|
Status |
Public on May 03, 2012 |
Title |
cmt3-11 mRNA EMS batch 1 |
Sample type |
SRA |
|
|
Source name |
leaf tissue, SDC::GFP cmt3-11, mRNA
|
Organism |
Arabidopsis thaliana |
Characteristics |
genotype: SDC::GFP cmt3-11 (eco. Columbia) tissue: leaf
|
Extracted molecule |
total RNA |
Extraction protocol |
Isolated mRNAs from total RNA Trizol preparation. Illumina TruSeq RNA.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
Purified mRNAs.
|
Data processing |
mRNA-Seq reads were mapped with Bowtie (Langmead, et al. 2009 Genome Biol. (PMID 19261174)) to TAIR8 chr1..5, allowing up to 2 mismatches and retaining only uniquely-mapping reads.
Supplementary_files_format_and_content: Each processed file gives 10- or 20-basepair resolution signal normalized as mapped reads per genomic kilobasepair per million mapped reads in the form of a UCSC Genome Browser wiggle file in plain text format with UNIX-style line endings (single `fixedStep start=1 step=10/20 span=10/20' header per chromosome in order chr1..5; non-negative decimal values).
Supplementary_files_format_and_content: Quality scores in _qseq files are Phred scale with +64 ASCII offset... non-multiplexed: 1 lane.
Genome_build: TAIR8
|
|
|
Submission date |
May 01, 2012 |
Last update date |
May 15, 2019 |
Contact name |
Shawn J. Cokus |
Organization name |
UCLA
|
Street address |
UCLA, 3000 Terasaki Life Sciences Building, 610 Charles Young Drive East
|
City |
Los Angeles |
State/province |
CA |
ZIP/Postal code |
90095 |
Country |
USA |
|
|
Platform ID |
GPL13222 |
Series (1) |
GSE37644 |
MORC family ATPases required for heterochromatin condensation and gene silencing |
|
Relations |
SRA |
SRX145417 |
BioSample |
SAMN00990542 |
Named Annotation |
GSM925648_cmt3-11_mRNA_EMSbatch1_processed.linCvg10bpResolution.UCSCwigToAthTAIR8chr12345.wig.gz |