|
| Status |
Public on Jan 26, 2019 |
| Title |
ATAC-seq for patient CLL6 before Ibrutinib treatment |
| Sample type |
SRA |
| |
|
| Source name |
Primary peripheral blood mononucleated cells (PBMC) from chronic lymphocytic leukemia patient
|
| Organism |
Homo sapiens |
| Characteristics |
patient id: CLL6
library: ATAC-seq
cell type: CLL
processing batch: ATAC40
clinical centre: Vienna General Hospital
sample type: primary_tissue
clinical status: disease
disease: CLL
timepoint name: before_Ibrutinib
patient gender: F
patient years at diagnosis: 47.5041095890411
patient years at sample collection: 75.312329
disease at diagnosis: CLL
hospital: Vienna General Hospital
patient leukocyte count (10e3/ul): 270
sample lymphocyte percentage: 98
blood monocyte percentage: 0
blood granulocyte percentage: 2
blood hemoglobin: 9.5
blood platelets: 80
sample viability percentage: 97.39
sample viable cd3+ percentage: 2.69
sample viable cd14+ percentage: 0.58
sample viable cd19+ percentage: 85.7
sample viable cd19+cd5+ percentage: 85.5
sample viable cd19+cd5- percentage: 0.17
sample viable cd19-cd5+ percentage: 12.78
sample cd38+ percentage in viable cd19+cd5+: 76
sample clone number: 1
sample del11q percentage: 0
sample del13q percentage: 87
sample del17p percentage: 87
sample tri12 percentage: 0
sample tp53 mutation: TRUE
sample tp53 mutation description: c.365_366 delTG p.Val122Asp.fs*26; c609_610 delGGinsA p.Glu204Ser.fs*43; 609G>A pV203V 610del1
sample days since ibrutinib treatment: 0
patient preliminary response evaluation: SD
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Heparinized peripheral blood was obtained from CLL patients after signed informed consent. Peripheral blood mononuclear cells (PBMCs) were isolated using Ficoll-Hypaque (GE Healthcare, Uppsala, Sweden) centrifugation. Patients were screened for CLL characteristic chromosomal aberrations including deletions on 13q14, 11q22, and 17p13 and for trisomy 12 by FISH analysis. The IGHV and TP53 mutational status was determined by sequencing (LGC Genomics, Berlin, DE). PBMCs from CLL patients were cryopreserved in RPMI 1640 supplemented with 40% FCS and 10 % DMSO.
~10^5 cells were pelleted by centrifuging for 5 min at 4 °C at 300 x g. After centrifugation, the pellet was carefully resuspended in the transposase reaction mix (12.5 ml 2xTD buffer, 2 ml TDE1 (Illumina) and 10.25 ml nuclease-free water, 0.25 µl 5% Digitonin (Sigma)) for 30 min at 37 °C. Following DNA purification with the MinElute kit eluting in 11 µl, 1 µl of the eluted DNA was used in a quantitative PCR (qPCR) reaction to estimate the optimum number of amplification cycles. Library amplification was followed by SPRI size selection to exclude fragments larger than 1,200 bp. DNA concentration was measured with a Qubit fluorometer (Life Technologies). Library amplification was performed using custom Nextera primers. The libraries were sequenced by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq3000/4000 platform and the 25-bp paired-end configuration.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
ATAC-seq in primary peripheral blood mononucleated cells (PBMC) from patient CLL6 before Ibrutinib treatment
|
| Data processing |
Illumina Casava1.7 software was used for basecalling.
Sequenced reads were trimmed for adaptor and Nextera sequences
Reads were mapped to hg19 whole genome using bowtie2 v2.2.4 with the –very-sensitive parameter
Duplicate reads were marked and removed with picard tools version 1.118
Read were extended to the average fragment size and bigWig files containing counts of reads per basepair created
Peaks for ATAC-seq samples were called with MACS2 version 2.1.1.20160309 using the “–nomodel” and “–extsize 147” parameters
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files contain counts of reads per basepair; narrowPeak files contain peaks called by MACS2
|
| |
|
| Submission date |
Jun 29, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Christoph Bock |
| E-mail(s) |
cbock@cemm.oeaw.ac.at
|
| Organization name |
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
|
| Street address |
Lazarettgasse 14
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE100672 |
Combined chemosensitivity and chromatin profiling prioritizes drug combinations in CLL |
|
| Relations |
| BioSample |
SAMN07302304 |
| SRA |
SRX2972257 |
