GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2495747 Query DataSets for GSM2495747
Status Public on Feb 14, 2018
Title BMH17-DL
Sample type SRA
Source name MSCs_1MT (1mM)
Organism Homo sapiens
Characteristics subject id: healthy human donor #17
cell type: Mesenchymal stromal cells (MSC)
treated with: 1MT (1mM) for 24h
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
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
BioSample SAMN06348060
SRA SRX2576677

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap