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| Status |
Public on Apr 10, 2024 |
| Title |
RS411_PCap_HiC |
| Sample type |
SRA |
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| Source name |
RS411
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| Organism |
Homo sapiens |
| Characteristics |
cell line: RS411
cell type: ALL
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| Growth protocol |
RPMI 1640 + 10% serum
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Arima promoter capture HiC (Arima: A510008, A303010, A302010) was performed according to the manufacturers provided instructions using unspecified proprietary buffers, solutions, enzymes, and reagents. Briefly, 10 million ALL cells were harvested, suspended in 5ml RT PBS which was brought to 2% formaldehyde by adding 37% methanol-stabilized paraformaldehyde for a 10-minute fixation. The amount of fixed cell suspension equal to 5mg of cell DNA was used for HiC. Cells were lysed with Lysis Buffer and conditioned with Conditioning Solution before their DNA was digested in a cocktail consisting of Buffer A, Enzyme 1, and Enzyme 2. The digested, fixed chromatin was biotinylated using using Buffer B and Enzyme B before being ligated using Buffer C and Enzyme C. The fixed, biotinylated, ligated DNA was then subjected to reversal of crosslinking and digestion of proteins before being purified. 100ul containing 1500ug of purified large proximally ligated DNA was fragmented for 24 cycles (30s on/ 30s off) using a Diagenode Bioruptor Plus bath sonicator. The fragmented DNA was then subjected to two-sided size selection targeting fragments between 200-600bp using AMPure XP DNA purification beads. Size selected DNA was then subjected to biotin enrichment using T1 streptavidin beads. Bead bound, enriched HiC DNA was then subjected to Arima library prep. Briefly, the sample underwent end repair followed by adapter ligation, at which point the sample was then subjected to 10 cycles of PCR amplification. The library DNA was then purified using AMPure XP DNA purification beads. The HiC library was then subjected to Arima promoter capture enrichment. The library was precleared of biotinylated DNA using T1 streptavidin beads before being subjected to promoter enrichment with biotinylated RNA probes. After washing, the captured fragments were then amplified an additional 13 PCR cycles. These libraries were submitted for deep sequencing on an Illumina Nova-seq where >200M 150bp paired-end reads were obtained.
Promoter capture Hi-C
read length: 150bp
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Analysis of Promoter capture HiC data was performed using the Arima CHiC pipeline (v1.5, https://github.com/ArimaGenomics/CHiC). Briefly, this pipeline uses HiCUP v0.8.0 for mapping and quality assessment of promoter capture HiC data and CHiCAGO to identify significant looping interactions in the promoter capture HiC data using 5kb resolution and adj. p < 0.05.
Assembly: HG19
Supplementary files format and content: bedpe for significant loops called at 5kb resolution used to determine if SNVs were in a looping genomic region
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| Submission date |
Jan 31, 2023 |
| Last update date |
Apr 10, 2024 |
| Contact name |
Daniel Savic |
| E-mail(s) |
daniel.savic@stjude.org
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| Organization name |
St. Jude Children's Research Hospital
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| Department |
Pharmaceutical Sciences
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| Lab |
Savic
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| Street address |
262 Danny Thomas pl.
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| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE224203 |
Functional investigation of inherited noncoding genetic variation impacting the pharmacogenomics of childhood acute lymphoblastic leukemia treatment [HiC] |
| GSE224204 |
Functional investigation of inherited noncoding genetic variation impacting the pharmacogenomics of childhood acute lymphoblastic leukemia treatment |
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| Relations |
| BioSample |
SAMN32983290 |
| SRA |
SRX19237270 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7017375_2451871_RS411_PCap_HiC.cis_le_2Mb.bedpe.gz |
336.0 Kb |
(ftp)(http) |
BEDPE |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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