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| Status |
Public on Aug 07, 2013 |
| Title |
T12_Day1 |
| Sample type |
SRA |
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| Source name |
T12_Day 1 post-vaccine_circulating B cells
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| Organism |
Homo sapiens |
| Characteristics |
subject id: T12
time point: Day 1 post-vaccine
cell type: circulating B cells
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| Treatment protocol |
B cell samples were enriched from heparinized whole blood with RosetteSep Immunodensity separation (Stemcell Technologies, Vancouver, BC, Canada). Negative magnetic immunoaffinity bead separation columns (Miltenyi Biotec, Auburn, CA) were used with anti-CD3 (BD Bioscience, San Diego, CA) and anti-CD235 beads (Miltenyi Biotec, Auburn, CA) to further purify total Bc. Flow cytometric analysis was performed on all isolates, showing >90% purity of the isolates.
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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: T12_bcel.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) |
| GSE45734 |
Changes in gene expression profiles of circulating B cells 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 |
| SRA |
SRX259436 |
| BioSample |
SAMN01997628 |
| 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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