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Series GSE133000 Query DataSets for GSE133000
Status Public on Jun 20, 2019
Title RNA sequence of mRNA in HUVEC cells after depleting EGFL6
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Total RNA was isolated from each thymic sample using the standard TRIzol protocol (Invitrogen, Carlsbad, CA, USA). RNA quality was examined by gel electrophoresis and with a Nanodrop spectrophotometer (Thermo, Waltham, MA, USA). For RNA sequencing, RNA samples from 9 biological replicates were separated into three independent pools, each comprised of three distinct samples at equal amounts. Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA), and sequencing was carried out using the Illumina HiSeq X Ten instrument by the commercial service of Genergy Biotechnology Co. Ltd. (Shanghai, China). The raw data was delieved into NCBI’s Gene Expression Omnibius, and was handled by Perl and data quality was checked by FastQC v0.11.2. Clean reads were aligned to the chicken genome (release: Gallus gallus 4.0) from NCBI using Bowtie, with one mismatch allowed. As shown by previous study[2], the expression of the transcript was calculated by FPKM using Perl. Differentially expression transcripts (DETs) were determined using the MA-plot-based method with Random Sampling (MARS) model in the DEGseq package between different time points. The thresholds for determining DETs are P < 0.05 and absolute fold change ≥ 2. Then DETs were chosen for function and signaling pathway enrichment analysis using GO and KEGG database.
 
Overall design 3 samples of control group and 3 samples of knock-down group
 
Contributor(s) Tang C
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Submission date Jun 19, 2019
Last update date Jun 20, 2019
Contact name Chao-Tao Tang
E-mail(s) superwave_tang@163.com
Phone 18701867197
Organization name Renji hospital
Street address Shan Dong Middle road 145
City Shanghai
ZIP/Postal code 200003
Country China
 
Platforms (1)
GPL20795 HiSeq X Ten (Homo sapiens)
Samples (6)
GSM3897993 Hn_1_RNA-Seq
GSM3897994 Hn_2_RNA-Seq
GSM3897995 Hn_3_RNA-Seq
Relations
BioProject PRJNA549677
SRA SRP201878

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Supplementary file Size Download File type/resource
GSE133000_gene_exp_significant_addFPKM_with_symbol_GO_KEGG.xls.gz 273.9 Kb (ftp)(http) XLS
GSE133000_gene_exp_with_symbol.xls.gz 2.1 Mb (ftp)(http) XLS
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Raw data are available in SRA
Processed data are available on Series record

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