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| Status |
Public on May 29, 2019 |
| Title |
Human PH7 rep2 |
| Sample type |
SRA |
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| Source name |
231 cell line
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| Organism |
Homo sapiens |
| Characteristics |
exposure length: 48 hours in pH7.4 medium
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| Treatment protocol |
Upon 48 hours of exposure to pH7.4 or pH6.4 cells were harvested for RNA extraction.
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| Growth protocol |
Cells at passage 4 were plated at 70% confluency in either pH6.4 medium or pH7.4 medium for 48 hours.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from cell lines was extracted using RNeasy Plus Mini Kit (Qiagen), following manufacturer instruction
KAPA Hyper Prep Kit (Kapa Biosystems) was used for library preparation. Short read sequencing was performed on NextSeq500 platform using 75bp paired-end method and Nextseq150nt kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
D17-159031
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| Data processing |
Base-calling was performed using Illumina's NextSeq control software RTA
Quality control:QC was carried out by MIT BMC/BCC in house pipeline including sequencing error rate estimation, sequencing reads complexity estimation, fastqc report, sample contamination estimation, intergenic reads percentile calculation, intronic reads percentile calculation, UTR reads percentile calculation, gene coding reads percentile calculation, and rRNA contamination estimation. Besides, sense to antisense reads ratio was calculated to indicate strand specificity. Hierarchical clustering and heatmap creation were carried out by TIBCO Spotfire 7.6.1.17 basing on log2(fpkm+1) values of the expressed coding genes to observe sample relationship and to detect outliers.
RNA-Seq mapping: against GRCm38/mm10 reference for mouse sequences and GRCh38/hg38 reference for human sequences using STAR/2.5.3
Gene expression was quantitated using RSEM v. 1.3.0
Exon level qualitfication was performed by DEXSeq v.1.22.0
Genome_build: GRCm38/mm10, GRCh38/hg38
Supplementary_files_format_and_content: txt file with, for each gene and each sample (from RSEM);for each exon and each sample (from DEXSeq)
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| Submission date |
Sep 07, 2018 |
| Last update date |
May 19, 2023 |
| Contact name |
Dunaduan Ma |
| E-mail(s) |
maduanduan8@gmail.com
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| Organization name |
MIT
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| Department |
Koch Institute
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| Lab |
Bioinformatics Core
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| Street address |
77 Massachusetts Ave
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| City |
Cambridge |
| State/province |
Ma |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE119646 |
Acidification of tumor: stromal boundaries drive transcriptome alterations associated with aggressive phenotypes |
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| Relations |
| BioSample |
SAMN09990280 |
| SRA |
SRX4655779 |
| 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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