|
| Status |
Public on Dec 06, 2018 |
| Title |
RNAseq_B_ZF108DNAJ1inWT_NophenoControl_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
leaf
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
tissue: leaf
genotype/variation: ZF108DNAJ1inWT
|
| Growth protocol |
soil, 16 hour light, 8 hour dark cycle
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
2-3 leaves from individual plants (2-3 weeks old). Total RNA was extracted using TRIzol and Direct-zol RNA miniprep kit (Zymo, R2050) including in-column DNase treatment.
TruSeq Stranded mRNA Library Prep Kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
polyA RNA
|
| Data processing |
RNA-seq: 50bp single end reads were aligned using TopHat2 including the fr-firststrand option allowing for intron length of up to 10,000. bigWig tracks were generated using bamCoverage in DeepTools (https://deeptools.readthedocs.io/en/latest/).
genome build: TAIR 10
RNAseq bigWig tracks are normalised reads (by mapped library size), and binned into 25bp or 50bp bins.
|
| |
|
| Submission date |
Dec 21, 2017 |
| Last update date |
Dec 06, 2018 |
| Contact name |
C. Jake Harris |
| E-mail(s) |
jake.harris88@gmail.com
|
| Organization name |
UCLA
|
| Department |
MCDB
|
| Lab |
Jacobsen
|
| Street address |
4045 Terasaki Life Sciences Building
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL21785 |
| Series (1) |
| GSE108414 |
A DNA methylation reader complex that enhances gene transcription |
|
| Relations |
| BioSample |
SAMN08225546 |
| SRA |
SRX3503898 |
