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| Status |
Public on Mar 27, 2016 |
| Title |
Wildtype study NG66 rep1 |
| Sample type |
SRA |
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| Source name |
Spleen tissue mRNA
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| Organism |
Mus musculus |
| Characteristics |
tissue: Spleen
genotype: Wildtype
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| Treatment protocol |
No treatment
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated from spleen using GE Healthcare RNA isolation kit. RNA was quantified on Tecan's Infinite 200PRO Nanoquant.
Libraries were prepared according to Illumina's Instructions
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
ES333_WT_NG66_rep1
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequence reads were trimmed for data quality using sickle version 1.210 with parameters "pe -q 20 -l 20"
Trimmed sequence reads were aligned to mm10 using TopHat v2.0.4, with an associated transcript GTF file, using parameters "--solexa-quals --library-type fr-unstranded", "--mate-inner-dist" using average insert size minus the read lengths, "--mate-std-dev" using 10 percent the average insert size, and "--GTF" using the attached mm10_genes.gtf file representing mm10 transcripts.
Splice junction data from TopHat2 were merged based upon identical start and stop positions to produce union junction tracks.
Genome_build: mm10
Supplementary_files_format_and_content: Junction bed files are in bed12 format, suitable for viewing in UCSC genome browser so the splice sites are thin and anchors are thick.
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| Submission date |
Aug 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Perry J Blackshear |
| E-mail(s) |
black009@niehs.nih.gov
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| Phone |
919-541-4926
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| Organization name |
NIEHS
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| Department |
LST
|
| Lab |
LST
|
| Street address |
111 T.W. alexander drive
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| City |
Research Triangle Park |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE60243 |
Tristetraprolin (TTP) regulated splenic transcriptome in "Triple KO" mice |
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| Relations |
| BioSample |
SAMN02979117 |
| SRA |
SRX672434 |
| 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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