|
| Status |
Public on Aug 01, 2020 |
| Title |
SEC_Id |
| Sample type |
SRA |
| |
|
| Source name |
Somatic embryonic callus after somatic embryo induction
|
| Organism |
Picea abies |
| Characteristics |
cultivar: 11:18:1:1 (Nakamura et al. 2019)
tissue: Embryonic callus
condition: After somatic embryo induction
|
| Treatment protocol |
For somatic induction treatment, somatic embryonic and non-embryonic calli were incubated in BMI-SI medium for 1 week.
|
| Growth protocol |
Seedlings were germinated and grown in quarter-strength SH medium (von Arnold & Clapham, 2008) for 2 months in dark at 22˚C. Somatic embryonic calli and non-embryonic calli were proliferated in half-strength LP medium (von Arnold & Clapham, 2008) in dark at 22˚C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Digested genomic DNA by pA-MNase were collected by ethanol precipitation. Subsequently, larger fragments were removed from extracted DNA by x 0.6 volume Agencourt AMPure XP and then the remaining DNA was recovered by x 3.0 volume AMpure XP.
Libraries were constructed using MicroPlex Library Preparation Kit v2 following the manufacturer's procedure.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Library strategy: CUT&RUN
After removing low quality reads by fastq_quality_filter (-q 20 -p 80 -Q 33), reads were mapped by bwa mem -P (bwa-0.7.17). The paired-end reads mapped on the different contigs were discarded. Then, merged paired-end fragments shorter than 701 bp were selected. The reads were processed by bedtools and bedGraphToBigWig.
Genome_build: Pabies1.0-genome.fa (ftp://plantgenie.org/Data/ConGenIE/Picea_abies/v1.0/FASTA/GenomeAssemblies/)
Supplementary_files_format_and_content: Bigwig
|
| |
|
| Submission date |
Feb 14, 2020 |
| Last update date |
Aug 02, 2020 |
| Contact name |
Miyuki Nakamura |
| E-mail(s) |
[email protected]
|
| Organization name |
Swedish University of Agricultural Sciences
|
| Street address |
Ulls Grand1
|
| City |
Uppsala |
| ZIP/Postal code |
75007 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL19695 |
| Series (1) |
| GSE145331 |
Profiling of histone modification H3K27me3 in Norway spruce embryonic calli and non-embryonic calli |
|
| Relations |
| BioSample |
SAMN14113404 |
| SRA |
SRX7729830 |
