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| Status |
Public on Feb 24, 2017 |
| Title |
X-52-30344430 |
| Sample type |
SRA |
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| Source name |
Stem cell
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Stem cell
age: 52
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| Growth protocol |
Subcutaneous abdominal adipose tissues were excised from informed and consented donors during abdominoplasties (University of Pennsylvania IRB approval Protocol number 812150). The tissues were immediately transferred to the laboratory on ice. Adipose tissue were dissected from skin and stored at -70oC until ASC isolations. ASCs were isolated from 29 tissue samples of female individual between 24 to 39 years, according to a protocol described in (Percec, Stem Cells International 2015). Fibroblasts were isolated from 7 procured specimens of female donors with age between 25 and 64, using the method described in (Huschtscha et al., 2012).
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| Extracted molecule |
total RNA |
| Extraction protocol |
ASCs and fibroblasts were detached from culture plates by trypsin digestion at confluence and cell numbers were counted using Countess Automated Cell Counter (Invitrogen, Carlsbad, CA). Approximately 500,000 cells from each sample were collected and frozen at -80oC until RNA isolation. Total RNA was extracted from the cells using TRIzol (Thermo Fisher Scientific, Grand Island, NY) and quality was examined by electrophoresis.
Poly (A)+RNA were isolated from the total RNA samples using the NEBNext Poly (A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA). RNA-seq libraries were generated for each sample from 1 ug of mRNA using the NEBNext Ultra Directional RNA Library Prep Kit with NEBNext® Multiplex Oligos for Ilumina according to the manufacture’s protocol (New England Biolabs, Ipswich, MA). Size distribution of the libraries was determined using the Agilent Bioanalyzer High Sensitivity Chip on Agilent Bioanalyzer 2100 (Santa Clara, CA). The concentration of the libraries were quantified by quantitative PCR using the the KAPA SYBR® FAST ABI Prism qPCR Kit and Applied Biosystems® 7500 Real-Time PCR System (Thermo Fisher Scientific, Grand Island, NY). The libraries were pooled and diluted to 1.8 pM with sequencing reagents from the Illumina NextSeq 500/550 High Output kit and sequenced on the NextSeq 500 desktop sequencer (Illumina Inc., San Diego, CA)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
FINAL_master_list_of_genes_counts_MIN.RNA_Pooling_Experiment_29_samples.highExp.txt
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| Data processing |
Basecalls performed using CASAVA
Alignment using STAR 2.4.1d
Normalized using PORT (https://github.com/itmat/Normalization), v0.8-beta for fibroblast and IMR, v0.7.5-beta for stem
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files
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| Submission date |
Aug 30, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Gregory Robert Grant |
| E-mail(s) |
ggrant@upenn.edu
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| Phone |
215-573-3736
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| Organization name |
University of Pennsylvania
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| Department |
Genetics
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| Lab |
ITMAT Bioinformatics
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| Street address |
3400 Civic Center Blvd.
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE86244 |
Early Chronological Aging in Human Adipose-Derived Stem Cells Marked by Distinct Transcriptional Regulation Compared to Differentiated Cells |
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| Relations |
| BioSample |
SAMN05716968 |
| SRA |
SRX2068704 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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