Lunardon et al. 2020

Genome and annotations summary

Version v3.0 of Populus trichocarpa cv. Nisqually 1 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

black_cottonwood_all_reference_set

78,245,274

28,037,378

none

mixed

refset1

merge of 7 libraries - reference set 1

Invidiual alignments (7)

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
GSM717875	3,804,781	668,030	GEO	0	leaf	unknown	wt	A	1	leaf -- control conditions
GSM717876	3,676,194	882,428	GEO	0	xylem	unknown	wt	B	1	xylem -- control conditions
GSM717877	3,397,328	575,498	GEO	0	xylem	unknown	wt	C	1	xylem -- mechnically treated
SRR4010495	25,140,590	1,855,164	SRA	0	unknown	unknown	wt	D	1	unknown -- control conditions
SRR4010496	28,592,769	1,952,088	SRA	0	unknown	unknown	wt	E	1	unknown -- drought stress
SRR926847	7,866,019	10,862,774	SRA	0	female flower bud	unknown	wt	F	1	female flower bud -- control conditions
SRR926848	5,767,593	11,241,396	SRA	0	female flower bud	unknown	wt	G	1	female flower bud -- control conditions

	miRBase21-BestBlastHit	ShortStack
MIRNA	123	65
nearMIRNA	67	55
siRNA20	4	36
siRNA21	70	1,445
siRNA22	7	272
siRNA23	4	30
siRNA24	52	7,557
OtherRNA	37	927
NotExpressed	80	0

Data from Lunardon et al. (2020)

Genome and annotations summary

Populus trichocarpa (Black Cottonwood) genome build 3.0 (ptc-b3.0)

Go to genome browser

Download genome assembly FASTA file

BLAST search

Small RNA Loci

Small RNA-seq data

Reference Set

Invidiual alignments (7)