A non-radioactive, improved PAR-CLIP and small RNA cDNA library preparation protocol

A non-radioactive, improved PAR-CLIP and small RNA cDNA library preparation protocol

Crosslinking and immunoprecipitation (CLIP) strategies are highly effective strategies to interrogate direct protein-RNA interactions and dissect posttranscriptional gene regulatory networks. One broadly used CLIP variant is photoactivatable ribonucleoside enhanced CLIP (PAR-CLIP) that entails in vivo labeling of nascent RNAs with the photoreactive nucleosides 4-thiouridine (4SU) or 6-thioguanosine (6SG), which might effectively crosslink to interacting proteins utilizing UVA and UVB mild.

Crosslinking of 4SU or 6SG to interacting amino acids adjustments their base-pairing properties and leads to attribute mutations in cDNA libraries ready for high-throughput sequencing, which could be computationally exploited to take away ample background from non-crosslinked sequences and assist pinpoint RNA binding protein binding websites at nucleotide decision on a transcriptome-wide scale.

Right here we current a streamlined protocol for fluorescence-based PAR-CLIP (fPAR-CLIP) that eliminates the necessity to use radioactivity. It’s primarily based on direct ligation of a fluorescently labeled adapter to the three’finish of crosslinked RNA on immobilized ribonucleoproteins, adopted by isolation of the adapter-ligated RNA and environment friendly conversion into cDNA with out the beforehand wanted measurement fractionation on denaturing polyacrylamide gels. These enhancements reduce the experimentation by half to 2 days and will increase sensitivity by 10-100-fold.

Characterization and evaluation of the transcriptome response to drought in Larix kaempferi utilizing PacBio full-length cDNA sequencing built-in with de novo RNA-seq reads

A hypothetical mannequin of drought tolerance mechanism of Larix kaempferi was established via SMRT-seq and Illumina HiSeq. Larix kaempferi is a vital financial and ecological species and a significant afforestation species in north-eastern China. Up to now, no info has been reliably derived concerning full-length cDNA sequencing info on L. kaempferi. By single-molecule long-read isoform sequencing (SMRT-seq), right here we report a complete of 26,153,342 subreads (21.24 Gb) and 330,371 round consensus sequence (CCS) reads after the modification of web site mismatch, and 35,414 unigenes have been efficiently collected.

To achieve deeper insights into the molecular mechanisms of L. kaempferi response to drought stress, we mixed Illumina HiSeq with SMRT-seq to decode full-length transcripts. On this examine, we report 27 differentially expressed genes (DEGs) concerned within the notion and transmission of drought stress indicators in L. kaempferi.

Numerous DEGs responding to drought stress have been detected in L. kaempferi, particularly DEGs concerned within the reactive oxygen species (ROS) scavenging, lignin biosynthesis, and sugar metabolism, and DEGs encoding drought stress proteins. We detected 73 transcription components (TFs) below drought stress, together with AP2/ERF, bZIP, TCP, and MYB. This examine offers primary full sequence sources for L. kaempferi analysis and can assist us to raised perceive the capabilities of drought-resistance genes in L. kaempferi.

A non-radioactive, improved PAR-CLIP and small RNA cDNA library preparation protocol

cDNA-derived RNA phage meeting reveals important residues within the maturation protein of the Pseudomonas aeruginosa leviphage, PP7

PP7 is a leviphage with single-stranded RNA genome, which infects Pseudomonas aeruginosa PAO1. A reverse genetic system for PP7 was beforehand created through the use of reverse-transcribed cDNA (PP7O) from virion-derived RNA genome. Right here, we’ve discovered that the PP7O cDNA contained 20 nucleotide variations from the PP7 genome sequence deposited within the database.

We created one other reverse genetic system exploiting chemically synthesized cDNA (PP7S) primarily based on the database sequence. In contrast to PP7O that rendered infectious PP7 virions, PP7S-derived particles have been incapable of plaque formation on PAO1 cells, which was restored on the PAO1 cells expressing the maturation protein (MP) from PP7O Utilizing this reverse genetic system, we revealed two amino acid residues concerned within the identified roles of MP (i.e. adsorption and genome replication), fortuitously offering a lesson that the viral RNA genome sequencing wants purposeful verification presumably by a reverse genetic system.

