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Sample GSM4079652 Query DataSets for GSM4079652
Status Public on Jul 29, 2020
Title shINCA1-C3
Sample type SRA
Source name Brain
Organism Homo sapiens
Characteristics genotype/variation: shRNA targeting INCA1
treatment: control
cell line: U251
passages: 14-18
cell type: MG Glioblastoma Cell Line
Extracted molecule total RNA
Extraction protocol 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
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing 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.
Genome_build: hg19
Supplementary_files_format_and_content: text files include read count for each Sample
Submission date Sep 15, 2019
Last update date Jul 29, 2020
Contact name Marco Mineo
Phone 6175255656
Organization name Brigham and Women's Hospital
Street address 60 Fenwood Rd, BTM 8012
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
Platform ID GPL24676
Series (2)
GSE137454 Long noncoding RNA INCA1 regulates tumor interferon signaling
GSE137489 Long noncoding RNA INCA1 regulates tumor interferon signaling.
BioSample SAMN12752306
SRA SRX6850559

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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