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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 01, 2024 |
| Title |
Genomic binding of NF-Y in mouse and human cells |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
NF-Y is a Transcription Factor that regulates transcription through binding to the CCAAT-box. To understand its strategy, we analyzed 16 ChIP-seq datasets from human and mouse cells. Shared loci, mostly located in promoters of expressed genes of cell cycle, metabolism and gene expression pathways, are associated with histone marks of active chromatin and specific modules of TFs. Other peaks are in enhancers and Transposable Elements -TE- of retroviral origin in human and mouse. We evaluated the relationship with USF1, a common synergistic partner in promoters and MLT1 TEs, upon NF-YB inactivation: USF1 binding decreases in promoters, modestly in MLT1, suggesting a pioneering role of NF-Y in formers, not in the latters. These data define a common set of NF-Y functional targets across different mammalian cell types, suggesting a pioneering role in promoters with respect to TEs.
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| Overall design |
NF-YB ChIP-seq data analysis on human and mouse cell lines for the identification of shared and specific binding locations.
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| Contributor(s) |
Ronzio M, Dolfini D |
| Citation(s) |
39025317 |
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| Submission date |
Jul 24, 2022 |
| Last update date |
Oct 31, 2024 |
| Contact name |
Diletta Dolfini |
| E-mail(s) |
diletta.dolfini@unimi.it
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| Organization name |
University of Milan
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| Department |
Bioscience
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| Street address |
Via Celoria, 26
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| City |
Milano |
| State/province |
MI |
| ZIP/Postal code |
20133 |
| Country |
Italy |
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| Platforms (4)
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| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (27)
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| GSM6380866 |
CCRF, NFYB, IP, rep2 |
| GSM6380867 |
B cells, NFYB, IP, rep1 |
| GSM6380868 |
B cells, NFYB, IP, rep2 |
| GSM6380869 |
C1R, input, rep1 |
| GSM6380870 |
C1R, input, rep2 |
| GSM6380871 |
B cells, input |
| GSM6380872 |
MEL, input |
| GSM6380873 |
CH27, input |
| GSM6380874 |
MEL, NFYB, IP, rep1 |
| GSM6380875 |
MEL, NFYB, IP, rep2 |
| GSM6380876 |
CH27, NFYB, IP1 |
| GSM6380877 |
CH27, NFYB, IP2 |
| GSM6380878 |
Fetal Myoblasts, input |
| GSM6380879 |
Fetal Myoblasts, NFYB, IP |
| GSM6380880 |
Fetal Myocytes, input |
| GSM6380881 |
Fetal Myocytes, NFYB, IP |
| GSM6380882 |
Keratinocytes, NFYB, IP |
| GSM6380883 |
Keratinocytes, input |
| GSM6380884 |
HeLa, Ctr, input |
| GSM6380885 |
HeLa, SiYB, input |
| GSM6380886 |
HeLa, Ctr, NFYB, IP |
| GSM6380887 |
HeLa, SiYB, NFYB, IP |
| GSM6380888 |
HeLa, Ctr, USF1, IP |
| GSM6380889 |
HeLa, SiYB, USF1, IP |
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| Relations |
| BioProject |
PRJNA861853 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE209627_NFYB_B_cells_ENCODEpipeline_hg38.bed.gz |
109.0 Kb |
(ftp)(http) |
BED |
| GSE209627_NFYB_B_cells_ENCODEpipeline_hg38_fc_signal.bigwig |
613.5 Mb |
(ftp)(http) |
BIGWIG |
| GSE209627_NFYB_C1R_ENCODEpipeline_hg38.bed.gz |
110.3 Kb |
(ftp)(http) |
BED |
| GSE209627_NFYB_C1R_ENCODEpipeline_hg38_fc_signal.bigwig |
822.4 Mb |
(ftp)(http) |
BIGWIG |
| GSE209627_NFYB_CCRF_ENCODEpipeline_hg38.bed.gz |
136.6 Kb |
(ftp)(http) |
BED |
| GSE209627_NFYB_CCRF_ENCODEpipeline_hg38_fc_signal.bigwig |
873.9 Mb |
(ftp)(http) |
BIGWIG |
| GSE209627_NFYB_CH27_ENCODEpipeline_mm10.bed.gz |
126.3 Kb |
(ftp)(http) |
BED |
| GSE209627_NFYB_CH27_ENCODEpipeline_mm10_fc_signal.bigwig |
584.8 Mb |
(ftp)(http) |
BIGWIG |
| GSE209627_NFYB_MEL_ENCODEpipeline_mm10.bed.gz |
148.6 Kb |
(ftp)(http) |
BED |
| GSE209627_NFYB_MEL_ENCODEpipeline_mm10_fc_signal.bigwig |
712.2 Mb |
(ftp)(http) |
BIGWIG |
| GSE209627_RAW.tar |
3.8 Gb |
(http)(custom) |
TAR (of BED, BIGWIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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