title: Smad4-KO  E13.5

data_processing:
The RNA-seq data were analyzed by following the procedure described below. Briefly, after sequence quality filtering at a cutoff of a minimum quality score Q20 in at least 90% bases, the good-quality reads aligned to Reads were processed and aligned to the University of California Santa Cruz (UCSC) mouse reference genome and transcriptome (build mm9) using the Burrows-Wheeler Aligner (BWA) (Li and Durbin 2009).
The reads that are uniquely aligned to the exon and splicing junction sites for each transcript were combined to calculate an expression level for a corresponding transcript and further normalized based on reads per kilobase per million reads in order to compare transcription levels among samples. The transcripts with a low raw read count <100 in all the samples were excluded for downstream analysis. Gene expression value was transformed to the log 2 base scale.
Principle Component Analysis (PCA) was firstly performed to assess the sample correlations using the expression data of all the genes. The differentially expressed genes for mRNA and lncRNA in tumor compared with normal were identified by the R package and we selected the genes based on limma test adjusted P<0.05 and 1.5-fold change. The gene ontology (GO) and pathway analysis for the differentially expressed genes were then performed with fold change cutoff of ≥1.5 using INGENUITY© IPA (www.ingenuity.com/products/ipa) and the online tool Enrichr.
The read coverage of gene functional elements was also visualized by the Integrative Genome Viewer tool (www.broadinstitute.org/igv/) from the genome alignment file. Heatmap was used to visualize the top 50 differentially expressed genes using the limma test after the median center was transformed using Multi-Experiment Viewer software (Saeed, Sharov et al. 2003).
Genome_build: mm9
Supplementary_files_format_and_content: Normalized gene expression data was generated in tab delimited files

extract_protocol:
Total RNA was isolated from the forelimbs of mouse embryos using Trizol reageant (Invitrogen, USA). RNA-seq Sample Preparation Kit (Illumina) was used to generate sequencing libraries according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample group

value: Embryonic day 13.5


title: Smad4-KO  E14.5

status: Public on May 07 2018

type: SRA

city: New York

first: Chengguo

last: Wei

state: NY

address: 1428 Madison Ave1468 Madison Ave

department: Medicine

country: USA

institute: Icahn School of Medicine at Mount Sinai

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: forelimb

tag: tissue

value: forelimb

tag: age

value: Embryonic day 14.5


title: Smad4-KO E12.5

value: Embryonic day 12.5


title: WT E14.5

value: wild type


title: WT E13.5


title: WT E12.5


title: WT E11.5

value: Embryonic day 11.5


title: Smad4-KO E11.5


title: Plus-tree_380

type: genomic

city: Hitachi

first: Kentaro

last: Mishima

state: Ibaraki

address: 3809-1 Juochoishi

department: Breeding Department

country: Japan

institute: Forest Tree Breeding Center

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix GeneTitan Multi-Color Instrument.

data_processing: The array image was acquired using Affymetrix GeneChip Operating Software (GCOS).  Genotypes were produced by AxiomGTv1 algorithm (Axiom Analysis Suite).

label: Biotin

molecule: genomic DNA

organism: Cryptomeria japonica

source_name: Plus-tree

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from  leaf of Japanese cedar using a Qiagen Dneasy Plant Mini Kit. A quality and quantity was assessed using a Nanodrop PlantSpectrophotometer.

value: Needle leaf


title: Plus-tree_367


title: Plus-tree_361


title: Plus-tree_384


title: Plus-tree_366


title: Plus-tree_381


title: Plus-tree_368


title: Plus-tree_359


title: Plus-tree_372


title: Plus-tree_373


title: Plus-tree_383


title: Plus-tree_375


title: Plus-tree_362


title: Plus-tree_374


title: Plus-tree_360


title: Plus-tree_371


title: Plus-tree_376


title: Plus-tree_370


title: Plus-tree_378


title: Plus-tree_363


title: Plus-tree_382


title: Plus-tree_364


title: Plus-tree_365


title: Plus-tree_369


title: Plus-tree_379


title: Plus-tree_356


title: Plus-tree_358


title: Plus-tree_357


title: Plus-tree_354


title: Plus-tree_353


title: Plus-tree_351


title: Plus-tree_349


title: Plus-tree_350


title: Plus-tree_352


title: Plus-tree_347


title: Plus-tree_348


title: Plus-tree_346


title: Plus-tree_335


title: Plus-tree_345


title: Plus-tree_330


title: Plus-tree_341


title: Plus-tree_329


title: Plus-tree_343


title: Plus-tree_338


title: Plus-tree_337


title: Plus-tree_332


title: Plus-tree_340


title: Plus-tree_328


title: Plus-tree_324


title: Plus-tree_333


title: Plus-tree_336


title: Plus-tree_334


title: Plus-tree_323


title: Plus-tree_331


title: Plus-tree_327


title: Plus-tree_325


title: Plus-tree_342


title: Plus-tree_318


title: Plus-tree_321


title: Plus-tree_339


title: Plus-tree_320


title: Plus-tree_317


title: Plus-tree_316


title: Plus-tree_326


title: Plus-tree_319


title: Plus-tree_344


title: Plus-tree_311


title: Plus-tree_315


title: Plus-tree_312


title: Plus-tree_313


title: Plus-tree_310


title: Plus-tree_309


title: Plus-tree_296


title: Plus-tree_314


title: Plus-tree_307


title: Plus-tree_305


title: Plus-tree_304


title: Plus-tree_303


title: Plus-tree_299


title: Plus-tree_308


title: Plus-tree_295


title: Plus-tree_293


title: Plus-tree_297


title: Plus-tree_300


title: Plus-tree_289


title: Plus-tree_306


title: Plus-tree_291


title: Plus-tree_302


title: Plus-tree_290


title: Plus-tree_301


title: Plus-tree_292


title: Plus-tree_286


title: Plus-tree_287


title: Plus-tree_294


title: Plus-tree_288


title: Plus-tree_284


title: Plus-tree_283


title: Plus-tree_279


title: Plus-tree_277


title: Plus-tree_272


title: Plus-tree_266


title: Plus-tree_280


title: Plus-tree_285


title: Plus-tree_278


title: Plus-tree_273


title: Plus-tree_281


title: Plus-tree_267


title: Plus-tree_264


title: Plus-tree_282


title: Plus-tree_274


title: Plus-tree_262


title: Plus-tree_265


title: Plus-tree_260


title: Plus-tree_270


title: Plus-tree_271


title: Plus-tree_263


title: Plus-tree_269


title: Plus-tree_276


title: Plus-tree_275


title: Plus-tree_261


title: Plus-tree_259


title: Plus-tree_268


title: smallRNA gmax NAM64 PI574.486

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

description: small RNA

data_processing:
MethylC-seq analysis was performed as described in (Schmtiz et al. 2013).
RNA-seq was performed using TopHat v2.0.13 and Cufflinks v2.2.1.
Small RN-seq was performed using Illumina small RNA TruSeq library prep kit.
Genome_build: Glycine max
Supplementary_files_format_and_content: Tab-delimited text files: see "allc_header_descriptions.txt", "genome.sort.txt_description.txt" and "RNA_column_header_descriptions.txt" for column headers.

organism: Glycine max

extract_protocol: MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.

tag: cultivar

value: leaf


title: smallRNA gmax NAM54 PI404.188A

description: small RNA


title: smallRNA gmax NAM50 PI561.370

description: small RNA


title: Plus-tree_253


title: Plus-tree_251


title: Plus-tree_247


title: Plus-tree_252


title: Plus-tree_250


title: Plus-tree_244


title: Plus-tree_249


title: Plus-tree_257


title: Plus-tree_248


title: Plus-tree_243


title: Plus-tree_238


title: Plus-tree_239


title: Plus-tree_233


title: Plus-tree_237


title: Plus-tree_245


title: Plus-tree_255


title: Plus-tree_242


title: Plus-tree_256


title: Plus-tree_240


title: Plus-tree_234


title: Plus-tree_241


title: Plus-tree_254


title: Plus-tree_246


title: Plus-tree_235


title: Plus-tree_236


title: smallRNA gmax NAM48 PI518.751

description: small RNA


title: smallRNA gmax NAM41 PI427.136

description: small RNA


title: smallRNA gmax NAM40 PI398.881

description: small RNA


title: smallRNA gmax NAM42 PI437.169B

description: small RNA


title: smallRNA gmax NAM37 LG98-1605

description: small RNA


title: smallRNA gmax NAM38 LG00-3377

description: small RNA


title: smallRNA gmax NAM36 LG97-7012

description: small RNA


title: smallRNA gmax NAM34 LG94-1906

description: small RNA


title: Plus-tree_232


title: smallRNA gmax NAM32 LG92-1255

description: small RNA


title: Plus-tree_230


title: Plus-tree_231


title: smallRNA gmax NAM30 LG05-4832

description: small RNA


title: Plus-tree_225


title: Plus-tree_224


title: smallRNA gmax NAM39 LG04-6000

description: small RNA


title: Plus-tree_227


title: Plus-tree_228


title: Plus-tree_226


title: smallRNA gmax NAM46 PI507.681B

description: small RNA


title: smallRNA gmax NAM29 LG05-4464

description: small RNA


title: smallRNA gmax NAM28 LG05-4317

description: small RNA


title: Plus-tree_229


title: smallRNA gmax NAM27 LG05-4292

description: small RNA


title: smallRNA gmax NAM31 LG90-2550

description: small RNA


title: smallRNA gmax NAM26 LG04-4717

description: small RNA


title: smallRNA gmax NAM33 LG94-1128

description: small RNA


title: Plus-tree_223


title: smallRNA gmax NAM25 LG03-3191

description: small RNA


title: Plus-tree_220


title: Plus-tree_217


title: smallRNA gmax NAM24 LG03-2979

description: small RNA


title: smallRNA gmax NAM23 U03-100612

description: small RNA


title: Plus-tree_219


title: Plus-tree_218


title: Plus-tree_216


title: Plus-tree_222


title: Plus-tree_214


title: Plus-tree_298


title: Plus-tree_215


title: smallRNA gmax NAM18 NE3001

description: small RNA


title: smallRNA gmax NAM15 Maverick

description: small RNA

source_name: NAM15 Maverick

value: NAM15 Maverick


title: smallRNA gmax NAM17 S06-13640

description: small RNA


title: smallRNA gmax NAM22 Skylla

description: small RNA

source_name: NAM22 Skylla

value: NAM22 Skylla


title: Plus-tree_221


title: smallRNA gmax NAM14 Magellan

description: small RNA

source_name: NAM14 Magellan

value: NAM14 Magellan


title: Plus-tree_211


title: Plus-tree_210


title: Plus-tree_213


title: Plus-tree_212


title: Plus-tree_209


title: smallRNA gmax NAM13 LD02-9050

description: small RNA


title: smallRNA gmax NAM12 LD02-4485

description: small RNA


title: Plus-tree_208


title: Plus-tree_258


title: Plus-tree_205


title: smallRNA gmax NAM09 Prohio

description: small RNA

source_name: NAM09 Prohio

value: NAM09 Prohio


title: Plus-tree_206


title: Plus-tree_207


title: Plus-tree_204


title: smallRNA gmax NAM10 LD00-3309

description: small RNA


title: smallRNA gmax NAM08 HS6-3976

description: small RNA


title: smallRNA gmax NAM05 CL0J095-4-6

description: small RNA


title: smallRNA gmax NAM06 CL0J173-6-8

description: small RNA


title: smallRNA gmax NAM03 4J105-3-4

description: small RNA


title: smallRNA gmax NAM11 LD01-5907

description: small RNA


title: smallRNA gmax NAM IA3023

description: small RNA

source_name: NAM IA3023

value: NAM IA3023


title: smallRNA gmax PI548356 Kanro

description: small RNA

source_name: PI548356 Kanro

value: PI548356 Kanro


title: smallRNA gmax NAM04 5M20-2-5-2

description: small RNA


title: smallRNA gmax PI548348 Illini

description: small RNA

source_name: PI548348 Illini

value: PI548348 Illini


title: smallRNA gmax NAM02 TN05-3027

description: small RNA


title: Plus-tree_198


title: smallRNA gmax PI88788 unnamed

description: small RNA

source_name: PI88788 unnamed

value: PI88788 unnamed


title: smallRNA gmax PI548318 Dunfield

description: small RNA

source_name: PI548318 Dunfield

value: PI548318 Dunfield


title: Plus-tree_203


title: Plus-tree_202


title: Plus-tree_201


title: smallRNA gmax PI641156 NC-Raleigh

description: small RNA

source_name: PI641156 NC-Raleigh

value: PI641156 NC-Raleigh


title: Plus-tree_195


title: smallRNA gmax PI548311 Capital

description: small RNA

source_name: PI548311 Capital

value: PI548311 Capital


title: Plus-tree_192


title: Plus-tree_196


title: Plus-tree_193


title: Plus-tree_197


title: Plus-tree_199


title: smallRNA gmax PI553039 Davis

description: small RNA

source_name: PI553039 Davis

value: PI553039 Davis


title: smallRNA gmax PI553046 Gasoy17

description: small RNA


title: smallRNA gmax PI630984 5601T

description: small RNA


title: smallRNA gmax PI572239 Holladay

description: small RNA

source_name: PI572239 Holladay

value: PI572239 Holladay


title: smallRNA gmax PI548989 Ransom

description: small RNA

source_name: PI548989 Ransom

value: PI548989 Ransom


title: smallRNA gmax PI548988 Pickett

description: small RNA

source_name: PI548988 Pickett

value: PI548988 Pickett


title: smallRNA gmax PI548987 Dare

description: small RNA

source_name: PI548987 Dare

value: PI548987 Dare


title: Plus-tree_194

source_name: Plus-tree

value: Needle leaf


title: Plus-tree_185


title: smallRNA gmax PI548983 Tracy

description: small RNA

source_name: PI548983 Tracy

value: PI548983 Tracy

value: leaf


title: Plus-tree_190


title: smallRNA gmax PI548986 Brim

description: small RNA

source_name: PI548986 Brim

value: PI548986 Brim


title: Plus-tree_186


title: Plus-tree_184


title: Plus-tree_189


title: Plus-tree_187


title: smallRNA gmax PI548298 A.K.(Harrow)

