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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 26, 2017 |
| Title |
mouse_HL_W3_4_rep2 |
| Sample type |
SRA |
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| Source name |
mouse_HL_W3_4
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| Organism |
Mus musculus |
| Characteristics |
tissue: hind-limb
developmental stage: W3
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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 |
SAMN07417346 |
| SRA |
SRX3040060 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2718709_mouse_W3_4_HL3R_CTTGTA_L004_R1_001_genes.fpkm_tracking.gz |
1.1 Mb |
(ftp)(http) |
FPKM_TRACKING |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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