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Sample GSM4119325 Query DataSets for GSM4119325
Status Public on Oct 12, 2019
Title BMT 3D10 treated_2
Sample type RNA
 
Source name Tissue samples from day9 post BMT_3D10
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 3.13594
17200003 2.38029
17200005 2.26643
17200007 3.25311
17200009 3.53055
17200011 1.76129
17200013 3.16172
17200015 4.19015
17200017 2.8318
17200019 2.62578
17200021 2.55227
17200023 3.4556
17200025 4.58087
17200027 2.61272
17200029 2.61109
17200031 2.27441
17200033 1.8611
17200035 2.74587
17200037 3.61305
17200039 1.78887

Total number of rows: 41345

Table truncated, full table size 682 Kbytes.




Supplementary file Size Download File type/resource
GSM4119325_Yujun_Yang_6_3D10_3_gut.CEL.gz 8.2 Mb (ftp)(http) CEL
GSM4119325_Yujun_Yang_6_3D10_3_gut.chp.gz 230.2 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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