LegumeIP V3: From Models to Crops - An Integrative Gene Discovery Platform for Translational Genomics in Legumes

Details

Name	SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing.
Description	IN THIS POPULATION BASED TRANSCRIPTOME ANALYSIS WHOLE MRNA WAS EXTRACTED FROM DEVELOPING XYLEM OF 20 P. TRICHOCARPA NATURAL ACESSIONS AND SEQUENCED WITH ILLUMINA%u2019S GA II ANALYZER AFTER CONVERSION TO CDNA AND PREPARATION OF PAIRED END LIBRARIES. THESE DATA WERE MAPPED TO THE REFERENCE GENOME OF P. TRICHOCARPA (version 2) AND USED TO DISCOVER SNPS IN GENES THAT ARE EXPRESSED DURING WOOD FORMATION.
Contact	University of British Columbia
Xref	PRJNA79827
Reference	Geraldes A et al . 2011;
Conditions	20
Species	Populus trichocarpa
Metadata export	.CSV .JSON

Analysis

Mapped Genomes	PtV3.1
Expression Analysis	Expression Profile / Differential Expression / Co-expression

Conditions

Name	Treatment	Samples	Xref	Download alignments
ALSC	ALSC	ALSC_1 ALSC_2 ALSC_3 ALSC_4	SRR073187 SRR073188 SRR073189 SRR073190	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
BELA	BELA	BELA_1 BELA_2 BELA_3 BELA_4	SRR073112 SRR073113 SRR073114 SRR073115	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
CNYH	CNYH	CNYH_1 CNYH_2 CNYH_3 CNYH_4	SRR073116 SRR073117 SRR073118 SRR073119	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
DENA	DENA	DENA_1 DENA_2 DENA_3 DENA_4	SRR072980 SRR072990 SRR073110 SRR073111	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
DESC	DESC	DESC_1 DESC_2 DESC_3 DESC_4	SRR073196 SRR073197 SRR073198 SRR073199	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
ELAD	ELAD	ELAD_1 ELAD_2 ELAD_3 ELAD_4	SRR073175 SRR073176 SRR073177 SRR073178	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
GLCA	GLCA	GLCA_1 GLCA_2 GLCA_3 GLCA_4	SRR073171 SRR073172 SRR073173 SRR073174	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
HIXN	HIXN	HIXN_1 HIXN_2 HIXN_3 HIXN_4	SRR073156 SRR073157 SRR073158 SRR073159	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
JASP	JASP	JASP_1 JASP_2 JASP_3 JASP_4 JASP_5 JASP_6 JASP_7	SRR073160 SRR073161 SRR073162 SRR073163 SRR073164 SRR073165 SRR073166	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
LONG	LONG	LONG_1 LONG_2 LONG_3 LONG_4	SRR073167 SRR073168 SRR073169 SRR073170	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
MCGR	MCGR	MCGR_1 MCGR_2 MCGR_3 MCGR_4	SRR073124 SRR073153 SRR073154 SRR073155	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
MCHB	MCHB	MCHB_1 MCHB_2 MCHB_3 MCHB_4	SRR073179 SRR073180 SRR073181 SRR073182	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
STKG	STKG	STKG_1 STKG_2 STKG_3 STKG_4	SRR073216 SRR073217 SRR073218 SRR073219	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
STKI	STKI	STKI_1 STKI_2 STKI_3 STKI_4	SRR073200 SRR073201 SRR073202 SRR073203	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
TAKA	TAKA	TAKA_1 TAKA_2 TAKA_3 TAKA_4	SRR073192 SRR073193 SRR073194 SRR073195	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
TATA	TATA	TATA_1 TATA_2 TATA_3 TATA_4	SRR073204 SRR073205 SRR073206 SRR073207	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
TATB	TATB	TATB_1 TATB_2 TATB_3 TATB_4	SRR073212 SRR073213 SRR073214 SRR073215	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
TNZA	TNZA	TNZA_1 TNZA_2 TNZA_3 TNZA_4	SRR073208 SRR073209 SRR073210 SRR073211	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
TOBA	TOBA	TOBA_1 TOBA_2 TOBA_3 TOBA_4	SRR073183 SRR073184 SRR073185 SRR073186	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi
VNDL	VNDL	VNDL_1 VNDL_2 VNDL_3 VNDL_4	SRR073120 SRR073121 SRR073122 SRR073123	.bam .bai .csi .bam .bai .csi .bam .bai .csi .bam .bai .csi