|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Feb 18, 2016 |
Title |
Metazome_Amphimedon_timecourse_sample_0068 |
Sample type |
SRA |
|
|
Source name |
single embryo 68
|
Organism |
Amphimedon queenslandica |
Characteristics |
developmental stage: cloud
|
Treatment protocol |
samples staged by morphology and imaged before being stored in 20 μl RNA later.
|
Growth protocol |
Embryos, larvae and post-larvae were collected individually at Heron Island, the Great Barrier Reef, Australia.
|
Extracted molecule |
polyA RNA |
Extraction protocol |
RNA was isolated using TRIzol as previously described (Levin et al., 2012). The CEL-Seq protocol (Hashimshony, et al. 2012) was used to amplify and sequence. CEL-seq multiplexing barocdes were used.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
Libraries were sequenced on the Illumina HiSeq2000 according to standard, paired-end sequencing, protocols. Primary analysis done in RTA 1.17.20,1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA-1.8 (configureBclToFastq.pl--fastq-cluster-count 1234567890 --mismatches 0 --use-bases-mask Y15n,I6n,Y35n) Filter and read trimming (barcode minimum quality of 10. trimming of read2 to 35 bases - not required). CEL-Seq (Hashimshony, et a. 2012l) demultiplexing of second mate, using first mate barcode, allowing no mismatches in barcode. bowtie2, version 2.1.0, against A. queenslandica genome Aqu1 Read counting with htseq-count version 0.5.4p3. Using on Ensemble Aqu2.1 annotations Genome_build: Aqu1 Supplementary_files_format_and_content: AQ_exp.tab is a tabular Expression matrix
|
|
|
Submission date |
Aug 18, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Itai Yanai |
E-mail(s) |
yanai@technion.ac.il
|
Organization name |
Technion - Israel Institute of Technology
|
Department |
Biology
|
Lab |
Yanai
|
Street address |
Technion City
|
City |
Haifa |
ZIP/Postal code |
30200 |
Country |
Israel |
|
|
Platform ID |
GPL18214 |
Series (2) |
GSE60483 |
Amphimedon queenslandica high resolution developmental transcriptomic time-course |
GSE70185 |
The mid-developmental transition and the evolution of animal body plans |
|
Relations |
BioSample |
SAMN02997032 |
SRA |
SRX682553 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
|