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| Status |
Public on Dec 30, 2020 |
| Title |
cmt/dnmt3b_rep1 |
| Sample type |
SRA |
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| Source name |
protonema
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| Organism |
Physcomitrium patens |
| Characteristics |
genotype: cmt/dnmt3b
cultivar: Grandsen
age: 7 days
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| Growth protocol |
7 days on BCDAT media, 25 °C, 16-h light and 8-h dark regime
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 7 days old protonema using SV Total RNA Isolation System (Promega, USA) and DNase treatment (Thermo Fisher Scientific, USA).
The polyA fraction (mRNA) was purified from 500 ng of total input RNA, followed by fragmentation and the generation of double-stranded cDNA. Then, Agencourt Ampure XP beads cleanup (Beckman Coulter), end repair, A base addition, adapter ligation and PCR amplification steps were performed. Libraries were quantified by Qubit (Thermo fisher scientific) and TapeStation (Agilent).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
batch2
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| Data processing |
Adaptor and quality trimming using TrimGalore v0.6.0 with Cutadapt v1.15
Alignment to the reference genome and counting reads per gene/TE in the supplied annotation file, using STAR v2.7.0f
Genome_build: Ppatens v3.0
Supplementary_files_format_and_content: tab-delimited text file with raw read counts assigned to each of the annotated features (gene or transposable element), in each sample
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| Submission date |
Dec 15, 2019 |
| Last update date |
Dec 30, 2020 |
| Contact name |
Katherine Domb |
| E-mail(s) |
[email protected]
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| Organization name |
Tel Aviv University
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| Department |
School of Plant Sciences and Food Security
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| Lab |
Assaf Zemach
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| Street address |
Haim Levanon st.
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| City |
Tel-Aviv |
| ZIP/Postal code |
6997801 |
| Country |
Israel |
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| Platform ID |
GPL27916 |
| Series (2) |
| GSE142053 |
Non-CG methylation is more potent than CG methylation in moss genome regulation [Ppatens RNA-Seq] |
| GSE142054 |
Non-CG methylation is more potent than CG methylation in moss genome regulation |
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| Relations |
| BioSample |
SAMN13566895 |
| SRA |
SRX7371480 |
| 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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