|
| Status |
Public on Dec 15, 2020 |
| Title |
24hrMockA RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
callus on CIM for 5 days with mock treatment
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
cultivar: L.er
tissue: callus
transgenic: 35S:LFY-GR
mutant: WT
deseq2 analyzed for differential expression: yes
|
| Treatment protocol |
24hr Mock treatment
|
| Growth protocol |
Plants were grown on 1/2MS plates for 3 weeks. Roots were harvested from 3-week-old seedlings and put on CIM for up to 5 days with either 1hr of mock or dex treatment, 6hr of mock or dex treatment and 24hr of mock or dex treatment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNAs were extracted by trizol and chloroform and further purified by Qiagen RNA cleanup kit
Manual library preparation with multiple steps -- steps described in detail in paper
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Base-calling was performed automatically in Illumina BaseSpace
FASTQ reads were trimmed using TRIMMOMATIC v0.36 (SE -phred33 ILLUMINACLIP:adapters.fasta:2:30:10 HEADCROP:15 MINLEN:70 TOPHRED33)
Sequencing quality metrics were obtained for the raw and trimmed FASTQ files with FASTQC v0.11.5
Trimmed sequencing reads were mapped to Release 10 of the Arabidopsis Genome (TAIR10) using STAR v2.5.3a (--sjdbOverhang 100 --outSAMprimaryFlag AllBestScore --outSJfilterCountTotalMin 10 5 5 5 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --alignIntronMin 60 --alignIntronMax 6000 --outFilterMismatchNmax)
Read counts at each gene for each sample and replicates was calculated with HT-Seq v0.7.2 htseq-count parameters: --stranded='no' --minaqual=30
Genome_build: TAIR10
Supplementary_files_format_and_content: htseq_result: unormalized read counts of each gene feature in the Arabidopsis genome for each individual RNA-seq sample and replicate calculated via HTSeq.
*A/B.bigwig: Bigwig showing 10RPM-normalized coverage
*Bigwigs on series record: showing 10RPM-normalized coverage after averaging the read counts from two biological replicates
|
| |
|
| Submission date |
Dec 09, 2019 |
| Last update date |
Dec 19, 2020 |
| Contact name |
Doris Wagner |
| E-mail(s) |
wagnerdo@sas.upenn.edu
|
| Phone |
2158980483
|
| Organization name |
University of Pennsylvania
|
| Department |
Department of Biology
|
| Lab |
Wagner Lab
|
| Street address |
103G Carolyn Lynch Laboratory
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL19580 |
| Series (2) |
| GSE141703 |
LFY is pioneer transcription factor [RNA-seq] |
| GSE141706 |
LFY is pioneer transcription factor |
|
| Relations |
| BioSample |
SAMN13515893 |
| SRA |
SRX7293421 |
