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Sample GSM4218389 Query DataSets for GSM4218389
Status Public on Dec 30, 2020
Title met/dnmt3b_rep2
Sample type SRA
 
Source name protonema
Organism Physcomitrium patens
Characteristics genotype: met/dnmt3b
cultivar: Grandsen
age: 7 days
Growth protocol 7 days on BCDAT media, 25 °C, 16-h light and 8-h dark regime
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).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description batch1
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
 
Submission date Dec 15, 2019
Last update date Dec 30, 2020
Contact name Katherine Domb
E-mail(s) [email protected]
Organization name Tel Aviv University
Department School of Plant Sciences and Food Security
Lab Assaf Zemach
Street address Haim Levanon st.
City Tel-Aviv
ZIP/Postal code 6997801
Country Israel
 
Platform ID GPL17793
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
Relations
BioSample SAMN13566897
SRA SRX7371478

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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