 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 04, 2021 |
| Title |
atg2 12 hours light replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
atg2 seedlings harvested at 12h light replicate 2
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
genotype: atg2
treatment: light
time (hrs): 12
tissue: seedlings
|
| Treatment protocol |
Seeds were grown for five days in the dark, then transferred to light (100-125 µmolm-2s-1) at 22oC. Samples were collected at 0 hours (0 h), 12 hours (12 h), and 24 hours (24 h)of growth in light.
|
| Growth protocol |
About 50 mg (5 mL) Arabidopsis thaliana seeds of genotype: WT (Col-0), atg2, atg5, and atg9 seeds were surface-sterilized (Desfeux et al 2000 Plant Physiology), washed five times with sterilized water, and sown on a mesh platform (mesh size 1 mm; 3 cm x3 cm x 3 cm) layered with 1% sterilized agarose. Plants were grown in a round plastic vessel (diameter 120 mm, height 140 mm) containing approximately 300 ml liquid medium (¼x Murashige & Skoog medium without vitamins, ¼x Gamborg B5 vitamins solution, 2 mM MES, 1% [w/v] sucrose, pH 5.8) (Lee et al 2008 Molecular & Cellular Proteomics). Seeds were grown for five days in the dark, then transferred to light (100-125 µE) at 22oC. Samples were collected at 0 hours (0 h), 12 hours (12 h), and 24 hours (24 h) of growth in light.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using an adapted CTAB/chloroform/LiCl extraction protocol (Chang et al 1993 Plant Mol Biol Rep). Full details are available on protocols.io: dx.doi.org/10.17504/protocols.io.3f6gjre.
Total RNA-sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, CA, USA) as per manufacterers instructions but with reaction volumes adjusted 1/3x.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw read quality was first diagnosed using FastQC (v0.11.7).
Trim Galore! (v0.4.4) was used for adapter and low-quality read trimming with PHRED score < 20 (-q 20).
Transcript abundance was quantified as TPM using Kallisto with flags --bias --single -b 10 -l 300 -s 100 (Bray et al 2016).
Kallisto index was used to build the an index from transcripts defined by AtRTDv2_QUASI_19April2016.fa (Zhang et al 2017 Plant Cell)
Genome_build: AtRTDv2_QUASI_19April2016.fa; https://ics.hutton.ac.uk/atRTD/ (Zhang et al 2017 Plant Cell)
Supplementary_files_format_and_content: h5: HDF5 file containing run info, abundance esimates (TPM), bootstrap estimates, and transcript length information length ; tsv: plaintext file of the abundance estimates (TPM).
|
| |
|
| Submission date |
Aug 22, 2020 |
| Last update date |
Aug 04, 2021 |
| Contact name |
Diep R Ganguly |
| E-mail(s) |
dganguly@sas.upenn.edu
|
| Phone |
+1 215-898-0808
|
| Organization name |
University of Pennsylvania
|
| Department |
Department of Biology
|
| Lab |
Brian Gregory
|
| Street address |
433 S University Ave
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19103 |
| Country |
USA |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE156677 |
Autophagy mutants show delayed chloroplast development during de-etiolation in carbon limiting conditions |
|
| Relations |
| BioSample |
SAMN15880537 |
| SRA |
SRX8986855 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4736595_atg2_12h_5.h5 |
3.8 Mb |
(ftp)(http) |
H5 |
| GSM4736595_atg2_12h_5.tsv.gz |
1.0 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
