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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 07, 2018 |
| Title |
3_683_Thalamus |
| Sample type |
SRA |
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| Source name |
Brain tissue
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| Organism |
Homo sapiens |
| Characteristics |
donor id: A
age: 64
brain region: Thalamus
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the QIAGEN miRNeasy kit.
RNA CaptureSeq was performed as per the protocol from Mercer, T.R. et al Nature Protocols 9, 989-1009 (2014), using the KAPA Stranded RNA-seq library prep kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Illumina base-calling
Adapters trimmed from reads using CutAdapt with Trim Galore wrapper script
Reads aligned to hg38 (plus ERCC sequences and in silico chromosome) using STAR v2.5.3a
Alignments assembled intro transcript models using Stringtie v1.3.3
Individual sample transcriptomes merged into consensus using Stringtie --merge
Genome_build: hg38
Supplementary_files_format_and_content: .gtf files provide assembled transcript coordinates and expression values (FPKM) for each sample
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| Submission date |
Aug 06, 2018 |
| Last update date |
Aug 07, 2018 |
| Contact name |
Simon Andrew Hardwick |
| E-mail(s) |
s.hardwick@garvan.org.au
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| Phone |
+61401264672
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| Organization name |
Garvan Institute of Medical Research
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| Lab |
Transcriptomic Research
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| Street address |
384 Victoria Street
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| City |
Darlinghurst |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE118158 |
Targeted, long-read RNA sequencing of non-coding genomic regions associated with neuropsychiatric functions. |
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| Relations |
| BioSample |
SAMN09768289 |
| SRA |
SRX4510469 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3319635_3_683_Thalamus.stringtie.out.gtf.gz |
9.6 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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