Comprehensive Cell Line RNA Isolation

Thirty-four neuroblastoma cell lines were grown to subconfluency according to standard culture conditions. RNA was isolated using the RNeasy Midi Kit (Qiagen) according to the manufacturer's instructions. Nine RNA samples from pooled normal human tissues (heart, brain, fetal brain, lung, trachea, kidney, mammary gland, small intestine and uterus) were obtained from Clontech. Blood and fibroblast biopsies were obtained from different normal healthy individuals. Thirteen leukocyte samples were isolated from 5 ml fresh blood using Qiagen's erythrocyte lysis buffer. Fibroblast cells from 20 upper-arm skin biopsies were cultured for a short time (3-4 passages) and harvested at subconfluency as described [22 (link)]. Bone marrow samples were obtained from nine patients with no hematological malignancy. Total RNA of leukocyte, fibroblast and bone marrow samples was extracted using Trizol (Invitrogen), according to the manufacturer's instructions.

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Vandesompele J., De Preter K., Pattyn F., Poppe B., Van Roy N., De Paepe A, & Speleman F. (2002). Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biology, 3(7), research0034.1-research0034.11.

Publication 2002

Biopsies Blood Bone marrow Brain Buffer Cell lines Erythrocyte Fetal Fibroblast Heart Hematological malignancy Human Kidney Leukocyte Lung Mammary gland Neuroblastoma Normal tissues Patients Skin Small intestine Trachea Trizol Upper arm Uterus

Corresponding Organization :

Other organizations : Ghent University Hospital

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Variable analysis

independent variables

Cell lines (thirty-four neuroblastoma cell lines)

dependent variables

Gene expression (measured by RNA isolation and analysis)

control variables

Standard culture conditions
Normal human tissue samples (nine RNA samples from pooled heart, brain, fetal brain, lung, trachea, kidney, mammary gland, small intestine and uterus)
Blood and fibroblast biopsies from different normal healthy individuals
Leukocyte samples isolated from fresh blood
Fibroblast cells from upper-arm skin biopsies
Bone marrow samples from patients with no hematological malignancy

controls

Positive control: Not explicitly mentioned
Negative control: Not explicitly mentioned

Annotations

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