|
| Status |
Public on Jun 18, 2018 |
| Title |
Whole Bone Marrow in vivo tamoxifen treated R26CreERT2 Srsf2 P95H from animal 136 |
| 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 136
age: 50-60 weeks
Sex: female
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).
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| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
SVI_SRSF2_136_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.
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| |
|
| 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 |
SAMN07175244 |
| SRA |
SRX2867106 |
