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Sample GSM4745857 Query DataSets for GSM4745857
Status Public on Aug 26, 2020
Title MM.1S BR-SI2-Pol II-IP
Sample type SRA
 
Source name MM.1S
Organism Homo sapiens
Characteristics cell line: MM.1S
cell type: B lymphoblast
tumor: 42 years black female immunoglobulin A lambda myeloma
chip antibody: Rpb1 NTD(Cell signaling technology, 14958, lot:1)
treatment: treated with SI2 for 24 hours
Treatment protocol MM.1S BR cell was 25nM SI-2 treated for 24 hours.
Growth protocol MM.1S BR cell was cultured in RPMI-1640 medium with 10% FBS.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to the TruePrep® DNA Library Prep Kit V2 for Illumina (TD503-02). Briefly, TruePrep Tagment Enzyme Mix (TTEMix) contains transposase and two kinds of adapters (Adapter 1 and Adapter 2) with equal molar. Input DNA are fragmented and linked with adapters on both ends just by mixing with TTE Mix, followed by a 10-minute incubation at 55℃. The tagged DNA fragments can be further amplified with two pairs of primers N5 (N5XX) / N7 (N7XX) and P5 / P7 (PCR Primer Mix, PPM). After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq X following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model HiSeq X Ten
 
Data processing Basecalls performed using HiSeqX
ChIP-seq reads were aligned to the hg19 genome assembly using BWA version 0.7.13 with the following configurations -q 5 -l 32 -k 2
Data were filtered using Picard-tools version 1.126
peaks were called using macs2 version 2.1.0 with the following setting: -pvalue 0.01 --keep-dup all --extsize -1 --shift 0
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using macs2; Scores represent an average read coverage
Supplementary_files_format_and_content: narrowpeak files
 
Submission date Aug 25, 2020
Last update date Aug 26, 2020
Contact name Liu Zhiqiang
E-mail(s) zhiqiangliu@tmu.edu.cn
Organization name Tianjin Medical University
Street address 22 Qxiangtai Rd
City Tianjin
ZIP/Postal code 300070
Country China
 
Platform ID GPL20795
Series (2)
GSE156870 Targeting steroid receptor co-activator 3 sensitizes myeloma cell to proteasome inhibitor treatment through NSD2-mediated phase separation and chromatin remodeling [ChIP-Seq]
GSE156872 Targeting steroid receptor co-activator 3 sensitizes myeloma cell to proteasome inhibitor treatment through NSD2-mediated phase separation and chromatin remodeling
Relations
SRA SRX9006275
BioSample SAMN15904187

Supplementary file Size Download File type/resource
GSM4745857_BS-P_R1_val_1.PE2SE.nodup.tagAlign_x_BSinput_R1_val_1.PE2SE.nodup.tagAlign.fc.signal.bw 284.7 Mb (ftp)(http) BW
GSM4745857_BS-P_R1_val_1.PE2SE.nodup.tagAlign_x_BSinput_R1_val_1.PE2SE.nodup.tagAlign.pval0.01.500K.narrowPeak.gz 897.8 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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