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| Status |
Public on Dec 12, 2013 |
| Title |
m_4_2_i12 |
| Sample type |
SRA |
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| Source name |
Macaque milk
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| Organism |
Macaca mulatta |
| Characteristics |
time point (days post-partum): 30
tissue type: Cells
animal id: M6
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Qiagen Universal Kit (Qiagen, Netherlands), followed by treatment with DNAse. RNA yield and quality (260/280 nm, 260/230 nm) were measured by Nanodrop spectrophotometry (Thermo Fisher Scientific Inc., Wilmington, DE). RNA integrity was assessed with an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA).
RNA libraries were prepared for sequencing using standard Illumina TruSeq protocol with polyA selection
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
FASTQ files were de-multiplexed to assign the 100bp reads to the originating sample
Reads were first trimmed to remove adaptor sequences using Scythe [17] and then adaptively trimmed for quality on both the 5’ and 3’ ends using Sickle [18]
Resulting reads were checked for quality using FastQC
The rhesus macaque genome assembly rheMac2 was indexed using Bowtie
Reads were then mapped to the indexed genome using TopHat
Transcript abundances were estimated as fragments per kilobase of exon per million fragments mapped (FPKMs) using Cufflinks and all MMUL1.0 Ensembl transcripts from the Ensembl database, release 67
Genome_build: rheMac2
Supplementary_files_format_and_content: Tab-delimited text file contains FPKMs for each transcript in each sample
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| Submission date |
Aug 11, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Danielle G Lemay |
| E-mail(s) |
dglemay@ucdavis.edu
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| Organization name |
University of California Davis
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| Department |
Genome Center
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| Street address |
451 Health Sciences Dr
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| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
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| Platform ID |
GPL14954 |
| Series (1) |
| GSE49765 |
Sequencing of milk fat, milk cell, and mammary tissue RNA from rhesus macaques |
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| Relations |
| BioSample |
SAMN02315379 |
| SRA |
SRX333505 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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