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Effect of HES6 knockdown on gene expression in vitro differentiated megakaryocytes, erythroblasts and precursor cells, cultured from CB CD34+ HSPCs.

GSE229196 Homo sapiens (human) RNA-seq (gene expression) 36 samples Submitted 2024/11/13 Platform GPL20301
At a glance

RNA-seq (gene expression) · human · 36 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
36 samples: 12 conditions, mostly in duplicateGroups 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.
Paper
<i>HES6</i>knockdown in human hematopoietic precursor cells reduces their <i>in vivo</i> engraftment potential and their capacity to differentiate into erythroid cells, B cells, T cells and plasmacytoid dendritic cellsHaematologica · 2024
Summary (written by the submitters)
Cord blood CD34+ hematopoietic precursors (3 donors) were control or HES6 shRNA (HES6 knockdown) transduced and cultured for four days in media containing SCF, TPO and EPO to drive differentiation towards megakaryocytes and erythroid cells. After four days four subpopulations were sorted for RNA isolation to research the effect of HES6 knockdown on gene expression. We sorted megakaryocytes (CD41+) and early (CD71+ CD235-) and late (CD71+ CD235+) erythroblasts (CD41-) and CD34- precursor cells (CD41- CD71- CD235- CD34-).
Published in
<i>HES6</i>knockdown in human hematopoietic precursor cells reduces their <i>in vivo</i> engraftment potential and their capacity to differentiate into erythroid cells, B cells, T cells and plasmacytoid dendritic cells
De Vos T, Oatman N, Boehme L et al. · Haematologica 2024 · PMID 38572564 · doi:10.3324/haematol.2023.283432
This dataset
Open GSE229196 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 GSE229196_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 PRJNA953389 and SRA study SRP431500. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38572564) ↗
Study design
12 conditions, mostly in duplicate
Biol rep1 mgk HES6 knockdown ×2 Biol rep1 CD34- HES6 knockdown ×2 Biol rep1 early ery HES6 knockdown ×2 Biol rep1 late ery HES6 knockdown ×2 Biol rep2 mgk HES6 knockdown ×2 Biol rep2 CD34- HES6 knockdown ×2 Biol rep2 early ery HES6 knockdown ×2 Biol rep2 late ery HES6 knockdown ×2 +16 more

Supports a case/control comparison: 24 samples read as cases, 12 as controls.

How we read this: 12 replicated groups read from 36 sample titles; they account for 24 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
Datasets on a similar topic

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