Rice 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
G1_5 Total sRNA, extract from 1-5 days grain after fertilizationSBS640,003552,9131,713,52339,2642M3318GSM278571
G6_10 Total sRNA, extract from 6-10 days grain after fertilizationSBS582,848472,8241,713,52358,0342M3318GSM278572
AGO1a_IP sRNAs from AGO1a IP, extracted from 3-week-old seedlingsSBS3,791,0133,775,85822,09515,1262M3418GSM455962
AGO1b_IP sRNAs from AGO1b IP, extracted from 3-week-old seedlingsSBS1,230,6681,134,9824,48995,6862M2619GSM455963
AGO1c_IP sRNAs from AGO1c IP, extracted from 3-week-old seedlingsSBS3,891,6873,853,53615,31838,1512M2519GSM455964
AGO_CT sRNA control for IP, total small RNA extracted from 3-weeks-old seedlingsSBS4,029,4623,593,4611,959,081435,7312M2719GSM455965
AGO4a_IP sRNA from AGO4a IP, extracted from 3-week-old seedlingsSBS3,084,4102,614,0391,489,4558,5412M3018GSM520634
AGO4b_IP sRNA from AGO4b IP, extracted from 3-week-old seedlingsSBS7,503,1106,215,7733,312,99526,1442M3018GSM520635
AGO16_IP sRNA from AGO16 IP, extracted from 3-week-old seedlingsSBS6,950,5764,315,9251,672,62948,5042M3418GSM520636
dcl1_sdl sRNA from os dcl1, extracted from 3-week-old seedlingsSBS6,919,6713,923,7041,787,3431,658,4982M3118GSM520637
dcl3_sdl sRNA from os dcl3, extracted from 3-week-old seedlingsSBS7,863,1944,417,4821,594,5081,678,9842M3118GSM520638
rdr2_sdl sRNA from os rdr2, extracted from 3-week-old seedlingsSBS8,823,3923,614,261631,9921,549,8102M3118GSM520639
wt_sdl sRNA from wildtype, extracted from 3-week-old seedlingsSBS7,957,2204,407,2811,599,6731,326,9272M3118GSM520640
ME5a 14-day seedling leaf, Xoo inoculated, bacterial mutant ME5SBS4,592,7903,020,363329,578437,1612M3418
Pxo99a 14-day seedling leaf, Xoo inoculated, strain WR or PXO99ASBS7,362,8783,659,885721,065332,3182M3418
OsMock Rice leaves, mock treated with 10 mM MgCl2SBS4,734,1403,386,6621,009,539539,3222M3118
Leaf Rice leaf, from Zhonghua 10SBS10,777,3754,867,944617,1824,772,1112M3018
Root Rice root, from Zhonghua 10SBS10,424,0664,081,720974,2884,546,8002M3018
BCP Rice bicellular pollen, from Zhonghua 10SBS10,256,8524,264,6891,469,4984,724,0192M3018
Callus Rice callus cells, from Zhonghua 10SBS10,884,5334,868,1061,292,1134,289,5642M3018
TCP Rice tricellular pollen, from Zhonghua 10SBS12,212,9733,306,772569,1037,718,2482M3018
UNM Rice uninucleate microspores, from Zhonghua 10SBS5,513,7401,918,341956,9612,568,4932M3018
LACt1 leaves, Wildtype control for AGO mutant librarySBS6,270,2013,591,9021,236,5461,006,2672M3418
La706 leaves, argonaute mutant, T-DNA insertion in AGO706SBS3,265,9981,973,849825,851116,5212M3418
La706c Leaves, argonaute mutant in AGO706. Repeated SBS run.SBS2,236,1211,011,698472,81063,6002M3418
Lros1b Leaves, ros1 mutant. Repeated SBS run.SBS3,683,3451,505,920355,181149,0242M3418
LOsNpb Nipponbare leaf, sRNA librarySBS15,068,8568,209,7841,370,1753,532,6092M3418
