Mutual repression of the RNA-binding protein PCBP2 and long non-coding RNAs in induced pluripotent stem cells
RNA-seq (gene expression) · human · 10 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
- 10 samples: 3 × 2day_PCBP2_KD_b vs 3 × 6day_PCBP2_KD_b vs 2 × 2day_Control_b vs 2 × 6day_Control_bGroups 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 GSE139626_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 PRJNA580509 and SRA study SRP227552. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 4 replicated groups read from 10 sample titles; they account for 10 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.
- GSM4144811 2day_Control_b1 2day_Control_b
- GSM4144812 2day_Control_b2 2day_Control_b
- GSM4144813 2day_PCBP2_KD_b1 2day_PCBP2_KD_b
- GSM4144814 2day_PCBP2_KD_b2 2day_PCBP2_KD_b
- GSM4144815 2day_PCBP2_KD_b3 2day_PCBP2_KD_b
- GSM4144816 6day_Control_b1 6day_Control_b
- GSM4144817 6day_Control_b2 6day_Control_b
- GSM4144818 6day_PCBP2_KD_b1 6day_PCBP2_KD_b
- GSM4144819 6day_PCBP2_KD_b2 6day_PCBP2_KD_b
- GSM4144820 6day_PCBP2_KD_b3 6day_PCBP2_KD_b
- GSE262419 Informing Hazard Identification and Risk Characterization of Environmental Chemicals by Combining Transcriptomic and Functional Data from Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes 4558 samples shares pluripotent, induced
- GSE226482 Single cell RNA sequencing of spinal motor neurons and interneurons differentiated from isogenic FUS and TARDBP human induced pluripotent stem cell lines harbouring ALS-causative mutations 1415 samples shares pluripotent, induced
- GSE290248 Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection 97 samples shares rna-binding, protein
- GSE324961 microRNA-132 attenuates inflammation in induced pluripotent stem-cell derived microglia from Alzheimer’s disease patients 95 samples shares pluripotent, induced
- GSE290282 Large-scale tethered screen of RNA-binding proteins reveals novel regulators of poly(A) site selection [RNA-Seq] 92 samples shares rna-binding, protein
- GSE293777 A high-risk osteoarthritis mutation in COL6A3 alters the mechanobiologic response of chondrocytes derived from human induced pluripotent stem cells 84 samples shares pluripotent, induced
- GSE293032 Transcriptomic comparison of hepatocytes derived from a panel of human induced pluripotent stem cells with different ethnicities 54 samples shares pluripotent, induced
- GSE255982 Persistent epigenome anomalies in induced pluripotent stem cells from late-onset sporadic Alzheimer’s disease cases [RNA-seq] 52 samples shares pluripotent, induced
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.