LINE-1 retrotransposons are reduced in bone of osteoporotic patients, correlate positively to BMD, and stimulate bone anabolism in transfected mesenchymal stem cells
RNA-seq (gene expression) · human · 16 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
- 16 samples: 8 conditions, mostly in duplicateGroups 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
- LINE-1 RNA triggers matrix formation in bone cells via a PKR-mediated inflammatory responseThe EMBO journal · 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 GSE201774_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 PRJNA832979 and SRA study SRP372672. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 8 replicated groups read from 16 sample titles; they account for 16 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.
- GSM6071112 9RFP, d6 9RFP, d
- GSM6071113 9L1, d6 9L1, d
- GSM6071114 12RFP, d6 12RFP, d
- GSM6071115 12L1, d6 12L1, d
- GSM6071116 16RFP, d6 16RFP, d
- GSM6071117 16L1, d6 16L1, d
- GSM6071118 19RFP, d6 19RFP, d
- GSM6071119 19L1, d6 19L1, d
- GSM6071120 9RFP, d10 9RFP, d
- GSM6071121 9L1, d10 9L1, d
- GSM6071122 12RFP, d10 12RFP, d
- GSM6071123 12L1, d10 12L1, d
- GSM6071124 16RFP, d10 16RFP, d
- GSM6071125 16L1, d10 16L1, d
- GSM6071126 19RFP, d10 19RFP, d
- GSM6071127 19L1, d10 19L1, d
- GSE269105 Investigation of Chimeric Transcripts Derived from LINE-1 and Alu Retrotransposons in Cerebellar Tissues of Individuals with Autism Spectrum Disorder (ASD) 13 samples shares line-1, retrotransposons
- GSE296212 LINE-1 locus transcription nucleates oncogenic chromatin architecture [RNA-Seq] 80 samples shares line-1
- GSE283597 LINE-1 transposable elements regulate the exit of human pluripotency and early brain development [bulkRNA-seq] 45 samples shares line-1
- GSE287105 LINE-1 ORF1p immune evasion mechanisms in pancreatic ductal adenocarcinoma 24 samples shares line-1
- GSE284086 LINE-1 transposable elements regulate the exit of human pluripotency and early brain development [snRNA-seq] 19 samples shares line-1
- GSE293846 Identification of known and novel long non-coding RNAs potentially responsible for the effects of BMD GWAS loci [hFOB RNA-seq] 18 samples shares bmd
- GSE313499 Identification of Novel Regulators of LINE-1 Expression via CRISPR/Cas9 Screening 12 samples shares line-1
- GSE273369 The oncogenic microRNA miR-222 promotes human LINE-1 retrotransposition 8 samples shares line-1
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.