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Status |
Public on Apr 26, 2013 |
Title |
PA-1 scramble |
Sample type |
SRA |
|
|
Source name |
embryonal carcinoma PA-1 cells, scrambled ASO
|
Organism |
Homo sapiens |
Characteristics |
cell line: PA-1 cell type: embryonal carcinoma (EC) cells ploidy: diploid aso: scrambled
|
Growth protocol |
Embryonal carcinoma (EC) cell line PA-1 was cultured using standard protocols provided by ATCC.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNAs were prepared using Trizol Reagent. After treatment with DNase I, total RNAs were used for RNA-Seq libraries preparation with Illumina TruSeq RNA Sample Preparation Kits according to the manufacturer's instructions.
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
Poly(A)+ RNA. This Sample represents 2 replicates.
|
Data processing |
Sequencing reads were obtained with Illumina HiSeq 2000. All reads were uniquely aligned to the human hg19 genome by using Bowtie with up to 2 mismatches. Genome_build: GRCh37 Supplementary_files_format_and_content: bigWig files were generated from the relevant bedGraph files according to the step-by-step protocol at http://genome.ucsc.edu/goldenPath/help/bigWig.html basically using the bedGraphToBigWig program. The bigWig format is for display of dense, continuous data that will be displayed in the Genome Browser as a graph. The resulting bigWig files are in an indexed binary format.
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|
|
Submission date |
Jun 06, 2012 |
Last update date |
May 15, 2019 |
Contact name |
Ling-Ling Chen |
E-mail(s) |
linglingchen@sibcb.ac.cn
|
Organization name |
Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
|
Street address |
320 Yue-Yang Road
|
City |
Shanghai |
ZIP/Postal code |
200031 |
Country |
China |
|
|
Platform ID |
GPL11154 |
Series (1) |
GSE38541 |
Human PA-1 cells treated with scrambled or specific ASOs |
|
Relations |
BioSample |
SAMN02056411 |
SRA |
SRX272036 |