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| Status |
Public on Mar 03, 2020 |
| Title |
stage3_SAM rep2 |
| Sample type |
SRA |
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| Source name |
Shoot apical meristem
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| Organism |
Arabis alpina |
| Characteristics |
cultivar: Pajares
tissue: Shoot apical meristem
developmental stage: after four weeks of cold treatment
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| Growth protocol |
All the experiments were performed using A. alpina Pajares accession (Wang et al., 2009). A. alpina seeds were stratified on wet filter paper for 4 days at 4°C in dark and then transferred to soil in a Bronson growth chamber (LD) with day-time temperature of 24°C and a night-time temperature of 18°C. Cold treatments were performed at 4°C in LD condition (16h light, 8h darkness) for seven weeks. Young buds with single leaf primordium and their corresponding shoot apical meristem including one leaf primordium were harvested. For each sample three biological replicates were prepared except for stage1_AB (two replicates). 120-150 buds and SAMs were harvested per replicate.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Spectrum™ Plant Total RNA Kit (Sigma Aldrich), following protocol A and on-column DNase digestion
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
1X150 bp single end
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| Data processing |
NGS analysis package: CLC genomics server 9.1.1 was used for processing and mapping reads. Data was further analysed using CLC genomics workbench 12.0
data-filtering: FASTQC was used to assess quality of reads. CLC genomics server was used to trim low quality sequences and ambiguous nucleotides using following parameters- Ambiguous trim = Yes, Ambiguous limit = 2, Quality trim = Yes, Quality limit = 0.05
read mapping: Reads were mapped to the latest annotation of the Arabis alpina genome V5 with the following settings: Mismatch cost = 2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8, Maximum number of hits for a read = 10.
adundance measurement: reads counts were normalised for differences in gene and library size using RPKM
differential expression analysis: Fold change between the two developmental stages of buds was calculated in CLC genomics workbench. The resulting candidate list was filtered for genes with statistically significant difference in expression of atleast two-fold at FDR adjusted p-value <0.05
Genome_build: Arabis alpina genome http://arabis-alpina.org/refseq.html/Arabis_alpina.MPIPZ.V5.chr.all.fasta.gz
Supplementary_files_format_and_content: excel file including geneIds, total mapped reads, normalised counts RPKM, TPM, CPM, average counts, DE test results including Fold Chnage, logFold change, FDR
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| Submission date |
Nov 13, 2019 |
| Last update date |
Mar 03, 2020 |
| Contact name |
Udhaya Ponraj |
| E-mail(s) |
vijaya.udhaya@gmail.com
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| Phone |
+492215062472
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| Organization name |
Max Planck Institute for Plant Breeding research
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| Department |
Department of chromosome biology
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| Street address |
carl-von-linne-weg-10
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| City |
cologne |
| State/province |
NRW |
| ZIP/Postal code |
50829 |
| Country |
Germany |
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| Platform ID |
GPL26216 |
| Series (1) |
| GSE140316 |
Keep a distance to be different: axillary bud initiating at a distance to the shoot apical meristem are crucial for the perennial life style of Arabis alpina |
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| Relations |
| BioSample |
SAMN13228255 |
| SRA |
SRX7135270 |
| 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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