|
| Status |
Public on Jun 06, 2020 |
| Title |
adr-1- L1 neural cells |
| Sample type |
SRA |
| |
|
| Source name |
Neural cells
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
sample type: Rab-3 driven GFP expressed neural cells
strain: BB77
age: 6 hr after hatching
|
| Treatment protocol |
Worms were grown under optimum conditions.
|
| Growth protocol |
After hatching L1 was plated to grow upto 50 hr to obtain adults.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Worms were digested into single cell suspension and GFP positive neural cells were isolated using FACS.
Poly-A selected mRNA library preparation was done using KAPPA stranded library preparation kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
poly-A selected RNA
adr1.L1.sailoroutput.csv
|
| Data processing |
Reads were aligned to C. elegans reference genome using STAR (v2.5.2b)
Differential gene expression analysis was performed using Feature counts and DeSeq2
A-to-I editing sites were de novo identified using SAILOR program
Variant calling was performed to quantify editing levels throughout C. elegans neural development.
Genome_build: C. elegans WS269
Supplementary_files_format_and_content: tab-delimited text files include the counts for each gene in L1 and adult neural RNA in WT and adr-2(-) backgrounds
Supplementary_files_format_and_content: .bed files from the de novo identification of SAILOR output include all the predicted sites and the confidence score for each predicted site
|
| |
|
| Submission date |
Jun 05, 2020 |
| Last update date |
Jun 06, 2020 |
| Contact name |
Heather Ann Hundley |
| E-mail(s) |
[email protected]
|
| Phone |
812-855-0675
|
| Organization name |
Indiana University, Bloomington
|
| Department |
Biology
|
| Lab |
Hundley
|
| Street address |
1001 E 3rd St,
|
| City |
Bloomington |
| State/province |
IN |
| ZIP/Postal code |
47405 |
| Country |
USA |
| |
|
| Platform ID |
GPL19757 |
| Series (1) |
| GSE151916 |
A molecular mechanism to regulate neural-specific A-to-I editing during development |
|
| Relations |
| BioSample |
SAMN15147710 |
| SRA |
SRX8483135 |
