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Status |
Public on Aug 26, 2020 |
Title |
MM.1S BR-Input |
Sample type |
SRA |
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|
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: none treatment: untreated
|
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.
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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
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|
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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 |
SRX9006276 |
BioSample |
SAMN15904186 |