|
| Status |
Public on Mar 31, 2016 |
| Title |
Endodermis line1 RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Endodermis line1
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
cell type: FACSorted endodermis cells
strain: ProSCR:GFP line1
tissue: root
|
| Growth protocol |
Seedlings were grown vertically for 6 days after plating on 1x Murashige and Skoog media supplemented with 1% sucrose and 1% agar. All seedlings were grown under standard long day conditions (16 hours of light, 8 hrs of darkness, 22 °C).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fluorescent Activated Cell Sorting (FACS) was performed using cell specific GFP lines. Sorted cells were collected directly into specific lysis buffers that were compatible with downstream applications. Cells used for bisulfite sequencing, mRNA-seq, smRNA-seq were lysed in Buffer AP1 (Qiagen), Buffer RLT (Qiagen), Trizol (Invitrogen). All samples were immediately stored at -80 °C until gDNA and RNA was extracted using DNeasy Plant mini kit (Qiagen) and RNeasy Plant mini kit (Qiagen) or Trizol, respectively.
RNA-seq library preparation was performed using the Illumina TruSeq RNA Library Prep kit from polyA+ selected mRNA as per manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using tophat 1.3.1 implemented with bowtie 0.12.7 with parameters --solexa1.3-quals -F 0 -g 1
FPKM ( fragments per kilobase of exon per million fragments mapped) were quantified using Cufflinks 2.0.2 with parameters --library-type fr-unstranded
Genome_build: TAIR10
Supplementary_files_format_and_content: FPKM ( fragments per kilobase of exon per million fragments mapped) for all genes in the TAIR10 reference annotation as defined by Cufflinks
|
| |
|
| Submission date |
Mar 30, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Joseph R Ecker |
| E-mail(s) |
ecker@salk.edu
|
| Phone |
8584534100
|
| Organization name |
HHMI-Salk-Institute
|
| Department |
Genomic Analysis Laboratory
|
| Lab |
Ecker lab
|
| Street address |
10010 North Torrey Pines Road
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL13222 |
| Series (2) |
| GSE79709 |
Unique cell-type specific patterns of DNA methylation in the root meristem (RNA-seq) |
| GSE79710 |
Unique cell-type specific patterns of DNA methylation in the root meristem |
|
| Relations |
| BioSample |
SAMN04590195 |
| SRA |
SRX1669853 |
