Name | Sequence | Scale | Purification | Index | |
3' Adapter | |||||
TLC-L3 | /5Phos/AGATCGGAAGAGCACACGTCTGAAAAAAAAAAAAAAAAAAAAAAAAA/3IR800CWN/ | 250nm | RNASE | ||
5' Adapter | |||||
TLC_L01 | /5Phos/NNNNATCACGNNNNNAGATCGGAAGAGCGTCGTG/3ddC/ | 100nm | STD | CGTGAT | |
TLC_L02 | /5Phos/NNNNCGATGTNNNNNAGATCGGAAGAGCGTCGTG/3ddC/ | 100nm | STD | ACATCG | |
TLC_L03 | /5Phos/NNNNTTAGGCNNNNNAGATCGGAAGAGCGTCGTG/3ddC/ | 100nm | STD | GCCTAA | |
TLC_L04 | /5Phos/NNNNTGACCANNNNNAGATCGGAAGAGCGTCGTG/3ddC/ | 100nm | STD | TGGTCA | |
TLC_L05 | /5Phos/NNNNACAGTGNNNNNAGATCGGAAGAGCGTCGTG/3ddC/ | 100nm | STD | CACTGT | |
TLC_L06 | /5Phos/NNNNGCCAATNNNNNAGATCGGAAGAGCGTCGTG/3ddC/ | 100nm | STD | ATTGGC | |
TLC_L07 | /5Phos/NNNNCAGATCNNNNNAGATCGGAAGAGCGTCGTG/3ddC/ | 100nm | STD | GATCTG | |
TLC_L08 | /5Phos/NNNNACTTGANNNNNAGATCGGAAGAGCGTCGTG/3ddC/ | 100nm | STD | TCAAGT | |
TLC_L09 | /5Phos/NNNNGATCAGNNNNNAGATCGGAAGAGCGTCGTG/3ddC/ | 100nm | STD | CTGATC | |
TLC_L10 | /5Phos/NNNNTAGCTTNNNNNAGATCGGAAGAGCGTCGTG/3ddC/ | 100nm | STD | AAGCTA | |
TLC_L11 | /5Phos/NNNNATGAGCNNNNNAGATCGGAAGAGCGTCGTG/3ddC/ | 100nm | STD | GCTCAT | |
TLC_L12 | /5Phos/NNNNCTTGTANNNNNAGATCGGAAGAGCGTCGTG/3ddC/ | 100nm | STD | TACAAG | |
cDNA Amplification | |||||
P5short_TLC-CLIP | ACACGACGCTCTTCCGATCT | 100nm | PAGE | ||
P7short_TLC-CLIP | TGACGTGTGCTCTTCCGATCT | 100nm | PAGE | ||
PCR amplification | |||||
P5_Universal_adapter | AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT | 1um | PAGE | ||
P7-1_TLC-CLIP | CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T | 250nm | PAGE | ATCACG | |
P7-2_TLC-CLIP | CAAGCAGAAGACGGCATACGAGATACATCGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T | 250nm | PAGE | CGATGTAT | |
P7-3_TLC-CLIP | CAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T | 250nm | PAGE | TTAGGCAT | |
P7-4_TLC-CLIP | CAAGCAGAAGACGGCATACGAGATTGGTCAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T | 250nm | PAGE | TGACCAAT | |
P7-5_TLC-CLIP | CAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T | 250nm | PAGE | ACAGTGAT | |
P7-6_TLC-CLIP | CAAGCAGAAGACGGCATACGAGATATTGGCGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T | 250nm | PAGE | GCCAATAT | |
P7-7_TLC-CLIP | CAAGCAGAAGACGGCATACGAGATGATCTGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T | 250nm | PAGE | CAGATCAT | |
P7-8_TLC-CLIP | CAAGCAGAAGACGGCATACGAGATTCAAGTGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T | 250nm | PAGE | ACTTGAAT |
Final Concentration | Stock Solution | For 500 ml | |
50 mM Tris-HCl, pH 7.4 | 1 M Tris-HCl, pH 7.5 | 25 ml | |
100 mM NaCl | 5 M NaCl | 10 ml | |
1% Igepal-CA-630 | 100% Igepal CA-630 | 5 ml | |
0.1% SDS | 10% SDS | 5 ml | |
0.5% sodium deoxycholate | 2.5 g | ||
Add H2O | 455 ml |
Final Concentration | Stock Solution | For 500 ml | |
