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| Status |
Public on May 28, 2020 |
| Title |
WT rep2 |
| Sample type |
SRA |
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| Source name |
flowers
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| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: WT (Col-0)
biological replicate: replicate 2
reference sequence: TAIR10
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| Growth protocol |
Arabidopsis plantlets of Col-0 accession were grown on soil with 16 hr light (21 °C) /8h (18 °C) darkness cycles
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from flowers with TRI Reagent® (Molecular Research Center) according to manufacturer’s instructions
TAILseq libraries according to Chang et al., 2014 (https://doi.org/10.1016/j.molcel.2014.02.007) and Zuber et al., 2016 (doi: 10.1016/j.celrep.2016.02.060) with some modifications of the protocol, see related publication.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Description |
Processed_data_TAILseq.txt
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| Data processing |
Library strategy: TAIL-seq
The base calling-based pipeline was adapted from Zuber et al. 2016 (doi: 10.1016/j.celrep.2016.02.060) .
The base calls were retrieved after initial data processing by the MiSeq Control Software v 2.6 and the sequences having completely identical nucleotides in the 1st to 15th cycle in read 2 (degenerate bases in 3’ adapter) were deduplicated.
In order to identify transcripts, read 1 sequences were mapped onto the Arabidopsis thaliana reference genome (TAIR 10) using Hisat2 (v2.1.0) (Kim et al. 2015, https://doi.org/10.1038/nmeth.3317).
The resulting alignment was annotated using the intersectBed tool from the BEDTools suite (v2.17.5) (Quinlan and Hall, 2010, https://doi.org/10.1093/bioinformatics/btq033) and the Arabidopsis annotation file TAIR10_GFF3_genes.gff (http://www.arabidopsis.org).
Reads 1 that map onto cytosolic mRNAs and their corresponding reads 2 were extracted and used for further analyses.
Reads 2 that contain the delimiter sequence were selected and subsequently trimmed from their random and delimiter sequences.
A homemade python script was then used to extract poly(A) tails (>5 nt) and their potential 3’ end modification from the remaining read 2. Poly(A) were detected with a constraint that it must begin within the first 30 cycles, so the maximum detectable 3’ end modification of poly(A) tails was limited to the last 29 nucleotides of insert.
Detected poly(A) and 3’ extensions were finally analyzed for their size and composition using a homemade script based on Python 2.7.
Genome_build: TAIR10
Supplementary_files_format_and_content: One processed data file is given. It includes the processed data for the three biological replicate.
Supplementary_files_format_and_content: For each read, we indicate read ID (read.ID), gene AGI (AGI), TruSeq index (index), biological replicate (rep), poly(A) tail sequence (polyA), poly(A) tail length (polyA.size), non-A extension sequence (modification), length of the non-A extension (modification.size), tail sequence (extension), tail size (extension.size), and a tag (classification) indicating the category of the tail.
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| Submission date |
Apr 09, 2020 |
| Last update date |
May 28, 2020 |
| Contact name |
Dominique Gagliardi |
| E-mail(s) |
[email protected]
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| Organization name |
CNRS
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| Department |
IBMP
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| Street address |
12, rue du General Zimmer
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| City |
Strasbourg |
| ZIP/Postal code |
67084 |
| Country |
France |
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| Platform ID |
GPL17970 |
| Series (2) |
| GSE148417 |
Global investigation by TAILseq of mRNA 3' ends in Arabidopsis thaliana flowers |
| GSE148449 |
Molecular connection between the TUTase URT1 and decapping activators |
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| Relations |
| BioSample |
SAMN14569696 |
| SRA |
SRX8092700 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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