|
| Status |
Public on Jul 20, 2020 |
| Title |
NGP_ARID1A_mut#1 |
| Sample type |
SRA |
| |
|
| Source name |
Neuroblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: NGP
cell type: ARID1A-/- #1
|
| Growth protocol |
The NGP neuroblastoma cell line was maintained in RPMI 1640 Medium (GIBCO) supplemented with 10% fetal bovine serum (Sigma) and 1X penicillin-streptomycin (GIBCO),and 0.5ug/ml puromycin (Sigma #P8833).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was depleted of ribosomal RNA with the SMARTer Universal Low Input RNA Kit (Clontech). Enriched mRNA was then applied to library preparation according to manufacturer’s protocol (NEBNext Ultra). After repeated quality control for average DNA input size of 300 bp, the samples were sequenced on aIllumina NextSeq 500 with 75bp single-end reads.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using HISAT2 version 2.1.0 with defalt parameters for single end reads.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using GFold version 1.1.2
Genome_build: hg19
|
| |
|
| Submission date |
Jul 22, 2019 |
| Last update date |
Jul 20, 2020 |
| Contact name |
Ting Tao |
| E-mail(s) |
taot@zju.edu.cn
|
| Organization name |
Children's Hospital, Zhejiang University School of Medicine
|
| Lab |
Ting Tao
|
| Street address |
3333 Binsheng Road
|
| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310052 |
| Country |
China |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE134631 |
ARID1A Loss in Neuroblastoma Promotes the Adrenergic-to-Mesenchymal Transition by Regulating Enhancer-Mediated Gene Expression [RNA-seq] |
| GSE134632 |
ARID1A Loss in Neuroblastoma Promotes the Adrenergic-to-Mesenchymal Transition by Regulating Enhancer-Mediated Gene Expression |
|
| Relations |
| BioSample |
SAMN12335355 |
| SRA |
SRX6483144 |
