) |
BED |
| GSE164498_M2_ID2_KD_bATACseq_IDRoutput.bed.gz |
644.4 Kb |
(ftp)(http) |
BED |
| GSE164498_M2_IRF1_KD_bATACseq_IDRoutput.bed.gz |
540.0 Kb |
(ftp)(http) |
BED |
| GSE164498_M2_IRF7_KD_bATACseq_IDRoutput.bed.gz |
599.3 Kb |
(ftp)(http) |
BED |
| GSE164498_M2_IRF9_KD_bATACseq_IDRoutput.bed.gz |
666.7 Kb |
(ftp)(http) |
BED |
| GSE164498_M2_Neg_Ctrl_KD_bATACseq_IDRoutput.bed.gz |
625.6 Kb |
(ftp)(http) |
BED |
| GSE164498_M2_Pos_Ctrl_KD_bATACseq_IDRoutput.bed.gz |
667.8 Kb |
(ftp)(http) |
BED |
| GSE164498_Mac_0hrs_bATACseq_IDRoutput.bed.gz |
498.0 Kb |
(ftp)(http) |
BED |
| GSE164498_RAW.tar |
469.0 Mb |
(http)(custom) |
TAR (of BED, CSV, TXT) |
| GSE164498_TPGSE164498_M_table.csv.gz |
1.9 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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