description: small RNA

source_name: PI548298 A.K.(Harrow)

value: PI548298 A.K.(Harrow)


title: smallRNA gmax PI617045 NC-Roy

description: small RNA

source_name: PI617045 NC-Roy

value: PI617045 NC-Roy


title: Plus-tree_183


title: Plus-tree_182


title: Plus-tree_181


title: Plus-tree_180


title: smallRNA gmax PI548980 Hood

description: small RNA

source_name: PI548980 Hood

value: PI548980 Hood


title: smallRNA gmax PI548654 Hill

description: small RNA

source_name: PI548654 Hill

value: PI548654 Hill


title: Plus-tree_191


title: smallRNA gmax PI548975 Centennial

description: small RNA

source_name: PI548975 Centennial

value: PI548975 Centennial


title: Plus-tree_200


title: Plus-tree_188


title: 13CT

city: Nashville

first: Kaylon

last: Bruner-Tran

state: TN

address: 1161 21st Avenue South

institute: Vanderbilt University Medical Center

description:
biological replicate 3 of 3
13CT_251527911473_S01_1_2

hyb_protocol: Samples were hybridized using the Agilent Hybridization master mix as described by the manufacturer and incubated 40 hrs at 67 C in a closed chamber. After hybridization, slides were washed with Agilent Oligo aCGH/ChIP-on-Chip Wash Buffer 2 followed by washing in ultrapure water.

scan_protocol: Images were scanned with SureScan microarray scanner (Agilent)

data_processing:
GeneSpring GX 13.1 software (Agilent Technologies) for background adjustment, summarization, log transformation and baseline transformation.
the sample data table contains normalized/processed data (88,321 data rows) after removal of technical controls.
Relative DNA methylation levels for each probe were determined by examining the Cyanine 5/Cyanine 3 ratios.

source_name: Control Placenta; Unexposed Parents

label_protocol: Methylated regions of a DNA sample were isolated with a monoclonal antibody to 5-methylcytosine which was then labeled with Cyanine 5 and competitively hybridized against similarly Cyanine 3-labeled DNA on a single microarray.

extract_protocol: Placental DNA was isolated by standard methods using the DNeasy Blood & Tissue Kit (QIAGEN, Valencia CA).

treatment_protocol: Pregnant mice (F0) were exposed to TCDD (10μg/kg) in corn oil or vehicle alone by gavage at 1100 hours local time on E15.5.  Adult males (control or F1) were mated to control females and euthanized on E18.5 for collection of placentae.

tag: strain

tag: mouse status

value: Parents exposed to vehicle alone

value: embryonic day 18.5

value: placenta

tag: molecule subtype

value: methylated DNA


title: Plus-tree_178


title: 3F1M

description:
biological replicate 3 of 5
3F1M_251527911471_S01_1_1

source_name: Placenta; Paternal exposure to TCDD

value: Paternal exposure to TCDD


title: 7CT

description:
biological replicate 1 of 3
7CT_251527911471_S01_1_2


title: smallRNA gmax PI548632 Woodworth

description: small RNA

source_name: PI548632 Woodworth

value: PI548632 Woodworth


title: Plus-tree_176


title: smallRNA gmax PI548657 Jackson

description: small RNA

source_name: PI548657 Jackson

value: PI548657 Jackson


title: Plus-tree_173


title: 9F1M

description:
biological replicate 4 of 5
9F1M_251527911472_S01_1_1


title: 12CT

description:
biological replicate 2 of 3
12CT_251527911472_S01_1_2


title: Plus-tree_172


title: Plus-tree_174


title: Plus-tree_177


title: 14F1M

description:
biological replicate 2 of 5
14F1M_251527911470_S01_1_2


title: Plus-tree_179


title: 10F1M

description:
biological replicate 5 of 5
10F1M_251527911473_S01_1_1


title: smallRNA gmax PI548634 Zane

description: small RNA

source_name: PI548634 Zane

value: PI548634 Zane


title: Plus-tree_175

value: Needle leaf


title: smallRNA gmax PI548631 Williams

description: small RNA

source_name: PI548631 Williams

value: PI548631 Williams


title: Standard immunosuppression SIS2

type: RNA

city: Jacksonville

first: Catherine

last: Dumur

state: FL

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133A 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GC3000 scanner.

data_processing: After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.

label: biotin

organism: Homo sapiens

source_name: Kidney

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: gender

value: F

tag: condition

value: Standard immunosuppression


title: Standard immunosuppression SIS5


title: Standard immunosuppression SIS1


title: smallRNA gmax PI548628 Wayne

description: small RNA

source_name: PI548628 Wayne

value: PI548628 Wayne

value: leaf


title: Standard immunosuppression SIS8


title: smallRNA gmax PI548603 Perry

description: small RNA

source_name: PI548603 Perry

value: PI548603 Perry


title: smallRNA gmax PI548586 Kent

description: small RNA

source_name: PI548586 Kent

value: PI548586 Kent


title: smallRNA gmax PI518673 Lawrence

description: small RNA

source_name: PI518673 Lawrence

value: PI518673 Lawrence


title: Standard immunosuppression SIS3


title: Rejection R9

value: M

value: Rejection


title: smallRNA gmax PI548577 Hawkeye

description: small RNA

source_name: PI548577 Hawkeye

value: PI548577 Hawkeye


title: Rejection R15


title: Rejection R4


title: Rejection R8


title: Rejection R11


title: Plus-tree_171

source_name: Plus-tree


title: Tolerance FCRx7

value: Tolerance


title: Rejection R2


title: Tolerance FCRx6


title: Rejection R1


title: Rejection R14


title: Standard immunosuppression SIS4


title: Rejection R13


title: Tolerance FCRx5


title: Rejection R12


title: Tolerance FCRx3


title: Plus-tree_169


title: Tolerance FCRx4


title: Plus-tree_168


title: Plus-tree_170


title: Plus-tree_165


title: Plus-tree_164


title: Plus-tree_166


title: Plus-tree_167


title: Tolerance FCRx1


title: smallRNA gmax PI548573 Harosoy

description: small RNA

source_name: PI548573 Harosoy

value: PI548573 Harosoy


title: smallRNA gmax PI548574 Shelby

description: small RNA

source_name: PI548574 Shelby

value: PI548574 Shelby


title: smallRNA gmax PI548570 Harcor

description: small RNA

source_name: PI548570 Harcor

value: PI548570 Harcor


title: smallRNA gmax PI548562 Ford

description: small RNA

source_name: PI548562 Ford

value: PI548562 Ford


title: smallRNA gmax PI548555 Douglas

description: small RNA

source_name: PI548555 Douglas

value: PI548555 Douglas


title: smallRNA gmax PI548545 Merit

description: small RNA

source_name: PI548545 Merit

value: PI548545 Merit


title: Donor D6

value: Donor


title: Donor D5


title: Donor D7


title: Donor D4


title: Donor D2


title: smallRNA gmax PI548542 Cumberland

description: small RNA

source_name: PI548542 Cumberland

value: PI548542 Cumberland


title: smallRNA gmax PI548540 Corsoy

description: small RNA

source_name: PI548540 Corsoy

value: PI548540 Corsoy


title: smallRNA gmax PI548543 Oakland

description: small RNA

source_name: PI548543 Oakland

value: PI548543 Oakland

value: leaf


title: Tolerance FCRx2


title: smallRNA gmax PI518671 Williams82

description: small RNA

source_name: PI518671 Williams82

value: PI518671 Williams82


title: Donor D1

source_name: Kidney


title: Donor D3


title: Plus-tree_161

value: Needle leaf


title: Plus-tree_163


title: smallRNA gmax PI548530 Chippewa

description: small RNA

source_name: PI548530 Chippewa

value: PI548530 Chippewa


title: 2F1M

description:
biological replicate 1 of 5
2F1M_251527911470_S01_1_1

source_name: Placenta; Paternal exposure to TCDD

value: Paternal exposure to TCDD

value: embryonic day 18.5

value: placenta

value: methylated DNA


title: smallRNA gmax PI548527 Calland

description: small RNA

source_name: PI548527 Calland

value: PI548527 Calland


title: Plus-tree_162


title: Normoxia_PANC-1_Control_rep2

city: Guangzhou

first: Huilin

last: Ye

state: Guangdong

address: No.107 YanJiang West Road

department: Sun Yat-sen Memorial Hospital

country: China

institute: Sun Yat-sen University

description: Gene expression data

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA). After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner.

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.

data_processing: Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization.All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Differentially expressed genes were identified through Fold Change filtering.

source_name: PANC-1 pancreatic cancer cells alone under normoxia

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). One μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.

growth_protocol: PANC-1 cells and tumor-associated macrophages were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin, and 100 mg/ml streptomycin and cultured at 37˚C in humidified air with 5% CO2.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Using transwell coculture system, we cocultured PANC-1 pancreatic cancer cells and tumor-associated macrophages both under normoxia and hypoxia for 4 days.

