 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 01, 2015 |
| Title |
hua2 seedling, biological replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Seedling, emergence of fourth true leaf, HUA2 T-DNA insertion
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
strain/background: Col-0
genotype/variation: HUA2 T-DNA insertion
tissue: seedling
developmental stage: emergence of fourth true leaf
|
| Growth protocol |
Plants were germinated on soil and grown until emergence of the fourth true leaf (16 hours light, 8 hours dark, at 20C).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Aerial seedling tissue was frozen in liquid nitrogen, ground to a fine power in liquid nitrogen, and RNA was extracted with the Plant Reagent (Invitrogen using the manufacturer's recommendations). Specific details are as given in Gan et al. 2011. Nature, 477:419-23; see Supplementary Information Section 7.
Illumina non-strand-specific (a minor adaptation of the Illumina mRNA-seq methods as reported by Gan et al. 2011. Nature, 477:419-23; see Supplementary Information Section 7).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
hua2_biol_rep_1
HUA2 T-DNA insertion (Col-0 background)
PolyA RNA
Barcode for sample: ACGT
|
| Data processing |
Read data was acquired from an Illumina Genome IIx sequencer using the SR_Amplification_Linearization_Blocking_PrimerHyb_v7 protocol. Base calling was performed with the Illumina version SCS2.6 software. For the "Real Time Analysis (RTA)" that is implemented in the SCS control software, we used "per lane" parameters for basecalling.
Barcode splitting was performed as described by Gan et al. 2011. Nature, 477(7365):419-23; see Supplementary Information Section 7, page 13.
Reads from FASTQ files that were the output of the Illumina SCS analysis pipeline were aligned to the genome and processed with TopHat/Bowtie (parameters: -a 5, -i 5, -I 32000, --solexa1.3-quals, -g 1, --segment-mismatches 3, -p 5) for calculation of gene expression levels determined as reads aligned to exons using the TAIR10 annotation.
Genome_build: TAIR10
Supplementary_files_format_and_content: A single tab-delimited text file per sample with Gene IDs and RPM values.
|
| |
|
| Submission date |
Jan 15, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard M Clark |
| Organization name |
University of Utah
|
| Department |
Department of Biology
|
| Lab |
Clark Laboratory
|
| Street address |
257 So. 1400 East, RM 204 SB
|
| City |
Salt Lake City |
| State/province |
Utah |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
|
| Platform ID |
GPL11221 |
| Series (1) |
| GSE54125 |
Seedling transcriptomes of Arabidopsis thaliana HULK mutants |
|
| Relations |
| BioSample |
SAMN02585100 |
| SRA |
SRX433982 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1308344_single_rep1.RPM.txt.gz |
147.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
