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Sample GSM4292743

Query DataSets for GSM4292743

Status

Public on Nov 09, 2020

Title

input_plus

Sample type

SRA

Source name

human breast cancer cell

Organism

Homo sapiens

Characteristics

antibody: none
cell line: MCF7
treatment: with estrogen

Treatment protocol

MCF7 cells were treated with or without 10nM estrodiol in culture medium for 48 hours

Growth protocol

Cells were cucltured into DMEM medium with 10% FBS

Extracted molecule

genomic DNA

Extraction protocol

Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with anti-BAP18.
The steps of DNA library construction are as follows:1.Fix the ends of the DNA from the IP with base A,and repair to add A DNA add sequencing joint processing;2.Magnetic beads were used to recover the target size fragment and PCR amplification was performed to obtain the library to be sequenced;3.The libraries were examined by agarose electrophoresis;4.Qubit 2.0 was used to quantify the library to determine whether the library concentration was suitable for computer;5.After the libraries passed the quality inspection, different libraries were sequenced on Illumina sequencer according to the requirements of effective concentration and target data volume.

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina HiSeq 2500

Data processing

The transcriptome sequencing project was completed on Illumina sequencing platform, Illumina PE library (~300bp) was constructed for sequencing, quality control was carried out on the obtained sequencing data, and then the transcriptome data was analyzed by means of bioinformatics
ChIP-seq reads were aligned to the hg18/Ch37 genome
The original image data sequenced by Illumina Hiseq was transformed into sequence data via Base Calling, namely in FASTQ format, to obtain the most original sequencing data file. FASTQ format file can record the base and its mass fraction of read. FASTQ format is stored as a unit of sequencing read segments, with each read segment accounting for 4 lines. The first and third lines are composed of sequence identifiers and read segment names (the first line begins with "@" and the third line begins with "+"). In the third line, ID can be omitted, but "+" cannot be omitted), the second behavior base sequence, and the fourth behavior the sequencing quality fraction of the corresponding position base.
Genome_build: human Ch37
Supplementary_files_format_and_content: After the sequencing data is taken off the machine, the original sequencing sequence of each sample, which we call raw data or raw reads, is stored in FASTQ (fq for short) file format. Raw data is evaluated for quality (software: FastQC). FastQC is a data quality visualization software that aims to provide an easy way to evaluate data quality to guide downstream analysis on whether or how to proceed.

Submission date

Feb 01, 2020

Last update date

Nov 09, 2020

Contact name

Ge Sun

E-mail(s)

[email protected]

Organization name

China Medical University

Street address

No.77 Puhe Road, Shenyang North New Area