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| Status |
Public on Mar 17, 2020 |
| Title |
Lymphatic Untreated #2 |
| Sample type |
SRA |
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| Source name |
Lymphatic Untreated
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Lymphatic endothelial cells
treated with: none (untreated)
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA isolation was performed with RNeasy Mini Kit (QIAGEN).
RNA libraries were generated starting from 1 µg of total RNA. RNA quality was assessed by using a Tape Station instrument (Agilent). To avoid over-representation of 3’ends, only high-quality RNA with RNA Integrity Number (RIN) ≥ 8 was used.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
G1M2L
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| Data processing |
Fastq files were adapter-trimmed and quality-filtered with Trimmomatic.
High quality fastq files were aligned to the human genome by using STAR.
Gene read counts were calculated with featureCounts.
Differential gene expression was performed with DESeq2.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: gene counts, tabular
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| Submission date |
Feb 22, 2018 |
| Last update date |
Mar 20, 2020 |
| Contact name |
Luca Massimino |
| E-mail(s) |
admin@lucamassimino.com
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| Phone |
3389039500
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| Organization name |
Ospedale San Raffaele
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| Department |
Gastroenterology
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| Street address |
Via Olgettina, 58
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| City |
Milano |
| State/province |
MI |
| ZIP/Postal code |
20100 |
| Country |
Italy |
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| Platform ID |
GPL21290 |
| Series (1) |
| GSE110990 |
Activation of the VEGFC/VEGFR3 pathway induces cancer immune escape through tumor-associated lymphatic vessels and macrophages in colorectal cancer |
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| Relations |
| BioSample |
SAMN08580510 |
| SRA |
SRX3733578 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3019785_G1M2LReadsPerGene.out.tab.gz |
301.1 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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