|
| Status |
Public on Jan 08, 2020 |
| Title |
Tumor GNP cell 5980_cul |
| Sample type |
SRA |
| |
|
| Source name |
5980 Cul
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Tumor GNP cell
strain: C57BL/7
rna extraction methods: Laser capture microdissection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The laser capture microdissection (LCM) experiment was designed and modified according to previous studies (Janes et al., 2010; Wang and Janes, 2013). Briefly, tumor brains were removed and slowly lowered into liquid nitrogen-cooled methyl-butane. Keep fully submerged for 1 minute then store at -80ºC. Tumor tissue was cut at 8 μm thickness on a cryostat and sections were collected on positively-charged slides. Slides were fixed in 100% ethanol for 5 minutes at room temperature and then transferred into 100% xylene for 5 minutes at room temperature. Slide was then air-dried for 5 minutes. Laser capture microdissection of individual cells was performed on an ArcturusXT LCM system (Applied Biosystems) with an infrared laser using CapSure HS LCM caps after optimization of laser power and duration.
Reamplified cDNA (~500 bp 3’ ends) was tagmented with the Nextera XT kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Adaptor Trimming by bioconductor
Initial quality assessment of sequencing reads using FastQC
Genome alignment with STAR
Genome_build: mm10
Supplementary_files_format_and_content: counts
|
| |
|
| Submission date |
Mar 12, 2018 |
| Last update date |
Jan 08, 2020 |
| Contact name |
Kevin A. Janes |
| E-mail(s) |
kjanes@virginia.edu
|
| Organization name |
University of Virginia
|
| Department |
Department of Biomedical Engineering
|
| Street address |
Box 800759 Health System
|
| City |
Charlottesville |
| State/province |
VA |
| ZIP/Postal code |
22908 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE111734 |
Astrocytic trans-differentiation completes a multicellular paracrine feedback loop required for medulloblastoma tumor growth |
|
| Relations |
| BioSample |
SAMN08688557 |
| SRA |
SRX3783274 |
