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Sample GSM3678632

Query DataSets for GSM3678632

Status

Public on Jan 30, 2020

Title

CHB6: 5 Premotor (BA6)

Sample type

SRA

Source name

5 Premotor (BA6)

Organism

Pan troglodytes

Characteristics

individual: cb
brain region: 5 Premotor (BA6)

Extracted molecule

polyA RNA

Extraction protocol

Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, California).
Sequencing libraries were prepared with TruSeq RNA Sample Preparation Kit (Illumina) according to manufacturer’s instruction. Briefly, poly-T oligo-attached magnetic beads were used to isolate long polyadenylated RNA from 1 μg of total RNA. After fragmentation, first-strand cDNA was reverse transcribed with random hexamer-primers, followed by second-strand cDNA synthesis, end repair, adenylation of 3′ ends, and ligation of the adapters. Fragments were then enriched by PCR.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

Data processing

Read trimming: trimmomatic-0.36 PE -phred33 ILLUMINACLIP:all.fa:2:30:10:2:true SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:20
Read alignment: hisat2 --no-softclip --max-intronlen 1000000 -k 20 –no-unal -q
abundance (TPM) estimation: stringtie -e -A -G -b; TPM outputed by -A option was used as expression estimates and provided in processed data files
Genome_build: Ensemble genomes and annotation were used for all species: GRCh38.91, Pan_tro_3.0.91, panpan1.1.91, Mmul_8.0.1
Supplementary_files_format_and_content: csv files with TPM for all samples

Submission date

Mar 19, 2019

Last update date

Jan 30, 2020

Contact name

Pavel Mazin

Organization name

Skolkovo Institute of Science and Technology

Department

Biomed

Street address

Skolkovo Innovation Center, Building 3