Isolation of biologically active small peptide from KSHV LANA protein sequence, which induces CHD4 degradation to promote cell differentiation and inhibits leukemic cell growth
RNA-seq (gene expression) · human · 30 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
- 30 samples: 13 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.
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 GSE228657_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 PRJNA950956 and SRA study SRP430335. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 30 samples.
How we read this: 13 replicated groups read from 30 sample titles; they account for 30 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.
- GSM7123951 PMA_1 PMA
- GSM7123952 PMA_2 PMA
- GSM7123953 PMA_3 PMA
- GSM7123954 VGN73_1 VGN73
- GSM7123955 VGN73_2 VGN73
- GSM7123956 VGN73_3 VGN73
- GSM7123957 PMA_VGN4_1 PMA_VGN4
- GSM7123958 PMA_VGN4_2 PMA_VGN4
- GSM7123959 PMA_VGN4_3 PMA_VGN4
- GSM7123960 PMA_VGN8_1 PMA_VGN8
- GSM7123961 PMA_VGN8_2 PMA_VGN8
- GSM7123962 PMA_VGN8_3 PMA_VGN8
- GSM7134511 BC3_Ctrl1 BC3_Ctrl
- GSM7134515 BC3_Wt2 BC3_Wt
- GSM7134518 BC3_Mut2 BC3_Mut
- GSM7134520 BCBL1_Ctrl1 BCBL1_Ctrl
- GSM7134521 BCBL1_Ctrl2 BCBL1_Ctrl
- GSM7134523 BCBL1_Wt1 BCBL1_Wt
- GSM7134524 BCBL1_Wt2 BCBL1_Wt
- GSM7134527 BCBL1_Mut2 BCBL1_Mut
- GSM7134529 Raji_Ctrl1 Raji_Ctrl
- GSM7134532 Raji_Wt1 Raji_Wt
- GSM7134536 Raji_Mut2 Raji_Mut
- GSM7181590 BC3_Ctrl2 BC3_Ctrl
- GSM7181591 BC3_Wt1 BC3_Wt
- GSM7181592 BC3_Mut1 BC3_Mut
- GSM7181593 BCBL1_Mut1 BCBL1_Mut
- GSM7181594 Raji_Ctrl2 Raji_Ctrl
- GSM7181595 Raji_Wt2 Raji_Wt
- GSM7181596 Raji_Mut1 Raji_Mut
- GSE228656 Isolation of biologically active small peptide from KSHV LANA protein sequence, which induces CHD4 degradation to promote cell differentiation and inhibits leukemic cell growth (SLAM-seq) 18 samples shares kshv, lana, chd4, biologically, degradation, isolation, inhibits, leukemic
- GSE228553 Isolation of biologically active small peptide from KSHV LANA protein sequence, which induces CHD4 degradation to promote cell differentiation and inhibits leukemic cell growth (RNA-seq) 12 samples shares kshv, lana, chd4, biologically, degradation, isolation, inhibits, leukemic
- GSE247621 Increased PTCHD4 expression via m6A modification of PTCHD4 mRNA promotes senescent-cell survival 30 samples shares chd4
- GSE280380 DNA virus infections shape transposable element activity in vitro and in vivo (HCMV,KSHV,DUX4) 54 samples shares kshv
- GSE250393 Transcriptomic effects of caspase cleavage at TFIIB residue D207 during apoptosis and KSHV infection [TFIIB(D207A)] 32 samples shares kshv
- GSE260925 Unveiling the Role of KSHV-Infected Human Mesenchymal Stem Cells in Kaposi's Sarcoma Initiation 24 samples shares kshv
- GSE309397 Virally encoded interleukin-6 (vIL-6) coordinates with human IL-6 to modulate cytokine expression during KSHV infection 24 samples shares kshv
- GSE320561 Effect of eIF5B silencing on KSHV-reactivated human iSLK.219 cells from 0-72 Hours reactivation 24 samples shares kshv
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.