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Sample GSM2655966 Query DataSets for GSM2655966
Status Public on Jun 18, 2018
Title Whole Bone Marrow in vivo tamoxifen treated R26CreERT2 Srsf2 P95H from animal 108
Sample type SRA
 
Source name Whole Bone Marrow in vivo tamoxifen treated R26CreERT2 Srsf2 P95H
Organism Mus musculus
Characteristics strain: C57BL/6
animal id: animal 108
age: 50-60 weeks
Sex: male
srsf2 genotype: R26CreERT2 Srsf2 P95H
tissue: Bone Marrow
Extracted molecule genomic DNA
Extraction protocol Exome sequencing data was acquired for 6 samples from 50-60 weeks post tamoxifen treatment (time of euthanasia due to animals becoming moribund). Genomic DNA was isolated from both whole BM and matched ear tissue from three independent animals (two R26-CreERT2 Srsf2P95H/+ and one hScl-CreERT R26eYFP Srsf2P95H/+ ). The genomic DNA was isolated using the PureGene DNA isolation kit (Qiagen) as directed by the manufacturer.
The gDNA was subjected to exome capture using the Agilent SureSelect Mouse Exon (50Mb; performed by BGI) system and sequenced using the Illumina X10 platform at a mean depth of 100x coverage by BGI Ltd (Hong Kong).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model HiSeq X Ten
 
Description SVI_SRSF2_108_BM
Data processing Illumina Casava1.7 software used for basecalling.
For RNA-seq (gene abundance and differential expression the following protocol was used)
The datasets were assessed using FastQC and all reads having quality greater than 30 (Phred score) were kept for further analysis.
Raw data was aligned to Mus musculus genome (Ensembl GRCm38.72) using the Bowtie2 aligner with allowance for one mismatch. More than 98% of reads aligned to reference genome in all samples.
Variants (SNP and Indels) were detected using samtools mpileup from each sample. Identified variants were filtered for ≥ 10 reads supporting allele (Sum of reads supporting (DP4): reference forward, reference reverse, alternate forward and alternate reverse bases).
Somatic mutations were identified using two algorithms (Strelka & VarScan2) by considering ear sample as germline control and bone marrow as tumour. Strelka detects somatic SNVs and small Indels from the aligned sequencing reads of matched tumour (BM) – normal (Ear) samples. Passed somatic variants (SNPs and Indels) are the somatic variants which have passed all filters and have a quality score of at least 15 (SNPs) or 30 (Indels) assuming a homozygous reference genotype in the normal.
Genome_build: mm9
Supplementary_files_format_and_content: *BM_All_variant_calling_samtools_RD10.vcf. VCF format. All variants called using samtools.
Supplementary_files_format_and_content: *BM_All_variants_samtools_RD10_SnpEff_Annotated.txt TXT format. All variants called using samtools, with SnpEff annotations.
Supplementary_files_format_and_content: *Somatic_mutation_detection_Stelka_Passed_Somatic_Indels.vcf. VCF format. Stelka somatic mutation Indels that pass cutoff. (BM (tumor) vs Ear (Normal))
Supplementary_files_format_and_content: *Somatic_mutation_detection_Stelka_Passed_Somatic_SNPs.vcf. VCF format. Stelka somatic mutation SNPs that pass cutoff. (BM (tumor) vs Ear (Normal))
Supplementary_files_format_and_content: *Somatic_mutation_detection_VarScan2_Filtered_Somatic_Indels.txt. TXT format. VarScan2 called somatic mutation Indels that pass cutoff. (BM (tumor) vs Ear (Normal))
Supplementary_files_format_and_content: *Somatic_mutation_detection_VarScan2_Filtered_Somatic_SNPs.txt TXT format. VarScan2 called somatic mutation SNPs that pass cutoff. (BM (tumor) vs Ear (Normal))
Supplementary_files_format_and_content: *Somatic_variants_strelka_Passed_Somatic_Indels_SnpEff_Annotated.txt TXT format. Stelka somatic mutation Indels that pass cutoff. (BM (tumor) vs Ear (Normal)). Annotated by SnpEff.
Supplementary_files_format_and_content: *Somatic_variants_strelka_Passed_Somatic_SNPs_SnpEff_Annotated.txt TXT format. Stelka somatic mutation SNPs that pass cutoff. (BM (tumor) vs Ear (Normal)). Annotated by SnpEff.
Supplementary_files_format_and_content: *Somatic_variants_VarScan2_Filtered_Somatic_Indels_SnpEff_Annotated.txt TXT format. VarScan2 called somatic mutation Indels that pass cutoff. (BM (tumor) vs Ear (Normal)) Annotated by SnpEff.
Supplementary_files_format_and_content: *Somatic_variants_VarScan2_Filtered_Somatic_SNPs_SnpEff_Annotated.txt TXT format. VarScan2 called somatic mutation SNPs that pass cutoff. (BM (tumor) vs Ear (Normal)) Annotated by SnpEff.
 
Submission date Jun 09, 2017
Last update date May 15, 2019
Contact name Alistair Morgan Chalk
E-mail(s) achalk@svi.edu.au, alistair.chalk@gmail.com
Organization name St Vincent's Institute of Medical Research
Department Stem Cell Regulation Unit
Lab Walkley
Street address 9 Princes st, Fitzroy
City Melbourne
State/province VIC
ZIP/Postal code 3065
Country Australia
 
Platform ID GPL21273
Series (2)
GSE99850 Physiologic expression of Srsf2(P95H) causes myeloid expansion, impaired competitive stem cell function and initiates the myeloproliferative/myelodysplastic syndrome in vivo [WES]
GSE99852 Physiologic expression of Srsf2(P95H) causes myeloid expansion, impaired competitive stem cell function and initiates the myeloproliferative/myelodysplastic syndrome in vivo.
Relations
BioSample SAMN07175248
SRA SRX2867108

Supplementary file Size Download File type/resource
GSM2655966_SVI_SRSF2_108_BM_All_variant_calling_samtools_RD10.vcf.gz 3.2 Mb (ftp)(http) VCF
GSM2655966_SVI_SRSF2_108_BM_All_variants_samtools_RD10_SnpEff_Annotated.txt.gz 6.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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