|
| Status |
Public on Dec 01, 2012 |
| Title |
Total RNA |
| Sample type |
SRA |
| |
|
| Source name |
Myeloid Leukemia
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HL60
rna fraction: Total RNA
|
| Growth protocol |
HL-60 were grown in DMEM supplemented with 10%FBS, at 37 °C in a humidified atmosphere with 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with TRI REAGENT® (MRC). Total RNA was extracted with TRI Reagent® (MRC). RNA samples were treated with DNase I (10 U of DNase I (Roche) per 3 ug of total RNA; 37ºC for one hour; in the presence of RNase inhibitor). Non-polyadenylated RNA fractions were selected with the MicroPoly (A) PuristTM purification kit (Ambion). Total and not-polyadenylated RNA were depleted of ribosomal RNA with Ribo-ZeroTM Magnetic Gold Kit (cat. # MRZG126 Epicentre).
Double stranded cDNA libraries were constructed using ScriptSeq™ v2 RNA-Seq Library Preparation Kit (cat. # SSV21106 Epicentre) followed by Duplex Specific Nuclease (DSN) normalization (Evrogen, EA001). DSN treated libraries were subjected to final size-selection in 3% agarose gel. 250-500 bp fragments were excised and recovered using the Qiaquick Gel Extraction Kit (Qiagen). Libraries were sequenced (1/lane) on a HiSeq 2000 Illumina instrument.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Bases were called using Casava 1.8.4 with default settings.
76-bp paired-end reads were aligned to human genome (hg19) using tophat 2.0.2 with default settings and without a reference assembly.
Assemblies were generated using Cufflinks 2.0.2 again, without reference assembly
Overlap with DNMT1-RIP-Seq was calculated using Bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: Whole-transcriptome .gtf assemblies of Total and polyA(-) RNA samples, including FPKM values.
|
| |
|
| Submission date |
Oct 02, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Touati Benoukraf |
| E-mail(s) |
tbenoukraf@mun.ca
|
| Phone |
+1 (709) 864-6671
|
| Organization name |
Memorial University of Newfoundland
|
| Department |
Faculty of Medicine, Discipline of Genetics
|
| Street address |
Craig L. Dobbin Genetics Research Centre,
|
| City |
St. John's |
| State/province |
NL |
| ZIP/Postal code |
A1B 3V6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE32260 |
Relationship between DNMT1-RNA interactions, DNA methylation and gene expression |
| GSE41279 |
RNA-seq HL60 cells |
|
| Relations |
| SRA |
SRX190848 |
| BioSample |
SAMN01737708 |
