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Platform GPL15657 Query DataSets for GPL15657
Status Public on Jun 05, 2012
Title [CINT06a520380F] Affymetrix Ciona intestinalis custom-designed array
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Ciona intestinalis
Manufacturer Affymetrix
Manufacture protocol See manufacturer's website (www.affymetrix.com).
Catalog number CINT06a520380F
 
Description Probe identifiers:

There are a few different types of probe identifiers, including:

* MKG.<number>.<number>_s<OptionalNumber>_at
* Fis_ciad<number>_at
* TGxxxxx_at
* Gastxxx_at
* Zellerxxx_at

A probe identifier in the format MKG.7.115_s_at indicates that this probe targets the gene model KYOTOGRAIL2005.7.115 described in the http://aniseed.cnrs.fr database. The suffixes s0, s1, s2, etc. signify different "supplemental" gene models for the same locus.

The Aniseed transcript model pages for these models are located at URLs such as: http://www.aniseed.cnrs.fr/molecule-gene.php?name=KYOTOGRAIL2005.7.115.1

The Fis and TG probe identifiers refer to additional gene models based on EST data that were not covered by the KyotoGrail predictions. A probe identifier like Fis_ciad008l03 is based on a full-insert sequence. These have been submitted to GenBank and can be found in the GenBank EST section, e.g., http://www.ncbi.nlm.nih.gov/nucest?term=ciad008l03 .

The GastmiR and ZellerMiR identifiers are probe sets against Ciona microRNAs models. The models were generated by the labs of Terry Gaasterland (UCSD) and Robert Zeller (SDSU), respectively.

Gene identifiers:

The Platform table includes a "jgi1_GeneID" column with JGI1 gene model identifiers. JGI1 identifiers have the format ci0100<number>.

Further information on these JGI1 gene models can be found at URLs such as:
http://genome.jgi-psf.org/cgi-bin/dispGeneModel?db=ciona4&id=142570
http://ghost.zool.kyoto-u.ac.jp/cgi-bin/gb2/gbrowse/kh/?name=mRNA%3Aci0100142570;dbid=clone%3Adatabase
http://www.aniseed.cnrs.fr/molecule-gene.php?name=ci0100142570

This array is also described in ArrayExpress (http://www.ebi.ac.uk/arrayexpress/arrays/A-AFFY-106).

The oligonucleotide sequences are available in the supplementary file GPL15657_probe.fa.gz.
 
Contributor(s) Kawashima T
Citation(s) 18535245
Submission date Jun 04, 2012
Last update date Jun 05, 2012
Contact name Bradley J Davidson
E-mail(s) bjd18@email.arizona.edu
Phone 520 626-8113
URL http://www.mcrp.med.arizona.edu/html/braddavidson
Organization name University of Arizona
Department Molecular Cardiovascular Research Program
Lab Davidson
Street address PO Box 245217
City Tucson
State/province AZ
ZIP/Postal code 85724
Country USA
 
Samples (131) GSM942940, GSM942941, GSM942942, GSM942943, GSM942944, GSM942945 
Series (6)
GSE38313 Transcriptional analysis of fluorescence-activated sorted Mesp-GFP-labeled B7.5 founder trunk ventral cell lineage cells from Ciona intestinalis
GSE42267 Expression profiling of Ciona intestinalis neurula and mid-tailbud stage embryos expressing altered forms of the transcription factor Ci-Tbx2/3 in the notochord
GSE46751 Expression profiling of Ciona intestinalis initial tailbud stage embryos expressing mutant forms of the transcription factor Ci-XBP1 in the notochord.

Data table header descriptions
ID
KYOTOGRAIL2005 KyotoGrail gene model
JGI1_GeneID JGI gene model identifier
CLONE_ID Fis clone identifier
SPOT_ID

Data table
ID KYOTOGRAIL2005 JGI1_GeneID CLONE_ID SPOT_ID
18s-3_at 18s-3_at
18s-5_at 18s-5_at
18s-M_at 18s-M_at
28s-3_at 28s-3_at
28s-5_at 28s-5_at
28s-M_at 28s-M_at
b-actin-3_s_at b-actin-3_s_at
b-actin-5_s_at b-actin-5_s_at
b-actin-M_x_at b-actin-M_x_at
eIF-4a-3_s_at eIF-4a-3_s_at
eIF-4a-M_s_at eIF-4a-M_s_at
elF-4a-5_s_at elF-4a-5_s_at
ENSCINT00000021948_at Ensembl:ENSCINT00000021948
ENSCINT00000021990_at ci0100138327 Ensembl:ENSCINT00000021990
ENSCINT00000022469_at Ensembl:ENSCINT00000022469
ENSCINT00000022469_x_at Ensembl:ENSCINT00000022469
ENSCINT00000024814_at ci0100146942 Ensembl:ENSCINT00000024814
ENSCINT00000025135_at Ensembl:ENSCINT00000025135
ENSCINT00000025261_at Ensembl:ENSCINT00000025261
Fis_ciad001e01_20_s_at ciad001e01

Total number of rows: 30969

Table truncated, full table size 1909 Kbytes.




Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp

Supplementary file Size Download File type/resource
GPL15657_CINT06a520380F.cdf.gz 7.6 Mb (ftp)(http) CDF
GPL15657_probes.fa.gz 6.1 Mb (ftp)(http) FA

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