Balancing the CKS1/CKS2 proteostasis axis is critical to maintain hematopoietic stem cell function
RNA-seq (gene expression) · mouse · 14 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
- Mus musculus (mouse)
- Samples
- 14 samples: 14 samples, each with a distinct title — no replicated groupsGroups 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
- The CKS1/CKS2 Proteostasis Axis Is Crucial to Maintain Hematopoietic Stem Cell FunctionHemaSphere · 2023
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 GSE212789_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 PRJNA877261 and SRA study SRP395884. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 9 samples read as cases, 5 as controls.
How we read this: Read from 14 sample titles: 14 distinct titles with little repetition. 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.
- GSM6552417 WT lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [WT_LSK_1]
- GSM6552418 WT lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [WT_LSK_2]
- GSM6552419 WT lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [WT_LSK_3]
- GSM6552420 WT lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [WT_LSK_4]
- GSM6552421 WT lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [WT_LSK_5]
- GSM6552422 CKS1b knockout lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [Cks1KO_LSK_1]
- GSM6552423 CKS1b knockout lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [Cks1KO_LSK_3]
- GSM6552424 CKS1b knockout lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [Cks1KO_LSK_4]
- GSM6552425 CKS1b knockout lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [Cks1KO_LSK_5]
- GSM6552426 CKS2 knockout lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [Cks2KO_LSK_1]
- GSM6552427 CKS2 knockout lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [Cks2KO_LSK_2]
- GSM6552428 CKS2 knockout lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [Cks2KO_LSK_3]
- GSM6552429 CKS2 knockout lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [Cks2KO_LSK_4]
- GSM6552430 CKS2 knockout lineage marker negative, cKit positive, Sca1 positive bone marrow derived cells [Cks2KO_LSK_5]
- GSE266509 A Bcl11a-driven mechanism maintaining hematopoietic stem cell functionality gives rise to dysfunction during aging [RNA-Seq] 52 samples shares hematopoietic, maintain
- GSE293047 20S proteasome-regulated proteostasis in ELVAs is critical for oocyte-to-embryo transition and female fertility 16 samples shares proteostasis, critical
- GSE188525 A critical requirement for IκBα in controlling dormancy in Hematopoietic stem cells via retinoic acid during embryonic development 20 samples shares hematopoietic, critical
- GSE274544 Single cell profiling reveals three endothelial to hematopoietic transitions with divergent isoform expression landscapes [scRNA-Seq] 1494 samples shares hematopoietic
- GSE265909 yHSC and oHSC scRNAseq with oHSC AThi ATlo Index Sorting. Assessing the transcriptional changes associated with autophagy engagement in old hematopoietic stem cells at single cell resolution. [scRNA-Seq] 563 samples shares hematopoietic
- GSE309071 Single cell profiling reveals three endothelial to hematopoietic transitions with divergent isoform expression landscapes [RNA-seq] 221 samples shares hematopoietic
- GSE274979 ER-phagy and proteostasis defects create a pre-malignant injury state in Kras-mediated tumourigenesis (Spatial transcriptomics) 95 samples shares proteostasis
- GSE165881 Establishment of hematopoietic stem cell compartment after single cell transplantation tracked by FIT approach 62 samples shares hematopoietic
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.