Long-read Sequencing and Hi-C Profiling

Sequel ^® Sequencing Kit 2.1 (PacBio) was used to construct an SMRT library, and high-quality long reads were generated using an RSII system. For Hi-C, libraries were performed according to a previously described method (Wang et al., 2020 (link); Wu et al., 2020 (link)), via HindIII digestion and sequencing using a Hiseq X platform (Illumina) with an average depth of 69 ×. Poly (A) strand-specific libraries were constructed using the KAPA Stranded mRNA-Seq Library Preparation kit (KK8421; Roche, Pleasanton, CA, United States). All libraries were sequenced using an Illumina Hiseq 4000 sequencing system.

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Wang S., Gao S., Nie J., Tan X., Xie J., Bi X., Sun Y., Luo S., Zhu Q., Geng J., Liu W., Lin Q., Cui P., Hu S, & Wu S. (2022). Improved 93-11 Genome and Time-Course Transcriptome Expand Resources for Rice Genomics. Frontiers in Plant Science, 12, 769700.

Publication 2021

Sequel ® Sequencing Kit 2.1 Hiseq X platform KAPA Stranded mRNA-Seq Library Preparation kit Hiseq 4000 sequencing system

Digestion Library Mrna Poly a Smrt

Corresponding Organization : Austrian Academy of Sciences

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Variable analysis

independent variables

Type of sequencing kit used (Sequel® Sequencing Kit 2.1 (PacBio))
Sequencing platform used (RSII system)
Hi-C library preparation method (described by Wang et al., 2020 and Wu et al., 2020)
Restriction enzyme used for Hi-C (HindIII)
Sequencing platform used for Hi-C (Hiseq X, Illumina)
Library preparation method for poly(A) strand-specific libraries (KAPA Stranded mRNA-Seq Library Preparation kit)
Sequencing platform used for all libraries (Illumina Hiseq 4000)

dependent variables

Quality of long reads generated
Sequencing depth for Hi-C libraries (average of 69×)

control variables

Not explicitly mentioned

controls

No positive or negative controls were explicitly mentioned in the provided information.

Annotations

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