|
| Status |
Public on Aug 10, 2021 |
| Title |
Cut&Tag_WTC11 iPSCs - CTCF_rep2 |
| 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 |
KJ209
|
| 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 |
SAMN17925155 |
| SRA |
SRX10109399 |
