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Sample GSM4563982 Query DataSets for GSM4563982
Status Public on May 22, 2020
Title Col0_A
Sample type SRA
 
Source name Col0 replicate 1
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
genotype/variation: wild type
developmental stage: Boyes: 1.0
tissue: roots
Treatment protocol No treatment.
Growth protocol Media = MS/10 +P (KH2PO4 500µM), hygrometry = 33% humidity, Temperature = 24°C day/ 21°c night, Light = 16 hours day / 8 hours night.
Extracted molecule total RNA
Extraction protocol Roots 50µg (QuickRNA Zymo).
RNA libraries were prepared for sequencing using standard Illumina protocols for TruSeq RNA.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Sequenced reads were trimmed using trimmomatic V0.36 to remove adapters and low quality bases. Ribosomal RNA were removed using SortMeRNA (v2.1).
Trimmed reads were aligned to the TAIR10 genome using STAR (2.5.2b).
Reads were counted using featureCounts from subreads package (v1.6.5) using strand specific mode.
Genome_build: TAIR10
Supplementary_files_format_and_content: *_counts.txt: Tab-delimited text files include raw count values by gene for each Sample.
 
Submission date May 21, 2020
Last update date May 22, 2020
Contact name Thomas Blein
E-mail(s) thomas.blein@cnrs.fr
Organization name CNRS
Lab IPS2
Street address rue de Noetzlin
City Gif-sur-Yvette
ZIP/Postal code 91190
Country France
 
Platform ID GPL19580
Series (1)
GSE151005 Analysis of NPC48 overexpressing in Arabidopsis roots
Relations
BioSample SAMN14992924
SRA SRX8377624

Supplementary file Size Download File type/resource
GSM4563982_Col0_A_counts.txt.gz 117.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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