|
| Status |
Public on Mar 13, 2019 |
| Title |
EGFRvIII driven glioma; biological rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Cell explanted from EGFRvIII driven glioma and sorted by FACS for DsRed Expression
|
| Organism |
Mus musculus |
| Characteristics |
strain: Balb/c
genotype: Ink/Arf -/-
|
| Growth protocol |
Embryonic neural precursors were obtained from Balb/c or Ink/Arf -/- Balb/c mouse embryos at day 14. Cells were plated at a density of 3.6e5 cells per cm^2 onto Matrigel-coated 24-well plates in DMEM-F12 added with B27 supplement, human bFGF and EGF (10 ng/ml). Immediately after plating, Balb/c cells were transduced with retroviral vectors encoding PDGF-B and DsRed; Ink/Arf -/- Balb/c cells were transduced with retroviral vectors encoding EGFRvIII and DsRed. After 10 days, 2e4 transduced cells were intracranially inoculated in adult BALB/c mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At the apparence of first neurogical symptoms, brain tumors were removed, microdissected and sorted by FACS by using teh fluorescent reported DsRed. RNA was harvested using Trizol reagent. Samples were sent to BGI (Hong Kong) for sequencing on BGISEQ-500 platform.
Library were prepared by BGI (Hong Kong) Oligo (dT) magnetic beads are used to selectmRNA with polyA tail, or hybridize the rRNA with DNA probe and digest the DNA/RNA hybrid strand, followed by DNase I reaction to remove DNA probe. Then obtain the targetRNA after purification. 2) Fragmentthe targetRNA and reverse transcription to double-strand cDNA (dscDNA) by N6 randomprimer. 3) End repair the dscDNA with phosphate at5' end and stickiness 'A' at3' end, then ligate and adaptor with stickiness 'T' at 3' end to the dscDNA. 4) Two specific primers are used to amplify the ligation product. 5) Denature the PCR productby heatand the single strand DNA is cyclized by splintoligo and DNA ligase
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
The sequence reads passed quality filters and were analyzed at gene level with the following methods:
STAR for the alignment;
Rsem for generating read counts;
edgeR for normalization.
genome build: mm10
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million values for each sample, generated by edgeR
|
| |
|
| Submission date |
Jan 25, 2018 |
| Last update date |
Mar 14, 2019 |
| Contact name |
Paolo Malatesta |
| E-mail(s) |
paolo.malatesta@unige.it
|
| Phone |
+390105558403
|
| Organization name |
IRCCS Ospedale Policlinico San Martino
|
| Street address |
Largo Rosanna Benzi 10
|
| City |
Genoa |
| ZIP/Postal code |
16132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE109614 |
RNAseq of murine models of high-grade gliomas induced by overexpression of PDGF-B or EGFRvIII |
|
| Relations |
| BioSample |
SAMN08394894 |
| SRA |
SRX3599149 |
