Lunardon et al. 2020

Genome and annotations summary

Version v2 of Setaria italica cv. Yugu1 from Phytozome

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

foxtail_millet_all_reference_set

104,140,864

19,564,562

none

mixed

refset1

merge of 9 libraries - reference set 1

Invidiual alignments (9)

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
ERR1292961	16,674,287	885,379	SRA	0	leaf	An04-4783	wt	A	1	leaf (2-weeks-old plants) - control conditions
ERR1292962	13,340,952	1,128,935	SRA	0	leaf	An04-4783	wt	B	1	leaf (2-weeks-old plants) - moderate drought stress
GSM803573	4,203,206	592,534	GEO	0	leaf	Yugu1	wt	C	1	leaf (5-6-weeks-old plants) - control conditions
GSM803574	4,809,152	688,682	GEO	0	inflorescence	Yugu1	wt	D	1	flower spike (2 pre-anthesis stages) - control conditions
GSM803575	3,696,938	695,099	GEO	0	root	unknown	wt	E	1	root - control conditions
SRR630983	16,987,601	3,963,497	SRA	0	shoot	Yugu1	wt	F	1	shoot (2-weeks-old plants) - control conditions
SRR631007	15,403,398	3,710,086	SRA	0	shoot	Yugu1	wt	F	1	shoot (2-weeks-old plants) - control conditions
SRR631008	14,117,009	3,888,173	SRA	0	shoot	Yugu1	wt	G	1	shoot (2-weeks-old plants) - PEG-simulated drought stress
SRR631010	14,908,321	4,012,177	SRA	0	shoot	Yugu1	wt	G	1	shoot (2-weeks-old plants) - PEG-simulated drought stress

	ShortStack	Yi_et_al_2013
MIRNA	78	132
nearMIRNA	55	25
siRNA20	19	0
siRNA21	308	78
siRNA22	102	8
siRNA23	15	3
siRNA24	26,736	43
OtherRNA	2,392	13
NotExpressed	0	1

Data from Lunardon et al. (2020)

Genome and annotations summary

Setaria italica (Foxtail Millet) genome build 2 (sit-b2)

Go to genome browser

Download genome assembly FASTA file

BLAST search

Small RNA Loci

Small RNA-seq data

Reference Set

Invidiual alignments (9)