|
| Status |
Public on Aug 04, 2019 |
| Title |
ETP-ALL3 (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 HiSeq 4000 |
| |
|
| Description |
Primary T-ALL, classified as Early T Progenitor (ETP) subtype 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 |
Aug 04, 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 |
GPL20301 |
| Series (2) |
| GSE115896 |
Dynamic 3D chromosomal landscapes in acute leukemia |
| GSE134761 |
Dynamic 3D chromosomal landscapes in acute leukemia [Hi-C] |
|
| Relations |
| BioSample |
SAMN12348940 |
| SRA |
SRX6578977 |
