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Sample GSM3133394

Query DataSets for GSM3133394

Status

Public on Feb 18, 2019

Title

sgGAL4-INPUT rep2

Sample type

SRA

Source name

HEK293T

Organism

Homo sapiens

Characteristics

cell type: HEK293T
passages: 10-15

Growth protocol

HEK293T cells were cultured at 37°C under 5% CO2 in high-glucose Dulbecco’s Modified Eagle’s Medium (DMEM; Life Technologies, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (Sigma, St. Louis, MO, USA), 1% penicillin/streptomycin (Life Technologies), and passaged at 1:5 every 2 days.

Extracted molecule

genomic DNA

Extraction protocol

The cells were lysed and sonicated, biotinylated protein-DNA complexes were affinity purified with M-280 Streptavidin Dynabeads. DNA was purified with QIAquick PCR Purification Kit (Qiagen, Hilden, Germany).
DNA libraries were prepared using the Ultra II DNA Library Prep Kit for Illumina (NEB)
CAPLOCUS-seq

Library strategy

OTHER

Library source

genomic

Library selection

other

Instrument model

Illumina Genome Analyzer

Data processing

ChIP-seq reads were aligned to the hg19 genome assembly using bwa aln version 0.7.15 with default parameters
data were filter with the following specification: 1. keep only unique mapped reads(except C13); 2. remove PCR duplicates with samtools version 1.5
peaks were called using MACS version 2.1 with parameters “-t chip -c input -g hs -f BAMPE -B”
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file were generated using UCSC utility bedGraphToBigWig

Submission date

May 07, 2018

Last update date

Feb 18, 2019

Contact name

Yun Liu

Organization name

Fudan University

Street address

Dongan Road 130

City

Shanghai