|
| Status |
Public on Sep 03, 2020 |
| Title |
SB_03_Fibro_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
human fibroblast cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: non-induced cells from donors
donor_age: NA
tissue: human fibroblast 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).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
iVEC_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)
|
| |
|
| 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 |
SAMN13380003 |
| SRA |
SRX7207645 |
