Arabidopsis Small RNA Library Information

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Code Title Technology Total
Sequences
Genome
Matched
Reads*
Distinct
Genome
Matched
Reads*
t/r/sn/snoRNA
Matched
Reads
Norm.
Base
Value
Max.
Len. of
Reads
Min.
Len. of
Reads
GEO
Accession
Number
Col0 Col-0 wildtype, control for Ecker libraries (met1, rdd, ddc libraries); unopened, immature flower budsSBS2,609,1962,516,337976,11492,8171M2818GSM277608
ddc drm1-2 drm2-2 cmt3-11 triple mutant plants in a Col-0 background; unopened, immature flower budsSBS1,625,9181,511,746605,897113,3671M2818GSM277610
met1 met1-3 mutant plants in a Col-0 background; unopened, immature flower budsSBS1,694,1671,506,711503,581187,1041M2818GSM277609
rdd ros1-3 dml2-1 dml3-1 triple mutant plants in a Col-0 background; unopened, immature flower budsSBS4,094,7543,919,4621,284,034173,5551M2818GSM277611
Col0b Col-0 wildtype, control for Ecker libraries (abh1, ein5, ein5/abh1 libraries); unopened, immature flower budsSBS2,165,5871,884,391874,305107,3571M3318GSM284747
abh11 abh1-1 mutant plants in a Col-0 background; unopened, immature flower budsSBS2,897,0832,487,0911,175,115143,7391M3318GSM284748
ein56 ein5-6 mutant plants in a Col-0 background; unopened, immature flower budsSBS2,110,7761,836,942885,466118,7131M3318GSM284749
ein56abh11 ein5-6/abh1-1 mutant plants in a Col-0 background; unopened, immature flower budsSBS1,709,1381,473,904816,81790,6551M3318GSM284750
SUr2a Arabidopsis untreated rdr2 flowers - replicated run "a"SBS2,576,6571,586,518354,158298,7181M3218GSM280229
SUr2b Arabidopsis untreated rdr2 flowers - replicated run "b"SBS2,611,1791,642,149383,299372,6321M3318GSM280230
SWT1 Arabidopsis untreated wt flowersSBS1,674,2961,037,336492,39687,0921M3218GSM280228
S234a Arabidopsis untreated flowers, triple mutant dcl234 - replicated run "a"SBS2,641,8321,647,464370,548312,5261M3218GSM280231
S234b Arabidopsis untreated dcl234 flowers - replicated run "b"SBS2,251,4501,337,345329,125289,2631M3318GSM280232
RMMT49 Col-0 inflorescence; Slotkin et al., 2009SBS5,280,4703,200,3981,419,736849,0521M3118
RMKS02 ddm1 inflorescence in Col-0 background; Slotkin et al., 2009SBS4,952,3233,568,2261,113,648387,5761M3118
RMKS01 Col-0 pollen cells; Slotkin et al., 2009SBS2,540,585551,394297,771781,7661M3118
RMKS03 Col-0 sperm cells; Slotkin et al., 2009SBS1,925,202524,532275,844350,8601M3118
RMMT10 Col-0 callus; Tanurdzic et al., 2008SBS4,146,450811,656323,0351,397,9911M3218
RMMT11 Col-0 cultured cells at 4 days; Tanurdzic et al., 2008SBS4,123,0351,400,968517,8981,814,2921M3118
RMMT05 A. arenosa leavesSBS3,882,1891,307,566183,684416,8061M3418
RMMT12 A. arenosa inflorescenceSBS7,266,139413,834122,224650,8951M3418
MTSRNA2 Col-0 cultured cells at 7 days; Tanurdzic et al., 2008SBS2,863,628665,270237,650482,7621M3418
MTSRNA1 Col-0, leaf; Tanurdzic et al., 2008SBS2,870,734926,951251,560507,3451M3418