OsTCP_b Rice tricellular pollen (TCP), from GEO record GSM722128SBS6,479,4842,868,603180,4341,753,1922M3418GSM722128
rdr6_HT rol_1, sterile, panicle of rdr6 grown in high temperatureSBS13,403,7849,960,3244,168,579591,14610M3518GSM648140
rdr6_LT rol_4, normal, panicle of rdr6 grown in low temperatureSBS13,517,2029,974,3023,856,982699,92110M3518GSM648142
zh_HT zh_1, normal, panicle of wildtype Zhonghua11 in high temperatureSBS15,926,14412,138,5494,234,530572,68110M3518GSM648139
zh_LT zh_4, normal, panicle of wildtype Zhonghua11 in low temperatureSBS15,795,92411,675,3224,129,233879,79010M3518GSM648141
704f Young inflorescence enclosed in sheaths from dcl4-1 mutant in 93-11 backgroundSBS3,487,1842,401,9891,428,9634,5872M2618GSM562945
704s 6-day old seedlings from dcl4-1 mutant in 93-11 backgroundSBS1,224,300905,849582,6954,4362M2618GSM562944
9311f young inflorescence enclosed in sheaths from wildtype 93-11SBS3,328,2062,312,4071,176,3402,9552M2618GSM562943
9311s 6-day old seedlings from wildtype 93-11SBS1,847,6421,418,197728,8645,7212M2618GSM562942
waf1-1 wavy leaf 1-1 (waf1-1), hen1 mutant alleleSBS45,297,54017,012,6222,779,55015,971,5275M3415GSM913520
waf1-2 wavy leaf 1-2 (waf1-2), hen1 mutant alleleSBS44,151,19915,733,0512,907,96515,246,8105M3415GSM913522
Wt_waf1-1 Wildtype control (for waf1-1)SBS51,198,09435,632,4665,269,1959,369,8725M3415GSM913521
Wt_waf1-2 Wildtype control (for waf1-2)SBS46,055,74529,837,7384,345,80310,609,5995M3415GSM913523
Wt_HEN1b wild type Dongjin control for hen1-3 alleleSBS23,979,62115,006,1082,245,5295,359,6545M3415GSM913525
Seg_Wt_HEN1b segregating wild type for hen1-3SBS37,538,20724,140,2022,780,1338,431,7485M3415GSM913526
Os hen1-3 Rice oshen1-3 mutant, T-DNASBS15,769,9084,817,170574,9986,017,6615M3415GSM913524
58N_1 Young panicles of Nongken 58, normal fertile lineSBS17,707,75515,794,3146,942,684494,9272M3418
58S_1 Young panicles of Nongken 58S, a male-sterile lineSBS19,936,96717,755,9797,603,674521,7412M3418
total_mel1 Small RNAs from total RNA of mel1 mutant young inflorescences, control for RIP-seqSBS4,950,9923,958,9201,703,812248,9705M3418
total_WT Small RNAs from total RNA of wildtype young inflorescences, control for RIP-seqSBS7,038,6435,860,2732,767,460333,4885M3418
MEL1IP_WT RIP-seq of MEL1-bound small RNAs, from wildtype young inflorescencesSBS13,594,33410,519,668920,4692,522,8685M3418
MEL1IP_mel1 RIP-seq of MEL1-bound small RNAs, from mel1 mutant young inflorescencesSBS65,04919,10512,10426,2365M3418
WTLamina Wildtype rice, material from lamina joints of the flag leafSBS31,885,56521,820,4438,892,3604,370,3578M3418SRX348485
3A1Lamina DCL3a-1 RNAi rice, material from lamina joints of flag leafSBS34,074,48920,177,3517,230,9175,576,2718M3418SRX348486
3A3Lamina DCL3a-3 RNAi rice, material from lamina joints of flag leafSBS44,077,38528,346,7619,692,8327,471,5128M3418SRX348487



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