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Sample GSM1936859 Query DataSets for GSM1936859
Status Public on May 01, 2016
Title mild chronic hepatitis C, male, C203
Sample type RNA
Source name plasma
Organism Homo sapiens
Characteristics gender: male
age: 46
ishak fiborosis score: 0
Extracted molecule total RNA
Extraction protocol We extracted RNAs from plasma samples in 16 healthy controls, 16 CHC patients with mild fibrosis and 16 with significant fibrosis.
Total RNAs including miRNAs in plasma were purified with miRNeasy Serum/Plasma kit (Qiagen, Hilden, Germany) respectively, following the manufacturer’s instructions.
Label biotin
Label protocol Total RNA derived from 400 μL of plasma in each subject was poly(A) tailed and then directly ligated to a fluorescent dendrimer (a branched single and double-stranded DNA molecule conjugated to biotin) using the FlashTag™ Biotin HSR RNA Labeling Kit (Affymetrix), following the manufacturer’s instructions (User manual of the FlashTag™ Biotin HSR RNA Labeling Kit, Affymetrix)
Hybridization protocol The biotin-labeled samples with hybridization master mix were hybridized at 48 °C and 60 rpm for 16 hours on Affymetrix GeneChip miRNA 4.0 Array, following the manufacturer’s instructions (User manual of the FlashTag™ Biotin HSR RNA Labeling Kit, Affymetrix) . Thereafter, the GeneChips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix), following the manufacturer’s instructions.
Scan protocol The GeneChips were scanned using GeneChip® Scanner 3000 7G (Affymetrix), following the manufacturer’s instructions.
Data processing Raw microarray data (CEL files) were imported into Partek Genomics Suite (Partek Inc., St. Louis, MO), and probe set summaries were computed using Robust Multi-Array algorithm. To adjust for differences in labeling intensities and hybridization, a global normalization was made by aligning signal intensities of data arrays across the medians.
Submission date Nov 10, 2015
Last update date May 01, 2016
Contact name Kentaro Matsuura
Phone 12404983888
Organization name National Institutes of Health
Department Department of Transfusion Medicine
Street address 5411 McGrath Blvd.
City North Bethesda
State/province Maryland
ZIP/Postal code 20852
Country USA
Platform ID GPL19117
Series (1)
GSE74872 Circulating let-7 levels in plasma correlate with hepatic fibrosis progression in chronic hepatitis C

Data table header descriptions
VALUE log2 Robust Multi-Array (RMA) signal intensity

Data table
14q0_st 1.62201
14qI-1_st 2.56636
14qI-1_x_st 2.4834
14qI-2_st 0.756368
14qI-3_x_st 0.868349
14qI-4_st 0.625141
14qI-4_x_st 0.939366
14qI-5_st 0.802294
14qI-6_st 0.772685
14qI-7_st 1.58049
14qI-8_st 1.53085
14qI-8_x_st 1.9238
14qI-9_x_st 1.08814
14qII-10_st 0.853257
14qII-11_st 0.521801
14qII-12_st 0.913684
14qII-12_x_st 0.949603
14qII-13_st 1.19641
14qII-14_st 0.961498
14qII-14_x_st 0.711499

Total number of rows: 36353

Table truncated, full table size 858 Kbytes.

Supplementary file Size Download File type/resource
GSM1936859_mild_M_C203_miRNA-4_0_.CEL.gz 686.0 Kb (ftp)(http) CEL
Processed data included within Sample table

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