|
| Status |
Public on Feb 16, 2018 |
| Title |
im-nc_Col_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
im-nc_Col, 7-day-old seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Colombia
genotype: wild-type
age: 7-day-old
tissue: root
|
| Treatment protocol |
-
|
| Growth protocol |
7-day-old seedlings horizontally grown on ΒΌ MS media containing 0.5% sucrose.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Seedling roots were flash frozen immediately after harvesting and subjected to total RNA extraction using miRNeasy Plant Mini kit (QIAGEN).
The total RNA was submitted to Texas A&M AgriLife Genomics & Bioinformatics Service for RNA-seq analysis (paired-end, 125-bp). After validating the integrity and purity of total RNA using Nanodrop, sequencing libraries were prepared using TruSeq Stranded Total RNA with Ribo-Zero Plant kit. To enrich intermediate non-coding RNA (im-ncRNA), fragmentation step was omitted, and library cDNA with 100-500nt were purified using Pippin (Sage Science) prior to sequencing by Illumina HiSeq (125 nt, paired-end).
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
im-ncRNA-seq_Col(3)
im-nc_samtools_bedcov.txt
|
| Data processing |
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's HCS 2.2.68 and RTA 1.18.66.3 software with default parameter settings. Sequencer .bcl basecall files were demultiplexed and formatted into .fastq files using bcl2fastq 2.17.1.14 script configureBclToFastq.pl.
Raw sequenced reads (.fastq files) were uploaded to Galaxy (https://usegalaxy.org/). The following data processing was done using Galaxy.
Sequenced reads were trimmed for adapter and low-quality sequences by using Trim Galore! (v0.4.0), then mapped with Tophat (v2.0.14) against reference assembly Ensembl TAIR10 from Illumina iGenome, using default parameters except -i/--min-intron-length 60 -I/--max-intron-length 6000.
Coverage depth of regions of interest was calculated by SAMtools_BedCov (v1.2).
Genome_build: Arabidopsis TAIR10 (Ensembl)
Supplementary_files_format_and_content: im-nc_samtools_bedcov.txt file includes raw coverage counts (a sum of coverage depth per base in each region of interest) for each sample, computed by SAMtools_BedCov.
|
| |
|
| Submission date |
Apr 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Akihito Fukudome |
| Organization name |
Texas A&M University
|
| Street address |
Dept. Horticultural Sciences MS2133 Texas A&M Univ.
|
| City |
College Station |
| State/province |
Texas |
| ZIP/Postal code |
77843-2133 |
| Country |
USA |
| |
|
| Platform ID |
GPL17639 |
| Series (2) |
| GSE98046 |
Salt-stress and CTD phosphatase-like 4 mediate switching of snRNA to mRNA transcription in Arabidopsis thaliana [im-nc] |
| GSE98047 |
Salt-stress and CTD phosphatase-like 4 mediate switching of snRNA to mRNA transcription in Arabidopsis thaliana |
|
| Relations |
| BioSample |
SAMN06808100 |
| SRA |
SRX2751241 |
