Cells treated with siRNA for ADAR1p110 - SRA

SRX24162060: Cells treated with siRNA for ADAR1p110
1 ILLUMINA (Illumina MiSeq) run: 59,127 spots, 20.9M bases, 10.5Mb 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

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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: siADAR1-rep3-G

SAMN40757013 • SRS20942561 • All experiments • All runs

Organism: Chikungunya virus

Library:

Name: siADAR1-rep3-G

Instrument: Illumina MiSeq

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: PolyA

Layout: PAIRED

Runs: 1 run, 59,127 spots, 20.9M bases, 10.5Mb

Run	# of Spots	# of Bases	Size	Published
SRR28562814	59,127	20.9M	10.5Mb	2025-01-22

ID:: 32472966

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