|
| Status |
Public on Apr 26, 2013 |
| Title |
PA-1 knockdown |
| Sample type |
SRA |
| |
|
| Source name |
embryonal carcinoma PA-1 cells, specific ASO
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PA-1
cell type: embryonal carcinoma (EC) cells
ploidy: diploid
aso: specific to PWS-associated sno-lncRNAs
|
| 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.
|
| |
|
| 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.
|
| |
|
| 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 |
SAMN02056412 |
| SRA |
SRX272037 |
