|
| Status |
Public on Jun 30, 2022 |
| Title |
Differentiated HL-60 neutrophil-like cells processed by capsaicin for 8 hours rep-3 |
| Sample type |
SRA |
| |
|
| Source name |
human leukemic cell line (HL-60)
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: 400uM capsaicin for 8 hours
|
| Treatment protocol |
Capsaicin (Sigma-Aldrich) was solved in DMSO until the final concentration reached 400uM and then added into the medium
|
| Growth protocol |
Differentiated HL-60 neutrophil-like cells (dHL-60) sourced from the human leukemic cell line (HL-60) (ATCC CCL-240) after the stimulation with the percent of 1.2% dimethyl sulfoxide (DMSO) in medium for 5 days. dHL-60 were maintained in the RPMI 1640 medium containing 1% penicillin and streptomycin (P/S) and 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total cell RNA was extracted using Trizol (Ambion, USA), every 5*10^6 cells for 1ml Trizol. Then add one-fifth of the total volume of chloroform, shake vigorously for 15 seconds, stand at room temperature for 3 minutes, and rotate at 12000 rpm for 15 minutes at 4°C. Then the upper water phase was transferred to a new centrifuge tube with equal volume of isopropyl alcohol and bottom-up to mix, and incubate at room temperature for 10 minutes. Centrifuged at 12000 rpm for 10 minutes at 4℃. Discard the up and added 1ml 75% alcohol diluted with RNase free water. RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the Nanophotometer ® spectrophotometer (IMPLEN, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer’s recommendations and index codes were added to the attribute sequences for each sample
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The image data of the sequencing fragments measured by the high-throughput sequencer were converted into sequence data (reads) by Illumina Casava 1.8 base recognition.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Assembly: human NCBI genome build 36
Supplementary files format and content: xls file with raw gene counts for every gene and every sample
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| |
|
| Submission date |
Mar 10, 2022 |
| Last update date |
Jun 30, 2022 |
| Contact name |
Kexin Chen |
| E-mail(s) |
[email protected]
|
| Phone |
86-13896212948
|
| Organization name |
West China hospital
|
| Department |
Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
|
| Lab |
Lab of Inflammatory bowel disease, Frontiers Science Center for Disease-Related Molecular Network
|
| Street address |
No.37 guoxue Lane, Wuhou District, Chengdu city
|
| City |
Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
610044 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE198304 |
Next Generation Sequencing Facilitates Quantitative Analysis Transcriptomes of dHL-60 cells after capsaicin processed |
|
| Relations |
| BioSample |
SAMN26559640 |
| SRA |
SRX14427410 |
