#transcriptome

Growing Liver

Study of the genes being read (transcriptome) in organoids [3D lab-grown tissue] grown from human foetal liver cells (hepatocytes) reveals the molecules they require for their metabolism and to undergo cell division as they mature from development to adulthood

Read the published research article here

Image from work by Delilah Hendriks and Benedetta Artegiani, and colleagues

Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands

Image originally published with a Creative Commons Attribution 4.0 International (CC BY 4.0)

Published in Nature Communications, May 2024

Sequencing Platform

Illumina NovaSeq X Plus high-throughput sequencing platform for large-scale genomic projects

NovaSeq X Plus:

As one of the two latest Illumina sequencing systems, the NovaSeq X Plus allows us to offer maximum throughput and accuracy, as well as exceptional sequencing capabilities for data-intensive applications.

10 B (PE150) Flow Cell available:   ~1.25 B paired reads per lane.

25 B (PE150) Flow Cell available:   ~3.2 B paired reads per lane.

NovaSeq 6000:

With the NovaSeq 6000, we are able to sequence up to 64 human genomes with 90 Gb and produce 6 Tb of data per single run as short as 40 hours, providing users with the speed and flexibility to complete projects faster and with greater output.

50 G raw data per lane, 3.4 T raw data per Flowcell, and 2 × 150 bp read length.

800 M raw reads per flow cell, with 2 × 250 bp and 2 × 50 bp read lengths.

Single Cell Platform:

The Chromium X makes single-cell analysis easy, reliable, and scalable thanks to its proprietary Next GEM technology. With Chromium X, we can conduct any 10x Genomics single-cell experiment on the scale you need, including single-cell transcriptomes, single-cell immunobanks, single-cell ATACs, and multi-omics consortia.

Automated intelligent NGS library preparation workstation in LC Sciences genomics laboratory

Intelligent NGS Workstation:

LC Sciences provides industry-leading speed from sample to data, powered by its fully automated, round-the-clock NGS solutions. Introducing the UnityFX series—an all-in-one automation platform for NGS library construction and pooling. Engineered for true walkaway operation, UnityFX enables continuous, unmanned processing, dramatically increasing workflow efficiency and accelerating project turn-around time for clients. This highly integrated system sets a new benchmark in robustness and reproducibility, helping to push the boundaries of genomic science and foster a more scalable NGS ecosystem.

Computing Platform

We have constructed a substantial data processing facility that encompasses an area of over 150 square meters. This facility, comprises more than 300 computing nodes and features a distributed storage capacity of over 50 petabytes.

DOI: doi.org/10.1111/jse.70034

[[ Phylogenetic relationships and proposed infrageneric classification of Encephalartos. Major clades identified in this study are shown on the left, with representative taxa illustrated on the right. Clades and their representatives are as follows:

Cycadifolius Clade: (1) E. cycadifolius (Jacq.) Lehm. and (2) E. laevifolius Stapf & Burtt Davy; #Inopinus Clade: (3) E. hirsutus P. J. H. Hurter; Altensteinii Clade: (4) E. woodii Sander of woodii subclade, (5) E. trispinosus (Hook. f.) R. A. Dyer and (6) E. horridus (Jacq.) Lehm. of longifolius subclade, (7) E. lebomboensis I. Verd. of altensteinii subclade;

Afer Clade: (😎 E. villosus Lem. and (9) E. cerinus Lavranos & D. L. Goode; Eugene-maraisii Clade: (10) E. middelburgensis Vorster, Robbertse & S. van der Westh; Ferox Clade: (11) E. ferox G. Bertol; Manikensis Clade: (12) E. concinnus R. A. Dyer & I. Verd. and (13) E. chimanimaniensis R. A. Dyer & I. Verd.; Turneri Clade: (14) E. turneri Lavranos & D. L. Goode, (15) and (16) E. gratus Prain of turneri subclade, (17) E. barteri Carruth. ex Miq. of hildebrandtii subclade, (18) E. delucanus R. A. Dyer & I. Verd. of poggei subclade. Photographs by A. Lindstrom (4, 11–18) and J. A. R. Clugston (1–3, 5–10). ]]

Integrative #phylogenomics and morphology reveal the evolution and biogeography of Encephalartos (#Zamiaceae) We aimed to conduct phylogenetic analyses of Encephalartos, a cycad genus endemic to #Africa, using 3545 single-copy nuclear genes extracted from transcriptome data, covering 64/65 of the recognized species, along with inference of divergence times using two secondary calibration points. Integrating analyses of phylogenomics, spatio-temporal distribution, and morphology, the eight major clades within the genus were resolved. Dated analyses to estimate the origins and diversification patterns for the genus Encephalartos species yielded divergence age estimates corresponding to the Oligo-Miocene. Comprehensive phylogenetic analyses reveal new higher level phylogenetic relationships among taxa in Encephalartos, providing a stable framework for clarifying the evolutionary history of this #cycad group.

以前横市にも頻繁に来て下さっていた農研機構の孫さん、当グループの清水先生、爲重さん、岡田さんも一緒に書いた論文が出ました。コムギで多検体のトランスクリプトーム解析をするのに優れた手法開発の論文です。