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Sample GSM4119322 Query DataSets for GSM4119322
Status Public on Oct 12, 2019
Title BMT untreated_1
Sample type RNA
 
Source name Tissue samples from day9 post BMT_control
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 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 2.91203
17200003 4.30522
17200005 1.75697
17200007 1.0506
17200009 3.66124
17200011 1.31594
17200013 2.55352
17200015 1.61107
17200017 3.36867
17200019 2.05912
17200021 2.59664
17200023 4.08045
17200025 4.26
17200027 4.07841
17200029 0.718814
17200031 3.64512
17200033 1.73953
17200035 1.71019
17200037 2.94573
17200039 1.19814

Total number of rows: 41345

Table truncated, full table size 682 Kbytes.




Supplementary file Size Download File type/resource
GSM4119322_Yujun_Yang_1_Tcon_2_SP.CEL.gz 7.0 Mb (ftp)(http) CEL
GSM4119322_Yujun_Yang_1_Tcon_2_SP.chp.gz 231.8 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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