|
| Status |
Public on Feb 01, 2017 |
| Title |
SM Dev rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Developed Somites at Forelimb Bud Level
|
| Organism |
Homo sapiens |
| Characteristics |
developmental stage: 4.5-5 weeks embryo
cell type: Developed Somites at Forelimb Bud Level
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Different mesoderm tissues were micro-dissected and RNA was extracted using the QIAGEN RNeasy Plus Micro Kit. 10-100 ng of total RNA was used for the sequencing library construction.
The Nugen Ovation RNA-Seq System V2 kit was used to make and amplify cDNA, and the sequencing libraries were constructed followed the standard operation procedures at the UCLA Clinical Microarray Core Facility.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
HiSeq Control Software v2.0 was used for basecalling on an Illumina HiSeq 3000 sequencer
Raw sequencing reads were processed using the packages available through the UCLA Galaxy resources (galaxy.hoffman2.idre.ucla.edu). Low quality bases found in the raw FASTQ files were removed by FASTQ Trimmer (v1.0.0) to ensure high quality base reads examined by FastQC (v0.4). The trimmed reads were mapped to the hg19 reference genome via Tophat for Illumina (v1.3.3) using default settings.
Gene expression values (Fragments Per Kilobase exons per Million mapped reads; FPKM) were obtained through Cufflinks (v2.0.2) using the iGenomes UCSC hg19 gene annotation and the mapped reads generated from Tophat, with default settings in Galaxy.
Differentially expressed gene (DEG) analysis was performed through Cuffdiff (v2.0.2) using the iGenomes UCSC hg19 gene annotation and the mapped reads generated from Tophat. Galaxy default settings were applied for Cuffdiff except that Bias Correction was performed using the hg19 reference genome.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample in Cufflinks files. Cuffdiff files also contained fold change and statistics comparing different sample groups (replicates of the same mesoderm type).
|
| |
|
| Submission date |
Dec 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Haibin Xi |
| Organization name |
UCLA
|
| Department |
MIMG
|
| Lab |
April Pyle
|
| Street address |
615 Charles E Young Dr South, BSRB 257
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE90876 |
Transcriptomic Profiling of Developing Human Paraxial Mesoderm from 4.5-5 Weeks of Gestation Human Embryos |
|
| Relations |
| BioSample |
SAMN06111353 |
| SRA |
SRX2396106 |
