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Sample GSM780433

Query DataSets for GSM780433

Status

Public on Mar 01, 2012

Title

C. remanei_rep1_stage7

Sample type

RNA

Source name

C. remanei,stage7

Organism

Caenorhabditis remanei

Characteristics

developmental stage: Ventral enclosure stage

Treatment protocol

For the embryo collection of all species adult hermaphrodites or females were collected and cut to obtain embryos. Embryos were washed with a bleach solution (70% DDW, 20% bleach, 10% 5M KOH) for 30 seconds and subsequently with a 5% BSA solution for 30 seconds. 4-cell embryos were collected,washed 4 times in clear DDW and incubated at 20°C for the appropriate time for each species to reach stages 1-10. After incubation embryos were frozen in liquid nitrogen and kept at -80°C until RNA extraction.

Growth protocol

Standard C. elegans techniques were followed to grow worms (Stiernagle 2006).

Extracted molecule

polyA RNA

Extraction protocol

RNA was extracted from embryos using Trizol. Each sample comprised 48 individually staged embryos. Total RNA was amplified by two round of in vitro transcription (IVT)and cy3 labeled using the MessageAmpII kit (Ambion). We also added to this reaction RNA from a Spike-in kit (Agilent) that included 10 different species of RNA at various concentrations.

Label

cy3

Label protocol

6μg of RNA was labeled with Cy-3 and 1.65μg of labeled aRNA was incubated on each microarray. Each embryonic stage was measured in independent biological triplicates.

Hybridization protocol

The hybridization and washing of the microarrays were performed following the Agilent protocol for single-channel arrays.

Scan protocol

Agilent Microarray Scanner was used to scan the slides

Description

C. remanei_rep1_stage7

Data processing

Feature Extraction was used for data processing with protocol GE1_105_Dec08

Submission date

Aug 16, 2011

Last update date

Mar 01, 2012

Contact name

Itai Yanai

E-mail(s)

yanai@technion.ac.il

Organization name

Technion - Israel Institute of Technology

Department

Biology

Lab

Yanai

Street address

Technion City

City

Haifa

ZIP/Postal code

30200

Country

Israel

Platform ID

GPL14146

Series (1)

GSE31422

Developmental milestones punctuate gene expression in the Caenorhabditis embryo

Data table header descriptions
ID_REF
VALUE	gProcessedSignal

Data table
ID_REF	VALUE
CRE03029_447-506_0.966_2_A	2.535119e+003
CRE18994_459-518_0.930_5_A	1.782931e+000
CRE19082_559-618_0.910_12_A	3.666877e+003
CRE13894_228-287_0.941_3_B	1.786315e+000
CRE16144_1989-2048_0.934_8_A	4.890865e+003
CRE12791_2344-2403_0.893_18_C	1.019927e+003
CRE27157_3017-3076_0.858_56_A	1.074128e+004
CRE21878_1138-1197_0.936_2_C	1.782612e+000
CRE08869_72-131_0.833_96_C	1.779868e+000
CRE24804_1510-1569_0.801_43_C	2.164420e+002
CRE22482_821-880_0.949_1_A	6.270975e+000
CRE24279_413-472_0.916_3_A	1.094432e+001
CRE01042_516-575_0.794_131_C	1.762891e+000
CRE07354_1168-1227_0.893_22_B	1.607793e+003
CRE00791_1862-1921_0.877_36_C	2.897924e+002
CRE17285_234-293_0.707_18_C	1.443201e+004
CRE29591_711-770_0.955_1_A	3.731232e+001
CRE13913_430-489_0.815_6_A	5.735026e+000
CRE17633_1159-1218_0.950_7_B	2.371933e+003
CRE05800_1347-1406_0.788_141_A	4.318248e+002

Total number of rows: 43803

Table truncated, full table size 1799 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM780433_US90803649_252577610006_S01_GE1_105_Dec08_1_3.txt.gz	6.4 Mb	(ftp)(http)	TXT
Processed data included within Sample table
Processed data provided as supplementary file