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Sample GSM3378768 Query DataSets for GSM3378768
Status Public on Nov 20, 2018
Title M2R
Sample type SRA
 
Source name Cell line, MC116
Organism Homo sapiens
Characteristics cell line: MC116
infection status: uninfected
rnase treatment: yes
infection type: uninfected
Treatment protocol Some conditions included KSHV infection. Some conditions included RNase R treatment of the purified RNA.
Growth protocol MC116 cells were grown in RPMI media. HUVEC cells were grown in EGM2 media.
Extracted molecule total RNA
Extraction protocol Total RNA (20 µg) was purified using miRNeasy System (Qiagen).
Total RNA samples were depleted of ribosomal RNA using RiboMinus Eukaryote System v2 (ThermoFisher). Ribo-depleted RNA was treated with 6 U of RNase R (Epicenter Biotechnologies) at 37° for 15 min. Libraries were generated using TruSeq Stranded Total RNA System (Illumina). Paired-end 150bp RNA-Seq sequencing reads (35.3 million reads per sample in average) were aligned with STAR version 2.4.2a (31) to a modified reference human genome of GRCh37, which included the complete genome sequence of KSHV, NC009333.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Ribominus RNA
Data processing Illumina RTA 1.18.64 software used for demultiplexing.
Illumina Bcl2fastq 1.8.4 software used for barcode demultiplexing by allowing 1 mismatch.
Paired-end reads were aligned to a modified reference human genome of GRCh37, which included the complete genome sequence of KSHV, NC009333, using two-pass alignment with chimeric alignment detection.
CIRCexplorer version 1.1.1 was used to detect circular RNA
Genome_build: GRCh37 plus KSHV genome sequence (NC009333)
Supplementary_files_format_and_content: tab-delimited text files include each circular RNA specification for each sample
 
Submission date Sep 06, 2018
Last update date Nov 22, 2018
Contact name Joseph M Ziegelbauer
Organization name NIH / National Cancer Institute
Street address 10 Center Dr. 6N110
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL16791
Series (1)
GSE119608 RNA sequencing with KSHV infection and enrichment for circular RNAs
Relations
BioSample SAMN09986337
SRA SRX4650548

Supplementary file Size Download File type/resource
GSM3378768_M2R_CIRCexplorer_circ_5.txt.gz 150.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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