tag: cell line

value: PANC-1 pancreatic cancer cells


title: smallRNA gmax PI548533 Clark

description: small RNA

source_name: PI548533 Clark

value: PI548533 Clark


title: Normoxia_PANC-1_Macrophage_rep3

description: Gene expression data

source_name: PANC-1 pancreatic cancer cells cocultured with tumor-associated macrophages under normoxia


title: Plus-tree_158

source_name: Plus-tree


title: Plus-tree_160


title: smallRNA gmax PI548523 Pella

description: small RNA

source_name: PI548523 Pella

value: PI548523 Pella


title: Normoxia_PANC-1_Control_rep1

description: Gene expression data


title: Normoxia_PANC-1_Macrophage_rep1

description: Gene expression data


title: Normoxia_PANC-1_Macrophage_rep2

description: Gene expression data


title: Plus-tree_159


title: Normoxia_PANC-1_Control_rep3

description: Gene expression data


title: Plus-tree_155


title: Hypoxia_PANC-1_Macrophage_rep3

description: Gene expression data

source_name: PANC-1 pancreatic cancer cells cocultured with tumor-associated macrophages under hypoxia


title: Plus-tree_154


title: smallRNA gmax PI548517 Bonus

description: small RNA

source_name: PI548517 Bonus

value: PI548517 Bonus


title: Hypoxia_PANC-1_Macrophage_rep2

description: Gene expression data


title: Plus-tree_157


title: Plus-tree_156


title: Plus-tree_151


title: Hypoxia_PANC-1_Macrophage_rep1

description: Gene expression data


title: Hypoxia_PANC-1_Control_rep3

description: Gene expression data

source_name: PANC-1 pancreatic cancer cells alone under hypoxia


title: Hypoxia_PANC-1_Control_rep2

description: Gene expression data


title: smallRNA gmax PI548516 Blackhawk

description: small RNA

source_name: PI548516 Blackhawk

value: PI548516 Blackhawk


title: smallRNA gmax PI548512 Century

description: small RNA

source_name: PI548512 Century

value: PI548512 Century


title: smallRNA gmax PI548505 Amcor

description: small RNA

source_name: PI548505 Amcor

value: PI548505 Amcor


title: smallRNA gmax PI548510 Beeson

description: small RNA

source_name: PI548510 Beeson

value: PI548510 Beeson


title: Hypoxia_PANC-1_Control_rep1

description: Gene expression data


title: smallRNA gmax PI548493 Tokyo

description: small RNA

source_name: PI548493 Tokyo

value: PI548493 Tokyo

value: leaf


title: Plus-tree_153

value: Needle leaf


title: Plus-tree_148


title: smallRNA gmax PI508266 Young

description: small RNA

source_name: PI508266 Young

value: PI508266 Young


title: Plus-tree_149


title: Plus-tree_147


title: Plus-tree_146


title: Plus-tree_152


title: smallRNA gmax PI548488 S-100

description: small RNA


title: smallRNA gmax PI548485 Roanoke

description: small RNA

source_name: PI548485 Roanoke

value: PI548485 Roanoke


title: Plus-tree_150


title: smallRNA gmax PI548484 Ralsoy

description: small RNA

source_name: PI548484 Ralsoy

value: PI548484 Ralsoy


title: Plus-tree_608


title: Plus-tree_609


title: Plus-tree_602


title: Plus-tree_604


title: Plus-tree_606


title: Plus-tree_607


title: Plus-tree_144


title: Plus-tree_603


title: Plus-tree_142


title: Plus-tree_145


title: Plus-tree_605


title: Plus-tree_601


title: Plus-tree_600


title: Plus-tree_143


title: Plus-tree_598


title: smallRNA gmax PI548456 Haberlandt

description: small RNA

source_name: PI548456 Haberlandt

value: PI548456 Haberlandt


title: Plus-tree_597


title: Plus-tree_141


title: smallRNA gmax PI548406 Richland

description: small RNA

source_name: PI548406 Richland

value: PI548406 Richland


title: Plus-tree_596


title: smallRNA gmax PI548477 Ogden

description: small RNA

source_name: PI548477 Ogden

value: PI548477 Ogden


title: smallRNA gmax PI548391 Mukden

description: small RNA

source_name: PI548391 Mukden

value: PI548391 Mukden


title: smallRNA gmax PI548379 Mandarin

description: small RNA

source_name: PI548379 Mandarin

value: PI548379 Mandarin


title: smallRNA gmax PI548362 Lincoln

description: small RNA

source_name: PI548362 Lincoln

value: PI548362 Lincoln


title: Plus-tree_593

source_name: Plus-tree


title: Plus-tree_139


title: Plus-tree_140


title: Plus-tree_594


title: Plus-tree_591


title: Plus-tree_138


title: Plus-tree_595


title: smallRNA gmax FC33243 Anderson

description: small RNA

source_name: FC33243 Anderson

value: FC33243 Anderson


title: Plus-tree_587


title: Plus-tree_590


title: Plus-tree_584


title: Plus-tree_585


title: Plus-tree_589


title: Plus-tree_599


title: Plus-tree_592


title: Plus-tree_135


title: Plus-tree_588


title: Plus-tree_586


title: Plus-tree_136


title: Plus-tree_582


title: mRNA gmax NAM IA3023

description:
mRNA RNA
Parent
processed data file: RNA_soybean_FPKM_table.txt

source_name: NAM IA3023

value: NAM IA3023


title: Plus-tree_583


title: Plus-tree_134


title: smallRNA gmax PI548360 Korean

description: small RNA

source_name: PI548360 Korean

value: PI548360 Korean


title: Plus-tree_137


title: mRNA gmax NAM64 PI574.486

description:
mRNA RNA
NAM64
processed data file: RNA_soybean_FPKM_table.txt


title: Plus-tree_581


title: mRNA gmax NAM54 PI404.188A

description:
mRNA RNA
NAM54
processed data file: RNA_soybean_FPKM_table.txt


title: mRNA gmax NAM50 PI561.370

description:
mRNA RNA
NAM50
processed data file: RNA_soybean_FPKM_table.txt


title: mRNA gmax NAM48 PI518.751

description:
mRNA RNA
NAM48
processed data file: RNA_soybean_FPKM_table.txt


title: mRNA gmax NAM46 PI507.681B

description:
mRNA RNA
NAM46
processed data file: RNA_soybean_FPKM_table.txt


title: Plus-tree_580


title: Plus-tree_579


title: mRNA gmax NAM42 PI437.169B

description:
mRNA RNA
NAM42
processed data file: RNA_soybean_FPKM_table.txt


title: Plus-tree_578


title: Plus-tree_133


title: CjMSF2_204


title: CjMSF2_203


title: CjMSF2_205


title: mRNA gmax NAM41 PI427.136

description:
mRNA RNA
NAM41
processed data file: RNA_soybean_FPKM_table.txt


title: CjMSF2_198


title: Plus-tree_577


title: Plus-tree_132


title: CjMSF2_197


title: Plus-tree_129


title: Plus-tree_128


title: Plus-tree_130


title: CjMSF2_201


title: CjMSF2_200


title: CjMSF2_SHK7


title: Plus-tree_127


title: Plus-tree_131


title: CjMSF2_196


title: CjMSF2_199


title: Plus-tree_126


title: CjMSF2_202


title: CjMSF2_194


title: mRNA gmax NAM39 LG04-6000

description:
mRNA RNA
NAM39
processed data file: RNA_soybean_FPKM_table.txt


title: Plus-tree_125


title: mRNA gmax NAM40 PI398.881

description:
mRNA RNA
NAM40
processed data file: RNA_soybean_FPKM_table.txt


title: mRNA gmax NAM37 LG98-1605

description:
mRNA RNA
NAM37
processed data file: RNA_soybean_FPKM_table.txt


title: mRNA gmax NAM34 LG94-1906

description:
mRNA RNA
NAM34
processed data file: RNA_soybean_FPKM_table.txt


title: mRNA gmax NAM38 LG00-3377

description:
mRNA RNA
NAM38
processed data file: RNA_soybean_FPKM_table.txt


title: mRNA gmax NAM36 LG97-7012

description:
mRNA RNA
NAM36
processed data file: RNA_soybean_FPKM_table.txt


title: CjMSF2_191


title: mRNA gmax NAM33 LG94-1128

description:
mRNA RNA
NAM33
processed data file: RNA_soybean_FPKM_table.txt


title: mRNA gmax NAM32 LG92-1255

description:
mRNA RNA
NAM32
processed data file: RNA_soybean_FPKM_table.txt


title: CjMSF2_190


title: Plus-tree_123


title: Plus-tree_122


title: CjMSF2_189


title: CjMSF2_195


title: CjMSF2_180


title: Plus-tree_124


title: CjMSF2_184


title: CjMSF2_188


title: CjMSF2_181


title: CjMSF2_187


title: CjMSF2_179


title: CjMSF2_178


title: CjMSF2_182


title: CjMSF2_174


title: CjMSF2_183


title: Plus-tree_118


title: Plus-tree_121


title: CjMSF2_176


title: CjMSF2_173


title: mRNA gmax NAM31 LG90-2550

description:
mRNA RNA
NAM31
processed data file: RNA_soybean_FPKM_table.txt


title: CjMSF2_172


title: Plus-tree_119


title: Plus-tree_120


title: mRNA gmax NAM29 LG05-4464

description:
mRNA RNA
NAM29
processed data file: RNA_soybean_FPKM_table.txt


title: mRNA gmax NAM28 LG05-4317

description:
mRNA RNA
NAM28
processed data file: RNA_soybean_FPKM_table.txt


title: mRNA gmax NAM30 LG05-4832

description:
mRNA RNA
NAM30
processed data file: RNA_soybean_FPKM_table.txt


title: mRNA gmax NAM27 LG05-4292

description:
mRNA RNA
NAM27
processed data file: RNA_soybean_FPKM_table.txt


title: mRNA gmax NAM26 LG04-4717

description:
mRNA RNA
NAM26
processed data file: RNA_soybean_FPKM_table.txt


title: mRNA gmax NAM25 LG03-3191

description:
mRNA RNA
NAM25
processed data file: RNA_soybean_FPKM_table.txt


title: CjMSF2_170


title: CjMSF2_167


title: mRNA gmax NAM24 LG03-2979

description:
mRNA RNA
NAM24
processed data file: RNA_soybean_FPKM_table.txt


title: mRNA gmax NAM23 U03-100612

description:
mRNA RNA
NAM23
processed data file: RNA_soybean_FPKM_table.txt


title: CjMSF2_161


title: Plus-tree_115


title: Plus-tree_114


title: CjMSF2_171


title: CjMSF2_169


title: CjMSF2_162


title: CjMSF2_165


title: CjMSF2_158


title: Plus-tree_113


title: Plus-tree_116


title: CjMSF2_168


title: CjMSF2_163


title: CjMSF2_160


title: Plus-tree_110


title: CjMSF2_157


title: CjMSF2_159


title: Plus-tree_112


title: CjMSF2_166


title: CjMSF2_156


title: Plus-tree_111


title: CjMSF2_154


title: Plus-tree_108


title: CjMSF2_155


title: mRNA gmax NAM18 NE3001

description:
mRNA RNA
NAM18
processed data file: RNA_soybean_FPKM_table.txt


title: Plus-tree_117


title: mRNA gmax NAM17 S06-13640

description:
mRNA RNA
NAM17
processed data file: RNA_soybean_FPKM_table.txt


title: mRNA gmax NAM22 Skylla

description:
mRNA RNA
NAM22
processed data file: RNA_soybean_FPKM_table.txt

source_name: NAM22 Skylla

value: NAM22 Skylla


title: mRNA gmax NAM14 Magellan

description:
mRNA RNA
NAM14
processed data file: RNA_soybean_FPKM_table.txt

source_name: NAM14 Magellan

value: NAM14 Magellan


title: CjMSF2_150


title: CjMSF2_152


title: mRNA gmax NAM13 LD02-9050

description:
mRNA RNA
NAM13
processed data file: RNA_soybean_FPKM_table.txt


title: CjMSF2_148


title: Plus-tree_106


title: Plus-tree_105


title: Plus-tree_109


title: CjMSF2_145


title: CjMSF2_146


title: mRNA gmax NAM12 LD02-4485

description:
mRNA RNA
NAM12
processed data file: RNA_soybean_FPKM_table.txt


title: CjMSF2_153


title: mRNA gmax NAM15 Maverick

description:
mRNA RNA
NAM15
processed data file: RNA_soybean_FPKM_table.txt

source_name: NAM15 Maverick

value: NAM15 Maverick


title: Plus-tree_107


title: Plus-tree_104


title: Plus-tree_103


title: CjMSF2_143


title: CjMSF2_141


title: Plus-tree_102


title: mRNA gmax NAM10 LD00-3309

description:
mRNA RNA
NAM10
processed data file: RNA_soybean_FPKM_table.txt

value: leaf


title: CjMSF2_147

value: Needle leaf


title: CjMSF2_142


title: mRNA gmax NAM09 Prohio

description:
mRNA RNA
NAM09
processed data file: RNA_soybean_FPKM_table.txt

source_name: NAM09 Prohio

value: NAM09 Prohio


title: CjMSF2_144


title: CjMSF2_138


title: CjMSF2_139


title: CjMSF2_137


title: CjMSF2_140


title: CjMSF2_136


title: Plus-tree_100


title: mRNA gmax NAM06 CL0J173-6-8

description:
mRNA RNA
NAM06
processed data file: RNA_soybean_FPKM_table.txt


title: Plus-tree_101


title: mRNA gmax NAM08 HS6-3976

description:
mRNA RNA
NAM08
processed data file: RNA_soybean_FPKM_table.txt


title: mRNA gmax NAM05 CL0J095-4-6

description:
mRNA RNA
NAM05
processed data file: RNA_soybean_FPKM_table.txt


title: mRNA gmax NAM04 5M20-2-5-2

description:
mRNA RNA
NAM04
processed data file: RNA_soybean_FPKM_table.txt


title: mRNA gmax NAM11 LD01-5907

description:
mRNA RNA
NAM11
processed data file: RNA_soybean_FPKM_table.txt


title: CjMSF2_134


title: CjMSF2_131


title: CjMSF2_133


title: Plus-tree_097


title: CjMSF2_135


title: Plus-tree_096


title: Plus-tree_099


title: mRNA gmax NAM03 4J105-3-4

description:
mRNA RNA
NAM03
processed data file: RNA_soybean_FPKM_table.txt


title: mRNA gmax NAM02 TN05-3027

description:
mRNA RNA
NAM02
processed data file: RNA_soybean_FPKM_table.txt


title: CjMSF2_129


title: CjMSF2_130


title: CjMSF2_127


title: Plus-tree_094


title: CjMSF2_126


title: Plus-tree_095


title: Plus-tree_SxHK7


title: CjMSF2_124


title: CjMSF2_128


title: CjMSF2_125


title: CjMSF2_121


title: mRNA gmax PI548348 Illini

description:
mRNA RNA
8
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548348 Illini

value: PI548348 Illini


title: mRNA gmax PI548318 Dunfield

description:
mRNA RNA
7
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548318 Dunfield

value: PI548318 Dunfield


title: Plus-tree_SxK6


title: mRNA gmax PI88788 unnamed

description:
mRNA RNA
61
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI88788 unnamed

value: PI88788 unnamed


title: mRNA gmax PI548356 Kanro

description:
mRNA RNA
9
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548356 Kanro

value: PI548356 Kanro


title: CjMSF2_119


title: CjMSF2_117


title: mRNA gmax PI641156 NC-Raleigh

description:
mRNA RNA
60
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI641156 NC-Raleigh

value: PI641156 NC-Raleigh


title: Plus-tree_093


title: CjMSF2_118


title: Plus-tree_092


title: CjMSF2_111


title: CjMSF2_113


title: CjMSF2_120


title: CjMSF2_116


title: CjMSF2_114


title: mRNA gmax PI630984 5601T

description:
mRNA RNA
59
processed data file: RNA_soybean_FPKM_table.txt


title: CjMSF2_112


title: CjMSF2_115


title: Plus-tree_086


title: Plus-tree_088


title: CjMSF2_110


title: mRNA gmax PI572239 Holladay

description:
mRNA RNA
57
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI572239 Holladay

value: PI572239 Holladay


title: mRNA gmax PI548311 Capital

description:
mRNA RNA
6
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548311 Capital

value: PI548311 Capital


title: Plus-tree_085


title: CjMSF2_108


title: CjMSF2_151


title: CjMSF2_109


title: CjMSF2_104


title: mRNA gmax PI553046 Gasoy17

description:
mRNA RNA
56
processed data file: RNA_soybean_FPKM_table.txt


title: CjMSF2_107


title: Plus-tree_084


title: Plus-tree_087


title: Plus-tree_083


title: CjMSF2_103


title: CjMSF2_105


title: CjMSF2_106


title: CjMSF2_102


title: mRNA gmax PI617045 NC-Roy

description:
mRNA RNA
58
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI617045 NC-Roy

value: PI617045 NC-Roy


title: mRNA gmax PI553039 Davis

description:
mRNA RNA
55
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI553039 Davis

value: PI553039 Davis


title: CjMSF2_101


title: CjMSF2_100


title: Plus-tree_082

source_name: Plus-tree


title: CjMSF2_098


title: mRNA gmax PI548989 Ransom

description:
mRNA RNA
54
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548989 Ransom

value: PI548989 Ransom


title: Plus-tree_081


title: mRNA gmax PI548987 Dare

description:
mRNA RNA
52
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548987 Dare

value: PI548987 Dare


title: CjMSF2_097


title: mRNA gmax PI548986 Brim

description:
mRNA RNA
51
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548986 Brim

value: PI548986 Brim


title: Plus-tree_080


title: mRNA gmax PI548983 Tracy

description:
mRNA RNA
50
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548983 Tracy

value: PI548983 Tracy


title: mRNA gmax PI548298 A.K.(Harrow)

description:
mRNA RNA
5
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548298 A.K.(Harrow)

value: PI548298 A.K.(Harrow)


title: mRNA gmax PI548988 Pickett

description:
mRNA RNA
53
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548988 Pickett

value: PI548988 Pickett

value: leaf


title: CjMSF2_096

value: Needle leaf


title: CjMSF2_093


title: CjMSF2_092


title: CjMSF2_095


title: CjMSF2_099


title: Plus-tree_079


title: CjMSF2_094


title: Plus-tree_076


title: Plus-tree_078


title: CjMSF2_SK6


title: CjMSF2_090


title: CjMSF2_091


title: Plus-tree_077


title: mRNA gmax PI548975 Centennial

description:
mRNA RNA
48
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548975 Centennial

value: PI548975 Centennial


title: mRNA gmax PI548980 Hood

description:
mRNA RNA
49
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548980 Hood

value: PI548980 Hood


title: Plus-tree_074


title: CjMSF2_089


title: mRNA gmax PI548657 Jackson

description:
mRNA RNA
47
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548657 Jackson

value: PI548657 Jackson


title: Plus-tree_075


title: mRNA gmax PI548654 Hill

description:
mRNA RNA
46
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548654 Hill

value: PI548654 Hill


title: CjMSF2_086


title: CjMSF2_085


title: mRNA gmax PI548634 Zane

description:
mRNA RNA
45
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548634 Zane

value: PI548634 Zane


title: CjMSF2_083


title: mRNA gmax PI548632 Woodworth

description:
mRNA RNA
44
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548632 Woodworth

value: PI548632 Woodworth


title: CjMSF2_084


title: Plus-tree_070


title: Plus-tree_072


title: Plus-tree_071


title: CjMSF2_087


title: CjMSF2_079


title: mRNA gmax PI548631 Williams

description:
mRNA RNA
43
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548631 Williams

value: PI548631 Williams


title: CjMSF2_080


title: CjMSF2_082


title: Plus-tree_073


title: CjMSF2_077


title: CjMSF2_081


title: mRNA gmax PI548628 Wayne

description:
mRNA RNA
42
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548628 Wayne

value: PI548628 Wayne


title: Plus-tree_068


title: Plus-tree_069


title: CjMSF2_076


title: CjMSF2_078


title: mRNA gmax PI548603 Perry

description:
mRNA RNA
41
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548603 Perry

value: PI548603 Perry


title: CjMSF2_073


title: CjMSF2_074


title: CjMSF2_072


title: mRNA gmax PI548586 Kent

description:
mRNA RNA
40
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548586 Kent

value: PI548586 Kent


title: Plus-tree_066

source_name: Plus-tree


title: Plus-tree_067


title: mRNA gmax PI518673 Lawrence

description:
mRNA RNA
4
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI518673 Lawrence

value: PI518673 Lawrence


title: CjMSF2_075


title: CjMSF2_069


title: CjMSF2_070


title: CjMSF2_068


title: mRNA gmax PI548577 Hawkeye

description:
mRNA RNA
39
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548577 Hawkeye

value: PI548577 Hawkeye


title: CjMSF2_071


title: Plus-tree_065


title: mRNA gmax PI548574 Shelby

description:
mRNA RNA
38
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548574 Shelby

value: PI548574 Shelby


title: mRNA gmax PI548573 Harosoy

description:
mRNA RNA
37
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548573 Harosoy

value: PI548573 Harosoy


title: CjMSF2_067


title: mRNA gmax PI548570 Harcor

description:
mRNA RNA
36
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548570 Harcor

value: PI548570 Harcor


title: Plus-tree_063


title: CjMSF2_063


title: mRNA gmax PI548562 Ford

description:
mRNA RNA
35
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548562 Ford

value: PI548562 Ford

value: leaf


title: CjMSF2_065

value: Needle leaf


title: Plus-tree_064


title: CjMSF2_066


title: CjMSF2_062


title: CjMSF2_064


title: Plus-tree_061


title: CjMSF2_058


title: Plus-tree_060


title: Plus-tree_062


title: CjMSF2_061


title: mRNA gmax PI548555 Douglas

description:
mRNA RNA
34
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548555 Douglas

value: PI548555 Douglas


title: Plus-tree_059


title: CjMSF2_057


title: CjMSF2_055


title: CjMSF2_059


title: CjMSF2_056


title: Plus-tree_058


title: mRNA gmax PI548545 Merit

description:
mRNA RNA
33
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548545 Merit

value: PI548545 Merit


title: CjMSF2_054


title: mRNA gmax PI548543 Oakland

description:
mRNA RNA
32
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548543 Oakland

value: PI548543 Oakland


title: CjMSF2_060


title: CjMSF2_053


title: CjMSF2_052


title: mRNA gmax PI548542 Cumberland

description:
mRNA RNA
31
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548542 Cumberland

value: PI548542 Cumberland


title: CjMSF2_051


title: CjMSF2_047


title: CjMSF2_049


title: Plus-tree_056


title: Plus-tree_055


title: mRNA gmax PI518671 Williams82

description:
mRNA RNA
3
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI518671 Williams82

value: PI518671 Williams82


title: CjMSF2_048


title: CjMSF2_050


title: Plus-tree_053


title: mRNA gmax PI548540 Corsoy

description:
mRNA RNA
30
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548540 Corsoy

value: PI548540 Corsoy


title: CjMSF2_046


title: mRNA gmax PI548533 Clark

description:
mRNA RNA
29
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548533 Clark

value: PI548533 Clark


title: CjMSF2_045


title: mRNA gmax PI548530 Chippewa

description:
mRNA RNA
28
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548530 Chippewa

value: PI548530 Chippewa


title: CjMSF2_040


title: CjMSF2_042


title: CjMSF2_043


title: Plus-tree_052


title: CjMSF2_036


title: Plus-tree_054


title: CjMSF2_041


title: CjMSF2_044


title: CjMSF2_039


title: CjMSF2_038


title: Plus-tree_050


title: Plus-tree_051


title: CjMSF2_035


title: mRNA gmax PI548523 Pella

description:
mRNA RNA
26
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548523 Pella

value: PI548523 Pella


title: mRNA gmax PI548516 Blackhawk

description:
mRNA RNA
24
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548516 Blackhawk

value: PI548516 Blackhawk


title: mRNA gmax PI548527 Calland

description:
mRNA RNA
27
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548527 Calland

value: PI548527 Calland


title: mRNA gmax PI548517 Bonus

description:
mRNA RNA
25
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548517 Bonus

value: PI548517 Bonus


title: mRNA gmax PI548512 Century

description:
mRNA RNA
23
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548512 Century

value: PI548512 Century


title: Plus-tree_048

source_name: Plus-tree


title: mRNA gmax PI548510 Beeson

description:
mRNA RNA
22
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548510 Beeson

value: PI548510 Beeson


title: CjMSF2_033


title: Plus-tree_049


title: mRNA gmax PI548505 Amcor

description:
mRNA RNA
21
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548505 Amcor

value: PI548505 Amcor


title: CjMSF2_029


title: CjMSF2_031


title: CjMSF2_027


title: Plus-tree_047


title: mRNA gmax PI548493 Tokyo

description:
mRNA RNA
20
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548493 Tokyo

value: PI548493 Tokyo

value: leaf


title: Plus-tree_046

value: Needle leaf


title: CjMSF2_030


title: CjMSF2_028


title: CjMSF2_023


title: CjMSF2_026


title: Plus-tree_044


title: Plus-tree_045


title: CjMSF2_020


title: CjMSF2_022


title: CjMSF2_017


title: CjMSF2_018


title: CjMSF2_025


title: CjMSF2_024


title: mRNA gmax PI508266 Young

description:
mRNA RNA
2
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI508266 Young

value: PI508266 Young


title: CjMSF2_021


title: Plus-tree_043


title: mRNA gmax PI548488 S-100

description:
mRNA RNA
19
processed data file: RNA_soybean_FPKM_table.txt


title: Plus-tree_042


title: Plus-tree_041


title: CjMSF2_016


title: mRNA gmax PI548485 Roanoke

description:
mRNA RNA
18
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548485 Roanoke

value: PI548485 Roanoke


title: mRNA gmax PI548484 Ralsoy

description:
mRNA RNA
17
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548484 Ralsoy

value: PI548484 Ralsoy


title: mRNA gmax PI548477 Ogden

description:
mRNA RNA
16
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548477 Ogden

value: PI548477 Ogden


title: mRNA gmax PI548456 Haberlandt

description:
mRNA RNA
15
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548456 Haberlandt

value: PI548456 Haberlandt


title: mRNA gmax PI548391 Mukden

description:
mRNA RNA
13
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548391 Mukden

value: PI548391 Mukden


title: Plus-tree_057


title: CjMSF2_011


title: Plus-tree_039


title: CjMSF2_007


title: Plus-tree_037


title: CjMSF2_010


title: CjMSF2_014


title: mRNA gmax PI548406 Richland

description:
mRNA RNA
14
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548406 Richland

value: PI548406 Richland


title: CjMSF2_012


title: CjMSF2_013


title: CjMSF2_005


title: CjMSF2_006


title: CjMSF2_015


title: Plus-tree_040


title: CjMSF2_008


title: Plus-tree_035


title: Plus-tree_038


title: CjMSF2_002


title: CjMSF2_009


title: CjMSF2_003


title: Plus-tree_033


title: Plus-tree_036


title: Plus-tree_034


title: CjMSF2_004


title: mRNA gmax PI548379 Mandarin

description:
mRNA RNA
12
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548379 Mandarin

value: PI548379 Mandarin


title: mRNA gmax PI548362 Lincoln

description:
mRNA RNA
11
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548362 Lincoln

value: PI548362 Lincoln


title: mRNA gmax PI548360 Korean

description:
mRNA RNA
10
processed data file: RNA_soybean_FPKM_table.txt

source_name: PI548360 Korean

value: PI548360 Korean


title: Plus-tree_576


title: CjMSF2_001


title: mRNA gmax FC33243 Anderson

description:
mRNA RNA
1
processed data file: RNA_soybean_FPKM_table.txt

source_name: FC33243 Anderson

value: FC33243 Anderson


title: Plus-tree_032


title: methylome gmax NAM IA3023

library_source: genomic

data_processing:
Library strategy: MethylC-seq
MethylC-seq analysis was performed as described in (Schmtiz et al. 2013).
RNA-seq was performed using TopHat v2.0.13 and Cufflinks v2.2.1.
Small RN-seq was performed using Illumina small RNA TruSeq library prep kit.
Genome_build: Glycine max
Supplementary_files_format_and_content: Tab-delimited text files: see "allc_header_descriptions.txt", "genome.sort.txt_description.txt" and "RNA_column_header_descriptions.txt" for column headers.