IMPORTANCE Organic significance of RNA phages has been largely ignored, mockingly as a result of few research have been specializing in RNA phages. As an preliminary try to correctly signify RNA phages within the phageome, we beforehand created, through the use of reverse-transcribed cDNA, a reverse genetic system for the small RNA phage, PP7 that infects the opportunistic human pathogen, Pseudomonas aeruginosa We right here report one other system through the use of chemically synthesized cDNA primarily based on the database genome that has 20 nucleotide variations from the earlier cDNA.

Investigation of these cDNA-derived phage virions unveiled that two amino acids of the maturation protein are essential for the traditional phage lifecycle at totally different steps. Our examine offers an perception into the molecular foundation for the RNA phage lifecycle and a lesson that the RNA genome sequencing must be rigorously validated by cDNA-based phage meeting methods.

RNAcDNA hybrids mediate transposition by way of totally different mechanisms

Retrotransposons can signify half of eukaryotic genomes. Retrotransposon dysregulation destabilizes genomes and has been linked to varied human ailments. Rising regulators of retromobility embrace RNA-DNA hybrid-containing constructions generally known as R-loops. Accumulation of those constructions on the transposons of yeast 1 (Ty1) parts has been proven to extend Ty1 retromobility via an unknown mechanism. Right here, by way of a focused genetic display screen, we recognized the rnh1Δ rad27Δ yeast mutant, which lacked each the Ty1 inhibitor Rad27 and the RNA-DNA hybrid suppressor Rnh1.

The mutant exhibited elevated ranges of Ty1 cDNA-associated RNA-DNA hybrids that promoted Ty1 mobility. Furthermore, on this rnh1Δ rad27Δ mutant, however not within the double RNase H mutant rnh1Δ rnh201Δ, RNA-DNA hybrids preferentially existed as duplex nucleic acid constructions and elevated Ty1 mobility in a Rad52-dependent method.

POLR1D cDNA Clone

MBS1275119-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 200

POLR1D cDNA Clone

MBS1275119-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 855

POLR2E cDNA Clone

MBS1275816-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 200

POLR2E cDNA Clone

MBS1275816-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 855

POLR3C cDNA Clone

MBS1277466-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 330

POLR3C cDNA Clone

MBS1277466-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 1430

POLR2J cDNA Clone

MBS1277649-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 200

POLR2J cDNA Clone

MBS1277649-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 855

POLR3E cDNA Clone

MBS1267767-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 435

POLR3E cDNA Clone

MBS1267767-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 1910

POLR1C cDNA Clone

MBS1268317-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 200

POLR1C cDNA Clone

MBS1268317-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 855

POLR2L cDNA Clone

MBS1268529-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 200

POLR2L cDNA Clone

MBS1268529-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 855

POLR1E cDNA Clone

MBS1268796-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 425

POLR1E cDNA Clone

MBS1268796-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 1860

POLR1A cDNA Clone

MBS1269025-INQUIRE INQUIRE Ask for price

POLR1D cDNA Clone

MBS1269118-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 190

POLR1D cDNA Clone

MBS1269118-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 815

POLR3D cDNA Clone

MBS1269487-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 405

POLR3D cDNA Clone

MBS1269487-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 1770

POLR2C cDNA Clone

MBS1269787-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 295

POLR2C cDNA Clone

MBS1269787-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 1295

POLR2K cDNA Clone

MBS1271511-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 200

POLR2K cDNA Clone

MBS1271511-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 855

POLR2L cDNA Clone

MBS1272106-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 200

POLR2L cDNA Clone

MBS1272106-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 855

POLR2H cDNA Clone

MBS1272766-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 205

POLR2H cDNA Clone

MBS1272766-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 870

POLR2I cDNA Clone

MBS1272835-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 200

POLR2I cDNA Clone

MBS1272835-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 855

POLR1E cDNA Clone

MBS1266175-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 200

POLR1E cDNA Clone

MBS1266175-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 855

POLR2D cDNA Clone

MBS1269925-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 200

POLR2D cDNA Clone

MBS1269925-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 855

POLR2A cDNA Clone

MBS1270824-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 200

POLR2A cDNA Clone

MBS1270824-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 855

POLR3GL cDNA Clone

MBS1271550-001mgPlasmid02mLGlycerolStock 0.01mgPlasmid+0.2mLGlycerol-Stock
EUR 200

