|
| Status |
Public on Jan 20, 2023 |
| Title |
Glioblastoma, high-functional connectivity, patient 11748 |
| Sample type |
SRA |
| |
|
| Source name |
glioblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: glioblastoma
functional connectivity: high
age: 29
Sex: M
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted from the glioblatoma samples using the Qiagen RNeasy Plus Universal Kit (CAT# 73404)
RNA libraries were prepared for sequencing using the Illumina TruSeq Stranded RNA Library Prep Kit v2 (CAT# RS-122-2001)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RED_11748
gbm_tpm.csv
|
| Data processing |
Standard Illumina software was used for basecalling
Sequenced reads were trimmed using Trimmomatic, then mapped to hg38 transcriptome using HISAT2 2.1.0
Exon level count data were extracted from the mapped reads using featureCounts
Transcripts per million (TPM) were calculated from the count data
Assembly: hg38
Supplementary files format and content: Matrix table with TPMs for every gene and every sample
|
| |
|
| Submission date |
Jan 17, 2023 |
| Last update date |
Jan 20, 2023 |
| Contact name |
Abrar Choudhury |
| Organization name |
University of California, San Francisco
|
| Street address |
1450 3rd St
|
| City |
San Francisco |
| State/province |
California |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE223064 |
Bulk RNA sequencing of high- and low-functional connectivity glioblastomas |
| GSE223065 |
Glioblastoma remodeling of neural circuits in the human brain decreases survival |
|
| Relations |
| BioSample |
SAMN32769898 |
| SRA |
SRX19052024 |
