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| Status |
Public on Mar 15, 2023 |
| Title |
acc.6220.rep4 |
| Sample type |
SRA |
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| Source name |
leaves
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: leaves
developmental stage: 14-leaf-rosette
accession: 6220
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| Treatment protocol |
no treatment
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| Growth protocol |
22 degrees Celsius, on soil, long-day conditions (16h light, 8h dark)
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated and DNAse I (NEB) treated using a KingFisher Robot with an in-house magnetic RNA isolation kit. RNA was diluted in nuclease free water (Ambion) and stored at -80oC.
TruSeq Stranded mRNA
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
125bp PE
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| Data processing |
raw RNA-seq reads were aligned to the TAIR10 genome using STAR (v.2.7.1.). First the genomebuild was performed for TAIR10 accounting for the genome size and not providing the annotated splice junctions. The genomebuild command: STAR --runMode genomeGenerate --genomeSAindexNbases 12.5 --genomeDir $stargenomedir --genomeFastaFiles genome.fasta . The command used for alignment: STAR --readFilesIn $fastq.gz --readFilesCommand zcat --runThreadN 4 --alignIntronMax 6000 --alignMatesGapMax 6000 --genomeDir $stargenomedir --outFilterIntronMotifs RemoveNoncanonical --outFilterMismatchNoverReadLmax 0.1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --outFilterMultimapNmax 10 --outReadsUnmapped None --alignSJoverhangMin 8 --outSAMattributes NH HI AS nM NM MD jM jI XS --outSAMtype BAM SortedByCoordinate --runMode alignReads --twopassMode Basic --outFileNamePrefix $out
read counts were calculated using featurecounts from the subread package (v.2.0.0). Command used: featureCounts -T 4 -p -F SAF -O -s 2 -t exon -g gene_id -a $saf -o $out.txt $bam
TPMs were calculated by dividing the raw counts number by the total number of raw counts in the sample (in million reads) and the length (in kb). Command used sum=`cat $out.txt| awk -v OFS="\t" '{ sum += $7} END {print sum}'` cat $out.txt| grep -v Geneid| awk -v OFS="\t" -v sum="$sum" ' {print $1,$6,$7,$7*1000000*1000/($6*sum)}' > $out.counts_tpm.bed
Assembly: TAIR10
Supplementary files format and content: Kornienko_et_al_annotation.TPMs.28accessions.rosette.txt contains a table with TPMs for 5 gene types in the new annotation (PC genes, AS lncRNAs, TE genes, lincRNAs and AS_to_TEgenes lncRNAs) for every RNAseq sample
Supplementary files format and content: BED files: The 13 bed files are gene annotations created and used in the study (for example they are used to create the table with expression values (TPMs): Kornienko_et_al_annotation.TPMs.28accessions.rosette.txt).
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| Submission date |
Feb 07, 2023 |
| Last update date |
Mar 15, 2023 |
| Contact name |
Aleksandra Kornienko |
| E-mail(s) |
kornienkoalexandra@gmail.com
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| Phone |
00431790449000
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| Organization name |
Gregor Mendel Institute
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| Lab |
Nordborg
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| Street address |
Dr. Bohrgasse 3
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| City |
Vienna |
| State/province |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
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| Platform ID |
GPL17639 |
| Series (2) |
| GSE224760 |
Population-level annotation of lncRNAs in Arabidopsis thaliana reveals extensive expression and epigenetic variability associated with TE-like silencing [lncRNA] |
| GSE224761 |
Population-level annotation of lncRNAs in Arabidopsis thaliana reveals extensive expression and epigenetic variability associated with TE-like silencing |
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| Relations |
| BioSample |
SAMN33228399 |
| SRA |
SRX19323599 |
| 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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