Deep sequencing reads for stem-loop sequence MI0000456

Stem-loop ID hsa-mir-140
Reads 
                      hsa-miR-140-5p                        hsa-miR-140-3p                            Count     RPM (mean number of reads per million)
......................CAGUGGUUUUACCCUAUGGUAG........................................................  50        9.89
......................CAGUGGUUUUACCCUAUGGUA.........................................................  10        0.651
......................CAGUGGUUUUACCCUAUGGU..........................................................  3         3.11
......................CAGUGGUUUUACCCUAUGGUAGG.......................................................  3         0.395
......................CAGUGGUUUUACCCUAUGG...........................................................  1         40.6
..........................................AGGUUACGUCAUGCUGUUCUAC....................................  2         0.0275
...........................................GGUUACGUCAUGCUGUUCUA.....................................  6         0.0633
............................................................CUACCACAGGGUAGAACCACGGAC................  32        0.383
............................................................CUACCACAGGGUAGAACCACGGA.................  21        0.256
............................................................CUACCACAGGGUAGAACCACGGACA...............  7         0.0737
............................................................CUACCACAGGGUAGAACCACGG..................  2         0.0147
.............................................................UACCACAGGGUAGAACCACGGAC................  122596    1.63e+03
.............................................................UACCACAGGGUAGAACCACGGA.................  35346     516
.............................................................UACCACAGGGUAGAACCACGGACA...............  29506     371
.............................................................UACCACAGGGUAGAACCACGG..................  2936      155
.............................................................UACCACAGGGUAGAACCACG...................  159       3.8
.............................................................UACCACAGGGUAGAACCACGGACAG..............  37        0.478
.............................................................UACCACAGGGUAGAACC......................  17        0.228
.............................................................UACCACAGGGUAGAACCA.....................  4         0.0422
.............................................................UACCACAGGGUAGAACCAC....................  3         0.0413
..............................................................ACCACAGGGUAGAACCACGGA.................  40852     564
..............................................................ACCACAGGGUAGAACCACGGAC................  37336     506
..............................................................ACCACAGGGUAGAACCACGG..................  2916      130
..............................................................ACCACAGGGUAGAACCACGGACA...............  2909      38.4
..............................................................ACCACAGGGUAGAACCACG...................  22        0.278
..............................................................ACCACAGGGUAGAACCACGGACAG..............  8         0.0682
..............................................................ACCACAGGGUAGAACCA.....................  5         0.0462
...............................................................CCACAGGGUAGAACCACGGA.................  1055      14.7
...............................................................CCACAGGGUAGAACCACGGAC................  769       10.4
...............................................................CCACAGGGUAGAACCACGGACA...............  136       2.5
...............................................................CCACAGGGUAGAACCACGG..................  40        0.587
................................................................CACAGGGUAGAACCACGGA.................  26        0.409
................................................................CACAGGGUAGAACCACGGAC................  22        0.31
................................................................CACAGGGUAGAACCACGGACA...............  10        0.146
.................................................................ACAGGGUAGAACCACGGACAGGA............  32        0.383
.................................................................ACAGGGUAGAACCACGGAC................  14        0.157
.................................................................ACAGGGUAGAACCACGGA.................  13        0.146
.................................................................ACAGGGUAGAACCACGGACA...............  2         0.0124
.................................................................ACAGGGUAGAACCACGGACAGGAU...........  2         0.0124
.................................................................ACAGGGUAGAACCACGGACAGG.............  2         0.0275
..................................................................CAGGGUAGAACCACGGAC................  1         0.181
...................................................................AGGGUAGAACCACGGACA...............  1         12.8
UGUGUCUCUCUCUGUGUCCUGCCAGUGGUUUUACCCUAUGGUAGGUUACGUCAUGCUGUUCUACCACAGGGUAGAACCACGGACAGGAUACCGGGGCACC
.(((((((.....((((((((((.(((((((((((((.(((((((..(((......)))))))))).))))))))))))))).)))))))).))))))). (-55.00)

