 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 05, 2023 |
| Title |
ARAC-gradual-TR1-PCR1-011119 |
| 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 |
SAMN38046816 |
| SRA |
SRX22292452 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7872608_ARAC-gradual-TR1-PCR1-011119_S79_R1_001_rawcounts.txt.gz |
8.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
