|
Status |
Public on Sep 03, 2020 |
Title |
RS14_iSM_young_rep3 |
Sample type |
SRA |
|
|
Source name |
human induced smooth muscle cells
|
Organism |
Homo sapiens |
Characteristics |
treatment: induced cells donor_age: young tissue: human induced smooth muscle cells
|
Treatment protocol |
Both iVECs and iSM cells were selected with antibiotic treatment during reprogramming. iVECs were FACS sorted for CD31 before analyses.
|
Growth protocol |
iVECs were obtained from skin fibroblasts by expressing the master regulator ETV2 while iSM cells were obtained from fibroblasts by expressing MYOCD. iVECs were cultured on collagen-coated dishes in EGM-2MV (Lonza), while iSM cells were cultured in EGM-2 (Lonza).
|
Extracted molecule |
polyA RNA |
Extraction protocol |
RNA was extracted following standard procedures based on Trizol and chloroform. The RNeasy Mini kit was used to purify RNA (Qiagen). Samples were incubated with DNAse I for 30 min to degrade genomic DNA. RNA was resuspended in RNAse-free water. The amount of RNA was quantified with Nanodrop. mRNA-Seq libraries were prepared using the TruSeq RNA Library Preparation Kit according to the manufacturer’s instructions (Illumina).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
iSM_exons.raw.xlsx
|
Data processing |
Sequenced reads were quality tested using FASTQC v0.11.2 using the default parameters. Alignment to the hg19 genome (from illumina iGenome) was performed using the STAR aligner version 2.5.3a using the --outFilterIntronMotifs RemoveNoncanonical parameter Gene expression was quantified using the HOMER analysis suite version 4.9.1, makeTagDirectory, analyzeRepeats.pl across exons of RefSeq genes. Genome_build: hg19 (illumina iGenome) Supplementary_files_format_and_content: iVEC_exons.raw.xlsx (raw count table for the induced vescular endothelial cells dataset) Supplementary_files_format_and_content: iSM_exons.raw.xlsx(raw count table for the induced smooth muscle cells dataset, including three controls samples from published GEO accessions) Supplementary_files_format_and_content: iSM_HGPS_exons.raw.txt (raw count table for the induced smooth muscle cells progeria dataset)
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|
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Submission date |
Nov 24, 2019 |
Last update date |
Mar 28, 2022 |
Contact name |
April Elizabeth Williams |
E-mail(s) |
apriljack06@gmail.com, awilliams@salk.edu
|
Phone |
7345461645
|
Organization name |
Salk Institute for Biological Studies
|
Department |
IGC
|
Street address |
10010 N Torrey Pines Rd
|
City |
San Diego |
State/province |
California |
ZIP/Postal code |
92037 |
Country |
USA |
|
|
Platform ID |
GPL16791 |
Series (1) |
GSE140898 |
Direct reprogramming of fibroblasts identifies signatures of vascular dysfunction in physiological aging and Hutchinson-Gilford Progeria Syndrome |
|
Relations |
BioSample |
SAMN13380026 |
SRA |
SRX7207667 |