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Status |
Public on Sep 07, 2023 |
Title |
L31423_K562_endogenous_RNA_IFNA_replicate3 |
Sample type |
SRA |
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Source name |
K562
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Organism |
Homo sapiens |
Characteristics |
cell line: K562 cell type: Lymphoblast cells genotype: wildtype treatment: IFNA
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Treatment protocol |
In this data set, 6 replicate flasks of K562 cells were treated for 6 hours with each of the following treatments: dexamethasone (1 uM), IFNA2b (2,000U/ml), or vehicle control (media). Cells were then collected for mRNA-Seq to assess the endogenous gene expression response of K562 cells to treatment.
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Growth protocol |
We made 18 replicate T75 flasks, each containing 12 million K562s. 42 hours later, K562s were stimulated with treatment, and cells were collected 6 hours post-treatment.
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Extracted molecule |
polyA RNA |
Extraction protocol |
We extracted RNA from the separately aliquoted cells using the Qiagen RNEasy kit. We prepared RNA-Seq libraries using the NEBNext Ultra II RNA Library Prep Kit for Illumina.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
L31423
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Data processing |
Reads were trimmed with Trim Galore (Trim Galore version 0.6.4_dev; Cutadapt version 2.3) to remove basepairs with a Phred score less than 20, and end sequences that matched at least two basepairs of the adapter sequence. Only trimmed reads longer than 25 basepairs were retained. We used the STAR package (version 2.5.0) (Dobin et al., 2013) two-pass mapping to map the filtered reads to the hg38 genome. We retained uniquely mapped reads by filtering the output SAM file to keep reads with MAPQ = 255. We then used htseq (version 0.6.0) (Anders et al., 2014) to quantify read counts per gene. We only retained genes that had TPM > 3 in at least 3 of 6 samples in at least one of the three conditions (baseline, IFNA, or dex). Only protein-coding genes were retained for final analysis, resulting in a total of 10,676 testable genes. Assembly: hg38 Supplementary files format and content: Tab delimited text file with data matrix of raw read counts mapping to a gene, where each row represents a gene, and each column represents a biological replicate (i.e., library). Only protein-coding genes that had transcripts per million > 3 in at least 3 of 6 samples in at least 1 of the 3 conditions (baseline, IFNA, or dex) are included.
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Submission date |
Jan 11, 2023 |
Last update date |
Sep 07, 2023 |
Contact name |
Rachel A Johnston |
E-mail(s) |
racheljohnston7@gmail.com
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Organization name |
Duke University
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Department |
Evolutionary Anthropology
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Lab |
Jenny Tung
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Street address |
130 Science Dr, Rm 108 Biological Sciences
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City |
Durham |
State/province |
NC |
ZIP/Postal code |
27708 |
Country |
USA |
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Platform ID |
GPL24676 |
Series (1) |
GSE222643 |
DNA methylation-environment interactions in the human genome |
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Relations |
BioSample |
SAMN32677786 |
SRA |
SRX19003515 |
Supplementary data files not provided |
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Raw data are available in SRA |
Processed data are available on Series record |
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