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Sample GSM2430333 Query DataSets for GSM2430333
Status Public on Jan 31, 2017
Title SHM_Patient1_Idelalisib_post
Sample type SRA
 
Source name Peripheral blood
Organism Homo sapiens
Characteristics tissue: peripheral blood, Human Chronic Lymphocytic Leukemia
cell type: human chronic lymphocytic leukemia B cells
treatment: idelalisib
Treatment protocol post-idelalisib treatment
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
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina MiSeq
 
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' .
 
Submission date Dec 15, 2016
Last update date May 15, 2019
Contact name Roberto Chiarle
E-mail(s) Roberto.Chiarle@childrens.harvard.edu
Organization name Children’s Hospital Boston and Harvard Medical School
Department Department of Pathology
Lab Roberto Chiarle
Street address 300 Longwood Avenue
City Boston
State/province Massachusetts
ZIP/Postal code 02115
Country USA
 
Platform ID GPL15520
Series (1)
GSE77788 Phosphatidylinositol 3-Kinase (PI3K) delta blockade increases genomic instability in B cells
Relations
BioSample SAMN06146226
SRA SRX2428951

Supplementary file Size Download File type/resource
GSM2430333_SHM_Patient9_Idelalisib_post.AvgBMF.txt.gz 434 b (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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