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Status |
Public on Feb 07, 2024 |
Title |
WT2, maize inbred line B104, segregating wild-type 2, sample A6 [WTCHG_960488_73595335] |
Sample type |
SRA |
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|
Source name |
pooled leaf primordia (SAM, plastochron 0 to plastochron 5, leaf sheath)
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Organism |
Zea mays |
Characteristics |
tissue: pooled leaf primordia (SAM, plastochron 0 to plastochron 5, leaf sheath) cell type: WT2, maize inbred line B104, segregating wild-type 2, sample A6 [WTCHG_960488_73595335] [WTCHG_960488_73595335] genotype: B104 treatment: CRISPR/Cas9 segregating TML wild-type
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Treatment protocol |
CRISPR/Cas9 gene editing was emploted to generate tml1;tml2 knock-outs. Seeds were genotyped by seed chipping to select segregating wild-type and homozygous tml1;tml2 prior to germination.
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Growth protocol |
Maize seeds were germinated in vermiculite for 7 days. Germinated seedlings were dissected to isolate the SAM, P0 - P5 primordia (including the leaf sheath) and to excise the root, embryo and coleoptile tissue. All isolated samples were immediately kept in RNAse-later prior to further processing.
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from three individual shoot apices, per genotype (mutant and wild-type) pool, using the Qiagen RNeasy Plant Mini Kit (Cat. No. 74904). Subsequent DNase treatment was done using the Ambion® TURBO DNA-free™ Kit (Cat. No. AM1907). RNA quantity was checked and normalized using a Qubit™ RNA HS Assay Kit (Cat. No. Q32852). RNA quality was assessed with an Agilent RNA 6000 Nano Kit (5067-1511) ensuring that all RNA used for library preparation had a RIN value of 9.0. Strand-specific RNA sequencing library preparation and sequencing was conducted by the Oxford Genomics Centre at the Wellcome Centre for Human Genetics (funded by Wellcome Trust grant reference 203141/A/16/Z) RNA-Seq was performed on an Illumina NovaSeq 6000 with paired-end 150-bp reads
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
WTCHG_960488_73595335
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Data processing |
Sequenced reads were mapped to the Zea Mays B73 RefGen V4 genome (https://phytozome-next.jgi.doe.gov/info/Zmays_RefGen_V4) using STAR, transcript quantification was done with Salmon and differential gene expression was determined using DESEq2. Assembly: Zea Mays B73 RefGen V4 genome (https://phytozome-next.jgi.doe.gov/info/Zmays_RefGen_V4) Supplementary files format and content: tab-delimited file includes raw counts, abundance and length of each gene assayed per sample Supplementary files format and content: tab-delimited file includes transcript-based differential expression relative to the WT samples at padj <0.05
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Submission date |
Feb 06, 2024 |
Last update date |
Feb 07, 2024 |
Contact name |
Maricris Zaidem |
E-mail(s) |
mzaidem@gmail.com, maricris.zaidem@biology.ox.ac.uk
|
Organization name |
University of Oxford
|
Department |
Department of Biology
|
Street address |
South Parks Rd
|
City |
Oxford |
State/province |
Oxfordshire |
ZIP/Postal code |
OX2 6GF |
Country |
United Kingdom |
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|
Platform ID |
GPL25410 |
Series (1) |
GSE255222 |
Profiling trancriptome changes that affect vein specification in maize (Zea mays) tml (TOO MANY LATERALS) mutants |
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Relations |
BioSample |
SAMN39848214 |
SRA |
SRX23554576 |