Filter reads

by experiment
Accession Read count Tissue Link Comment Reference
ER0000000001 80embryonic stem cell GEO : GSM541796 [ Bar M et al.]
ER0000000002 150embryonic stem cell GEO : GSM541797 [ Bar M et al.]
ER0000000103 64301melanoblast GEO : GSM458535 [ Stark MS et al.]
ER0000000104 17411melanocyte GEO : GSM458536 [ Stark MS et al.]
ER0000000105 46725 GEO : GSM458537 cell line: primary giant congental nevus [ Stark MS et al.]
ER0000000106 11369melanoma GEO : GSM458538 cell line: secondary acral melanoma [ Stark MS et al.]
ER0000000107 11612melanoma GEO : GSM458539 cell line: secondary mucosal melanoma [ Stark MS et al.]
ER0000000108 37826melanoma GEO : GSM458540 cell line: secondary cutaneous melanoma [ Stark MS et al.]
ER0000000109 17804melanoma GEO : GSM458541 cell line: primary uveal melanoma [ Stark MS et al.]
ER0000000110 19422melanoma GEO : GSM458542 cell line: secondary cutaneous melanoma [ Stark MS et al.]
ER0000000111 15394melanoma GEO : GSM458543 cell line: secondary cutaneous melanoma [ Stark MS et al.]
ER0000000112 13542melanoma GEO : GSM458544 cell line: secondary cutaneous melanoma [ Stark MS et al.]
ER0000000113 85098melanoma GEO : GSM458545 cell line: secondary cutaneous melanoma from a chronically sun-damaged body site [ Stark MS et al.]
ER0000000114 11327melanoma GEO : GSM458546 cell line: secondary cutaneous melanoma [ Stark MS et al.]
ER0000000135 1 GEO : GSM532871 normal cervix [ Witten D et al.]
ER0000000136 15squamous cell GEO : GSM532872 [ Witten D et al.]
ER0000000140 1squamous cell GEO : GSM532876 [ Witten D et al.]
ER0000000141 4 GEO : GSM532877 normal cervix [ Witten D et al.]
ER0000000142 6squamous cell GEO : GSM532878 [ Witten D et al.]
ER0000000147 6 GEO : GSM532883 normal cervix [ Witten D et al.]
ER0000000150 1squamous cell GEO : GSM532886 [ Witten D et al.]
ER0000000154 1squamous cell GEO : GSM532890 [ Witten D et al.]
ER0000000155 1 GEO : GSM532891 normal cervix [ Witten D et al.]
ER0000000156 1squamous cell GEO : GSM532892 [ Witten D et al.]
ER0000000157 8 GEO : GSM532893 normal cervix [ Witten D et al.]
ER0000000158 1squamous cell GEO : GSM532894 [ Witten D et al.]
ER0000000160 4squamous cell GEO : GSM532896 [ Witten D et al.]
ER0000000161 11 GEO : GSM532897 normal cervix [ Witten D et al.]
ER0000000164 1squamous cell GEO : GSM532900 [ Witten D et al.]
ER0000000165 12 GEO : GSM532901 normal cervix [ Witten D et al.]
ER0000000166 1squamous cell GEO : GSM532902 [ Witten D et al.]
ER0000000169 2 GEO : GSM532905 normal cervix [ Witten D et al.]
ER0000000170 1adenosquamous cell GEO : GSM532906 [ Witten D et al.]
ER0000000171 14 GEO : GSM532907 normal cervix [ Witten D et al.]
ER0000000174 7squamous cell GEO : GSM532910 [ Witten D et al.]
ER0000000176 9adenosquamous cell GEO : GSM532912 [ Witten D et al.]
ER0000000180 1squamous cell GEO : GSM532916 [ Witten D et al.]
ER0000000181 6 GEO : GSM532917 normal cervix [ Witten D et al.]
ER0000000182 3squamous cell GEO : GSM532918 [ Witten D et al.]
ER0000000184 8squamous cell GEO : GSM532920 [ Witten D et al.]
ER0000000185 2 GEO : GSM532921 normal cervix [ Witten D et al.]
ER0000000193 1 GEO : GSM532929 normal cervix [ Witten D et al.]
ER0000000194 1squamous cell GEO : GSM532930 [ Witten D et al.]
ER0000000262 4 GEO : GSM337570 antibody: anti-Ago1 4B8
ER0000000263 11 GEO : GSM337571 antibody: anti-Ago2 11A9
ER0000000264 45 GEO : GSM368181 tissue: undifferentiated NPC [ Zhu JY et al.]
ER0000000265 4 GEO : GSM368182 tissue: clinically negative of NPC [ Zhu JY et al.]
ER0000000266 21 GEO : GSM368183 tissue: undifferentiated NPC [ Zhu JY et al.]
ER0000000267 4 GEO : GSM368184 tissue: clinically negative of 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).