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Sample GSM659352 Query DataSets for GSM659352
Status Public on Jun 15, 2011
Title HCT-116 si TUT1 replicate 1 canonical assay
Sample type RNA
Source name HCT-116 cells
Organism Homo sapiens
Characteristics cell type: HCT-116
transfection: si TUT1
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 38.24754178
hsa-miR-146a 34.07317883
hsa-miR-134 7.357492902
hsa-miR-128 34.90805125
hsa-miR-149 8.192329128
hsa-miR-1308 1.514815492
hsa-miR-200b 113.3861858
hsa-miR-92b 61.62399635
hsa-miR-455-5p 22.38498008
hsa-miR-34c-5p 12.36658747
hsa-miR-99b 59.11937518
hsa-let-7e 127.5790471
hsa-miR-199a-5p 4.853062919
hsa-miR-18b 9.862020945
hsa-miR-509-3p 19.04550423
hsa-miR-320a 7.357492902
hsa-miR-10b 11.53172923
hsa-let-7c 56.61475418
hsa-miR-103 320.4350096
hsa-miR-886-5p 10.69687351

Total number of rows: 125

Table truncated, full table size 2 Kbytes.

Supplementary file Size Download File type/resource
GSM659352_tut_1_canonical.RCC.gz 6.4 Kb (ftp)(http) RCC
Processed data included within Sample table

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