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Sample GSM3391971 Query DataSets for GSM3391971
Status Public on Mar 14, 2019
Title BJ/hTERT LT/ST HDAC4 TM cells, rep1
Sample type RNA
 
Source name BJ/hTERT LT/ST HDAC4 TM
Organism Homo sapiens
Characteristics cell type: human fibroblasts
Growth protocol BJ/TERT cells were cultured in Earle’s salts minimal essential medium (EMEM) (Euroclone) completed with nonessential amino acids (HyClone). Media was supplemented with 10% fetal bovine serum (FBS), L-glutamine (2mM), penicillin (100U/ml), and streptomycin (100µg/ml) (Lonza)
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using Direct-zol RNA mini prep (Zymo Research). RNA samples concentration and purity (assessed as 260/280 nm and 260/230 nm ratios) were evaluated by NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies; Wilmington, DE), while RNA integrity was assessed by using the Agilent 2100 Bioanalyzer (Agilent Technologies; Waldbrunn, Germany).
Label biotin
Label protocol RNA samples were labeled according to the standard one-cycle amplification and labeling protocol (Affymetrix, Santa Clara, CA).
 
Hybridization protocol Labeled cRNA was hybridized on Affymetrix Clariom S Human array
Scan protocol Scanning was performed using a GeneChip Scanner 3000 7G (Affymetrix).
Data processing Data processing was performed with BioConductor packages (http://www.bioconductor.org/). Robust Multi-Array Average (RMA) normalization was applied. Normalized intensity values for all probes on the Affymetrix chip are presented in the Matrix table. Data analysis was performed using the moderated t-test as implemented in the limma package. P values were adjusted for multiple testing using the False Discovery Rate method.
 
Submission date Sep 17, 2018
Last update date Mar 14, 2019
Contact name raffaella picco
E-mail(s) raf.picco@uniud.it
Organization name university of Udine
Department department of medical and biological sciences
Lab bioinformatics
Street address piazzale kolbe 4
City udine
ZIP/Postal code 33100
Country Italy
 
Platform ID GPL23159
Series (1)
GSE120040 Unscheduled HDAC4 repressive activity in human fibroblasts triggers TP53-dependent senescence and favours cell transformation

Data table header descriptions
ID_REF
VALUE RMA signal intensity

Data table
ID_REF VALUE
AFFX-BkGr-GC03_st 1.933861963
AFFX-BkGr-GC04_st 1.883251909
AFFX-BkGr-GC05_st 1.881924781
AFFX-BkGr-GC06_st 1.908420307
AFFX-BkGr-GC07_st 1.947811396
AFFX-BkGr-GC08_st 1.967471052
AFFX-BkGr-GC09_st 2.01100532
AFFX-BkGr-GC10_st 2.062641361
AFFX-BkGr-GC11_st 2.177221673
AFFX-BkGr-GC12_st 2.353471568
AFFX-BkGr-GC13_st 2.531199457
AFFX-BkGr-GC14_st 2.996477155
AFFX-BkGr-GC15_st 3.41070067
AFFX-BkGr-GC16_st 4.247850883
AFFX-BkGr-GC17_st 4.732100932
AFFX-BkGr-GC18_st 5.336460692
AFFX-BkGr-GC19_st 5.891764785
AFFX-BkGr-GC20_st 6.102234303
AFFX-BkGr-GC21_st 6.473641655
AFFX-BkGr-GC22_st 7.001491712

Total number of rows: 24351

Table truncated, full table size 731 Kbytes.




Supplementary file Size Download File type/resource
GSM3391971_R1361_B_HDAC4-TM_1st.CEL.gz 1.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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