GEO help: Mouse over screen elements for information.
Status
Public on May 13, 2019
Title
USC/ACUIGEN-Ruditapes philippinarum-8 × 15 k-designID: 072098
Technology type
spotted oligonucleotide
Distribution
non-commercial
Organism
Ruditapes philippinarum Manufacturer
Acuigen group, Dpto de Zoología, Genética y Antropología Física,Facultad Veterinaria, Campus de Lugo, Universidade de Santiago de Compostela
Manufacture protocol
A total of 14,615 oligo-probes corresponding to 11,288 different Manila clam transcripts, 10,987 of them (97.9%) annotated. A total of 9,094 oligo-probes came from the HS-transcriptome, while 5,521 oligo-probes were from MR- and ML-transcriptomes. Among the HS-transcriptome probes, 5,770 corresponded to consistently annotated transcripts in the NCBI nr protein database and 236 DE to non-annotated transcripts, but showing a high DE between infected and control clams (Hasanuzzamann et al., 2017). This latter set consisted in 472 probes since forward and reverse oligo-probes were necessary. Finally, 2,852 transcripts annotated to well-known proteins were replicated. Regarding the other two reported transcriptomes, a total of 3,627 oligo-probes corresponded to the MR-transcriptome (584 of them associated with immune response), 1,605 to the ML-transcriptome, and 289 were common to both MR and ML transcriptomes.The probes were synthesized in a random layout using the Agilent methodology.
Submission date
May 22, 2017
Last update date
May 13, 2019
Contact name
Belen G Pardo
E-mail(s)
belen.gomez@usc.es Phone
+34 982822428
Organization name
University of Santiago de Compostela
Department
Zoology, Genetics and Physical Anthropology
Lab
Acuigen
Street address
Avda. Carballo Calero s/n
City
LUGO
State/province
LUGO
ZIP/Postal code
27002
Country
Spain
Samples (48)
GSM2634665 , GSM2634666 , GSM2634667 , GSM2634668 , GSM2634669 , GSM2634670
GSM2634671 ,
GSM2634672 ,
GSM2634673 ,
GSM2634674 ,
GSM2634675 ,
GSM2634676 ,
GSM2634677 ,
GSM2634678 ,
GSM2634679 ,
GSM2634680 ,
GSM4221963 ,
GSM4221964 ,
GSM4221965 ,
GSM4221966 ,
GSM4221967 ,
GSM4221968 ,
GSM4221969 ,
GSM4221970 ,
GSM4221971 ,
GSM4221972 ,
GSM4221973 ,
GSM4221974 ,
GSM4221975 ,
GSM4221976 ,
GSM4221977 ,
GSM4221978 ,
GSM4221979 ,
GSM4221980 ,
GSM4221981 ,
GSM4221982 ,
GSM4221983 ,
GSM4221984 ,
GSM4221985 ,
GSM4221986 ,
GSM4221987 ,
GSM4221988 ,
GSM4221989 ,
GSM4221990 ,
GSM4221991 ,
GSM4221992 ,
GSM4221993 ,
GSM4221994 Series (3)
GSE99162 Gene Expression Analysis of Ruditapes philippinarum Haemocytes after Experimental Perkinsus olseni Zoospore Challenge and Infection in the Wild
GSE142172 Manila clam - Perkinsus olseni interaction based on gene expression analysis of clam hemocytes and parasite trophozoites [Manila clam]
GSE142666 New insights into the Manila clam – Perkinsus olseni interaction based on gene expression analysis of clam hemocytes and parasite trophozoites through in vitro challenges
Data table header descriptions ID Row Matrix Row
Col Matrix Column
ControlType Control Probe : 1; otherwise : 0