POLR3GL cDNA Clone

MBS1271550-5x001mgPlasmid5x02mLGlycerolStock 5x0.01mgPlasmid+5x0.2mLGlycerol-Stock
EUR 855

Lenti ORF clone of Polr3f (mGFP-tagged) - Mouse polymerase (RNA) III (DNA directed) polypeptide F (Polr3f)

MR204539L4 10 µg Ask for price

Lenti ORF clone of Polr3f (Myc-DDK-tagged) - Mouse polymerase (RNA) III (DNA directed) polypeptide F (Polr3f)

MR204539L3 10 µg Ask for price

POLR3F cloning plasmid

CSB-CL884440HU-10ug 10ug
EUR 279.6
Description: A cloning plasmid for the POLR3F gene.

Lenti ORF clone of Polr3f (mGFP-tagged ORF) - Rat polymerase (RNA) III (DNA directed) polypeptide F, 39 kDa (Polr3f), (10 ug)

RR202392L4 10 µg Ask for price

Lenti ORF clone of Polr3f (Myc-DDK-tagged ORF) - Rat polymerase (RNA) III (DNA directed) polypeptide F, 39 kDa (Polr3f), (10 ug)

RR202392L3 10 µg Ask for price

POLR3F

CSB-CL884440HU 10 μg plasmid + 200μl Glycerol Ask for price

POLR3F

enz-650 5µg
EUR 60
Description: Recombinant Human Polymerase III Polypeptide F

POLR3F

MBS8535555-01mL 0.1mL
EUR 325

POLR3F

MBS8535555-01mLAF405L 0.1mL(AF405L)
EUR 565

POLR3F

MBS8535555-01mLAF405S 0.1mL(AF405S)
EUR 565

POLR3F

MBS8535555-01mLAF610 0.1mL(AF610)
EUR 565

POLR3F

MBS8535555-01mLAF635 0.1mL(AF635)
EUR 565

POLR3F siRNA

20-abx929231
  • Ask for price
  • Ask for price
  • 15 nmol
  • 30 nmol

POLR3F siRNA

20-abx929232
  • Ask for price
  • Ask for price
  • 15 nmol
  • 30 nmol

POLR3F Peptide

4727P 0.05 mg
EUR 197.7
Description: (NT) POLR3F peptide

POLR3F Peptide

MBS152583-005mg 0.05mg
EUR 175

POLR3F Peptide

MBS152583-5x005mg 5x0.05mg
EUR 770

POLR3F Antibody

24726 100ul
EUR 479

POLR3F Antibody

24726-100ul 100ul
EUR 468

POLR3F Antibody

4727-002mg 0.02 mg
EUR 206.18
Description: POLR3F Antibody: The human POLR3F is a component of RNA III polymerase. RNA polymerase III transcribes many essential, small, noncoding RNAs, including the 5S rRNAs and tRNAs. While most pol III-transcribed genes are found scattered throughout the linear chromosome maps or in multiple linear clusters, there is increasing evidence that many of these genes prefer to be spatially clustered, often at or near the nucleolus. This association could create an environment that fosters the coregulation of transcription by pol III with transcription of the large ribosomal RNA repeats by RNA polymerase I (pol I) within the nucleolus. Given the high number of pol III-transcribed genes in all eukaryotic genomes, the spatial organization of these genes is likely to affect a large portion of the other genes in a genome. POLR3F has also been recently identified as an HIV dependency factor (HDF), suggesting that POLR3F may be an important drug target in HIV treatment. At least two isoforms of POLR3F are known to exist.

