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Status |
Public on Mar 18, 2014 |
Title |
Pancreas mmPCR-Seq R1 |
Sample type |
SRA |
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Source name |
Pancreas
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Organism |
Homo sapiens |
Characteristics |
tissue: Pancreas
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Extracted molecule |
total RNA |
Extraction protocol |
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. mmPCR-Seq libraries were prepared as previously described in Zhang R, et al. (Nature Methods 2013)
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Library strategy |
OTHER |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina MiSeq |
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Description |
library strategy: mmPCR-Seq
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Data processing |
Aligned samples to reference genome (hg19) with STAR (v2.1.4) Sorted aligned files (.sam) using Samtools (v0.1.18) Performed variant calling using Samtools mpileup command Calculated allelic ratio for each genomic loci by dividing the number of reads mapped to the non-ref allele divided by the total reads per site Genome_build: hg19 Supplementary_files_format_and_content: Allelic read counts for each genomic loci and corresponding gene tested by mmPCR-Seq
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Submission date |
Oct 28, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Stephen Montgomery |
E-mail(s) |
smontgom@stanford.edu
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Organization name |
Stanford University
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Street address |
300 Pasteur Lane
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City |
Stanford |
ZIP/Postal code |
94305 |
Country |
USA |
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Platform ID |
GPL15520 |
Series (1) |
GSE51769 |
Allele-specific expression of multiple tissues |
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Relations |
BioSample |
SAMN02384962 |
SRA |
SRX368965 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1252250_index9.R1.ase.txt.gz |
25.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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