CxC5d Siliques, 5 days after pollination; Col x Col, F1 hybrid. Mosher et al., 2009SBS243,803109,04553,17124,3511M2718GSM385393
CxL5d Siliques, 5 days after pollination; Col x Ler, F1 hybrid. Mosher et al., 2009SBS362,309171,49578,90122,9921M2718GSM385394
LxL5d Siliques, 5 days after pollination; Ler x Ler, F1 hybrid. Mosher et al., 2009SBS349,141126,81058,35912,7511M2718GSM385395
LxC5d Siliques, 5 days after pollination; Ler x Col, F1 hybrid. Mosher et al., 2009SBS552,982231,36392,97533,1911M2718GSM385396
Cola 135 Col-0 flowers (stage 12) none 1SBS2,637,9862,503,011774,875134,9431M3018GSM342999
Colb 136 Col-0 flowers (stage 12) none 2SBS2,454,6532,361,376565,65993,2621M3018GSM343000
Colc 137 Col-0 flowers (stage 12) none 3SBS2,483,4412,365,792513,170117,6171M3018GSM343001
ago1a 138 ago1-25 flowers (stage 12) none 1SBS3,526,9722,999,843761,821527,0851M3018GSM343002
ago1b 139 ago1-25 flowers (stage 12) none 2SBS3,310,8592,689,518736,193621,3041M3018GSM343003
ago1c 140 ago1-25 flowers (stage 12) none 3SBS2,790,8472,481,621799,223309,1941M3018GSM343004
Col7a 141 Col-0 whole-aerial mock 7dpi 1SBS684,539601,534282,70582,9981M2718GSM506656
Col7b 142 Col-0 whole-aerial mock 7dpi 2SBS633,127540,559255,37192,5541M2718GSM506657
Col7c 143 Col-0 whole-aerial mock 7dpi 3SBS535,636488,026252,95447,6021M2718GSM506658
Col10a 155 Col-0 whole-aerial mock 10dpi 1SBS676,128615,198218,00860,9161M2718GSM506662
Col10b 156 Col-0 whole-aerial mock 10dpi 2SBS822,492728,109246,40594,3771M2718GSM506663
Col10c 157 Col-0 whole-aerial mock 10dpi 3SBS1,975,8441,759,692312,485216,1161M2718GSM506664
dcl17a 161 dcl1-7 whole-aerial mock 7dpi 1SBS701,602588,211334,666113,3851M2718GSM506668
dcl110a 165 dcl1-7 whole-aerial mock 10dpi 1SBS817,766666,509357,756151,2411M2718
dcl2347a 169 dcl234 whole-aerial mock 7dpi 1SBS577,980497,72253,12780,2191M2718
dcl23410a 173 dcl234 whole-aerial mock 10dpi 1SBS919,014774,84567,186144,1221M2718
dcl17b 162 dcl1-7 whole-aerial mock 7dpi 2SBS834,943680,358371,862154,5691M2718GSM506669
dcl17c 163 dcl1-7 whole-aerial mock 7dpi 3SBS770,214595,987337,376174,2091M2718GSM506670
dcl110b 179 dcl1-7 whole-aerial mock 10dpi 2SBS785,849691,969370,69793,8731M2718
dcl110c 180 dcl1-7 whole-aerial mock 10dpi 3SBS880,289764,810427,923115,4651M2718
dcl2347b 181 dcl234 whole-aerial mock 7dpi 2SBS1,070,752824,93782,581245,7651M2718
Col7d 182 Col-0 whole-aerial mock 7dpi 4SBS706,832584,725158,326121,9721M2718
dcl23410b 183 dcl234 whole-aerial mock 10dpi 2SBS865,167778,40978,59686,7111M2718
dcl23410c 184 dcl234 whole-aerial mock 10dpi 3SBS1,092,353852,57879,412239,7091M2718
TuMV7dpiA Col0 TumV treated 7dpi Replicate 1 w/o TumV tagsSBS741,486648,852301,52792,6251M2718GSM506659
TuMV7dpiB Col0 TumV treated 7dpi Replicate 2 w/o TuMV tagsSBS953,728811,345284,121142,3701M2718GSM506660
TuMV7dpiC Col0 TumV treated 7dpi Replicate 3 w/o TuMV tagsSBS837,363741,151297,28796,1971M2718GSM506661
