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Sample GSM2210918 Query DataSets for GSM2210918
Status Public on Jun 22, 2017
Title 53-1cm
Sample type SRA
Source name breast fibroblasts_adjacent normal 1 cm
Organism Homo sapiens
Characteristics cell type: fibroblasts
tissue: breast
culture protocol: primary culture Passage 2
tumor status: adjacent normal tissue
patient id: 53
Growth protocol Primary culture according to Stampfer, 1985 PMID: 3857588. Grown in DMEM 10%FBS. Passage 2 cells
Extracted molecule total RNA
Extraction protocol Qiagen RNAEasy kit
DNaseI treatment, Thermo Fisher Ribo Minus, Ion Total RNASeq Library Kit v2
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
Data processing BaseCalling with IonTorrent BaseCaller version 5.0.13
Aligned with IonTorrent tmap version 5.0.13
Aligned with STAR version 2.5.1b
Feature Counts generated with htseq-count 0.61p1, options -f bam --stranded=no -m union
Normalization and pairwise differential expression analysis using R 3.2.2, edgeR 3.12.0 and DESeq 1.22.0
Genome_build: Human GRCh37 PII d5
Supplementary_files_format_and_content: csv table of feature counts per gene per sample
Submission date Jun 22, 2016
Last update date May 15, 2019
Contact name Kristina Antonia Trujillo
Phone 575-644-1361
Organization name University of New Mexico
Department Cell Biology and Physiology
Lab Trujillo
Street address 915 Camino de Salud NE
City Albuquerque
State/province New Mexico
ZIP/Postal code 87131
Country USA
Platform ID GPL17303
Series (1)
GSE83611 Field cancerized fibroblasts in primary culture, P2
BioSample SAMN05281865
SRA SRX1870057

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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