With the identification of Lgr5 as a definitive marker for intestinal stem cells, we used the highly novel, recently described, Lgr5-EGFP-IRES-cre ERT2knock in mouse model. Mice were injected with azoxymethane (AOM, a colon carcinogen) or saline (control) and fed a chemo-protective diet containing n-3 fatty acids and fermentable fiber (n-3 PUFA+pectin) or a control diet (n-6 PUFA + cellulose). Single cells were isolated from colonic mucosa crypts and three discrete populations of cells were collected via fluorescence activated cell sorting (FACS): Lgr5high (stem cells), Lgr5low (daughter cells) and Lgr5negative (differentiated cells). microRNA profiling and RNA sequencing were performed from the same sample and analyzed. These data refer to ‘Comparative effects of diet and carcinogen on microRNA expression in the stem cell niche of the mouse colonic crypt’ (Shah et al., 2016) [5]

Callaway, Evelyn S.

Chapkin, Robert S.

Davidson, Laurie A.

Goldsby, Jennifer S.

Ivanov, Ivan

Kim, Eunjoo

Knight, Jason M.

Shah, Manasvi S.

Zhou, Beyian

Zoh, Roger S.

Data in Brief

PubMed

AbstractWith the identification of Lgr5 as a definitive marker for intestinal stem cells, we used the highly novel, recently described, Lgr5-EGFP-IRES-cre ERT2 knock in mouse model. Mice were injected with azoxymethane (AOM, a colon carcinogen) or saline (control) and fed a chemo-protective diet containing n-3 fatty acids and fermentable fiber (n-3 PUFA+pectin) or a control diet (n-6 PUFA + cellulose). Single cells were isolated from colonic mucosa crypts and three discrete populations of cells were collected via fluorescence activated cell sorting (FACS): Lgr5high (stem cells), Lgr5low (daughter cells) and Lgr5negative (differentiated cells). microRNA profiling and RNA sequencing were performed from the same sample and analyzed. These data refer to ‘Comparative effects of diet and carcinogen on microRNA expression in the stem cell niche of the mouse colonic crypt’ (Shah et al., 2016) [5]

