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Sample GSM3832686 Query DataSets for GSM3832686
Status Public on Dec 31, 2020
Title BAHD1-V5 OE R3 (RNA-seq)
Sample type SRA
 
Source name HUDEP-2
Organism Homo sapiens
Characteristics cell line: HUDEP-2
cell type: erythroblast cells
tissue: Umbilical Cord blood derived
genotype: BAHD1-V5 overexpression
Growth protocol Cells were expanded in StemSpan serum-free expansion medium (SFEM; Stem Cell Technologies) supplemented with 1 µM dexamethasone, 1 µg/mL doxycycline, 50 ng/mL human stem cell factor (SCF), 3 units/mL erythropoietin (EPO), and 1% penicillin–streptomycin.
Extracted molecule total RNA
Extraction protocol HUDEP-2 cells' RNA was harvested using RLT reagent (Qiagen). 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 4000
 
Description RNA.count.all.txt.gz
BAHD1-V5-R3
Data processing Illumina Casava software used for basecalling.
Sequenced reads were aligned and counted by RNA-seq pipeline(WARDEN) at https://www.stjude.cloud/tools.html
Briefly, paired-end reads were aligned to hg19 by STAR and counted by HTSEQ.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes raw counts for each gene for each sample
 
Submission date May 30, 2019
Last update date Dec 31, 2020
Contact name Mitch Weiss
E-mail(s) mitch.weiss@stjude.org
Phone 9015953760
Organization name st jude children's research hospital
Department Hematology
Street address 262 Danny Thomas Place
City Memphis
State/province Tennessee
ZIP/Postal code 38105
Country USA
 
Platform ID GPL20301
Series (1)
GSE115357 FBXO11-Mediated Proteolysis of BAHD1 Relieves PRC2-dependent Transcriptional Repression in Erythropoiesis
Relations
BioSample SAMN11891815
SRA SRX5931583

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

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