Arabidopsis MPSS Plus Library Information

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

Our MPSS small RNA data was described in Science 309: 1567-1569 and Genome Research 16:1276-1288, with additional data on this site gathered from other labs' publications. For general information on this dataset, please visit the following GEO Series links: GSE3008, GSE5343, GSE8994. You can click on the GEO Accession Number to open the direct link to view the information about each library and download its data.

Small RNA Libraries    Download data files (for some of the 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
FLR Inflorescence tissues, small RNA MPS MPSS
721,044
424,124
54,829
46,688
 250K GSM65747
RDR rdr2 inflorescence, small RNA MPSS MPSS
915,856
478,145
6,403
85,404
 250K GSM120717
SD1 Seedlings, small RNA MPSS set 1MPSS
686,124
252,759
13,746
226,609
 250K GSM65748
SD2 Seedlings, small RNA MPSS set 2 MPSS
802,978
244,132
16,741
268,536
 250K GSM65749
SDC Seedlings, small RNA MPSS sets 1 and 2 combined MPSS
1,489,102
496,891
20,454
495,145
 250K GSM65750
AB1 ABA-treated seedlings, small RNA MPSS set 1MPSS
744,203
206,734
23,721
282,638
 250K  
AB2 ABA-treated seedlings, small RNA MPSS set 2 MPSS
593,196
154,619
25,775
187,686
 250K  
ABC ABA-treated seedlings, small RNA MPSS sets 1 and 2 combinedMPSS
1,337,399
361,353
35,280
470,324
 250K  
FABAm Seedlings control without ABA treatment, small RNA 454 454
14,024
7,838
4,189
660
 10K 
FABAp ABA-treated seedlings, small RNA 454 454
6,186
3,463
1,848
352
 10K 
FCol0 Col-0 wildtype inflorescence tissues, small RNA 454 454
11,510
7,229
5,492
253
 10K GSM121455
Fdcl17 dicer1 (dcl1-7) inflorescence 454 454
16,768
8,519
7,813
167
 10K GSM121456
Fdcl234 dicer2/3/4 (dcl234) inflorescence 454 454
10,631
6,074
1,557
174
 10K GSM121457
Frdr2 rdr2 inflorescence 454 454
7,064
4,393
533
185
 10K GSM121453
Frdr6 rdr6 inflorescence 454 454
11,959
6,214
2,415
426
 10K GSM121454
FBFL wt - Flower, Bartel 454 expt 454
197,630
166,337
88,230
31,293
 250K 
FBLE wt - Leaf (rosette), Bartel 454 expt454
173,762
147,459
58,417
26,303
 250K 
FBSE wt - Seedling, Bartel 454 expt 454
184,651
140,886
63,667
43,765
 250K 
FBSI wt - Silique, Bartel 454 expt454
300,113
263,160
129,247
36,953
 250K 
FHag1 Immunopurified Arabidopsis AGO1 complex 454
152,088
150,857
6,050
1,231
 250K 
FHag4 Immunopurified Arabidopsis AGO4 complex 454
42,394
41,178
16,234
1,216
 50K 
FHwe whole plant extracts, Arabidopsis thaliana, wild-type Col-0 454
51,293
39,329
18,368
11,963
 50K 
FJWt wildtype, control for PolIV expt 454
75,618
55,318
37,348
1,090
 50K 
FJ1ab nrpd1a/1b 454
105,257
76,507
6,670
4,602
 50K 
FJ2ab nrpd2a/2b 454
71,914
47,493
6,983
2,143
 50K 
FJF1 F1 of nrpd1a/1b X nrpd2a/2b454
76,590
52,562
36,199
2,411
 50K 
JCWt Col-0, whole seedlings 454
22,467
19,483
10,903
2,984
 10K 
JC1hr Col-0, leaf tissue, inoculated with Pseudomonas syringae pv. tomato (DC3000hrcC), 1 hr p.i.454
18,388
16,184
10,747
2,204
 10K 
JC3hr Col-0, leaf tissue, inoculated with Pseudomonas syringae pv. tomato (DC3000hrcC), 3 hr p.i 454
10,387
8,986
5,925
1,401
 10K 
JCcmp Composite small RNA sequences454
123,113
113,993
19,733
9,115
 100K 
JCd1 dcl1-7, inflorescence tissue (stage 1-12 flowers) 454
17,840
15,900
13,819
1,940
 10K 
JCd2 dcl2-1, inflorescence tissue (stage 1-12 flowers) 454
13,688
12,534
9,629
1,154
 10K 
JCd3 dcl3-1, inflorescence tissue (stage 1-12 flowers)454
30,320
26,647
21,202
3,673
 10K 
JCd4 dcl4-2, inflorescence tissue (stage 1-12 flowers) 454
29,501
26,905
21,083
2,596
 10K 
JCinf Col-0, inflorescence tissue (stage 1-12 flowers)454
78,596
73,294
54,885
5,302
 10K 
JClef Col-0, leaf tissue 454
15,833
11,982
7,069
3,851
 10K 
JCr1 rdr1-1, inflorescence tissue (stage 1-12 flowers)454
19,761
18,418
13,813
1,343
 10K 
JCr2 rdr2-1, inflorescence tissue (stage 1-12 flowers)454
19,636
13,907
3,327
5,729
 10K 
JCr6a rdr6-15, whole seedlings454
23,988
18,688
13,718
5,300
 10K 
JCr6b rdr6-15, inflorescence tissue (stage 1-12 flowers)454
46,896
44,721
36,418
2,175
 10K 

