|
| Status |
Public on Jul 29, 2020 |
| Title |
Control_3 |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: GBM patient-derived cells
passages: 3 to 6
tissue: glioblastoma
treatment: control
|
| 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 |
SAMN12752300 |
| SRA |
SRX6850547 |
