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Sample GSM5271249 Query DataSets for GSM5271249
Status Public on May 25, 2022
Title RNA-Seq HUDEP2 cells GFP control rep1
Sample type SRA
 
Source name HUDEP2 cells
Organism Homo sapiens
Characteristics tissue: Immortalized Human Erythroid Progenitor
cell type: Erythroid cells
differentiation: Differentiated for 5 days
genotype: GFP OE
Growth protocol Human CD34+ HSPCs were cultured using a three-phase protocol. For Phase I medium, IMDM was supplemented with 100 ng/mL human SCF, 50 ng/mL IL3, 3 units/ml erythropoietin, 1% penicillin/streptomycin, 330 μg/ml holo-transferrin, 10 μg/ml insulin, 5% human A/B plasma and 2 units/ml heparin. For Phase II medium, the IL3 was withdrawn after 9 days of culture. For Phase III medium, the cells were cultured with IMDM supplemented with 3 units/ml erythropoietin, 1% penicillin/streptomycin, 330 μg/ml holo-transferrin, 10 μg/ml insulin, 5% human A/B plasma and 2 units/ml heparin.
HUDEP2 cells were cultured with StemSpan SFEM (Stem Cell Technologies) supplemented with 1 μg/ml doxycycline, 1 μM dexamethasone, 100 ng/ml human SCF, 3 units/ml erythropoietin and 1% penicillin/streptomycin.
Extracted molecule total RNA
Extraction protocol Cells were homogenized using TRIzol (Life Technologies). RNA was extracted using RNeasy Mini Kit (Qiagen).
Sequencing libraries were constructed from 500 ng of DNase-treated, total RNA using the NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (NEB cat# 6310) for rRNA depletion, followed by the TruSeq Stranded Total kit (Illumina cat# 20020598) for cDNA synthesis and library preparation according to manufacturer’s specifications.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 2000
 
Data processing Basecalls using DRAGEN BCL Data Conversion (version 3.7.4), bcl2fastq2 v2.20, and parameters --no-eamss --mismatches 1
Reads were mapped to reference genome hg38 with ENCODE RNA-seq pipeline.
Genome_build: hg38
Supplementary_files_format_and_content: tsv files with FPKM and TPM values for each gene
 
Submission date Apr 29, 2021
Last update date May 27, 2022
Contact name Peng Huang
E-mail(s) waliays@gmail.com
Organization name Guangzhou Medical University
Department GMU-GIBH Joint School of Life Sciences
Lab Peng Huang
Street address Xinzao, Panyu District
City Guangzhou
State/province Guangdong
ZIP/Postal code 511436
Country China
 
Platform ID GPL30173
Series (2)
GSE173586 HIC2 represses BCL11A transcription to regulate hemoglobin switching during development (RNA-Seq)
GSE173587 HIC2 represses BCL11A transcription to regulate hemoglobin switching during development
Relations
BioSample SAMN18925836
SRA SRX10714863

Supplementary file Size Download File type/resource
GSM5271249_2888.hg38.tsv.gz 1.5 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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