|
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 |