Elsevier - Publisher Connector 

Contents lists available at ScienceDirect
Data in Brief
Data in Brief 6 (2016) 398–404http://d
2352-34
(http://c
DOI
n Corr
TX, Uni
E-m
1 Bojournal homepage: www.elsevier.com/locate/dibData ArticleData describing the effects of dietary bioactive
agents on colonic stem cell microRNA and
mRNA expression
Manasvi S. Shah a,b,h,i,1, Eunjoo Kim a,c,1, Laurie A. Davidson a,
Jason M. Knight a,d,g, Roger S. Zoh a,e, Jennifer S. Goldsby a,g,
Evelyn S. Callaway a, Beyian Zhou f,g, Ivan Ivanov a,f,g,
Robert S. Chapkin a,b,g,n
a Program in Integrative Nutrition & Complex Diseases, United States
b Intercollegiate Faculty of Genetics, United States
c Department of Molecular and Cellular Medicine, United States
d Department of Electrical Engineering, United States
e Department of Statistics, United States
f Department of Veterinary Physiology & Pharmacology, United States
g Center for Translational Environmental Health Research, Texas A&M University, College Station, TX, United
States
h Divison of Endocrinology, Boston Children’s Hospital, United States
i Department of Pediatrics, Harvard Medical School, Boston, MA, United Statesa r t i c l e i n f o
Article history:
Received 20 October 2015
Received in revised form
16 December 2015
Accepted 16 December 2015
Available online 19 December 2015x.doi.org/10.1016/j.dib.2015.12.026
09/& 2015 The Authors. Published by Else
reativecommons.org/licenses/by/4.0/).
of original article: http://dx.doi.org/10.1016
esponding author at: Center for Translatio
ted States.
ail address: r-chapkin@tamu.edu (R.S. Chap
th authors contributed equally to this mana b s t r a c t
With the identiﬁcation of Lgr5 as a deﬁnitive marker for intestinal
stem cells, we used the highly novel, recently described, Lgr5-EGFP-
IRES-cre ERT2 knock in mouse model. Mice were injected with
azoxymethane (AOM, a colon carcinogen) or saline (control) and fed
a chemo-protective diet containing n-3 fatty acids and fermentable
ﬁber (n-3 PUFAþpectin) or a control diet (n-6 PUFA þ cellulose).
Single cells were isolated from colonic mucosa crypts and three
discrete populations of cells were collected via ﬂuorescence acti-
vated cell sorting (FACS): Lgr5high (stem cells), Lgr5low (daughter
cells) and Lgr5negative (differentiated cells). microRNA proﬁling and
RNA sequencing were performed from the same sample and ana-
lyzed. These data refer to ‘Comparative effects of diet andvier Inc. This is an open access article under the CC BY license
/j.bbadis.2015.10.012
nal Environmental Health Research, Texas A&M University, College Station,
kin).
uscript.
S
M
T
H
D
E
E
D
D
M.S. Shah et al. / Data in Brief 6 (2016) 398–404 399carcinogen on microRNA expression in the stem cell niche of the
mouse colonic crypt’ (Shah et al., 2016) [5].
& 2015 The Authors. Published by Elsevier Inc. This is an open access
article under the CC BY license
(http://creativecommons.org/licenses/by/4.0/).Speciﬁcations tableubject area Biology
ore speciﬁc sub-
ject areaIntestinal stem cellsype of data Tables
ow data was
acquiredThe raw data was generated using an Illumina sequencer and was statistically
analyzed and displayed in tabular format.ata format Analyzed
xperimental
factorsThe samples were collected from mice fed with either corn oilþ cellulose or ﬁsh
oilþpectin. Both groups of mice were then either injected with Azoxymethane
