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Sample GSM780537

Query DataSets for GSM780537

Status

Public on Mar 01, 2012

Title

C. elegans_rep3_stage1

Sample type

RNA

Source name

C. elegans, stage1

Organism

Caenorhabditis elegans

Characteristics

developmental stage: 4-cell 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. elegans_rep3_stage1

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

GPL14144

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
F58D5.1a_1211-1270_0.904_3_C	1.002550e+002
C09H10.9_374-433_0.913_9_A	3.631483e+000
C34F11.6_48-107_0.881_1_A	6.934567e+001
AC3.7_1046-1105_0.896_11_C	1.248701e+001
Y15E3A.3_461-520_0.860_37_A	9.833109e+000
Y87G2A.4_501-560_0.903_5_C	2.920385e+001
Y56A3A.3_213-272_0.954_1_A	2.999431e+003
W06E11.5a_376-435_0.938_3_C	2.516562e+002
C05D10.2a_1015-1074_0.931_8_B	3.681499e+001
Y37D8A.2_1579-1638_0.946_1_A	3.875954e+003
ZK669.5a_77-136_0.924_6_A	1.243294e+001
C11D2.2_722-781_0.936_3_B	3.594933e+000
ZK1073.1_555-614_0.908_8_B	1.653592e+001
Y39G8B.10_455-514_0.970_1_A	3.583541e+000
C50E3.7_545-604_0.926_4_B	3.577952e+000
ZC317.5_888-947_0.719_108_A	3.572024e+000
Y42A5A.2_1663-1722_0.956_1_A	1.166794e+001
T24C4.4_413-472_0.965_1_A	6.748436e+000
ZK1067.1c_3356-3415_0.901_10_B	4.070044e+001
F35C12.2a_905-964_0.885_24_A	2.904481e+001

Total number of rows: 43803

Table truncated, full table size 1780 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM780537_US90803649_252577510006_S01_GE1_105_Dec08_1_2.txt.gz	6.5 Mb	(ftp)(http)	TXT
Processed data included within Sample table
Processed data provided as supplementary file