|
| Status |
Public on Sep 21, 2015 |
| Title |
Mxplus_Flt3ITD_2 |
| Sample type |
SRA |
| |
|
| Source name |
c-Kit+ cells purified from bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
tissue: bone marrow
cell type: c-Kit+ cells
genotype: Flt3-ITD
|
| Growth protocol |
Whole bone marrow from individual mice was positively selected for Cd117 (c-Kit) using antibody-conjugated magnetic beads (Cd117 microbeads, Miltenyi Biotec Inc).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using Trizol (Invitrogen), and cDNA was synthesized using the SuperScript First-Strand kit (Invitrogen). Sequencing libraries were constructed using the Nextflex Rapid Directional RNA-seq kit (Bioo Scientific).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Flt3_RNA_Seq_1
Cells were purified from whole bone marrow 4-weeks following PIpC injection; mice harbor Mx1-cre and Flt3-ITD allele
|
| Data processing |
expression levels: Gene-level expression measurements for 23,021 Ensembl mouse genes were reported in fragments per kilobase per million reads (FPKM) by Cufflinks 2.0.0 (http://cufflinks.cbcb.umd.edu/) (Trapnell et al., 2010). Cufflinks assembles transcripts, estimates their abundance, and tests for differential expression and regulation in RNA-Seq samples. Cufflinks command line-cufflinks --GTF <gtf_file> -q -p 3 -u -b <genome.fa> -o <output directory> <bam_file_from_tophat>
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM files for each sample
|
| |
|
| Submission date |
Sep 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
James Bradner |
| E-mail(s) |
bradner_computation@dfci.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Bradner Lab
|
| Street address |
450 Brookline
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE73216 |
Dose-dependent role of the cohesin complex in normal and malignant hematopoiesis [RNA-Seq] |
| GSE73218 |
Dose-dependent role of the cohesin complex in normal and malignant hematopoiesis |
|
| Relations |
| BioSample |
SAMN04096894 |
| SRA |
SRX1262255 |
