|
| Status |
Public on May 04, 2016 |
| Title |
WT rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
embryo
|
| Organism |
Mus musculus |
| Characteristics |
strain: 3H1 Balb
tissue: rostrum
Stage: E9 (18-22 somites)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rostrums dissected, homogenized in QIAzol Lysis Reagent from QIAgen Rnasy Plus Universal Kit. Samples purified for RNA. Remaining embryonic tissue used for genotyping.
30 ng from 3 biological replicates with RIN of at least 9 pooled for library construction. Standard protocols for sequencing with Ion Torrent were used
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
Ion Torrent Suite used to obtain FASTQ data
Single-end reads trimmed and filtered using PRINSEQ (Schmieder and Edwards 2011). Low quality sequences trimmed from ends until a bp of Phred quality score of at least 20 (at least 99% accurate) not found, and filtered out sequences having < 20 nt
UCSC mm10 reference genome indexed by Bowtie2 v2.2.5. Processed reads then aligned with ref genome using Tophat v2.0.14 (Kim et al., 2013).
Resulting .BAM files were then analyzed with Cufflinks v2.1.1 (Trapnell et al., 2010) to quantify transcript abundance as Reads Per Kilobase of exon model per Million mapped reads (RPKM)
SAMtools v0.1.18 (Li et al., 2009) used for sorting and BAM conversion. Htseq-count script (HTSeq package) used to count reads mapped to mouse gene models
Differential gene expression from count data identified using the non-parametric NOISeq-sim program (Tarazona et al., 2011) with default parameters. A trimmed mean of M-values normalization and estimated probablity of differential expression PNOI > 0.95 as a threshold.
Genome_build: mm10
Supplementary_files_format_and_content: counts, tab-delimited text files
|
| |
|
| Submission date |
Nov 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Keith S Fong |
| E-mail(s) |
ksfong@hawaii.edu
|
| Phone |
808 692-1421
|
| Organization name |
University of Hawai'i John A. Burns School of Medicine
|
| Department |
Anatomy, Biochemistry and Physiology
|
| Street address |
651 Ilalo Street; BSB 110
|
| City |
Honolulu |
| State/province |
HI |
| ZIP/Postal code |
96813 |
| Country |
USA |
| |
|
| Platform ID |
GPL18635 |
| Series (1) |
| GSE75001 |
Differential expression of RNAs in E9 tuft rostrums with NTDs |
|
| Relations |
| BioSample |
SAMN04267294 |
| SRA |
SRX1431780 |
