GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1256956 Query DataSets for GSM1256956
Status Public on Jun 01, 2014
Title central cell
Sample type RNA
Source name pool of central cells isolated by laser assisted microdissection
Organism Boechera gunnisoniana
Characteristics tissue: female reproductive tissues, germline
cell type: central cell
Treatment protocol no treatment
Growth protocol Seeds were surface sterilized and grown on MS plates for 10-14 days before transfer to a mixture of soil (ED73, Universalerde, Germany) and sand (5:1) fertilized with Plantomaag (Syngenta, Switzerland) and Osmocote (Scotts, Marysville, USA). Plants were grown in a greenhouse chamber with 60% humidity and 16 h light/ 8 h darkness at 20 °C and 16 °C, respectively.
Extracted molecule total RNA
Extraction protocol For total RNA isolation from cells or tissues isolated by laser assisted microdissection, caps were covered with 10 ul extraction buffer from the PicoPure RNA isolation kit (Arcturus Engineering, Mountain View, USA), incubated at 42°C for 30 min before isolation according to manufacturers instructions. The DNAse treatment was performed on-column using the RNAse-free DNase set (QIAGEN, Hilden, Germany).
Label biotin
Label protocol During the second round of amplification with the Message AmpII Kit (Ambion), biotin-11-UTP (ambion) was incorporated in th amplified aRNA for microarray analysis.
Hybridization protocol Hybridization-EukGE-WS2v4
Scan protocol GCOS
Description RNA amplification with Ambion Message AmpII Kit
Data processing BgPANP algorith with R/Bioconductor
presence absence p-values with BgPANP
Submission date Nov 01, 2013
Last update date Jun 01, 2014
Contact name Marc William Schmid
Organization name MWSchmid GmbH
Street address Hauptstrasse 34
City Glarus
ZIP/Postal code 8750
Country Switzerland
Platform ID GPL16112
Series (1)
GSE51996 Cell-type specific transcriptome analysis to study germline development and reproduction in apomictic Boechera gunnisoniana- ATH1 arrays

Data table header descriptions
VALUE RMA signal

Data table
AFFX-Athal-25SrRNA_s_at 13.1378922155406
AFFX-Athal-5SrRNA_at 2.76287444062546
AFFX-Athal-Actin_3_f_at 5.28698065800188
AFFX-Athal-Actin_5_r_at 6.8691388207477
AFFX-Athal-Actin_M_at 5.53405643337358
AFFX-Athal-GAPDH_3_s_at 3.10712450963903
AFFX-Athal-GAPDH_5_s_at 4.96948957827347
AFFX-Athal-GAPDH_M_s_at 5.45590638609908
AFFX-Athal-Ubq_3_f_at 7.139066122472
AFFX-Athal-Ubq_5_f_at 6.16900868905813
AFFX-Athal-Ubq_M_f_at 5.89929960579389
AFFX-BioB-3_at 9.50517081704811
AFFX-BioB-5_at 9.18828387188297
AFFX-BioB-M_at 9.45524661363684
AFFX-BioC-3_at 10.4866342214612
AFFX-BioC-5_at 10.5488131897156
AFFX-BioDn-3_at 12.6131404027591
AFFX-BioDn-5_at 11.8096932754814
AFFX-CreX-3_at 13.710599722261
AFFX-CreX-5_at 13.3925370559259

Total number of rows: 21492

Table truncated, full table size 627 Kbytes.

Supplementary file Size Download File type/resource
GSM1256956_BG_central_cell.CEL.gz 3.0 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap