GEO series

Title: RNA-seq analysis of b0-HUDEP2 and HUDEP2 cells following erythroid differentiation

GSE200504 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2024/04/04 Platform GPL16791

At a glance

RNA-seq (gene expression) · human · 12 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Homo sapiens (human)
Samples: 12 samples: 3 × HUDEP2 (Day 0) vs 3 × b0-HUDEP2 (Day 0) vs 3 × HUDEP2 (Day 8) vs 3 × b0-HUDEP2 (Day 8)Groups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.

Summary (written by the submitters)

Purpose: The goal of this study is to compare the altered transcriptional program (RNA-seq) and cellular adaptation to stress caused by excess a-globin synthesis. Results: 100bp paired-end polyA-enriched RNA sequencing were performed with a depth of minimum of 20 million read counts per sample. The sequencing library was sequenced on the Illumina HiSeq2500 at Azenta.

Read the full summary ↓

Raw data then went through read quality assessment by FastQC (version 0.11.5), mapping to the human genome (GRch38) by the STAR aligner and gene-level reads quantification using the Rsubread package. RNA-seq data analysis identified 1870 upregulated and 1549 down regulated genes on Day 0 (FDR <=0.05) and 1924 upregulated and 1960 down regulated genes on Day 8 (FDR <=0.05). MA plot analysis of differentially expressed genes uncovered an altered transcriptional program favouring γ-globin expression not solely dependent upon the HRI ATF4-BCL11A axis. Instead, we noted attenuated expression of several key γ-globin co-repressors, including SOX6, ZBTB7A, KLF1 and GATA1, which coincided with increased expression of co-activators such as CBFB/NY-FB and GATA2 following erythroid differentiation. Gene Set Enrichment Analysis (GSEA) software was used to determine significantly enriched gene sets. Downregulated DEGs in β0 HUDEP 2 cells in pathways related to haeme metabolism, hypoxia, MTORC1, unfolded protein response and TNFA/NFkB signalling were enriched. Meanwhile, upregulated DEGs in β0 HUDEP-2 cells related to G-protein-coupled receptors (GPCR) signalling, IL-2/STAT5 and hypoxia signalling pathway were also retrieved. Pathways shown to be significantly altered in both β0 HUDEP-2 cells and patient group include apoptosis, MAPK signalling and NFKB pathway thus provided complementary insights in transcriptome profiling. Conclusions: Our study represents analysis of HUDEP2 transcriptomes, with biologic replicates, generated by RNA-seq technology. The data analysis reported here should provide a framework for comparative investigations of expression profiles. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of the cellular adaptation to intrinsic stress caused by excess a-globin synthesis.

This dataset

Open GSE200504 in finder → Find more human RNA-seq datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE200504_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA824843 and SRA study SRP368309. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

3 × HUDEP2 (Day 0) vs 3 × b0-HUDEP2 (Day 0) vs 3 × HUDEP2 (Day 8) vs 3 × b0-HUDEP2 (Day 8)

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM6035271 HUDEP2 (Day 0) Rep 1 HUDEP2 (Day 0)
GSM6035272 HUDEP2 (Day 0) Rep 2 HUDEP2 (Day 0)
GSM6035273 HUDEP2 (Day 0) Rep 3 HUDEP2 (Day 0)
GSM6035274 b0-HUDEP2 (Day 0) Rep 1 b0-HUDEP2 (Day 0)
GSM6035275 b0-HUDEP2 (Day 0) Rep 2 b0-HUDEP2 (Day 0)
GSM6035276 b0-HUDEP2 (Day 0) Rep 3 b0-HUDEP2 (Day 0)
GSM6035277 HUDEP2 (Day 8) Rep 1 HUDEP2 (Day 8)
GSM6035278 HUDEP2 (Day 8) Rep 2 HUDEP2 (Day 8)
GSM6035279 HUDEP2 (Day 8) Rep 3 HUDEP2 (Day 8)
GSM6035280 b0-HUDEP2 (Day 8) Rep 1 b0-HUDEP2 (Day 8)
GSM6035281 b0-HUDEP2 (Day 8) Rep 2 b0-HUDEP2 (Day 8)
GSM6035282 b0-HUDEP2 (Day 8) Rep 3 b0-HUDEP2 (Day 8)

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