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Sample GSM1208099 Query DataSets for GSM1208099
Status Public on Jan 16, 2014
Title Hu_Mock_pCalu3_3h_4
Sample type RNA
 
Source name Human, virus, polarized calu-3 cells, timepoint, replicate
Organism Homo sapiens
Characteristics cell line: polarized Calu3 cells
infection: Mock Infection
time: 3h
Treatment protocol Confluent monolayers of polarized Calu-3 achieving stable transepithelial resistance were infected apically at a MOI of 1. After a 1-hour incubation, monolayers were washed to remove nonadherent virus and 2 ml of MEM-BSA was added to both apical and basolateral reservoirs of cells and left for the duration of the experiment.
Growth protocol The human bronchial epithelial cell line Calu-3 was originally derived from subbronchial epithelium of a lung adenocarcinoma (ATCC) and cells were grown in Eagle's minimal essential medium (MEM) supplemented with 2 mM l-glutamine, 1 mM sodium pyruvate, 0.1 mM nonessential amino acids, 1.5 g/liter sodium bicarbonate, and 10% fetal bovine serum. Calu-3 cells (5 × 105) were seeded onto Corning 24-mm-diameter semipermeable membrane inserts with a 0.4-μm pore size (Corning, NY) and cultured for 1 week with the addition of fresh culture medium every 2 to 3 days. Confluent monolayers of polarized Calu-3 achieving stable transepithelial resistance were infected apically at a MOI of 1. After a 1-hour incubation, monolayers were washed to remove nonadherent virus and 2 ml of MEM-BSA was added to both apical and basolateral reservoirs of cells and left for the duration of the experiment.
Extracted molecule total RNA
Extraction protocol All Trizol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.
Label Cy3
Label protocol The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.
 
Hybridization protocol The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing.
Scan protocol Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.
Data processing After control probes filtering : 58,717 probes including 8118 duplicated probes 3. After SUMMARIZATION OF non-CTRL PROBES: 50,599 probes 4. Filtering of probes: we require that the probes pass the following QC in at least 100% samples of 1 infected time-point: gIsFound, gIsWellAboveBG, gIsSaturated: no probe was excluded based on that criteria, gIsFeatNonUnifOL, and gIsFeatPopnOL. Probes passing qc: 29,382 probes only.
 
Submission date Aug 13, 2013
Last update date Jan 17, 2014
Contact name Michael Katze
E-mail(s) data@viromics.washington.edu
Organization name University of Washington
Department Microbiology
Lab Michael G. Katze, Ph.D
Street address Rosen Building 960 Republican St.
City Seattle
State/province WA
ZIP/Postal code 98109-4325
Country USA
 
Platform ID GPL17077
Series (1)
GSE49840 Transcriptomic characterization of the novel avian-origin influenza A (H7N9) virus: specific and intermediate host-response between avian (H5N1 and H7N7) and human (H3N2) viruses.

Data table header descriptions
ID_REF
VALUE gProcessedSignal

Data table
ID_REF VALUE
A_19_P00315459 6.42084505
A_19_P00315493 5.816871561
A_19_P00315502 13.01216819
A_19_P00315506 9.611895764
A_19_P00315524 4.276979345
A_19_P00315528 4.846338103
A_19_P00315529 4.756357923
A_19_P00315543 5.233125516
A_19_P00315550 7.477703218
A_19_P00315551 7.657412451
A_19_P00315581 11.73409558
A_19_P00315583 5.961944969
A_19_P00315584 6.382970428
A_19_P00315593 4.961222743
A_19_P00315601 10.9576194
A_19_P00315603 10.2197905
A_19_P00315627 4.769226762
A_19_P00315631 5.374008726
A_19_P00315633 5.58289541
A_19_P00315649 6.48582448

Total number of rows: 29382

Table truncated, full table size 724 Kbytes.




Supplementary file Size Download File type/resource
GSM1208099_US93503719_253949410486_S01_GE1_107_Sep09_2_2.txt.gz 12.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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