|
Status |
Public on Nov 03, 2022 |
Title |
CTRL_shRNA_rep2_1 |
Sample type |
SRA |
|
|
Source name |
Thyroid
|
Organism |
Homo sapiens |
Characteristics |
cell type: human thyroid cancer cells tissue: Thyroid cell line: 8505C genotype: wild-type treatment: untreated
|
Treatment protocol |
Not applicable
|
Growth protocol |
1x106 cells/well were plated in 6-well plate and placed in a 5% CO2 37 °C incubator for 24 hours
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was isolated by Trizol. libraries were prepared using the TIANSeq mRNA Capture Kit (TIANGEN) and TIANSeq Fast RNA Library Kit (Illumina), according to the manufacturer’s instructions.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific), Agilent 2100 Bioanalyzer and 2100 RNA nano 6000 assay kit (Agilent Technologies) were used to quantify and qulify RNA sample The RNA with poly-A in eukaryotic total RNA was enriched by TIANSeq mRNA Capture Kit (TIANGEN) and TIANSeq Fast RNA Library Kit (Illumina) was used to construct the transcriptome sequencing libraries. Library concentration was first quantified using Qubit 2.0 fluorometer (Life Technologies), and checking insert size on an Agilent 2100 and quantifying to greater accuracy by quantitative PCR (Q-PCR) (library activity >2 nM). The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions Assembly: three biological replicates per cell infection HHEX/CTRL shRNA virus Supplementary files format and content: tab-delimited text files include log2 counts per million (CPM) values for each Sample
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|
|
Submission date |
Oct 29, 2022 |
Last update date |
Nov 03, 2022 |
Contact name |
Zhongyun Xu |
E-mail(s) |
xzhongyun@126.com
|
Phone |
17702148820
|
Organization name |
Shanghai Jiao Tong University School of Medicine
|
Street address |
1665 Kongjiang Road
|
City |
Shanghai |
ZIP/Postal code |
200092 |
Country |
China |
|
|
Platform ID |
GPL18573 |
Series (1) |
GSE216850 |
RNAseq of 8505c cell line with HHEX knockdown |
|
Relations |
BioSample |
SAMN31521046 |
SRA |
SRX18076146 |