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| Status |
Public on Jan 17, 2021 |
| Title |
Tumor-MDSC |
| Sample type |
SRA |
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| Source name |
myeloid cell
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| Organism |
Mus musculus |
| Characteristics |
cell type: myeloid cell
strain: NOD-SCID-IL2Rg-/-
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from cell pellets using TRIzol™ Reagent (Invitrogen), and RNA quality was determined using the Bioanalyzer 2100 (Agilent). 23S and 16S rRNAs were depleted using a MicrobExpress kit (Ambion). Genomic DNA was removed with two digestions using amplification-grade DNase 1 (Invitrogen). The processed RNA was sheared and reverse transcribed using random primers to obtain cDNA, which was used for library construction
RNase H was used to remove the rRNA, DNase I was used to digest double-stranded and single-stranded DNA in total RNA. Purified RNA from previous steps was fragmented into small pieces with fragment buffer at appropriate temperature. Then, First-strand cDNA was generated in First Strand Master Mix by PCR, and the second-strand cDNA was generated as well. The reaction product was purified by magnetic beads, afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments were amplified with adapters by PCR, and the products was purified by Ampure XP Beads. Library was validating on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR product from previous step was heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29(Thermo Fisher Scientific, MA, USA) to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGISEQ500 platform (BGI-Shenzhen, China).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| Data processing |
DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and single-end read of 50 bp were read through on the BGISEQ-500 platform for the following data analysis study. For this step, the BGISEQ-500 platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.
All the generated raw sequencing reads were filtered to remove reads with adaptors, reads in which unknown bases are more than 10%, and low quality reads. Clean reads were then obtained and stored as FASTQ format. HISAT was used to map clean reads to genome of PDL-0 (HISAT parameters for PE reads: HISAT was used to map clean reads to reference genome (-p 8 --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000).
Gene expression levels were quantified by the software package RSEM. The DEGseq method was used to screen differentially expressed genes between groups (cutoff criteria: fold change absolute value of log2-Ratio ≥1 and a false discovery rate (FDR) ≤ 0.001).
Genome_build: NCBI_GRCh38.p11
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample; tab-delimited text files include RPKM values for each Sample
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| Submission date |
Sep 05, 2019 |
| Last update date |
Jan 19, 2021 |
| Contact name |
Shouheng Lin |
| E-mail(s) |
[email protected]
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| Organization name |
Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences
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| Street address |
190 Kaiyuan Avenue, Science Park, Guangzhou
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| City |
Guagzhou |
| ZIP/Postal code |
510530 |
| Country |
China |
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| Platform ID |
GPL23479 |
| Series (1) |
| GSE136949 |
Myeloid-derived suppressor cells promote lung cancer metastasis |
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| Relations |
| BioSample |
SAMN12700606 |
| SRA |
SRX6806519 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4063565_Tumor-MDSC.gene.rpkm.txt.gz |
340.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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