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| Status |
Public on Sep 12, 2022 |
| Title |
ips_PC054_p59 |
| Sample type |
SRA |
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| Source name |
hIPSc
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| Organism |
Homo sapiens |
| Characteristics |
cell type: hIPSc
disease state: HGPS-l
batch: II
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| Growth protocol |
The hIPSc were differentiated into MSC, cultivated in KO DMEM supplemented 15% FBS, 10ng Beta FGF, 1mM ascobic acid 2-P, 1X glutamax, 1X NEAA, 50 µM Beta mercaptoethanol
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNAeasy kit (Qiagen) following manufacturer’s instructions. Quality, quantitation and sizing of total RNA was evaluated using the RNA 6000 Pico assay. (Agilent Technologies Ref. 5067-1513) on an Agilent 2100 Bioanalyzer system.
RNA-Seq libraries were generated from 600 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
We assessed fastq sequence data quality using FastQC v0.11.5 (Andrews, 2010) and trimmed the reads to remove adapter sequences and low quality bases using Trimmomatic v0.36
Pair end reads were aligned using STAR v2.5.3a to the GRCh38 human genome release
BAMS index were generated using Sambamba v0.6.6
DEGs and abundance measurements were identified using StringTie v1.3.1c and R package DESeq2 v1.18.1 (median of ratio)
Assembly: GRCh38 human genome
Supplementary files format and content: tab-delimited text file (.csv) include RAW counts for each Sample
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| Submission date |
May 06, 2022 |
| Last update date |
Sep 12, 2022 |
| Contact name |
Frederique Magdinier |
| Organization name |
Aix-Marseille Université - Marseille Medical Genetics
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| Department |
MMG- U1251
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| Street address |
27 Bvd Jean Moulin, Aix-Marseille Université. Faculté de Médecine. Campus La Timone
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| City |
Marseille |
| ZIP/Postal code |
13005 |
| Country |
France |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE202364 |
Mesenchymal stem cells derived from patients with premature ageing syndromes display hallmarks of physiological ageing [RNA-Seq] |
| GSE202369 |
Mesenchymal stem cells derived from patients with premature ageing syndromes display hallmarks of physiological ageing |
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| Relations |
| BioSample |
SAMN28109436 |
| SRA |
SRX15185703 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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