LINE-1 transposable elements regulate the exit of human pluripotency and early brain development
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 83 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Homo sapiens (human)
- Samples
- 83 samples: 70 distinct titles, 13 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.
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 GSE283600_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1194596 and SRA study SRP549633. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 83 sample titles: 70 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.
- GSM8667515 MN07_LacZ_Rep1_bulkRNA_hiPS6_LV3599_L1_CRISPRi_batch1
- GSM8667516 MN07_LacZ_Rep2_bulkRNA_hiPS6_LV3599_L1_CRISPRi_batch1
- GSM8667517 MN07_LacZ_Rep3_bulkRNA_hiPS6_LV3599_L1_CRISPRi_batch1
- GSM8667518 MN07_gRNA1_Rep1_bulkRNA_hiPS6_LV3824_L1_CRISPRi_batch1
- GSM8667519 MN07_gRNA1_Rep2_bulkRNA_hiPS6_LV3824_L1_CRISPRi_batch1
- GSM8667520 MN07_gRNA1_Rep3_bulkRNA_hiPS6_LV3824_L1_CRISPRi_batch1
- GSM8667521 MN07_gRNA1_Rep1_bulkRNA_hiPS48_LV3824_L1_CRISPRi_batch2
- GSM8667522 MN07_gRNA1_Rep2_bulkRNA_hiPS48_LV3824_L1_CRISPRi_batch2
- GSM8667523 MN07_gRNA1_Rep3_bulkRNA_hiPS48_LV3824_L1_CRISPRi_batch2
- GSM8667524 MN07_LacZ_Rep1_bulkRNA_hiPS48_LV3599_L1_CRISPRi_batch2
- GSM8667525 MN07_LacZ_Rep2_bulkRNA_hiPS48_LV3599_L1_CRISPRi_batch2
- GSM8667526 MN07_LacZ_Rep3_bulkRNA_hiPS48_LV3599_L1_CRISPRi_batch2
- GSM8667527 MN07_gRNA2_Rep1_bulkRNA_hiPS6_LV3822_L1_CRISPRi_batch3
- GSM8667528 MN07_gRNA2_Rep2_bulkRNA_hiPS6_LV3822_L1_CRISPRi_batch3
- GSM8667529 MN07_gRNA2_Rep3_bulkRNA_hiPS6_LV3822_L1_CRISPRi_batch3
- GSM8667530 MN07_LacZ_Rep1_bulkRNA_hiPS6_LV3599_L1_CRISPRi_batch3
- GSM8667531 MN07_LacZ_Rep2_bulkRNA_hiPS6_LV3599_L1_CRISPRi_batch3
- GSM8667532 MN07_LacZ_Rep3_bulkRNA_hiPS6_LV3599_L1_CRISPRi_batch3
- GSM8667533 MN07_LacZ_Rep1_bulkRNA_org_hiPS48_LV3599_L1_CRISPRi_d15_batch4
- GSM8667534 MN07_LacZ_Rep2_bulkRNA_org_hiPS48_LV3599_L1_CRISPRi_d15_batch4
- GSM8667535 MN07_LacZ_Rep3_bulkRNA_org_hiPS48_LV3599_L1_CRISPRi_d15_batch4
- GSM8667536 MN07_gRNA1_Rep1_bulkRNA_org_hiPS48_LV3824_L1_CRISPRi_d15_batch4
- GSM8667537 MN07_gRNA1_Rep2_bulkRNA_org_hiPS48_LV3824_L1_CRISPRi_d15_batch4
- GSM8667538 MN07_gRNA1_Rep3_bulkRNA_org_hiPS48_LV3824_L1_CRISPRi_d15_batch4
- GSM8667539 MN07_WT_Rep1_bulkRNA_hiPS48_batch5
- GSM8667540 MN07_WT_Rep1_bulkRNA_hiPS6_batch5
- GSM8667541 MN07_WT_Rep2_bulkRNA_hiPS6_batch5
- GSM8667542 MN07_WT_Rep3_bulkRNA_hiPS6_batch5
- GSM8667543 MN07_WT_Rep2_bulkRNA_hiPS48_batch5
- GSM8667544 MN07_WT_Rep3_bulkRNA_hiPS48_batch5
- GSM8667545 MN07_gRNA1_Rep1_bulkRNA_org_hiPS6_LV3824_L1_CRISPRi_d15_batch6
- GSM8667546 MN07_gRNA1_Rep2_bulkRNA_org_hiPS6_LV3824_L1_CRISPRi_d15_batch6
- GSM8667547 MN07_gRNA1_Rep3_bulkRNA_org_hiPS6_LV3824_L1_CRISPRi_d15_batch6
- GSM8667548 MN07_LacZ_Rep1_bulkRNA_org_hiPS6_LV3599_L1_CRISPRi_d15_batch6
- GSM8667549 MN07_LacZ_Rep2_bulkRNA_org_hiPS6_LV3599_L1_CRISPRi_d15_batch6
- GSM8667550 MN07_LacZ_Rep3_bulkRNA_org_hiPS6_LV3599_L1_CRISPRi_d15_batch6
- GSM8667551 MN07_LacZ_Rep1_bulkRNA_org_hiPS6_LV3599_L1_CRISPRi_d15_batch7
- GSM8667552 MN07_LacZ_Rep2_bulkRNA_org_hiPS6_LV3599_L1_CRISPRi_d15_batch7
- GSM8667553 MN07_LacZ_Rep3_bulkRNA_org_hiPS6_LV3599_L1_CRISPRi_d15_batch7
- GSM8667554 MN07_gRNA2_Rep1_bulkRNA_org_hiPS6_LV3822_L1_CRISPRi_d15_batch7
+ 43 more — browse all 83 samples with per-sample file links →
- 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, exit
- GSE284086 LINE-1 transposable elements regulate the exit of human pluripotency and early brain development [snRNA-seq] 19 samples shares line-1, transposable, pluripotency, elements, regulate, early, brain, exit
- 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
- 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
- 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
- GSE234237 Transposable Elements Shape Stemness in Normal and Leukemic Hematopoiesis 215 samples shares transposable, elements
- GSE270454 Epigenetic dysregulation of transposable elements in cognitive impairment and Alzheimer’s disease 135 samples shares transposable, elements
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.