NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM659324 Query DataSets for GSM659324
Status Public on Jun 15, 2011
Title HCT-116 si PAPD1 replicate 2 variant 2 assay
Sample type RNA
 
Source name HCT-116 cells
Organism Homo sapiens
Characteristics cell type: HCT-116
transfection: si PAPD1
Treatment protocol Treated with 30 nM Dharmacon SMARTpool siRNAs against enzyme of interest or Cyclophilin B as a negative control
Growth protocol HCT-116 cells grown in McCoy's media with 10% FBS
Extracted molecule total RNA
Extraction protocol RNA was isolated using the miRNeasy RNA isolation kit from Qiagen. 400 ng of RNA was used as input for the nCounter sample prep reaction.
Label N/A
Label protocol N/A
 
Hybridization protocol Hybrdization reactions were performed according to the manufacturer's instructions (NanoString) with 5 µl of the 5-fold diluted sample preparation reaction. All hybridization reactions were incubated at 65°C for a minimum of 18 h.
Scan protocol Hybridized probes were purified and counted on the nCounter Prep Station and Digital Analyzer (NanoString) following the manufacturer’s instructions. For each assay, a high-density scan (600 fields of view) was performed.
Description Variant 2
Replicate 2
Data processing The data were normalized for lane-to-lane variation with a dilution series of six spike-in positive controls using the vsn R package
 
Submission date Jan 21, 2011
Last update date Jun 15, 2011
Contact name Muneesh Tewari
E-mail(s) mtewari@fhcrc.org
Organization name Fred Hutchinson Cancer Research Center
Department Human Biology
Lab Tewari
Street address 1100 Fairview Ave, N
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platform ID GPL11642
Series (2)
GSE26803 Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity (KD)
GSE26970 Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity

Data table header descriptions
ID_REF
VALUE Normalized miRNA counts

Data table
ID_REF VALUE
hsa-miR-140-5p 20.20334852
hsa-miR-146a 14.68440415
hsa-miR-134 10.08532666
hsa-miR-128 15.6042257
hsa-miR-149 5.486392468
hsa-miR-1308 128.74348
hsa-miR-200b 17.44387229
hsa-miR-92b 11.00513644
hsa-miR-455-5p 6.406153028
hsa-miR-34c-5p 11.92494974
hsa-miR-99b 18.36369698
hsa-let-7e 32.16112162
hsa-miR-199a-5p 8.245722357
hsa-miR-18b 8.245722357
hsa-miR-509-3p 5.486392468
hsa-miR-320a 4.566660922
hsa-miR-10b 6.406153028
hsa-let-7c 29.40163186
hsa-miR-103 10.08532666
hsa-miR-886-5p 12.84476581

Total number of rows: 125

Table truncated, full table size 2 Kbytes.




Supplementary file Size Download File type/resource
GSM659324_papd1_2_V2.RCC.gz 6.0 Kb (ftp)(http) RCC
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap