|
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 |