|
| Status |
Public on Jun 23, 2016 |
| Title |
NR_mir-ctrl-2 |
| Sample type |
SRA |
| |
|
| Source name |
SHSY5Y_mir-control
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SHSY5Y
cell type: neural progenitors/neuroblastoma
|
| Treatment protocol |
SHSY5Y cells were treated either with 50 nM of miR-143-3p mimic or 100 nM of siRNA specific for LncND. Scrambled siRNA or miRNA sequences were used as a negative control.
|
| Growth protocol |
SHSY5Y cells were grown in DMEM/F12 media supplemented with 10%FBS and antibiotic.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were harvested after 72h and RNA was extracted using MirVana isolation kit
PolyA+ libraries were prepared using Illumina's TrueSeq mRNA Stranded Kit according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data file: mir-filtered.merged.genes.fpkm.txt
|
| Data processing |
The Illumina Next Seq500 Next Generation Sequencer software was used.
pair-end data were upload to Illumina Basespace(https://basespace.illumina.com/),TopHat Alignment(Version: 1.0.0) of Basespace app was used to map the reads to hg19.
Cufflinks Assembly & DE(Version: 1.1.0) from Basespace app was used to call the DE genes.
Genome_build: hg19
Supplementary_files_format_and_content: txt files with fpkm values for each gene
|
| |
|
| Submission date |
Oct 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Kenneth S. Kosik |
| Organization name |
UCSB
|
| Department |
NRI
|
| Lab |
Kosik
|
| Street address |
UC Santa Barbara
|
| City |
Santa Barbara |
| State/province |
California |
| ZIP/Postal code |
93106 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE73982 |
A Primate lncRNA Mediates Notch Signaling During Neuronal Development by Sequestering miRNA [SHSY5Y cells] |
| GSE74210 |
A Primate lncRNA Mediates Notch Signaling During Neuronal Development by Sequestering miRNA |
|
| Relations |
| BioSample |
SAMN04161379 |
| SRA |
SRX1332632 |
