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| Status |
Public on Mar 25, 2018 |
| Title |
FAIRE-seq RPMI-8226 |
| Sample type |
SRA |
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| Source name |
Multiple myeloma
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| Organism |
Homo sapiens |
| Characteristics |
cell line: RPMI-8226
tissue: peripheral blood
cell type: B lymphocyte
age: 61
disease state: Multiple myeloma
gender: male
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| Growth protocol |
Cells were cultured in RPMI-1640 medium (ATCC, Catalog No. 30-2001) with 15% fetal bovine serum and air, 95%, carbon dioxide (CO2), 5% at 37℃.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For FAIRE-seq, about 5M cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Formaldehyde was quenched by 0.2M glycine. Nuclei were isolated and sonicated. Sonicate was extracted with phenol–chloroform–isoamyl alcohol (25:24:1) and reverse crosslinked. DNA were purified and size selected before Illumina libraries generation.
Sequencing libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina (E7645, NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
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| Library strategy |
FAIRE-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Description |
No treatment
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| Data processing |
FAIRE-seq reads were aligned to hg19 using BWA-MEM
FAIRE-seq peaks and OCEAN-seq HOCIs were defined using ZINBA
genome build: hg19
processed data files format and content: bed files for FAIRE-seq samples with peaks
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| Submission date |
Jul 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
lumeng Jia |
| E-mail(s) |
lumeng_j@pku.edu.cn
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| Organization name |
Peking university
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| Street address |
Yiheyuan road
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| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE100832 |
OCEAN-C: mapping hubs of open chromatin interactions across the genome reveals gene regulatory networks |
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| Relations |
| BioSample |
SAMN07325867 |
| SRA |
SRX2986027 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2694180_RPMI-8226_faire-seq_broadpeak.bed.gz |
1.1 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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