In Vitro transcription - SRA

Links from BioSample

SRX24162074: In Vitro transcription
1 ILLUMINA (Illumina MiSeq) run: 40,875 spots, 14.2M bases, 7.6Mb downloads

Design: Total RNA was extracted using TRIzol (Thermo Fisher) according to the suppliers protocol and TURBO DNA-free Kit (Thermo Fisher) was used to remove any contaminating DNA from RNA samples. Isolated RNA was further purified by ethanol precipitation and 30-40 g of total RNA were subjected to poly(A)-selection with the use of Dynabeads Oligo (dT)25 (Thermo Fisher) according to the manufacturers instructions. Poly(A)+ RNA samples were concentrated before LC-MS/MS analysis with the use of an RNA clean & concentrator kit (Zymo Research). For isolation of gRNA and sgRNA, poly(A)+ RNA was first passed through an RNA clean & concentrator kit (Zymo Research) and then at least 5 g of poly(A)+ RNA wasere separated in a native 1% (w/v) agarose gel (containing ethidium bromide) which was prepared and ran in 1x tris-acetate-EDTA (TAE) buffer. gRNA and sgRNA bands were then gel-extracted with the Zymoclean gel RNA recovery kit (Zymo Research) following the manufacturers instructions.

Submitted by: University of Padova

Study: RNA seq data of HEK293T cells infected with Chikungunya virus

PRJNA1096462 • SRP499890 • All experiments • All runs

show Abstracthide Abstract

Cytoplasmically-replicating positive-sense (+) single-stranded RNA (ssRNA) viruses are believed to be subjected to a wide range of RNA modifications in their genomes. Here, we focused on one of such viruses, the mosquito-transmitted chikungunya virus (CHIKV), as a model virus to study the landscape of viral RNA modifications in CHIKV-infected human embryonic kidney cells (HEK 293T). RNA-seq analysis at base-resolution showed that the CHIKV RNA does not contain inosine modification at biological relevant levels, only after the overexpression of ADAR1 was possible to trace putative RNA editing sites along the viral genome.

Sample: CHIKV-rep3

SAMN40757008 • SRS20942575 • All experiments • All runs

Organism: Chikungunya virus

Library:

Name: CHIKV-rep3

Instrument: Illumina MiSeq

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: PolyA

Layout: PAIRED

Runs: 1 run, 40,875 spots, 14.2M bases, 7.6Mb

Run	# of Spots	# of Bases	Size	Published
SRR28562800	40,875	14.2M	7.6Mb	2025-01-22

ID:: 32472980

SRA

Sequence Read Archive

Result Filters

Send to:

Links from BioSample

Supplemental Content

Related information

Recent activity