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Sample GSM3873136

Query DataSets for GSM3873136

Status

Public on Aug 08, 2019

Title

Input_TT(-)_Day 5

Sample type

SRA

Source name

Human iPS-derived cells on day 5 of TT(-) protocol

Organism

Homo sapiens

Characteristics

cell type: Human iPS cells
tissue: Dermal fibroblasts
days after differentiation: 5
antibody: None

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

ATAC-seq

Library source

genomic

Library selection

other

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 08, 2019

Contact name

Manabu Kawata

E-mail(s)

manabukawata@hotmail.com

Organization name

The University of Tokyo

Street address

7-3-1 Hongo