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Sample GSM5086289 Query DataSets for GSM5086289
Status Public on Aug 10, 2021
Title Cut&Tag_WTC11 iPSCs - CTCF_rep1
Sample type SRA
 
Source name human iPSCs
Organism Homo sapiens
Characteristics cell type: WTC11 iPSCs
antibody: CTCF (Millipore, 07-729, Lot 3059608)
cell line: WTC11
Growth protocol WTC11 iPS cells were cultured on Matrigel-coated (Corning, 354277) plates with Essential 8™ Medium (Life Technologies, A1517001). WTC11 iPSCs were passaged using Accutase (STEMCELL Technologies, 07922) and 10 μM ROCK inhibitor Y-27632 (STEMCELL Technologies, 72302).
Extracted molecule genomic DNA
Extraction protocol Cells were washed with PBS and nuclei were extracted prior to library construction.
CUT&Tag libraries were prepaed according to the published protocol (Kaya-Okur, H.S. et al. 2019).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description KJ207
Data processing Library strategy: CUT&Tag
Sequencing reads were mapped to hg38 using bowtie2 with the following options: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Picard Tools was used to remove blacklisted regions and duplicate reads
SEACR (Meers et al. 2019) was used to call peaks on merged replicates.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig file was generated with bamCoverage --binSize=1
Supplementary_files_format_and_content: Peaks called by MACS2
 
Submission date Feb 16, 2021
Last update date Aug 10, 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)
GSE166836 Parallel characterization of cis-Regulatory Elements for Multiple Genes using CRISPRpath [Cut&Tag]
GSE166839 Parallel characterization of cis-Regulatory Elements for Multiple Genes using CRISPRpath
Relations
BioSample SAMN17925156
SRA SRX10109398

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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