|
| Status |
Public on Jul 27, 2024 |
| Title |
Endosperm, clsy3-kd |
| Sample type |
SRA |
| |
|
| Source name |
Endosperm (20 days after anthesis)
|
| Organism |
Oryza sativa |
| Characteristics |
tissue: Endosperm (20 days after anthesis)
subspecies: Indica
cultivar: Pusa Basmati 1 (PB1)
|
| Treatment protocol |
Endosperm tissues were handled in the same manner.
|
| Growth protocol |
The plants were grown in green house with natural day-night cycles with temperature maintained around 28 degrees celsius.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA was extracted from the tissues using CTAB method.
The DNA samples were sheared by ultrasonication (Covaris) avarage 350bp. Bisulfite convertion by EZ DNA Methylation-Gold Kit (Catalog no-D5005) as per manufacturer’s protocol. Adapters used: Read1-AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and Read2-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
xGen™ Methyl-Seq DNA Library Prep Kit (Catalog no. 10009860)
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Adapter was removed and low quality bases were trimmed from sequenced reads using Trimmomatic.
The reads were aligned to genome using Bismark and methylation extraction was done using Bismark protocol.
The methylation was calculated using the Bismark tool and cytosine coverage report was used to create the bedgraph files for methylation density.
Assembly: Genome built from Oryza sativa japonica nipponbare genome – IRGSP1
Supplementary files format and content: Genome-wide cytosine reports are the output file
|
| |
|
| Submission date |
Feb 29, 2024 |
| Last update date |
Jul 27, 2024 |
| Contact name |
Shivaprasad Padubidri V. |
| E-mail(s) |
shivaprasad@ncbs.res.in, epigeneticsncbsindia@gmail.com, harshith200cy@gmail.com
|
| Phone |
+91-80-2366-6511
|
| Organization name |
National Centre for Biological Sciences - TIFR
|
| Street address |
UAS-GKVK Campus
|
| City |
Bangalore |
| ZIP/Postal code |
560065 |
| Country |
India |
| |
|
| Platform ID |
GPL27660 |
| Series (2) |
| GSE229961 |
Upstream regulator of genomic imprinting in rice is a small RNA-associated chromatin remodeler |
| GSE260651 |
Upstream regulator of genomic imprinting in rice is a small RNA-associated chromatin remodeler [Bisulfite_seq] |
|
| Relations |
| BioSample |
SAMN40210330 |
| SRA |
SRX23802524 |
