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| Status |
Public on Sep 12, 2022 |
| Title |
Balanced SET levels favor the correct enhancer repertoire during cell fate acquisition |
| Organisms |
Danio rerio; Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
To understand the effect of SET protein accumulation on genomic function we used different accumulating models, cells and in vivo, that we analyzed with different techinques up to the single level. SET accumulation is known to be caused by the accumulation of its direct interactor SETBP1, when mutated, the causative gene of Schinzel Giedion syndrome. SET has been shown to be able to interfere with histones acetylation, thus we wanted to investigated the functional effect on the genome function and cell fate commitment.
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| Overall design |
Genomic analysis of human cells (IPSCs, NPCs, Neurons), Zebrafish brain embryo, mouse embryonic and post natal cortex, to understand the effect of SET accumulation on genome function
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| Contributor(s) |
Zaghi M, Massimino L, Bellini E, Sessa A, Broccoli V |
| Citation(s) |
37270547 |
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| Submission date |
Aug 29, 2022 |
| Last update date |
Jun 15, 2023 |
| Contact name |
Luca Massimino |
| E-mail(s) |
admin@lucamassimino.com
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| Phone |
+393389039500
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| Organization name |
Ospedale San Raffaele
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| Department |
Gastroenterology
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| Street address |
Via Olgettina, 58
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| City |
Milano |
| State/province |
MI |
| ZIP/Postal code |
20100 |
| Country |
Italy |
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| Platforms (3) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
| GPL24995 |
Illumina NovaSeq 6000 (Danio rerio) |
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| Samples (80)
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| Relations |
| BioProject |
PRJNA874714 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE212252_NUCLEI_EMBRYO_CRE_NEGATIVE_processed_data.tar.gz |
458.3 Mb |
(ftp)(http) |
TAR |
| GSE212252_NUCLEI_EMBRYO_CRE_POSITIVE_processed_data.tar.gz |
175.7 Mb |
(ftp)(http) |
TAR |
| GSE212252_NUCLEI_POST_NATAL_CRE_NEGATIVE_processed_data.tar.gz |
446.0 Mb |
(ftp)(http) |
TAR |
| GSE212252_NUCLEI_POST_NATAL_CRE_POSITIVE_processed_data.tar.gz |
533.7 Mb |
(ftp)(http) |
TAR |
| GSE212252_RAW.tar |
12.3 Gb |
(http)(custom) |
TAR (of BROADPEAK, HIC, NARROWPEAK, TAB) |
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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