POLR3F Antibody

4727-01mg 0.1 mg
EUR 523.7
Description: POLR3F Antibody: The human POLR3F is a component of RNA III polymerase. RNA polymerase III transcribes many essential, small, noncoding RNAs, including the 5S rRNAs and tRNAs. While most pol III-transcribed genes are found scattered throughout the linear chromosome maps or in multiple linear clusters, there is increasing evidence that many of these genes prefer to be spatially clustered, often at or near the nucleolus. This association could create an environment that fosters the coregulation of transcription by pol III with transcription of the large ribosomal RNA repeats by RNA polymerase I (pol I) within the nucleolus. Given the high number of pol III-transcribed genes in all eukaryotic genomes, the spatial organization of these genes is likely to affect a large portion of the other genes in a genome. POLR3F has also been recently identified as an HIV dependency factor (HDF), suggesting that POLR3F may be an important drug target in HIV treatment. At least two isoforms of POLR3F are known to exist.

POLR3F Antibody

1-CSB-PA884440LA01HU
  • Ask for price
  • Ask for price
  • 100ug
  • 50ug
Description: A polyclonal antibody against POLR3F. Recognizes POLR3F from Human. This antibody is Unconjugated. Tested in the following application: ELISA, WB; Recommended dilution: WB:1:500-1:2000

POLR3F Antibody

1-CSB-PA018348GA01HU
  • Ask for price
  • Ask for price
  • 150ul
  • 50ul
Description: A polyclonal antibody against POLR3F. Recognizes POLR3F from Human, Mouse, Rat. This antibody is Unconjugated. Tested in the following application: ELISA, WB

POLR3F Antibody

E94441 100μg
EUR 255
Description: Available in various conjugation types.

POLR3F Antibody

E912224 100ul
EUR 255
Description: Available in various conjugation types.

POLR3F Antibody

E38PA2497 100ul
EUR 225
Description: Available in various conjugation types.

POLR3F antibody

70R-19415 50 ul
EUR 289
Description: Rabbit polyclonal POLR3F antibody

POLR3F antibody

70R-2038 50 ug
EUR 467
Description: Rabbit polyclonal POLR3F antibody raised against the middle region of POLR3F

POLR3F antibody

70R-2962 50 ug
EUR 467
Description: Rabbit polyclonal POLR3F antibody raised against the N terminal of POLR3F

