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Sample GSM2976727 Query DataSets for GSM2976727
Status Public on Dec 25, 2018
Title preproB_EnhDel_rep2
Sample type RNA
Source name preproB Cebpa enhancer-deleted replicate 2
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: bone marrow
gender: male
age: 24 wks
genotype/variation: without the +37 kb Cebpa enhancer
Treatment protocol pIpC 300 mg s.q. every other day for 3 doses, then wait 5 wks to isolate marrow and then preproB cells
Extracted molecule total RNA
Extraction protocol cells were sorted into Trizol, chloroform extracted, and upper phase added to equal volume ethanol and then applied to RNA Clean and Concentrator-5 (Zymo Research) columns and Eluted with 15 ml water to isolate RNA.
Label Cy3
Label protocol Sample amplification and labeling were carried out by using Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). The labeled cRNA were purified using RNeasy mini kit (Qiagen).
Hybridization protocol 0.825 ug of each Cy3-labeled sample was used for hybridization at 65ÂșC for 17 hours in a hybridization oven with rotation. After hybridization, microarrays are washed and dried according to Agilent microarray processing protocol in a walk-in ozone-controlled enclosure.
Scan protocol Microarrays were scanned using an Agilent G2565A Scanner controlled by Agilent Scan Control 7.0 software. Data were extracted with Agilent Feature Extraction software.
Description Gene expression, enhancer deletion
Data processing Agilent FE processed signal intensities were imported into GeneSpring GX 10 (Agilent Technologies). Normalization was done by setting intensity thresheld to 5 and log2 transformation.
Submission date Feb 01, 2018
Last update date Dec 25, 2018
Contact name Alan D Friedman
Phone 410-955-2095
Organization name Johns Hopkins University
Department Oncology
Lab CRB I, Rm. 253
Street address 1650 Orleans St.
City Baltimore
State/province MD
ZIP/Postal code 21231
Country USA
Platform ID GPL10333
Series (1)
GSE110029 RNA Expression (log2) in preproB Cells from Two Cebpa +37 kb Enhancer(f/f) or Cebpa +37 kb Enhancer(f/f);Mx1-Cre Mice Exposed to pIpC 5 Weeks Earlier

Data table header descriptions
VALUE processed Cy3 signal intensity (Agilent gProcessedSignal)

Data table
1 2.427708e+004
2 3.037774e+000
3 3.033308e+000
4 3.028608e+000
5 3.023687e+000
6 3.018644e+000
7 3.014268e+000
8 3.009387e+000
9 3.005574e+000
10 3.002126e+000
11 2.998453e+000
12 9.348144e+001
13 8.774383e+000
14 5.029089e+003
15 7.884925e+001
16 2.605254e+003
17 2.500561e+003
18 2.985137e+000
19 3.062908e+003
20 1.037606e+001

Total number of rows: 44397

Table truncated, full table size 856 Kbytes.

Supplementary file Size Download File type/resource
GSM2976727_preproB_EnhDel_2.txt.gz 8.9 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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