|
| Status |
Public on Feb 28, 2023 |
| Title |
ChIP_H3K4me3_nrpd1-kd_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
pre-emerged panicle
|
| Organism |
Oryza sativa |
| Characteristics |
tissue: pre-emerged panicle
subspecies: Indica
cultivar: Pusa Basmati 1 (PB1)
genotype: nrpd1-kd
chip antibody: H3K4me3
|
| Treatment protocol |
WT and pol IV knockdown lines 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 |
Sheared chromatin from the equally developed pre emerged panicle of WT and kd plants were incubated with appropriate antibodies bound to Protein G Dynabeads (Thermo Fisher, catalog number 10003D). Washes, elution, de-crosslinking and DNA purification was done as described. The purified DNA was taken for library preparation.
The ChIP library was constructed using NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads (Catalog no-E7103L) as per manufacturer's instructions. The adapter sequence used is AGATCGGAAGAGCACACGTCTGAACTCCAGTCA. The sequencing was done in single end mode in a Illumina HiSeq2500 platform.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The reads obtained were trimmed using cutadapt and aligned to IRGSP rice genome with parameters -q -v 1 -m 100 -y -a --best –strata
The alignment files are converted to coverage files using bam coverage tool of Deeptools with the 100bp bin size.
Genome_build: Oryza sativa japonica nipponbare genome – IRGSP1
Supplementary_files_format_and_content: The coverage files of the ChIP seq alignments were provided in bigwig format.
|
| |
|
| Submission date |
Jul 18, 2021 |
| Last update date |
Feb 28, 2023 |
| Contact name |
Shivaprasad Padubidri V. |
| E-mail(s) |
shivaprasad@ncbs.res.in
|
| Phone |
+91 80 2366 6511
|
| Organization name |
National Center for Biological Sciences
|
| Department |
Plant epigenetics
|
| Street address |
GKVK Campus, Bellary road
|
| City |
Bangalore |
| ZIP/Postal code |
560065 |
| Country |
India |
| |
|
| Platform ID |
GPL19290 |
| Series (2) |
| GSE180311 |
RNA Polymerase IV sensitizes the chromatin via histone modifications modulating protein coding genes [ChIP-Seq] |
| GSE180457 |
RNA Polymerase IV sensitises the chromatin via histone modifications modulating protein coding genes |
|
| Relations |
| BioSample |
SAMN20295775 |
| SRA |
SRX11490553 |
