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Sample GSM1015703

Query DataSets for GSM1015703

Status

Public on Oct 25, 2012

Title

C.elegans XX 2

Sample type

SRA

Source name

whole animal

Organism

Caenorhabditis elegans

Characteristics

strain: JK574 fog-2(q71)
temperature (deg.c): 20
developmental stage: L4 & adult pseudo-females
rna: poly-A RNA
base calling software version: RTA 1.10.36

Growth protocol

C. remanei, C. japonica, C. brenneri, and C. elegans were maintained at 20˚C on OP50-seeded NGM agar plates , using 2.2% agar to discourage burrowing. C. briggsae was maintained at 25˚C to prevent production of intersexual germ cells in the XX sex. To avoid inbreeding depression in obligately outcrossing strains, large populations were maintained by transferring large chunks from two independent plates per passage.

Extracted molecule

total RNA

Extraction protocol

Worms were roughly synchronized by hypochlorite / bleach treatment, and at least 400 XX or 600 XO L4 and young adult worms per replicate were hand-picked. Worms were washed and resuspended in 50 microliters of RNA-ase free water. 250mL of TRI-Reagent (Molecular Research Center) were added and the samples were frozen at ‑80˚C. Samples were thawed and lysed using a plastic pestle. RNA was purified using phenol/chloroform extractions, isopropanol precipitations, and DNaseI treatment.
Single-ended cDNA libraries were prepared according to manufacturer’s protocol (Illumina)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

base were called with RTA (specific release indicated for each raw file; see column E below)
C. briggsae reads were trimmed to 36bp to correspond to data obtained for the other species
reads were used to generate de novo transcriptome assemblies using SOAPdenovo v1.05, k-mer size 23. The contigs shorter than 50bp, at the tips smaller than 2k or whose coverage was low were removed.
reads were aligned to either genome reference sequences using TopHat v1.2.0 (-p 4 -i 40) or to the do novo assemblies using Bowtie v0.12.7 (-v 2 -m 3 -p 4 -q --best)
expression values for contigs were calculated as Reads Per Kilobase of contigs per Million mapped reads, expression values for gene models were assessed using Cufflinks v1.0.3 (default parameters, using gene annotation files from ENSEMBL release 9 and 14 for C. briggsae)
only genes or contigs whose expression were detected consistently across the three biological replicates were considered for further analyses. Statistical differential expression between sexes was assessed by linear regression models taking into account effect of sex and machine variation (HiSeq vs GAII)
Genome_build: C. japonica, C. elegans, C. brenneri, C.remanei, C. briggsae: Wormbase release WS224
C. japonica CJ302, C. elegans WS220, C. brenneri CB601, C.remanei CR2, C. briggsae CB4

Submission date

Oct 05, 2012

Last update date

May 15, 2019

Contact name

Eric S. Haag

E-mail(s)

ehaag@umd.edu

Phone

301-405-8534

Organization name

University of Maryland