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| Status |
Public on Apr 08, 2010 |
| Title |
Brain MAQC Human s_3_1 |
| Sample type |
SRA |
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| Source name |
Human brain tissue
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| Organism |
Homo sapiens |
| Characteristics |
tissue: mixed human brain
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| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA is purified from total RNA with oligo-dT magnetic beads. cDNA is synthesized with random primer priming. ds-cDNA is sequenced using Illumina Genome Analyzers as recommended by the manufacturer.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
RNA_Seq.
Brain MAQC Human s_x_y:
In the sequencing experiment, there are 8 lanes in one run. The data uploaded to GEO were from three lanes of one run. That is, x=3,6 or 8 are the indexes of the lanes, which do not have any biological significance. y=1 or 2 represents the paired data. In a pair of data, y=1 represents the reads on 5' end while y=2 represents the ones on 3' end.
The average insert size is about 200bp. But we do not have any estimate of standard deviation.
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| Data processing |
The processed files are the mapping results of the reads on human genome(hg18) by SeqMap. Up to 2 mismatches are allowed.
Contents of processed data files (fastq.out):
The first column is the combination of the data file name and the read index, which are separated by dash.
The second column is the sequence of the raw data.
The third column is the numbers of the mapping hits that allow no mismatch, 1 mismatch and 2 mismatch, respectively.
The forth column are the mapping hits that describe the chromosomal positions.
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| Submission date |
Nov 24, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Kin Fai Au |
| Organization name |
Stanford University
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| Department |
Statistics
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| Lab |
Wong Lab
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| Street address |
390 Serra Mall, Stanford University
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305-4065 |
| Country |
USA |
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| Platform ID |
GPL9052 |
| Series (1) |
| GSE19166 |
Next generation sequencing of human brain tissues transcriptome |
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| Relations |
| SRA |
SRX018974 |
| BioSample |
SAMN00011078 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM475204_brain_s_3_1_sequence.fastq.out.txt.gz |
256.7 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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