NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5592541 Query DataSets for GSM5592541
Status Public on Mar 21, 2022
Title CD34+ differentiation Day8-KD1, RNA-seq
Sample type SRA
 
Source name human CD34+ cells
Organism Homo sapiens
Characteristics genotype: KD
time: differentiation Day8
cell type: CD34+ cells
Growth protocol Primary CD34+ umbilical cord cells (Lonza, cat. 2C-101) were cultured as described (Wilber et al., 2010). HUDEP2 cells was cultured in SFEM medium and induced in DMEM medium as described (Vinjamur and Bauer, 2018). K562 cells were cultured in RPMI 1640 medium containing 10 % fetal bovine serum.Hemogen WT and KO mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Fetal livers isolated from E14.5 control and knockout mice.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using RNeasy Plus Micro Kit
RNA sequencing libraries were generating from 100ng-1 ug of RNA using Illumina TruSeq Stranded mRNA Library Preparation kit (20020594) following manufacturer’s protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 and mm10 whole genome using hisat2 v2.1.0 with default parameters respectively. Multimappnig reads were filtered using samtoools 1.9, uniquely aligned reads were then mapped to gene features using Subread featureCounts v1.6.4
Differential expression between groups of samples was tested using R version 3.5.1 with DESeq2 1.20.0
Genome_build: hg38 , mm10
Supplementary_files_format_and_content: tab-delimited text files include gene count values for each Sample ...
 
Submission date Sep 21, 2021
Last update date Mar 21, 2022
Contact name Xiang Guo
E-mail(s) xguoellen@gmail.com
Phone 2402052897
Organization name NIH
Department NIDDK
Lab LCDB
Street address 50 south drive, blg50
City bethesda
State/province MD
ZIP/Postal code 20814
Country USA
 
Platform ID GPL20301
Series (2)
GSE184558 Hemogen /BRG1 cooperativity modulates promoter and enhancer activation during erythropoiesis [RNA-seq]
GSE184606 Hemogen /BRG1 cooperativity modulates promoter and enhancer activation during erythropoiesis
Relations
BioSample SAMN21541035
SRA SRX12286520

Supplementary file Size Download File type/resource
GSM5592541_CD34D8KDRep1.cutadapt.bam.featurecounts.s2.txt.gz 4.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.