|
| 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 |
