|
| Status |
Public on Apr 30, 2024 |
| Title |
SEP3Δtet-AGΔtet |
| Sample type |
SRA |
| |
|
| Source name |
seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: seedlings
cell type: bulk
genotype: SEP3{delta}tet3M-AG
treatment: no treatment
|
| Growth protocol |
2-weeks old seedlings of Arabidopsis thaliana
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted by chloroform isoamyl alcohol dna extraction protocol
Libraries were contructed using Truseq Illumina kits
Illumina TruSeq adaptors with single end index
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Alignment to genome is done by Bowtie2
poor quality and multimapped reads are filtered out using samtools
peak-calling is done by MACS2 with parameters (-q 0.001 --call-summits)
Peaks called where Control read coverage is too high are removed from analysis
replicates are treated by MSPC to create consensus peaks
Assembly: Consensus peaks are reworked around maximum of peaks.
|
| |
|
| Submission date |
Mar 09, 2023 |
| Last update date |
Apr 30, 2024 |
| Contact name |
Romain BLANC-MATHIEU |
| E-mail(s) |
romain.blancmathieu@cea.fr
|
| Organization name |
CEA
|
| Lab |
LPCV
|
| Street address |
17 Avenue des martyrs
|
| City |
Grenoble |
| ZIP/Postal code |
38000 |
| Country |
France |
| |
|
| Platform ID |
GPL21785 |
| Series (1) |
| GSE227012 |
sequential DNA affinity purification sequencing (seq-DAP-seq) data of MADS SEP3-AG tetramerization mutants. |
|
| Relations |
| BioSample |
SAMN33699271 |
| SRA |
SRX19611852 |
