|
| Status |
Public on Oct 04, 2022 |
| Title |
Sorghum Shoot RNA-seq Rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Sorghum shoot
|
| Organism |
Sorghum bicolor |
| Characteristics |
strain: BTx623
technique: RNA-seq
tissue: Shoot
|
| Growth protocol |
Plants grown for four weeks with standard 16H daylight conditions at room temperature
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using Monarch Total RNA Extraction and Purification kit (NEB #T2010)
Libraries where prepared using the novel smar2C2 method described in the related manuscript
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequences were quality trimmed and adaptors were identified and filtered using CutAdapt v2.8
UMI sequences were extracted from processed fasta files using UMI-tools v1.0.1
Sequences were aligned to their respective genome using STAR v2.7.2
Sequences were deduplicated using the UMI and mapping location using UMI-tools v1.0.1
Transcriptoinal start sites were determined using the R library TSRchitect v1.2.0 in R v4.0.0
Genome_build: Maize genome = AGPv4.38, Sorghum genome = NCBIv3.52, Rice genome = IRGSP-1.0.51, Wheat genome = IWGSC.51, Soy genome = Wm82.a4.v1
Supplementary_files_format_and_content: Text file containing single nucleotide position of transcription start site, read count, and strand
|
| |
|
| Submission date |
Feb 22, 2022 |
| Last update date |
Oct 04, 2022 |
| Contact name |
Robert J Schmitz |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Georgia
|
| Department |
Genetics
|
| Street address |
B416 Davison Life Sciences
|
| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
| |
|
| Platform ID |
GPL28998 |
| Series (1) |
| GSE197144 |
Simple and Accurate Transcriptional Start Site Identification Using Smar2C2 |
|
| Relations |
| BioSample |
SAMN26156414 |
| SRA |
SRX14249639 |
