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Sample GSM3446998

Query DataSets for GSM3446998

Status

Public on Jan 01, 2019

Title

mouse3

Sample type

SRA

Source name

lung tissue

Organism

Mus musculus

Characteristics

strain: C3H/HeN
infection: uninfected control
tissue: lung

Extracted molecule

total RNA

Extraction protocol

Total RNA from lung tissues was extracted using TRIzol reagent according to the manufacturer’s instructions (Invitrogen).
RNA samples were subjected to treatment with DNaseI (NEB) to remove any contaminating DNA and then enriched with Ribo-Zero rRNA Removal kit (Illumina). Concentration of RNA in sample preparations using the MultiSkan Go UV/Vis instrument for microsample analysis (Thermo Scientific) and the quality of RNA was evaluated on a bioanalyzer (Agilent Technologies). The samples with an RNA integrity number (RIN) of >9 were subjected to RNA-sequencing (Chowdhury et al., 2017). Briefly, RNA fragments of 50 bases were generated by incubating purified total RNA in a fragmentation buffer (Ambion) and fragmented RNA was then 140 ligated with 5′ and 3′-adaptors using a T4 RNA ligase (NEB). Adaptor-ligated RNAs were reverse transcribed and subjected to PCR amplification with barcoded primers (Illumina) (Narra et al., 2016; Schroeder et al., 2016). Finally, amplified cDNA libraries were purified using standard gel purification procedures.
RNA sequencing was performed on an Illumina HiSeq 1500 equipment at the Next Generation Sequencing Core facility at the UTMB. Briefly, 50 base long reads were obtained from the RNA derived from the lungs of R. conorii-infected and uninfected control (n=3 for each) mice.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 1500

Data processing

Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed by 14 bases from the 5' end, reads containing nucleotides with a phred quality score below 15 were removed.
CLC Genomics Workbench 9.0.1 RNA Seq Analysis tool was used to map all of the reads to the Noncode v4 lncRNA allowing up to 2 mismatches
Genome_build: mm9
Supplementary_files_format_and_content: Excel file with read counts and coverage for each lncRNA from Noncode v4

Submission date

Oct 25, 2018

Last update date

Jan 01, 2019

Contact name

Kamil Khanipov

Organization name

University of Texas Medical Branch

Street address

301 University Blvd

City

GALVESTON