Deep sequencing reads for mature sequence MIMAT0004702

Stem-loop ID hsa-mir-339
Mature ID hsa-miR-339-3p
Reads 
              hsa-miR-339-5p                     hsa-miR-339-3p                                 Count     RPM (mean number of reads per million)
.............CUCCCUGUCCUCCAGGAGCUCA...........................................................  1         0.201
..............UCCCUGUCCUCCAGGAGCUCA...........................................................  236       8.04
..............UCCCUGUCCUCCAGGAGCUCACG.........................................................  178       6.78
..............UCCCUGUCCUCCAGGAGCUCAC..........................................................  87        8.57
..............UCCCUGUCCUCCAGGAGCU.............................................................  85        2.22
..............UCCCUGUCCUCCAGGAGCUC............................................................  77        7.58
..............UCCCUGUCCUCCAGGAGCUCACGU........................................................  43        1.34
..............UCCCUGUCCUCCAGGAGC..............................................................  4         0.0733
..............UCCCUGUCCUCCAGGAG...............................................................  3         0.0583
................CCUGUCCUCCAGGAGCUCACGU........................................................  3         0.0519
................CCUGUCCUCCAGGAGCUCACG.........................................................  3         0.226
.................................................UGAGCGCCUCGACGACAGAGCCG......................  478       8.44
.................................................UGAGCGCCUCGACGACAGAGCC.......................  134       5.14
.................................................UGAGCGCCUCGACGACAGAGC........................  43        2.38
.................................................UGAGCGCCUCGACGACAGAG.........................  30        0.601
.................................................UGAGCGCCUCGACGACAGA..........................  2         0.0389
.................................................UGAGCGCCUCGACGACAG...........................  2         6.83
..................................................GAGCGCCUCGACGACAGAGCCG......................  27        0.364
...................................................AGCGCCUCGACGACAGAGCCG......................  124       2.07
...................................................AGCGCCUCGACGACAGAGCCGG.....................  32        0.605
...................................................AGCGCCUCGACGACAGAGCC.......................  9         0.168
CGGGGCGGCCGCUCUCCCUGUCCUCCAGGAGCUCACGUGUGCCUGCCUGUGAGCGCCUCGACGACAGAGCCGGCGCCUGCCCCAGUGUCUGCGC
.(((((((.((((..(.(((((.((.(((.(((((((.((....)).))))))).))).)).))))).)..)))).))))))).(((....))) (-49.20)

