|
| Status |
Public on Mar 23, 2021 |
| Title |
con rep2 |
| Sample type |
SRA |
| |
|
| Source name |
con_BaF3
|
| Organism |
Mus musculus |
| Characteristics |
cell line: BaF3
cell type: pro-B chronic lymphocytic leukemia (CLL) cell line
transfected plasmid: pmax-Clover
|
| Treatment protocol |
BaF3 cells were nucleofected with plasmids(pmax-Clover/pmax-Clover-ICN/pmax-Clover-CTdel) and cell sorting after 24 hours.
|
| Growth protocol |
Cells were cultured in Gibco RPMI 1640 containing 10% FBS and 2ng/mL mouse IL-3 at 37°C with 5% CO2 and were maintained between a density of 5 × 10^5 cells/ml and 2 × 10^6 cells/ml.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue blocks were lysed in TRIzol reagent (Sigma-Aldrich). The lysate was well mixed with chloroform and spun for 15 min at 13000 g at 4 °C. RNA in top aqueous phase was collected and mixed with propan-2-ol to precipitate total RNA.
RNA libraries were prepared for sequencing using MGIEasymRNA Library Prep Kit V2.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
processed data file: con_ICN_CTdel_2.GeneExpression.FPKM.txt
con_FPKM
|
| Data processing |
Basecalls performed using BGISEQ-500.
SOAPnuke was used to get the "clean reads".
Mapping clean reads to hg19 whole genome using HISAT2.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Genome_build: UCSC_mm10
Supplementary_files_format_and_content: tab-delimited text files include fpkm values for each Sample.
|
| |
|
| Submission date |
Jun 13, 2018 |
| Last update date |
Mar 23, 2021 |
| Contact name |
Maolin Ge |
| E-mail(s) |
MGE1@mgh.harvard.edu
|
| Phone |
8577578190
|
| Organization name |
Harvard Medical School
|
| Department |
MGH Cancer Center
|
| Lab |
Bar-Peled
|
| Street address |
149 13th Street
|
| City |
Charlestown |
| State/province |
Massachusetts |
| ZIP/Postal code |
02129 |
| Country |
USA |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE115728 |
RNA-seq of NOTCH1 mutation in chronic lymphocytic leukemia cell BaF3. |
|
| Relations |
| BioSample |
SAMN09404989 |
| SRA |
SRX4202544 |
