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| Status |
Public on Jan 30, 2020 |
| Title |
CHD39: 26 Internal Capsule |
| Sample type |
SRA |
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| Source name |
26 Internal Capsule
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| Organism |
Pan troglodytes |
| Characteristics |
individual: cd
brain region: 26 Internal Capsule
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| 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
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| Submission date |
Mar 19, 2019 |
| Last update date |
Jan 30, 2020 |
| Contact name |
Pavel Mazin |
| Organization name |
Skolkovo Institute of Science and Technology
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| Department |
Biomed
|
| Street address |
Skolkovo Innovation Center, Building 3
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| City |
Moscow |
| ZIP/Postal code |
143026 |
| Country |
Russia |
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| Platform ID |
GPL23423 |
| Series (1) |
| GSE127898 |
Transcriptome map of the human brain at the single-cell resolution |
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| Relations |
| BioSample |
SAMN11166056 |
| SRA |
SRX5541657 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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