NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6696770 Query DataSets for GSM6696770
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
 
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

Supplementary file Size Download File type/resource
GSM6696770_control1-R3_fastqc_data.rtf.gz 8.2 Kb (ftp)(http) RTF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.