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Sample GSM3873119 Query DataSets for GSM3873119
Status Public on Aug 08, 2019
Title β-catenin_std_Day 2-1
Sample type SRA
 
Source name Human iPS-derived cells on day 2 of the standard 2C protocol
Organism Homo sapiens
Characteristics cell type: Human iPS cells
tissue: Dermal fibroblasts
days after differentiation: 2
antibody: Rabbit anti-non-phospho β-catenin antibody (Cell Signaling Technology, 8814)
Treatment protocol Human iPS cells were differentiated to chondrocytes by the standard or altered 2C differentiation protocols.
Extracted molecule genomic DNA
Extraction protocol For ATAC-seq, 50,000 cells were lysed to obtain nuclei in cold lysis buffer, and incubated in the Tn5 transposase reaction mix, as described previously (Buenrostro et al., 2013). For ChIP-seq, cells were cross-linked with 1% formaldehyde, and after lysis of cells, chromatin was fragmented by sonication. Protein-DNA complexes were purified with antibody.
For ATAC-seq, DNA fragments were PCR-amplified using previously-designed barcoded primers, as described previously (Buenrostro et al., 2013).For ChIP-seq, libraries were constructed with ThruPLEX DNA-seq Kit (Takara Bio), according to manufacturer’s instruction.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model HiSeq X Ten
 
Data processing DNA-sequence information was aligned to the human genome reference sequence (hg19) by bowtie aligner (Langmead et al., 2009).
Peak calling was performed by two-sample analysis on CisGenome software (Ji et al., 2008) with a P-value cutoff of 10-5 comparing with the input control.
Genome_build: hg19
Supplementary_files_format_and_content: .bed file reports peaks
 
Submission date Jun 11, 2019
Last update date Aug 09, 2019
Contact name Manabu Kawata
E-mail(s) manabukawata@hotmail.com
Organization name The University of Tokyo
Street address 7-3-1 Hongo
City Bunkyo-ku
State/province Tokyo
ZIP/Postal code 113-0033
Country Japan
 
Platform ID GPL20795
Series (1)
GSE132532 β-catenin ChIP-seq, RARα ChIP-seq, and ATAC-seq datasets in the standard or altered 2C protocols.
Relations
BioSample SAMN12018384
SRA SRX6039031

Supplementary file Size Download File type/resource
GSM3873119_b-catenin_std_D2-1_ChIP.2s.FDR1.peaks.bed.gz 34.4 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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