NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3466751 Query DataSets for GSM3466751
Status Public on Mar 19, 2020
Title pif4 pif5 pif7 RNA-seq replicate 3
Sample type SRA
 
Source name pif4 pif5 pif7 RNA-seq
Organism Arabidopsis thaliana
Characteristics ecotype: Columbia (Col-0)
genotype/variation: pif4-101 pif5(pil6-1) pif7-1
age: 14 days old
time of harvest: ZT4
tissue: Apical portions of plants (cut in hypocotyl)
Growth protocol 22°C constant temperature with long-day photoperiod (16h light/8h darkness) under white fluorescent light (~35-55 μmol/m2/sec) on sucrose-free 1X MS medium containing 0.6% Gelzan CM
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy Plant Mini Kit (QIAGEN) according to manufacturer's instructions, including on-column DNase digestion to eliminate genomic DNA.
Isolated RNA was subjected to library preparation using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems) with NEBNext Multiplex Oligos for Illumina (New England Biolabs) used as adapters and Agencourt AMPure XP (Beckman Coulter) beads used instead of KAPA Pure Beads.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description RNA-seq for pif4 pif5 pif7 (triple LOF pif mutant) replicate 3
Data processing Generation of fastq files: Raw data files (bcl format) were converted to fastq files by bcl2fastq (Illumina).
Alignment: Reads were mapped to the Arabidopsis reference using Bowtie 1.2.1 with the following parameters: '-all -best -strata'.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited data with transcript CPM (counts per million mapped reads) values for each sample
 
Submission date Nov 13, 2018
Last update date Mar 19, 2020
Contact name David Seth Favero
E-mail(s) davefavero@gmail.com
Phone +81-45-503-9575
Organization name RIKEN
Department CSRS
Lab Keiko Sugimoto
Street address 1-7-22 Suehirocho, Tsurumi-ku
City Yokohama
State/province International
ZIP/Postal code 230-0045
Country Japan
 
Platform ID GPL19580
Series (2)
GSE122454 AT-hook transcription factors repress petiole growth by antagonizing PIF4 [RNA-seq]
GSE122456 AT-hook transcription factors repress petiole growth by antagonizing PIF4
Relations
BioSample SAMN10414061
SRA SRX5001347

Supplementary file Size Download File type/resource
GSM3466751_p4p5p7_RNA-seq_Rep3.txt.gz 201.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap