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Sample GSM3593770 Query DataSets for GSM3593770
Status Public on Jun 15, 2019
Title CUT&RUN-CTCF_iPSC-induced lower motor neurons_rep1
Sample type SRA
 
Source name iPSC-induced lower motor neurons
Organism Homo sapiens
Characteristics cell type: iPSC-induced excitatory neurons
cut&run antibody: CTCF (Millipore, cat# 07-729, lot# 305960)
Extracted molecule genomic DNA
Extraction protocol Cells were washed with PBS and nuclei were extracted prior to library construction.
CUT&RUN libraries were prepared according to the published protocol (Skene and Henikoff 2017).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description MN.CTCF.merged.0.05_peaks.narrowPeak
MN.CTCF.merged.hg19.bw
Data processing library strategy: CUT&RUN
All reads were trimmed to 50 bp with fastp.
Alignment was performed using bowtie2 with the following options: -local -very-sensitive-local -nomixed -no-discordant -phred33 -I 10 -X 700. Picard Tools was used to remove duplicate reads.
Narrow peaks called using MACS2 with a q-value threshold of 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Narrow peaks called using MACS2 and signal tracks in bigwig format
 
Submission date Feb 07, 2019
Last update date Apr 08, 2021
Contact name Yin Shen
E-mail(s) Yin.Shen@ucsf.edu
Phone 4155023403
Organization name UCSF
Department Department of Neurology
Lab Shen Lab
Street address 513 Parnassus Ave
City SAN FRANCISCO
State/province CALIFORNIA
ZIP/Postal code 94143-0410
Country USA
 
Platform ID GPL24676
Series (2)
GSE113483 Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes
GSE126211 Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes [CUT&RUN]
Relations
BioSample SAMN10883279
SRA SRX5346383

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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