|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Jan 01, 2019 |
Title |
mouse8 |
Sample type |
SRA |
|
|
Source name |
lung tissue
|
Organism |
Mus musculus |
Characteristics |
strain: C3H/HeN infection: R. conorii 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 |
State/province |
TX |
ZIP/Postal code |
77555 |
Country |
USA |
|
|
Platform ID |
GPL18480 |
Series (1) |
GSE121808 |
Enhancer associated long non-coding RNA transcription and immune gene regulation in experimental models of rickettsial infection |
|
Relations |
BioSample |
SAMN10311421 |
SRA |
SRX4938168 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
|