(carcinogen) or saline (control). Total ¼ 20 mice in all.xperimental
featuresColonic crypts were isolated from the stem cell reporter mice and were sorted
based on GFP into high, low and negative cell populations using a BD FACS Aria II
cytometer/sorter (BD Biosciences). Total RNA was isolated from the sorted cells
using a miRVana miRNA isolation kit. After checking the quality of the RNA,
libraries were subjected to RNA sequencing and microRNA proﬁling.ata source
locationCollege Station, Texas, USA (30.6014oN, 96.3144oW)ata accessibility All the datasets mentioned in this manuscript will be uploaded to the Gene
Expression Omnibus (GEO) (accession no.- SRP061188) in NCBI.Value of the data
 These data will serve as a basis to compare Lgr5high stem cells that have been perturbed by
inﬂammation, radiation or knockout of tumor suppressors/oncogenes.
 These data describe expression values for miRNAs in Lgr5high, Lgr5low and Lgr5neg cells. For
example, if a researcher wants to know if a certain miRNA is expressed in the colonic crypt, this
database will provide that information. The data set also details the location of the miRNA
throughout the entire crypt.
 RNA sequencing data from Lgr5high, Lgr5low and Lgr5neg cells also provides the basis for deter-
mining the expression of different mRNAs throughout the crypt. This database will serve as a
comparative platform for future studies to determine correlations between current and future
datasets.1. Data
The data presented in this article represent: (a) Ct values of miRNAs expressed in mouse colonic
epithelial cells (Table 1), (b) differentially expressed miRNAs in Lgr5high versus Lgr5negative cells (i.e.,
stem cells vs. differentiated cells) (Table 2), (c) the effect of diet on miRNA expression in Lgr5high
sorted cells (Table 3), (d) the effect of carcinogen on miRNA expression in Lgr5 high sorted cells
(Table 4) and (e) the effect of diet and carcinogen combination on miRNA expression in GFPnegative
sorted cells (Table 5).
M.S. Shah et al. / Data in Brief 6 (2016) 398–404400These data refer to our recently published paper ‘Comparative effects of diet and carcinogen on
microRNA expression in the stem cell niche of the mouse colonic crypt’ (Shah et al., 2016) [5].2. Experimental design, materials and methods
2.1. Experimental diets
Lgr5-EGFP-IRES-creERT2 mice were assigned to one of the two diet groups (ﬁsh oil / pectin or corn
oil / cellulose), which differed only in the type of fat and ﬁber. Diets contained (g/100 g diet): dex-
trose, 51.00; casein, 22.40; D,L-methionine, 0.34; American Institute of Nutrition (AIN)-76 salt mix,
3.91; AIN-76 vitamin mix, 1.12; choline chloride, 0.13; pectin or cellulose, 6.00. The total fat content of
each diet was 15% by weight with the n-6 PUFA diet containing 15.0 g corn oil/100 g diet (Dyets,
Bethlehem, PA) and the n-3 PUFA diet containing 11.5 g ﬁsh oil/100 g diet (Omega Protein, Houston,Table 1
Ct values of 103 miRNAs expressed in mouse colonic epithelial cells.
miRNA Ct values miRNA Ct values miRNA Ct values
mmu-miR-31 11.44 mmu-miR-671-3p 26.81 mmu-let-7g- 28.94
rno-miR-190b 14.92 mmu-miR-215 26.81 mmu-miR-103 28.95
mmu-miR-872 17.72 mmu-miR-151-3p 26.9 mmu-miR-320 29
mmu-miR-124 20.88 mmu-let-7b 26.96 mmu-miR-218 29.02
mmu-miR-128a 20.99 mmu-miR-203 26.97 mmu-miR-30d 29.2
mmu-miR-429 21.89 mmu-miR-484 27.02 mmu-miR-125b-5p 29.2
mmu-miR-148b 22.68 mmu-miR-29a 27.11 mmu-miR-205 29.63
