Summary of Study ST001962

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001249. The data can be accessed directly via it's Project DOI: 10.21228/M88974 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001962
Study TitleNontargeted metabolomics of UGT71 CRISPR knockouts in Poplar
Study SummaryNon-targeted metabolomic analysis of UGT71L1 CRISPR-Cas9 knockouts in populus tremula x populus alba
Institute
University of Victoria
Last NameGordon
First NameHarley
Address3800 Finnerty Rd
Emailharleygordon@uvic.ca
Phone2507217211
Submit Date2021-10-29
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2022-12-01
Release Version1
Harley Gordon Harley Gordon
https://dx.doi.org/10.21228/M88974
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001249
Project DOI:doi: 10.21228/M88974
Project Title:Nontargeted metabolomics of UGT71 CRISPR knockouts in Poplar
Project Type:non-targeted metabolomics
Project Summary:HRMS non-targeted analysis of knockout, empty vector, and wild-type populus tremula x populus alba plants. CRISPR-Cas9 knockout gene was UGT71L1 and mutants were selected with Kanamycin resistance.
Institute:University of Victoria
Department:Biology
Laboratory:Constabel
Last Name:Gordon
First Name:Harley
Address:3800 Finnerty Rd
Email:harleygordon@uvic.ca
Phone:2507217211

Subject:

Subject ID:SU002042
Subject Type:Plant
Subject Species:Populus tremula x Populus alba
Taxonomy ID:80863
Genotype Strain:INRA-717-1B4

Factors:

Subject type: Plant; Subject species: Populus tremula x Populus alba (Factor headings shown in green)

mb_sample_id local_sample_id sample_type
SA18463171-9_35blankBlank
SA18463271-9_33blankBlank
SA18463371-10_26blankBlank
SA18463471-9_38blankBlank
SA18463571-9_39blankBlank
SA184636Empty-2_43blankBlank
SA184637Empty-2_42blankBlank
SA18463871-10_24blankBlank
SA18463971-10_22blankBlank
SA18464071-3_14blankBlank
SA18464171-3_13blankBlank
SA18464271-3_12blankBlank
SA18464371-3_15blankBlank
SA18464471-3_16blankBlank
SA184645Empty-2_44blankBlank
SA18464671-10_21blankBlank
SA18464771-10_23blankBlank
SA184648Empty-2_46blankBlank
SA184649WT_64blankBlank
SA184650Empty-6_61blankBlank
SA184651Empty-6_59blankBlank
SA184652WT_65blankBlank
SA184653WT_66blankBlank
SA184654WT_69blankBlank
SA184655WT_67blankBlank
SA184656Empty-6_58blankBlank
SA184657Empty-6_56blankBlank
SA184658Empty-5_50blankBlank
SA184659Empty-5_49blankBlank
SA18466071-5_7blankBlank
SA184661Empty-5_51blankBlank
SA184662Empty-5_52blankBlank
SA184663Empty-6_55blankBlank
SA184664Empty-5_53blankBlank
SA184665Empty-2_45blankBlank
SA18466671-9_36blankBlank
SA18466771-5_2blankBlank
SA18466871-5_4blankBlank
SA18466971-5_5blankBlank
SA18467071-5_1blankBlank
SA184688Empty-5_49cempty_vector
SA184689Empty-5_50aempty_vector
SA184690Empty-5_50cempty_vector
SA184691Empty-5_50bempty_vector
SA184692Empty-5_51aempty_vector
SA184693Empty-2_46aempty_vector
SA184694Empty-2_44bempty_vector
SA184695Empty-2_45aempty_vector
SA184696Empty-2_44aempty_vector
SA184697Empty-2_43cempty_vector
SA184698Empty-2_43bempty_vector
SA184699Empty-2_45bempty_vector
SA184700Empty-2_45cempty_vector
SA184701Empty-5_49aempty_vector
SA184702Empty-2_46cempty_vector
SA184703Empty-2_46bempty_vector
SA184704Empty-5_51bempty_vector
SA184705Empty-5_49bempty_vector
SA184706Empty-5_53bempty_vector
SA184707Empty-6_58cempty_vector
SA184708Empty-6_58bempty_vector
SA184709Empty-6_58aempty_vector
SA184710Empty-6_56cempty_vector
SA184711Empty-6_59aempty_vector
SA184712Empty-6_59bempty_vector
SA184713Empty-6_61cempty_vector
SA184714Empty-6_61bempty_vector
SA184715Empty-6_61aempty_vector
SA184716Empty-6_59cempty_vector
SA184717Empty-6_56bempty_vector
SA184718Empty-6_56aempty_vector
SA184719Empty-5_53aempty_vector
SA184720Empty-5_52cempty_vector
SA184721Empty-5_52bempty_vector
SA184722Empty-5_52aempty_vector
SA184723Empty-2_43aempty_vector
SA184724Empty-5_53cempty_vector
SA184725Empty-6_55cempty_vector
SA184726Empty-6_55bempty_vector
SA184727Empty-6_55aempty_vector
SA184728Empty-5_51cempty_vector
SA184729Empty-2_44cempty_vector
SA184730Empty-2_42aempty_vector
SA184731Empty-2_42bempty_vector
SA184732Empty-2_42cempty_vector
SA18473371-10_24aintermediate
SA18473471-10_23cintermediate
SA18473571-10_24bintermediate
SA18473671-10_26bintermediate
SA18473771-10_23bintermediate
SA18473871-10_26aintermediate
SA18473971-10_24cintermediate
SA18474071-10_22bintermediate
SA18474171-10_21bintermediate
SA18474271-10_21aintermediate
SA18474371-10_21cintermediate
SA18474471-10_22aintermediate
SA18474571-10_26cintermediate
SA18474671-10_23aintermediate
SA18474771-10_22cintermediate
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Collection:

Collection ID:CO002035
Collection Summary:Samples are fully expanded leaf tissue with midvein excised of three month old greenhouse grown poplar. Tissue was flash frozen and stored at -80 prior to metabolite extraction.
Sample Type:Leaves

Treatment:

Treatment ID:TR002054
Treatment Summary:Leaf tissue from Populus tremula x Populus alba was transformed using CRISPR-Cas9 to create functional knockouts of the UGT71L1 gene. Positive transformants were selected with Kanamycin and sequencing was conducted to confirm transformation. Clones of either wild type plants, knockouts (frame shift mutations, both alleles), intermediates (Frameshift mutation, one allele), or empty vectors (no gRNA for Cas9 construct). Plants were then grown under identical conditions for three months in a greenhouse.
Treatment:Genetic
Plant Growth Location:Greenhouse
Plant Watering Regime:As required

Sample Preparation:

Sampleprep ID:SP002048
Sampleprep Summary:Flash frozen leaf tissue was homogenized under liquid nitrogen with mortar and pestle. Tissue was then freeze dried and stored at room temperature prior to analysis. For extraction, 50 mg of freeze-dried tissue was weighed into a 2 mL cryo-vial with 4 x 5 mm steel ball bearings and 750 mL of chilled methanol. Samples were homogenized 2 x 45 seconds at 5500 rpm using a Precellys 24 Homogenizer, then sonicated for 2 minutes in a sonicating water bath. Samples were centrifuged at 12,000 rpm for 2 minutes and the supernatant was filtered through 0.22 µm PTFE filters into glass vials. Methanol extractions were repeated twice and extracts were pooled. Extracts were dried under vacuum at ambient temperature. Final extraction weight was determined, vials were sealed and stored at -20°C until analysis. Each biological replicate included an extraction

Combined analysis:

Analysis ID AN003198 AN003199
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column Phenomenex Kinitex C18 (50 x 2.1 mm,1.7um) Phenomenex Kinitex C18 (50 x 2.1 mm,1.7um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo LTQ XL Thermo LTQ XL
Ion Mode POSITIVE NEGATIVE
Units Area Area

Chromatography:

Chromatography ID:CH002365
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Phenomenex Kinitex C18 (50 x 2.1 mm,1.7um)
Flow Rate:0.35 ml/min
Chromatography Type:Reversed phase

MS:

MS ID:MS002976
Analysis ID:AN003198
Instrument Name:Thermo LTQ XL
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:voltage of 35 V m/z from 100 – 2000.00 MS1 data was processed using MZMine2
Ion Mode:POSITIVE
  
MS ID:MS002977
Analysis ID:AN003199
Instrument Name:Thermo LTQ XL
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:voltage of -35 V m/z from 100 – 2000.00 MS1 data was processed using MZMine2
Ion Mode:NEGATIVE
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