TuMV10dpiA Col0 TumV treated 10dpi Replicate 1 w/o TuMV tagsSBS954,631880,060281,35374,5651M2718GSM506665
TuMV10dpiB Col0 TumV treated 10dpi Replicate 2 w/o TuMV tagsSBS768,234714,409271,24353,8131M2718GSM506666
TuMV10dpiC Col0 TumV treated 10dpi Replicate 3 w/o TuMV tagsSBS522,084469,180185,66652,8951M2718GSM506667
Vector_IP Vector control for AGO IP data, from Col-0 mixed-stage inflorescenceSBS54,588,22144,311,365207,8142,411,1721M3618GSM989350
AGO1_DDH_IP AGO IP data for DDH mutant, Arabidopsis mixed-stage inflorescenceSBS27,365,11120,428,1391,019,824188,7361M3618GSM989351
AGO1_DAH_IP AGO IP data for DAH mutant, Arabidopsis mixed-stage inflorescenceSBS153,301,335135,804,5392,456,656548,2071M3618GSM989352
Col_1 "Col rep1" in Lee et al. (2012) Inflorescence of Arabidopsis Columbia (Col-0) plants, replication 1SBS3,711,1781,662,202755,834533,1751M3418GSM893112
Col_2 "Col rep2" in Lee et al. (2012) Inflorescence of Arabidopsis Columbia (Col-0) plants, replication 2SBS11,396,0676,188,5082,096,0171,299,8161M3418GSM893113
Col_3 "Col rep3" in Lee et al. (2012) Inflorescence of Arabidopsis Columbia (Col-0) plants, replication 3SBS9,690,0244,946,0441,710,8641,119,1371M3418GSM893114
nrpe_1 "nrpe rep1" in Lee et al. (2012) Inflorescence of Arabidopsis nrpd1b-11 mutant, replication 1SBS4,537,2221,314,919577,4101,128,8701M3418GSM893115
nrpe_2 "nrpe rep2" in Lee et al. (2012) Inflorescence of Arabidopsis nrpd1b-11 mutant, replication 2SBS9,787,1404,593,2701,609,5211,441,7561M3418GSM893116
nrpe_3 "nrpe rep3" in Lee et al. (2012) Inflorescence of Arabidopsis nrpd1b-11 mutant, replication 3SBS9,343,0334,327,8561,524,3431,406,9741M3418GSM893117
FRDR2a “rdr2” library in Lee et al. (2012) Inflorescence of Arabidopsis rdr2-1 mutantSBS9,001,7334,322,052172,3013,664,2581M3418GSM893124
pd1_b “nrpd1” library in Lee et al. (2012) Inflorescence of Arabidopsis nrpd1a-4 mutantSBS13,580,5752,858,557491,7708,889,9371M3418GSM893123
edt Wt(T+S) control in Lee et al. (2012) Inflorescence of Arabidopsis transgenic line containing “target+silencer”SBS6,670,9215,106,2821,348,941325,8331M3418GSM893118
dms4 "dms4-1" library in Lee et al. (2012) Inflorescence of Arabidopsis EMS mutant dms4-1SBS5,809,2354,043,5491,085,912549,9281M3418GSM893119
AtD1 “drd1-1” library in Lee et al. (2012) Inflorescence of Arabidopsis EMS mutant drd1-1SBS25,062,88413,235,0152,203,1961,575,6151M3118GSM893120
AtS3 “dms3-1” library in Lee et al. (2012) Inflorescence of Arabidopsis EMS mutant dms3-1SBS29,196,14216,592,0692,750,6271,670,1431M3118GSM893121
AtS7 “rdm1-4” library in Lee et al. (2012) Inflorescence of Arabidopsis EMS mutant rdm1-4SBS28,859,67313,549,2312,407,9711,804,2361M3118GSM893122
Ath_ovule wild type ovules of ArabidopsisSBS4,198,5112,441,563506,684471,0191M3418GSM709567
ZhuSaltA Salt stress library, shoots, stress: 300mM NaCl for 5 hours, 10-day-old plantsSBS19,547,3569,031,8123,325,2578,304,1611M3117GSM832032
ZhuSaltB Col-0, shoots, stress: 300mM NaCl for 5 hours, 10-day-old plantsSBS11,606,2601,344,325827,1698,583,3461M3117GSM832033
FAta control for rdr2 library in Lee et al. (2012), from inflorescence of Arabidopsis Columbia (Col-0) plantsSBS12,155,0558,671,640842,1071,727,6291M3418GSM870550
hen1_1b Biological replicate, hen1-1 mutant, Ler background, inflorescenceSBS18,950,8225,138,5891,607,9163,389,3791M3118GSM870547
hen1_8_bcm hen1-8 mutant, Col background, inflorescenceSBS9,944,8703,502,8781,124,8062,700,0551M3118GSM870549
Ler_b Biological replicate, Landsberg erecta (Ler), wildtype, control for hen1-1b, inflorescence.SBS20,892,25511,435,5202,417,7211,465,6171M3118GSM870548
Control_hen1 small RNAs from AGO1 IP in hen1-8 and heso1-1/hen1-8, together with the input controlsSBS25,103,758441,487239,49417,490,3691M3415GSM1178870
Control_hen1heso small RNAs from AGO1 IP in hen1-8 and heso1-1/hen1-8, together with the input controlsSBS27,588,154516,679275,66320,079,1071M3415GSM1178871
AGO1IP_hen1 small RNAs from AGO1 IP in hen1-8 and heso1-1/hen1-8, together with the input controlsSBS24,134,85410,934,6161,314,0143,005,6901M3415GSM1178872
AGO1IP_hen1heso1 small RNAs from AGO1 IP in hen1-8 and heso1-1/hen1-8, together with the input controlsSBS11,156,0774,961,377478,8392,239,8291M3415GSM1178873
hen1_2 hen1-2SBS34,286,0953,790,976951,96625,530,6471M3415GSM1178867
ago1_11 ago1-11SBS29,458,7282,832,285407,68524,537,8721M3415GSM1178866
wt_4_ago1 wt_4_ago1SBS33,184,7252,813,402553,81527,760,5551M3415GSM1178869
hen1_ago1_db hen1_ago1_dbSBS29,734,0012,025,746457,77725,383,8211M3415GSM1178868
JZ_Ler_rep1 Arabidopsis Ler wildtype, control for hen1-1 rep1SBS2,374,442407,570166,229547,6581M4615GSM1178874
JZ_Ler_rep2 Arabidopsis Ler wildtype, control for hen1-1 rep2SBS5,321,574829,947311,9691,387,3851M4615GSM1178875
JZ_Ler_rep3 Arabidopsis Ler wildtype, control for hen1-1 rep3SBS6,088,8531,877,373565,4172,446,7161M4615GSM1178876
JZ_hen1_1_rep1 Arabidopsis hen1-1 mutant rep1SBS2,378,069344,253184,593452,7741M4615GSM1178877
JZ_hen1_1_rep2 Arabidopsis hen1-1 mutant rep2SBS5,791,631843,201394,5971,228,9091M4615GSM1178878
JZ_hen1_1_rep3 Arabidopsis hen1-1 mutant rep3SBS19,140,3794,611,3581,463,2915,813,9661M4615GSM1178879
JZ_Col_rep1 Arabidopsis Col wildtype, control for hen1-8 rep1SBS1,928,261369,206183,999472,0111M4615GSM1178880
JZ_Col_rep2 Arabidopsis Col wildtype, control for hen1-8 rep2SBS9,695,4642,864,856948,8344,078,7381M4615GSM1178881
JZ_Col_rep3 Arabidopsis Col wildtype, control for hen1-8 rep3SBS2,226,455700,925320,426986,8411M4615GSM1178882
JZ_hen1_8_rep1 Arabidopsis hen1-8 mutant rep1SBS4,264,177898,564475,595579,2881M4615GSM1178883
JZ_hen1_8_rep2 Arabidopsis hen1-8 mutant rep2SBS23,722,4869,595,0502,820,1995,351,8951M4615GSM1178884
JZ_hen1_8_rep3 Arabidopsis hen1-8 mutant rep3SBS14,077,0035,583,6731,911,2073,267,9191M4615GSM1178885



* Does not include the data listed in the column "t/r/sn/snoRNA Matched Reads".