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| Status |
Public on Nov 08, 2013 |
| Title |
UFK467_RNAseq |
| Sample type |
SRA |
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| Source name |
pancreatic islets
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| Organism |
Homo sapiens |
| Characteristics |
tissue: pancreatic islets
Sex: M
age: 16
purity: 70
viability: 93
rin: 8.5
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| Growth protocol |
Fresh human pancreatic islets were obtained from the Islet Cell Resource (ICR) and National Disease Research Interchange (NDRI). Upon receipt, islets were warmed to 37 C in CMRL shipping medium for 1-2 hours. After equilibration, islets were washed with calcium- and magnesium-free Dulbecco's phosphate-buffered saline (Invitrogen, Carlsbad, CA).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and purified using Trizol (Invitrogen, Carlsbad, CA).
Non-directional RNA-seq libraries were prepared using standard Illumina protocol, and run on Illumina HiSeq 2000 as 101bp paired-end reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
PolyA RNA
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| Data processing |
Base calling was performed by CASAVA version 1.8.
Reads that fail Illumina chastity filter were removed, and reads were trimmed to 76bp, to match ENCODE data sets and prevent bias due to mappability issues.
Reads were mapped to hg19 using STAR version 2.1.1a_r109 with default parameters.
Duplicate reads were removed using samtools rmdup.
Reads from all four islets were combined prior to counting reads overlapping features.
Gene-level counts were calculated using only uniquely-mapped (MAPQ=255) reads with HTSeq, with parameters --stranded=no, with Ensembl 68 annotations.
Standard RPKMs (not quantile-normalized) were calculated using the CQN R library.
Only RPKMs for protein-coding genes present in the Gene Ontology Database are included in the final table.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text file includes RPKM values for combined samples; see Islets column for results from this dataset.
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| Submission date |
Nov 08, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Francis S Collins |
| E-mail(s) |
collinsf@mail.nih.gov
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| Organization name |
NHGRI
|
| Department |
Genome Technology Branch
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| Lab |
Molecular Genetics Section
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| Street address |
1 Center Drive, Rm 126
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE51310 |
Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants (RNA-seq) |
| GSE51312 |
Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants |
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| Relations |
| BioSample |
SAMN02400867 |
| SRA |
SRX375280 |
| 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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