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Sample GSM1936872 Query DataSets for GSM1936872
Status Public on May 01, 2016
Title severe chronic hepatitis C, female, C477
Sample type RNA
Source name plasma
Organism Homo sapiens
Characteristics gender: female
age: 54
ishak fiborosis score: 4
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 0.808256
14qI-1_st 1.93283
14qI-1_x_st 1.74209
14qI-2_st 1.02593
14qI-3_x_st 1.33516
14qI-4_st 0.988832
14qI-4_x_st 0.993176
14qI-5_st 1.03663
14qI-6_st 1.02243
14qI-7_st 1.79631
14qI-8_st 1.0226
14qI-8_x_st 0.974513
14qI-9_x_st 1.15997
14qII-10_st 1.01912
14qII-11_st 1.1249
14qII-12_st 1.38351
14qII-12_x_st 1.08227
14qII-13_st 0.794919
14qII-14_st 3.84153
14qII-14_x_st 1.30909

Total number of rows: 36353

Table truncated, full table size 859 Kbytes.

Supplementary file Size Download File type/resource
GSM1936872_severe_F_C477_miRNA-4_0_.CEL.gz 728.6 Kb (ftp)(http) CEL
Processed data included within Sample table

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