NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4079641 Query DataSets for GSM4079641
Status Public on Jul 29, 2020
Title IFNg_1
Sample type SRA
 
Source name Brain
Organism Homo sapiens
Characteristics cell type: GBM patient-derived cells
passages: 3 to 6
tissue: glioblastoma
treatment: interferon gamma
Extracted molecule total RNA
Extraction protocol RNA was harvested from cells using RNeasy Mini Kit (Qiagen Cat#74104). Illumina RiboZero was used with 1 ug of total RNA and sequencing libraries were constructed using NEBNext Ultra II RNA library Prep Kit for Illumina (Cat#E7770)
RNA libraries were prepared for sequencing using standard NEB protocols
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 4000
 
Data processing Raw reads were examined for quality issues using FastQC.
Trimmed reads were aligned to UCSC build 38 of the human genome (hg38), augmented with transcript information from Ensembl release GRCh38 using STAR, where adapter sequences and other contaminating sequences with low PHRED quality scores were trimmed.
Count of reads aligning known genes was generated by HT-Seq. Differential expression at the gene level was calculated with DESeq.
Genome_build: hg38
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
E-mail(s) mmineo@bwh.harvard.edu
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 GPL20301
Series (2)
GSE137453 Long noncoding RNA expression profiles analysis in GBM patient-derived cells stimulated with interferon gamma
GSE137489 Long noncoding RNA INCA1 regulates tumor interferon signaling.
Relations
BioSample SAMN12752299
SRA SRX6850548

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap