|
| Status |
Public on Dec 01, 2021 |
| Title |
empty vector rIIS Rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole worm
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: rrf-3(pk1426);daf-2(e1368)
Stage: L4/YA
temerature: 20 ˚C
|
| Treatment protocol |
Stains were kept on empty vector and transcription specific RNAi clones
|
| Growth protocol |
Worms were grown on nematode growth medium (NGM) supplemented with 100 µg/ml ampicillin and 2mM IPTG.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Worms grown on empty vector or transcription factors RNAi plates. RNA was harvested using Trizol reagent. The cDNA libraries were constructed with TruSeq RNA Library Prep Kit v2 (Illumina Inc., USA).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
rrf-3;daf-2_EV_BR1
|
| Data processing |
Imaging, base calling and quality scoring were done as per standard manufacturer’s guidelines (Illumina Inc.).
The demultiplexing and conversion of BCL file format reads to FASTQ file format was done with the Illumina-supported CASAVA v1.8.2 software package.
Read counts were then aligned to the reference genome (WBcel 235) and their normalized abundance were calculated as Reads Per Kilobase Million (RPKM) using QIAGEN CLC Genomics Workbench v12.0.3.
Genes fold change was calculated among samples based on negative binomial Generalized Linear Model (GLM) which corrects for differences in library size between samples and the effects of cofounding factors.
Genes with absolute fold change of at least 1.5 and standard-p value below 0.05 were considered as differentially expressed.
Genome_build: WBcel 235
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample.
|
| |
|
| Submission date |
Sep 20, 2021 |
| Last update date |
Dec 01, 2021 |
| Contact name |
Neeraj Kumar |
| E-mail(s) |
[email protected]
|
| Phone |
01126593945
|
| Organization name |
All India Institute of Medical Sciences, New Delhi
|
| Street address |
Ansari Nagar
|
| City |
New Delhi |
| State/province |
Delhi |
| ZIP/Postal code |
110029 |
| Country |
India |
| |
|
| Platform ID |
GPL13776 |
| Series (1) |
| GSE184415 |
Transcriptome of insulin signalling associated transcription factor targets |
|
| Relations |
| BioSample |
SAMN21509258 |
| SRA |
SRX12259617 |
