|
Status |
Public on Dec 01, 2020 |
Title |
Input MpoDNA |
Sample type |
SRA |
|
|
Source name |
21-d-old gemmalings
|
Organism |
Marchantia polymorpha |
Characteristics |
protein: Input MpoDNA sample 26 gene id: Input MpoDNA sample 26 protein expression: Input DNA
|
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 HiSeq 2500 |
|
|
Description |
Sample 27 Input MpoDNA sample 26
|
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 01, 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 |
GPL28942 |
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 |
SAMN15662429 |
SRA |
SRX8840858 |