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Sample GSM4861707 Query DataSets for GSM4861707
Status Public on Apr 14, 2021
Title U2OS cells - input DNA - siMLL3
Sample type SRA
 
Source name U2OS
Organism Homo sapiens
Characteristics cell line: U2OS
treatment: transfected with siMLL3.1 or siMLL3.2
chip-antibody: none
Treatment protocol Cells were transfected with control or two different MLL3 siRNAs for 48 h
Growth protocol U2OS cells were cultured in RPMI 1640 media supplemented with 10% FBS at 37℃ with 5% CO2
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from MNase digested nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed by VATHS Universal DNA Library Prep Kit for Illumina (Vazyme ND606). 
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model HiSeq X Ten
 
Description Input for sample 4, 5, 7, 8
Data processing All ChIP-seq raw fastq data was cleaned by removing adaptor sequence.
ChIP-seq reads were aligned to the hg19 genome assembly using with bowtie2-align-s version 2.3.5.1
Data were filtered using cutadapt version 1.18 with parameters -u 10 -u -15 -U 10 -U -15 -m 30
peaks were called using macs2 2.1.1.20160309 with the following setting -p 1E-10 --nomodel --keep-dup all --SPMR --extsize 147 --broad --broad-cutoff 1E-10
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using deeptools 3.1.3; Scores represent RPKM
 
Submission date Oct 26, 2020
Last update date Apr 14, 2021
Contact name Jun-Yi Zheng
Organization name Wuhan Univisity
Street address No. 299 Of Bayi Road
City Wuhan
ZIP/Postal code 430072
Country China
 
Platform ID GPL20795
Series (2)
GSE160164 MLL3 suppresses tumorigenesis through regulating TNS3 enhancer activity [ChIP-seq]
GSE160254 MLL3 suppresses tumorigenesis through regulating TNS3 enhancer activity
Relations
BioSample SAMN16560301
SRA SRX9366231

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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