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Sample GSM1673629 Query DataSets for GSM1673629
Status Public on Oct 15, 2015
Title Cd-low rep3
Sample type RNA
 
Source name Daphnia pulex neonates <96hours
Organism Daphnia pulex
Characteristics developmental stage: neonate
stress: Cd
dose: 20 ppb
tissue: whole organsim
Treatment protocol Fifty D. pulex were randomly selected from each replicate for small RNA extraction
Growth protocol D. pulex were cultured in moderatly reconstituted hard water
Extracted molecule total RNA
Extraction protocol Small RNAs including miRNAs were extracted by PureLink miRNA extraction kit by invitrogen.
Label biotin
Label protocol In brief, 300ng of small RNA from each sample was labeled using the Affymetrix FlashTag Bioton HSR kit.
 
Hybridization protocol The labeled samples were hybridized to the arrays for 17 hours and were stained and washed using the standard miRNA protocol.
Scan protocol Affymetrix GeneChip Command Console Software was used to scan the arrays and generate CEL files.
Description Gene expression data from Cd-low
small RNAs
Data processing Arrays were visually scanned for abnormalities or defects. CEL files were imported into Genespring 12.0 (Agilent, Santa Clara, CA, USA) to generate RMA (robust multi-array average) expression levels (Lrizarry et al., 2003) using the RMA normalization option.
 
Submission date May 03, 2015
Last update date Oct 15, 2015
Contact name SHUAI CHEN
E-mail(s) shuai@PURDUE.EDU
Phone 7653373586
Organization name PURDUE UNIVERSITY
Department Forestry and Natural Resources
Lab 105
Street address 195 Marsteller Street
City West Lafayette
State/province IN
ZIP/Postal code 47907
Country USA
 
Platform ID GPL19117
Series (1)
GSE68481 Daphnia miRNA expression data from Cadmium exposed and none-exposed samples

Data table header descriptions
ID_REF
VALUE log2 RMA signal

Data table
ID_REF VALUE
MIMAT0000001_st 9.18
MIMAT0015091_st 1.08
MIMAT0000002_st 1.52
MIMAT0015092_st 1.52
MIMAT0020301_st 1.48
MIMAT0000003_st 2.05
MIMAT0020302_st 1.21
MIMAT0000004_st 8.12
MIMAT0000005_st 12.15
MIMAT0015093_st 1.70
MIMAT0020303_st 0.81
MIMAT0000006_st 1.18
MIMAT0020304_st 1.04
MIMAT0000007_st 1.11
MIMAT0015094_st 1.52
MIMAT0000008_st 0.85
MIMAT0020305_st 0.51
MIMAT0000009_st 3.14
MIMAT0020306_st 0.96
MIMAT0000010_st 0.88

Total number of rows: 36249

Table truncated, full table size 737 Kbytes.




Supplementary file Size Download File type/resource
GSM1673629_SC01mi006_miRNA-4_0_.CEL.gz 756.0 Kb (ftp)(http) CEL
Processed data included within Sample table

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