|
| Status |
Public on Apr 02, 2015 |
| Title |
RNA-seq in lin-35 mutants, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
L3 larvae
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole larvae
strain: JA1507
Stage: L3
genotype/variation: lin-35 mutant
|
| Treatment protocol |
Total RNA was extracted in TriPure Reagent according to manufacturer's protocol, treated with baseline-zero DNAse (Epicentre, Madison, WI, USA), and purified using the Qiagen Rneasy kit.
|
| Growth protocol |
Worms grown in liquid culture were bleached and then hatched in M9 for 24-42 hrs. Hatched L1 larvae were inoculated in a proper volume of liquid culture. Next day when larvae reached the L3 stage they were cleaned by M9 washes and sucrose gradient and collected by freezing in liquid nitrogen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was used to make mRNA libraries using the TruSeq RNA Sample Preparation Kit according to the manufacturer's instructions (Illumina, Inc., San Diego, CA, USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample name: lin35_0910_RNAseq_MC006
processed data file: N2_lin-35_htz-1_processed_RNAseq.xlsx
|
| Data processing |
ChIP-seq and RNA-seq reads were aligned to the WS220 assembly of the C. elegans genome using BWA (Li and Durbin, 2010) with default settings.
ChIP-seq data were normalized using BEADS algorithm (Cheung et al, 2011).
ChIP-seq signals were exported to bigWig tracks at native resolution.
RNA-seq tag counts for each gene were extracted from BAM alignment files using HTSeq method working in ”union” mode. An exon model based on WS235 genes (taken from Ensembl Gene 74 December 2013) was lifted over to ce10/WS220.
RNA-seq tag counts were used to build the expression matrix. Differential gene expression between N2, lin-35 mutant, and htz-1 mutant was tested using DESeq2
Genome_build: ce10/WS220
Genome_build: http://ws220.wormbase.org/
Genome_build: http://hgdownload.soe.ucsc.edu/goldenPath/ce10/bigZips/
Supplementary_files_format_and_content: "linear" scores in bigWig tracks represent BEADS values; files were generated using BEADS normalization pipeline in R
Supplementary_files_format_and_content: "zscore" scores in bigWig tracks represent standardized BEADS values; files were generated using BEADS normalization pipeline in R
Supplementary_files_format_and_content: xslx spreadsheet contains: reads per kilobase (kb) of transcript per millions reads in library (RPKM) for all RNA-seq experiments, averaged RPKM values for replicates, plus log2 fold changes, p-values and adjusted p-values (FDR) calculated with DEseq2 for gene knock-out replicates versus N2 (wild-type) replicate
|
| |
|
| Submission date |
Oct 29, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Przemyslaw Aleksander Stempor |
| Organization name |
University of Cambridge
|
| Department |
The Gurdon Institute
|
| Lab |
Ahringer Lab
|
| Street address |
Tennis Court Road
|
| City |
Cambridge |
| State/province |
United Kingdom |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13657 |
| Series (1) |
| GSE62833 |
The DREAM complex promotes gene body deposition of H2A.Z for target repression |
|
| Relations |
| BioSample |
SAMN03152269 |
| SRA |
SRX747311 |
