|
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 |