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Sample GSM659361 Query DataSets for GSM659361
Status Public on Jun 15, 2011
Title HCT-116 si ZCCHC11 replicate 2 canonical assay
Sample type RNA
Source name HCT-116 cells
Organism Homo sapiens
Characteristics cell type: HCT-116
transfection: si ZCCHC11
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 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
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 49.4125838
hsa-miR-146a 18.2311556
hsa-miR-134 6.53835431
hsa-miR-128 53.31027016
hsa-miR-149 15.3079166
hsa-miR-1308 6.53835431
hsa-miR-200b 218.9620746
hsa-miR-92b 129.3152033
hsa-miR-455-5p 27.97532909
hsa-miR-34c-5p 14.33350622
hsa-miR-99b 113.7244445
hsa-let-7e 254.0412868
hsa-miR-199a-5p 0.695356358
hsa-miR-18b 22.12881944
hsa-miR-509-3p 19.20557054
hsa-miR-320a 2.641285052
hsa-miR-10b 19.20557054
hsa-let-7c 74.74755275
hsa-miR-103 614.5776457
hsa-miR-886-5p 2.641285052

Total number of rows: 125

Table truncated, full table size 2 Kbytes.

Supplementary file Size Download File type/resource
GSM659361_zcchc11_2_canonical.RCC.gz 6.4 Kb (ftp)(http) RCC
Processed data included within Sample table

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