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| Status |
Public on Mar 02, 2019 |
| Title |
KD2 |
| Sample type |
SRA |
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| Source name |
Kidney cell line
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| Organism |
Homo sapiens |
| Characteristics |
genotype/variation: Eoxc5 knockdown
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA samples were isolated from independent experiments performed in triplicate using Qiagen RNAeasy Mini Kit.
RNA libraries were prepared for sequencing using standard HiSeq/MiSeq Illumina platform for the RNA sequencing
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Downstream bioinformatics analyses was performed by using a combination of programs including Bowtie2, Tophat2, HTseq and Cufflink .
Reference genome and gene model annotation files were acquired from NCBI/UCSC/Ensemble genome browser.
Indexes of the reference genome were built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
Gene expression level quantification was done using HTSeq v0.6.1 and for each gene read numbers counts were mapped, whereas, Reads Per Kilobase of exon model (RPKM) of each gene was calculated based on the length of the gene and expression levels were analyzed
DESeq2 R package (2_1.6.3) database was used for the differential expression (DE) analyses. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach and adjusted P-value <0.05 found by DESeq2 were assigned as DE. Analyses of DE of two conditions was performed using the DEGSeq R package (1.12.0). The P-values were also adjusted using Benjamini & Hochberg method. Corrected P-value of 0.005 and log2 (Fold change) of 1 were set as threshold for significantly differential expression.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
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| Submission date |
Mar 01, 2019 |
| Last update date |
Mar 03, 2019 |
| Contact name |
Deepak Nihalani |
| E-mail(s) |
nihalani@musc.edu
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| Organization name |
Medical University of South Carolina
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| Department |
Medicine
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| Lab |
Deepak Nihalani
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| Street address |
70 President street
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| City |
Charleston |
| State/province |
SC |
| ZIP/Postal code |
29407 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE127736 |
Disruption of the exocyst induces podocyte loss and dysfunction |
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| Relations |
| BioSample |
SAMN11042274 |
| SRA |
SRX5453225 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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