|
Status |
Public on Nov 01, 2013 |
Title |
ldl1 ldl2 RNA-seq |
Sample type |
SRA |
|
|
Source name |
3 week leaf tissue
|
Organism |
Arabidopsis thaliana |
Characteristics |
genotype: jmj14-1 ldl1-2 ldl2 ecotype: Columbia
|
Growth protocol |
All plants were grown at 22 degrees celsius in constant light.
|
Extracted molecule |
total RNA |
Extraction protocol |
Trizol (Life Technologies) Illumina TruSeq mRNA Total RNA isolated by a standard Trizol (Life Technologies) extraction. mRNA was selectively sequenced by bead purification as part of library generation. Total RNA Trizol extracted from leaf tissue\n\!Sample_data_processing = Raw file content: quality scores in _qseq files are Phred scale with +64 ASCII offset... multiplexed: 1/4 lane
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
RNA-seq -- Reads were filtered for full-length (50bp) reads. Reads containing adapter were discarded. Reads were mapped with Tophat2 (Kim et al. 2011 Genome Bio) to the nuclear genome, allowing for 1 mismatch and retaining only uniquely mapping reads. Identical reads (potential PCR or optical duplicates) were flattened to 1 read. Genome_build: TAIR10 Supplementary_files_format_and_content: Fixed step (25bp) UCSC Genome Browser wiggle format files for each chromosome with the the relative read counts given (reads in 25bp bins / total unique mapping reads)
|
|
|
Submission date |
Jul 22, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Christopher Joel Hale |
E-mail(s) |
chris.joel.hale@gmail.com
|
Organization name |
University of Washington
|
Department |
Pathology
|
Lab |
Center for Precision Diagnostics
|
Street address |
1959 NE Pacific St., HSC H-458
|
City |
Seattle |
State/province |
WA |
ZIP/Postal code |
98195 |
Country |
USA |
|
|
Platform ID |
GPL13222 |
Series (1) |
GSE49090 |
Interplay Between Active Chromatin Marks and RNA-directed DNA Methylation in Arabidopsis thaliana |
|
Relations |
BioSample |
SAMN02261595 |
SRA |
SRX326952 |