|
| Status |
Public on May 16, 2022 |
| Title |
Empty vector_1 [1_BB] |
| Sample type |
SRA |
| |
|
| Source name |
BM progenitor cells_Empty vector
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57B/6
cell type: Lineage negative bone marrow cells
genotype/variation: Empty vector
sort: GFP+
|
| Treatment protocol |
The mice were not treted prior to the bone marrow isolation
|
| Growth protocol |
The cells were cultured for five days in-vitro (IL3, IL6, SCF), sorted for GFP positive cells and sent for bulk RNA-sequencing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lineage negative cells were isolated using magnetic beads from fresh bone marrow of 6 weeks C57B/6 female. The cell were retrovirally infected with ETV6-NCOA2, KAT6A-NCOA2 or empty vector and cultured in RPMI supplemented with IL-3, IL-6 and SCF for 5 days. The positive cells were sorted (GFP). We extracted RNA from the samples and performed bulk RNA-sequencing.
Inhouse poly A based RNA seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
1-BB_S1_L003
Murine lineage negative bone marrow cells were retroviraly infected with MigR1-IRES-GFP expression.
|
| Data processing |
Reads were trimmed using cutadapt
After trimming the reads were mapped to the human genome using STAR v2.4.2a (using options outFilterMismatchNmax 2 and alignEndsType EndToEnd)
Counting proceeded over genes annotated in Ensembl using htseq-count
Normalization was performed using DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel file includes the normalized counts
|
| |
|
| Submission date |
Nov 18, 2020 |
| Last update date |
May 16, 2022 |
| Contact name |
Gilgi Friedlander |
| Organization name |
Weizmann Institute of Science
|
| Street address |
Hertzel st
|
| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE161703 |
ETV6-NCOA2 expression profile in T/M mixed-phenotype acute leukemia [ETV6_NCOA2_Mouse_in_vitro] |
| GSE162338 |
ETV6-NCOA2 expression in CD34 positive cord blood cells |
|
| Relations |
| BioSample |
SAMN16826066 |
| SRA |
SRX9526942 |
