|
| Status |
Public on Oct 03, 2022 |
| Title |
INR1.1 |
| Sample type |
SRA |
| |
|
| Source name |
DNA from radicles germinated 20°C dark_R1
|
| Organism |
Medicago truncatula |
| Characteristics |
cultivar: A17
treatment: 1mm radicle+desiccation
harvest: seeds from 2017 and 2018
tissue: dried radicles
chip antibody: anti-H3K27me3
|
| Treatment protocol |
desiccation or PEG and desiccation
|
| Growth protocol |
Plants were grown in a culture room in trays containing a sterile soil at 20°C/18°C, with a 16 h light photoperiod at 200 μmol photons m -²s-².
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction protocol as explained in Cortijo et al, 2018 (https://doi.org/10.1007/978-1-4939-7747-5_18)
Library construction by Microplex diagenodef protocol. Samples were sent to BGI, Hong Kong, for sequencing. https://www.diagenode.com/en/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
Rep1
|
| Data processing |
TrimGalore to trim short reads (remove adapters)
Fastqc to check sequencing quality control
STAR mapper to map reads against the genome: STAR --readFilesIn read1.fq.gz read2.fq.gz --genomeDir genome index --outFileNamePrefix results_file --runThreadN 20 --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06 --alignIntronMax 1 --outSAMtype BAM SortedByCoordinate --readFilesCommand 'gunzip -c'
Read deduplication using Picard Markduplicates algorithm
BAMcoverage to transform raw data in bigwig
Peak calling using macs2 callpeak function to statistically identify binding sites using INPUT and IP files. Broad peak calling setting for H3K27me3 and narrow peak calling setting for H3ac according to ENCODe recommendations.
Assembly: MtrunA17r5.0-20161119-ANR.fasta
Supplementary files format and content: bigwig files representing the chromatin accessibility (more reads = chromatin regions bound with h3K27me3)
|
| |
|
| Submission date |
Sep 26, 2022 |
| Last update date |
Oct 03, 2022 |
| Contact name |
Jerome Verdier |
| E-mail(s) |
Jerome.verdier@inrae.fr
|
| Organization name |
INRAE / IRHS
|
| Lab |
SEED
|
| Street address |
Rue Georges Morel
|
| City |
Angers |
| ZIP/Postal code |
49000 |
| Country |
France |
| |
|
| Platform ID |
GPL30653 |
| Series (1) |
| GSE214220 |
DNA sequencing of Medicago truncatula from ChIP-seq experiment - roots of germinated seeds at 1mm, 1mm+PEG, 5mm (after immunoprecipitation of H3k27me3) |
|
| Relations |
| BioSample |
SAMN31023074 |
| SRA |
SRX17711012 |
