|
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 |