|
| Status |
Public on Oct 01, 2019 |
| Title |
tm1473_NGM_1 |
| Sample type |
SRA |
| |
|
| Source name |
L4 Larvae
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
cell type: Whole Organism
passages: Synchronized L4 Larvae
strain: tm1473 allele backcrossed to N2 Bristol
|
| Treatment protocol |
Worms were grown on NGM plates seeded with OP50 E. coli
|
| Growth protocol |
N2 wild-type and nhr-14 (tm1473) mutants were synchronized by hypochlorite treatment at the L1 larval stage, and grown to the L4 larval stage on NGM plates seeded with OP50 E. coli before RNA extraction.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Worms were rinsed with M9 buffer and RNA was extracted using a modified Trizol protocol.
Library construction was performed using the Illumina TruSeq RNA Sample Preparation Kit v2 with oligo dT selection (RS-122-2001 and RS-122-2002), and was sequenced with the Illumina HiSeq (50 cycle, single read).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
10578X7
|
| Data processing |
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned to Ce10 (Wormbase Build 220) using Novoalign
Differentially expressed reads were determined by Useq 8.7.4
DESeq's log2 ratio for differential expression, log2(mean(varCorT1,varCorT2, ...)/mean(varCorC1,varCorC2,...)). Note these varCor values will differ somewhat from the blinded varCor values exported to the spreadsheet since they use a different variance estimation.
DESeq's negative binomial p-value following the Benjamini and Hochberg multiple testing correction.
Genome_build: Ce10 Wormbase Build 220
|
| |
|
| Submission date |
Nov 12, 2016 |
| Last update date |
Oct 01, 2019 |
| Contact name |
Elizabeth A Leibold |
| E-mail(s) |
bleibold@genetics.utah.edu
|
| Organization name |
University of Utah
|
| Department |
Molecular Medicine
|
| Lab |
Leibold lab
|
| Street address |
15 North 2030 East
|
| City |
Salt lake city |
| State/province |
Utah |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
|
| Platform ID |
GPL9309 |
| Series (1) |
| GSE89783 |
NHR-14 loss of function couples intestinal iron uptake with innate immunity in C. elegans through PQM-1 signaling |
|
| Relations |
| BioSample |
SAMN06013561 |
| SRA |
SRX2343546 |
