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| Status |
Public on Dec 31, 2020 |
| Title |
Exchange of molecular and cellular information: a hybrid model that integrates stem cell divisions and key regulatory interactions [an3] |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We performed a transcriptome analysis on the meristematic root tissue from the loss-of-function line an3 and WT plants.
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| Overall design |
Three biological replicates of an3 and WT seeds were plated. After 5 days of growth, ∼5 mm of an3 and WT root tips were collected. RNA was extracted using the Qiagen RNeasy Micro kit and libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs). Libraries were sequenced on an Illumina HiSeq 2500 with 100 bp single-end reads. Gene expression analysis of raw RNA-seq data was performed using the TuxNet interface (Spurney et al, 2019). Specifically, TuxNet uses ea-utils fastq-mcf (Aronesty, 2011, Aronesty, 2013) for preprocessing, hisat2 (Kim et al., 2015) for genome alignment, and Cufflinks (Trapnell et al., 2012) for differential expression analysis.
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| Web link |
https://doi.org/10.1017/qpb.2021.1
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| Contributor(s) |
Van den Broeck L, Fisher AP, Sozzani R |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Jul 30, 2020 |
| Last update date |
Apr 13, 2021 |
| Contact name |
Lisa Van den Broeck |
| E-mail(s) |
lfvanden@ncsu.edu, lisa.vandenbroeck@hotmail.com
|
| Organization name |
North Carolina State University
|
| Department |
Plant and Microbial Biology
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| Lab |
Thomas Hall 2577
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| Street address |
112 Derieux Place
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| City |
Raleigh |
| State/province |
NORTH CAROLINA |
| ZIP/Postal code |
27606 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL17639 |
Illumina HiSeq 2500 (Arabidopsis thaliana) |
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| Samples (6)
|
| GSM4704876 |
an3 - meristematic root tissue - Replicate 1 |
| GSM4704877 |
an3 - meristematic root tissue - Replicate 2 |
| GSM4704878 |
an3 - meristematic root tissue - Replicate 3 |
| GSM4704879 |
Col - meristematic root tissue - Replicate 1 |
| GSM4704880 |
Col - meristematic root tissue - Replicate 2 |
| GSM4704881 |
Col - meristematic root tissue - Replicate 3 |
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| This SubSeries is part of SuperSeries: |
| GSE155464 |
Exchange of molecular and cellular information: a hybrid model that integrates stem cell divisions and key regulatory interactions |
|
| Relations |
| BioProject |
PRJNA649798 |
| SRA |
SRP274406 |
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