 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 20, 2023 |
| Title |
ccr bio rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Inflorescence stems
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Inflorescence stems
genotype: ccr1-3 mutant
age: 2- months -old
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from the main inflorescence stems of 2-month-old wild-type Col-0, ccr1-3, fer4, and ccr1-3/fer4 double mutant plants. Total RNA was isolated with Trizol reagent (Invitrogen, USA) and treated with TURBO DNA-free Kit (Ambion) to remove genomic DNA contaminants. RNA was cleaned using an RNA cleanup kit (Qiagen). Purified RNA was quantified using a Nanodrop ND-100 spectrophotometer (NanoDrop Technologies) and evaluated for purity with an Agilent 4200 TapeStation system (Agilent Technologies).
Libraries were constructed using a TruSeq stranded mRNAseq prep kit following the standard protocols and run on an Illumina Nextseq 500 platform (2 × 75 bp).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
For each sample, RNA-seq raw reads were trimmed and filtered using in-house perl scrips.
Clean reads were mapped to the A. thaliana genome sequence and the reference-annotated genes (TAIR10) using Bowtie v2.3.2.0 (3) and TopHat v2.1.1 (4) with default parameters.
The gene expression levels for each sample were estimated by Cufflinks v2.2.1(5) based on the FPKM (fragments per kilobase of exon model per million mapped fragments) method.
Significantly differentially expressed genes were analyzed by Cuffdiff in the cufflinks package (6) using twofold change and multiple test p-value < 0.05.
Assembly: TAIR10
Supplementary files format and content: Excel files include FPKM values for each Sample
|
| |
|
| Submission date |
Aug 08, 2022 |
| Last update date |
Mar 20, 2023 |
| Contact name |
Chang Liu |
| E-mail(s) |
nmgliuchang@gmail.com
|
| Organization name |
University of North Texas
|
| Street address |
1155 Union Circle #311428
|
| City |
Denton |
| ZIP/Postal code |
76203-5017 |
| Country |
USA |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE210734 |
RNA-seq analysis of total RNA from inflorescence stems of Arabidopsis Col-0, ccr-1, fer-4 and ccr-1/fer-4 |
|
| Relations |
| BioSample |
SAMN30194135 |
| SRA |
SRX16984278 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
