|
| Status |
Public on Feb 13, 2018 |
| Title |
Lats12_tumor_GFP2 |
| Sample type |
SRA |
| |
|
| Source name |
nerve tumor-FACS GFP cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: paraspinal tumors
developmental stage: Adult
genotype: Lats1fl/fl;Lats2fl/+;CcGFPfl/+;Dhh-Cre
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Dhh+ Schwann cell lineage-derived GFP+ cell populations from 3-4-month-old control:ccGFP SNs and Lats1/2-mutant:ccGFP paraspinal tumors were sorted by fluorescence activated cell sorting (FACS). RNA of GFP+ cells were extracted using TRIZOL (Life Technologies) followed by purification using a Direct-zol RNA MicroPrep Kit (Zymo Research).
RNA-seq libraries were prepared using Illumina RNA-Seq Preparation Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Reads mapped to mm10 whole genome by Tophat with default options
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file.
genome build: mm10
processed data files format and content: format:fpkm_traking; Contain the estimated expression values produced by Cufflinks.
|
| |
|
| Submission date |
May 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard Lu |
| Organization name |
Cincinnati Children's Hospital Medical Center
|
| Department |
CBDI
|
| Lab |
Lu Lab,T6.525
|
| Street address |
3333 Burnet Ave
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE99040 |
Reprogramming of Schwann Cells by LATS1/2-TAZ/YAP Signaling Drives Malignant Peripheral Nerve Sheath Tumorigenesis |
|
| Relations |
| BioSample |
SAMN07138918 |
| SRA |
SRX2832610 |
