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Sample GSM8043552 Query DataSets for GSM8043552
Status Public on Feb 01, 2024
Title P7,Mus musculus,Liver,293,24
Sample type SRA
 
Source name Liver
Organism Mus musculus
Characteristics tissue: Liver
vector treatment: 293
timepoint _(weeks): 24
genotype: C57BL/6J
Extracted molecule genomic DNA
Extraction protocol Flash-Frozen mouse liver tissue was manually disassociated, isolated nuclei were quantified using a hemocytometer, and 100,000 nuclei were tagmented as previously described (Buenrostro et al. 2013), with some modifications based on (Corces et al. 2017) using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina)
Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter). Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina).
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Description PE42 protocol
Data processing BWA-mem
MACS2
Assembly: GRCm38.p6
Supplementary files format and content: bam- aligned reads
Supplementary files format and content: narrowPeak- MACS2 output from bam files
 
Submission date Jan 29, 2024
Last update date Feb 01, 2024
Contact name Evan Witt
E-mail(s) evan.witt@bmrn.com
Organization name Biomarin Pharmaceutical
Street address 791 Lindaro Street
City San Rafael
State/province California
ZIP/Postal code 94901
Country USA
 
Platform ID GPL19057
Series (1)
GSE254503 The longitudinal kinetics of AAV5 vector integration profiles and evaluation of clonal expansion in mice
Relations
BioSample SAMN39659189
SRA SRX23431134

Supplementary file Size Download File type/resource
GSM8043552_17_0DAR_01XGBiomarin_S17-P7_ATAC_mm10_i203_peaks.narrowPeak.gz 2.7 Mb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA

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