 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 29, 2015 |
| Title |
MLM-P9A |
| Sample type |
SRA |
| |
|
| Source name |
P9_ocular lens_miRNA-seq
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
developmental stage: Postnatal day 9
tissue: Ocular Lens
|
| Extracted molecule |
total RNA |
| Extraction protocol |
To obtain the lenses, mice were first anesthetized by isoflurane and subsequently euthanized through cervical dislocation. The lenses were isolated using forceps under a microscope. Two biological replicates, each consisting of 8-9 pups, were used for each developmental stage. Lenses were dissolved immediately in the Trizol reagent (Invitrogen; Carlsbad, CA) and total RNA was extracted.
Illumina TruSeq RNA Sample Preparation Kit v2 and TruSeq Small RNA Sample Prep Kit was used to prepare mRNA and small RNA sequencing libraries
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.8 used for basecalling and de-indexing.
The analysis included preprocessing of FASTQ file format sequencing reads by removing the adapter sequences using SeqPrep (https://github.com/jstjohn/SeqPrep).
The preprocessed sequencing reads were aligned against the Mus musculus (GRCm38/mm10) transcriptome using default parameters
Subsequently, duplicates reads caused by PCR amplification were removed using the rmdup option of SAMtools (version 0.1.18)
The expression data were normalized by calculating the reads per kilobase per million mapped reads (RPKM) values for each gene (Mortazavi et al., Nat Methods, 2008)
Small RNA sequencing reads were aligned against the Mus musculus (GRCm38/mm10) reference genome with the mapper module of miRDeep2 that uses Bowtie (version 0.12.8)
Reported microRNAs were identified by miRDeep2 through reported miRNA hairpins and mature miRNA sequences downloaded from the miRBase (Release 20) database
Genome_build: mm10
Supplementary_files_format_and_content: xlsx files include RPKM and RPM values for mRNA and microRNA data, respectively.
|
| |
|
| Submission date |
May 26, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
S. Amer Riazuddin |
| E-mail(s) |
OMGenetics@jhmi.edu
|
| Phone |
410-955-3656
|
| Organization name |
Johns Hopkins University School of Medicine
|
| Street address |
600 N. Wolfe St
|
| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21287 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE69221 |
Transcriptome Profiling of Developing Murine Lens through RNA Sequencing |
|
| Relations |
| BioSample |
SAMN03734505 |
| SRA |
SRX1038175 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1695574_MLM-P9A.xlsx |
50.9 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
