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SRX3471678: GSM2889337: shHdac6.rep2; Mus musculus; RNA-Seq
1 ILLUMINA (Illumina HiSeq 3000) run: 47.3M spots, 14G bases, 5.2Gb downloads

Submitted by: NCBI (GEO)
Study: Epigenetic control of genes and transposable elements [Knockdown RNA-seq]
show Abstracthide Abstract
Epigenetic control is an elaborate system the cell uses to control aspects of cell type and gene control. Histones and DNA are chemically modified to signal epigenetic information as to whether a gene is active or inactive, and so maintain cell type stability. Whilst epigenetic control of genes has been explored, the control of the rest of the genome is less well explored. The bulk of DNA and chromatin consists of repetitive elements, not genes, and these TEs must be tightly regulated to provide structure and function for nearby genes and, ultimately, cell type control. In this project we explore the intereaction of epigenetic control factors, and inhibitors, and how perturbation of the epigenetic control system disrupts TE regulation inside embryonic stem cells. Overall design: We analyzed the transcriptome expression profiles(RNA-seq) and chromation accessibility(ATAC-seq) upon specific epigenetic perturbation
Sample: shHdac6.rep2
SAMN08177848 • SRS2758325 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina HiSeq 3000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: VAHTS mRNA-seq V2 Library Prep Kit for Illumina was used according to the manufacturer's instruction. Briefly, 1ug total RNA was used and mRNA was enriched using olig-dT dynabeads, followed by fragmentation by divalent cation at elevated temperature. First-strand cDNA synthesis by random hexamers and reverse transcriptase was followed by the second-strand cDNA synthesis. Then the reverse product was purified using AMPure XP beads. The cDNA was end repaired and a dA was added, followed by ligation, two round purification using AMPure XP beads, PCR amplification and PCR product purification. The library was quantified with an Invitrogen Qubit.
Experiment attributes:
GEO Accession: GSM2889337
Links:
Runs: 1 run, 47.3M spots, 14G bases, 5.2Gb
Run# of Spots# of BasesSizePublished
SRR637688547,304,08114G5.2Gb2018-12-13

ID:
4833242

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