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Sample GSM1329859 Query DataSets for GSM1329859
Status Public on Jul 01, 2014
Title Treated.1
Sample type SRA
 
Source name AML3
Organism Homo sapiens
Characteristics cell line: AML3
treatment: Aza Treated
Treatment protocol AzaC was dissolved from lyophilised powder into culture-sterile DMSO to produce a 20 mM stock solution and stored as 15μl aliquots at -80°C. For each new experiment a fresh aliquot of AzaC was diluted in RPMI/20% FBS to produce a 2 mM working stock which was diluted directly onto cells in culture.
Growth protocol OCI-AML3 cells were cultured in suspension in RPMI media supplemented with FBS 20%, Penicllin 5% and L-Glutamine 5%, incubated at 37°C in humidified conditions and 5% CO2. To passage, cells were counted by haemocytometer and either centrifuged to a pellet and resuspended in fresh media or resuspended in 50% fresh media at a concentration of 0.5 x 106/ml every 2-3 days.
Extracted molecule polyA RNA
Extraction protocol RNA was extracted using RNA easy mini kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Description RNA-Seq of Aza treated AML3 cells
Data processing Basecalls performed using CASAVA 1.8.2 and filtered to only sequences passing the Illumina QC filter
Sequenced reads were mapped to hg18 whole genome using tophat 1.4.1 with parameters –solexa-quals, -p 12, --segment-length 18, -M, -G Homo_sapiens.NCBI36.54.gtf
Aligned reads normalised by library size (number of fragments) and subsequent reads piledup and converted to bigWig format
Genome_build: hg18
Supplementary_files_format_and_content: bigWig files represent pileups of the reads at each base. bigWig files were normalised by library size and represent the number of reads at a given genomic location per million mapped reads and generated using UCSC wigToBigWig.
 
Submission date Feb 18, 2014
Last update date Mar 17, 2021
Contact name Xue Lei
E-mail(s) xlei@sbpdiscovery.org
Organization name SBP medical discovery institute
Lab Peter Adams Lab
Street address 10901 N Torrey Pines Rd
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL10999
Series (2)
GSE55123 Expression data from untreated and Aza treated AML3 cells
GSE55125 Aza treated AML3 cells
Relations
BioSample SAMN02645178
SRA SRX472607
Named Annotation GSM1329859_Aza.treated.KL1.bigWig

Supplementary file Size Download File type/resource
GSM1329859_Aza.treated.KL1.bigWig 87.2 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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