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Sample GSM7872611 Query DataSets for GSM7872611
Status Public on Nov 05, 2023
Title ARAC-gradual-TR1-PCR1-151119
Sample type SRA
 
Source name in vitro
Organism Mus musculus
Characteristics tissue: in vitro
cell line: MLL-AF9
cell type: mouse leukaemia MLL-AF9
genotype: C57BL6/J background
treatment: Cytarabine
Treatment protocol Dose escalation cultures were supplemented with either 0.1% v/v DMSO, 400nM IBET or 300nM AraC. For the high dose arms, liquid cultures were supplemented with 800nM IBET or 700nM AraC. Drugs were replenished every three days by replating in fresh medium with drug. For the dose escalation, every 7 days, 5×10^5 cells were replated into fresh medium supplemented with an increased concentration of IBET (TP1 - 400nM, TP-2 - 600nM, TP-3 – 800nM and TP-4 - 1000nM), AraC (TP1 - 300nM, TP-2 - 300nM, TP-3 – 300nM and TP-4 - 500nM) or maintained in 0.1% v/v DMSO.
Growth protocol Mouse MLL-AF9 leukaemia cells were generated from the bone marrow of female C56BL6/J mice as previously described (Fennell & Vassiliadis, Nature, 2022) and cultured in RPMI-1640 medium supplemented with mouse IL-3 (10 ng ml−1), human IL-6 (10 ng ml−1), mouse SCF (50 ng ml−1) 20% fetal bovine serum, streptomycin (100 µg ml−1), penicillin (100 U ml−1) and 2 mM GlutaMAX (Thermo Fisher Scientific) in 5% CO2 at 37 °C
Extracted molecule genomic DNA
Extraction protocol 5x10^5 cells were lysed in 40 µl Viagen lysis buffer containing 0.5 mg ml−1 proteinase K (Invitrogen) and split into technical replicates.
Barcode libraries were constructed using a two step PCR strategy using Q5 polymerase (NEB).
dual indexed PCR amplicon
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Description DNA barcode amplicon sequencing of MLL-AF9 cells cultured in vitro
Data processing Raw sequence data from population-based dose-escalation were processed using BARtab v1.3 with the following parameters: --mode “single-bulk”, --upconstant “CGATTGACTA”, --downconstant “TGCTAATGCG”, --alnmismatches 1, --minqual 20, --pctqual 80, --constants “up”, --constantmismatches 0.1, --barcode_length 60. Count files were imported into R v4.2 and further analysed with bartools v0.2.5.
Assembly: SPLINTR BFP V1 reference barcode list (Addgene #179776)
Supplementary files format and content: tab delimited text file contains raw counts per barcode for each sample
 
Submission date Oct 30, 2023
Last update date Nov 05, 2023
Contact name Dane Aaron McKay Vassiliadis
E-mail(s) dane.vassiliadis@unimelb.edu.au
Organization name University of Melbourne
Street address Parkville VIC 3000
City Melbourne
ZIP/Postal code 3000
Country Australia
 
Platform ID GPL19057
Series (1)
GSE246611 An integrated toolkit for the analysis of synthetic cellular barcodes in the genome and transcriptome
Relations
BioSample SAMN38046813
SRA SRX22292455

Supplementary file Size Download File type/resource
GSM7872611_ARAC-gradual-TR1-PCR1-151119_S63_R1_001_rawcounts.txt.gz 2.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA

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