source_name: NAM IA3023

value: NAM IA3023


title: Plus-tree_575


title: methylome gmax NAM64 PI574.486


title: methylome gmax NAM54 PI404.188A


title: methylome gmax NAM50 PI561.370


title: Plus-tree_029


title: CjMSF2_034


title: Plus-tree_031


title: Plus-tree_030


title: methylome gmax NAM48 PI518.751


title: Plus-tree_028


title: Plus-tree_574


title: Plus-tree_564


title: Plus-tree_566


title: Plus-tree_569


title: Plus-tree_573


title: Plus-tree_572


title: Plus-tree_562


title: Plus-tree_570


title: methylome gmax NAM46 PI507.681B


title: Plus-tree_568


title: Plus-tree_565


title: Plus-tree_571


title: Plus-tree_567


title: Plus-tree_026


title: Plus-tree_561


title: methylome gmax NAM42 PI437.169B


title: methylome gmax NAM41 PI427.136


title: Plus-tree_025


title: Plus-tree_559


title: Plus-tree_027


title: Plus-tree_560


title: methylome gmax NAM40 PI398.881


title: Plus-tree_558


title: Plus-tree_024


title: methylome gmax NAM38 LG00-3377


title: Plus-tree_554


title: Plus-tree_557


title: methylome gmax NAM39 LG04-6000


title: Plus-tree_555


title: Plus-tree_553


title: Plus-tree_563


title: Plus-tree_550


title: Plus-tree_021


title: methylome gmax NAM37 LG98-1605


title: Plus-tree_552


title: Plus-tree_551


title: Plus-tree_022


title: Plus-tree_023


title: Plus-tree_556


title: Plus-tree_549


title: Plus-tree_020


title: Plus-tree_019


title: methylome gmax NAM33 LG94-1128


title: methylome gmax NAM34 LG94-1906


title: Plus-tree_548


title: Plus-tree_546


title: methylome gmax NAM36 LG97-7012


title: Plus-tree_017


title: Plus-tree_547


title: Plus-tree_544


title: Plus-tree_016


title: methylome gmax NAM31 LG90-2550


title: Plus-tree_541


title: Plus-tree_018


title: Plus-tree_015


title: Plus-tree_545


title: methylome gmax NAM32 LG92-1255


title: Plus-tree_543


title: methylome gmax NAM30 LG05-4832


title: Plus-tree_538


title: methylome gmax NAM28 LG05-4317


title: Plus-tree_540


title: Plus-tree_014


title: Plus-tree_013


title: Plus-tree_537


title: Plus-tree_535


title: Plus-tree_542


title: methylome gmax NAM29 LG05-4464


title: methylome gmax NAM27 LG05-4292


title: Plus-tree_539


title: methylome gmax NAM26 LG04-4717


title: Plus-tree_534


title: Plus-tree_533


title: methylome gmax NAM25 LG03-3191


title: Plus-tree_012


title: Plus-tree_010


title: Plus-tree_531


title: Plus-tree_532


title: Plus-tree_530


title: Plus-tree_536


title: methylome gmax NAM24 LG03-2979


title: Plus-tree_527


title: Plus-tree_525


title: Plus-tree_528


title: methylome gmax NAM23 U03-100612


title: Plus-tree_526


title: Plus-tree_009


title: methylome gmax NAM22 Skylla

source_name: NAM22 Skylla

value: NAM22 Skylla


title: Plus-tree_008

source_name: Plus-tree


title: Plus-tree_521


title: Plus-tree_523


title: Plus-tree_520


title: Plus-tree_529


title: Plus-tree_007


title: methylome gmax NAM18 NE3001


title: Plus-tree_005


title: Plus-tree_006


title: methylome gmax NAM17 S06-13640


title: Plus-tree_522


title: Plus-tree_004


title: Plus-tree_518


title: Plus-tree_524


title: Plus-tree_519


title: Plus-tree_011


title: methylome gmax NAM15 Maverick

source_name: NAM15 Maverick

value: NAM15 Maverick


title: Plus-tree_517


title: Plus-tree_003


title: Plus-tree_515


title: Plus-tree_516


title: methylome gmax NAM14 Magellan

source_name: NAM14 Magellan

value: NAM14 Magellan


title: methylome gmax NAM13 LD02-9050

value: leaf


title: methylome gmax NAM12 LD02-4485


title: Plus-tree_002

value: Needle leaf


title: methylome gmax NAM11 LD01-5907


title: Plus-tree_512


title: Plus-tree_514


title: Plus-tree_511


title: methylome gmax NAM10 LD00-3309


title: Plus-tree_510


title: Plus-tree_001


title: Plus-tree_507


title: Plus-tree_509


title: methylome gmax NAM09 Prohio

source_name: NAM09 Prohio

value: NAM09 Prohio


title: Plus-tree_506


title: Plus-tree_513


title: methylome gmax NAM08 HS6-3976


title: F1_MAP1_OT1


title: F1_MAP1_181


title: Plus-tree_508


title: Plus-tree_504


title: methylome gmax NAM06 CL0J173-6-8


title: F1_MAP1_179


title: methylome gmax NAM05 CL0J095-4-6


title: Plus-tree_500


title: F1_MAP1_183


title: Plus-tree_503


title: Plus-tree_501


title: Plus-tree_505


title: Plus-tree_498


title: Plus-tree_502


title: methylome gmax NAM04 5M20-2-5-2


title: F1_MAP1_MN2


title: F1_MAP1_175


title: methylome gmax NAM03 4J105-3-4


title: F1_MAP1_173


title: F1_MAP1_171


title: Plus-tree_499


title: Plus-tree_497


title: Plus-tree_496


title: methylome gmax NAM02 TN05-3027


title: methylome gmax PI548356 Kanro

source_name: PI548356 Kanro

value: PI548356 Kanro


title: Plus-tree_495


title: methylome gmax PI548348 Illini

source_name: PI548348 Illini

value: PI548348 Illini


title: Plus-tree_493


title: F1_MAP1_167


title: Plus-tree_492


title: Plus-tree_489


title: Plus-tree_488


title: Plus-tree_490


title: F1_MAP1_165


title: Plus-tree_494


title: Plus-tree_484


title: Plus-tree_486


title: methylome gmax PI548318 Dunfield

source_name: PI548318 Dunfield

value: PI548318 Dunfield


title: Plus-tree_491


title: Plus-tree_487


title: Plus-tree_483


title: Plus-tree_482


title: F1_MAP1_169


title: F1_MAP1_159


title: F1_MAP1_161


title: methylome gmax PI641156 NC-Raleigh

source_name: PI641156 NC-Raleigh

value: PI641156 NC-Raleigh


title: methylome gmax PI88788 unnamed

source_name: PI88788 unnamed

value: PI88788 unnamed


title: methylome gmax PI630984 5601T


title: Plus-tree_480


title: Plus-tree_481


title: Plus-tree_479


title: F1_MAP1_157


title: methylome gmax PI617045 NC-Roy

source_name: PI617045 NC-Roy

value: PI617045 NC-Roy


title: Plus-tree_476


title: Plus-tree_477


title: F1_MAP1_153


title: methylome gmax PI548311 Capital

source_name: PI548311 Capital

value: PI548311 Capital


title: F1_MAP1_155


title: methylome gmax PI572239 Holladay

source_name: PI572239 Holladay

value: PI572239 Holladay


title: Plus-tree_475


title: F1_MAP1_151


title: Plus-tree_474


title: methylome gmax PI553046 Gasoy17


title: F1_MAP1_149


title: methylome gmax PI548989 Ransom

source_name: PI548989 Ransom

value: PI548989 Ransom


title: F1_MAP1_177


title: Plus-tree_472


title: Plus-tree_473


title: F1_MAP1_147


title: Plus-tree_467


title: Plus-tree_470


title: Plus-tree_469


title: Plus-tree_468


title: Plus-tree_471


title: methylome gmax PI548988 Pickett

source_name: PI548988 Pickett

value: PI548988 Pickett


title: F1_MAP1_145


title: methylome gmax PI548987 Dare

source_name: PI548987 Dare

value: PI548987 Dare


title: methylome gmax PI548986 Brim

source_name: PI548986 Brim

value: PI548986 Brim


title: Plus-tree_478


title: F1_MAP1_143


title: Plus-tree_465


title: F1_MAP1_141


title: Plus-tree_463


title: Plus-tree_464


title: Plus-tree_461


title: Plus-tree_462


title: methylome gmax PI548983 Tracy

source_name: PI548983 Tracy

value: PI548983 Tracy


title: F1_MAP1_139


title: Plus-tree_459

source_name: Plus-tree


title: methylome gmax PI548298 A.K.(Harrow)

source_name: PI548298 A.K.(Harrow)

value: PI548298 A.K.(Harrow)


title: Plus-tree_458


title: methylome gmax PI548657 Jackson

source_name: PI548657 Jackson

value: PI548657 Jackson

value: leaf


title: methylome gmax PI548975 Centennial

source_name: PI548975 Centennial

value: PI548975 Centennial


title: Plus-tree_460

value: Needle leaf


title: F1_MAP1_135


title: F1_MAP1_163


title: methylome gmax PI548654 Hill

source_name: PI548654 Hill

value: PI548654 Hill


title: Plus-tree_451


title: Plus-tree_453


title: Plus-tree_449


title: F1_MAP1_133


title: Plus-tree_457


title: Plus-tree_454


title: F1_MAP1_137


title: methylome gmax PI548634 Zane

source_name: PI548634 Zane

value: PI548634 Zane


title: Plus-tree_456


title: methylome gmax PI548632 Woodworth

source_name: PI548632 Woodworth

value: PI548632 Woodworth


title: Plus-tree_450


title: F1_MAP1_129


title: Plus-tree_455


title: F1_MAP1_131


title: Plus-tree_448


title: Plus-tree_447


title: Plus-tree_485


title: methylome gmax PI548631 Williams

source_name: PI548631 Williams

value: PI548631 Williams


title: F1_MAP1_127


title: Plus-tree_444


title: F1_MAP1_125


title: Plus-tree_446


title: methylome gmax PI548603 Perry

source_name: PI548603 Perry

value: PI548603 Perry


title: Plus-tree_445


title: F1_MAP1_123


title: Plus-tree_443


title: F1_MAP1_121


title: methylome gmax PI548586 Kent

source_name: PI548586 Kent

value: PI548586 Kent


title: methylome gmax PI548628 Wayne

source_name: PI548628 Wayne

value: PI548628 Wayne


title: Plus-tree_442


title: methylome gmax PI548577 Hawkeye

source_name: PI548577 Hawkeye

value: PI548577 Hawkeye


title: Plus-tree_438


title: methylome gmax PI548574 Shelby

source_name: PI548574 Shelby

value: PI548574 Shelby


title: F1_MAP1_119


title: methylome gmax PI518673 Lawrence

source_name: PI518673 Lawrence

value: PI518673 Lawrence


title: F1_MAP1_117


title: Plus-tree_433


title: Plus-tree_440


title: F1_MAP1_115


title: Plus-tree_439


title: Plus-tree_435


title: Plus-tree_441


title: methylome gmax PI548573 Harosoy

source_name: PI548573 Harosoy

value: PI548573 Harosoy


title: Plus-tree_434


title: Plus-tree_437


title: F1_MAP1_113


title: F1_MAP1_111


title: methylome gmax PI548570 Harcor

source_name: PI548570 Harcor

value: PI548570 Harcor


title: Plus-tree_432


title: Plus-tree_436


title: F1_MAP1_109


title: Plus-tree_430


title: Plus-tree_431


title: F1_MAP1_107


title: F1_MAP1_105


title: Plus-tree_426


title: Plus-tree_427


title: Plus-tree_424


title: Plus-tree_429


title: Plus-tree_428


title: F1_MAP1_103


title: methylome gmax PI548555 Douglas

source_name: PI548555 Douglas

value: PI548555 Douglas


title: Plus-tree_425

source_name: Plus-tree


title: methylome gmax PI548545 Merit

source_name: PI548545 Merit

value: PI548545 Merit


title: methylome gmax PI548543 Oakland

source_name: PI548543 Oakland

value: PI548543 Oakland

value: leaf


title: methylome gmax PI548562 Ford

source_name: PI548562 Ford

value: PI548562 Ford


title: methylome gmax PI548542 Cumberland

source_name: PI548542 Cumberland

value: PI548542 Cumberland


title: methylome gmax PI548540 Corsoy

source_name: PI548540 Corsoy

value: PI548540 Corsoy


title: methylome gmax PI548530 Chippewa

source_name: PI548530 Chippewa

value: PI548530 Chippewa


title: methylome gmax PI518671 Williams82

source_name: PI518671 Williams82

value: PI518671 Williams82


title: methylome gmax PI548533 Clark

source_name: PI548533 Clark

value: PI548533 Clark


title: methylome gmax PI548527 Calland

source_name: PI548527 Calland

value: PI548527 Calland


title: Plus-tree_422

value: Needle leaf


title: Plus-tree_414


title: Plus-tree_417


title: Plus-tree_421


title: F1_MAP1_085


title: F1_MAP1_099


title: Plus-tree_419


title: Plus-tree_416


title: F1_MAP1_101


title: Plus-tree_410


title: Plus-tree_423


title: Plus-tree_406


title: F1_MAP1_089


title: Plus-tree_418


title: Plus-tree_420


title: Plus-tree_411


title: F1_MAP1_093


title: F1_MAP1_095


title: Plus-tree_407


title: Plus-tree_413


title: Plus-tree_405


title: Plus-tree_409


title: F1_MAP1_083


title: Plus-tree_404


title: methylome gmax PI548523 Pella

source_name: PI548523 Pella

value: PI548523 Pella


title: Plus-tree_415


title: Plus-tree_408


title: F1_MAP1_097


title: Plus-tree_412


title: F1_MAP1_091


title: F1_MAP1_087


title: methylome gmax PI548516 Blackhawk

source_name: PI548516 Blackhawk

value: PI548516 Blackhawk


title: methylome gmax PI548512 Century

source_name: PI548512 Century

value: PI548512 Century


title: methylome gmax PI548510 Beeson

source_name: PI548510 Beeson

value: PI548510 Beeson


title: methylome gmax PI548517 Bonus

source_name: PI548517 Bonus

value: PI548517 Bonus


title: methylome gmax PI548505 Amcor

source_name: PI548505 Amcor

value: PI548505 Amcor


title: Plus-tree_403


title: methylome gmax PI548493 Tokyo

source_name: PI548493 Tokyo

value: PI548493 Tokyo


title: Plus-tree_400

source_name: Plus-tree


title: methylome gmax PI508266 Young

source_name: PI508266 Young

value: PI508266 Young


title: F1_MAP1_077


title: Plus-tree_401


title: Plus-tree_398


title: F1_MAP1_075


title: Plus-tree_397


title: Plus-tree_399


title: methylome gmax PI548488 S-100

value: leaf


title: F1_MAP1_079


title: Plus-tree_394


title: Plus-tree_402


title: Plus-tree_392


title: Plus-tree_395


title: F1_MAP1_081


title: Plus-tree_396


title: F1_MAP1_069


title: Plus-tree_393


title: F1_MAP1_073


title: F1_MAP1_071


title: Plus-tree_391


title: methylome gmax PI548485 Roanoke

source_name: PI548485 Roanoke

value: PI548485 Roanoke


title: Plus-tree_388


title: Plus-tree_389


title: methylome gmax PI548484 Ralsoy

source_name: PI548484 Ralsoy

value: PI548484 Ralsoy


title: F1_MAP1_067


title: methylome gmax PI548477 Ogden

source_name: PI548477 Ogden

value: PI548477 Ogden


title: Plus-tree_387


title: Plus-tree_386


title: Plus-tree_390


title: methylome gmax PI548406 Richland

source_name: PI548406 Richland

value: PI548406 Richland


title: methylome gmax PI548391 Mukden

source_name: PI548391 Mukden

value: PI548391 Mukden


title: methylome gmax PI548456 Haberlandt

source_name: PI548456 Haberlandt

value: PI548456 Haberlandt


title: methylome gmax PI548379 Mandarin

source_name: PI548379 Mandarin

value: PI548379 Mandarin


title: Plus-tree_672

value: Needle leaf


title: methylome gmax PI548362 Lincoln

source_name: PI548362 Lincoln

value: PI548362 Lincoln


title: F1_MAP1_063


title: Plus-tree_671


title: F1_MAP1_057


title: Plus-tree_385


title: Plus-tree_667


title: F1_MAP1_055


title: Plus-tree_669


title: Plus-tree_663


title: methylome gmax PI548360 Korean

source_name: PI548360 Korean

value: PI548360 Korean


title: F1_MAP1_061


title: Plus-tree_670


title: F1_MAP1_059


title: Plus-tree_660


title: Plus-tree_659


title: F1_MAP1_053


title: Plus-tree_664


title: Plus-tree_666


title: Plus-tree_662


title: Plus-tree_668


title: Plus-tree_661


title: Plus-tree_665


title: methylome gmax FC33243 Anderson

source_name: FC33243 Anderson

value: FC33243 Anderson


title: F1_MAP1_065


title: F1_MAP1_049


title: F1_MAP1_051


title: SIIIRTMg +CMC

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

description: total RNA >200 nt

data_processing:
Trim adaptor using Trimmomatic v0.32 and Python script
End trimming for each read, Python script
Align using Bowtie 1.0
Calculate mutation and stop frequency at each position, Python script
Genome_build: NR_003286 and NR_003287.2
Supplementary_files_format_and_content: text file

growth_protocol: Human embryonic kidney (HEK) cell line HEK293T/17 was obtained from the American Type Culture Collection (ATCC) and cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) with high glucose and L-glutamine, without sodium pyruvate (HyClone, SH30022.01) in a 37 °C incubator with a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA was isolated from confluent 100-mm plates of HEK293T cells by Trizol extraction (Life Technologies, 15596-018) and size-selected for RNAs over 200 nucleotides long with the mirVana miRNA isolation kit (Life Technologies, AM1561).
RNA was fragmented, CMC- or mock-treated, end-repaired, ligated to a 3' adapter, and reverse transcribed with one of three conditions. The cDNA was then size-selected by PAGE, circularized, amplified with barcodes, size-selected by PAGE, and sequenced in a single lane.

tag: chemical treatment

value: CMC

tag: reverse transcriptase

value: SuperScript III RT

tag: divalent cation for rt

value: magnesium

tag: barcode

value: CTGATC


title: SIIIRTMg -CMC

description: total RNA >200 nt

value: mock

value: TTTCAC


title: SIIIRTMn -CMC

description: total RNA >200 nt

value: manganese

value: TCAAGT


title: Plus-tree_657


title: SIIIRTMn +CMC

description: total RNA >200 nt

value: GCCTAA


title: Plus-tree_658


title: F1_MAP1_047


title: Plus-tree_655


title: Plus-tree_656


title: Plus-tree_652


title: Plus-tree_654


title: HIVRT +CMC

description: total RNA >200 nt

value: HIV RT

value: CGTGAT


title: Plus-tree_653


title: Plus-tree_649


title: HIVRT -CMC

description: total RNA >200 nt

value: ACATCG


title: Plus-tree_647


title: F1_MAP1_039


title: Plus-tree_650


title: Plus-tree_646


title: Plus-tree_645


title: Plus-tree_651


title: F1_MAP1_035


title: F1_MAP1_043


title: F1_MAP1_045


title: Plus-tree_641


title: F1_MAP1_041


title: Plus-tree_648


title: Plus-tree_644


title: F1_MAP1_037


title: Plus-tree_640


title: F1_MAP1_033


title: Plus-tree_642


title: Plus-tree_643


title: Plus-tree_639


title: F1_MAP1_027


title: Plus-tree_637


title: Plus-tree_635


title: Plus-tree_638


title: F1_MAP1_029


title: Plus-tree_636


title: Plus-tree_633


title: F1_MAP1_025


title: Plus-tree_634


title: F1_MAP1_031


title: F1_MAP1_021


title: Plus-tree_628


title: Plus-tree_631


title: F1_MAP1_019


title: Plus-tree_626


title: F1_MAP1_017


title: Plus-tree_632


title: Plus-tree_630


title: Plus-tree_624


title: F1_MAP1_023


title: Plus-tree_625


title: Plus-tree_629


title: Plus-tree_622


title: PMNs_iRBCs_1h_rep3

city: Obihiro

first: Ryo

last: Takano

state: Hokkaido

address: Inada-cho

department: National Research Center for Protozoan Diseases

institute: Obihiro University of Agriculture and Veterinary Medicine

hyb_protocol: Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarrays ver. 3.0 (G4858) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned with an Agilent's High-Resolution Microarray Scanner using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software ver. 10.7.3.1. using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Human neutrophils, iRBCs, 1hour, replicate 3

label_protocol: Cy3-labeled cRNA probe synthesis was initiated with 50 ng of total RNAs by using the Agilent Low Input Quick Amp Labeling kit, one color (Agilent Technologies).

growth_protocol: Human PMNs were separated from the peripheral blood of a healthy donor by using Ficoll-Paque™ PLUS (GE Healthcare) and cultured in a humidified atmosphere containing 5% CO2, in RPMI-1640 medium (Sigma-Aldrich) supplemented with 20% human serum (Sigma), 25 mg/L penicillin/streptomycin. Mononuclear layer cells, plasma, Ficoll, and interface layer of RBC pellets with Ficoll were discarded and RBC pellets were lysed by RBC lysis buffer (Sigma) to obtain PMNs.

extract_protocol: At 1 hour post co-cultivation, the cells were lysed with TRIzol Reagent (Invitrogen) and chloroform-isoamyl alchol (5:1) was added. The cells were then vortexed and centrifuged for 15 min at 12,000 g at 4 °C. The resulting aqueous layer was subjected to RNA extraction by using RNeasy Mini kit columns (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Freshly isolated PMNs were co-cultured with either uninfected RBCs or enriched Plasmodium falciparum parasite-infected RBCs (iRBCs, 1:20) for 1 h in the presence of interferon-gamma (IFN-γ, 250 ng/ml) in a humidified atmosphere containing 5% CO2 at 37 °C.

