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Status |
Public on Jan 31, 2017 |
Title |
SHM_Patient6_Ibrutinib_post |
Sample type |
SRA |
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Source name |
Peripheral blood
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Organism |
Homo sapiens |
Characteristics |
tissue: peripheral blood, Human Chronic Lymphocytic Leukemia cell type: human chronic lymphocytic leukemia B cells treatment: ibruitinib
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Treatment protocol |
post-ibrutinib treatment
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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) PCR amplicons
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina MiSeq |
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Data processing |
For SHM data, sequences with mean quality score < 20 and length < 50 were removed. The remained sequences were used to calculate mutation rate. Sequences obtained from each designed region were aligned to the reference sequence using BLASTN with alignment length > 200. Mutations to be considered valid were calculated after filtering steps, as previously described(Liu, M. et al.,Nature 2008). Briefly, mutations first had to pass a Neighbourhood Quality Standard (NQS) criteria requiring a minimum Phred score of 30 for the mutation itself, and 20 for the five adjacent bases on either side. Mutations that were within five bases of more than two additional mutations were excluded. Mutations within two bases of a deletion or insertion were also excluded. In addition, bases with mutation rate > 0.01 were excluded as a result of overwhelming influence of sequence error or SNP, of which bases with mutation rate > 0.2 were further regarded as SNP and were excluded. Finally, the average base mutation rate of 1-200 bp passing the above criteria were calculated from forward sequence, as well as reverse sequences if applicable. For average base mutation rates of C-to-T or G-to-A transitions, only C or G bp sites we counted.
processed data files format and content: tab-delimited text file gives average C>T|G>A transitions/mut frequency for each re-sequenced genomic region. Regions with reads less than 100 were excluded and shown as 'NA'.
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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 |
SAMN06146252 |
SRA |
SRX2429011 |
Supplementary file |
Size |
Download |
File type/resource |
GSM2430363_SHM_Patient24_Ibrutinib_post.AvgBMF.txt.gz |
427 b |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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