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Sample GSM3408438 Query DataSets for GSM3408438
Status Public on Dec 01, 2018
Title Nasal Mucosa ALI at day 0, biological rep 4 (miRNA)
Sample type RNA
 
Source name Control NM ALI at day 0
Organism Homo sapiens
Characteristics individual: healthy subject
age (years): 67
gender: M
previous treatment: No
atopy: No
cell type: BSC
cells isolated from: NM
protocol: ALI culture
time: day 0
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 (300 ng, RIN ≥ 9) was processed for global transcriptional analysis using the microRNA 4.1 Array Plate (Affymetrix, Santa Clara, CA, USA), following the manufacturer’s directions.
 
Hybridization protocol Global microRNA transcriptional analysis using the microRNA 4.1 Array Plate (Affymetrix, Santa Clara, CA, USA), following the manufacturer’s directions.
Scan protocol GeneTitan Affymetrix genetic analysis system
Description microRNA expression data from CONTROL NM ALI Cultures at day 0
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.
Only the normalized data for human mature microRNA is available.
 
Submission date Oct 01, 2018
Last update date Dec 02, 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 GPL19117
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
MIMAT0000416_st 1.15347
MIMAT0004512_st 1.19903
MIMAT0000098_st 7.77152
MIMAT0000099_st 1.19153
MIMAT0004513_st 1.53678
MIMAT0009196_st 1.46526
MIMAT0000101_st 10.51250
MIMAT0007402_st 1.27128
MIMAT0004516_st 1.07307
MIMAT0000102_st 1.48049
MIMAT0004517_st 1.26656
MIMAT0000103_st 9.64236
MIMAT0004672_st 5.66324
MIMAT0000680_st 8.72825
MIMAT0000104_st 9.92461
MIMAT0004555_st 0.78695
MIMAT0000253_st 1.79029
MIMAT0004556_st 1.66320
MIMAT0000254_st 1.52013
MIMAT0005823_st 1.39059

Total number of rows: 2560

Table truncated, full table size 60 Kbytes.




Supplementary file Size Download File type/resource
GSM3408438_NASAL_MUCOSA_4_0D_miRs.CEL.gz 863.9 Kb (ftp)(http) CEL
Processed data included within Sample table

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