|
| Status |
Public on Jun 29, 2020 |
| Title |
hMSCs NIR MoS2 2 |
| Sample type |
SRA |
| |
|
| Source name |
Mesenchymal stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Bone marrow derived mesenchymal stem cells
|
| Treatment protocol |
hMSCs were cultured and treated with/without low-intensity NIR exposure and/or exfoliated MoS2 (25 µg/mL, 48 h).
|
| Growth protocol |
hMSCs were cultured under normal media conditions consisting of α-minimal essential media (alpha-MEM, Hyclone, GE Sciences) with 16.5% fetal bovine serum (Atlanta Biologicals, USA) and 1% penicillin/streptomycin (100 U/100 µg/mL, Gibco). After every 2-3 days, half of culture media was exchanged for fresh media. Cells were passaged with 0.5% trypsin-EDTA upon reaching confluency of ~70% and seeded at ~2500 cells/cm2. All experiments were completed with cell populations under P5.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At the end of 7 days of culture, total RNA was extracted (High Pure RNA Isolation, Roche Life Sciences), and then converted into cDNA (>1 μg).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
NIR MoS2 treatment
|
| Data processing |
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's NCS 1.0.2 and RFV 1.0.2 software with default parameter settings. Sequencer .cbcl basecall files were demultiplexed and formatted into .fastq files using bcl2fastq 2 2.19.0 script configureBclToFastq.pl.
Sequenced reads were trimmed for adaptor sequence and aligned by STAR aligner
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons (excluding 5UTR and 3UTR) of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library (only reads mapping to annotated regions of the genome were used for the total libraray size).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all samples
|
| |
|
| Submission date |
Dec 04, 2019 |
| Last update date |
Jun 29, 2020 |
| Contact name |
Irtisha Singh |
| E-mail(s) |
[email protected]
|
| Organization name |
Texas A&M Health Science Center
|
| Street address |
8447 Riverside Pkwy Medical Research and Education Building II
|
| City |
Bryan |
| State/province |
TX |
| ZIP/Postal code |
77807 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE141456 |
Photothermal Modulation of Human Stem Cells Using Light-responsive 2D Nanomaterials |
|
| Relations |
| BioSample |
SAMN13480542 |
| SRA |
SRX7267432 |
