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| Status |
Public on Sep 25, 2023 |
| Title |
RC17 Master Cell Bank |
| Sample type |
SRA |
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| Source name |
RCe021-A (RC17)
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| Organism |
Homo sapiens |
| Characteristics |
cell line: RCe021-A (RC17)
cell type: embryonic stem cells
treatment: embryonic stem cell culture
time: Day 0
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA was extracted using the QIAamp DNA mini kit (Qiagen). 10 ng of gDNA was used for the construction of sequencing libraries.
gDNA libraries were prepared using the AmpliSeq Illumina Cancer Hotspot panel v2 Kit following manufacturer's instruction.
targeted gDNA sequencing
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Data processing |
Fastq files are generated with Illumina Local Run Manager Generate Fastq workflow.
Raw data is de-multiplexed, aligned to the Human reference genome GRCh37/h19 (BWA-MEM Whole Genome Aligner v0.7.12-r1039), and genomic variant were called with DNA Amplicon analysis module (Basespace workflow v2.1.1).
The generated variant call format (vcf) files were visualized and annotated with Illumina Variant Studio software v3.0.
Genetic variants are cross-referenced to public databases (dbSNP, ClinVar, COSMIC).
The identified variants are reported as benign, pathogenic or of unknown significance based on available clinical classification.
Assembly: GRCh37/h19
Supplementary files format and content: The processed datafiles are text files (.vcf) listing the identified genomic varinats.
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| Submission date |
Apr 14, 2023 |
| Last update date |
Sep 25, 2023 |
| Contact name |
Malin Parmar |
| E-mail(s) |
malin.parmar@med.lu.se
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| Organization name |
Wallenberg Neuroscience Center, MultiPark and Lund Stem Cell Centre
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| Department |
Department of Experimental Medical Science, Lund University
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| Street address |
221 84 Lund
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| City |
Lund |
| ZIP/Postal code |
Box 117, SE-221 00 |
| Country |
Sweden |
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| Platform ID |
GPL15520 |
| Series (2) |
| GSE229766 |
Preclinical quality, safety and efficacy of a human embryonic stem cell-derived product for treatment of people with moderate Parkinson’s Disease (STEM-PD) I |
| GSE229769 |
Preclinical quality, safety and efficacy of a human embryonic stem cell-derived product for treatment of people with moderate Parkinson’s Disease (STEM-PD) |
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| Relations |
| SRA |
SRX19973577 |
| BioSample |
SAMN34191962 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7177497_RC17-MCB_S2.vcf.gz |
4.3 Kb |
(ftp)(http) |
VCF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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