Rice MPSS Library Information

The data in this database are from an obsolete technology. Our SBS data and our other short-read-based Rice databases are accessible and described on our index page.

The rice mRNA and small RNA data is described in Nature Biotechnology 25: 473-477. For general information on this dataset, please visit the following GEO Series links: GSE7107, GSE10523. You can also click on the GEO Accession Number to open the direct link to view the information about each library.

Small RNA Libraries

Code Title Technology Total
Sequences		 Genome
Matched
Reads		 Distinct
Genome
Matched
Reads		 t/r/sn/snoRNA
Matched
Reads		 Norm.
Base
Value		 GEO
Accession
Number
STM Stem MPSS 520,676 362,484 49,495 19,427 250K GSM170921
SNU Germinating seedlings MPSS 701,631 523,754 27,828 19,026 250K GSM170919
FLR Nipponbare Immature panicles- 90 days old plants MPSS 1,731,548 1,062,314 216,927 50,234 250K GSM170917
SNM Germinating seedlings infected with Magnaporthe grisea (strain 70-15) MPSS 541,360 412,013 24,839 17,116 250K GSM265797
ABA Seedlings treated with ABA MPSS 448,763 364,230 29,468 8,712 250K GSM265798
UNT Seedling control for ABA treatment MPSS 529,886 428,420 47,593 10,441 250K GSM265799

mRNA Libraries

Code Title Technology 17 bp Total
Sequences		 20 bp Total
Sequences		 GEO
Accession
Number
NYR 14 days - Young Roots MPSS
1,944,785
1,330,133
GSM170914
NRA 60 days - Mature Roots - Replicate A MPSS
2,675,567
1,925,649
 
NRB 60 days - Mature Roots - Replicate B MPSS
2,617,770
1,955,815
 
NGD 10 days - Germinating seedlings grown in dark MPSS
2,512,579
1,963,932
GSM169569
NST 60 days - Stem MPSS
2,095,983
1,438,617
GSM170909
NYL 14 days - Young leaves MPSS
2,249,147
1,675,313
GSM170912
NLA 60 days - Mature Leaves - Replicate A MPSS
1,073,991
774,721
 
NLB 60 days - Mature Leaves - Replicate B MPSS
1,348,557
1,001,565
 
NLC 60 days - Mature Leaves - Replicate C MPSS
1,263,549
958,846
 
NLD 60 days - Mature Leaves - Replicate D MPSS
1,254,824
944,407
 
NME 60 days - Crown vegetative meristematic tissue MPSS
2,568,641
2,018,455
GSM170902
NPO Mature Pollen MPSS
2,310,574
1,836,178
GSM170903
NOS Ovary and mature stigma MPSS
2,499,264
1,922,660
 
NIP 90 days - Immature panicle MPSS
2,661,421
2,042,459
GSM170900
NGS 3 days - Germinating seed MPSS
1,861,571
1,271,334
GSM169568
NCA 35 days - Callus MPSS
2,131,255
1,523,370
GSM169562
NSR 14 days - Young roots stressed in 250 mM NaCl for 24h MPSS
1,842,226
1,281,591
GSM170907
NSL 14 days - Young leaves stressed in 250 mM NaCl for 24h MPSS
2,531,362
1,973,678
GSM170905
NDR 14 days - Young roots stressed in drought for 5 days MPSS
2,190,870
1,580,846
GSM169568
NDL 14 days - Young leaves stressed in drought for 5 days MPSS
2,613,140
1,926,066
GSM169567
NCR 14 days - Young roots stressed in 4C cold for 24h MPSS
2,401,553
1,824,875
GSM169566
NCL 14 days - Young leaves stressed in 4C cold for 24h MPSS
2,322,924
1,720,104
GSM169564
XC00 Unwounded Control-Nipponbare Xa21-0hr MPSS
1,190,318
902,921
 
