Log In Sign up
The largest database of trusted experimental protocols

Thruplex dna seq library preparation kit

Manufactured by Takara Bio
Visit Supplier

The Thruplex DNA-seq library preparation kit is a tool used for the generation of DNA sequencing libraries. The kit provides the necessary reagents and protocols to prepare DNA samples for downstream sequencing analysis.

Automatically generated - may contain errors

Lab products found in correlation

Picogreen, by Thermo Fisher Scientific (4 mentions) Bioanalyzer, by Agilent Technologies (4 mentions) Ab4729, by Abcam (2 mentions) Hi seq 2000 100bp, by Illumina (2 mentions) Hiseq 2500, by Illumina (2 mentions) Pippin prep, by Sage Science (1 mentions)

Close spelling variants of this product

ThruPLEX DNA-seq (7 citations) ThruPLEX Kit (7 citations)

5 protocols using thruplex dna seq library preparation kit

1

ChIP-seq of Primary Glioblastoma Tumors

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
Chromatin immunoprecipitation (ChIP) of 5–10 mg of flash-frozen primary GBM tumors was performed by using 5 μg H3K27ac antibody per ChIP experiment (Active Motif; 39133). In the case of cells, 5 million cells were used for ChIP studies. ChIPs were performed as described previously (Wang et al., 2018b (link)). Enriched DNA was quantified by using PicoGreen (Invitrogen) and ChIP libraries were amplified and barcoded by using the Thruplex DNA-seq library preparation kit (Rubicon Genomics) according to the manufacturer’s recommendations. Following library amplification, DNA fragments were agarose gel (1.0%) size selected (<1 kb), assessed by using a Bioanalyzer (Agilent Technologies), and sequenced at The Centre for Applied Genomics (The Hospital for Sick Children) by using Illumina Hi-Seq 2500 150-bp single-end reads (GeneWiz).
Mack S.C., Singh I., Wang X., Hirsch R., Wu Q., Villagomez R., Bernatchez J.A., Zhu Z., Gimple R.C., Kim L.J., Morton A., Lai S., Qiu Z., Prager B.C., Bertrand K.C., Mah C., Zhou W., Lee C., Barnett G.H., Vogelbaum M.A., Sloan A.E., Chavez L., Bao S., Scacheri P.C., Siqueira-Neto J.L., Lin C.Y, & Rich J.N. (2019). Chromatin landscapes reveal developmentally encoded transcriptional states that define human glioblastoma. The Journal of Experimental Medicine, 216(5), 1071-1090.
+ Open protocol
+ Expand
2

ChIP-seq of Ependymoma Tumor Samples

Check if the same lab product or an alternative is used in the 5 most similar protocols
Chromatin immunoprecipitation (ChIP) of 5-10 mg of flash frozen primary ependymoma tumours was performed using 5 mg of H3K27ac antibody per ChIP experiment (Abcam-AB4729 (Toronto) or Active Motif-39133 (Heidelberg)). Enriched DNA was quantified using Picogreen (Invitrogen) and ChIP libraries were amplified and barcoded using the Thruplex DNA-seq library preparation kit (Rubicon Genomics) according to manufacturer recommendations. Following library amplification, DNA fragments were Agarose gel (1.0%) size selected (< 1 kb), assessed using Bioanalyzer (Agilent Technologies) and sequenced at The Centre for Applied Genomics (The Hospital for Sick Children) using Illumina Hi-Seq 2000 100bp (Toronto cohort) and 50bp (Heidelberg) single-end sequencing.
Mack S.C., Pajtler K.W., Chavez L., Okonechnikov K., Bertrand K.C., Wang X., Erkek S., Federation A., Song A., Lee C., Wang X., McDonald L., Morrow J.J., Saiakhova A., Sin-Chan P., Wu Q., Michaelraj A., Miller T.E., Hubert C.G., Ryzhova M., Garzia L., Donovan L., Dombrowski S., Factor D.C., Luu B., Valentim C.L., Gimple R.C., Morton A., Kim L., Prager B.C., Lee J.J., Wu X., Zuccaro J., Thompson Y., de Borja López Holgado F., Reimand J., Ke S.Q., Tropper A., Lai S., Vijayarajah S., Doan S., Mahadev V., Miñan A.F., Gröbner S.N., Lienhard M., Zapatka M., Huang Z., Aldape K.D., Carcaboso A.M., Houghton P.J., Keir S.T., Milde T., Witt H., Li Y., Li C.J., Bian X.W., Jones D.T., Scott I., Singh S.K., Huang A., Dirks P.B., Bouffet E., Bradner J.E., Ramaswamy V., Jabado N., Rutka J.T., Northcott P.A., Lupien M., Lichter P., Korshunov A., Scacheri P.C., Pfister S.M., Kool M., Taylor M.D, & Rich J.N. (2017). Therapeutic Targeting of Ependymoma as Informed by Oncogenic Enhancer Profiling. Nature, 553(7686), 101-105.
+ Open protocol
+ Expand
3

