|
| Status |
Public on Feb 14, 2018 |
| Title |
BMH14-NoRx |
| Sample type |
SRA |
| |
|
| Source name |
MSCs_vehicle (NoRx)
|
| Organism |
Homo sapiens |
| Characteristics |
subject id: healthy human donor #14
cell type: Mesenchymal stromal cells (MSC)
treated with: vehicle (NoRx)
|
| Treatment protocol |
Cells treated with vehicle (RPMI 1640 +Pen/Strep, +L-glut, +1-% fetal calf serum), with TCDD (10nM) or 1MT (1mM) for 24h, then trypsinized, washed with PBS and stored at -80˚C until RNA analysis.
|
| Growth protocol |
Mesenchymal stromal cells (MSC) were isolated from the marrow of five healthy human donors, passaged in α-MEM supplemented with penicillin, streptomycin and 10% human platelet lysate. Cells were trypsinized and 50,00 were plated per well in a 12-welled plate, in duplicate. Cells were plated in RPMI 1640 +Pen/Strep, +L-glut, +1-% fetal calf serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using RNAeasy Micro Kit (Qiagen). Standard quality control steps were included to determine total RNA quality using Agilent 2100 Bioanalyzer (RNA integrity number (RIN) >8.5; Eukaryote Total RNA Pico Kit, Agilent, USA)
RNA libraries were prepared for sequencing using standard Illumina TruSeq protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the GRCh38 human genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
Genome_build: Homo_sapiens.GRCh38.dna.primary_assembly.fa, Homo_sapiens.GRCh38.86.gtf
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).
|
| |
|
| Submission date |
Feb 19, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Gregory K Tharp |
| E-mail(s) |
gktharp@emory.edu
|
| Phone |
404-727-7797
|
| Organization name |
Yerkes National Primate Research Center
|
| Department |
Developmental and Cognitive Neuroscience
|
| Lab |
Genomics Core
|
| Street address |
954 Gatewood Dr
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30329-4208 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE95072 |
RNAseq data from Mesenchymal stem cells treated with TCDD or 1-methyl tryptophan |
|
| Relations |
| BioSample |
SAMN06348067 |
| SRA |
SRX2576672 |
