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Sample GSM659364 Query DataSets for GSM659364
Status Public on Jun 15, 2011
Title HCT-116 si ZCCHC6 replicate 1 canonical assay
Sample type RNA
Source name HCT-116 cells
Organism Homo sapiens
Characteristics cell type: HCT-116
transfection: si ZCCHC6
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 58.22973547
hsa-miR-146a 47.07210602
hsa-miR-134 9.880190607
hsa-miR-128 52.03105185
hsa-miR-149 14.83904891
hsa-miR-1308 13.59932797
hsa-miR-200b 285.1017246
hsa-miR-92b 74.34631729
hsa-miR-455-5p 30.95554439
hsa-miR-34c-5p 34.67474841
hsa-miR-99b 126.4152918
hsa-let-7e 291.3004137
hsa-miR-199a-5p 4.921519914
hsa-miR-18b 16.07877246
hsa-miR-509-3p 17.31849805
hsa-miR-320a 12.35961042
hsa-miR-10b 18.55822528
hsa-let-7c 83.02447838
hsa-miR-103 355.7667803
hsa-miR-886-5p 19.79795385

Total number of rows: 125

Table truncated, full table size 2 Kbytes.

Supplementary file Size Download File type/resource
GSM659364_zcchc6_1_canonical.RCC.gz 6.3 Kb (ftp)(http) RCC
Processed data included within Sample table

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