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Sample GSM659331 Query DataSets for GSM659331
Status Public on Jun 15, 2011
Title HCT-116 si PAPD4 replicate 2 canonical assay
Sample type RNA
Source name HCT-116 cells
Organism Homo sapiens
Characteristics cell type: HCT-116
transfection: si PAPD4
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 26.41608699
hsa-miR-146a 14.22277353
hsa-miR-134 11.60994506
hsa-miR-128 31.64181384
hsa-miR-149 15.0937197
hsa-miR-1308 2.030532844
hsa-miR-200b 168.382046
hsa-miR-92b 96.96355596
hsa-miR-455-5p 20.31941686
hsa-miR-34c-5p 8.997141881
hsa-miR-99b 90.86685646
hsa-let-7e 185.8011914
hsa-miR-199a-5p 2.030532844
hsa-miR-18b 2.901083384
hsa-miR-509-3p 10.73900694
hsa-miR-320a 0.001183052
hsa-miR-10b 12.48088585
hsa-let-7c 57.77049478
hsa-miR-103 469.7332762
hsa-miR-886-5p 2.030532844

Total number of rows: 125

Table truncated, full table size 2 Kbytes.

Supplementary file Size Download File type/resource
GSM659331_papd4_2_canonical.RCC.gz 6.3 Kb (ftp)(http) RCC
Processed data included within Sample table

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