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Series GSE233927 Query DataSets for GSE233927
Status Public on Sep 28, 2023
Title Comparative analysis of nascent transcription among plant species
Organisms Chlamydomonas reinhardtii; Physcomitrium patens; Carica papaya; Arabidopsis thaliana; Hordeum vulgare; Zea mays; Drosophila melanogaster; Selaginella moellendorffii
Experiment type Expression profiling by high throughput sequencing
Other
Non-coding RNA profiling by high throughput sequencing
Summary Comparative analysis of nascent transcription among plant species
 
Overall design A.thaliana Col-0 mature leaves were collected from plants grown as described (M. Wang et al. 2023), while A.thaliana Col-0 suspension cells were grown in 250-mL baffled flasks containing 50 mL of growth medium (3.2 g/L Gamborg’s B-5 medium, 3 mM MES, 3% [v/v] Suc, 1.1 mg L−1 2,4-dichlorophenoxyacetic acid). The cultures were maintained at 23°C under continuous light on a rotary shaker (160 rpm) and kindly provided as a frozen pellet by Dr. Ashley M. Brooks. Barley (Hordeum vulgare) RNA was isolated by Dr. Pete Hedley from embryonic tissue (including mesocotyl and seminal roots; EMB) isolated from grain tissues 4 days past germination (Mascher et al. 2017). Physcomitrium (Physcomitrella) patens (Gransden) was grown on plates with BCDA medium in a growth cabinet at 21°C under 16h light. Selaginella moellendorffii was purchased from Plant Delights Nursery and grown at the window under normal daylight for 1 week prior to isolating RNA from stems and leaves. C. reinhardtii, which was kindly provided by Dr. Will Ansari and Dr. Stephen Mayfield (UC San Diego), was grown to late logarithmic phase in TAP (Tris–acetate–phosphate) medium at 23°C under constant illumination of 5000 lux on a rotary shaker. Adult 2nd and 3rd leaves from Z. mays L. cultivar B73 was kindly provided by Dr. Lauri Smith (UC San Diego). Plants were grown in 4-inch pots in a greenhouse (temp: 23°C-29°C) without supplemental lighting or humidification (humidity in the 15 hours following inoculation ranged between 70 and 90%) year round in La Jolla, CA. RNA from Z. mays L. cultivar B73 7d old shoot, root and leaves were grown in the Schmitz laboratory (University of Georgia) as described in (Ricci et al. 2019).
 
Contributor(s) McDonald B, Duttke S, Brabb I
Citation(s) 37808859
Submission date Jun 01, 2023
Last update date Apr 02, 2024
Contact name Sascha Duttke
Organization name Washington State University
Department School of Molecular Biosciences
Lab Dr. Duttke Lab
Street address BLS 202, 100 Dairy Road
City Pullman
State/province Washington
ZIP/Postal code 99163
Country USA
 
Platforms (17)
GPL19132 Illumina NextSeq 500 (Drosophila melanogaster)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
GPL20156 Illumina NextSeq 500 (Zea mays)
Samples (68)
GSM7439207 Arabidopsis thaliana col-0 cells csRNA-seq r1
GSM7439208 Arabidopsis thaliana col-0 cells csRNA-seq r2
GSM7439209 Arabidopsis thaliana col-0 cells sRNA-seq r1
Relations
BioProject PRJNA978596

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE233927_A.thaliana-6dseedling-10.tss.txt.gz 1.0 Mb (ftp)(http) TXT
GSE233927_A.thaliana-cells-10.tss.txt.gz 1.8 Mb (ftp)(http) TXT
GSE233927_A.thaliana-leaf-10.tss.txt.gz 1.2 Mb (ftp)(http) TXT
GSE233927_C.papaya-10.tss.txt.gz 1.7 Mb (ftp)(http) TXT
GSE233927_C.reinhardtii-10.tss.txt.gz 1.1 Mb (ftp)(http) TXT
GSE233927_D.melanogaster-S2cells-10.tss.txt.gz 773.0 Kb (ftp)(http) TXT
GSE233927_D.melanogaster-embryo-10.tss.txt.gz 1.1 Mb (ftp)(http) TXT
GSE233927_D.melanogaster_total_RNA-seq.bed.gz 80.6 Mb (ftp)(http) BED
GSE233927_GEOsubmissionSheet.xlsx 48.3 Kb (ftp)(http) XLSX
GSE233927_H.vulgare-10.tss.txt.gz 1.7 Mb (ftp)(http) TXT
GSE233927_P.patens-Gransden-10.tss.txt.gz 1.6 Mb (ftp)(http) TXT
GSE233927_RAW.tar 963.3 Mb (http)(custom) TAR (of BED)
GSE233927_S.moellendorffii-10.tss.txt.gz 1.9 Mb (ftp)(http) TXT
GSE233927_Z.mays-leaf-10.tss.txt.gz 1.5 Mb (ftp)(http) TXT
GSE233927_Z.mays-leaves7d-10.tss.txt.gz 1.1 Mb (ftp)(http) TXT
GSE233927_Z.mays-root7d-10.tss.txt.gz 1.7 Mb (ftp)(http) TXT
GSE233927_Z.mays-shoot7d-10.tss.txt.gz 1.9 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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