50 mM Tris-HCl, pH 7.4 | 1 M Tris-HCl, pH 7.5 | 25 ml | |
1 M NaCl | 5 M NaCl | 100 ml | |
1 mM EDTA | 0.5M EDTA, pH 8.0 | 1 ml | |
1% Igepal-CA-630 | 100% Igepal CA-630 | 5 ml | |
0.1% SDS | 10% SDS | 5 ml | |
0.5% sodium deoxycholate | 2.5 g | ||
Add H2O | 364 ml |
Final Concentration | Stock Solution | For 500 ml | |
20 mM Tris-HCl, pH 7.4 | 1 M Tris-HCl, pH 7.5 | 10 ml | |
10 mM MgCl2 | 2 M MgCl2 | 2.5 ml | |
0.2% Tween-20 | 100% Tween-20 | 1 ml | |
Add H2O | 486.5 ml |
Final Concentration | Stock Solution | For 10 ml | |
350 mM Tris-HCl, pH 6.5 | 1 M Tris-HCl, pH 6.5 | 3.5 ml | |
50 mM MgCl2 | 2 M MgCl2 | 0.25 ml | |
5 mM DTT | 1M DTT | 0.05 ml | |
Add H2O | 6.2 ml |
Final Concentration | Stock Solution | For 10 ml | |
200 mM Tris-HCl, pH 7.8 | 1 M Tris-HCl, pH 7.8 | 2 ml | |
40 mM MgCl2 | 2 M MgCl2 | 0.2 ml | |
4 mM DTT | 1M DTT | 0.04 ml | |
Add H2O | 7.76 ml |
Final Concentration | Stock Solution | For 50 ml | |
100 mM Tris-HCl, pH 7.4 | 1 M Tris-HCl, pH 7.4 | 5 ml | |
50 mM LiCl | 8 M LiCl | 0.3125 ml | |
1 mM EDTA | 0.5 M EDTA | 0.1 ml | |
0.2% LiDS | 1% LiDS | 10 ml | |
Add H2O | 34.5875 ml |
Final Concentration | Stock Solution | For 50 ml | |
20 mM Tris-HCl, pH 7.4 | 1 M Tris-HCl, pH 7.4 | 1 ml | |
1 M LiCl | 8 M LiCl | 6.25 ml | |
2 mM EDTA | 0.5 M EDTA | 0.2 ml | |
Add H2O | 42.55 ml |
Final Concentration | Stock Solution | For 50 ml | |
10 mM Tris-HCl, pH 7.4 | 1 M Tris-HCl, pH 7.4 | 0.5 ml | |
150 mM LiCl | 8 M LiCl | 0.9375 ml | |
0.1 mM EDTA | 0.5 M EDTA | 0.01 ml | |
Add H2O | 48.5525 ml |
Final Concentration | Stock Solution | For 10 ml | |
250 mM Tris-HCl, pH 8.3 | 1 M Tris-HCl, pH 8.3 | 2.5 ml | |
375 mM KCl | 1 M KCl | 3.75 ml | |
15 mM MgCl2 | 1 M MgCl2 | 0.15 ml | |
Add H2O | 3.6 ml |
PNK Reaction | x 1 | x # | |
5X PNK Buffer | 4 µl | ||
SuperaseIN | 0.5 µl | ||
T4 PNK | 0.5 µl | ||
H2O | 15 µl |
Ligation Mix | x 1 | x # | |
4X Ligation Buffer | 5 µl | ||
T4 RNA Ligase | 1 µl | ||
1 µM L3 Adapter | 1 µl | ||
SuperaseIN | 0.5 µl | ||
H2O | 8.5 µl | ||
PEG400 | 4 µl |
Reverse Transcription | x1 | x # | |
5X FS Buffer | 2 µl | ||
10mM dNTPs | 0.5 µl | ||
0.1M DTT | 0.1 µl | ||
SuperaseIN | 0.3 µl | ||
Superscript IV | 0.1 µl | ||
H2O | 7 µl |
5' Adapter Mix | x1 | x # | |
10X T4 RNA Ligase Buffer | 2 µl | ||
10 µM L## oligo | 2 µl | ||
DMSO | 1 µl |
Ligation mix | x1 | x # | |
0.1 M ATP | 0.5 µl | ||
TdT (14U/µl) | 0.5 µl | ||
T4 RNA Ligase High Conc. (30U/µl) | 0.5 µl | ||
H20 | 2.5 µl |
cDNA amplification | x1 | x # | |
2X Phusion HF PCR Mastermix | 12.5 µl | ||
10 µM P7&P5 short | 1.25 µl | ||
H2O | 11.25 µl |
Test qPCR | x 1 | x # | |
2X PowerUP SYBR Green Mastermix | 5 µl | ||
10 µM P5 + P7 primers | 0.5 µl | ||
H2O | 3.5 µl |
PCR | x 1 | x # | |
2X Phusion HF Mastermix | 20 µl | ||
10 µM P5 + P7 primers | 1 µl | ||
H2O | 9 µl |