|
Status |
Public on May 21, 2019 |
Title |
RNA-seq in ARID1A KO cells, replicate 1 |
Sample type |
SRA |
|
|
Source name |
RMG1_ARID1A CRISPR
|
Organism |
Homo sapiens |
Characteristics |
cell line: RMG1 arid1a: KO 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)
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
RNA.ARID1A.KO.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
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|
|
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 |
SAMN10079393 |
SRA |
SRX4704639 |