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Status |
Public on Jan 31, 2017 |
Title |
HTGTS_MEC1.KO-Duvelisib rep2 |
Sample type |
SRA |
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Source name |
DSMZ ACC 497
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Organism |
Homo sapiens |
Characteristics |
tissue: peripheral blood, Human Chronic Lymphocytic Leukemia cell line: MEC1 AID KO cell type: human chronic lymphocytic leukemia B cells treatment: Duvelisib
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Treatment protocol |
1 micromolar Duvelisib
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Growth protocol |
RPMI 1640+10% FBS,Human chronic lymphocytic leukemia B cells transduced with c-MYC CRISPR #1 /Cas9 lentivirus 8 h post treatment with duvelisib.
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Extracted molecule |
genomic DNA |
Extraction protocol |
Cells were lysed in lysis buffer (NaCl 200 mM, Tris.HCl 100 mM, EDTA 5mM, SDS 0.2%) containing 10 μg/ml Proteinase K at 56°C overnight. Genomic DNA was precipitated with isopropanol at room temperature, washed in ethanol 70% and resuspended in TE buffer (10mM Tris-HCl plus 1mM EDTA) See Supplemental Experimental procedures from Chiarle et al. Cell 2011, paragraph Generation of HTGTS libraries by adapter-PCR.
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina MiSeq |
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Data processing |
Library strategy: High-Throughput Genomic Translocation Sequencing approach, HTGTS
For HTGTS data, we applied prinseq 0.2 to remove sequences with exact PCR duplicates, mean quality score < 20 and length < 50. Next, effect reads for each sample were recognized by designed barcode, primer and bait portion. Lastly,the barcode, primer and bait portion of the remained sequences were masked for alignment analysis to determine translocation junctions as previously described(Chiarle et al.,Cell 2011). Briefly, we aligned sequences to the mouse reference genome (GRCm37/mm9) or human genome (GRCh38/hg38) using BLAT, and then filtered artificial junctions by removing PCR repeats (reads with same junction position in alignment to the reference genome and a start position in the read less than 3 bp apart), invalid alignments (including alignment scores < 30, reads with multiple alignments having a score difference < 4 and alignments having 10-nucleotide gaps) and ligation artifacts (for example, random HaeIII restriction sites ligated to bait breaksite). Translocation junction position was determined based on the genomic position of the 5’ end of the aligned read.
genome build: hg38
processed data files format and content: BED files of HTGTS data contain all obtained translocation junctions information including chromosome,corrdinate,read name,align score and strand.
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Submission date |
Dec 15, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Roberto Chiarle |
E-mail(s) |
Roberto.Chiarle@childrens.harvard.edu
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Organization name |
Children’s Hospital Boston and Harvard Medical School
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Department |
Department of Pathology
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Lab |
Roberto Chiarle
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Street address |
300 Longwood Avenue
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City |
Boston |
State/province |
Massachusetts |
ZIP/Postal code |
02115 |
Country |
USA |
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Platform ID |
GPL15520 |
Series (1) |
GSE77788 |
Phosphatidylinositol 3-Kinase (PI3K) delta blockade increases genomic instability in B cells |
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Relations |
BioSample |
SAMN06146205 |
SRA |
SRX2428913 |
Supplementary file |
Size |
Download |
File type/resource |
GSM2430314_HTGTS_MEC1.KO-Duvelisib.C1_2.bed.gz |
64.3 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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