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| Status |
Public on Feb 09, 2015 |
| Title |
corrected R14del-CMs (clone L2GC2) |
| Sample type |
SRA |
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| Source name |
Cardiomyocytes derived from PLN-R41del iPSC cells infected with AAV6-EGFP-miR-PLN
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| Organism |
Homo sapiens |
| Characteristics |
cell type: iPS-derived cardiomyocytes
differentiation stage: Day 30 post-differentiation
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA samples were assessed for quantity by Qubit fluorometry (Life Technologies, Grand Island, NY) and for quality by the 2100 Bioanalyzer system (Agilent). Initial shearing of 0.5–1 µg genomic DNA to an average of 200-300 bp fragments was performed using the Covaris E210 focused acoustic energy system (Covaris). Whole genome libraries were prepared using the NEBNext DNA Library Prep kit according to the standard manufacturer's protocol (New England Biolabs). Illumina compatible paired-end adapters were used and the adapter-ligated DNA fragments was amplified by ligation-mediated PCR (KAPA Biosystems) using a reverse PCR primer containing a six nucleotide barcode that allowed for multiples samples to be pooled and sequenced in the same run. The library was enriched for human exomic sequences using the SeqCap EZ Human Exome Library v3.0 capture system (Roche NimbleGen).
The libraries were sequenced with a 100bp paired-end protocol on the Illumina HiSeq 2500 according to the manufacturer's protocol (Illumina)
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Library strategy: Exome-Seq
Paired end exom-seq reads were aligned to the hg19 genome assembly using Bowtie2 version 2.1 with default configurations
After conversion into bam files same sample files were merged using samtools version 0.1.7_x86_64-linux
Picard-tools version 1.110 was used to coordinate sort the merged files, to mark duplicates, to add read groups and to create BamIndexes
GenomeAnalysisTK version 3.1-1 was used for local realignement under consideration of the known indels specified in the files 1000G_phase1.indels.hg19.sites.vcf Mills_and_1000G_gold_standard.indels.hg19.sites.vcf (downloaded from Broad Institute website) and default configurations
Base Quality Scores were recalibrated using GenomeAnalysisTK version 3.1-1 under consideration of known SNPs specified in dbsnp_138.hg19.vcf (downloaded from Broad Institute website) and default configurations
Variants were called using the GenomeAnalysisTK version 3.1-1 HaplotypeCaller
GenomeAnalysis TK version 3.1-1 was used for variant (indel) recalibration with the following configurations:
Variant Recalibrator: -nt 8 --maxGaussians 4 -resource:mills,known=false,training=true,truth=true,prior=12.0 /Data/reference_genomes/hg19_broad/Variation/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /Data/reference_genomes/hg19_broad/Variation/dbsnp_138.hg19.vcf -an QD -an FS -an ReadPosRankSum -an MQRankSum -mode INDEL
ApplyRecalibration: --ts_filter_level 99.5 -mode INDEL
GenomeAnalysis TK version 3.1-1 was used for variant (SNP) recalibration with the following configurations:
Variant Recalibrator: -nt 8 -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg19.sites.vcf -resource:omni,known=false,training=true,truth=true,prior=12.0 1000G_omni2.5.hg19.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.high_confidence.hg19.sites.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg19.vcf -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -mode SNP
ApplyRecalibration: -nt 8 -o francesca_recalibrated_snps_recalibrated_indels.vcf --ts_filter_level 99.5 -mode SNP
Genome_build: hg19
Supplementary_files_format_and_content: vcf data (will be submitted to dbVar or dbSNP)
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| Submission date |
Feb 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
FRANCESCA STILLITANO |
| E-mail(s) |
francesca.stillitano@mssm.edu
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| Phone |
+12128249020
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| Organization name |
Mount Sinai School of Medicine
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| Department |
CARDIOVASCULAR RESEARCH
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| Street address |
1470 Madison Avenue
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| City |
NEW YORK |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE65762 |
Correction of human phospholamban R14del mutation associated with cardiomyopathy using targeted nucleases and combination therapy [Exome-Seq] |
| GSE65763 |
Correction of human phospholamban R14del mutation associated with cardiomyopathy using targeted nucleases and combination therapy |
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| Relations |
| BioSample |
SAMN03333468 |
| SRA |
SRX869322 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data not provided for this record |
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