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| Status |
Public on Aug 07, 2013 |
| Title |
T15_Day6 [PBMC] |
| Sample type |
SRA |
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| Source name |
T15_Day 6 post-vaccine_PBMCs
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| Organism |
Homo sapiens |
| Characteristics |
subject id: T15
time point: Day 6 post-vaccine
cell type: peripheral blood mononuclear cells (PBMCs)
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| Treatment protocol |
Blood was collected in heparinized tubes and a portion was removed for PBMC analysis. Lymphocytes were isolated using discontinuous Ficoll gradient centrifugation from buffy coat samples. Magnetic anti-CD235 immunoaffinity beads (Miltenyi Biotec, Auburn, CA) were used to remove RBC contaminants.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted with the Qiagen RNeasy micro kit. Concentrations were determined by UV spectrophotometry (Nanodrop) and integrity of ribosomal RNA was confirmed with an Agilent Bioanalyzer.
Polyadenylated RNA was extracted from total RNA, fragmented, ligated to sequencing and indexing adapters, and PCR amplified using Illumina TruSeq RNA kits as recommended by the kit instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
processed data file: T15_pbmc.txt
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| Data processing |
CASAVA version 1.7 pipeline was used to call bases, demultiplex indexes, align reads to the genome, and count the number of reads aligned with each annotated gene transcript.
RefSeq gene annotations ( hg19 refFlat.txt.gz) were downloaded from UCSC genome broswer and modified to add hg19 loci for constant regions of IGHA2 (chr14:106053890-106054215), IGHG4 (chr14:106090816-106091565), IGHG2 (chr14:106109959-106110289), IGHA1 (chr14:106173508-106173900,106174696-106174994), IGHG1 (chr14:106207813-106208562), IGHG3 (chr14:106235440-106235898), IGHD (chr14:106306703-106307026,106307237-106307563), IGHM (chr14:106320321-106320843) & IGKC (chr2:89156874-89157196).
Base counts per gene (i.e. bases aligned with RefSeq transcripts) were divided by 65 (read length) to obtain reads per gene.
Reads per gene were divided by the total number of RefSeq reads to obtain reads per gene per total reads.
Reads per million RefSeq reads (RPM) were obtained by multilying reads per total reads by one million.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files contain data from an individual subject (specified in file name), tab delimited text with 12 columns and 21967 rows. The first column contains official gene symbols. The first row indicates study day (0-10). Matrix contains RPM values as defined in description of data processing steps.
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| Submission date |
Apr 03, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephen Welle |
| E-mail(s) |
swelle@rochester.rr.com
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| Organization name |
University of Rochester
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| Street address |
601 Elmwood Avenue
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| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14642 |
| Country |
USA |
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| Platform ID |
GPL10999 |
| Series (2) |
| GSE45735 |
Changes in PBMC gene expression profiles after influenza vaccination in healthy human subjects |
| GSE45764 |
Effect of influenza vaccination on PBMC and B cell gene expression profiles in healthy humans |
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| Relations |
| Reanalyzed by |
GSE122515 |
| SRA |
SRX259529 |
| BioSample |
SAMN01997721 |
| 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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