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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 26, 2020 |
| Title |
Transcriptional Heterogeneity within the Glucocorticoid Response |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Steroid hormone receptors such as the Glucocorticoid Receptor (GR) mediate the transcriptional response to hormones and are frequently targeted in the treatment of human diseases. Experiments using bulk populations of cells have provided a detailed picture of the global transcriptional hormone response but are unable to interrogate cell-to-cell transcriptional heterogeneity. To examine the glucocorticoid response in individual cells, we performed single cell RNA sequencing (scRNAseq). The transcriptional response to hormone was robustly detected in individual cells and scRNAseq provided additional statistical power to identify over 100 GR-regulated genes that were not detected in bulk RNAseq. scRNAseq also revealed a large degree of cell-to-cell variability in the hormone response. On average, individual hormone-treated cells showed a response at only 30% of the total set of GR target genes. Understanding the basis of this heterogeneity will be critical for the development of more precise models of steroid hormone signaling.
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| Overall design |
Single-cell RNAseq and bulk total RNAseq in A1-2 human breast cancer cells
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| Web link |
https://www.nature.com/articles/s42003-020-0837-0
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| Contributor(s) |
Hoffman JA, Papas BN, Trotter KW, Archer TK |
| Citation(s) |
32170217 |
| Submission date |
Dec 11, 2019 |
| Last update date |
Mar 29, 2020 |
| Contact name |
Jackson Andrew Hoffman |
| E-mail(s) |
jackson.hoffman@nih.gov
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| Organization name |
NIEHS
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| Department |
DIR
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| Lab |
ESCBL
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| Street address |
111 TW Alexander Dr, Building 101 Room C432
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| City |
Research Triangle Park |
| State/province |
North Carolina |
| ZIP/Postal code |
27709 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (26)
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| GSM4213970 |
A1-2 cells, D1hr_rep1, Bulk RNAseq |
| GSM4213971 |
A1-2 cells, D1hr_rep2, Bulk RNAseq |
| GSM4213972 |
A1-2 cells, D1hr_rep3, Bulk RNAseq |
| GSM4213973 |
A1-2 cells, D2hr_rep1, Bulk RNAseq |
| GSM4213974 |
A1-2 cells, D2hr_rep2, Bulk RNAseq |
| GSM4213975 |
A1-2 cells, D2hr_rep3, Bulk RNAseq |
| GSM4213976 |
A1-2 cells, D4hr_rep1, Bulk RNAseq |
| GSM4213977 |
A1-2 cells, D4hr_rep2, Bulk RNAseq |
| GSM4213978 |
A1-2 cells, D4hr_rep3, Bulk RNAseq |
| GSM4213979 |
A1-2 cells, D8hr_rep1, Bulk RNAseq |
| GSM4213980 |
A1-2 cells, D8hr_rep2, Bulk RNAseq |
| GSM4213981 |
A1-2 cells, D8hr_rep3, Bulk RNAseq |
| GSM4213982 |
A1-2 cells, D18hr_rep1, Bulk RNAseq |
| GSM4213983 |
A1-2 cells, D18hr_rep2, Bulk RNAseq |
| GSM4213984 |
A1-2 cells, D18hr_rep3, Bulk RNAseq |
| GSM4213985 |
A1-2 cells, EtOH, single-cell RNAseq |
| GSM4213986 |
A1-2 cells, Dex1hr, single-cell RNAseq |
| GSM4213987 |
A1-2 cells, Dex2hr, single-cell RNAseq |
| GSM4213988 |
A1-2 cells, Dex4hr_rep1, single-cell RNAseq |
| GSM4213989 |
A1-2 cells, Dex4hr_rep2, single-cell RNAseq |
| GSM4213990 |
A1-2 cells, Dex8hr_rep1, single-cell RNAseq |
| GSM4213991 |
A1-2 cells, Dex8hr_rep2, single-cell RNAseq |
| GSM4213992 |
A1-2 cells, Dex18hr, single-cell RNAseq |
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| Relations |
| BioProject |
PRJNA594939 |
| SRA |
SRP236872 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE141834_RAW.tar |
5.6 Gb |
(http)(custom) |
TAR (of BW) |
| GSE141834_bulkRNAseq_normalized_counts.txt.gz |
4.5 Mb |
(ftp)(http) |
TXT |
| GSE141834_scRNAseq_rawCounts.txt.gz |
12.8 Mb |
(ftp)(http) |
TXT |
| GSE141834_scRNAseq_seuratV3_normalized.txt.gz |
121.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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