HDAC7 is essential in early pre-germinal center formation and its deregulation is associated with DLBCL
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)
- Topic
- Diffuse large B-cell lymphomaThis series is part of our curated briefing on it.
- Samples
- 12 samples: 4 × GC_KO vs 3 × GC_WT vs 3 × HDAC7 vs 2 × EmptyGroups 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.
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE228738_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA951374 and SRA study SRP430474. Searching any of these in the dataset finder brings you back here.
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.
- GSM7135738 GC_KO1 GC_KO
- GSM7135739 GC_KO2 GC_KO
- GSM7135740 GC_KO3 GC_KO
- GSM7135741 GC_KO4 GC_KO
- GSM7135742 GC_WT1 GC_WT
- GSM7135743 GC_WT2 GC_WT
- GSM7135744 GC_WT4 GC_WT
- GSM7135745 Empty_1 Empty
- GSM7135746 Empty_2 Empty
- GSM7135747 HDAC7_1 HDAC7
- GSM7135748 HDAC7_2 HDAC7
- GSM7135749 HDAC7_3 HDAC7
- GSE228736 HDAC7 is essential in early pre-germinal center formation and its deregulation is associated with DLBCL [Xenografts] 5 samples same disease briefing · shares hdac7, dlbcl, pre-germinal, deregulation, essential, formation, center, early
- GSE231624 (1) Effect of KLHL6 loss on the transcriptome in DLBCL upon NOTCH ligand stimulation. (2) Effect of KLHL6 and NOTCH2 loss on the transcriptome in DLBCL. (3) Effect of DLBCL-associated NOTCH2 mutants on the transcriptome in DLBCL. 48 samples same disease briefing · shares dlbcl
- GSE277665 DOT1L and EZH2 cooperatively repress PRC2 targets to maintain the GC B cell identity in DLBCL [RNA-seq] 48 samples same disease briefing · shares dlbcl
- GSE224867 RNA-seq analysis of DLBCL cell lines in response to chemotherapy 36 samples same disease briefing · shares dlbcl
- GSE252690 Increased CCL2/CCR2 axis in MYC/BCL2 double-expressor DLBCL promotes tumor progression by increasing M2 macrophages 28 samples same disease briefing · shares dlbcl
- GSE280799 Expression Data from DLBCL Cell Line U2932 (Parental, CDC-Treated, and CDC-Resistant) and 8 DLBCL Patient Samples (5 High CDC-Sensitive, 3 Low CDC-Sensitive) 20 samples same disease briefing · shares dlbcl
- GSE242115 Morusinol is a Potent Therapeutic Agent Against DLBCL II 12 samples same disease briefing · shares dlbcl
- GSE249466 Bendamustine combined with rituximab induces pyroptosis to shape an "immunologically hot" tumor microenvironment in DLBCL cells via the STING pathway 12 samples same disease briefing · shares dlbcl
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.