|
| Status |
Public on Apr 29, 2024 |
| Title |
BEL-A cells, wildtype, day 2 of differentiation 1 |
| Sample type |
SRA |
| |
|
| Source name |
BEL-A
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BEL-A
cell type: Erythroid progenitor
genotype: WT
treatment: Erythroid differentiation
|
| Treatment protocol |
Cells were seeded in differentiation medium, Iscove’s Modified Basal Medium (IMDM) with glutamine (Biochrom; Merck Millipore), supplemented with 3% (v/v) human AB serum (Sigma-Aldrich), 2% (v/v) fetal bovine serum (Hyclone), 10 μg/ml insulin (Sigma-Aldrich), 3 U/ml heparin (Sigma-Aldrich), 200 μg/ml holo-transferrin (Sanquin), 1 ng/ml interleukin‐3 (IL-3; Roche), 3 U/ml EPO, 10 ng/ml SCF and 1 U/ml penicillin / streptomycin with DOX 1 μg/ml, at 2.0 × 105 cells/ml.
|
| Growth protocol |
Cells were maintained in expansion medium (Stemspan SFEM (Stem Cell Technologies) supplemented with 50 ng/ml stem cell factor (SCF; R&D Systems), 3 U/ml erythropoietin (EPO; Roche), 1 uM dexamethasone (DEX; Sigma-Aldrich) and 1 ug/ml doxycycline (DOX; Clontech) at 1.0 × 10^5 cells/ml.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 3 biological repeats using RNeasy mini kit (Qiagen) according to the manufacturer’s protocol.
Library construction and sequencing were performed by Novogene Co. Ltd. using the NEB Next® Ultra™ RNA Library Prep Kit according to the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
WT1
|
| Data processing |
Hisat2 v2.0.5
For gene expression quantification, featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM (Fragments Per Kilobase of transcript sequence per Millions base pair sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 R package (1.20).
The resulting P-values were adjusted using the Benjamini-Hochberg approach for controlling the false discovery rate. Genes with an adjusted P-value ≤0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing fpkm values for all samples
|
| |
|
| Submission date |
Mar 07, 2023 |
| Last update date |
Apr 29, 2024 |
| Contact name |
Jan Frayne |
| E-mail(s) |
jan.frayne@bristol.ac.uk
|
| Organization name |
University of Bristol
|
| Department |
School of Biochemistry
|
| Street address |
Biomedical Sciences Building, University Walk
|
| City |
Bristol |
| ZIP/Postal code |
BS8 1TD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE226782 |
Novel human cellular model of CDA IV enables comprehensive analysis revealing molecular basis of disease phenotype. |
|
| Relations |
| BioSample |
SAMN33610435 |
| SRA |
SRX19585022 |
