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Sample GSM4497331

Query DataSets for GSM4497331

Status

Public on Apr 27, 2020

Title

Brain, Ipsi21_1

Sample type

SRA

Source name

brain

Organism

Rattus norvegicus

Characteristics

strain: Sprague Dawley
tissue: brain
treatment: intracerebral hemorrhage
age: 21-month

Treatment protocol

Rats were anesthetized with isoflurane at 3.5% for induction and 1.5% in maintenance and then immobilized on the stereotaxic apparatus (RWD Life Science Co., Shenzhen, China) followed by drilling of a 1-mm diameter burr hole at the location of 0.2 mm anterior and 3.5 mm lateral to the bregma. We then injected a total of 75-μL autologous blood into the striatum after attached a Hamilton needle to the micropump (RWD Life Science Co.) at 5.5 mm ventral to the skull surface.

Growth protocol

Aging male Sprague Dawley rats (13- and 22-month old) were used for our experiments. These rats were obtained from Animal Center of Daping Hospital, the Army Medical University (the Third Military Medical University, Chongqing, China) and housed in specific pathogen free conditions. The rats were randomly enrolled in each experimental group. Protocols of our animal studies were approved by and conducted in accordance with the Animal Ethics Committee of the Army Medical University (Third Military Medical University, Chongqing, China).

Extracted molecule

polyA RNA

Extraction protocol

To construct an RNA-Seq library, we first isolated total cellular RNA from brain tissue samples using TRIzol reagent (Ambion, Austin, TX, USA) according to the manufacturer’s protocol and then treated them with RQ1 DNase (Promega, Madison, WI, USA) to remove contaminated DNA and quantified them by measuring the absorbance at 260 /280 nm with the Smartspec plus (BioRad, Hercules, CA, USA). The integrity of the RNA samples was further assessed using 1.5% agarose gel electrophoresis.
Ten μg of each total RNA sample was used to construct the RNA-seq library. Specifically, polyadenylated mRNA samples were isolated, purified, and concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen, Carlsbad, CA, USA) and fragmented at 95oC and ligated by the end repair and 5' adaptor. Next, these mRNA samples were reversely transcribed into cDNA using the RT primer harboring 3'-end adaptor sequences and randomized hexamer, which was purified and amplified using PCR, leading to 200-500 bp PCR products, which was purified, quantified and stored at -80oC before DNA sequencing.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

HiSeq X Ten

Description

expressed_gene_FPKM.txt
expressed_gene_reads.txt

Data processing

Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 16 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2, Qvalue <= 0.05.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: tab-delimited text files including gene FPKM values for each sample.

Submission date

Apr 24, 2020

Last update date

Apr 27, 2020

Contact name

dong chen

Organization name

ablife

Street address

GaoXin 2nd Road

City

wuhan