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Sample GSM1936855 Query DataSets for GSM1936855
Status Public on May 01, 2016
Title mild chronic hepatitis C, female, C208
Sample type RNA
 
Source name plasma
Organism Homo sapiens
Characteristics gender: female
age: 40
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
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 1.0075
14qI-1_st 2.13986
14qI-1_x_st 1.9544
14qI-2_st 1.15347
14qI-3_x_st 0.786641
14qI-4_st 0.865937
14qI-4_x_st 0.925725
14qI-5_st 1.06447
14qI-6_st 0.965064
14qI-7_st 1.08406
14qI-8_st 1.12823
14qI-8_x_st 0.998591
14qI-9_x_st 0.944268
14qII-10_st 0.986385
14qII-11_st 1.08769
14qII-12_st 1.14637
14qII-12_x_st 0.971164
14qII-13_st 1.20813
14qII-14_st 1.10281
14qII-14_x_st 1.04134

Total number of rows: 36353

Table truncated, full table size 857 Kbytes.




Supplementary file Size Download File type/resource
GSM1936855_mild_F_C208_miRNA-4_0_.CEL.gz 718.3 Kb (ftp)(http) CEL
Processed data included within Sample table

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