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SRX19003517: GSM6928213: L31425_K562_endogenous_RNA_Dex_replicate4; Homo sapiens; RNA-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 22.2M spots, 4.5G bases, 1.3Gb downloads

External Id: GSM6928213_r1
Submitted by: Jenny Tung, Evolutionary Anthropology, Duke University
Study: DNA methylation-environment interactions in the human genome
show Abstracthide Abstract
This project uses the massively parallel reporter assay, mSTARR-seq (Lea et al., 2018) to simultaneously test for both enhancer-like activity and DNA methylation-dependent enhancer activity across nearly the entire human genome. We assessed enhancer activity at almost all CpG sites profiled either on the commonly used Illumina Infinium MethylationEPIC array or via reduced representation bisulfite sequencing. Experiments were performed in K562 and HepG2 cells. Overall design: In this data set, 6 replicate flasks of K562 cells were treated for 6 hours with each of the following treatments: dexamethasone (1 uM), IFNA2b (2,000U/ml), or vehicle control (media). Cells were then collected for mRNA-Seq to assess the endogenous gene expression response of K562 cells to treatment.
Sample: L31425_K562_endogenous_RNA_Dex_replicate4
SAMN32677784 • SRS16423430 • All experiments • All runs
Organism: Homo sapiens
Library:
Name: GSM6928213
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: We extracted RNA from the separately aliquoted cells using the Qiagen RNEasy kit. We prepared RNA-Seq libraries using the NEBNext Ultra II RNA Library Prep Kit for Illumina.
Runs: 1 run, 22.2M spots, 4.5G bases, 1.3Gb
Run# of Spots# of BasesSizePublished
SRR2305004822,182,6284.5G1.3Gb2023-09-07

ID:
26153185

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