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| Status |
Public on Feb 04, 2016 |
| Title |
C57.2 |
| Sample type |
SRA |
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| Source name |
C57Bl/6 mouse lens
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| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
genotype: wild type
tissue: Lens
age: E13.5
lenses per replicate: 30
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from pooled samples of 30 mouse lenses using the SV total RNA isolation System (Promega, Madison, WI) acording to the manufacturers recommended protocol.
cDNA libraries were constructed from total RNA by were used to purifying mRNA from the total RNA samples using poly-T oligo attached magnetic beads and converted to a library of template molecules for cluster generation and DNA sequencing using the Illumina® TruSeq™ RNA Sample Preparation Kit v2. Sequencing performed on a Illumina HiSeq 2500 using single-end 51bp sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
30 C57Bl/6 E13.5 Biological replicate 2
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| Data processing |
Reads were trimmed using CLC Genomics Workbench 5.5.1with the following parameters: Max ambiguous bases:0; Minimum Q>0.01; minimum length 35bp
Reads were aligned to the Mus musculus genome using CLC Genomics Workbench 5.5.1
Unique gene counts were determined using CLC Genomics Workbench 5.5.1
Counts were normalized (CPM and RPKM) using R BioConductor EdgeR
Genome_build: Mus musculus GRCm38.77
Supplementary_files_format_and_content: tab-delimited: mgc gene symbol, ensembl gene ID, MGID, ensembl gene description, cpm, rpkm, raw count
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| Submission date |
Jun 17, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Melinda K. Duncan |
| E-mail(s) |
duncanm@udel.edu
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| Phone |
3028310533
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| Organization name |
University of Delaware
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| Department |
Biological Sciences
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| Lab |
Vertebrate Development
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| Street address |
327 Wolf Hall
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| City |
Newark |
| State/province |
DE |
| ZIP/Postal code |
19716 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE69940 |
Genome-wide analysis of embryonic gene epression in the absence of Prox1 compared to wild type |
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| Relations |
| BioSample |
SAMN03777443 |
| SRA |
SRX1060439 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1713507_C57-2.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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