U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SRX8166523: GSM4494509: WOXINTP; Solanum lycopersicum; ATAC-seq
1 ILLUMINA (NextSeq 500) run: 14.9M spots, 1.2G bases, 446.8Mb downloads

Submitted by: NCBI (GEO)
Study: Atlas of chromatin accessibility and translatome of tomato and rice root tip cell types
show Abstracthide Abstract
Plant species have evolved specialized cell types and regulatory programs. To understand this diversity, we profiled tomato cell type translatomes and chromatin accessibility. While cell type expression signatures are diverse, some genes exhibit robust cell type expression across time and environments. Using xylem differentiation as a model, newly described, repurposed and conserved genes illustrate this spatial variation. Data integration into regulatory networks demonstrates the function of molecularly uncharacterized cell types. Analyses of rice, tomato and Arabidopsis tissues suggest that root meristems are more conserved, while other cell types/tissues exhibit species-specific genes and processes. Several transcriptional properties observed in animals were also observed in plants and suggest cross-kingdom higher-order organizational properties. These data serve as a community resource, paving the way for engineering resilient crops. Overall design: Examination of cell type-specific ATAC and TRAP seq profiles in tomato and rice roots. Tomato plate-based experiments (the nuclear and translating ribosome affinity purification experiments) were conducted with four independent replicates of each of the 12 lines, with T1 seed stocks (and T2 as needed). Tomato pot-based experiments were conducted with four independent replicates of the meristematic cortex and cortex lines and each root tissue was dissected for the lateral roots and the adventitious (hypocotyl-derived) roots. Following filtering steps only four samples were included, one lateral and one adventitious root sample of the meristematic cortex and cortex lines. Tomato field-based experiment was performed with six independent replicates of the meristematic cortex, endodermis, meristematic zone and 35S lines. Following filtering steps, one replicate was removed from the endodermis and one from the meristematic cortex. Rice plate-based experiments were conducted with three independent replicates of the endodermis, vasculature and 35S lines, with T1 seed stocks (and T2 as needed), except for the meristematic cortex for which two independent replicates of two lines were used. Arabidopsis plate-based experiments were done with two independent replicates of the meristematic cortex, endodermis, vasculature and 35S lines as described in Mustroph et al., 2009.
Sample: WOXINTP
SAMN14679948 • SRS6527800 • All experiments • All runs
Library:
Instrument: NextSeq 500
Strategy: ATAC-seq
Source: GENOMIC
Selection: other
Layout: PAIRED
Construction protocol: Nuclei were purified from frozen and pulverized tissue as previously described (Reynoso et al. 2019). Tissue was resuspended in an ice-cold mortar containing 10 mL of freshly prepared nuclei purification buffer (NPB: 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, pH, 7.0) containing 200 uL Protease Inhibitor Cocktail (0.4X, Sigma, P9599) per 50 mL of buffer. The homogenized extracts were filtered through a 30 µM nylon mesh to remove cell debris and centrifuged at 1000 x g for 15 min at 4° C to pellet nuclei. Nuclei were resuspended in 1 mL of NPB and 25 µL of streptavidin-coated beads (NEB) were added to the nuclei. This mixture was slowly rotated in a cold room at 4° C for 30 min. The nuclei/beads suspension was diluted to 14 mL with NPB supplemented with 0.1% (v/v) Triton X-100 (NPB-T), in a 15 mL Falcon tube, mixed thoroughly and placed in a 15 ml magnet to capture bead-bound nuclei for 1 min at 4° C. The supernatant was carefully removed using a plastic Pasteur pipette, taking care to remove bubbles to avoid disturbing the beads. Beads were resuspended in 14 ml of cold NPB-T, placed on a rotating mixer for 30 sec, and then placed back in the 15 ml magnet to capture the beads-nuclei at 4° C for 1 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube. Libraries were size selected for under 750nt and up to 24 barcoded libraries were pooled together. ATAC-seq libraries were sequenced on the NextSeq 500 at the UC Davis DNA Technologies Core to obtain 40-bp paired-end reads.
Experiment attributes:
GEO Accession: GSM4494509
Links:
Runs: 1 run, 14.9M spots, 1.2G bases, 446.8Mb
Run# of Spots# of BasesSizePublished
SRR1159980114,889,8611.2G446.8Mb2021-03-24

ID:
10643756

Supplemental Content

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...