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Sample GSM1936869 Query DataSets for GSM1936869
Status Public on May 01, 2016
Title severe chronic hepatitis C, female, C289
Sample type RNA
 
Source name plasma
Organism Homo sapiens
Characteristics gender: female
age: 40
ishak fiborosis score: 5
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
E-mail(s) kmatsuura0528@gmail.com
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
ID_REF
VALUE log2 Robust Multi-Array (RMA) signal intensity

Data table
ID_REF VALUE
14q0_st 2.07666
14qI-1_st 0.995951
14qI-1_x_st 0.839943
14qI-2_st 1.16193
14qI-3_x_st 0.787971
14qI-4_st 0.973058
14qI-4_x_st 0.748371
14qI-5_st 0.935773
14qI-6_st 0.99367
14qI-7_st 1.19595
14qI-8_st 1.26793
14qI-8_x_st 1.30296
14qI-9_x_st 0.694714
14qII-10_st 1.16938
14qII-11_st 0.731222
14qII-12_st 0.629182
14qII-12_x_st 0.845901
14qII-13_st 1.15889
14qII-14_st 1.42573
14qII-14_x_st 1.54099

Total number of rows: 36353

Table truncated, full table size 858 Kbytes.




Supplementary file Size Download File type/resource
GSM1936869_severe_F_C289_miRNA-4_0_.CEL.gz 645.8 Kb (ftp)(http) CEL
Processed data included within Sample table

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