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Sample GSM4912911 Query DataSets for GSM4912911
Status Public on May 16, 2022
Title Empty vector_3 [3_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 3-BB_S7_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 SAMN16826062
SRA SRX9526944

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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