XC06 Mock treatment-6hr MPSS
1,367,076
1,051,340
 
XC24 Mock treatment-24hr MPSS
1,165,716
914,150
 
XR03 X.oryzae-R-3hr MPSS
1,134,269
874,545
 
XR06 X.oryzae-R-6hr MPSS
1,269,616
962,174
 
XR12 X.oryzae-R-12hr MPSS
1,542,183
1,263,925
 
XR24 X.oryzae-R-24hr MPSS
1,055,586
826,749
 
XR48 X.oryzae- R-48hr MPSS
1,248,814
1,022,364
 
XS03 X.oryzae-S-3hr MPSS
1,466,965
1,162,447
 
XS06 X.oryzae-S-3hr MPSS
1,419,178
1,113,297
 
XS12 X.oryzae- S-12hr MPSS
1,444,840
1,177,043
 
XS24 X.oryzae- S24hr MPSS
1,264,383
1,017,047
 
XS48 X.oryzae-S-48hr MPSS
1,175,368
912,629
 
MR03 M. grisea-R-3hr MPSS
1,422,272
1,167,077
 
MR06 M. grisea-R-6hr MPSS
1,054,700
834,384
 
MR12 M. grisea-R-12hr MPSS
1,331,343
995,468
 
MR24 M. grisea-R-24hr MPSS
1,435,098
1,063,532
 
MR48 M. grisea-R-48hr MPSS
1,367,250
1,136,745
 
MS03 M. grisea-S-3hr MPSS
1,584,229
1,289,755
 
MS06 M. grisea-S-6hr MPSS
1,354,948
826,456
 
MS12 M. grisea-S-12hr MPSS
1,086,361
812,566
 
MS24 M. grisea-S-24hr MPSS
1,022,535
812,221
 
MS48 M. grisea-S-48hr MPSS
1,518,407
1,176,137
 
MS96 M. grisea-S-96hr MPSS
1,061,873
809,692
 
MC00 Mock treatment-0hr MPSS
1,372,860
1,112,770
 
MC24 Mock treatment-24hr MPSS
1,402,116
1,167,682
GSM629189
I9RO Roots MPSS
2,162,940
1,593,078
 
I9RR Roots - Replicate MPSS
2,156,164
1,594,323
 
I9LA Leaves MPSS
1,606,175
1,235,049
 
I9LB Leaves - Replicate MPSS
1,005,937
802,077
 
I9LC Leaves MPSS
1,144,192
875,786
 
I9LD Leaves - Replicate MPSS
1,146,212
848,298
 
I9ME Merismatic Tissue MPSS
2,112,790
1,495,639
 
FRO F1 Hybrid 60days Mature Root MPSS
2,436,387
1,902,752
 
FRR F1 Hybrid 60days Mature Root-Repl MPSS
2,205,884
1,708,041
 
FLA F1 Hybrid 60days Mature Leaf Replicate A MPSS
1,171,478
855,097
 
FLB F1 Hybrid 60days Mature Leaf Replicate B MPSS
1,040,468
777,927
 
FLC F1 Hybrid 60days Mature Leaf Replicate C MPSS
1,056,621
802,877
 
FLD F1 Hybrid 60days Mature Leaf Replicate D MPSS
1,419,115
1,158,992
 
FME F1 Hybrid 60days Meristematic tissue MPSS
3,045,290
2,226,486
 
PSC rice developing seeds, 6 days old cypress high milling(99-1710) MPSS
1,266,713
1,046,055
 
PSI rice developing seeds,6 days old, Ilpumbyeo - High Taste MPSS
1,201,584
991,832
 
PSL rice developing seeds, 6 days old, LaGrue-Low Milling MPSS
1,082,099
885,188
 
PSN rice developing seed, 6 days old, Nipponbare-Grain quality control MPSS
1,207,914
969,922
 
PSY rice developing seeds,6 days old, YR15965Acp33 - Low Taste MPSS
1,190,250
970,285
 
PLA rice leaf, beet armyworm damaged, 24 hr(99-1726) MPSS
1,150,869
927,594
 
PLW rice leaf, water weevil damaged, 24 hr MPSS
1,012,170
799,900
 
PLC rice leaf, mechanical damaged, 24 hr MPSS
1,213,577
980,722