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Sample GSM3967121 Query DataSets for GSM3967121
Status Public on Aug 04, 2019
Title T-ALL4 (Hi-C)
Sample type SRA
 
Source name Peripheral blood primary T-ALL cells
Organism Homo sapiens
Characteristics tissue: Peripheral blood
cell type: primary T-ALL cells
disease state: Primary T-ALL
treatment: N/A
enzymatic restriction: commercial Arima kit
Treatment protocol CUTLL1 cells were treated with DMSO or gamma-secretase inhibitor (1 uM) for 72 hours or THZ1 (100 nM) for 24 hours.
Growth protocol CUTLL1 and Jurkat cells were grown in RPMI medium with 10% FBS ; Primary T-ALL cells isolated from the peripheral blood of T-ALL patients were xenogroafted in immunocompromised NOD SCID gamma mice (NSG) . Following xenograft, T-ALL cells were isolated from spleen by flow cytometer using hCD45 as marker; Healthy T cells were purchased from Lonza (catalog no: 2W-200)
Extracted molecule genomic DNA
Extraction protocol Nuclear extraction and DNA purification using Amicon Ultra 30K
End-repair was performed using T4 DNA polymerase (NEB), T4 DNA polynucleotide kinase (NEB), Klenow (NEB) and dNTPs in 1× T4 DNA ligase reaction buffer (NEB), followed by dATP-addition with Klenow. Paired-end (PE) adapters (Illumina) were ligated to DNA fragments using 15 U of the T4 DNA ligase (Invitrogen) for 2 hours at room temperature. Bead-bound DNA was amplified with 6 PCR amplification cycles using PE PCR 1.0 and PE PCR 2.0 primers (Illumina). Library prepartion of samples prcoessed using Arima HiC kit were prepared using Kap Hper library prep kit (KK8504)as per manufacturer's guidelines.
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description Primary T-ALL, classified as canonical T-ALL based on transcriptomic profiling. Enzymatic restriction was peformed using commercial Arima kit.
HiC_cscore_compartment-scores.tsv
HiC_hicratio-scores.tsv
Data processing Read alignment: bowtie2 2.2.3. Paired-end reads were mapped against the hg19 reference sequence using bowtie2 (special paramters: --very-sensitive-local --local)
Filtering: GenomicTools "gtools-hic filter". Discards read-pairs marked as multihits, only one mappable read, positional duplicates, low mapping quality (MAPQ < 20), self-ligated fragments, short-range interactions (<25 kb)
Matrix generation: HicBench. For each sample and each chromosome, a matrix with binned interactions (bin-size 40kb) was generated.
Normalization: ICE normalization as described in Imakaev et al. (2012) was employed first. We then applied normalization by distance as recently described (Gong et al., 2018)
Topologically Associated Domains (TAD) calls: TADs were called using the algorithm developed within hic-bench, setting the insulating window to 500kb.
Genome_build: hg19
Supplementary_files_format_and_content: TAD bed files, scores.tsv files
 
Submission date Jul 24, 2019
Last update date Nov 02, 2019
Contact name Andreas Kloetgen
Organization name Helmholtz Centre for Infection Research
Department Department for Computational Biology of Infection Research
Street address Inhoffenstr 7
City Braunschweig
State/province NI
ZIP/Postal code 38124
Country Germany
 
Platform ID GPL24676
Series (2)
GSE115896 Dynamic 3D chromosomal landscapes in acute leukemia
GSE134761 Dynamic 3D chromosomal landscapes in acute leukemia [Hi-C]
Relations
BioSample SAMN12348931
SRA SRX6578974

Supplementary file Size Download File type/resource
GSM3967121_TALL_4_TADs_hicratio-500kb-activity.bed.gz 17.6 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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