Lunardon et al. 2020

Genome and annotations summary

Version v1 of Brassica rapa var. pekinensis cv. Chiifu-401-42 from Ensembl Plants

Small RNA Loci

Click links below to show sub-sets of annotations

Small RNA-seq data

Reference Set

accession

aligned reads

unaligned reads

source db

is refset? Alignments that are reference sets (value of 1) are mergers of other component libraries used to compile master small RNA annotations for a species.

tissue

ecotype / cultivar

genotype

replicate id Alignments that are biological replicates have the same replicate ids

refset id If set, the alignment is part of the indicated reference set

description

chinese_cabbage_all_reference_set

65,338,894

27,771,726

none

mixed

refset1

merge of 5 libraries - reference set 1

Invidiual alignments (5)

accession	aligned reads	unaligned reads	source db	is refset? Alignments that are reference sets (value of 1) are mergers of other component libraries used to compile master small RNA annotations for a species.	tissue	ecotype / cultivar	genotype	replicate id Alignments that are biological replicates have the same replicate ids	refset id If set, the alignment is part of the indicated reference set	description
SRR2136646	13,000,896	8,629,674	SRA	0	flower bud	Tyms	wt	A	1	flower bud (less than 6 mm length -- contain the entire developmental progress from anther generation to pollen abortion) -- control conditions
SRR2136647	15,434,200	8,399,156	SRA	0	flower bud	231-330	wt	B	1	flower bud (less than 6 mm length -- contain the entire developmental progress from anther generation to mature pollen) -- control conditions
SRR2912891	12,337,076	2,146,427	SRA	0	root	Chiifu	wt	C	1	root -- control conditions
SRR2912893	13,582,000	2,192,482	SRA	0	stem	Chiifu	wt	D	1	stem -- control conditions
SRR2912894	10,984,722	6,403,987	SRA	0	leaf	Chiifu	wt	E	1	leaf -- control conditions

	ShortStack	miRBase21-BestBlastHit
MIRNA	87	56
nearMIRNA	24	7
siRNA20	31	0
siRNA21	492	21
siRNA22	110	1
siRNA23	129	0
siRNA24	34,693	11
OtherRNA	1,410	2
NotExpressed	0	10

Data from Lunardon et al. (2020)

Genome and annotations summary

Brassica rapa var. pekinensis (Chinese Cabbage) genome build 1 (bra-b1)

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Download genome assembly FASTA file

BLAST search

Small RNA Loci

Small RNA-seq data

Reference Set

Invidiual alignments (5)