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| Status |
Public on Jan 26, 2021 |
| Title |
WT_rep3 [RNA-seq] |
| Sample type |
SRA |
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| Source name |
Mature pollen
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| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-gl
genotype: wild type
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| Extracted molecule |
total RNA |
| Extraction protocol |
For analysis of dme-2/+ pollen, dry pollen was harvested from Col-gl and BASTA-sprayed dme-2/+ plants using a method published previously. Pollen grains were disrupted in a Precellys tissue homogenizer (Bertin Instruments) and total RNA isolated using an RNeasy Micro Kit (Qiagen). For vegetative cell nuclei, FACS-isolated nuclei from the ProVCK:NTF line were sorted directly into Trizol reagent and precipitated with isopropanol.
RNA-seq libraries were generated from the resulting RNA with Smart-seq2 using independent biological replicates. The libraries were sequenced on an Illumina Hiseq 2500 using 50 bp paired-end and single-end reads for VN and pollen samples, respectively.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
wild type pollen
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| Data processing |
Raw, unaligned BAM files were first sorted with samtools sort -n and then converted to fastq files with bedtools bamtofastq.
Adapter trimming was performed using TrimGalore version 0.4.1.
Reads were aligned to the Arabidopsis genome (TAIR10) using the STAR aligner version 2.5.2a.
Transcripts per million (TPM) values were generated using Kallisto version 0.43.1 (21) with an index built on TAIR10 cDNA sequences.
Differential gene expression analysis of WT and dme-2/+ was performed using DESeq2 1.22.2 for transcripts that had 10 counts or more in at least one sample.
Differentially expressed genes (DEGs) were classified as having a p-value < 0.1 after correction for multiple testing (i.e. adjusted p-value).
Genome_build: TAIR10 cDNA sequences (Arabidopsis_thaliana.TAIR10.cdna.all.fa.gz)
Supplementary_files_format_and_content: *.tsv: Kallisto quantification abundance.tsv output
Supplementary_files_format_and_content: *.txt: TPM values for VN and Sperm
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| Submission date |
Jul 29, 2020 |
| Last update date |
Jan 30, 2021 |
| Contact name |
Michael Borg |
| E-mail(s) |
borgmichael@gmail.com
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| Organization name |
Gregor Mendel Institute
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| Lab |
Berger Lab
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| Street address |
Dr. Bohr-Gasse 3
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| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
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| Platform ID |
GPL17639 |
| Series (2) |
| GSE155365 |
Epigenetic reprogramming events rewire transcription during the alternation of generations in Arabidopsis [RNA-Seq] |
| GSE155369 |
Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidopsis |
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| Relations |
| BioSample |
SAMN15667720 |
| SRA |
SRX8844293 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4700184_kallisto_123727_AGGCAGAATCGTCGGC_CEAB6ANXX_1_20200630B_20200630.tsv.gz |
347.0 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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