|
| Status |
Public on Oct 19, 2020 |
| Title |
wt-proB-Rep1 (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
wt proB cells, Replicate1
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: wt proB (Fraction BC) bone marrow
cell type: wt proB cells
genotype: Ebf1+/+ Pax5+/+ Rag2+/+
|
| Growth protocol |
dHet leukemic cells were derived from the lymph node of Ebf1+/-Pax5+/- leukemic mice. dHet proB cells were derived by culturing the single-cell suspensions of freshly isolated c-Kit positive fetal liver cells were plated on OP9 feeder cells in OptiMEM medium, supplemented with 4% FCS, 1% PSG, 50 μM β-mercaptoethanol, 5 ng/ml interleukin 7 (IL-7), 10 ng/ml Flt3 ligand (Flt3L) and 10 ng/ml stem cell factor (SCF). wt proB (FrBC) cells were sorted from the control mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-seq: Total RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.
The RNA-seq libraries were prepared by using the NEB E6420 RNA library preparation kit according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Gene expression in wt proB cells
|
| Data processing |
The base calling was performed by using BCL2Fastq pipeline (version: 0.3.1) and bcl2fastq (version 2.20.0.422).
RNA-seq: The paired-end RNA-seq datasets were mapped to the mouse reference genome (mm9) using STAR aligner (2.5.3a).
RNA-seq: The mapped reads were further assembled by using Cufflinks (v2.2.1) and the expression level of the annotated genes (UCSC, mm9) was calculated by Cuffquant. The differential gene expression between the conditions was calculated by using Cuffdiff.
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq: The normalized gene expression values (FPKM) calculated by Cuffnorm (v2.2.1) are provided in TXT format.
|
| |
|
| Submission date |
Sep 28, 2020 |
| Last update date |
Oct 19, 2020 |
| Contact name |
Senthilkumar Ramamoorthy |
| E-mail(s) |
[email protected]
|
| Phone |
00497615108731
|
| Organization name |
Max Planck Institute of Immunobiology and Epigenetics
|
| Department |
Cellular & Molecular Immunology
|
| Lab |
Laboratory Rudolf Grosschedl
|
| Street address |
Stübeweg 51
|
| City |
Freiburg |
| ZIP/Postal code |
D-79108 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE158661 |
RNASeq analysis to unravel molecular networks driving leukemia in Ebf1+/-Pax5+/- (dHet) B-ALL mice |
| GSE158673 |
EBF1 and Pax5 safeguard leukemic transformation by limiting IL-7 signaling, Myc expression and folate metabolism |
|
| Relations |
| BioSample |
SAMN16281361 |
| SRA |
SRX9203767 |
