|
| Status |
Public on Jan 01, 2021 |
| Title |
CCF 3255_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Meningioma tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue/sample type: Meningioma tissue
|
| Growth protocol |
First-passage arachnoid granulation cells were grown in DMEM supplemented with 7% FBS and 1% penicillin/streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted flash frozen, pulverized tissue using the miRNeasy mini kit (Qiagen, cat #217004) in accordance with the manufacturer protocols.
Libraries were prepared and sequenced by Genewiz. Stranded RNA library preparation was performed with ribosomal RNA depletion according to instructions from the manufacturer (Epicentre).
Paired-end sequencing was performed on the Illumina HiSeq 2500 with single-end read configuration.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
3255_S15
|
| Data processing |
Single-end reads were trimmed to 75 bp using BBDuk from the BBMap toolset to match the sample format from GSE101638.
Trim Galore was used to trim adaptors and remove low quality reads.
Reads were quantified against Gencode v29 using Salmon with correction for fragment-level GC bias, positional bias and sequence-specific biases.
Transcripts were summarized to gene level and processed to transcripts per million (TPM) using the R/Bioconductor package DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: meningioma_TPM.csv
|
| |
|
| Submission date |
Oct 31, 2019 |
| Last update date |
Jan 01, 2021 |
| Contact name |
Briana Prager |
| E-mail(s) |
briana.prager@gmail.com
|
| Organization name |
Cleveland Clinic
|
| Street address |
9500 Euclid Ave.
|
| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44195 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE139651 |
Enhancer landscape of meningioma [RNA-seq] |
| GSE139652 |
Enhancer landscape of meningioma |
|
| Relations |
| BioSample |
SAMN13168717 |
| SRA |
SRX7079242 |
