|
Status |
Public on Jul 31, 2024 |
Title |
WT_Embryo_sRNA_Rep2 |
Sample type |
SRA |
|
|
Source name |
Embryo
|
Organism |
Oryza sativa |
Characteristics |
subspecies: Indica cultivar: Pusa Basmati1 (PB1) developmental stage: Embryo (20-25 days after anthesis)
|
Treatment protocol |
WT and clsy3 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 |
total RNA |
Extraction protocol |
Total RNA from endosperm was extracted using Trizol (Invitrogen) reagent. Size fractionation. adaptor_seq TGGAATTCTCGGGTGCCAAGG
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|
|
Library strategy |
ncRNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
Illumina HiSeq 2500 |
|
|
Data processing |
Adapter was removed and low quality bases were trimmed from sequenced reads using UEA sRNA workbench. The sRNAs of appropriate size class(16-35nt) was chosen further. The processed reads were aligned to the rice genome using Bowtie with one allowed mismatch. Assembly: Oryza sativa japonica nipponbare genome – IRGSP1 Supplementary files format and content: Text delimited files showing the sequence and raw abundance of the sRNAs.
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|
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Submission date |
Apr 18, 2023 |
Last update date |
Jul 31, 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 |
GPL19290 |
Series (1) |
GSE229958 |
Upstream regulator of genomic imprinting in rice is a small RNA-associated chromatin remodeler [ncRNA-Seq] |
|
Relations |
BioSample |
SAMN34234237 |
SRA |
SRX20001561 |