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Sample GSM659336 Query DataSets for GSM659336
Status Public on Jun 15, 2011
Title HCT-116 si PAPD5 replicate 2 variant 2 assay
Sample type RNA
Source name HCT-116 cells
Organism Homo sapiens
Characteristics cell type: HCT-116
transfection: si PAPD5
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
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 23.83349804
hsa-miR-146a 14.88084241
hsa-miR-134 9.183768456
hsa-miR-128 17.32246864
hsa-miR-149 6.742224696
hsa-miR-1308 71.03869915
hsa-miR-200b 30.34454606
hsa-miR-92b 15.69471692
hsa-miR-455-5p 11.62535781
hsa-miR-34c-5p 14.06696901
hsa-miR-99b 26.27513961
hsa-let-7e 53.94714531
hsa-miR-199a-5p 12.43922642
hsa-miR-18b 9.997628157
hsa-miR-509-3p 10.81149153
hsa-miR-320a 11.62535781
hsa-miR-10b 10.81149153
hsa-let-7c 40.92501592
hsa-miR-103 13.25309693
hsa-miR-886-5p 13.25309693

Total number of rows: 125

Table truncated, full table size 2 Kbytes.

Supplementary file Size Download File type/resource
GSM659336_papd5_2_V2.RCC.gz 6.1 Kb (ftp)(http) RCC
Processed data included within Sample table

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