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Sample GSM4119326 Query DataSets for GSM4119326
Status Public on Oct 12, 2019
Title no BMT
Sample type RNA
 
Source name no BMT
Organism Mus musculus
Characteristics strain: Balb/c
tissue: spleen
Treatment protocol Whole gut and spleen tissues were collected on stored on RNA stabilization solution (RNAlater Solution) Invitrogen
Growth protocol Balb/c were transplanted with T cell depleted BM (5x10^6 cell/mouse) and T cells (10^6 cells/mouse) of the B6 background. On day9 post bone marrow transplation the mice were euthanized and the tissues were harvested
Extracted molecule total RNA
Extraction protocol Total RNA was extraceted using an RNAeasy Micro Kit (Qiagen) and it's qulaity was assessed by an Agilent 2100 Bioanalyzer. Total RNA (from 500pg-2ng) was reverse transcribed into cDNA followed by in vitro transcription use GeneChip WT Pico (Affymetrix, Santta Clara, CA)
Label biotin
Label protocol The fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using a proprietary DNA Labeling Reagent that is covalently linked to biotin. 5.5 ug of total RNA was used
 
Hybridization protocol Labeled cRNSs were hybridized to (Affymetrix) according ot manufacturer's protocol
Scan protocol The chips were scanned using a GeneChip Scanner 3000 GeneChip Mouse 2.0ST- this is a whole transcript desogn with probed as well as exon (Catalog number: 902118 (Affymetric)
Description no BMT
Data processing Background correction, normalization and estimation of gene expression was performed using the Robust Multiarray (RMA) method in R/Bioconductor (www.bioconductor.org). Following aggregation, the samples were re-normalized using quantile normalization.
 
Submission date Oct 11, 2019
Last update date Oct 12, 2019
Contact name Panagiota Iliopoulou
E-mail(s) ilio@stanford.edu
Phone (650)723 5544
Organization name Stanford University
Street address 269 Campus Dr.
City Stanford
State/province CA
ZIP/Postal code 94070
Country USA
 
Platform ID GPL1261
Series (1)
GSE138785 Expression data from murine gut and spleen tissues

Data table header descriptions
ID_REF
VALUE Quantification

Data table
ID_REF VALUE
AFFX-BioB-5_at 8.38444
AFFX-BioB-M_at 9.08458
AFFX-BioB-3_at 8.55442
AFFX-BioC-5_at 9.51211
AFFX-BioC-3_at 10.0591
AFFX-BioDn-5_at 10.8579
AFFX-BioDn-3_at 11.6845
AFFX-CreX-5_at 12.9377
AFFX-CreX-3_at 13.0337
AFFX-DapX-5_at 5.70114
AFFX-DapX-M_at 9.62108
AFFX-DapX-3_at 11.2591
AFFX-LysX-5_at 4.23164
AFFX-LysX-M_at 7.41864
AFFX-LysX-3_at 9.15972
AFFX-PheX-5_at 4.7762
AFFX-PheX-M_at 6.69458
AFFX-PheX-3_at 8.98724
AFFX-ThrX-5_at 4.57068
AFFX-ThrX-M_at 4.94149

Total number of rows: 45101

Table truncated, full table size 850 Kbytes.




Supplementary file Size Download File type/resource
GSM4119326_Yujun_Yang_wt.CEL.gz 3.6 Mb (ftp)(http) CEL
GSM4119326_Yujun_Yang_wt.chp.gz 310.1 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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