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Sample GSM3416297 Query DataSets for GSM3416297
Status Public on Dec 18, 2019
Title ROSA26_rep_2
Sample type SRA
 
Source name MLL-AF9 I-BET resistant cells
Organism Mus musculus
Characteristics strain/background: C57BL/6
cell type: haematopoietic progenitors
condition: I-BET Resistant
treatment: ROSA26_sgRNA
Treatment protocol Cell lines were removed from IBET and transduced with sgRNA targeting HBO1/ROSA26. Following 24 hours of transduction, sgRNA positive cells were selected with puromycin (5ug/ml) for a further 72 hours.
Growth protocol Cell lines were grown in RPMI-1640 supplemented with mouse IL-3 (10ng/ml), 10% FCS, streptomycin (100ug/ml), penicillin (100 units/ml) and glutamax (2nM), under standard culture conditions (5% CO2, 37°C). MLL-AF9 I-BET resistant cells were cultured with constant I-BET treatment (1000nM, 0.1% DMSO).
Extracted molecule total RNA
Extraction protocol RNA was extracted using the Qiagen RNeasy kit.
Libraries were prepared using QuantSeq 3’ mRNA-seq Library Prep kit (Lexigen).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description ROSA26_2
PolyA RNA
processed data file: CPManno.txt
Data processing Illumina bcl2fastq v2 software was used for basecalling.
Reads were aligned to the mouse genome (GRCm38.78) using HISAT2.
Reads were assigned to genes using htseq-count. Differential expression was calculated using edgeR.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: CPManno.txt: Tab-delimited text file includes CPM values for each Sample.
 
Submission date Oct 03, 2018
Last update date Dec 18, 2019
Contact name Mark Dawson
E-mail(s) mark.dawson@petermac.org
Organization name Peter MacCallum Cancer Centre
Street address 305 Grattan St
City Melbourne
State/province VIC
ZIP/Postal code 3000
Country Australia
 
Platform ID GPL19057
Series (2)
GSE120811 HBO1 is required for the maintenance of leukaemia stem cells [RNA-seq]
GSE120813 HBO1 is required for the maintenance of leukaemia stem cells
Relations
BioSample SAMN10174397
SRA SRX4796153

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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