mRNA Libraries    Download data files (for some of the libraries)

Code Title Technology 17 bp Total
Sequences		 20 bp Total
Sequences		 GEO
Accession
Number
CAF Callus - actively growing, classic MPSS MPSS
1,959,539
1,637,407
  
INF Infloresence - mixed stage, immature buds, classic MPSS MPSS
1,774,306
1,455,847
  
LEF Leaves - 21 day, untreated, classic MPSS MPSS
2,884,598
2,457,736
  
ROF Root - 21 day, untreated, classic MPSS MPSS
3,642,632
3,002,218
  
SIF Silique - 24 to 48 hr post-fertilization, classic MPSS MPSS
2,012,859
1,673,908
  
AP1 ap1-10 infloresence - mixed stage, immature buds MPSS
2,964,724
2,558,992
 GSM226844
AP3 ap3-6 infloresence - mixed stage, immature buds MPSS
2,435,965
2,050,647
 GSM226845
AGM agamous infloresence - mixed stage, immature buds MPSS
2,575,670
2,165,628
 GSM226843
INS Infloresence - mixed stage, immature buds MPSS
2,890,894
2,516,138
 GSM226767
ROS Root - 21 day, untreated MPSS
2,458,436
2,047,569
 GSM226769
SAP sup/ap1 infloresence - mixed stage, immature buds MPSS
2,310,350
1,874,297
 GSM226846
S04 Leaves, 4 hr after salicylic acid treatment MPSS
3,006,975
2,626,946
 GSM226847
S52 Leaves, 52 hr after salicylic acid treatment MPSS
2,964,840
2,584,795
 GSM226848
LES Leaves - 21 day, untreated MPSS
3,109,385
2,752,425
 GSM226768
GSE Germinating seedlings MPSS
2,550,655
1,805,187
  
CAS Callus - actively growing, signature MPSS MPSS
1,919,458
1,433,143
 GSM226766
SIS Silique - 24 to 48 hr post-fertilization, signature MPSS MPSS
2,349,283
1,869,453
 GSM226770
OVL Ovule - fully differentiated prior to pollination, signature MPSS MPSS
2,699,824
2,174,447
 GSM1212493
NZZ nozzle ovule fully differentiated prior to pollination, signature MPSS MPSS
2,775,817
2,175,089
 GSM1212494