mmu-miR-324-5p 22.88 mmu-miR-29b 27.24 mmu-miR-18a 29.63
mmu-miR-322 23.04 mmu-miR-340-5p 27.41 mmu-miR-195 29.68
mmu-miR-142-3p 23.43 mmu-miR-139-5p 27.43 mmu-miR-28 29.7
mmu-miR-192 23.51 mmu-miR-15b 27.43 mmu-miR-574-3p 29.83
mmu-miR-200a 23.75 mmu-miR-93 27.49 mmu-miR-101a 29.83
mmu-miR-423-5p 23.88 mmu-let-7e 27.55 mmu-miR-29c 30.01
mmu-miR-375 23.94 mmu-miR-20b 27.71 rno-miR-345-3p 30.02
mmu-miR-10b 24.03 mmu-miR-27b 28.01 mmu-miR-301b 30.12
mmu-miR-19b 24.16 mmu-miR-30a 28.04 mmu-miR-146b 30.29
mmu-miR-30c 24.31 mmu-miR-27a 28.04 mmu-miR-744 30.34
mmu-miR-92a 24.36 mmu-miR-148a 28.06 mmu-miR-331-3p 30.37
mmu-miR-191 24.43 mmu-miR-222 28.13 mmu-miR-186 30.38
mmu-miR-30b 24.75 mmu-miR-141 28.18 mmu-miR-196b 30.39
mmu-miR-24 24.78 mmu-miR-188-5p 28.19 mmu-miR-340-3p 30.44
mmu-miR-126-3p 24.79 mmu-miR-106b 28.22 mmu-miR-301a 30.45
mmu-miR-17 24.91 mmu-miR-19a 28.23 mmu-miR-130b 30.49
mmu-miR-194 24.92 mmu-let-7d 28.23 mmu-miR-193b 30.68
mmu-miR-200b 24.99 mmu-miR-25 28.24 mmu-miR-155 30.77
mmu-miR-34b-3p 25.05 rno-miR-196c 28.46 mmu-miR-152 30.8
mmu-miR-20a 25.16 mmu-miR-130a 28.46 mmu-miR-23b 30.98
mmu-miR-106a 25.16 mmu-miR-100 28.5 mmu-miR-183 31.39
mmu-miR-200c 25.38 mmu-miR-30e 28.57 mmu-miR-125a-5p 31.84
mmu-let-7c 25.74 mmu-miR-182 28.57 mmu-miR-181a 31.94
mmu-miR-16 25.98 mmu-miR-328 28.59 mmu-miR-181c 34.76
mmu-miR-10a 26.11 mmu-let-7i 28.68
mmu-miR-145 26.32 mmu-miR-26b 28.84
mmu-miR-26a 26.33 mmu-miR-140 28.86
mmu-miR-21 26.48 mmu-miR-146a 28.87
mmu-miR-99a 26.67 mmu-miR-224 28.92
Expression of miRNAs was quantiﬁed by reverse transcription using miRNA-speciﬁc primers followed by real-time PCR TaqMan
low-density array analysis. Ct values represent means of 60 samples, mmu, mouse; rno, rat; Ct, cross threshold.
Table 2
Differentially expressed miRNAs in Lgr5high versus Lgr5negative cells.
Up-regulated in Lgr5high P-value Down-regulated in Lgr5high P-value
miRNA Expression ratio
Lgr5high/
Lgr5negative
miRNA Expression
ratio Lgr5high/
Lgr5negative
mmu-miR-342-3p 2.64 0.012 mmu-miR-652 0.32 0.000
mmu-miR-671-3p 2.29 0.008 mmu-miR-145 0.40 0.009
rno-miR-345-3p 2.14 0.022 mmu-miR-27a 0.42 0.000
rno-miR-190b 1.95 0.018 mmu-miR-215 0.42 0.000
mmu-miR-155 1.90 0.033 mmu-miR-532-5p 0.50 0.040
mmu-miR-191 1.81 0.001 mmu-miR-7b 0.60 0.027
mmu-miR-20b 1.68 0.011 mmu-miR-21 0.62 0.024
mmu-miR-17 1.68 0.000 mmu-miR-30d 0.62 0.017
mmu-miR-125a-5p 1.58 0.036 rno-miR-224 0.62 0.018
mmu-miR-186 1.58 0.006 mmu-miR-30a 0.66 0.000
mmu-miR-218 1.44 0.003 mmu-miR-200b 0.69 0.013
mmu-miR-10a 1.30 0.047 mmu-miR-203 0.76 0.003
mmu-miR-92a 1.29 0.018
mmu-miR-200a 1.27 0.031
Expression of miRNAs were quantiﬁed as described in Table 1. GFPhigh stem cells (n¼20, pooled samples); Lgr5negative cells
(n¼20, pooled samples). Only miRNAs with Po0.05 are shown. mmu, mouse; rno, rat.
Table 3
Effect of carcinogen on miRNA expression in Lgr5high sorted cells.
A.
miRNA Expression ratio AOM-Lgr5high /Saline-Lgr5high P-value
mmu-miR-532-3p 2.61 0.020
rno-miR-196c 1.66 0.008
mmu-miR-331-3p 1.45 0.032
mmu-miR-92a 1.41 0.042
mmu-miR-100 0.19 0.050
mmu-miR-124 0.25 0.021
B.
miRNA Expression ratio AOM-Lgr5neg /Saline-Lgr5neg P-value
mmu-let-7e 1.97 0.008
mmu-miR-18a 1.84 0.050
mmu-miR-20b 1.59 0.029
mmu-miR-101a 1.52 0.045
mmu-let-7i 1.45 0.039
mmu-miR-375 1.26 0.046
mmu-miR-224 0.65 0.030
mmu-miR-193b 0.65 0.045
mmu-miR-10a 0.62 0.008
