 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 23, 2017 |
| Title |
Capsella rubellla Cr A x Cr B R2 |
| Sample type |
SRA |
| |
|
| Source name |
Capsella rubella Cr48.21 x Cr75.2 endosperm
|
| Organism |
Capsella rubella |
| Characteristics |
tissue: 6 DAP seed endosperm
|
| Treatment protocol |
For all crosses, designated female partners were emasculated, and the pistils were hand-pollinated 2 days after emasculation.
|
| Growth protocol |
All seeds were surface sterilized using 5 % Sodium Hypochloride solution under the fume hood. After sterilization seeds were plated on MS media containing 1% sucrose. After stratification for two days in the dark at 4°C seedlings were grown in a growth room under long-day photoperiod (16 hrs light and 8 hrs darkness) at 22°C light and 20°C darkness temperature and a light intensity of 110 µE. All seedlings were transferred to pots and plants were grown in a growth chamber at 60 % humidity and daily cycles of 16 hrs light at 21°C and 8hrs darkness at 18°C. ts were grown in a growth cabinet under long day photoperiods (16 h light and 8 h dark) at 22°C. After 10 days, seedlings were transferred to soil and plants were grown in a growth chamber at 60% humidity and daily cycles of 16 h light at 22°C and 8 h darkness at 18°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For DNA-seq, 300 mg young fresh leaves were used as DNA source. For RNA-seq, dissected endosperm of 300-500 seeds per replicate was used. Seeds were harvested at 6 DAP and stored at -20oC in RNAlater® (Sigma-Aldrich, St Louis, USA). RNA extraction was done using RNAqueous® Kit with Plant RNA Isolation Aid (Life Technologies, Carlsbad, USA).
The RNA-sequencing libraries were prepared using TruSeq® RNA Sample Preparation Kit v2 (Illumina, San Diego, USA) according to the manufacturer's instructions.
DNA-seq and RNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
excess index clean up: fastq-mcf -L 100 -l 25
additional adapter cleanup: trimmomatic PE ILLUMINACLIP:adapter.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
DNA sequencing reads were aligned to the C. rubella genome v1.0 (Phytozome) using Bowtie 1.0, -m 1 option, RNA sequencing were aligned using TopHat with -g 1 -N 2 --bowtie1 option
Genome SNP calling was done using Freebayes with -i -X -u --min-coverage 20 --min-alternate-total 10 -q 30 option
Nucleotide counting for RNA-seq was done by running a loop of igvtools.jar count -w 1
Allele spectrum ratio for imprinting analysis was done by using a custom R-script and is available by request, p-value for imprinting status was calculated using chi.test(). Parental genotype is represented using integer value of A = 1, T= 3, G = 9, C = 27. For example, genotype AT will be A(1) + T(3) = 4, and TC will be T(3) + C(27) = 30.
Genome_build: C. rubella genome v1.0 (Phytozome)
Supplementary_files_format_and_content: Aligned reads
---------------------------
RNA-Seq CSV files contain the following:
#LOCUS_NAME","#POS","#A_COUNT", "#C_COUNT ", "#G_COUNT ", " #T_COUNT ", " #N_COUNT "
#POS: position at the locus
#A_COUNT: Number of A bases found in particular locus
#C_COUNT: Number of C bases found in particular locus
#G_COUNT: Number of G bases found in particular locus
#T_COUNT: Number of T bases found in particular locus
#N_COUNT: Number of unknown bases found in particular locus
|
| |
|
| Submission date |
Jan 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Marcelinus Rocky Hatorangan |
| E-mail(s) |
marcelinus.r.hatorangan@sinarmas-agri.com
|
| Organization name |
PT SMART, Tbk.
|
| Department |
Biotechnology
|
| Lab |
Genome Editing
|
| Street address |
Cijayanti, Babakan Madang
|
| City |
Sentul |
| State/province |
Jawa Barat |
| ZIP/Postal code |
16810 |
| Country |
Indonesia |
| |
|
| Platform ID |
GPL19953 |
| Series (1) |
| GSE76888 |
Imprinted genes in Capsella rubella |
|
| Relations |
| BioSample |
SAMN04414867 |
| SRA |
SRX1531632 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2039977_craxcrbr2.csv.gz |
1.3 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
