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Series GSE118633 Query DataSets for GSE118633
Status Public on Sep 05, 2020
Title SAMMY-seq, H3K9me3 and H3K27me3 ChIP-seq and RNA-seq of control and progeria fibroblasts
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Other
Summary We present a new high-throughput sequencing-based technique, named Sequential Analysis of MacroMolecules accessibilitY (SAMMY-seq), for the genome-wide mapping of chromatin regions separated by differential accessibility. The method is based on the sequential extraction of multiple chromatin fractions, corresponding to increasingly compacted and less accessible chromatin regions, which are mapped along the genome using high-throughput sequencing. Using SAMMY-seq we analyzed Hutchinson-Gilford progeria syndrome (HGPS) skin fibroblasts and normal control fibroblasts. Additionally we carried out ChIP-seq for the H3K9me3 and H3K27me3 histone modifications and RNA-seq for the characterization of transcriptome changes on the same HGPS and control fibroblasts.
 
Overall design Using SAMMY-seq we analyzed Hutchinson-Gilford progeria syndrome (HGPS) skin fibroblasts and normal control fibroblasts. Additionally we carried out ChIP-seq for the H3K9me3 and H3K27me3 histone modifications and RNA-seq for the characterization of transcriptome changes on the same HGPS and control fibroblasts.

Human raw data will be uploaded to dbGaP
 
Contributor(s) SebestyƩn E, Marullo F, Petrini C, Lucini F, Bianchi A, Valsoni S, Olivieri I, Antonelli L, Gregoretti F, Oliva G, Ferrari F, Lanzuolo C
Citation(s) 33293552
BioProject PRJNA483177
Submission date Aug 16, 2018
Last update date May 24, 2024
Contact name Chiara Lanzuolo
E-mail(s) [email protected]
Phone 0200660358
Organization name CNR and Istituto Nazionale Genetica Molecolare
Lab Lanzuolo Lab
Street address Via Francesco Sforza 35
City Milan
State/province ---
ZIP/Postal code 20122
Country Italy
 
Platforms (3)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (76)
GSM3335748 CTRL004 H3K9me3 ChIP-seq
GSM3335749 CTRL013 H3K9me3 ChIP-seq
GSM3335750 HGPS167 H3K9me3 ChIP-seq
Relations
SRA SRP155495

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE118633_RAW.tar 27.8 Gb (http)(custom) TAR (of BED, BIGWIG, BROADPEAK, BW, TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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