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|Public on Jul 29, 2020
|genotype/variation: shRNA control
treatment: interferon gamma
cell line: U251
cell type: MG Glioblastoma Cell Line
|RNA was harvested from cells using RNeasy Mini Kit (Qiagen Cat#74104). Illumina TruSeq stranded mRNA Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|Illumina NovaSeq 6000
|The quality of produced data is determined by the phred quality score at each cycle. Box plot containing the average quality at each cycle is created with FastQC.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data. Trimmed reads are mapped to reference genome hg19 with HISAT2
Known genes and transcripts are assembled with StringTie based on reference genome model. After assembly, the abundance of gene/transcript is calculated in the read count and normalized value as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) for a sample.
Supplementary_files_format_and_content: text files include read count for each Sample
|Sep 15, 2019
|Last update date
|Jul 29, 2020
|Brigham and Women's Hospital
|60 Fenwood Rd, BTM 8012
|Long noncoding RNA INCA1 regulates tumor interferon signaling
|Long noncoding RNA INCA1 regulates tumor interferon signaling.