GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM4075463

Query DataSets for GSM4075463

Status

Public on Jan 11, 2020

Title

Spinal cord, BCP rep1

Sample type

SRA

Source name

Spinal cord, Bone cancer pain (BCP)

Organism

Rattus norvegicus

Characteristics

strain: Wistar
tissue: spinal cord
treatment: breast cancer cells were implanted into medullary cavity of left tibia
time: 14 days after tumor inoculation of treated samples
condition: BCP

Treatment protocol

Approximately (1-5) ×10e5 living or heat-killed Walker 256 breast cancer cells were implanted into medullary cavity of left tibia

Extracted molecule

total RNA

Extraction protocol

The lumbar enlargement spinal cord was quickly isolated out, removed the meninges, and dissected longitudinally on ice; then the ipsilateral spinal cord was snap-frozen and preserved in liquid nitrogen. Total RNA was extracted using RNeasy Mini Kit (Cat#74106, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
Strand specific libraries were prepared using the TruSeq® Stranded Total RNA Sample Preparation kit (Illumina, USA). Briefly, ribosomal RNA was removed from total RNA by Ribo-Zero rRNA removal beads. Then fragmented RNA was copied into first strand cDNA using reverse transcriptase, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. After undergoing an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters, cDNA fragments were purified and enriched with PCR to create the final cDNA library.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

HiSeq X Ten

Description

Data processing

Sequencing raw reads were preprocessed by filtering out rRNA reads,sequencing adapters,short-fragments and other low-quality reads by Seqtk (https://github.com/lh3/seqtk)
Obtained clean reads were mapped to the rat Rnor_6.0 reference genome using Hisat2 (version:2.0.4)
Stringtie (version:1.3.0) was used to calculate Fragments Per Kilobase of exon model per Million mapped reads (FPKM) with a reference annotation.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: FPKMs, counts

Submission date

Sep 12, 2019

Last update date

Jan 11, 2020

Contact name

Xinran Hou

E-mail(s)

doctorhxr@csu.edu.cn

Organization name

Central South University

Street address

Xiangya Road 87