ChIP-seq of Ependymoma Tumor Samples

Check if the same lab product or an alternative is used in the 5 most similar protocols
Chromatin immunoprecipitation (ChIP) of 5-10 mg of flash frozen primary ependymoma tumours was performed using 5 mg of H3K27ac antibody per ChIP experiment (Abcam-AB4729 (Toronto) or Active Motif-39133 (Heidelberg)). Enriched DNA was quantified using Picogreen (Invitrogen) and ChIP libraries were amplified and barcoded using the Thruplex DNA-seq library preparation kit (Rubicon Genomics) according to manufacturer recommendations. Following library amplification, DNA fragments were Agarose gel (1.0%) size selected (< 1 kb), assessed using Bioanalyzer (Agilent Technologies) and sequenced at The Centre for Applied Genomics (The Hospital for Sick Children) using Illumina Hi-Seq 2000 100bp (Toronto cohort) and 50bp (Heidelberg) single-end sequencing.
Mack S.C., Pajtler K.W., Chavez L., Okonechnikov K., Bertrand K.C., Wang X., Erkek S., Federation A., Song A., Lee C., Wang X., McDonald L., Morrow J.J., Saiakhova A., Sin-Chan P., Wu Q., Michaelraj A., Miller T.E., Hubert C.G., Ryzhova M., Garzia L., Donovan L., Dombrowski S., Factor D.C., Luu B., Valentim C.L., Gimple R.C., Morton A., Kim L., Prager B.C., Lee J.J., Wu X., Zuccaro J., Thompson Y., de Borja López Holgado F., Reimand J., Ke S.Q., Tropper A., Lai S., Vijayarajah S., Doan S., Mahadev V., Miñan A.F., Gröbner S.N., Lienhard M., Zapatka M., Huang Z., Aldape K.D., Carcaboso A.M., Houghton P.J., Keir S.T., Milde T., Witt H., Li Y., Li C.J., Bian X.W., Jones D.T., Scott I., Singh S.K., Huang A., Dirks P.B., Bouffet E., Bradner J.E., Ramaswamy V., Jabado N., Rutka J.T., Northcott P.A., Lupien M., Lichter P., Korshunov A., Scacheri P.C., Pfister S.M., Kool M., Taylor M.D, & Rich J.N. (2017). Therapeutic Targeting of Ependymoma as Informed by Oncogenic Enhancer Profiling. Nature, 553(7686), 101-105.
+ Open protocol
+ Expand
4

Chromatin Immunoprecipitation of Meningioma Tumors

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
Chromatin immunoprecipitation (ChIP) was performed as previously described (22 (link)). Briefly, 5–10 mg of flash-frozen primary meningioma tumors was pulverized, crosslinked using 1.5% formaldehyde and sonicated to fragment sizes of 200-800 bp. Samples were incubated overnight with 5 μg H3K27ac antibody per ChIP experiment (Active Motif; 39133). Enriched DNA was quantified by using PicoGreen (Invitrogen) and ChIP libraries were amplified and barcoded by using the Thruplex DNA-seq library preparation kit (Rubicon Genomics) according to the manufacturer’s recommendations. Following library amplification, DNA fragments were agarose gel (1.0%) size selected (<1 kb), analyzed using a Bioanalyzer (Agilent Technologies) and sequenced at Genewiz by using Illumina HiSeq 2500 2x150-bp paired-end reads.
Prager B.C., Vasudevan H.N., Dixit D., Bernatchez J.A., Wu Q., Wallace L.C., Bhargava S., Lee D., King B.H., Morton A.R., Gimple R.C., Pekmezci M., Zhu Z., Siqueira-Neto J.L., Wang X., Xie Q., Chen C., Barnett G.H., Vogelbaum M.A., Mack S.C., Chavez L., Perry A., Raleigh D.R, & Rich J.N. (2020). The Meningioma Enhancer Landscape Delineates Novel Subgroups and Drives Druggable Dependencies. Cancer discovery, 10(11), 1722-1741.
+ Open protocol
+ Expand
5

ChIP-seq Library Preparation and Sequencing

Check if the same lab product or an alternative is used in the 5 most similar protocols
ChIP libraries were prepared using a ThruPlex DNA-seq library preparation Kit (Rubicon Genomics) following the manufacturer’s protocol. ChIP libraries were then size selected with PippinPrep (Sage Science) for a final library fragment size of 350–400 bp, and quantified with KAPPA qPCR. ChIP libraries were then sequenced on a HiSeq 2500 (Illumina) with 2 × 100 bp paired-end reads to a depth of >20 × 106 fragments per sample at the RUCDR, Infinite Biologics sequencing center (Rutgers University, NJ). Reads were de-multiplexed and concatenated, and delivered as fastq files.
Vazquez B.N., Thackray J.K., Simonet N.G., Chahar S., Kane-Goldsmith N., Newkirk S.J., Lee S., Xing J., Verzi M.P., An W., Vaquero A., Tischfield J.A, & Serrano L. (2019). SIRT7 mediates L1 elements transcriptional repression and their association with the nuclear lamina. Nucleic Acids Research, 47(15), 7870-7885.
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!