PHF6 cooperates with SWI/SNF complexes to facilitate transcriptional progression [RNA-seq]
RNA-seq (gene expression) · human · 38 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
- 38 samples: 11 × shPHF6 vs 9 × shCTRLGroups 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
- PHF6 cooperates with SWI/SNF complexes to facilitate transcriptional progressionNature communications · 2024
Read the full summary ↓
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 GSE180481_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 PRJNA748393 and SRA study SRP329125. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 20 samples.
How we read this: 2 replicated groups read from 38 sample titles; they account for 20 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.
- GSM5463686 shCTRL_1 shCTRL
- GSM5463687 shCTRL_2 shCTRL
- GSM5463688 shPHF6_1 shPHF6
- GSM5463689 shPHF6_2 shPHF6
- GSM5463690 shCTRL_3 shCTRL
- GSM5463691 shCTRL_4 shCTRL
- GSM5463692 shPHF6_3 shPHF6
- GSM5463693 shPHF6_4 shPHF6
- GSM5463694 shPHF6_5 shPHF6
- GSM5463695 shCTRL_5 shCTRL
- GSM5463696 shCTRL_6 shCTRL
- GSM5463697 shCTRL_7 shCTRL
- GSM5463698 shPHF6_6 shPHF6
- GSM5463699 shPHF6_7 shPHF6
- GSM5463700 shPHF6_8 shPHF6
- GSM5463701 shCTRL_8 shCTRL
- GSM5463702 shCTRL_9 shCTRL
- GSM5463703 shPHF6_9 shPHF6
- GSM5463704 shPHF6_10 shPHF6
- GSM5463705 shPHF6_11 shPHF6
- GSM7837956 2374641_G401_RNA_PGIPZ_1
- GSM7837957 2374642_G401_RNA_PGIPZ_2
- GSM7837958 2374643_G401_RNA_PGIPZ_3
- GSM7837959 2374647_G401_RNA_shBRD9_1
- GSM7837960 2374648_G401_RNA_shBRD9_2
- GSM7837961 2374649_G401_RNA_shBRD9_3
- GSM7837962 2424355_TTC549_RNA_shCTRL_NA_1
- GSM7837963 2424356_TTC549_RNA_shCTRL_NA_2
- GSM7837964 2424357_TTC549_RNA_shCTRL_NA_3
- GSM7837965 2424358_TTC549_RNA_shPHF6_NA_1
- GSM7837966 2424359_TTC549_RNA_shPHF6_NA_2
- GSM7837967 2424360_TTC549_RNA_shPHF6_NA_3
- GSM7837968 2424361_TTC709_RNA_shCTRL_NA_1
- GSM7837969 2424362_TTC709_RNA_shCTRL_NA_2
- GSM7837970 2424363_TTC709_RNA_shCTRL_NA_3
- GSM7837971 2424364_TTC709_RNA_shPHF6_NA_1
- GSM7837972 2424365_TTC709_RNA_shPHF6_NA_2
- GSM7837973 2424366_TTC709_RNA_shPHF6_NA_3
- GSE270787 ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency 205 samples shares swi, snf, progression
- GSE261988 SWI/SNF is a gatekeeper of chromatin access at enhancer networks controlling triple-negative breast cancer progression [ChIP-Seq] 79 samples shares swi, snf, progression
- GSE249258 Mammalian SWI/SNF complex activity regulates POU2F3 and constitutes a targetable dependency in small cell lung cancer 24 samples shares swi, snf
- GSE215024 Targeting DCAF5 suppresses SMARCB1-mutant cancer via stabilizing SWI/SNF 12 samples shares swi, snf
- GSE301505 Mutual Antagonism Between PRC1 Condensates and SWI/SNF in Chromatin Regulation 210 samples shares swi, snf
- GSE328578 CBFA2T3-GLIS2 fusion-mediated mSWI/SNF chromatin remodeler disruption generates cancer-specific dependencies in AMKL 156 samples shares swi, snf
- GSE299672 PHIP suppresses NuRD to enable the growth of SWI/SNF-mutant cancers [ChIP-seq] 132 samples shares swi, snf
- GSE245249 CRISPR activation screens identify the SWI-SNF ATPases as suppressors of ferroptosis 65 samples shares swi, snf
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.