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Sample GSM659322 Query DataSets for GSM659322
Status Public on Jun 15, 2011
Title HCT-116 si PAPD1 replicate 1 canonical 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 Canonical
Replicate 1
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
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
VALUE Normalized miRNA counts

Data table
hsa-miR-140-5p 29.55622244
hsa-miR-146a 30.59457172
hsa-miR-134 8.789393744
hsa-miR-128 21.24943935
hsa-miR-149 1.522421613
hsa-miR-1308 0.001045133
hsa-miR-200b 144.8132689
hsa-miR-92b 67.97520999
hsa-miR-455-5p 27.47952461
hsa-miR-34c-5p 4.636264544
hsa-miR-99b 88.74224926
hsa-let-7e 182.1939527
hsa-miR-199a-5p 0.004906817
hsa-miR-18b 15.01937846
hsa-miR-509-3p 11.90436911
hsa-miR-320a 3.598083422
hsa-miR-10b 9.827713093
hsa-let-7c 48.24653024
hsa-miR-103 414.7848902
hsa-miR-886-5p 8.789393744

Total number of rows: 125

Table truncated, full table size 2 Kbytes.

Supplementary file Size Download File type/resource
GSM659322_papd1_1_canonical.RCC.gz 6.4 Kb (ftp)(http) RCC
Processed data included within Sample table

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