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Sample GSM3439844 Query DataSets for GSM3439844
Status Public on Oct 20, 2021
Title A249
Sample type SRA
 
Source name Spleen
Organism Mus musculus
Characteristics tissue: Spleen
cell type: CD4+ splenoctyes
genotype/variation: plkcGAPDH transgenic mice
concentration sample (ng/nl): 1115
rin number: 9
Extracted molecule genomic DNA
Extraction protocol For whole exome sequencing genomic DNA was extracted from CD4+ T cells, isolated from plck-GAPDH tumors by negative microbead selection (see above), using the Nucleospin Tissue Kit (Macherey Nagel, #740901)
Paired-end DNA library was prepared according to the manufacturer’s instructions (Agilent). The adapter-modified gDNA fragments were enriched by six cycles of PCR. Whole exome capture was carried out using Agilent’s SureSelect All Exon V5 Kit. Finally, 50 Mb of DNA sequences of 33,4378 exons from 20,965 genes were captured. After DNA quality evaluation, pooled samples were sequenced on Illunima Hiseq 2000
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Data processing Library strategy: exome-seq
Raw data were first filtered using an in house quality control
Paired-end clean reads are aligned to the reference genome (UCSC mm9) using Burrows–Wheeler Aligner (BWA) software. If a read or reads pair is mapped to multiple positions, BWA will choose the most likely placement. While if two or more most-likely placements are present, BWA will choose any one randomly. Aligned reads were realigned to the genome. Genome Analysis Toolkit (GATK)34 was used to ignore those duplicates resulted from PCR amplification with Picard-tool. We utilized the Indelrealigner and RealignerTargetCreator in GATK do realignment around the indels according to GATK best practice. Furthermore, we performed base quality score recalibration with GATK to avoid system bias. After realignment to genome, we identified and filtered variants (SNP, INDELs) using GATK HaplotypeCaller and variantFiltration to guarantee meaningful analysis. Variants obtained from previous steps were compared based on the dbSNP35 and 1000 Genomes database36 and annotates with ANNOVAR
Genome_build: mm9
Supplementary_files_format_and_content: Variant call files of Single Nucleotide Polymorphisms (SNPs) and Indels
 
Submission date Oct 22, 2018
Last update date Oct 20, 2021
Contact name Kevin Lebrigand
Organization name IPMC/CNRS
Lab Functional Genomics Platform of Nice-Sophia-Antipolis, France.
Street address 660 route des lucioles
City Valbonne - Sophia-Antipolis
ZIP/Postal code 06560
Country France
 
Platform ID GPL13112
Series (2)
GSE121592 Identification of a T-cell lymphoma in plkcGAPDH transgenic mice (Exome)
GSE121748 Identification of a T cell lymphoma in plkcGAPDH transgenic mice
Relations
SRA SRX4912022
BioSample SAMN10319488

Supplementary file Size Download File type/resource
GSM3439844_A249_GATK_indel.vcf.gz 172.8 Kb (ftp)(http) VCF
GSM3439844_A249_GATK_snp.vcf.gz 379.3 Kb (ftp)(http) VCF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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