|
| Status |
Public on Aug 15, 2017 |
| Title |
Col-0 gDNA |
| Sample type |
SRA |
| |
|
| Source name |
Col-0, seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: seedlings
genotype: WT (Col-0)
developmental stage: two weeks old
|
| Growth protocol |
Seeds were sown on MS media, statified at 4 C for 2-d before being transferred to long-day conditions at 22°C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
QIAgen DNeasy extraction
Nextera DNA Library prep (Illumina)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were trimmed with trimgalore (v0.4.2) with options --phred33 --paired --nextera
mapped with bowtie2 (2.2.29) [Langmead 2012] with option -X 1500 onto the TAIR10 genome with the pROK2 T-DNA sequence as a supplementary chromosome [Baulcombe 1986, Ülker 2008]
Read pairs with one read mapping to the T-DNA and its mate mapping to the genome were extracted from the SAM output with awk ‘($3 == “pROK2_T-DNA_only” && $7 != “=”)’, to identify T-DNA insertion sites.
Genome_build: TAIR10 + pROK2 T-DNA
Supplementary_files_format_and_content: filtered alignments for read pairs mapping across the T-DNA – genome junction.
|
| |
|
| Submission date |
Aug 01, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Quentin Gouil |
| Organization name |
Olivia Newton-John Cancer Research Institute
|
| Lab |
Health and Epigenomics Across Life
|
| Street address |
Studley Road
|
| City |
Heidelberg |
| State/province |
VIC |
| ZIP/Postal code |
3085 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19580 |
| Series (2) |
| GSE94459 |
methylC-seq, RNA-seq and sRNA-seq data over Arabidopsis thaliana germination |
| GSE102126 |
Whole-genome resequencing of T-DNA insertion lines |
|
| Relations |
| BioSample |
SAMN07431841 |
| SRA |
SRX3052752 |
