|
| Status |
Public on May 21, 2019 |
| Title |
RNA-seq in CAPH2 WT cells, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
RMG1_shControl
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RMG1
arid1a: WT
caph2: WT
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol (Invitrogen) according to the manufacturer's instruction and digested with DNase I (Qiagen, 79254) and purified using RNeasy MinElute Cleanup Kit (Qiagen, 74106)
RNA-Seq libraries were prepared using TruSeq Total RNA Sample Prep Kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNA.CAPH2.ctr.1
|
| Data processing |
RNA-seq data was aligned using bowtie2 against hg19 version of the human genome and RSEM v1.2.12 software was used to estimate raw read counts using Ensemble transcriptome.
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains raw counts for each gene
|
| |
|
| Submission date |
Sep 17, 2018 |
| Last update date |
May 21, 2019 |
| Contact name |
Priyankara J Wickramasinghe |
| E-mail(s) |
priyaw@wistar.org
|
| Phone |
2154956837
|
| Organization name |
The Wistar Institute
|
| Department |
Bioinformatics
|
| Lab |
Genomics
|
| Street address |
3601 Spruce Street
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE120057 |
ARID1A regulates condensin II distribution and chromosomal partition [RNA-seq] |
| GSE120060 |
ARID1A regulates condensin II distribution and chromosomal partition |
|
| Relations |
| BioSample |
SAMN10079390 |
| SRA |
SRX4704641 |
