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Sample GSM3059545 Query DataSets for GSM3059545
Status Public on Apr 26, 2019
Title A549 BoRed-Seq Ctrl Rep 1
Sample type SRA
 
Source name A549 human lung adenocarcinoma cell line
Organism Homo sapiens
Characteristics cell line: A549
sample type: Control (non-reduced) RNA
Treatment protocol Total RNA, including miRNAs, was extracted from mammalian cells. m7G residues were specifically reduced by treatment with NaBH4 in the presence of high concentrations of free m7GTP. Control samples were treated with acid-quenched NaBH4. The reduced m7G residues were subjected to nucleoside hydrolysis at low pH. A biotin-coupled aldehyde reactive probe (ARP) was covalently bound to the abasic RNA sites resulting from m7G reduction and hydrolysis, allowing pull-down with streptavidin-conjugated beads.
Growth protocol A549 cells were cultured in DMEM (Invitrogen), supplemented with 10% FBS and 1% penicillin/streptomycin/glutamine.
Extracted molecule total RNA
Extraction protocol Cells were lysed in Qiazol (Qiagen) and total RNA was purified using the miRNAeasy mini kit (Qiagen)
Libraries were prepared using the NEBNext SmallRNA kit (NEB) according to the manufacturer’s recommendations
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 1500
 
Description profiling strategy:
BoRed-Seq
TK_LP_A549_BoRed-Seq_RAW_miRNA_counts.txt
Data processing Library strategy: BoRed-Seq
Raw sequencing .bcl files were demultiplexed in FASTQ format using Illumina Basespace
Library adaptors were trimmed with Trimmomatic
Reads were mapped to the human genome with Bowtie2
Reads were summarized using featureCounts according to miRbase21 annotation
Genome_build: NCBI GRCh38/hg38
Supplementary_files_format_and_content: Raw miRNA counts in tab-separated value file
 
Submission date Mar 21, 2018
Last update date Apr 26, 2019
Contact name Luca Pandolfini
E-mail(s) luca.pandolfini@iit.it
Organization name Istituto Italiano di Tecnologia - I
Department Center for Human Technologies
Street address Via Enrico Melen 83, Building B
City Genova
State/province Genova
ZIP/Postal code 16152
Country Italy
 
Platform ID GPL18460
Series (2)
GSE112181 m7G methylation by METTL1 regulates let-7 microRNAs [BoRed-Seq & m7G-RIP-Seq A549]
GSE112182 m7G methylation by METTL1 regulates let-7 microRNAs
Relations
BioSample SAMN08769850
SRA SRX3829848

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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