Filter reads

by experiment
Accession Read count Tissue Link Comment Reference
ER0000000001 51embryonic stem cell GEO : GSM541796 [ Bar M et al.]
ER0000000002 143embryonic stem cell GEO : GSM541797 [ Bar M et al.]
ER0000000103 142melanoblast GEO : GSM458535 [ Stark MS et al.]
ER0000000104 24melanocyte GEO : GSM458536 [ Stark MS et al.]
ER0000000105 77 GEO : GSM458537 cell line: primary giant congental nevus [ Stark MS et al.]
ER0000000106 27melanoma GEO : GSM458538 cell line: secondary acral melanoma [ Stark MS et al.]
ER0000000107 54melanoma GEO : GSM458539 cell line: secondary mucosal melanoma [ Stark MS et al.]
ER0000000108 314melanoma GEO : GSM458540 cell line: secondary cutaneous melanoma [ Stark MS et al.]
ER0000000109 117melanoma GEO : GSM458541 cell line: primary uveal melanoma [ Stark MS et al.]
ER0000000110 381melanoma GEO : GSM458542 cell line: secondary cutaneous melanoma [ Stark MS et al.]
ER0000000111 252melanoma GEO : GSM458543 cell line: secondary cutaneous melanoma [ Stark MS et al.]
ER0000000112 206melanoma GEO : GSM458544 cell line: secondary cutaneous melanoma [ Stark MS et al.]
ER0000000113 131melanoma GEO : GSM458545 cell line: secondary cutaneous melanoma from a chronically sun-damaged body site [ Stark MS et al.]
ER0000000114 219melanoma GEO : GSM458546 cell line: secondary cutaneous melanoma [ Stark MS et al.]
ER0000000135 4 GEO : GSM532871 normal cervix [ Witten D et al.]
ER0000000138 4squamous cell GEO : GSM532874 [ Witten D et al.]
ER0000000140 2squamous cell GEO : GSM532876 [ Witten D et al.]
ER0000000141 4 GEO : GSM532877 normal cervix [ Witten D et al.]
ER0000000142 3squamous cell GEO : GSM532878 [ Witten D et al.]
ER0000000147 8 GEO : GSM532883 normal cervix [ Witten D et al.]
ER0000000150 1squamous cell GEO : GSM532886 [ Witten D et al.]
ER0000000154 2squamous cell GEO : GSM532890 [ Witten D et al.]
ER0000000156 21squamous cell GEO : GSM532892 [ Witten D et al.]
ER0000000157 12 GEO : GSM532893 normal cervix [ Witten D et al.]
ER0000000160 11squamous cell GEO : GSM532896 [ Witten D et al.]
ER0000000161 28 GEO : GSM532897 normal cervix [ Witten D et al.]
ER0000000164 16squamous cell GEO : GSM532900 [ Witten D et al.]
ER0000000165 24 GEO : GSM532901 normal cervix [ Witten D et al.]
ER0000000169 7 GEO : GSM532905 normal cervix [ Witten D et al.]
ER0000000171 17 GEO : GSM532907 normal cervix [ Witten D et al.]
ER0000000172 1squamous cell GEO : GSM532908 [ Witten D et al.]
ER0000000174 14squamous cell GEO : GSM532910 [ Witten D et al.]
ER0000000176 4adenosquamous cell GEO : GSM532912 [ Witten D et al.]
ER0000000178 9squamous cell GEO : GSM532914 [ Witten D et al.]
ER0000000180 17squamous cell GEO : GSM532916 [ Witten D et al.]
ER0000000181 11 GEO : GSM532917 normal cervix [ Witten D et al.]
ER0000000183 4whole body GEO : GSM532919 normal cervix [ Witten D et al.]
ER0000000184 2squamous cell GEO : GSM532920 [ Witten D et al.]
ER0000000186 6squamous cell GEO : GSM532922 [ Witten D et al.]
ER0000000188 2squamous cell GEO : GSM532924 [ Witten D et al.]
ER0000000193 1 GEO : GSM532929 normal cervix [ Witten D et al.]
ER0000000262 1 GEO : GSM337570 antibody: anti-Ago1 4B8
ER0000000263 2 GEO : GSM337571 antibody: anti-Ago2 11A9
ER0000000266 3 GEO : GSM368183 tissue: undifferentiated NPC [ Zhu JY et al.]
by # mismatches     Display untemplated ends
by read count min max

References

1
PMID:18583537 "MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries" Bar M, Wyman SK, Fritz BR, Qi J, Garg KS, Parkin RK, Kroh EM, Bendoraite A, Mitchell PS, Nelson AM, Ruzzo WL, Ware C, Radich JP, Gentleman R, Ruohola-Baker H, Tewari M Stem Cells. 26:2496-2505(2008).
2
PMID:19144710 "Identification of novel Epstein-Barr virus microRNA genes from nasopharyngeal carcinomas" Zhu JY, Pfuhl T, Motsch N, Barth S, Nicholls J, Grasser F, Meister G J Virol. 83:3333-3341(2009).
3
PMID:20300190 "Characterization of the Melanoma miRNAome by Deep Sequencing" Stark MS, Tyagi S, Nancarrow DJ, Boyle GM, Cook AL, Whiteman DC, Parsons PG, Schmidt C, Sturm RA, Hayward NK PLoS One. 5:e9685(2010).
4
PMID:20459774 "Ultra-high throughput sequencing-based small RNA discovery and discrete statistical biomarker analysis in a collection of cervical tumours and matched controls" Witten D, Tibshirani R, Gu SG, Fire A, Lui WO BMC Biol. 8:58(2010).