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Sample GSM1444160 Query DataSets for GSM1444160
Status Public on Jun 03, 2015
Title BSW008i4
Sample type SRA
 
Source name mixed stage embryos
Organism Caenorhabditis elegans
Characteristics strain: N2
genotype: wild type
developmental stage: embryo
Growth protocol Wild-type N2 worms were grown at 20°C on NG agar plates with concentrated HB101 bacteria. For DC-mutant embryos, 10 ml of packed synchronous sdc-2(y93) L1 worms were placed onto 10 cm RNAi plates (NG agar with 1 mM IPTG and 100 mg/ml Carbenicillin) seeded with 2-3 ml of concentrated HT115 (DE3) bacteria carrying the Ahringer feeding library plasmid expressing the coding region of sdc-2. The RNAi plates were incubated at 25°C overnight before L1s were added. Mixed-stage embryos were harvested from gravid hermaphrodites.
Extracted molecule total RNA
Extraction protocol RNA was extracted using a the protocol described in Baugh, Hunter Development 2002 except that 10 µL of a 20 mg/mL glycogen solution was used as a carrier.
Libraries were prepared from 10 µg of total RNA. PolyA RNA was purified using the Dynabeads mRNA purification kit (Ambion) and fragmented using Fragmentation Reagent (Ambion). First strand cDNA was synthesized from polyA RNA using the SuperScript III Reverse Transcriptase Kit with random primers (Invitrogen). Second strand cDNA synthesis was performed using Second Strand Synthesis buffer, DNA Pol I, and RNAse H (Invitrogen). cDNA libraries were prepared for sequencing using the mRNA TruSeq protocol (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing 100 base single end Illumina sequences were trimmed to remove reads that failed quality control, barcodes were trimmed off reads using cutadapt version 0.9.5
Reads were aligned to the transcriptome using GSNAP version 2012-01-11
Uniquely mapping reads were assigned to genes using HTSeq version 0.5.4p3 using the union mode
Changes in gene expression were determined by analysis with DESeq
Genome_build: WormBase WS220
Supplementary_files_format_and_content: csv file with averaged FPKM values for N2 and sdc-2(y93).
 
Submission date Jul 23, 2014
Last update date May 15, 2019
Contact name Barbara J. Meyer
E-mail(s) bjmeyer@berkeley.edu
Phone 510 643 5583
Organization name HHMI/UCB
Department MCB
Lab Meyer
Street address 16 Barker Hall #3204
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
 
Platform ID GPL13657
Series (2)
GSE59715 Condensin-Driven Remodeling of X-Chromosome Topology during Dosage Compensation [RNA-Seq]
GSE59716 Condensin-Driven Remodeling of X-Chromosome Topology during Dosage Compensation
Relations
BioSample SAMN02935340
SRA SRX660419

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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