|
| Status |
Public on Mar 16, 2018 |
| Title |
SALK_059379 RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
SALK_059379
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
t-dna mutant: SALK_059379
tissue: leave, whole rosette
molecule subtype: total RNA
|
| Growth protocol |
grown in peat based, fertilized soil, controlled conditions, 21dC, 16h day, 8h dark
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen Rneasy Plant Mini kit
standard Illumina multiplexed library construction
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
RNA-seq:
base-calling using RTA 2.7.7
alignment using Bowtie2 2.3.0
smallRNA-seq:
base-calling using RTA 2.7.7
Adapter trimmed using fastqc
alignment using Bowtie2 2.3.0
bisulfite-seq:
base-calling using RTA 2.7.7
alignment using methpip_se map w/ Bowtie 0.12.7
mC calling using methpipe_se_post_map
Genome_build: pBIN_ROK2_pCSA110_sequences.txt
|
| |
|
| Submission date |
Dec 21, 2017 |
| Last update date |
Mar 16, 2018 |
| Contact name |
Joseph R Ecker |
| E-mail(s) |
ecker@salk.edu
|
| Phone |
8584534100
|
| Organization name |
HHMI-Salk-Institute
|
| Department |
Genomic Analysis Laboratory
|
| Lab |
Ecker lab
|
| Street address |
10010 North Torrey Pines Road
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL21785 |
| Series (1) |
| GSE108401 |
The Complex Architecture of Transgene Insertions |
|
| Relations |
| BioSample |
SAMN08224095 |
| SRA |
SRX3503018 |
