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Sample GSM659317 Query DataSets for GSM659317
Status Public on Jun 15, 2011
Title HCT-116 si Cyclophilin B replicate 4 variant 1 assay
Sample type RNA
Source name HCT-116 cells
Organism Homo sapiens
Characteristics cell type: HCT-116
transfection: si Cyclophilin B
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 1
Replicate 4
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 3.372300021
hsa-miR-146a 12.510039
hsa-miR-134 4.133677607
hsa-miR-128 4.133677607
hsa-miR-149 0.000790316
hsa-miR-1308 49.06321593
hsa-miR-200b 43.73252722
hsa-miR-92b 6.41802439
hsa-miR-455-5p 0.002293972
hsa-miR-34c-5p 0.006222535
hsa-miR-99b 34.59420864
hsa-let-7e 61.24765172
hsa-miR-199a-5p 0.001404006
hsa-miR-18b 0.001011377
hsa-miR-509-3p 4.895101958
hsa-miR-320a 0.001011377
hsa-miR-10b 4.895101958
hsa-let-7c 45.25558098
hsa-miR-103 17.8406688
hsa-miR-886-5p 7.179506834

Total number of rows: 125

Table truncated, full table size 2 Kbytes.

Supplementary file Size Download File type/resource
GSM659317_cyclo_4_V1.RCC.gz 6.1 Kb (ftp)(http) RCC
Processed data included within Sample table

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