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| Status |
Public on Jan 29, 2024 |
| Title |
snap33_5d_3 |
| Sample type |
SRA |
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| Source name |
snap33_5d_3
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| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: snap33 - mutant=knock-out,insertional mutagen,T-DNA-
developmental stage: planting-date=29-MAR-21,harvest-date=05-APR-21
tissue: seedling,whole plant
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| Treatment protocol |
no treatment
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| Growth protocol |
Long day conditions: 16 h light from 6 am to 10 pm (½ MS solid media prepared with Murashige Skoog Basal Salts (Sigma M6899), 0.05% MES hydrate (Sigma M8250), pH adjusted to 5.70 with KOH (5 M), 0.5% agar type E (Sigma A4675). Autoclaved 60% hygrometry 23°C 180 µmol.m-².s-1)
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| Extracted molecule |
total RNA |
| Extraction protocol |
snap33_5d_3(35ug)
rna_selection:selection polyA, single, stranded:yes, Protocol:truseq-stranded-mrna-sample-prep-guide-15031047-E.pdf
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Genome_build: genome of Arabidopsis thaliana TAIR10
genome mapping and counts of reads by gene locus are done with STAR/HTSeqcount; exact multihits are removed and count only consistent PE reads (in PE case).
Supplementary_files_format_and_content: type:count file (txt); content:GeneID,counts
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| Submission date |
Nov 07, 2023 |
| Last update date |
Jan 29, 2024 |
| Contact name |
Véronique BRUNAUD |
| E-mail(s) |
veronique.brunaud@inrae.fr
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| Organization name |
INRA - CNRS - UPSUD
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| Lab |
IPS2
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| Street address |
rue Noetzlin
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| City |
Gif-sur-Yvette |
| ZIP/Postal code |
91190 |
| Country |
France |
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| Platform ID |
GPL19580 |
| Series (1) |
| GSE247242 |
rna-seq snap33-1 vs wt -Description of Arabidopsis thaliana t-SNARE SNAP33 |
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| Relations |
| BioSample |
SAMN38148860 |
| SRA |
SRX22404035 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7885816_htseqcount_snap33_5d_3.txt.gz |
114.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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