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| Status |
Public on Nov 28, 2024 |
| Title |
DMSO_1_S37 |
| Sample type |
SRA |
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| Source name |
RPE-1
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| Organism |
Homo sapiens |
| Characteristics |
cell line: RPE-1
treatment: DMSO
time: 4hrs
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNAeasy mini columns (from QIAGEN) following vendor instructions
RNA libraries were prepared for sequencing using standard Illumina protocols
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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 |
Raw sequencing reads (in a FASTQ format) were trimmed of residual adaptor sequences using Scythe software. Low quality bases at the beginning or the end of sequencing reads were removed using sickle then the quality of remaining reads was confirmed with FastQC.
Reads were aligned to hg38 with STAR software then raw counts were computed with featureCounts for each gene in each sample.
Read-count normalization and differentially expressed analyses were performed using the edgeR package from Bioconductor.
Ingenuity Pathway Analysis (IPA, QIAGEN, Redwood City CA) was used to identify and interactively explore significantly altered pathways, functional sets and gene networks, enriched among the set of DE genes.
Assembly: GRCh38 (hg38)
Supplementary files format and content: rawCounts.txt: tab delimited text file with raw counts per gene per sample
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| Submission date |
Aug 20, 2024 |
| Last update date |
Nov 28, 2024 |
| Contact name |
Jonathan Wren |
| E-mail(s) |
[email protected]
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| Phone |
(405) 271-6989
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| Organization name |
OMRF
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| Department |
Genes & Human Disease Research Program
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| Street address |
825 N.E. 13th Street
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| City |
Oklahoma City |
| State/province |
OK |
| ZIP/Postal code |
73104 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE275316 |
SULFORAPHANE ACUTELY ACTIVATES MULTIPLE STARVATION RESPONSE PATHWAYS |
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| Relations |
| BioSample |
SAMN43275103 |
| SRA |
SRX25776234 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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