NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2718742 Query DataSets for GSM2718742
Status Public on Jul 26, 2017
Title opossum_HL_32_2
Sample type SRA
 
Source name opossum_HL_32
Organism Monodelphis domestica
Characteristics tissue: hind-limb
developmental stage: 32
Growth protocol Embryonic mice (ICR strain, Taconic) and opossums were obtained from timed matings [1, 2] in breeding colonies housed in the Sears Lab at the University of Illinois. Pig embryos were obtained through timed inseminations following ovulations at the University of Illinois pig farm [3]. Bat embryos were obtained from field collections in Trinidad and staged according to Cretekos et al. 2005 [4].
1. Keyte AL, Smith KK. Basic maintenance and breeding of the opossum monodelphis domestica. CSH Protoc. 2008;2008:pdb prot5073.
2. Suckow MA, Danneman P, Brayton C. The laboratory mouse. Boca Raton: CRC Press; 2001.
3. Artificial Insemination (AI) [http://livestocktrail.illinois.edu/swinerepronet/paperDisplay.cfm?ContentID=6267]. Accessed May-June 2016.
4. Cretekos CJ, Weatherbee SD, Chen CH, Badwaik NK, Niswander L, Behringer RR, Rasweiler JJ. Embryonic staging system for the short-tailed fruit bat, Carollia perspicillata, a model organism for the mammalian order Chiroptera, based upon timed pregnancies in captive-bred animals. Dev Dyn. 2005;233(3):721–38.
Extracted molecule total RNA
Extraction protocol Limbs were removed from embryos and stored in RNALater in -20° C until further processing. RNA was extracted from tissues using E.Z.N.A. Total RNA Kit I (OMEGA bio-tek #R6834), and converted into RNASeq libraries with the Illumina TruSeq RNA Sample Preparation Kit (Illumina RS-122-2001).
Libraries were sequenced on an Illumina HiSeq 2500 housed in the Roy G. Carver Biotechnology Center at the University of Illinois.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Sequenced reads werepreprocessed to remove Illumina adaptors, and bases with qualities below 20 at the read's 3 prime end were trimmed. Reads from mouse, opossum, and pig were aligned using STAR (--outFilterMultimapNmax 10, --outFilterMismatchNmax 3, --outFilterScoreMin 0, --clip3pNbases 0, --clip5pNbases 0). Reads from bat were aligned using RSEM (--fragment-length-mean 425.0 --fragment-length-sd 150.0).
Gene expression (fragments per kilobase of transcript per million mapped reads, FPKM) were computed using cufflinks (for mouse, opossum, and pig) and RSEM (bat).
Genome_build: For mouse, opossum, and pig, we used their corresponding Ensembl reference genomes and annotation assemblies: GRCm38 (mouse), BROADO5 (opossum), and Sscrofa10.2 (pig). For bat reads, we used as a reference a de novo assembly. In short, we merged all libraries (from all stages) and called a de novo transcriptome using Trinity, then from the resulting de novo transcriptome we filtered out any sequence not matching the SwissProt database (blastx, e-value<1e-20).
Supplementary_files_format_and_content: *.genes.results.txt: Tab-delimited text files include RSEM gene expression (FPKM).
Supplementary_files_format_and_content: *_genes.fpkm_tracking: Tab-delimited text files include CUFFLINKS gene expression (FPKM).
 
Submission date Jul 26, 2017
Last update date May 15, 2019
Contact name Marcelo Rivas
Organization name University of California San Diego
Department Bioengineering
Lab Sheng Zhong
Street address 9500 Gilman Drive, MC 0412
City La Jolla
State/province CA
ZIP/Postal code 92093-0412
Country USA
 
Platform ID GPL20141
Series (1)
GSE71390 The relationship between gene network structure and expression variation among individuals and species
Relations
BioSample SAMN07417358
SRA SRX3040094

Supplementary file Size Download File type/resource
GSM2718742_Mono_St32_HL2_GTGAAA_L005_R1_001_genes.fpkm_tracking.gz 688.2 Kb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap