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Sample GSM1899874 Query DataSets for GSM1899874
Status Public on Nov 09, 2015
Title SET4 L1 spikein rep2 RNAseq
Sample type SRA
 
Source name whole worms
Organisms Caenorhabditis briggsae; Caenorhabditis elegans
Characteristics strain: MT14911 & AF16
developmental stage: L1
Treatment protocol Packed larvae were resuspended in 10V of Trizol and frozen at -80C.
Growth protocol Larvae were collected after overnight embryo hatching and growth for 6 hours (L1) or 24 hours (L3) on NGM plates.
Extracted molecule total RNA
Extraction protocol RNA was extracted by freeze cracking samples by freezing in liquid nitrogen and thawing at 37C water bath five times. RNA was isolated according to the manufacturer's (Invitrogen) Trizol extraction protocol. Purified total RNA RNA was cleaned up through Qiagen RNeasy column.
mRNA was purified from .5-10 ug of total RNA using Sera-Mag Oligo(dT) beads (ThermoScientific). cDNA preparation was done in the presence of dUTP to prepare stranded RNA-seq libraries as in PMID:19620212
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description mRNA
RNAseq_spikeins_counts.txt
RNAseq_spikeins_counts_Cbriggsae.txt
Data processing Basecalls were performed using CASAVA version 1.8.
RNA-seq reads were aligned to the WS220 genome assembly using tophat version 2.0.11 using default parameters for a stranded library.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using cufflinks version 2.2.0 using default parameters supplying gene annotations.
Raw counts for each gene were generated using htseq-count version 0.6.0 using default parameters.
Genome_build: WS220
Supplementary_files_format_and_content: FPKM text file contains the FPKM values for each gene for each replicate.
 
Submission date Sep 30, 2015
Last update date May 15, 2019
Contact name Sevinc Ercan
Organization name New York University
Department Biology
Street address 12 Waverly Place
City New York
State/province NY
ZIP/Postal code 10003
Country USA
 
Platform ID GPL20977
Series (1)
GSE67650 Developmental dynamics of C. elegans dosage compensation
Relations
BioSample SAMN04124069
SRA SRX1297660

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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