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Sample GSM3721814 Query DataSets for GSM3721814
Status Public on Jun 29, 2020
Title Line 13 WT H3K27me3 rep1
Sample type SRA
Source name Line XIII DIPG
Organism Homo sapiens
Characteristics histone h3.3 status: WT
antibody: H3K27me3
Treatment protocol Single-stranded donor oligonucleotide (ssODN) templates were designed with the desired mutations to facilitate homology directed repair (HDR) after cleavage of H3F3A by Cas9n. cells were co-transfected with a combination of pSpCas9n(BB)-2A-GFP-guideA (0.5μg/well), pSpCas9n(BB)-2A-Puro-guideB (0.5μg/well), and ssODN HDR (1μg/well) template using XtremeGene-HP (Sigma).
Growth protocol All DIPG cells were cultured in Tumor Stem Medium (Nagaraja et al, 2017), which contains DMEM/F12 1:1 (Invitrogen), Neurobasal-A (Invitrogen), 10mM HEPES (Invitrogen), 1X MEM sodium pyruvate (Invitrogen), 1X MEM nonessential amino acids (Invitrogen), 1% GlutaMax (Invitrogen), human-bFGF (20 ng/ml) (Shenandoah), human-EGF (20 ng/ml) (Shenandoah), human PDGF-A and PDGF-B (20ng/ml) (Shenandoah), heparin (10 ng/ml) (StemCell Technologies) and B27 without Vitamin A (Invitrogen).
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibodies to H3K27me3 (Cell Signaling C36B11) or H3.3 (Millipore #09-838).
Libraries were prepared with the Nextera library prep kit
Libraries were sequenced on the NovaSeq machine with 150 base paired-end sequencing
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
Description Line 13 WT H3K27me3 rep1
Data processing Reads were called with illumina bclfastq
Reads were aligned to the hg19 genome with BWA (version 0.7.13-r1126 )
Peaks were called with MACS2 (version
Differential peak occupancy analysis was performed with DiffBind (R version 3.5.2)
Downstream analysis was performed on the Galaxy webserver
Genome_build: hg19
Supplementary_files_format_and_content: bed files of peaks
Submission date Apr 12, 2019
Last update date Jul 01, 2020
Contact name Paul Knoepfler
Organization name University of California Davis
Department Cell Biology and Human Anatomy
Street address 2425 Stockton Blvd, Room 633
City Sacramento
State/province CA
ZIP/Postal code 95817
Country USA
Platform ID GPL24676
Series (1)
GSE129765 Reciprocal gene editing defines targetable mutant H3.3 oncohistone effectors in pediatric glioma
BioSample SAMN11411048
SRA SRX5678416

Supplementary file Size Download File type/resource
GSM3721814_13_WT_H3K27me3_rep1_peaks.narrowPeak.gz 3.5 Mb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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