Transcriptome analysis for XBP1 overexpressing complete hydatidiform mole-derived cell lines
RNA-seq (gene expression) · human · 12 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
- 12 samples: 3 × Hmol1-2C_Ctrl vs 3 × Hmol1-2C_XBP1-OE vs 3 × Hmol1-3B_Ctrl vs 3 × Hmol1-3B_XBP1-OEGroups 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
- Elucidation of the role of XBP1 in the progression of complete hydatidiform mole to invasive mole through RNA-seqGynecologic oncology · 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 GSE252905_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 PRJNA1063209 and SRA study SRP482890. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8010105 Hmol1-2C_Ctrl_rep1 Hmol1-2C_Ctrl
- GSM8010106 Hmol1-2C_Ctrl_rep2 Hmol1-2C_Ctrl
- GSM8010107 Hmol1-2C_Ctrl_rep3 Hmol1-2C_Ctrl
- GSM8010108 Hmol1-2C_XBP1-OE_rep1 Hmol1-2C_XBP1-OE
- GSM8010109 Hmol1-2C_XBP1-OE_rep2 Hmol1-2C_XBP1-OE
- GSM8010110 Hmol1-2C_XBP1-OE_rep3 Hmol1-2C_XBP1-OE
- GSM8010111 Hmol1-3B_Ctrl_rep1 Hmol1-3B_Ctrl
- GSM8010112 Hmol1-3B_Ctrl_rep2 Hmol1-3B_Ctrl
- GSM8010113 Hmol1-3B_Ctrl_rep3 Hmol1-3B_Ctrl
- GSM8010114 Hmol1-3B_XBP1-OE_rep1 Hmol1-3B_XBP1-OE
- GSM8010115 Hmol1-3B_XBP1-OE_rep2 Hmol1-3B_XBP1-OE
- GSM8010116 Hmol1-3B_XBP1-OE_rep3 Hmol1-3B_XBP1-OE
- GSE252907 Gene expression profiles of complete hydatidiform moles and XBP1-overexpressing cell lines associated with progression to gestational trophoblastic tumors 25 samples shares xbp1, overexpressing, hydatidiform, complete, lines
- GSE49955 Genome-wide maps of XBP1 binding sites in different breast cancer cell lines. 19 samples shares xbp1, lines
- GSE49952 Genome-wide maps of XBP1 binding sites in different breast cancer cell lines [ChIP-Seq] 11 samples shares xbp1, lines
- GSE316572 Transcriptome analysis of Galectin-1 (LGALS1) knockout and overexpressing human gastric carcinoma 7901 cell lines 6 samples shares overexpressing, lines
- GSE252906 The gene expression profiles of complete hydatidiform mole which developed post molar gestational trophoblast neoplasia 13 samples shares hydatidiform, complete
- GSE206364 The IRE1α/XBP1 pathway expression is impaired in pediatric cholestatic liver disease explants 34 samples shares xbp1
- GSE272102 Effect of Knockdown of PAXBP1 on gene expression of HaCaT keratinocytes 6 samples shares xbp1
- GSE309488 Cucurbitacin B induces immunogenic cell death in cutaneous melanoma via ROS-STAT3-(EIF2α-ATF4/IRE1-XBP1) pathway mediated endoplasmic reticulum stress 6 samples shares xbp1
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.