LINE-1 transposable elements regulate the exit of human pluripotency and early brain development [snRNA-seq]
Single-nucleus RNA-seq · human · 19 samples
- What it is
- Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue).
- Organism
- Homo sapiens (human)
- Samples
- 19 samples: 15 distinct titles, 4 of them repeatedGroups 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.
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 GSE284086_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1196974 and SRA study SRP550918. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 19 sample titles: 15 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.
- GSM8677769 MN07_gRNA1_Rep1_snRNA_org_hiPS48_LV3824_L1_CRISPRi_d15_batch1
- GSM8677770 MN07_gRNA1_Rep1_snRNA_org_hiPS6_LV3824_L1_CRISPRi_d15_batch1
- GSM8677771 MN07_gRNA1_Rep1_snRNA_org_hiPS6_LV3824_L1_CRISPRi_d15_batch2
- GSM8677772 MN07_gRNA1_Rep2_snRNA_org_hiPS48_LV3824_L1_CRISPRi_d15_batch2
- GSM8677773 MN07_gRNA1_Rep2_snRNA_org_hiPS6_LV3824_L1_CRISPRi_d15_batch3
- GSM8677774 MN07_gRNA1_Rep2_snRNA_org_hiPS6_LV3824_L1_CRISPRi_d15_batch4
- GSM8677775 MN07_gRNA1_Rep3_snRNA_org_hiPS48_LV3824_L1_CRISPRi_d15_batch2
- GSM8677776 MN07_gRNA1_Rep3_snRNA_org_hiPS6_LV3824_L1_CRISPRi_d15_batch4
- GSM8677777 MN07_gRNA2_Rep1_snRNA_org_hiPS6_LV3822_L1_CRISPRi_d15_batch2
- GSM8677778 MN07_gRNA2_Rep2_snRNA_org_hiPS6_LV3822_L1_CRISPRi_d15_batch4
- GSM8677779 MN07_gRNA2_Rep3_snRNA_org_hiPS6_LV3822_L1_CRISPRi_d15_batch4
- GSM8677780 MN07_LacZ_Rep1_snRNA_org_hiPS48_LV3599_L1_CRISPRi_d15_batch1
- GSM8677781 MN07_LacZ_Rep1_snRNA_org_hiPS6_LV3599_L1_CRISPRi_d15_batch1
- GSM8677782 MN07_LacZ_Rep1_snRNA_org_hiPS6_LV3599_L1_CRISPRi_d15_batch2
- GSM8677783 MN07_LacZ_Rep2_snRNA_org_hiPS48_LV3599_L1_CRISPRi_d15_batch2
- GSM8677784 MN07_LacZ_Rep2_snRNA_org_hiPS6_LV3599_L1_CRISPRi_d15_batch3
- GSM8677785 MN07_LacZ_Rep2_snRNA_org_hiPS6_LV3599_L1_CRISPRi_d15_batch4
- GSM8677786 MN07_LacZ_Rep3_snRNA_org_hiPS48_LV3599_L1_CRISPRi_d15_batch2
- GSM8677787 MN07_LacZ_Rep3_snRNA_org_hiPS6_LV3599_L1_CRISPRi_d15_batch4
- GSE283597 LINE-1 transposable elements regulate the exit of human pluripotency and early brain development [bulkRNA-seq] 45 samples shares line-1, transposable, pluripotency, elements, regulate, early, brain
- GSE283600 LINE-1 transposable elements regulate the exit of human pluripotency and early brain development 83 samples shares line-1, transposable, pluripotency, elements, regulate, early, brain
- GSE261306 Early Prediction of Preeclampsia Based on Transposable Elements Deregulation in the Placenta [RNA-Seq] 30 samples shares transposable, elements, early
- GSE274217 METTL3-dependent m6A RNA methylation represses transposable elements derived enhancers to suppress naïve pluripotency in human pluripotent stem cells [RNA-Seq] 28 samples shares transposable, pluripotency, elements
- GSE275738 METTL3-dependent m6A RNA methylation represses transposable elements derived enhancers to suppress naïve pluripotency in human pluripotent stem cells 72 samples shares transposable, pluripotency, elements
- GSE275737 METTL3-dependent m6A RNA methylation represses transposable elements derived enhancers to suppress naïve pluripotency in human pluripotent stem cells [ChIP-Seq] 21 samples shares transposable, pluripotency, elements
- GSE254242 Cancer cell type-specific derepression of transposable elements by inhibition of chromatin modifier enzymes [RNA-Seq] 99 samples shares transposable, elements
- GSE324453 Dissecting the cellular architecture of breast cancer brain metastases reveals prognostically distinct immune landscapes [snRNA-Seq] 28 samples shares snrna-seq, brain
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.