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| Status |
Public on Aug 24, 2015 |
| Title |
mouse_FL_LS_rep2 |
| Sample type |
SRA |
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| Source name |
mouse_FL_LS
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| Organism |
Mus musculus |
| Characteristics |
breed: Embryonic mice obtained from timed matings in the breeding colonies housed in the Sears Lab at the Univ. of Illinois
tissue: fore-limb
developmental stage: late-stage
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| Extracted molecule |
total RNA |
| Extraction protocol |
Embryonic mice, opossums, bats and pigs with early (ES) or late (LS) stage forelimbs were obtained from a variety of sources. Forelimbs for the ES were harvested at Stage 14 for bat, E11 for mouse, Stage 28 for opossum and E22 for pig. For the LS, forelimbs were harvested at Stage 15 for bat, E12 for mouse, Stage 29 for opossum and E26 for pig. 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 (beginning, early, and late stages) and call a de novo transcriptome using Trinity, then from the resulting de novo transcriptome we filter out any sequence not matching the SwissProt database (blastx, e-value<1e-20).
Supplementary_files_format_and_content: Tab-delimited text files include either RSEM or CUFFLINKS gene expression FPKM values for each Sample
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| Submission date |
Jul 27, 2015 |
| 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 |
SAMN03939326 |
| SRA |
SRX1121055 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1833587_cufflinks_Mus_W6_FL1_CGATGT_L003_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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