 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 01, 2024 |
| Title |
S05 AtWT shoot control replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
shoot
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: shoot
genotype: AtWT
treatment: control
|
| Treatment protocol |
7 days on vermiculite with or without growth media
|
| Growth protocol |
9 days on agar, 12 days on vermiculite with growth media
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Plant tissues were grinded with mortar and pestle in liquid nitrogen. RNA used for sequencing was extracted using the RNeasy Plant Mini Kit from Qiagen, following the manufacturer’s instructions. The quality of the RNA, i.e. RNA integrity, for sequencing was checked by RIN measurement by ‘Dutch Genomics Service and Support Provider’ (MAD, Science Park, University of Amsterdam, The Netherlands), for which all root samples scored at least 6.5, and all shoot samples at least 9.0.
The total RNA was mixed with ERCC RNA Spike-In Control mix 1 (Thermo Fisher Scientific) and afterwards a poly- A enrichment was performed using Dynabeads mRNA DIRECT Micro Purification Kit (Invitrogen). With the Ion Total RNA-Seq kit v2 and the Ion Xpress RNA-Seq barcoding kit, bar-coded RNA libraries were generated by following the manufacturer’s instructions (Thermo Fisher Scientific)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
Data was cleaned using FastQC, filtering out all reads smaller than 25 nucleotides and any reads where >75% of the read had a quality score of 17 or less
Reads were aligned to the TAIR10_cdna_20101214_updated reference genome using the Kallisto package
For the number of alignments, 500 was chosen.
The Sleuth package (Pimentel et al., 2017) was used to determine differential gene expression (DEG), the Wald-test was used to determine fold-change difference between conditions or genotypes. Significance was deemed at q<0.05 as determined by the Likelihood-ratio test.
Assembly: TAIR10_cdna_20101214
Supplementary files format and content: abundance.tsv contain est count and tpm for each arabidpsis gene.
Supplementary files format and content: abundance.h5 contain est count and tpm for each of the 500 allignments performed by kallisto. Can be used by the Sleuth package to get average and confidence intervals for the est_counts and tpm
|
| |
|
| Submission date |
Jun 24, 2024 |
| Last update date |
Jul 01, 2024 |
| Contact name |
Max van Hooren |
| E-mail(s) |
max.v.hooren@gmail.com
|
| Organization name |
University of Amsterdam
|
| Department |
Plant Cell biology
|
| Street address |
Science park 904
|
| City |
Amsterdam |
| State/province |
Noord Holland |
| ZIP/Postal code |
1098 XH |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL20696 |
| Series (1) |
| GSE270544 |
Transcriptome analyses of Arabidopsis lines overexpressing distinct PLC genes to explore their contribution to drought tolerance |
|
| Relations |
| BioSample |
SAMN42017524 |
| SRA |
SRX25034858 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8346406_S05.abundance.h5 |
55.3 Mb |
(ftp)(http) |
H5 |
| GSM8346406_S05.abundance.tsv.gz |
504.6 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
