|
| Status |
Public on Feb 07, 2019 |
| Title |
Transplant BcorΔE9-10 RNA-seq (2) |
| Sample type |
SRA |
| |
|
| Source name |
Myeloid Progenitor Cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype: scl-Cre-ERT +; Bcorfl/y
tissue: Bone Marrow
cell type: Myeloid Progenitor Cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Donor-derived myeloid progenitor cells (CD45.2+Lin-cKIT+Sca-1- )were isolated from the BM of experimental mice by FACS and total RNA was extracted using the Direct-zol™ RNA kit (Zymo Research) as per the manufacturer's instructions.
cDNA libraries were prepared using the QuantSeq 3' mRNA seq kit, Lexogen.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
B3
|
| Data processing |
Sample QC was first performed and overrepresented sequences identified using FastQC (Babraham Bioinformatics, Babraham Institute)
The RNA sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using Hisat2 to the mouse reference genome (GRCm38/mm10)
Read counting was performed with featureCounts from the subread package
Genes with read counts under 10 were filtered before the Voom-LIMMA workflow was used to normalise data and compute statistical significance of differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: count file
|
| |
|
| Submission date |
Feb 06, 2019 |
| Last update date |
Feb 12, 2019 |
| Contact name |
Madison Kelly |
| E-mail(s) |
mjk4002@med.cornell.edu
|
| Organization name |
Weill Cornell Medicine
|
| Street address |
413 E69th Street
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE126183 |
Bcor loss perturbs myeloid differentiation and promotes leukaemogenesis [TransplantRNA-SEQ] |
| GSE126264 |
Bcor loss perturbs myeloid differentiation and promotes leukaemogenesis |
|
| Relations |
| BioSample |
SAMN10881530 |
| SRA |
SRX5342946 |
