NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2406734 Query DataSets for GSM2406734
Status Public on Nov 01, 2017
Title PBS_1
Sample type SRA
 
Source name G-CSF mobilized peripheral blood stem cells
Organism Homo sapiens
Characteristics source: CD34+ hematopoietic stem and progenitor cells
culture period-in vitro: 5 days-PBS control treated
type: in vitro expanded CD34+ cells
Extracted molecule total RNA
Extraction protocol CD34+ cells were re-isolated and total RNA was isolated using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing basecalling: bcl2fastq 2.1.17.4
alignment: alignment of single-end data against hg38 with gsnap version 2015-12-31; splice sites were supported by using Ensembl version 81 (gsnap -d hg38 --gunzip --use-sarray=1 -B 4 -t 16 -N 1 -s EnsemblGene-81.ss.hg38.iit -n 1 -A sam)
read counting: counting was done with featureCounts version 1.5.0 (-a EnsemblGene-81.hg38.TR.gtf -s 2 -Q 1) and the Ensembl version 81 gtf file
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited file from featureCounts (featureCounts.hg38.e81.csv.gz); columns are in the following order: Ensembl Gene ID, Chromosom, Exon Start Coordinates, Exon End Coordinates, Gene Length; Counts from the 2 Conditions and their 4 replicates
 
Submission date Nov 26, 2016
Last update date May 15, 2019
Contact name Guruchandar Arulmozhivarman
E-mail(s) guruschandar.arulmozhiv@crt-dresden.de
Organization name TU Dresden - Faculty of Medicine
Department Hematology department
Lab Dresden Stem Cell Lab
Street address Fetscherstra├če 74
City Dresden
ZIP/Postal code 01307
Country Germany
 
Platform ID GPL16791
Series (1)
GSE90552 In Vivo Chemical Screen Nominates Valproic Acid as Pharmacologic Modulator of Hematopoietic Stem and Progenitor Cell Activity
Relations
BioSample SAMN06056428
SRA SRX2378700

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