value: Polymorphonuclear leukocytes

value: cultured with Plasmodium falciparum parasite-infected RBCs for 1 hour


title: F1_MAP1_015

value: Needle leaf


title: Plus-tree_619


title: Plus-tree_623


title: Plus-tree_620


title: Plus-tree_618


title: F1_MAP1_013


title: PMNs_iRBCs_1h_rep4

source_name: Human neutrophils, iRBCs, 1hour, replicate 4


title: Plus-tree_627


title: Plus-tree_621


title: PMNs_iRBCs_1h_rep1

source_name: Human neutrophils, iRBCs, 1hour, replicate 1


title: KO2_contralateral

status: Public on May 06 2018

city: Zurich

first: Gianluca

last: Figlia

address: Otto-Stern-Weg 7

department: Institute for Molecular Health Sciences

country: Switzerland

institute: ETH Zurich

data_processing:
adapter sequences were removed, low quality ends trimmed, and reads with low quality (phred quality<20) filtered using Trimmomatic (Bolger et al., Bioinformatics, 2014)
high-quality reads were mapped to the mouse reference genome and quantification of gene level expression was carried out using RSEM (version 1.2.22)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads for each sample

source_name: Sciatic nerve

growth_protocol: Controls and mutants were injected with tamoxifen at 2 months of age

extract_protocol:
Nerves were extracted, flash frozen in liquid nitrogen after mechanical removal of the epineurium, and total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Sciatic nerves surgeries were performed 2 months after the last tamoxifen injection

value: Sciatic nerve

value: 5 days post-crush

tag: genotype

value: Raptor knockout

tag: surgery

value: Uninjured contrataleral


title: KO3_crush

value: Injured


title: Plus-tree_617


title: Plus-tree_614


title: KO4_contralateral


title: KO3_contralateral


title: KO2_crush


title: F1_MAP1_009


title: KO1_crush


title: F1_MAP1_007


title: PMNs_iRBCs_1h_rep2

source_name: Human neutrophils, iRBCs, 1hour, replicate 2


title: Plus-tree_616

source_name: Plus-tree


title: Control3_contralateral

value: Control


title: Plus-tree_611


title: F1_MAP1_011


title: F1_MAP1_005


title: PMNs_mock_1h_rep3

source_name: Human neutrophils, RBCs, 1hour, replicate 3

value: cultured with RBCs for 1 hour


title: F1_MAP1_003


title: Plus-tree_613


title: Plus-tree_612


title: Plus-tree_615


title: PMNs_mock_1h_rep4

source_name: Human neutrophils, RBCs, 1hour, replicate 4


title: Control3_crush


title: PMNs_mock_1h_rep2

source_name: Human neutrophils, RBCs, 1hour, replicate 2


title: Plus-tree_610


title: control_biological_rep3

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: LPS was injected into the calvarial periosteum of CX3CR1-EGFP mice, together with 10 mg/kg whole human IgG, and then 5 days later, EGFP+ cells were isolated from mouse calvaria using a cell sorter.

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm version 2.2.1.
Genome_build: mm10

source_name: CX3CR1-EGFP+ cells

extract_protocol:
Total RNA was extracted from the collected cells using the miRNeasy kit (QIAGEN), according to the manufacturer’s instructions.
The library was prepared using a TruSeq stranded mRNA sample prep kit (Illumina), according to the manufacturer's instructions.

treatment_protocol: For sample collection, LPS was injected into the calvarial periosteum of CX3CR1-EGFP mice, together with 10 mg/kg CTLA4-Ig or whole human IgG (Wako), and then 5 days later, EGFP+ cells were isolated from mouse calvaria using a cell sorter (SONY).

tag: treatment

value: control IgG

tag: cell type

value: CX3CR1-EGFP+ cells


title: control_biological_rep2


title: KO1_contralateral

tag: tissue


title: Control2_contralateral

tag: age


title: control_biological_rep1


title: Control2_crush


title: Control1_crush


title: Control1_contralateral


title: abatacept_biological_rep2

description: LPS was injected into the calvarial periosteum of CX3CR1-EGFP mice, together with 10 mg/kg CTLA4-Ig, and then 5 days later, EGFP+ cells were isolated from mouse calvaria using a cell sorter.


title: abatacept_biological_rep1


title: T_Thy_2

status: Public on May 05 2018

city: San Francisco

first: Joshua

last: Pollack

state: CA

address: 2 Tower Pl.  Ste 800

institute: Pionyr Immunotherapeutics

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed of any presence of the Illumina adapter, then mapped to GRCm38.78 whole genome using STAR: Dobin A, Gingeras TR et al. "STAR: Ultrafast Universal RNA-seq Aligner." Bioinformatics. 2013 Jan 1;29(1):15-21.
Unique alignments were aggregated across all isoforms on a per-gene basis, using only reads mapping to exons, using rna-STAR.
Normalization and differential expression estimation was performed using DESeq2: Love MI, Huber W, Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, 550.
Genome_build: GRCm38.78 (Ensembl)
Supplementary_files_format_and_content: tab-delimited text files include raw per-gene values for each sample

molecule: polyA RNA

source_name: thymus epithelium

extract_protocol:
For thymic epithelium, thymi were isolated, cleaned of fat and transferred to DMEM + 2% FBS on ice. Thymi were minced with a razor blade and tissue pieces were moved with a glass Pasteur pipette to 15 ml tubes and vortexed briefly in 10 ml of media. Fragments were allowed to settle before removing the media and replacing it with 4 ml of digestion media containing 2% FBS, 100 μg mL-1 DNase I (Roche), and 100 μg mL-1 Liberase TM (Sigma-Aldrich) in DMEM. Tubes were moved to a 37° C water bath and fragments were triturated through a glass Pasteur pipette at 0 min and 6 min to mechanically aid digestion. At 12 min, tubes were spun briefly to pellet undigested fragments and the supernatant was moved to 20 ml of 0.5% BSA (Sigma-Aldrich), 2 mM EDTA (TekNova), in PBS (MACS buffer) on ice to stop the enzymatic digestion. This was repeated twice for a total of three 12 min digestion cycles, or until there were no remaining tissue fragments. The single cell suspension was then pelleted and washed once in MACS Buffer. Density-gradient centrifugation using a three-layer Percoll gradient (GE Healthcare) with specific gravities of 1.115, 1.065, and 1.0 was used to enrich for stromal cells. Cells isolated from the Percoll- light fraction, between the 1.065 and 1.0 layers, were then washed and resuspended for staining.
Cells were sorted directly into lysis buffer from the Dynabead mRNA Direct Purification Kit (ThermoFisher). Sorted cells were pooled for bulk sequencing and poly A RNA was isolated according to the manufacturer’s protocol.
amplification protocol: Amplified cDNA was prepared using the NuGen Ovation RNA-Seq system V2 kit, according to the manufacturer’s protocol
Sequencing libraries were generated using the Nextera XT library preparation kit with multiplexing primers, according to manufacturer’s protocol (Illumina)

value: 12 weeks

tag: Sex

value: M

value: naive

value: thymus

tag: number of mice

value: tuft cells

tag: sorting gate

tag: cells sorted


title: T_Col_2

source_name: colon epithelium

extract_protocol:
For single cell epithelial preparations from small intestines, gall bladder, and colon, tissues were flushed with PBS, opened, and rinsed with PBS to remove intestinal contents. Intestinal tissue was cut into 2-5 cm pieces and incubated rocking at 37° C in 15 mL HBSS (Ca+2/Mg+2-free) supplemented with 5mM dithiothreitol (DTT, Sigma-Aldrich), 5% fetal calf serum (FCS, VWR), and 10mM HEPES (Gibco). Tissues were vortexed vigorously and supernatant was discarded. Tissues were then incubated rocking at 37° C in 15 mL HBSS (Ca+2/Mg+2-free) supplemented with 5mM EDTA (Invitrogen), 5% FCS, and 10mM HEPES. Tissues were vortexed thoroughly and released epithelial cells were passed through a 70 μm filter. Tissues were then incubated in fresh EDTA/HBSS solution for 15 minutes, vortexed, and filtered. Supernatants were pooled and washed once before staining for flow cytometry.
Cells were sorted directly into lysis buffer from the Dynabead mRNA Direct Purification Kit (ThermoFisher). Sorted cells were pooled for bulk sequencing and poly A RNA was isolated according to the manufacturer’s protocol.
amplification protocol: Amplified cDNA was prepared using the NuGen Ovation RNA-Seq system V2 kit, according to the manufacturer’s protocol
Sequencing libraries were generated using the Nextera XT library preparation kit with multiplexing primers, according to manufacturer’s protocol (Illumina)

tag: strain

tag: mouse status

value: colon


title: T_Col_1


title: T_Gall_3

source_name: gall bladder epitheliium

value: gall bladder


title: T_Tr_2

source_name: trachea epithelium

extract_protocol:
For tracheal epithelium, the trachea was dissected from mice, stored in DMEM + 5% FBS and cleaned of stroma using a dissecting microscope. Tissue was cut into 6 pieces and incubated at room temperature in 16U mL-1 Dispase (Corning) in DPBS without Ca2+/Mg2+. Incubation was monitored carefully and stopped by transfer into DMEM + 5% FBS when epithelium began to lift away from stroma (23-28 minutes). Epithelium was then peeled off under a dissecting microscope and collected in DMEM + 5% FBS on ice. Harvested epithelium was digested in 0.5% Trypsin + EDTA for 20 minutes at 37° C. After digest, cells were vortexed briefly and trypsin was quenched with DMEM + 5% FBS. Cells were washed once and stained for flow cytometry.
Cells were sorted directly into lysis buffer from the Dynabead mRNA Direct Purification Kit (ThermoFisher). Sorted cells were pooled for bulk sequencing and poly A RNA was isolated according to the manufacturer’s protocol.
amplification protocol: Amplified cDNA was prepared using the NuGen Ovation RNA-Seq system V2 kit, according to the manufacturer’s protocol
Sequencing libraries were generated using the Nextera XT library preparation kit with multiplexing primers, according to manufacturer’s protocol (Illumina)

value: 16 weeks

value: trachea


title: T_Col_4


title: T_SI_4

source_name: small intestine epithelium

value: small intestine


title: T_Thy_4


title: T_Thy_1


title: T_Tr_1


title: T_Col_3


title: abatacept_biological_rep3


title: T_SI_2


title: T_SI_3


title: E_SI_3

value: total epithelium (no tuft cells)


title: purmorphamine_8

city: Philadelphia

first: David

last: Manning

state: PA

address: 3620 Hamilton Walk

institute: University of Pennsylvania

description: FINAL_master_list_of_gene_counts_MIN.sense.manning_rnaseq_Nov17_7samples.txt.gz

data_processing:
RNA-Seq data were aligned to the mouse genome build mm9 (ensemblv67) by STAR-2.5.3a.
Data were normalized at the gene-level, using a resampling strategy PORT (v0.8.4-beta), the code is available at https://github.com/itmat/Normalization
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file from gene-level normalization contains counts from unique reads that only map to one gene.

growth_protocol: C3H10T1/2 cells (ATCC) were plated at 2.6 x 10^4 cells/cm^2 in Minimal Eagle Medium (MEM) plus 10% fetal bovine serum at 37°C at 5% CO2; cells were not used beyond 10 passages from purchase.

extract_protocol:
RNA was extracted with an RNeasy Minikit from QIAGEN.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After incubation of plated cells overnight, the medium was changed to Basal Medium Eagle (BME) without fetal bovine serum for 12 hours. The cells were then treated an additional 48 hours with 2 uM purmorphamine (Sigma) or vehicle (0.02% DMSO). RNA was then prepared.

tag: cell line

tag: agent

value: purmorphamine


title: E_SI_1


title: E_SI_2


title: DMSO_4

value: DMSO


title: purmorphamine_6


title: purmorphamine_7


title: purmorphamine_5


title: T_Tr_3

value: F


title: DMSO_3


title: T_Tr_4

value: 14 weeks


title: T_Gall_1


title: T_Thy_3


title: T_Gall_4


title: WT PP1 rep 1

first: Shuibing

last: Chen

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Illumina bcl2fastq2 v2.17 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the human hg19 reference genome using tophat v2.0.11.
The gene annotation file we used is based on RefSeq database and was downloaded from
ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz
We report expressions for mRNA only.
Transcript abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.1.1 package.
Genome_build: hg19
Supplementary_files_format_and_content: .txt file including gene name, RefSeq id, locus, RPKM value of each gene in each sample

source_name: early pancreatic progenitors

growth_protocol: ESCs were differentiated to pancreatic fate using the protocol described in the paper.

