|
| Status |
Public on Oct 15, 2017 |
| Title |
sgGFP, biological rep2 |
| Sample type |
SRA |
| |
|
| Source name |
SMB21 cell line
|
| Organism |
Mus musculus |
| Characteristics |
strain background: Ptch1tm1Mps/J (JAX003081)
age: Adult
cell line: SMB21
cell type: medulloblastoma cell line
genotype background: Ptch mutant
genotype/variation: CRISPR-GFP
|
| Treatment protocol |
Targeted knockout of Ofd1, or Kif3a was achieved using lentiCRISPR vector system. 2 weeks after viral infection, cells were collected for RNA extraction
|
| Growth protocol |
Cells were cultured as neurospheres at 37°C in a humidified incubator with 5% CO2 in DMEM/F12 media (2% B27, 1% Pen/Strep).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from cells using RNeasy Kit (Qiagen).
Libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on a single Illumina NextSeq500 run with single-end 75bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
CRISPR knockout
sgGFP_2
|
| Data processing |
Illumina software used for basecalling.
STAR aligner was used to map sequenced reads to the mm9 genome assembly and to quantify gene level expression. Comparative analysis was performed by DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads
|
| |
|
| Submission date |
Sep 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Xuesong Zhao |
| E-mail(s) |
xuesong_zhao@dfci.harvard.edu
|
| Phone |
6176326174
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Cancer Biology
|
| Lab |
Rosalind Segal
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE103525 |
Gene expression profiles of Ofd1 and Kif3a mutant SMB21 cells generated by CRISPR knockout |
| GSE103538 |
A transposon screen identifies loss of primary cilia as a mechanism of resistance to Smo inhibitors |
|
| Relations |
| BioSample |
SAMN07606675 |
| SRA |
SRX3162303 |
