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Sample GSM4912907 Query DataSets for GSM4912907
Status Public on May 16, 2022
Title Empty vector_in-vitro_2 [EV_2]
Sample type SRA
 
Source name CD34 positive cells
Organism Homo sapiens
Characteristics tissue/cell type: CD34 positive cells
genotype/treatment: empty vector after five days culture in-vitro
sort: GFP+
Treatment protocol Each CD34 biological replicate composed of three different cord blood units
Growth protocol Samples 1-4: bone marrow samples from ETV6-NCOA2 patients were transplanted into NSGS mice. Samples 5-12: CD34 cord blood cells were retroviraly infected with ETV6-NCOA2 (NGFR) or ETV6-NCOA2 (NGFR)+NOTCH1-L1601PdP (GFP) and transplanted into NSGS mice. Samples 13-18: The cells were cultured for five days in-vitro (SCF, Flt3L, and TPO) , sorted for GFP positive, and sent for bulk RNA-sequencing.
Extracted molecule total RNA
Extraction protocol CD34 positive cord blood cells were isolated using magnetic beads from fresh cord blood (For each biological replicate, three different cord blood samples were mixed). The cell were retrovirally infected with ETV6-NCOA2 or empty vector and cultured in IMDM supplemented with hSCF, hTPO, hFlt3L (100 ng/ml) for 5 days. The positive cells were sorted (GFP). ETV6-NCOA2 or ETV6-NCOA2+NOTCH1-L1601PdP were sorted (NGFR+/ GFP+NGFR+ respectively) from fresh bone marrow of engrafted NSGS mice. ETV6-NCOA2 patient derived xenografts were sorted with human CD45 from bone marrow of engrafted NSGS mice. 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 s_2_BB
CD34 positive cells transduced with empty vector after five days culture in-vitro
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)
Reads whose AS (alignment score) was higher in the mouse compared to human were discarded. The reads were aligned to both GRCm38 sequence and GRCh38 sequences. Reads with a higher mapping quality to the mouse genome were excluded from the analysis.
Counting proceeded over genes annotated in Ensembl using htseq-count
Normalization was performed using DESeq2
Genome_build: GRCh38
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 GPL16791
Series (2)
GSE161702 ETV6-NCOA2 expression profile in T/M mixed-phenotype acute leukemia [ETV6-NCOA2 human]
GSE162338 ETV6-NCOA2 expression in CD34 positive cord blood cells
Relations
BioSample SAMN16826056
SRA SRX9526894

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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