|
| Status |
Public on Apr 11, 2015 |
| Title |
RNA-seq_35d-2 |
| Sample type |
SRA |
| |
|
| Source name |
mature fully-expanded rosette leaf tissue, 35d
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia (Col-0)
cell type: predominantly leaf mesophyll
age: 35d
|
| Treatment protocol |
N/A
|
| Growth protocol |
Sunshine LC-1 soil mix, weekly feedings with Gro-Power Liquid 4-8-2. Percival AR-60 growth chamber, 30 micromoles photons m^-2 sec^-1, 20 hours of light 4 hours of dark.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol reagent was used for RNA isolation according to manufacturer's instructions, except one additional ethanol precipitation was added to remove residual phenol.
RNA libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2-Set A. Three samples were run per lane using multiplexing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNA-seq of 35d mature fully-expanded rosette leaf tissue - replicate 2.
|
| Data processing |
RNA-seq library reads were mapped to the TAIR10 reference genome and gene annotation using tophat-2.0.4 (Trapnell et al., 2009) calling bowtie-0.12.8 (Langmead et al., 2009) .
HTSeq (Anders et al., 2014) was used to perform gene counts.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text file of reads counts (not normalized) per gene (rows) for each sample (columns).
|
| |
|
| Submission date |
Apr 10, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Judy Brusslan |
| Organization name |
California State University Long Beach
|
| Department |
Department of Biological Sciences
|
| Lab |
MLSC-203
|
| Street address |
1250 Bellflower Blvd
|
| City |
Long Beach |
| State/province |
CA |
| ZIP/Postal code |
90840 |
| Country |
USA |
| |
|
| Platform ID |
GPL13222 |
| Series (2) |
| GSE67777 |
A Genome-wide Chronological Study of Gene Expression and Two Histone Modifications, H3K4me3 and H3K9ac, during Developmental Leaf Senescence [RNA-seq] |
| GSE67778 |
A Genome-wide Chronological Study of Gene Expression and Two Histone Modifications, H3K4me3 and H3K9ac, during Developmental Leaf Senescence |
|
| Relations |
| BioSample |
SAMN03473657 |
| SRA |
SRX986849 |
