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| Status |
Public on Mar 29, 2013 |
| Title |
E15.5 TGFβ3-HT BioRep1 Lane005 |
| Sample type |
SRA |
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| Source name |
Palate
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Palatal shelves
age: Embryonic day 14.5
genotype: TGF-beta3 +/-
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| Extracted molecule |
total RNA |
| Extraction protocol |
Palates were removed from fetuses as duplicates at E14.5, E15.5, and E16,5 and stored in RNALater until extraction; and RNA was harvested from tissues using RNeasy Kit (Qiagen, CA) and evaluated the RNA for purity and concentration by NanoDrop (Wilmington, DE). RNA integrity numbers (RIN) were evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Libraries were prepared using the Illumina mRNA-Seq Sample Preparation Kit (San Diego, CA) according to the manufacturer’s instructions. Briefly, poly(A) + RNA was recovered from 1 µg of total RNA using two rounds of isolation with oligo-dT-coated Sera-Mag magnetic beads. The recovered poly (A) + RNA was then chemically fragmented. RNA fragments were converted to cDNA using SuperScript II and random primers. The second strands were synthesized using RNaseH and DNA Pol I. The ends of the cDNA were repaired using T4 DNA polymerase, T4 polynucleotide kinase, and Klenow DNA polymerase. A single adenosine was added to the 3’ end using Klenow fragment (3’ to 5’ exo minus). Adaptors were attached to both ends of the cDNA using T4 DNA ligase. RNA fragments were extracted from a 2% low range ultra agarose sizing gel. The fragments were amplified by 15 cycles of PCR using Phusion DNA polymerase. Libraries were validated with Agilent Bioanalyzer (Palo Alto, CA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
T2 G2
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| Data processing |
fastq quality control:fastQC v0.10.1
alignment: TopHat v1.4.1
transcriptome assembly, transcripts quantification and tests for differentially expression: Cufflinks v1.3.0
visualizing the output from Cufflinks: CummeRbund v1.2.0
Genome_build: mm9, NCBI build 37
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Mar 28, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
You Li |
| E-mail(s) |
you.li@unmc.edu
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| Organization name |
University of Nebraska Medical Center
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| Department |
Department of Genetics, Cell Biology and Anatomy
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| Lab |
Guda Lab
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| Street address |
Emile St
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| City |
OMAHA |
| State/province |
NE |
| ZIP/Postal code |
68198 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE45568 |
Systematic analysis of palatal transcriptome to identify cleft palate genes within TGFbeta3-knockout mice alleles: RNA-Seq analysis of TGFbeta3 Mice |
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| Relations |
| SRA |
SRX256678 |
| BioSample |
SAMN01993627 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1109836_sample_15-5-14_L005_genesfpkm_tracking.txt.gz |
711.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
| Raw data are available in SRA |
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