|
| Status |
Public on May 11, 2017 |
| Title |
SlRootHair2 |
| Sample type |
SRA |
| |
|
| Source name |
root hair
|
| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar: Heinz 1706
reference annotation: Ensembl Release 19, SL2.4
age: 4-5 days after plating
|
| Treatment protocol |
Root tissue was stirred in liquid nitrogen and filtered with a 250-mm sieve.
|
| Growth protocol |
Seeds were surface sterilized and germinated on agarose-solidified MS media under constant light at 22C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Qiagen RNAeasy Plant Mini Kit.
RNA libraries were prepared for sequencing using SMART-Seq v4 Ultra Low Input RNA kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed data file: SlRootHair.xlsx
|
| Data processing |
Illumina Casava 1.8.2 was used for base calling.
The first 15bp of each read were trimmed.
Reads were mapped using Tophat v2.0.9. Default settings with --segment length 17 parameter were used to map the reads to the reference annotation (already mentioned in the sample information above).
FPKM values were calculated by Cufflinks2 v2.1.1 with multiread correction (-u -G).
Genome_build: See sample information above.
Supplementary_files_format_and_content: Excel files that contain the FPKM value generated by Cufflinks for the gene expression profiling for each of the six species.
|
| |
|
| Submission date |
Feb 08, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
John Schiefelbein |
| E-mail(s) |
schiefel@umich.edu
|
| Phone |
734-764-3580
|
| Organization name |
University of Michigan
|
| Department |
Molecular, Cellular, and Developmental Biology
|
| Street address |
830 North University Avenue
|
| City |
Ann Arbor |
| State/province |
Michigan |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL19694 |
| Series (1) |
| GSE85516 |
Diversification of Root Hair Development Genes in Vascular Plants |
|
| Relations |
| BioSample |
SAMN06312677 |
| SRA |
SRX2545790 |