miRNA expression was quantiﬁed as described in Table 1. AOM, azoxymethane (n¼20); saline (n¼20); Lgr5high, stem cells;
Lgr5neg, non-stem cells. Only miRNAs with Po0.05 are shown.
M.S. Shah et al. / Data in Brief 6 (2016) 398–404 401TX) plus 3.5 g corn oil/100 g diet to prevent essential fatty acid deﬁciency. All diet ingredients except
oils were obtained from Bio-serv (Frenchtown, NJ). To prevent the formation of oxidized lipids, diets
were stored at 20 °C and provided fresh to animals every day.
Table 4
Effect of diet on miRNA expression in Lgr5high sorted cells.
A. Carcinogen
miRNA Expression ratio CCA-Lgr5high /FPA-Lgr5high P-value
miR-21 2.2 0.030
miR-26b 2.0 0.010
miR-200a 1.8 0.000
miR-10a 1.7 0.040
miR-26a 1.7 0.020
miR-29c 1.6 0.010
miR-30c 1.5 0.040
miR-203 1.5 0.040
miR-30a 1.4 0.020
miR-19b 1.3 0.040
miR-181a 0.6 0.030
miR-34b-3p 0.1 0.000
B. Saline
miRNA Expression ratio CCS-Lgr5high/FPS-Lgr5high P-value
mmu-miR-188-5p 5.3 0.027
mmu-miR-218 0.6 0.016
mmu-miR-125a-5p 0.5 0.047
mmu-miR-574-3p 0.5 0.028
mmu-miR-200c 0.5 0.047
mmu-miR-222 0.4 0.016
mmu-miR-429 0.3 0.034
mmu-miR-106a 0.1 0.047
Expression of miRNAs was quantiﬁed as described in Table 1. CCA, Corn oilþcelluloseþazoxymethane (AOM) (n¼5); FPA, Fish
oilþpectinþAOM (n¼5); CCS, Corn oilþcelluloseþsaline (n¼5); FPS, Fish oilþpectinþsaline (n¼5); Lgr5high, stem cells. Only
miRNAs with P r0.05 are shown.
Table 5
Effect of diet and carcinogen combination on miRNA expression in GFPnegative sorted cells.
miRNA Expression ratio CCA- Lgr5neg/FPA- Lgr5neg P-value
miR-29b 3.8 0.008
let-7e 2.1 0.004
Let-7c 1.3 0.048
miR-19b 0.6 0.029
miR-484 0.5 0.019
miR-19a 0.4 0.034
miRNA Expression ratio CCA- Lgr5neg/FPA- Lgr5neg P-value
miR-29b 3.8 0.008
let-7e 2.1 0.004
Let-7c 1.3 0.048
miR-19b 0.6 0.029
miR-484 0.5 0.019
miR-19a 0.4 0.034
Expression of miRNAs was quantiﬁed as described in Table 1. CCA, Corn oilþcelluloseþazoxymethane (AOM) (n¼5); FPA, Fish
oilþpectinþAOM (n¼5); Lgr5neg, differentiated cells. Only miRNAs with Pr0.05 are shown.
M.S. Shah et al. / Data in Brief 6 (2016) 398–4044022.2. Fluorescence activated cell sorting of colonic stem cells
Colonic crypts from individual mice were isolated as previously described Sato et al. [1] with
minor modiﬁcation. The intact colons were everted on a disposable mouse gauge needle (Instech
M.S. Shah et al. / Data in Brief 6 (2016) 398–404 403Laboratories) and incubated with 20 mM EDTA in PBS at 37 °C for 30 min. Following transfer to
chilled Ca/Mg free HBSS, colons were vigorously vortexed to release crypts. The crypts were then
incubated with 50 ul of DNase (stock concentration – 20 units/ml) in 10 ml of trypsin solution and
single cells were then passed through a 40 micron cell strainer. Cells were counted and resuspended
to a ﬁnal cell density of 2106 cells/mL. FACS (Fluorescence activated cell sorting) was then carried
out to isolate the Lgr5high expressing stem cells, Lgr5low expressing daughter cells and Lgr5negative cells
isolated from the colon using a BD FACS Aria II cytometer /sorter (BD Biosciences). Cells from wild
type mice were used to set the gates for sorting.
2.3. RNA analyses
Total RNA from Lgr5high, Lgr5low and Lgr5negative sorted cells was isolated. For this purpose, cells
from individual mice from all 4 groups (total of 60 samples) were separately processed using the
mirVana miRNA Isolation Kit according to manufacturer’s instructions (Ambion, Austin, TX).
