|
| Status |
Public on Oct 17, 2017 |
| Title |
SJMMMB018134 |
| Sample type |
SRA |
| |
|
| Source name |
control G3 MB tumorspheres # 19568
|
| Organism |
Mus musculus |
| Characteristics |
cell description: Mouse MB cells
treatment: none
|
| Treatment protocol |
Tumorspheres were dissociated and infected six times over a 2-day period in virus collection media supplemented with N2, B27, EGF and FGF containing lentiviral particles encoding empty vector (pCDH-EF1-MCS-T2A-copGFP) or WDR11 (pCDH-EF1-WDR11-T2A-copGFP. The following day, infected tumorspheres were suspended in Matrigel (BD Bioscience, San Jose) at a concentration of 100,000 tumorspheres/5µl Matrigel and transplanted into the cortices of CD1-nu/nu mice, as described previously [19, 49]. When mice became moribund, tumors were isolated and tumor chunks flash frozen and stored at -80 degrees Celsius.
|
| Growth protocol |
G3 MB tumorspheres # 19568 were derived from tumors that developed in CD1nu/nu mice implanted with cerebellar granule neuronal progenitors transduced with MSCV retroviruses expressing Myc and the green fluorescent protein (GFP) from an internal ribosomal entry site (IRES) (Myc-IRES-GFP) as previously described (Kawauchi et al, 2012). Briefly, spheres were grown in grown in N2, B27, EGF and FGF supplemented neurobasal medium (“complete tumorsphere medium”).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted from tumor chunks using Trizol according to manufacturer’s instruction, and as previously published (Murphy et al., 2013).
Libraries were prepared from ~500 ng total RNA with the TruSeq RNA Library Preparation Kit v2 according to manufacturer’s instructions (Illumina, San Diego CA)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
SJMMMB018134
|
| Data processing |
Basecalling was performed using Illumina Casava 1.7
FASTQ sequences adapter trimmed (curtadapt) and mapped to the mouse mm9 genome by a pipeline that serially employs STAR and BWA
Mapped reads were counted with HTSEQ
Genome_build: mm9
Supplementary_files_format_and_content: count files are txt format files that contain raw read counts that map to transcripts for each defined gene.
|
| |
|
| Submission date |
Jul 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Lei Wei |
| E-mail(s) |
lei.wei@roswellpark.rog
|
| Phone |
7168451176
|
| Organization name |
Roswell Park Cancer Institute
|
| Department |
Biostatistics & Bioinformatics
|
| Street address |
Elm & Carlton Streets
|
| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14263 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE101767 |
Exome sequencing analysis of murine medulloblastoma models identifies Wdr11 as a potential tumor suppressor in Group 3 tumors |
|
| Relations |
| BioSample |
SAMN07376334 |
| SRA |
SRX3028090 |