extract_protocol:
RNA extraction was done using RNA extraction spin-column kits
Libraries were prepared using TruSeq RNA Sample Preparation (Non-Stranded and Poly-A selection)

tag: developmental stage

value: hESC-derived early pancreatic progenitors

tag: es cell line

value: WT


title: WT PP2 rep 1

source_name: late pancreatic progenitors

value: hESC-derived late pancreatic progenitors


title: DMSO_2


title: WT PP1 rep 2


title: GLIS3-/- INS-GFP+ PP2-beta rep 1

source_name: late pancreatic beta-like cells

value: hESC-derived late pancreatic beta-like cells

value: GLIS3-/- INS-GFP+


title: GLIS3-/- INS-GFP+ PP2-beta rep 2


title: WT INS-GFP+ PP1-beta rep 2

source_name: early pancreatic beta-like cells

value: hESC-derived early pancreatic beta-like cells

value: WT INS-GFP+


title: WT INS-GFP+ PP2-beta rep 2


title: WT PP2 rep 2


title: WT INS-GFP+ PP1-beta rep 1


title: GLIS3-/- PP2 rep 2


title: WT PP2 rep 3


title: WT INS-GFP+ PP2-beta rep 1


title: GLIS3-/- PP2 rep 3


title: GLIS3-/- PP2 rep 1


title: NF-null_2

city: London

first: Fernando

last: Calvo

state: London

address: 237 Fulham Road

department: Cancer Biology

country: United Kingdom

institute: The Institute of Cancer Research

description: Normal mammary fibroblasts, E6 immortalized, stable expression of empty vector, cultured for 48h in plastic, duplicate #2.

hyb_protocol: RNA was processed in collaboration with Eurofins Genomics following standard Affymetrix protocol (Mouse Gene 2.1 ST).

data_processing: Standard expression analysis data (SST-RMA) was used for the analysis.

growth_protocol: Cells were isolated from the defined tissues, immortalized using hpvE6, subjected to specific treatments (lentiviral infection and selection; or transient RNAi transfection) and seeded on plastic for 48 h on 10%FBS, 1% ITS DMEM.

extract_protocol: RNA was isolated using EZNA Total RNA Kit 1 (Omega Bio-tek).

treatment_protocol: Cells were stably transfected with empty vector by lentivirus infection followed by selection.

tag: strain/background

value: MMTV-PyMT (FVB/n background)

tag: gender

value: female

value: mammary gland

tag: Stage

value: normal mammary gland

value: fibroblasts


title: CAF-siDkk3#2_1

description: CAFs, E6 immortalized, transfection with DKK3 RNAi (#2.), cultured for 48h in plastic, duplicate #1.

scan_protocol: RNA was processed in collaboration with Eurofins Genomics following standard Affymetrix protocol (Mouse Gene 2.1 ST).

source_name: CAFs, E6 immortalized, transfection with DKK3 RNAi (#2), cultured for 48h in plastic

treatment_protocol: Cells were transiently transfected with Dkk3 RNAi (si#2) and cultured for 48 h.

value: carcinoma


title: Smolt, freshawater, fish 2

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol for 4x44k microarrays

scan_protocol: Arrays were scanned with Agilent microarray scanner

data_processing: Global normalization was performed by equalizing the mean intensities of all microarrays. The individual values for each feature were divided to the mean value of all samples and expression ratios (ER) were calculated. Log2-ER were normalized with the locally weighted non-linear regression (Lowess)

organism: Salmo salar

source_name: skin

label_protocol: Amplified and labeled with Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Salmon was fed with commercial feed

extract_protocol: Total RNA was extracted using the RNeasy® Mini Kit (Qiagen)

tag: treament

value: freshwater


title: Smolt, freshawater, fish 1


title: Smolt, freshawater, fish 6


title: Smolt, freshawater, fish 3


title: Smolt, freshawater, fish 7


title: NF-DKK3_1

description: Normal mammary fibroblasts, E6 immortalized, stable expression of DKK3, cultured for 48h in plastic, duplicate #1.

label_protocol: RNA was processed in collaboration with Eurofins Genomics following standard Affymetrix protocol (Mouse Gene 2.1 ST).

treatment_protocol: Cells were stably overexpressing DKK3 by lentivirus infection followed by selection.

tag: cell type


title: CAF-siDkk3#3_1

description: CAFs, E6 immortalized, transfection with DKK3 RNAi (#3), cultured for 48h in plastic, duplicate #1.

treatment_protocol: Cells were transiently transfected with Dkk3 RNAi (si#3) and cultured for 48 h.

tag: tissue


title: CAF-siDkk3#2_2

description: CAFs, E6 immortalized, transfection with DKK3 RNAi (#2.), cultured for 48h in plastic, duplicate #2.


title: CAF-siCtr_1

description: CAFs, E6 immortalized, transfection with control RNAi, cultured for 48h in plastic, duplicate #1.

treatment_protocol: Cells were transiently transfected with control RNAi and cultured for 48 h.


title: Close containment system, four months in seawater, fish 6

value: close containment system four  months in seawater


title: CAF-siDkk3#3_2

description: CAFs, E6 immortalized, transfection with DKK3 RNAi (#3), cultured for 48h in plastic, duplicate #2.


title: Close containment system, four months in seawater, fish 2


title: Smolt, freshawater, fish 12


title: Smolt, freshawater, fish 11


title: NF-DKK3_2

description: Normal mammary fibroblasts, E6 immortalized, stable expression of DKK3, cultured for 48h in plastic, duplicate #2.


title: NF-null_1

description: Normal mammary fibroblasts, E6 immortalized, stable expression of empty vector, cultured for 48h in plastic, duplicate #1.


title: CAF-siCtr_2

description: CAFs, E6 immortalized, transfection with control RNAi, cultured for 48h in plastic, duplicate #2.


title: Close containment system, four months in seawater, fish 7


title: Close containment system, four months in seawater, fish 12


title: Close containment system, one month in seawater, fish 7

value: close containment system one month in seawater


title: Close containment system, four months in seawater, fish 1


title: Close containment system, one month in seawater, fish 6


title: Close containment system, four months in seawater, fish 11


title: Close containment system, one month in seawater, fish 12


title: Close containment system, one month in seawater, fish 2


title: Close containment system, one month in seawater, fish 11


title: PMNs_mock_1h_rep1

source_name: Human neutrophils, RBCs, 1hour, replicate 1

value: Polymorphonuclear leukocytes

tag: condition

value: cultured with RBCs for 1 hour


title: Close containment system, one month in seawater, fish 1


title: Open cage, four months in seawater, fish 7

value: open cage four months in seawater


title: Open cage, four months in seawater, fish 2


title: Open cage, four months in seawater, fish 6


title: Open cage, four months in seawater, fish 12


title: Open cage, one month in seawater, fish 7

value: open cage one month in seawater


title: Open cage, four months in seawater, fish 11


title: Open cage, four months in seawater, fish 1


title: F1_MAP1_001

value: Needle leaf


title: Open cage, one month in seawater, fish 6


title: Rosi_10mgkg_M_28d_2 [mRNA]

city: Basel

first: Jonathan

last: Moggs

address: Fabrikstrasse 2

institute: Novartis

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent HI-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Oligo Microarrays (G4853A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent),  1 minute with 37°C GE Wash buffer 2 (Agilent),  10 Seconds with Acetonitrile (VWR HPLC Grade) and 30 Seconds with Wash 3 Stabilisation and Drying Solution (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Raw data has been background corrected and quantile normalized using the limma package for R/Bioconductor.

organism: Rattus norvegicus

source_name: bladder, male, Rosiglitazone, 10 mg/kg/day, 28 days

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low Input Quick Amp Labelling  kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Sprague-Dawley rats (10/sex/group) were treated orally with vehicle (0.5% methylcellulose 15), Pioglitazone hydrochloride (CAS No 112529-15-4) at 16 or 63 mg/kg/day, or Rosiglitazone maleate (CAS 155141-29-0) at 10 mg/kg/day.

extract_protocol: RNA was isolated using the Qiagen RNeasy kit following the manufacturer's recommendations. For extraction, the filter paper was trimmed, and transferred to the lysis buffer. All handling was done on dry ice.

treatment_protocol: The rats received a daily oral administration of 10 mL/kg body weight of vehicle or test compound solution for either 3, 28 or 90 days. One day after the last treatment, the animals were anaesthetised in isoflurane, exsanguinated from the abdominal aorta and subjected to necropsy. The bladder was rapidly isolated and cut longitudially into halves. The urothelium was scraped off with a scalpel and snap frozen in liquid nitrogen.

value: bladder urothelium

value: Sprague-Dawley

tag: Sex

value: male

value: Rosiglitazone

value: 10 mg/kg/day

value: 28 days

tag: group

value: yes


title: Rosi_10mgkg_M_90d_2 [mRNA]

source_name: bladder, male, Rosiglitazone, 10 mg/kg/day, 90 days

value: 90 days


title: Rosi_10mgkg_M_3d_1 [mRNA]

source_name: bladder, male, Rosiglitazone, 10 mg/kg/day, 3 days

value: 3 days


title: Rosi_10mgkg_M_28d_3 [mRNA]


title: Open cage, one month in seawater, fish 2


title: Rosi_10mgkg_M_3d_4 [mRNA]


title: Rosi_10mgkg_M_28d_4 [mRNA]


title: Rosi_10mgkg_F_90d_5 [mRNA]

source_name: bladder, female, Rosiglitazone, 10 mg/kg/day, 90 days

value: female


title: Rosi_10mgkg_M_90d_3 [mRNA]


title: Open cage, one month in seawater, fish 1


title: Rosi_10mgkg_M_90d_1 [mRNA]


title: Rosi_10mgkg_M_3d_5 [mRNA]


title: Open cage, one month in seawater, fish 11


title: Rosi_10mgkg_F_90d_1 [mRNA]


title: Rosi_10mgkg_M_90d_5 [mRNA]


title: Open cage, one month in seawater, fish 12


title: Rosi_10mgkg_M_3d_3 [mRNA]


title: Rosi_10mgkg_F_90d_2 [mRNA]


title: Rosi_10mgkg_M_28d_5 [mRNA]


title: Rosi_10mgkg_F_90d_4 [mRNA]


title: Rosi_10mgkg_M_90d_4 [mRNA]


title: Rosi_10mgkg_M_28d_1 [mRNA]


title: Rosi_10mgkg_F_28d_5 [mRNA]

source_name: bladder, female, Rosiglitazone, 10 mg/kg/day, 28 days


title: Rosi_10mgkg_M_3d_2 [mRNA]


title: Rosi_10mgkg_F_90d_3 [mRNA]


title: TFAM OE Aop RNAi rep2

first: Joseph

middle: M.

last: Bateman

state: (Click to Select US State)

address: Guy's campus

institute: King's College London

description: Gene expression data from CNS tissue over-expressing TFAM combined with Aop knock-down in neurons

hyb_protocol: 7mg of labelled cDNA was hybridised to Affymetrix Drosophila genome v2 GeneChips

scan_protocol: Genechips were washed, stained (GeneChip® Fluidics Station 450) and scanned (GeneChip Scanner 3000 7G) according to manufacturer’s instructions (Nugen Technologies Inc & Affymetrix)

data_processing: Data was processed using a MAS5.0 algorithm and analysed using the Transcriptome Analysis Console (ThermoFisher) using gene level differential expression analysis. Means were calculated using Tukey's Bi-weight average algorithm and differential expression between groups was calculated using un-paired one way one way analysis of variance (ANOVA). A statistical cutoff of p<0.05 was used and a fold change cutoff of ±1.5 fold were used.

organism: Drosophila melanogaster

source_name: CNS tissue from nsybGal4/UAS-TFAM3M + Aop RNAi larvae

label_protocol: 10ng of RNA per genotype was converted into labelled cDNA with the Nugen Ovation V2 protocol (NuGEN Technologies Inc.)

growth_protocol: Larvae were grown on standard fly food at 25 degrees.

extract_protocol: For the microarray analysis the complete CNS from 20 wandering third instar larvae were dissected in PBS and placed into PBS on ice and then transferred into 100ul of lysis buffer from the Absolutely RNA Microprep kit (Stratagene) and vortexed for 5 seconds. Total RNA was then prepared using this kit. For each genotype RNA samples were prepared in triplicate and stored at -80oC.

treatment_protocol: One control and five experimental genotypes were used: Control (nsybGal4/+), Experimental group 1: TFAM3M (nsybGal4>UAS-TFAM3M), Experimental group 2: Pnt RNAi (nsybGal4>UAS-Pnt RNAi #JF02227), Experimental group 3: Aop RNAi (nsybGal4>UAS-Aop RNAi #3166R1), Experimental group 4: TFAM3M, Pnt RNAi (nsybGal4>UAS-TFAM3M, UAS-Pnt RNAi #JF02227), Experimental group 5: TFAM3M, Aop RNAi (nsybGal4>UAS-TFAM3M, UAS-Aop RNAi #3166R1).

tag: genotype/variation

value: nsybGal4/UAS-TFAM3M, Aop RNAi


title: TFAM OE Aop RNAi rep3

value: CNS tissue from nsybGal4/UAS-TFAM3M + Aop RNAi larvae


title: Rosi_10mgkg_F_28d_2 [mRNA]