|
| Status |
Public on Nov 28, 2015 |
| Title |
non-polyA RNAs from nuclear extract, seedling |
| Sample type |
SRA |
| |
|
| Source name |
non-polyA RNAs from nuclear extract, seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
tissue: seedling
developmental stage: 14-day old
molecule: non-polyA RNA, rRNA depleted
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Arabidopsis ecotype Col-0 was surface steriled and planted on 1/2 MS medium. The culture condition was: 16 hour with light at 23℃, 70% humity, 8 hours without light at 18℃, 70% humity. 2 weeks old seedlings were harvested. The rest were transferred to soil medium for addtional two weeks and the inflorescence was harvested.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was extracted by using TRIzol reagent (Invitrogen, Cat. No. 15596018) with its standard protocol. RNAs were first fragmented by partial alkaline hydrolysis and separated on 12% PAGE gel. RNAs ranging from ~50 to ~75 were ligated to 3’ RNA adaptor and then ligated to 5’ RNA adaptor. The ligation products were then reverse transcribed to first strand cDNA, followed by PCR amplification.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Strand-specific RNA-seq
|
| Data processing |
Illumina Casava1.7 software was used for base-calling.
Adaptor sequences in the sequencing reads were removed using Cutadapt v1.0 with parameters '-O 4 -e 0.13 -m 35'.
Trimmed reads with a length no shorter than 35nt were aligned to Arabidopsis genome using TopHat v1.3.1 with parameters '-g 5 -i 20 -I 50000 -G TAIR10.gtf --solexa1.3-quals --library-type fr-secondstrand'.
For each sample, transcripts were assembled independently using Cufflinks v1.3.0 with parameters '--min-intron-length 20 -I 50000 -g TAIR10.gtf --library-type fr-secondstrand --min-frags-per-transfrag 1 -u'.
All assemblies from each samples as well as TAIR annotation (v10) were merged together by Cuffmerge using default parameters.
Cuffdiff were used to estimate the expression levels of each transcript in all samples.
genome build: TAIR10
processed data files format and content: tab-delimited text files include FPKM values for each Sample.
|
| |
|
| Submission date |
Dec 03, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Yijun Qi |
| E-mail(s) |
qiyijun@biomed.tsinghua.edu.cn
|
| Organization name |
National Institute of Biological Sciences
|
| Lab |
Yijun Qi's lab
|
| Street address |
#7 Science Park Road, Zhongguancun Life Science Park
|
| City |
Beijing |
| ZIP/Postal code |
102206 |
| Country |
China |
| |
|
| Platform ID |
GPL11221 |
| Series (1) |
| GSE42695 |
Genome-wide profiling of long non-coding RNAs in Arabidopsis |
|
| Relations |
| SRA |
SRX208111 |
| BioSample |
SAMN01822143 |
