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SRX7051001: GSM4138089: Primary Schwann Cell cAMP 3; Rattus norvegicus; RNA-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 84.5M spots, 25.5G bases, 8.1Gb downloads

Submitted by: NCBI (GEO)
Study: Schwann Cell Tn5Prime
show Abstracthide Abstract
Here we provide sequencing data derived from our efforts to identify SOX10-regulated promoters in Schwann cells genome-wide. We assess the activity of SOX10-bound promoters using Tn5Prime to identify and quantify transcription start sites in adult peripheral nerve, in differentiating primary Schwann cells, and upon ablation of SOX10 in vitro. Tn5Prime libraries were prepared essentially as described by Cole and colleagues (NAR, 2018). Analyses focused on transcription start sites associated with H3K4me3 and SOX10 ChIP-Seq peaks from sciatic nerve (ChIP-Seq data derived from previously published datasets). Overall design: Samples include two libraries derived from independent adult rat sciatic nerves (age 6-9 months), three libraries each from control- and CPT-cAMP-treated rat primary Schwann cells, two libraries from unmodified immortalized rat myelinating Schwann (S16) cells, and four libraries each derived from independent clonal ?SOX10 S16 cell lines. Each library was prepared from an independent RNA isolation.
Sample: Primary Schwann Cell cAMP 3
SAMN13107900 • SRS5567861 • All experiments • All runs
Library:
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: Total RNA was isolated using the Qiagen Rneasy Mini Kit (Catalog Number 74104) with on-column Dnase treatment (Catalog Number 79254) according to manufacturer protocol. Tn5Prime libraries were constructed essentially as described by Cole and colleagues (NAR, 2018). Briefly, RNA was reverse-transcribed by SMARTScribe RT in the presence of an oligo-dT primer and template-switching oligo. The reaction was treated with RNase and Exonuclease. The resulting DNA was subjected to an indexing PCR, tagmentation by purified Tn5 enzyme pre-loaded with Tn5ME-B/R adapters, and another round of PCR. Size selection to 400-1000bp was performed on a 0.8% low-melt agarose TAE gel. DNA was purified using the Qiagen Gel Extraction Kit (Catalog Number 28704). Libraries were sequenced on Illumina HiSeq or NovaSeq sequencers. Read 1 (corresponding to 5' end of mRNAs) was used for subsequent analyses.
Experiment attributes:
GEO Accession: GSM4138089
Links:
Runs: 1 run, 84.5M spots, 25.5G bases, 8.1Gb
Run# of Spots# of BasesSizePublished
SRR1034093784,492,19225.5G8.1Gb2020-07-20

ID:
9270033

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