|
| Status |
Public on Dec 01, 2020 |
| Title |
DAP-MYC4_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
10 days-old seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
protein: MYC4
gene id: AT4G17880
protein expression: E.coli expressed
|
| Growth protocol |
10 days-old seedlings grown in MS medium
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extraacted with the CTAB method and RNase A treated
gDNA fragmented to 200 bp fragments in average and ligated a a truncated Illumina TruSeq adapter (Y adapter). gDNA library is incubated with recombinant protein expressed in E.coli, previously immobilized with Amylose beads. After binding and washing, DNA is eluted and PCR-amplified with Truseq primers, including a single index.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Sample 8
Protein-DNA interaction
|
| Data processing |
Library strategy: DAP-seq
Adaptors were trimmed and low quality reads were filtered with Trim Galore
Alignment to genome sequence with Bowtie2
BAM files are used for peak calling with GEMv3.4, using input files as control
Genome_build: Arabidopsis TAIR10 genome (Ensemble Release 42)
Genome_build: Solanum lycopersicum SL4.0 assembly, ITAG4.0 annotation
Genome_build: Marchantia polymnorpha MpTak1v5 version
Supplementary_files_format_and_content: Significant peaks of protein-DNA interactions in narrowpeak fromat generated by GEMv3.4
|
| |
|
| Submission date |
Jul 28, 2020 |
| Last update date |
Dec 04, 2020 |
| Contact name |
Jose M. Franco-Zorrilla |
| Organization name |
Centro Nacinal de Biotecnologia-CSIC
|
| Department |
Plant Molecular Genetics
|
| Street address |
Darwin, 3
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28049 |
| Country |
Spain |
| |
|
| Platform ID |
GPL26208 |
| Series (2) |
| GSE155317 |
DNA features beyond the transcription factor binding sites specify target recognition by plant bHLHs [DAP-seq] |
| GSE155321 |
DNA features beyond the transcription factor binding sites specify target recognition by plant bHLHs |
|
| Relations |
| BioSample |
SAMN15662448 |
| SRA |
SRX8840839 |
