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| Status |
Public on May 25, 2022 |
| Title |
RNA-Seq HUDEP2 cells HIC2 OE rep1 |
| Sample type |
SRA |
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| Source name |
HUDEP2 cells
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Immortalized Human Erythroid Progenitor
cell type: Erythroid cells
differentiation: Differentiated for 5 days
genotype: HIC2 OE
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| 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 For Phase II medium, the IL3 was withdrawn after 9 days of culture.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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| 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
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| Submission date |
Apr 29, 2021 |
| Last update date |
May 27, 2022 |
| Contact name |
Peng Huang |
| E-mail(s) |
waliays@gmail.com
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| Organization name |
Guangzhou Medical University
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| Department |
GMU-GIBH Joint School of Life Sciences
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| Lab |
Peng Huang
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| Street address |
Xinzao, Panyu District
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
511436 |
| Country |
China |
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| 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 |
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| Relations |
| BioSample |
SAMN18925834 |
| SRA |
SRX10714865 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5271251_2890.hg38.tsv.gz |
1.5 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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