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Sample GSM2416867 Query DataSets for GSM2416867
Status Public on Feb 01, 2017
Title SM rep1
Sample type SRA
Source name Nascent Somites
Organism Homo sapiens
Characteristics developmental stage: 4.5-5 weeks embryo
cell type: Nascent Somites
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 ( 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
BioSample SAMN06111350
SRA SRX2396104

Supplementary file Size Download File type/resource
GSM2416867_Cufflinks_SM_R1_ID306.txt.gz 790.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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