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Sample GSM3790942 Query DataSets for GSM3790942
Status Public on Dec 07, 2020
Title N2 + 50% cco-1 RNAi + 50% atfs-1 RNAi_ rep1
Sample type SRA
 
Source name N2 + 50% cco-1 RNAi + 50% atfs-1 RNAi_ rep1
Organism Caenorhabditis elegans
Characteristics strain: N2
RNAi clone: E. coli HT115, cco-1 RNAi, atfs-1-1 RNAi
genotype/variation: Wild-type
stage at harvesting: L4/young adult
Treatment protocol RNAi treatment was started from the egg phase and treated until worms reached L4/young adult phase and then collected in 1.5 mL tubes
Growth protocol Worms were synchronized by bleaching. Synchronized worm eggs were plated in NGM plates under the described conditions and raised at 20 ̊C. Worms were harvested after 2 days (at L4/young adult stage) and washed with M9 buffer for three times to remove the bacteria, then snap frozen in liquid nitrogen.
Extracted molecule total RNA
Extraction protocol On the day of the extraction, 1 ml of TriPure Isolation Reagent (Cat. 11667165001, Roche) was added to each tube. The samples were then frozen and thawed quickly 8 times in liquid nitrogen to rupture cell membranes. RNA was then extracted by using a column-based kit from Macherey-Nagel (Cat. 740955.250).
RNA libraries were prepared for sequencing using standard BGISeq500 protocol with polyA enrichment
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model BGISEQ-500
 
Description L1
Data processing After sequencing on the BGIseq-500 platform, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality (phred quality < 20) reads from raw reads.
Sequenced reads were mapped to the WBcel235 assembly of the worm genome using ensembl release 89 gene annotation with STAR aligner version 2.6.0a
Reads were counted using htseq-count version 0.10.0 using these flags: -f bam -r pos -s no -m union -t exon -i gene_id
Genome_build: Caenorhabditis_elegans.WBcel235.89
Supplementary_files_format_and_content: xlsx file with counts per gene per sample
 
Submission date May 22, 2019
Last update date Dec 07, 2020
Contact name Terytty Yang Li
E-mail(s) teryttyliyang@fudan.edu.cn
Organization name EPFL
Street address EPFL SV IBI-SV LISP AI 1145
City Lausanne
ZIP/Postal code 1015
Country Switzerland
 
Platform ID GPL25145
Series (2)
GSE131611 The transcriptional coactivator CBP/p300 is an evolutionarily conserved node that promotes longevity in response to mitochondrial stress [C. elegans]
GSE131616 The transcriptional coactivator CBP/p300 is an evolutionarily conserved node that promotes longevity in response to mitochondrial stress
Relations
BioSample SAMN11812602
SRA SRX5882452

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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