ProbeName Probe Name
SPOT_ID SEQUENCE Probe Oligo
Ref_seq_Anot genebank number of annotating sequence
Annotation Sequence Annotation
Data table ID Row Col ControlType ProbeName SPOT_ID SEQUENCE Ref_seq_Anot Annotation 1
1
1
1
GE_BrightCorner
CONTROL
2
1
2
1
DarkCorner
CONTROL
3
1
3
1
DarkCorner
CONTROL
4
1
4
0
Contig7783reverse.0
CACTGCTGGTGTCTCAATTAAGCCGGCTTTGCTGCTGTTCATCTCTTCAGAGTTG
gb|EKC18506.1|
WD repeat-containing protein 55, partial [Crassostrea gigas]
5
1
5
0
comp369067_c0_seq1reverse.0
GGGAGCTGAAACCATTGAACATACTCTAAACTCACTGATGAATACACATAGCAGTC
ref|XP_005098445.1|
PREDICTED: uncharacterized protein C6orf62 homolog [Aplysia californica]
6
1
6
0
comp1759221_c0_seq1reverse.0
CTATTGAACAAAGAGAAGAGTCAAAGGGTACAAATGAGCAACGTGTACTATTGGCC
dbj|BAE96758.1|
putative 14-3-3 epsilon [Dugesia japonica]
7
1
7
0
ruditapes_c20663.0
TTATGTGTCCTGGTGAGCAATGTTATTCTGAGCACGACTTGACGCACCTGGTGTG
jagged 1
8
1
8
0
Rphi_c21948.0
ATGTTTCACTTCCCCAATGTGTGTCTGGCTATCAAAGTTGTGGAGGGACACCAGA
ref|XP_002157557.2|
PREDICTED: uncharacterized protein LOC100201718 [Hydra vulgaris]
9
1
9
0
ruditapes2_lrc4494.0
GGCACTGCACAGAGATCTACTAGACAATTACTGCTATTGAACTGTATCGGTTTTGT
ref|XP_005108000.1|
PREDICTED: 60S ribosomal protein L10a-2-like [Aplysia californica]
10
1
10
0
comp389257_c0_seq2reverse.1
CCTTGACCTTCCTGACCCATAACAGGCTAAATTATGACAGTATGCAGCAAGGAAA
gb|ESO96999.1|
hypothetical protein LOTGIDRAFT_115354 [Lottia gigantea]
12
1
12
0
Contig4067.1
CTGAAGGAATCCATGTATTTGCGTATATTGATCCGCCATAAACCACTATAAAGGGG
gb|EKC42922.1|
Amiloride-sensitive amine oxidase [copper-containing] [Crassostrea gigas]
13
1
13
0
Contig2140reverse.1
GCTCTTCTACAATAACAGTTACTGTTTGGCATTTCCGACCACATAACTATTGTGCG
NA
14
1
14
0
Contig8719.0
GCGGGAGGAAACACAACTTCGTGAAGAACTTGTCGCACAACAGATTAAGTATAGAG
gb|EKC35375.1|
Pleckstrin-like protein domain family B member 2 [Crassostrea gigas]
15
1
15
0
Rphi_rep_c38101.0
GAAGACAAGGCAACATGGAAGTCCAACTACTTCATCAAGATTGCTAAACTTTTGG
gb|EKC26031.1|
60S acidic ribosomal protein P0 [Crassostrea gigas]
16
1
16
0
Rphi_rep_c51350reverse.0
GAGGAACACCCCGTACTTCTCACTGAAGCCCCTCTAAATCCTAAGGCAAATAGAGA
gb|EJW72694.1|
actin-2, partial [Wuchereria bancrofti]
17
1
17
0
Contig7511reverse.0
GGCACTGTGTAATCAGACATAACATATGTCCAAACAGCAGCATTAGACCAAATGT
NA
18
1
18
0
comp388687_c0_seq1.0
TGGTCACAAAGTTCAAGTTGTTTCATTGTGCATCAACAATTTGGAGAAGGGGAAG
gb|EKC18810.1|
OTU domain-containing protein 6B [Crassostrea gigas]
19
1
19
0
comp385426_c0_seq1reverse.1
GATGGATGAACTTTCGCCTCAGAGGCTGTGTGAATTTTACAAGATTGGAGTAAAT
gb|EKC18912.1|
Cathepsin Z [Crassostrea gigas]
20
1
20
0
Rphi_rep_c46541reverse.0
GTGCTATGTTAGCTTTGGATTTTGAACAAGAAATGGCAACAGCTGCATCATCTAG
sp|Q00215.1|ACTC_STYPL
RecName: Full=Actin, cytoplasmic
21
1
21
0
comp385678_c1_seq1reverse.0
ATTGCTAAGGTCAATGCCATGTTAATAGCCAAAGGAAAGCTGAAACCTTCCCAGC
gb|ACH87543.1|
splicing factor 1 K-like RNA-binding domain protein [Platynereis dumerilii]gb|ACH87547.1| splicing factor 1 K-like RNA-binding domain protein [Platynereis dumerilii]
15151 2548 Kbytes .Supplementary data files not provided
Less...
More...