The effect of TRAF6 loss on the gene expression profiles in leukemia cells
RNA-seq (gene expression) · human · 32 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
- 32 samples: 12 conditions, mostly in triplicateGroups 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
- Metabolic reprogramming regulated by TRAF6 contributes to the leukemia progressionLeukemia · 2024
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 GSE254616_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 PRJNA1071139 and SRA study SRP486900. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 32 samples.
How we read this: 12 replicated groups read from 32 sample titles; they account for 32 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.
- GSM8047042 HEL_untreated_1 HEL_untreated
- GSM8047043 HEL_untreated_2 HEL_untreated
- GSM8047044 HEL_DOX_1 HEL_DOX
- GSM8047045 HEL_DOX_2 HEL_DOX
- GSM8047046 MV4;11_untreated_1 MV4;11_untreated
- GSM8047047 MV4;11_untreated_2 MV4;11_untreated
- GSM8047048 MV4;11_DOX_1 MV4;11_DOX
- GSM8047049 MV4;11_DOX_2 MV4;11_DOX
- GSM8047050 THP-1_untreated_1 THP-1_untreated
- GSM8047051 THP-1_untreated_2 THP-1_untreated
- GSM8047052 THP-1_untreated_3 THP-1_untreated
- GSM8047053 THP-1_DOX_1 THP-1_DOX
- GSM8047054 THP-1_DOX_2 THP-1_DOX
- GSM8047055 THP-1_DOX_3 THP-1_DOX
- GSM8047056 TF-1_untreated_1 TF-1_untreated
- GSM8047057 TF-1_untreated_2 TF-1_untreated
- GSM8047058 TF-1_untreated_3 TF-1_untreated
- GSM8047059 TF-1_DOX_1 TF-1_DOX
- GSM8047060 TF-1_DOX_2 TF-1_DOX
- GSM8047061 TF-1_DOX_3 TF-1_DOX
- GSM8047062 MOLM14_untreated_1 MOLM14_untreated
- GSM8047063 MOLM14_untreated_2 MOLM14_untreated
- GSM8047064 MOLM14_untreated_3 MOLM14_untreated
- GSM8047065 MOLM14_DOX_1 MOLM14_DOX
- GSM8047066 MOLM14_DOX_2 MOLM14_DOX
- GSM8047067 MOLM14_DOX_3 MOLM14_DOX
- GSM8047068 MLL-AF9;Traf6+/+_1 MLL-AF9;Traf6+/+
- GSM8047069 MLL-AF9;Traf6+/+_2 MLL-AF9;Traf6+/+
- GSM8047070 MLL-AF9;Traf6+/+_3 MLL-AF9;Traf6+/+
- GSM8047071 MLL-AF9;Traf6-/-_1 MLL-AF9;Traf6-/
- GSM8047072 MLL-AF9;Traf6-/-_2 MLL-AF9;Traf6-/
- GSM8047073 MLL-AF9;Traf6-/-_3 MLL-AF9;Traf6-/
- GSE317764 High-Fat Diet Causes Rapid Loss of Intestinal Group 3 Innate Lymphoid Cells Through Microbiota-Driven Inflammation 270 samples shares loss
- GSE216612 Gene expression profiles of hematopoietic stem/progenitor cells after stimulating CCL2. 2 samples shares profiles
- GSE278006 NK cell cytotoxicity shapes the clonal evolution of B cell leukemia [RNA-seq] 241 samples shares leukemia
- GSE297591 Cytotoxicity caused by 5-methylcytosine depletion on chromatin-associated RNA by 5-azacytosine in leukemia [RNA-seq] 96 samples shares leukemia
- GSE256272 Loss of NUMB drives aggressive bladder cancer via a RHOA/ROCK/YAP signaling axis. 65 samples shares loss
- GSE283531 MOZ and HBO1 Histone Acetyltransferase Complexes Are Molecular Dependencies and Therapeutic Targets in NUP98-Rearranged Acute Myeloid Leukemia [RNA-Seq] 54 samples shares leukemia
- GSE239350 Identifying STRN3-RARA as a new fusion gene for acute promyelocytic leukemia [RNA-seq 2] 6 samples shares leukemia
- GSE253138 A dual role for PSIP1/LEDGF in T-cell acute lymphoblastic leukemia [RNA-seq] 42 samples shares leukemia
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.