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SRX18756299: GSM6829691: CTCF_10:1_2uM_ACF_15min_biolrep2_techrep1; unidentified plasmid; OTHER
1 PACBIO_SMRT (Sequel II) run: 15,781 spots, 40.4M bases, 9.9Mb downloads

External Id: GSM6829691_r1
Submitted by: Ramani, Gladstone Institutes
Study: Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler
PRJNA813226 • SRP362791 • All experiments • All runs
show Abstracthide Abstract
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.
Sample: CTCF_10:1_2uM_ACF_15min_biolrep2_techrep1
SAMN32227412 • SRS16191754 • All experiments • All runs
Organism: unidentified plasmid
Library:
Name: GSM6829691
Instrument: Sequel II
Strategy: OTHER
Source: GENOMIC
Selection: other
Layout: SINGLE
Construction protocol: CTCF site 1 was purified using a GigaPrep kit (Qiagen), restriction enzyme digested, and purified by size exclusion chromatography. Chromatin was assembled using salt gradient dialysis Library preparation included DNA damage repair, end repair, blunt-end SMRTbell® ligation, Exonuclease treatment, and Ampure PB cleanup according to manufacturer's instruction. Library quality was assessed with Agilent Bioanalyzer High Sensitivity DNA kit or Agilent Tapestation D5000 Assay. PacBio SMRTbell® library preparation
Runs: 1 run, 15,781 spots, 40.4M bases, 9.9Mb
Run# of Spots# of BasesSizePublished
SRR2279658315,78140.4M9.9Mb2023-09-20

ID:
25839871

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