Expression of 368 mature miRNAs was determined using TaqMan Rodent MicroRNA A Array 2.0 (Life
Technologies, Grand Island, NY) as we have previously described [2,3]. For mRNA proﬁling, samples
were randomized prior to RNASeq library preparation. Sequencing libraries from RNA (10 ng) were
generated using the TruSeq RNA Sample Preparation kit (Illumina, San diego, CA). ERCC (Life Tech-
nologies, Grand Island, NY) was added at the appropriate level as per manufacturer instructions. The
libraries were pooled and sequenced using an Illumina HiSeq 2500 at SeqWright Genomic Services
(Houston, TX). Sequencing data was provided demultiplexed and aligned using STAR with default
parameters [4] and referenced against Mus musculus (UCSC version mm10).
2.4. Statistical analyses
For miRNA and mRNA proﬁling, two sided t-tests with Welch correction for unequal variance were
performed on select miRNA across the speciﬁc treatment comparisons of interest. Mann–Whitney U
nonparametric tests were also performed as a control against non-normal data and similar P-values
were obtained. Standard error bars were plotted in order to document the variation in the population
mean. P values o0.05 were considered to be statistically signiﬁcant, and genes were selected for
analysis using prior knowledge without considering P-values. Therefore, no multiple testing correc-
tion procedure was used. Standardized differences for the miRNAs and mRNAs were computed and a
two-sample t-test was utilized to compare them. Small p-values indicated strong evidence of the
hypothesized trend.Acknowledgments
We gratefully acknowledge grant support from the National Institutes of Health grants (CA168312,
CA129444, P30ES023512 and F32DK107108) and the American Institute for Cancer Research 208460.Appendix A. Supplementary material
Supplementary data associated with this article can be found in the online version at http://dx.doi.
org/10.1016/j.dib.2015.12.026.References
[1] T. Sato, R.G. Vries, H.J. Snippert, M. van de Wetering, N. Barker, D.E. Stange, et al., Single Lgr5 stem cells build crypt-villus
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Data describing the effects of dietary bioactive agents on colonic stem cell microRNA and mRNA expression 

Harvard University - DASH 

Data describing the effects of dietary bioactive agents on colonic stem cell microRNA and mRNA expression

With the identification of Lgr5 as a definitive marker for intestinal stem cells, we used the highly novel, recently described, Lgr5-EGFP-IRES-cre ERT2 knock in mouse model. Mice were injected with azoxymethane (AOM, a colon carcinogen) or saline (control) and fed a chemo-protective diet containing n-3 fatty acids and fermentable fiber (n-3 PUFA+pectin) or a control diet (n-6 PUFA + cellulose). Single cells were isolated from colonic mucosa crypts and three discrete populations of cells were collected via fluorescence activated cell sorting (FACS): Lgr5high (stem cells), Lgr5low (daughter cells) and Lgr5negative (differentiated cells). microRNA profiling and RNA sequencing were performed from the same sample and analyzed. These data refer to ‘Comparative effects of diet and carcinogen on microRNA expression in the stem cell niche of the mouse colonic crypt’ (Shah et al., 2016) [5]

Data describing the effects of dietary bioactive agents on colonic stem cell microRNA and mRNA expression

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