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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 10, 2022 |
| Title |
Integrating transcription factor abundance with chromatin accessibility in human erythroid lineage commitment |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
We present InTAC-seq, a method for simultaneous quantification of genome-wide open chromatin and intracellular protein abundance in fixed cells. Using InTAC we directly observe variation in chromatin accessibility and transcription factor motif occupancy driven by differences in transcription factor protein abundance. By purifying bone marrow progenitor cells based on GATA1 protein expression, we establish its role in both functional and epigenetic restriction of erythroid cell identity in human hematopoiesis.
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| Overall design |
ATAC-seq profiling of K562 cells, GM12878 cells, and primary human bone marrow progenitor cells
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| Contributor(s) |
Baskar R, Chen A |
| Citation(s) |
35463156 |
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| Submission date |
Mar 01, 2021 |
| Last update date |
May 05, 2022 |
| Contact name |
Amy Chen |
| E-mail(s) |
[email protected]
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| Organization name |
Stanford University
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| Street address |
279 Campus Drive West
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platforms (1) |
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| Samples (42)
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| GSM5115852 |
GM12878 InTAC-seq rep 1 |
| GSM5115853 |
GM12878 InTAC-seq rep 2 |
| GSM5115854 |
GM12878 InTAC-seq rep 3 |
| GSM5115855 |
Qiagen 25K cells rep 1 |
| GSM5115856 |
Qiagen 25K cells rep 2 |
| GSM5115857 |
Qiagen 5K cells rep 1 |
| GSM5115858 |
Qiagen 5K cells rep 2 |
| GSM5115859 |
Qiagen 1K cells rep 1 |
| GSM5115860 |
Qiagen 1K cells rep 2 |
| GSM5115861 |
Qiagen 100 cells rep 1 |
| GSM5115862 |
Qiagen 100 cells rep 2 |
| GSM5115863 |
Purigen 25K cells rep 1 |
| GSM5115864 |
Purigen 25K cells rep 2 |
| GSM5115865 |
Purigen 5K cells rep 1 |
| GSM5115866 |
Purigen 5K cells rep 2 |
| GSM5115867 |
Purigen 1K cells rep 1 |
| GSM5115868 |
Purigen 1K cells rep 2 |
| GSM5115869 |
Purigen 100 cells rep 1 |
| GSM5115870 |
Purigen 100 cells rep 2 |
| GSM5115871 |
K562 GATA1-low rep 1 |
| GSM5115872 |
K562 GATA1-high rep 1 |
| GSM5115873 |
K562 GATA1-low rep 2 |
| GSM5115874 |
K562 GATA1-high rep 2 |
| GSM5115875 |
Bone marrow progenitor GATA1+ biorep 1, techrep 1 |
| GSM5115876 |
Bone marrow progenitor GATA1+ biorep 1, techrep 2 |
| GSM5115877 |
Bone marrow progenitor GATA1- biorep 1, techrep 1 |
| GSM5115878 |
Bone marrow progenitor GATA1- biorep 1, techrep 2 |
| GSM5115879 |
Bone marrow progenitor GATA1+ biorep 2, techrep 1 |
| GSM5115880 |
Bone marrow progenitor GATA1+ biorep 2, techrep 2 |
| GSM5115881 |
Bone marrow progenitor GATA1- biorep 2, techrep 1 |
| GSM5115882 |
Bone marrow progenitor GATA1- biorep 2, techrep 2 |
| GSM5115883 |
MEP GATA1 high biorep 1, techrep 1 |
| GSM5115884 |
MEP GATA1 high biorep 1, techrep 2 |
| GSM5115885 |
MEP GATA1 low biorep 1, techrep 1 |
| GSM5115886 |
MEP GATA1 low biorep 1, techrep 2 |
| GSM5115887 |
MEP GATA1 high biorep 2, techrep 1 |
| GSM5115888 |
MEP GATA1 high biorep 2, techrep 2 |
| GSM5115889 |
MEP GATA1 low biorep 2, techrep 1 |
| GSM5115890 |
MEP GATA1 low biorep 2, techrep 2 |
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| Relations |
| BioProject |
PRJNA705610 |
| SRA |
SRP308675 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE167934_BMprogenitor_countmatrix.csv.gz |
4.4 Mb |
(ftp)(http) |
CSV |
| GSE167934_Fixed_vs_live_countsmatrix.csv.gz |
3.3 Mb |
(ftp)(http) |
CSV |
| GSE167934_K562_countmatrix.csv.gz |
2.0 Mb |
(ftp)(http) |
CSV |
| GSE167934_MEP_countmatrix.csv.gz |
4.1 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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