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Sample GSM4104622

Query DataSets for GSM4104622

Status

Public on Aug 31, 2020

Title

Kidney_4

Sample type

SRA

Source name

kidney

Organism

Ailuropoda melanoleuca

Characteristics

Sex: female
age: 0.5
death_time: Died_in_20180308
tissue: kidney
Cause of death: coronavirus infection

Treatment protocol

Stored in liquid nitrogen

Growth protocol

Collection of samples from newly dead pandas

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted using an RNeasy Mini Kit (Qiagen, Hilden, Germany)
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

Total RNA was extracted using an RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer protocol. RNA degradation and contamination were monitored using 1% agarose gels.
A NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) was used to check the purity of RNA, and a Qubit® RNA Assay Kit was used on samples, which were measured using a Qubit® 2.0 Flurometer (Life Technologies, CA, USA) to measure the concentration of RNA.
RNA integrity was assessed using an RNA Nano 6000 Assay Kit for the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 μg RNA per sample was used as input material for sequencing.
Libraries were generated using an NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations; index codes were added to the attribute sequences of each sample.
Index-coded samples were then clustered on a cBot Cluster Generation System using a TruSeq PE Cluster Kit v3-cBot-HS (Illumina) in accordance with the manufacturer’s instructions.
After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 150 bp paired-end reads were generated
Fastq format raw data (raw reads) were processed firstly through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing sequence reads with adaptor or ploy-N sequences with an uncertain base ratio of more than 10%, or low quality reads (reads with Qphred < 20 bases accounting for more than 50% of total read length) from raw data.
Genome_build: ailMel1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

Submission date

Oct 02, 2019

Last update date

Aug 31, 2020

Contact name

Feng Li

E-mail(s)

lifeng17512@126.com

Organization name

Sichuan Agricultural University

Street address

No.211, Huimin Road, Wenjiang District