|
| Status |
Public on Feb 07, 2024 |
| Title |
MT3, maize inbred line B104, tml1;tml2 HMZ CRISPR-Cas mutant 3, sample D6 [WTCHG_960488_73675343] |
| Sample type |
SRA |
| |
|
| Source name |
pooled leaf primordia (SAM, plastochron 0 to plastochron 5, leaf sheath)
|
| Organism |
Zea mays |
| Characteristics |
tissue: pooled leaf primordia (SAM, plastochron 0 to plastochron 5, leaf sheath)
cell type: MT3, maize inbred line B104, tml1;tml2 HMZ CRISPR-Cas mutant 3, sample D6 [WTCHG_960488_73675343] [WTCHG_960488_73675343]
genotype: B104 tml1;tml2
treatment: CRISPR/Cas9 homozygous tml1;tml2 mutant
|
| 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.
|
| 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.
|
| 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
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
WTCHG_960488_73675343
|
| 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
|
| |
|
| 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 |
| |
|
| Platform ID |
GPL25410 |
| Series (1) |
| GSE255222 |
Profiling trancriptome changes that affect vein specification in maize (Zea mays) tml (TOO MANY LATERALS) mutants |
|
| Relations |
| BioSample |
SAMN39848210 |
| SRA |
SRX23554580 |
