|
Status |
Public on Nov 01, 2017 |
Title |
Valproic_Acid_3 |
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-valproic acid 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 |
Fetscherstraße 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 |
SAMN06056430 |
SRA |
SRX2378706 |