|
| Status |
Public on Sep 04, 2012 |
| Title |
Kn1-N leaf homo #1 |
| Sample type |
SRA |
| |
|
| Source name |
young leaves from Kn1-N homozygote
|
| Organism |
Zea mays |
| Characteristics |
genotype: Kn1-N/Kn1-N
inbred: B73
tissue: young immature leaves
growth conditions: Greenhouse, flat tray, 10 days after germination (2 visible leaves with the third one emerging from the whorl)
|
| Growth protocol |
maize plants were grown in the greenhouse or the field as specified in column H
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Dissected tissue was flash frozen in liquid nitrogen and total RNA was isolated using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries. Ligated cDNA were amplified for 13 cycles instead of the 15 cycles specified in the TruSeq protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
dissected leaves were a tube of 1-2 mm by 7-8 mm (starting 2-3 mm above the SAM)
Leaf_Homo_WT.diff
Leaf_Homo_Het.diff
|
| Data processing |
Basecalls performed using CASAVA version 1.8
RNA-seq reads were aligned to the maize genome assembly version 2 using TopHat version 1.2.0 -G option using the gff file for Filtered Gene Set provided by maizegenome.org
Total number of reads to be considered in the next steps were counted from the alignment files. The gene region as appears for the protein-coding genes in the FGS gff provided by maizegenome.org. Reads were counted using the script htseq-count.py unique hits using union method and unique hits only.
Differential expression was tested between mutants and controls using DESeq version 1.4.1 with a P-value adjusted (this value is the P-value after FDR adjusted for multiple testing with the Benjamini-Hochberg procedure) < 0.01
Genome_build: Maize Golden Path B73 RefGen_v2
Supplementary_files_format_and_content: DESeq results for genes differentially expressed are reported as tabulated text files and reads count results as a excel spreadsheet
|
| |
|
| Submission date |
Jun 05, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Erich Grotewold |
| Organization name |
Michigan State University
|
| Lab |
Grotewold Laboratory
|
| Street address |
603 Wilson Road
|
| City |
East Lansing |
| State/province |
MI |
| ZIP/Postal code |
48823 |
| Country |
USA |
| |
|
| Platform ID |
GPL15463 |
| Series (1) |
| GSE38487 |
Unraveling the KNOTTED1 regulatory network in maize meristems |
|
| Relations |
| SRA |
SRX151740 |
| BioSample |
SAMN01041006 |
