Gene Expression Nebulas
A data portal of transcriptomic profiles across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species

PRJNA327871: Transcriptome profiling of ER+ breast cancer primary tumor and its tumorsphere derivative

Source: NCBI / GSE084054
Submission Date: Jul 05 2016
Release Date: Sep 24 2017
Update Date: May 15 2019

Summary: We profiled RNA expression in the ER+ primary tumor and the matching tumorspheres. The objective was to find genes differentially expressed between the tumorspheres and bulk tumor.

Overall Design: 12 pairs of matching ER+ bulk tumor and its tumorspheres

GEN Datasets:
GEND000024
Strategy:
Species:
Tissue:
Healthy Condition:
Cell Type:
Protocol
Growth Protocol: Surgical samples were collected from consenting breast cancer patients at Tan Tock Seng Hospital (Singapore) according to human subject research protocols approved by the Ethics Committee. Samples were washed with cold PBS with antibiotics three times, chopped with a sterile blade, and incubated by using MACS Tissue Dissociation Kits (Miltenyi Biotec) according to protocol. The resulting cell suspension were passed through 70 μm (BD Falcon, San Jose, CA, USA) and centrifuged at 800 rpm for 5 min at 4°C. cell were seeded in Single-cell suspensions (10,000 cell/well) were plated in 6-well ultra-low attachment plates (Corning) in DMEM/F12 medium containing 1X B27 (Invitrogen, cat. 12587-010), 50 ng/ml EGF, and 20 ng/ml βFGF for up to 1 months.
Treatment Protocol: -
Extract Protocol: Snap frozen human breast cancer tissues were disrupted using TissueLyser II (Qiagen). Total RNA including small RNAs from both human breast cancer tissue as well as the cell lines were isolated using miRNeasy Mini Kit (Qiagen, cat. 217004) according manual. In brief, c.a. 50 ng of total RNAs or 200 tumor cell were first lysed in reverse transcription buffer and the reaction is initiated with oligodT containing primer. Complete first strand synthesis is followed by template switching and the incorporation of SMARTer oligonucleotide. Full-length cDNAs are amplified using PCR to obtain DNA. Fragmentation and adapter introduction was performed using acoustic shearing to approximately 200 to 500 bp length and NEBNext® DNA Library Prep kit incorporating multiplex index primers. A pooled multiplexed library consisting equal amount of 6 individual libraries were sequenced on The HiSeq 2500 System by core facility.
Library Construction Protocol: RNA-seq libraries were generated by using the cDNA amplification kit SMARTer® Ultra™ Low RNA Kit (Cat. No. 634935, Clontech Laboratories, Inc. Mountain View, USA) for small amount of RNA or less than 200 cell according to manufacturer's manual followed by DNA library construction using the NEBNext® DNA Library Prep Master Mix Set for Illumina® kit (Cat. No. E6040S, New England Biolabs).
Sequencing
Molecule Type: poly(A)+ RNA
Library Source:
Library Layout: PAIRED
Library Strand: -
Platform: ILLUMINA
Instrument Model: Illumina HiSeq 2500
Strand-Specific: Unspecific
Publications
Chromosome 1q21.3 amplification is a trackable biomarker and actionable target for breast cancer recurrence.
Nature medicine . 2017-09-25 [PMID: 28967919]
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
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Assessing Quality:
Analysis:
Data Resource GEN Sample ID GEN Dataset ID Project ID BioProject ID Sample ID Sample Name BioSample ID Sample Accession Experiment Accession Release Date Submission Date Update Date Species Race Ethnicity Age Age Unit Gender Source Name Tissue Cell Type Cell Subtype Cell Line Disease Disease State Development Stage Mutation Phenotype Case Detail Control Detail Growth Protocol Treatment Protocol Extract Protocol Library Construction Protocol Molecule Type Library Layout Strand-Specific Library Strand Spike-In Strategy Platform Instrument Model Cell Number Reads Number Gbases AvgSpotLen1 AvgSpotLen2 Uniq Mapping Rate Multiple Mapping Rate Coverage Rate