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Status |
Public on Oct 12, 2019 |
Title |
BMT untreated_1 |
Sample type |
RNA |
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|
Source name |
Tissue samples from day9 post BMT_control
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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
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|
|
Hybridization protocol |
Labeled cRNSs were hybridized to (Affymetrix) according ot manufacturer's protocol
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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
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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.
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|
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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 |
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