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Sample GSM2872775 Query DataSets for GSM2872775
Status Public on Dec 01, 2018
Title Nasal Polyp ALI at day 14, biological rep 3 (mRNA)
Sample type RNA
 
Source name NP ALI at day 14
Organism Homo sapiens
Characteristics individual: CRSwNP patient
age (years): 42
gender: F
previous treatment: No
atopy: No
cell type: BSC
cells isolated from: NP
protocol: ALI culture
time: day 14
Treatment protocol Human primary basal stem/progenitor cells were not treated during ALI culture. Mucociliary differentiation was only induced by differentiation media (B-ALI (Lonza) supplemented with SingleQuots™ kit containing: BPE, hydrocortisone, hEGF, epinephrine, insulin, triiodothyronine, transferrin, GA-1000, inducer, and retinoic acid) and exposure to air.
Growth protocol Human primary basal cells were obtained from CRSwNP patients (n=7) and healthy subjects (NM, n=7) by the explant technique in BEGM™ (LONZA) media suplemented with SingleQuots™ (LONZA) containing: BPE, hydrocortisone, hEGF, epinephrine, insulin, triiodothyronine, transferrin, GA-1000, and retinoic acid. Cells were cultured and differentiated at the air-liquid interface (ALI) system for 28 days in differentiation media composed of B-ALI™ (Lonza) supplemented with suplemented with SingleQuots™ (LONZA) containing: BPE, hydrocortisone, hEGF, epinephrine, insulin, triiodothyronine, transferrin, GA-1000, and retinoic acid.
Extracted molecule total RNA
Extraction protocol Total RNA, including small RNAs, was isolated from cells using the miRNeasy Mini Kit from Qiagen (Valencia, CA, USA). Briefly, cells were lysed with Qiazol lysis buffer (Qiagen), with cells from three inserts pooled for each time point, followed by passage through a Qiashredder column (Qiagen). Total RNA was extracted via RNeasy mini spin columns. All incubation and washing steps were performed following the manufacturer’s instructions.
Label biotin
Label protocol Total RNA (100 ng, RIN ≥ 9) was processed for global transcriptional analysis using the GeneChip® 3’ IVT Express kit and the Human Genome U219 24-Array Plate (Affymetrix, Santa Clara, CA, USA), following the manufacturer’s directions.
 
Hybridization protocol Global transcriptional analysis using the GeneChip® 3’ IVT Express kit and the Human Genome U219 24-Array Plate (Affymetrix, Santa Clara, CA, USA), following the manufacturer’s directions.
Scan protocol GeneTitan Affymetrix genetic analysis system
Description Gene expression data from NP ALI Cultures at day 14
Data processing Microarray data (Affymetrix .cel files) were processed for raw data quality control analysis by using Robust Multichip Analysis (RMA) algorithm, which perform background correction, probe-level normalization, and probe-set summary.
 
Submission date Dec 02, 2017
Last update date Dec 01, 2018
Contact name Borja Callejas-Díaz
Organization name IDIBAPS, HOSPITAL CLÍNIC
Department Clinical and Experimental Respiratory Immunoallergy
Lab IRCE Lab
Street address Carrer de Casanova, 143, CELLEX Sector 2B
City BARCELONA
State/province CATALUÑA
ZIP/Postal code 08036
Country Spain
 
Platform ID GPL13667
Series (1)
GSE107624 Global Transcriptome Analysis during Mucociliary Differentiation of Human Nasal Polyp/Nasal Mucosa Basal Stem/Progenitor Cells

Data table header descriptions
ID_REF
VALUE normalized signal

Data table
ID_REF VALUE
AFFX-DapX-5_at 10.1657
AFFX-DapX-M_at 10.542
AFFX-DapX-3_at 11.2747
AFFX-LysX-5_at 6.57733
AFFX-LysX-M_at 7.54987
AFFX-LysX-3_at 8.2923
AFFX-PheX-5_at 7.6029
AFFX-PheX-M_at 8.33971
AFFX-PheX-3_at 7.86688
AFFX-ThrX-5_at 7.53241
AFFX-ThrX-M_at 8.89931
AFFX-ThrX-3_at 9.82558
AFFX-TrpnX-5_at 4.16393
AFFX-TrpnX-M_at 4.42297
AFFX-TrpnX-3_at 4.13556
AFFX-r2-Ec-bioB-5_at 8.1771
AFFX-r2-Ec-bioB-M_at 8.19313
AFFX-r2-Ec-bioB-3_at 8.50343
AFFX-r2-Ec-bioC-5_at 9.86315
AFFX-r2-Ec-bioC-3_at 10.3634

Total number of rows: 49386

Table truncated, full table size 1033 Kbytes.




Supplementary file Size Download File type/resource
GSM2872775_NASAL_POLYP_3_14D.CEL.gz 2.3 Mb (ftp)(http) CEL
GSM2872775_NASAL_POLYP_3_14D.chp.gz 344.0 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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