 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 10, 2024 |
| Title |
HiChIP_H3K27Ac_Nalm6 |
| Sample type |
SRA |
| |
|
| Source name |
NALM6
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: NALM6
cell type: ALL
|
| Growth protocol |
RPMI 1640 + 10% serum
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Arima H3K27Ac HiChIP (Arima: A101020) was performed according to the manufacturers provided instructions using unspecified proprietary buffers, solutions, enzymes, and reagents. Briefly, cells were fixed as in promoter capture Hi-C above and the amount of fixed cell suspension equal to 15g of cell DNA was used for the HiC reactions as in promoter capture Hi-C above. The samples were then sonicated 25 cycles (30s on/ 30s off) using a Diagenode Bioruptor Plus bath sonicator. Chromatin immunoprecipitation of the sonicated HiC samples was performed by first incubating the samples with 0.2ug of H3K27 antibody (Active Motif 91194) per 1ug of sample overnight. The next day antibody bound chromatin was collected using protein A beads included in the kit. The beads were washed three times with buffer R1, twice with buffer R3, once with buffer LC and then twice with LTE (buffers specified in Arima kit). Samples were eluted before undergoing decrosslinking. Libraries were prepared using Swift Biosciences Accel-NGS 2S Plus DNA Library Kit (Cat # or 21096) following instructions provided by Arima Genomics. The paired-end libraries were sequenced on the Illumina Novaseq to generate >200M 150bp reads. The provided FitHiChIP pipeline was used for analysis to call 5kb resolution loops in relaxed background mode (https://github.com/ay-lab/FitHiChIP)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
H3K27Ac HiChIP was processed using the Dovetail Genomics pipeline junt documented at https://hichip.readthedocs.io/en/latest/index.html. In preparation for peak calling processed HiChIP bam files were transformed into bed files using samtools (v. 1.14) and bedtools (v. 2.30.0) with command “samtools view -h -@ ${NCORE} -F 0x900 sorted.mapped.PT.bam | bedtools bamtobed -i stdin > primary.aln.bed”. Peak calling to define anchor regions of interest was performed using MACS2 (v. 2.1.1) with command “macs2 callpeak -t primary.aln.bed --nomodel --extsize 147 -q 0.05”. Final statistically significant loops were identified utilizing FitHiChIP (v. 11.0) with configuration parameters “IntType=3, BINSIZE=5000, UppDistThr=2000000, UseP2PBackgrnd=0, BiasType=1, MergeInt=1, QVALUE=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
Library strategy: Promoter capture Hi-C
|
| |
|
| Submission date |
Jan 31, 2024 |
| Last update date |
Apr 10, 2024 |
| Contact name |
Daniel Savic |
| E-mail(s) |
daniel.savic@stjude.org
|
| Organization name |
St. Jude Children's Research Hospital
|
| Department |
Pharmaceutical Sciences
|
| Lab |
Savic
|
| Street address |
262 Danny Thomas pl.
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE224204 |
Functional investigation of inherited noncoding genetic variation impacting the pharmacogenomics of childhood acute lymphoblastic leukemia treatment |
| GSE254783 |
Functional investigation of inherited noncoding genetic variation impacting the pharmacogenomics of childhood acute lymphoblastic leukemia treatment [HiChIP] |
|
| Relations |
| BioSample |
SAMN39711351 |
| SRA |
SRX23485695 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8057780_2505128_HiChIP_H3K27Ac_Nalm6.interactions_FitHiC_Q0.05_IGV.bedpe.gz |
1.1 Mb |
(ftp)(http) |
BEDPE |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
