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Sample GSM2882189 Query DataSets for GSM2882189
Status Public on Feb 01, 2018
Title HR-29-V1
Sample type RNA
 
Source name peripheral blood mononuclear cells
Organism Homo sapiens
Characteristics disease state: Crohn's disease;treatment:none;patient:HR-29;time:V1;status:Responder;CRP:4.9;HBI:0;BMI:21.4995968825585;status_time:W14
treatment: none
patient: HR-29
time: V1
status: Responder
crp: 4.9
hbi: 0
bmi: 21.4995968825585
status_time: W14
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from Paxgene-cryopreserved whole blood using PreAnalytiX standard protocol. Quality was verified using Agilent Bioanalyzer TapeStation
Label biotin
Label protocol The quality of total RNA was first assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Biotin-labeled cDNA targets were synthesized starting from 150 ng of total RNA. Double stranded cDNA synthesis and related cRNA was performed with GeneChip® WT Plus Kit (Affymetrix, Santa Clara, CA). With the same kit was synthesized the sense strand cDNA before to be fragmented and labeled. All steps of the labeling protocol were performed as suggested by Affymetrix, starting from 5.5 ug of ssDNA. Each eukaryotic GeneChip® probe array contains probe sets for several B. subtilis genes that are absent in the samples analyzed (lys, phe, thr, and dap). This Poly-A RNA Control Kit contains in vitro synthesized, polyadenylated transcripts for these B. subtilis genes that are pre-mixed at staggered concentrations to allow GeneChip® probe array users to assess the overall success of the assay. Poly-A RNA Controls final concentration in each target are lys 1:100,000, phe 1:50,000, thr 1:25,000 and dap 1:6,667.
 
Hybridization protocol Hybridization was performed using the GeneChip® Hybridization, Wash and Stain Kit. It contains mix for target dilution, DMSO at a final concentration of 7% and pre- mixed biotin-labelled control oligo B2 and bioB, bioC, bioD and cre controls (Affymetrix cat #900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM, respectively. Fragmented and labeled sscDNA were diluted in hybridization buffer at a concentration of 23 ng/ul for a 2.3 ug total and denatured at 99 °C for 5 minutes incubated at 45 °C for 5 minutes and centrifuged at maximum speed for 1 minute prior to introduction into the GeneChip® cartridge. A single GeneChip® Human Clariom S was then hybridized with each biotin-labeled sense target. Hybridizations were performed for 16 h at 45 °C in a rotisserie oven. GeneChip® cartridges were washed and stained with GeneChip® Hybridization, Wash and Stain Kit in the Affymetrix Fluidics Station 450 following the FS450_0007 standard protocol, including the following steps: (1) (wash) 10 cycles of 2 mixes/cycle with Wash Buffer A at 30 °C; (2) (wash) 6 cycles of 15 mixes/cycle with Wash Buffer B at 50 °C; (3) stain of the probe array for 5 min in SAPE solution at 35 °C; (4) (wash) 10 cycles of 4 mixes/cycle with Wash Buffer A at 30 °C; (5) stain of the probe array for 5 min in antibody solution at 35 °C; (6) stain of the probe array for 5 min in SAPE solution at 35 °C; (7) (final wash) 15 cycles of 4 mixes/cycle with Wash Buffer A at 35 °C; (8) fill the probe array with Array Holding buffer.
Scan protocol GeneChip arrays were scanned using an Affymetrix GeneChip® Scanner 3000 7G using default parameters. Affymetrix GeneChip® Command Console software (AGCC) was used to acquire GeneChip® images and generate .DAT and .CEL files, which were used for subsequent analysis.
Description PBMC from CD patient at baseline, Responder at week 14
Data processing Preprocessing was perfomed in R using the oligo package. Raw CEL files were summarized and normalized using RMA and quantile normalization (oligo::rma), using the probe definition and annotation packages pd.clariom.s.human and clariomshumantranscriptcluster.db
 
Submission date Dec 08, 2017
Last update date Feb 01, 2018
Contact name Shai S Shen-Orr
E-mail(s) shenorr@technion.ac.il
Organization name Rappaport Institute of Medical Research, Faculty of Medicine and Faculty of Biology, Technion
Department Immunology
Lab Systems Immunology
Street address 1st Efron Street
City Haifa
ZIP/Postal code 32000
Country Israel
 
Platform ID GPL23159
Series (1)
GSE107865 PBMC gene expression from Crohn's disease patients before Infliximab therapy.

Data table header descriptions
ID_REF
VALUE RMA-calculated signal intensity

Data table
ID_REF VALUE
TC0100006437.hg.1 5.10283011663092
TC0100006476.hg.1 6.98076177353111
TC0100006479.hg.1 6.69997364995678
TC0100006480.hg.1 6.27630158478766
TC0100006483.hg.1 6.24614221791768
TC0100006486.hg.1 6.72753875301188
TC0100006490.hg.1 5.03761822611215
TC0100006492.hg.1 6.48587016015605
TC0100006494.hg.1 6.30638892298396
TC0100006497.hg.1 5.45970463267308
TC0100006499.hg.1 6.35109353838831
TC0100006501.hg.1 6.18811681880393
TC0100006502.hg.1 5.05255622484214
TC0100006514.hg.1 5.99345264362386
TC0100006516.hg.1 5.97174253125472
TC0100006517.hg.1 4.08177381141048
TC0100006524.hg.1 6.80097558056167
TC0100006540.hg.1 5.68978757344337
TC0100006548.hg.1 3.88424791358874
TC0100006550.hg.1 6.49006335404363

Total number of rows: 24351

Table truncated, full table size 849 Kbytes.




Supplementary file Size Download File type/resource
GSM2882189_R1282_25_HR_29_V1.CEL.gz 1.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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