POLR3F antibody

70R-50816 100 ul
EUR 242
Description: Purified Polyclonal POLR3F antibody

POLR3F Antibody

GWB-MR240F 50ug Ask for price

POLR3F Antibody

GWB-MR241G 50ug Ask for price

POLR3F Antibody

MBS9406659-01mL 0.1mL
EUR 495

POLR3F Antibody

MBS9406659-5x01mL 5x0.1mL
EUR 2075

POLR3F Antibody

MBS9210018-01mL 0.1mL
EUR 415

POLR3F Antibody

MBS9210018-5x01mL 5x0.1mL
EUR 1841

POLR3F Antibody

MBS8581354-01mL 0.1mL
EUR 305

POLR3F Antibody

MBS8581354-01mLAF405L 0.1mL(AF405L)
EUR 465

POLR3F Antibody

MBS8581354-01mLAF405S 0.1mL(AF405S)
EUR 465

POLR3F Antibody

MBS8581354-01mLAF610 0.1mL(AF610)
EUR 465

POLR3F Antibody

MBS8581354-01mLAF635 0.1mL(AF635)
EUR 465

POLR3F Antibody

MBS8501471-01mg 0.1mg
EUR 325

POLR3F Antibody

MBS8501471-01mLAF405L 0.1mL(AF405L)
EUR 565

POLR3F Antibody

MBS8501471-01mLAF405S 0.1mL(AF405S)
EUR 565

POLR3F Antibody

MBS8501471-01mLAF610 0.1mL(AF610)
EUR 565

POLR3F Antibody

MBS8501471-01mLAF635 0.1mL(AF635)
EUR 565

POLR3F Antibody

MBS151394-01mg 0.1mg
EUR 445

POLR3F Antibody

MBS151394-5x01mg 5x0.1mg
EUR 1965

POLR3F Antibody

MBS1492228-005mg 0.05mg
EUR 190

POLR3F Antibody

MBS1492228-01mg 0.1mg
EUR 270

POLR3F Antibody

MBS1492228-5x01mg 5x0.1mg
EUR 1205

POLR3F Antibody

MBS5315434-01mL 0.1mL
EUR 470

POLR3F Antibody

MBS5315434-5x01mL 5x0.1mL
EUR 1955

POLR3F Rabbit pAb

A12224-100ul 100 ul
EUR 369.6

POLR3F Rabbit pAb

A12224-200ul 200 ul
EUR 550.8

POLR3F Rabbit pAb

A12224-20ul 20 ul
EUR 219.6

POLR3F Rabbit pAb

A12224-50ul 50 ul
EUR 267.6

POLR3F Rabbit pAb

E2510867 100ul
EUR 225
Description: Available in various conjugation types.

POLR3F Rabbit pAb

MBS8548176-01mL 0.1mL
EUR 305

POLR3F Rabbit pAb

MBS8548176-01mLAF405L 0.1mL(AF405L)
EUR 565

POLR3F Rabbit pAb

MBS8548176-01mLAF405S 0.1mL(AF405S)
EUR 565

POLR3F Rabbit pAb

MBS8548176-01mLAF610 0.1mL(AF610)
EUR 565

POLR3F Rabbit pAb

MBS8548176-01mLAF635 0.1mL(AF635)
EUR 565

POLR3F Rabbit pAb

A12224 100μL
EUR 70.85

POLR3F siRNA (Mouse)

MBS8228639-15nmol 15nmol
EUR 405

POLR3F siRNA (Mouse)

MBS8228639-30nmol 30nmol
EUR 565

POLR3F siRNA (Mouse)

MBS8228639-5x30nmol 5x30nmol
EUR 2450

POLR3F siRNA (Human)

MBS8240036-15nmol 15nmol
EUR 405

POLR3F siRNA (Human)

MBS8240036-30nmol 30nmol
EUR 565

POLR3F siRNA (Human)

MBS8240036-5x30nmol 5x30nmol
EUR 2450

Lenti ORF clone of Polr1e (mGFP-tagged) - Mouse polymerase (RNA) I polypeptide E (cDNA clone MGC:35831 IMAGE:4022372)

MR207725L4 10 µg Ask for price

anti- POLR3F antibody

FNab06632 100µg
EUR 658.5
Description: Antibody raised against POLR3F

POLR3F Blocking Peptide

20-abx063691
  • Ask for price
  • Ask for price
  • 1 mg
  • 5 mg

POLR3F Blocking Peptide

33R-5647 100 ug
EUR 119
Description: A synthetic peptide for use as a blocking control in assays to test for specificity of POLR3F antibody, catalog no. 70R-2962

POLR3F Blocking Peptide

33R-5238 100 ug
EUR 119
Description: A synthetic peptide for use as a blocking control in assays to test for specificity of POLR3F antibody, catalog no. 70R-2038

POLR3F Blocking Peptide

MBS823525-1mg 1mg
EUR 190

POLR3F Blocking Peptide

MBS823525-5mg 5mg
EUR 345

The info point out that in cells missing RNA-DNA hybrid and Ty1 repressors, elevated ranges of RNA-cDNA hybrids, that are related to duplex nucleic acid constructions, increase Ty1 mobility by way of a Rad52-dependent mechanism. In distinction, in cells missing RNA-DNA hybrid repressors alone, elevated ranges of RNA-cDNA hybrids, that are related to triplex nucleic acid constructions, increase Ty1 mobility by way of a Rad52-independent course of. We suggest that duplex and triplex RNA-DNA hybrids promote transposon mobility by way of Rad52-dependent or -independent mechanisms.

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