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| Status |
Public on Feb 13, 2022 |
| Title |
ATAC_MM1S_CO2 |
| Sample type |
SRA |
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| Source name |
Cell line derived from human plasma cell myelom
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MM.1S (ATCC, CRL-2974)
cell type: Human myeloma cell line
culture condition: in the lower chamber from a transwell coculture with HS5
repeat: r2
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were washed with cold PBS and pelleted by centrifugation (500g, 5min, 4°C). Nuclei were isolated by subjecting cells to 100uL of RSB-lysis buffer (10mM Tris-HCl ph 7.4, 10mM NaCl, 3mM MgCl2, 1uL/mL of Digitonin, 1uL/mL of Tween20, and 1uL/mL of NP40) for 3-5 min on ice. 1mL RSB buffer (10mM Tris-HCl ph 7.4, 10mM NaCl, 3mM MgCl2, and 1uL/mL of Tween20) was added to neutralize RSB-lysis buffer. Cells were pelleted by centrifugation (500g, 10min, 4°C) and supernatant was removed. Cells were resuspended in 50uL Transposase mix (25 uL of 2x TD buffer, 2.5 ul of transposase, 16.5 ul of PBS, 0.5 ul of digitonin, 0.5 ul Tween 20, and 5 uL of nuclease free water). The samples were incubated on a thermomixer at 37°C, 1000rpm for 30min. Samples were cleaned up using Zymo DNA Clean & Concentrator-5 kit (D4014) according to manufacturer’s instruction in 21uL water.
Libraries were prepared with approximately 5x10^4 sorted cells using a Tagment DNA Enzyme and Buffer Large Kit (Illumina, 20034198) and following the Omni-ATAC protocol (PMID: 28846090).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
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| Data processing |
Pair-end Omni-ATAC sequence reads were aligned to hg38 using Bowtie2 (PMID: 19261174). Reads mapped to multiple positions of the genome were excluded and only one read was kept if multiple reads mapped to the same position.
Read enriched regions (peaks) were predicted by MACS3 (PMID: 18798982).
We compiled a list of reference peaks for each MM cell line with in-house script: a peak is in the reference if it presents in at least three samples.
Genome_build: hg38
Supplementary_files_format_and_content: Txt file, from left to right represent chr, start, end, number of libs supporting the peak
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| Submission date |
Jan 13, 2022 |
| Last update date |
Feb 13, 2022 |
| Contact name |
Gangqing Hu |
| E-mail(s) |
michael.hu@hsc.wvu.edu
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| Organization name |
West Virginia University
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| Department |
MicroBiology, Immunology, and Cell Biology
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| Lab |
2072A, HSC North, Floor 2
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| Street address |
64 Medical Center Drive
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| City |
Morgantown |
| State/province |
West Virginia |
| ZIP/Postal code |
26506-9177 |
| Country |
USA |
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| Platform ID |
GPL30173 |
| Series (2) |
| GSE193657 |
Bone Marrow Stroma-induced Transcriptome and Regulome Signatures of Multiple Myeloma [ATAC-seq] |
| GSE193658 |
Bone Marrow Stroma-induced Transcriptome and Regulome Signatures of Multiple Myeloma |
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| Relations |
| BioSample |
SAMN24964732 |
| SRA |
SRX13778719 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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