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Series GSE197979 Query DataSets for GSE197979
Status Public on Aug 03, 2023
Title Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler
Organisms Mus musculus; unidentified plasmid
Experiment type Other
Summary SAMOSA, a method previously developed in the Ramani Lab, was employed to reveal nucleosome patterns from remodeling reactions in vitro with the Imitation Switch (ISWI) ATP-Dependent Remodeler ATPase, SNF2h. SAMOSA was further employed to reveal single-molecule nucleosome patterns in vivo from SNF2h knockout and re-expression murine embryonic stem cells.
 
Overall design Investigating an ATP-Dependent Chromatin Remodeler ATPase via single-molecule chromatin profiling with m6A methyltransferase footprinting and SMRT long-read sequencing. 128 in vitro chromatin samples were analyzed (two replicates per condition), including the following controls: unremodeled methylated arrays and methylated/unmethylated unassembled template DNA. 35 in vivo samples were analyzed, including SAMOSA SNF2h KO/WT re-expression/E14 mESC SAMOSA samples (three biological replicates and technical replicates) and unmethylated/methylated mESC controls.
 
Contributor(s) Abdulhay NJ, Hsieh LJ, McNally CP, Ostrowski MS, Moore CM, Ketavarapu M, Kasinathan S, Nanda AS, Wu K, Chio US, Zhou Z, Goodarzi H, Narlikar GJ, Ramani V
Citation(s) 37696956
Submission date Mar 06, 2022
Last update date Oct 31, 2023
Contact name Megan Ostrowski
E-mail(s) megan.ostrowski@gladstone.ucsf.edu
Organization name Gladstone Institutes
Lab Ramani
Street address 1700 Owens
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
 
Platforms (2)
GPL29177 Sequel II (Mus musculus)
GPL29466 Sequel II (unidentified plasmid)
Samples (235)
GSM5935098 S2, array, 20:1, +M, -ATP, ST
GSM5935099 S2, array 15:1 +M -ATP, ST
GSM5935100 S2, array 10:1 +M -ATP, ST
Relations
BioProject PRJNA813226

Download family Format
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Supplementary file Size Download File type/resource
GSE197979_RAW.tar 279.5 Gb (http)(custom) TAR (of PICKLE)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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