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Sample GSM780516

Query DataSets for GSM780516

Status

Public on Mar 01, 2012

Title

C. brenneri_rep3_stage10

Sample type

RNA

Source name

C. brenneri, stage10

Organism

Caenorhabditis brenneri

Characteristics

developmental stage: Juvenile L1 larvae

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. brenneri_rep3_stage10

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

GPL14142

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
CBN22734_964-1023_0.958_1_A	3.117487e+001
CBN08360_750-809_0.895_17_B	3.955939e+001
CBN20079_1480-1539_0.932_2_A	5.311454e+002
CBN17599_467-526_0.951_1_A	1.015431e+002
CBN00059_138-197_0.924_1_A	1.209925e+002
CBN08477_1317-1376_0.793_31_A	4.409786e+004
CBN03719_772-831_0.941_4_A	1.962920e+002
CBN00486_1915-1974_0.844_75_B	1.973363e+002
CBN29433_1140-1199_0.953_1_A	3.703282e+002
CBN06275_225-284_0.898_22_A	4.960243e+001
CBN24585_428-487_0.945_1_A	4.571546e+001
CBN05268_1686-1745_0.894_22_C	9.130612e+001
CBN08182_636-695_0.934_4_B	4.598448e+002
CBN02695_670-729_0.881_40_B	2.487984e+002
CBN19419_1009-1068_0.960_1_A	5.401619e+001
CBN00789_1004-1063_0.934_3_C	4.571873e+001
CBN03219_1966-2025_0.880_32_C	4.972395e+001
CBN03616_64-123_0.897_9_C	2.136516e+002
CBN11783_219-278_0.922_1_B	9.484724e+002
CBN15162_1360-1419_0.882_13_A	7.471788e+002

Total number of rows: 43803

Table truncated, full table size 1796 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM780516_US90803649_252577710003_S01_GE1_105_Dec08_1_3.txt.gz	6.5 Mb	(ftp)(http)	TXT
Processed data included within Sample table
Processed data provided as supplementary file