|
| Status |
Public on Jul 22, 2020 |
| Title |
LIN28Bwt_yDox_3 |
| Sample type |
SRA |
| |
|
| Source name |
LIN28Bwt_yDox
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BE2C
cell type: Neuroblastoma cells
genotype/variation: doxycycline-inducible overexpression of wild-type LIN28B
treatment: treated (yDox) with doxycycline
|
| Treatment protocol |
Cells were untreated (nDox) or treated (yDox) with doxycycline at 50 ng/ml for 3 days.
|
| Growth protocol |
The BE2C neuroblastoma cells were maintained in RPMI 1640 Medium (GIBCO) supplemented with 10% fetal bovine serum (Sigma) and 1X penicillin-streptomycin (GIBCO).
|
| 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 a Illumina 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 |
| |
|
| Description |
20180306_LWTplusD_3_TT5314_S6
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
RNA-seq reads were aligned to the hg19 revision of the human reference genome using TopHat with parameters –library-type fr-firststrand –no-novel-juncs and -G set to a GTF of Refseq genes downloaded 7/5/2017.
Counts of reads covering genes were quantified using HTSeq-count with parameters -I gene_id –stranded=reverse -f bam -m intersection-strict and a GTF of Refseq genes downloaded 7/5/2017.
Differentially expressed genes were called by the R Bioconductor package DESeq2.
Genome_build: hg19
|
| |
|
| Submission date |
Oct 10, 2019 |
| Last update date |
Jul 22, 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) |
| GSE138741 |
LIN28B Regulates Transcription and Potentiates MYCN-induced Neuroblastoma in a let-7-independent Manner [RNA-seq] |
| GSE138743 |
LIN28B Regulates Transcription and Potentiates MYCN-induced Neuroblastoma in a let-7-independent Manner |
|
| Relations |
| BioSample |
SAMN13014995 |
| SRA |
SRX6977263 |
