|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Feb 09, 2016 |
Title |
wrapped leaf R2 |
Sample type |
SRA |
|
|
Source name |
leaf number 6, wrapped
|
Organism |
Zea mays |
Characteristics |
genotype: B73 treatment: control, greenhouse conditions sampling time point: V5 developmental stage biological replicate: R2
|
Extracted molecule |
total RNA |
Extraction protocol |
For each tissue, samples from three-four plants were pooled together, flash-frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted from frozen tissue with Trizol and small RNA extracted with PAGE gel. The sRNA libraries were produced using the TruSeQ® small RNA Sample Preparation Kit (Illumina) and sequenced on an Illumina HiSeq 2500 platform
|
|
|
Library strategy |
ncRNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
Illumina HiSeq 2500 |
|
|
Data processing |
cutadapt was used to remove the 3' adapter (--discard-untrimmed -m 15) and to discard reads containing the 5' adapter Low quality reads were removed with FASTX-Toolkit (-q 20 -p 85 -Q 33 -v) Reads were aligned to the maize genome with ShortStack 3.3 Genome_build: (AGPv3) Supplementary_files_format_and_content: Tab-delimited text files contain two columns: the first column is the sequence of the unique, non-redundant sRNA read, the second column is its total raw abundance
|
|
|
Submission date |
Feb 08, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Michael J Axtell |
Organization name |
Penn State University
|
Department |
Department of Biology
|
Street address |
University Park
|
City |
State College |
State/province |
PA |
ZIP/Postal code |
16802 |
Country |
USA |
|
|
Platform ID |
GPL17628 |
Series (1) |
GSE77657 |
Reference annotation for small RNA-producing genes in maize |
|
Relations |
BioSample |
SAMN04479318 |
SRA |
SRX1564780 |
Supplementary file |
Size |
Download |
File type/resource |
GSM2055767_W-Leaf_R2_tag_count.txt.gz |
15.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
|
|
|
|
|