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Sample GSM4119323 Query DataSets for GSM4119323
Status Public on Oct 12, 2019
Title BMT untreated_2
Sample type RNA
 
Source name Tissue samples from day9 post BMT_control
Organism Mus musculus
Characteristics strain: Balb/c
tissue: gut
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 Gene expression data from tissue samples from day9 post 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 GPL16570
Series (1)
GSE138785 Expression data from murine gut and spleen tissues

Data table header descriptions
ID_REF
VALUE Quantification

Data table
ID_REF VALUE
17200001 3.34109
17200003 3.17092
17200005 1.6308
17200007 3.01189
17200009 4.6751
17200011 2.3629
17200013 3.01765
17200015 4.49759
17200017 2.01343
17200019 2.23003
17200021 2.65428
17200023 4.45232
17200025 3.47479
17200027 2.80035
17200029 2.6688
17200031 2.06756
17200033 1.61069
17200035 2.52575
17200037 3.61305
17200039 2.00139

Total number of rows: 41345

Table truncated, full table size 682 Kbytes.




Supplementary file Size Download File type/resource
GSM4119323_Yujun_Yang_2_Tcon_2_gut.CEL.gz 8.1 Mb (ftp)(http) CEL
GSM4119323_Yujun_Yang_2_Tcon_2_gut.chp.gz 231.5 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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