|
| Status |
Public on Apr 20, 2020 |
| Title |
MYC OFF 3_d4 |
| Sample type |
SRA |
| |
|
| Source name |
spleen
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB/N
tissue: splenic single cell suspension
age: post natal 6-10 weeks
genotype: Em-tTA/tet-O-MYC (MYC OFF)
|
| Treatment protocol |
MYC OFF splenic samples were obtained by treating Em-tTA/tet-O-MYC lymphoma bearing mice with doxycycline for 4 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single cell suspensions were made by homogenizing spleens using a 191/2 guage needle. Following filtration using a 70mm cell strainer and RBC lysis, cells were washed with PBS and used for RNA isolation. RNA isolation was performed using the Qiagen RNeasy Mini Kit (Catalog # 74104).
RNA libraries were prepared for sequencing using standard BGI protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
MYC OFF lymphoma spleen
|
| Data processing |
Primary sequencing data (raw reads) were subjected to quality control (QC).
After QC, raw reads were filtered into clean reads before alignment to the reference sequences. Once alignment passed QC, we proceeded with downstream analysis including gene expression and deep analysis based on gene expression (PCA/correlation/screening differentially expressed genes).
Data was filtered reads with adaptors, reads with greater than 10% unknown bases and low quality reads. Bowtie 2 was used to map clean reads to reference gene, and HISAT was used to map reads to reference genome (mm8).
RSEM was used to compute Maximum likelihood abundance estimates using the Expectation Maximization (EM) algorithm. FPKM method was used to calculate the expression levels of individual genes.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
|
| |
|
| Submission date |
Oct 24, 2017 |
| Last update date |
Apr 20, 2020 |
| Contact name |
Srividya Swaminathan |
| E-mail(s) |
sswaminathan@coh.org
|
| Phone |
3233337745
|
| Organization name |
City of Hope
|
| Department |
Systems Biology
|
| Lab |
Swaminathan Lab
|
| Street address |
1218 S. Fifth Ave
|
| City |
Monrovia |
| State/province |
CA |
| ZIP/Postal code |
91016 |
| Country |
USA |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE106078 |
MYC functions as a switch for natural killer cell-mediated immune surveillance of lymphoid malignancies |
|
| Relations |
| BioSample |
SAMN07829331 |
| SRA |
SRX3316238 |
