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Status |
Public on Jul 26, 2017 |
Title |
mouse_FL_W2_rep2 |
Sample type |
SRA |
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Source name |
mouse_FL_W2
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Organism |
Mus musculus |
Characteristics |
tissue: fore-limb developmental stage: W2
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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.
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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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).
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Submission date |
Jul 26, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Marcelo Rivas |
Organization name |
University of California San Diego
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Department |
Bioengineering
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Lab |
Sheng Zhong
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Street address |
9500 Gilman Drive, MC 0412
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City |
La Jolla |
State/province |
CA |
ZIP/Postal code |
92093-0412 |
Country |
USA |
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Platform ID |
GPL17021 |
Series (1) |
GSE71390 |
The relationship between gene network structure and expression variation among individuals and species |
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Relations |
BioSample |
SAMN07417354 |
SRA |
SRX3040054 |
Supplementary file |
Size |
Download |
File type/resource |
GSM2718703_Mus_W2_FL3_4_ACAGTG_L003_R1_001_genes.fpkm_tracking.gz |
1.0 Mb |
(ftp)(http) |
FPKM_TRACKING |
SRA Run Selector![Help](/coreweb/images/long_help4.gif) |
Raw data are available in SRA |
Processed data provided as supplementary file |
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