title: ∆arcS-LP3-2

city: Hachioji

first: Atsushi

last: Kouzuma

state: Tokyo

address: 1432-1 Horinouchi

country: Japan

institute: Tokyo University of Pharmacy and Life Sciences

description: Gene expression in ∆arcS exposed to LP

hyb_protocol: For each array, 20 μl of the purified Cy3-labeled cDNA (20 ng/μl) was mixed with 5 μL of 10× Blocking Agent and 25 μl of 2× GEx Hybridization Buffer HI-RPM. The resultant mixture (40 μl) was hybridized to an array at 65°C for 17h. After hybridization, each slide was washed in Gene Expression Wash Buffer I (Agilent Technologies) at room temperature for 1 min and in Gene Expression Wash Buffer II (Agilent Technologies) at 37°C for 1 min.

scan_protocol: After the slide was air dried for 1 min, it was scanned using an Agilent DNA Microarray Scanner at a 5 μm resolution.

data_processing: Gene expression data (fluorescent intensities) were extracted from the scanned image using the Feature Extraction Software version 8.1 (Agilent Technologies) and normalized and statistically analyzed using GeneSpring GX version 11.5 (Agilent Technologies).

organism: Shewanella oneidensis

source_name: ∆arcS exposed to LP, biological replicate 3, technical replicate 2

label_protocol: Cyanine 3 (Cy3)-labeled cDNA was synthesized from 5 μg of total RNA using the FairPlay III Microarray Labeling Kit (Stratagene) and CyDye Cy3 mono-Reactive Dye (GE Healthcare). The labeled cDNA was quantified using NanoDrop ND-1000 Spectrophotometer (Thermo Scientific).

growth_protocol: A single-chambered EC (electrochemical cell) was used for analyzing transcriptomes of WT and ∆arcS strains. The working electrode was poised at +0.2 V until the electric current became stable (for approximately 15 h), and then the potential was changed to +0.5 V (high potential; HP) or –0.1 V (low potential; LP).

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) and subsequently purified using an RNeasy Mini Kit and an RNase-Free DNase Set (Qiagen) according to the manufacturer’s instructions. The quality of extracted RNA was evaluated using an Agilent 2100 Bioanalyzer with RNA 6000 Pico reagents and RNA Pico Chips (Agilent Technologies).

treatment_protocol: After further cultivation in the ECs for 2 h, the bacterial cells attached to the working electrode were collected and subjected to RNA extraction.

tag: potential

value: LP


title: Kidney Tissue from UUO Mice Replicate 18

status: Public on Feb 22 2018

type: RNA

city: Stanford

first: Bo

last: Wu

state: Ca

address: 300 Pasteur Dr. Grant/S259

department: Urology

country: USA

institute: Stanford University

description:
Biological replicate 18 of 60.
UUO-rep18

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent Hybridization Chamber Kit. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent p/n G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (A. 7.0.1) was used for background subtraction and LOWESS normalization.

molecule: total RNA

organism: Mus musculus

source_name: Kidney Tissue from UUO Mice

label_protocol: 5 µg of total RNA were primed with T7 Promoter Primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of MMLV-RT, and 10 mM dNTP, Cy3- or Cy5-label

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Mice were anesthetized and subjected to unilateral obstruction for 0, 0.5h, 1h, 3h, 5h, 7h, 12h, 1 day, 3 days, 5 days or 7 days. The left ureter was ligated to generate an obstructed kidney. For each time point additional mice underwent dissection of the left ureter without ligation to serve as sham controls.

tag: stress (obstruction)

value: UUO

tag: time after stress (obstruction)

tag: tissue

value: Kidney

tag: strain

source_name: Mouse Universal Reference RNA

tag: cell line

value: Cell Line Mixture


title: spore mrna from totRNA-seq

type: SRA

city: Berkeley

first: Gloria

last: Brar

address: 626 Barker Hall

department: MCB

institute: UC Berkeley

description:
processed data column: spore totRNA rpkm
processed data file: timecourse replicate 2 totRNA.txt

library_source: transcriptomic

data_processing:
Basecalls performed with CASAVA bcl2fastq_v2.17
reads were trimmed
trimmed reads were aligned using bowtie2 and excluding multiple alignments
ribosome footprint reads were assigned to one genomic position based on a-site analysis of fragment length distribution
Genome_build: sk1_revised_100331 (published in Brar et. al, Science, 2012)
Supplementary_files_format_and_content: txt matrix files of RPKM measurements using standard SGD genome annotations

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: yeast cells were either grown in YEPD for exponential growth or sporulation medium

extract_protocol:
For ribosome profiling, cells were flash frozen and mixermilled at -80 together with ribosome profiling lysis buffer, extract was clarified with a low and high speed spin, all as described in Ingolia et. al, Science, 2009. For mRNA, cells were flash frozen and lysed using hot acid phenol and SDS as described in Ingolia et al., Science, 2009
As described in Ingolia et al, Science 2009

tag: strain background

tag: cellular state

value: meiotic cells in sporulation medium

tag: molecule subtype

value: mRNA


title: 6hr mrna from totRNA-seq

description:
processed data column: 6hr totRNA rpkm
processed data file: timecourse replicate 2 totRNA.txt


title: 3hr mrna from totRNA-seq

description:
processed data column: 3hr totRNA rpkm
processed data file: timecourse replicate 2 totRNA.txt


title: 4.5hr mrna from totRNA-seq

description:
processed data column: 4.5hr totRNA rpkm
processed data file: timecourse replicate 2 totRNA.txt


title: 1.5hr mrna from totRNA-seq

description:
processed data column: 1.5hr totRNA rpkm
processed data file: timecourse replicate 2 totRNA.txt


title: Kidney Tissue from UUO Mice Replicate 17

description:
Biological replicate 17 of 60.
UUO-rep17


title: 10hr mrna from totRNA-seq

description:
processed data column: 10hr totRNA rpkm
processed data file: timecourse replicate 2 totRNA.txt


title: 0hr mrna from totRNA-seq

description:
processed data column: 0hr totRNA rpkm
processed data file: timecourse replicate 2 totRNA.txt


title: Kidney Tissue from UUO Mice Replicate 13

description:
Biological replicate 13 of 60.
UUO-rep13


title: 8hr mrna from totRNA-seq

description:
processed data column: 8hr totRNA rpkm
processed data file: timecourse replicate 2 totRNA.txt


title: ∆arcS-LP2-2

description: Gene expression in ∆arcS exposed to LP

source_name: ∆arcS exposed to LP, biological replicate 2, technical replicate 2


title: Kidney Tissue from UUO Mice Replicate 14

description:
Biological replicate 14 of 60.
UUO-rep14


title: ∆arcS-LP3-1

description: Gene expression in ∆arcS exposed to LP

source_name: ∆arcS exposed to LP, biological replicate 3, technical replicate 1


title: ∆arcS-LP1-1

description: Gene expression in ∆arcS exposed to LP

source_name: ∆arcS exposed to LP, biological replicate 1, technical replicate 1


title: ∆arcS-LP2-1

description: Gene expression in ∆arcS exposed to LP

source_name: ∆arcS exposed to LP, biological replicate 2, technical replicate 1


title: ∆arcS-LP1-2

description: Gene expression in ∆arcS exposed to LP

source_name: ∆arcS exposed to LP, biological replicate 1, technical replicate 2


title: ∆arcS-HP3-2

description: Gene expression in ∆arcS exposed to HP

source_name: ∆arcS exposed to HP, biological replicate 3, technical replicate 2

value: HP


title: Kidney Tissue from UUO Mice Replicate 12

description:
Biological replicate 12 of 60.
UUO-rep12


title: Kidney Tissue from UUO Mice Replicate 15

description:
Biological replicate 15 of 60.
UUO-rep15


title: Kidney Tissue from UUO Mice Replicate 10

description:
Biological replicate 10 of 60.
UUO-rep10


title: Kidney Tissue from UUO Mice Replicate 11

description:
Biological replicate 11 of 60.
UUO-rep11


title: Kidney Tissue from UUO Mice Replicate 8

description:
Biological replicate 8 of 60.
UUO-rep8


title: Kidney Tissue from UUO Mice Replicate 9

description:
Biological replicate 9 of 60.
UUO-rep9


title: vegetative exponential mrna from totRNA-seq

description:
processed data column: vexp repl1 totrna rpkm
processed data file: timecourse replicate 2 totRNA.txt

value: vegetative exponential OD600=0.6


title: ∆arcS-HP2-1

description: Gene expression in ∆arcS exposed to HP

source_name: ∆arcS exposed to HP, biological replicate 2, technical replicate 1


title: ∆arcS-HP2-2

description: Gene expression in ∆arcS exposed to HP

source_name: ∆arcS exposed to HP, biological replicate 2, technical replicate 2


title: ∆arcS-HP1-2

description: Gene expression in ∆arcS exposed to HP

source_name: ∆arcS exposed to HP, biological replicate 1, technical replicate 2


title: MATa/a 4.5hr mrna

description:
processed data column: MATa/a mrna rpkm
processed data file: timecourse replicate 2 mRNA.txt

value: non-meiotic cells in sporulation medium


title: ∆arcS-HP3-1

description: Gene expression in ∆arcS exposed to HP

source_name: ∆arcS exposed to HP, biological replicate 3, technical replicate 1


title: Kidney Tissue from UUO Mice Replicate 7

description:
Biological replicate 7 of 60.
UUO-rep7


title: spore mrna

description:
processed data column: spore mrna rpkm
processed data file: timecourse replicate 2 mRNA.txt


title: 10hr mrna

description:
processed data column: 10hr mrna rpkm
processed data file: timecourse replicate 2 mRNA.txt


title: ∆arcS-HP1-1

description: Gene expression in ∆arcS exposed to HP

source_name: ∆arcS exposed to HP, biological replicate 1, technical replicate 1


title: WT-LP5

description: Gene expression in WT exposed to LP

source_name: Wild type exposed to LP, biological replicate 5

value: wild-type MR-1


title: Kidney Tissue from UUO Mice Replicate 44

description:
Biological replicate 44 of 60.
UUO-rep44


title: Kidney Tissue from UUO Mice Replicate 5

description:
Biological replicate 5 of 60.
UUO-rep5


title: 8hr mrna

description:
processed data column: 8hr mrna rpkm
processed data file: timecourse replicate 2 mRNA.txt


title: Kidney Tissue from UUO Mice Replicate 4

description:
Biological replicate 4 of 60.
UUO-rep4


title: 6hr mrna

description:
processed data column: 6hr mrna rpkm
processed data file: timecourse replicate 2 mRNA.txt


title: Kidney Tissue from UUO Mice Replicate 3

description:
Biological replicate 3 of 60.
UUO-rep3


title: V2a+ lumbar rep 2

city: La Jolla

first: Samuel

middle: L

last: Pfaff

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

description: rawGeneCounts.csv

data_processing:
Illumina adapters were trimmed down to minimum of 50bp with BBTools
Reads were filtered selecting reads with average base quality of > 15 using BBTools
Reads were mapped to combined UCSC/Ensembl/Refgene transcriptome with BWA ‘aln’ allowing up to 200 alignments per read.
Alignments were counted to genes from transcriptome alignments. Multi-gene mapped reads were down weighted by 1/n^2 where n = number of genes
Genome_build: mm10
Supplementary_files_format_and_content: processed data file is raw gene level counts per replicate in CSV format

molecule: polyA RNA

source_name: Lumbar spinal cord

extract_protocol:
Cervical and lumbar segments were dissected in aCSF, and cell dissociation was conducted using Papain following the manufacturer’s instruction (Worthington Biochemical). Via FACS (FACSDIVA or Influx, BD), cells were collected directly into Trizol (Life Technologies). 5-6 neonates at P0 were used from each litter, which typically yielded ~20K cells. ~100K Tom- cells were collected. 3 litters were used to obtain biological replicates. Total RNA was isolated and digested with TURBO DNase (Life Technologies). An Agilent Tape Station was used to determine RNA integrity (RIN) numbers prior to library preparation.
Stranded mRNA-Seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit according to the manufacturer’s instructions (Illumina). Briefly, poly-A RNA was isolated using magnetic beads conjugated to poly-T oligos. mRNA was then fragmented and reverse-transcribed into cDNA. dUTPs were incorporated, followed by second strand cDNA synthesis. dUTP-incorporated second strand was not amplified. cDNA was then end-repaired, index adapter-ligated and PCR amplified. AMPure XP beads (Beckman Coulter) were used to purify nucleic acid after each steps of the library prep.

value: Lumbar spinal cord

tag: age

value: mix of C57BL/6J and CB6F1/J


title: 4.5hr mrna

description:
processed data column: 4.5hr mrna rpkm
processed data file: timecourse replicate 2 mRNA.txt


title: Kidney Tissue from UUO Mice Replicate 6

description:
Biological replicate 6 of 60.
UUO-rep6


title: WT-LP1

description: Gene expression in WT exposed to LP

source_name: Wild type exposed to LP, biological replicate 1


title: V2a+ lumbar rep 3

description: rawGeneCounts.csv


title: V2a- lumbar rep 1

description: rawGeneCounts.csv


title: spore fps

description:
processed data column: spore fp rpkm
processed data file: timecourse replicate 2 fps.txt

data_processing:
library strategy: ribosome profiling
Basecalls performed with CASAVA bcl2fastq_v2.17
reads were trimmed
trimmed reads were aligned using bowtie2 and excluding multiple alignments
ribosome footprint reads were assigned to one genomic position based on a-site analysis of fragment length distribution
Genome_build: sk1_revised_100331 (published in Brar et. al, Science, 2012)
Supplementary_files_format_and_content: txt matrix files of RPKM measurements using standard SGD genome annotations

value: ribosome footprints


title: WT-LP4

description: Gene expression in WT exposed to LP

source_name: Wild type exposed to LP, biological replicate 4


title: V2a+ lumbar rep 1

description: rawGeneCounts.csv


title: 3hr mrna

description:
processed data column: 3hr mrna rpkm
processed data file: timecourse replicate 2 mRNA.txt


title: WT-LP3

description: Gene expression in WT exposed to LP

source_name: Wild type exposed to LP, biological replicate 3


title: V2a- lumbar rep 2

description: rawGeneCounts.csv


title: V2a- lumbar rep 3

description: rawGeneCounts.csv


title: WT-HP4

description: Gene expression in WT exposed to HP

source_name: Wild type exposed to HP, biological replicate 4


title: WT-LP2

description: Gene expression in WT exposed to LP

source_name: Wild type exposed to LP, biological replicate 2


title: 0hr mrna

description:
processed data column: 0hr mrna rpkm
processed data file: timecourse replicate 2 mRNA.txt

source_name: yeast cells


title: V2a+ cervical rep 2

description: rawGeneCounts.csv

source_name: Cervical spinal cord

value: Cervical spinal cord


title: WT-HP5

description: Gene expression in WT exposed to HP

source_name: Wild type exposed to HP, biological replicate 5


title: MATa/a 4.5hr fps

description:
processed data column: MATa/a fp rpkm
processed data file: timecourse replicate 2 fps.txt


title: Kidney Tissue from UUO Mice Replicate 1

description:
Biological replicate 1 of 60.
UUO-rep1

source_name: Kidney Tissue from UUO Mice

source_name: Mouse Universal Reference RNA


title: WT-HP2

description: Gene expression in WT exposed to HP

source_name: Wild type exposed to HP, biological replicate 2


title: WT-HP3

description: Gene expression in WT exposed to HP

source_name: Wild type exposed to HP, biological replicate 3


title: V2a+ cervical rep 3

description: rawGeneCounts.csv


title: 6hr fps

description:
processed data column: 6hr fp rpkm
processed data file: timecourse replicate 2 fps.txt


title: V2a- cervical rep 3

description: rawGeneCounts.csv


title: vegetative exponential mrna

description:
processed data column: vegrepl1-mrna-Jan2017-rpkm
processed data file: timecourse replicate 2 mRNA.txt


title: V2a+ cervical rep 1

description: rawGeneCounts.csv


title: 10hr fps

description:
processed data column: 10hr fp rpkm
processed data file: timecourse replicate 2 fps.txt


title: 8hr fps

description:
processed data column: 8hr fp rpkm
processed data file: timecourse replicate 2 fps.txt


title: WT-HP1

description: Gene expression in WT exposed to HP

source_name: Wild type exposed to HP, biological replicate 1


title: Kidney Tissue from UUO Mice Replicate 2

description:
Biological replicate 2 of 60.
UUO-rep2


title: 1.5hr mrna

description:
processed data column: 1.5 hr mrna rpkm
processed data file: timecourse replicate 2 mRNA.txt


title: Macrophages after 6 days of differentiation and 1 day without m-CSF used for analyses at 72h, replicate 2

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

hyb_protocol: Labelled RNA was hybridized onto microarray slides using a rotational oven at 55° C for 22 h.

scan_protocol: Mycroarrays were scanned in an Agilent microarray scanner (model G2565CA). Agilent Feature Extraction software version 10.5.1.1 was used for image analysis.

data_processing:
Raw microarray data were first filtered for the number of miRNAs presenting an expression value above background (allowed 50% of undetected values for each miRNA) and then normalized according loess cyclic algorithm.
Fluorescence intensity Raw values based on GeneView version

organism: Homo sapiens

source_name: Healthy male blood donor

label_protocol: 200 ng of total RNA were labelled using miRNA Complete Labeling and Hyb Kit (Agilent Technologies), according to the manufacturer protocol.

growth_protocol: Monocytes derived from buffy coats obtained from healthy blood donors were prepared as described previously (Amedei A et al., J Clin Invest 2006). For macrophage differentiation, 5 × 10^5 monocytes, seeded in 24-well plates, were cultured in RPMI 20% FBS in the presence of 100 ng/ml M-CSF (Miltenyi Biotec. Bergisch Gladbach, Germany) for a 6-d differentiation. Monocyte-derived macrophages were cultured for 1 d in culture medium without M-CSF, before stimuli application.

extract_protocol: Total RNA from macrophages was isolated with TRIzol reagent (ThermoFisher) according to manufacturer protocol. RNA quantification was performed using the NanoDrop 1000 spectrophotometer (Nanodrop, Wilmington, DE, USA). Total RNA integrity and content of miRNAs in each sample were assessed by capillary electrophoresis using the Agilent Bioanalyzer 2100 with the RNA 6000 Nano and the Small RNA Nano LabChips, respectively (Agilent Technologies, Palo Alto, CA, USA). Only total RNA samples with an RNA integrity number > 7 and small RNAs concentration < 30% were used for miRNA or mRNA gene expression analysis.

treatment_protocol: Monocyte-derived macrophages were cultured for 1 d in culture medium without M-CSF, before stimuli application. Cells were infected with bacteria (5 × 10^6 colony-forming units/mL, MOI=10) in RPMI 1640 containing 20% FCS. Helicobacter pylori strain N6 was maintained in 5% CO2 at 37°C on Columbia agar plates supplemented with 5% horse blood (ThermoFisher, Waltham, MA, USA). Colonies were taken directly from plates and suspended in RPMI 20% FBS without any antibiotic. Number of bacteria cells was determined by spectroscopic optical density measurement at 600 nm (1 O.D.= 10^9 Colony Forming Units –CFU- /ml). Before proceeding with the infection experiments, bacteria motility was verified at the optical microscope. Controls were produced treating macrophages with the veicle using to treat with Hp substituting Hp with PBS.

tag: cell type

value: monocyte-derived macrophages

tag: disease state

value: Healthy

tag: gender

value: male


title: V2a- cervical rep 2

description: rawGeneCounts.csv


title: 1.5hr fps

description:
processed data column: 1.5hr fp rpkm
processed data file: timecourse replicate 2 fps.txt


title: 3hr fps

description:
processed data column: 3hr fp rpkm
processed data file: timecourse replicate 2 fps.txt


title: Macrophages after 6 days of differentiation and 1 day without m-CSF used for analyses at 72h, replicate 3


title: Macrophages after 6 days of differentiation and 1 day without m-CSF used for analyses at 24h, replicate 2


title: Macrophages after 6 days of differentiation and 1 day without m-CSF used for analyses at 72h, replicate 1


title: Hp treated 72h replicate 2


title: 4.5hr fps

description:
processed data column: 4.5hr fp rpkm
processed data file: timecourse replicate 2 fps.txt


title: vegetative exponential fps

description:
processed data column: veg exp fp rpkm
processed data file: timecourse replicate 2 fps.txt


title: Hp treated 24h replicate 3


title: 0hr fps

description:
processed data column: 0hr fp rpkm
processed data file: timecourse replicate 2 fps.txt


title: Hp treated 72h replicate 1


title: Hp treated 24h replicate 2


title: Hp treated 72h replicate 3


title: Control 24h replicate 3


title: Control 24h replicate 2


title: Macrophages after 6 days of differentiation and 1 day without m-CSF used for analyses at 24h, replicate 1


title: V2a- cervical rep 1

description: rawGeneCounts.csv


title: Control 72h replicate 1


title: Control 24h replicate 1


title: Hp treated 24h replicate 1


title: Control 72h replicate 2


title: IMpTB3

status: Public on Feb 21 2018

city: Ithaca

first: Lu

last: Huang

state: NY

department: Microbiology and Immunology

institute: Cornell University

data_processing:
The Tophat program (v2.1) was used to align the reads, and the Cufflinks program (v2.2) was used for the measurements of transcript abundance represented by Fragments Per Kilobase of transcript per Million mapped reads (FPKM) and statistical analysis of differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Cuffdiff2 output files:
4comparisons_gene_exp.diff
4comparisons_genes.read_group_tracking (IMP 2)

source_name: Interstitial macrophages with Mtb

extract_protocol:
Lung macrophages were FACS-sorted, and total RNA was extracted using Trizol according to the commercial protocol, with the addition of a chloroform back-extraction step, addition of GlycoBlue as a carrier at the precipitation step, and a second 70% ethanol wash of the RNA pellet.
Libraries were generated with the NEBNext Ultra II RNA library prep kit.

value: Lung

value: Interstitial macrophages

tag: infection

value: Mtb


title: IMmTB2

data_processing:
The Tophat program (v2.1) was used to align the reads, and the Cufflinks program (v2.2) was used for the measurements of transcript abundance represented by Fragments Per Kilobase of transcript per Million mapped reads (FPKM) and statistical analysis of differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Cuffdiff2 output files:
4comparisons_gene_exp.diff
4comparisons_genes.read_group_tracking (IMM 1)

source_name: Interstitial macrophages without Mtb

value: without Mtb


title: IMmTB3

data_processing:
The Tophat program (v2.1) was used to align the reads, and the Cufflinks program (v2.2) was used for the measurements of transcript abundance represented by Fragments Per Kilobase of transcript per Million mapped reads (FPKM) and statistical analysis of differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Cuffdiff2 output files:
4comparisons_gene_exp.diff
4comparisons_genes.read_group_tracking (IMM 2)


title: IMpTB2

data_processing:
The Tophat program (v2.1) was used to align the reads, and the Cufflinks program (v2.2) was used for the measurements of transcript abundance represented by Fragments Per Kilobase of transcript per Million mapped reads (FPKM) and statistical analysis of differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Cuffdiff2 output files:
4comparisons_gene_exp.diff
4comparisons_genes.read_group_tracking (IMP 1)


title: wild type A549 _No3

city: Nanjing

first: Shizhi

last: Wang

state: Jiangsu

address: 87 Dingjiaqiao, Gulou District

department: Key Laboratory of Environmental Medicine Engineering, Ministry of Education

country: China

institute: Southeast University

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual.a,The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min. b, Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA). c, Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon)

scan_protocol: Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. Discriminant miRNAs and differences between groups were analyzed using Bayes moderated t test (limma) with Benjamini Hochberg false discovery rate (FDR) at P < 0.05. A two-fold cut-off difference was applied to select the up- and down-regulated miRNAs.

source_name: A549 cells

label_protocol: RNA labeling and array hybridization was according to Exiqon's manual.After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling by following steps:  a, 1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C. b, The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture.The labeling reaction was incubated for 1 h at 16°C. c,Terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.


title: Al2O3 nanoparticle treated A549_No1


title: Al2O3 nanoparticle treated A549_No2


title: FACS population P4

city: Worcester

first: Merav

last: Socolovsky

state: MA

address: 364 Plantation St

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

data_processing:
Raw sequencing data were processed using the previously described (Zilionis et al., Nature Protocols 2017) inDrops.py bioinformatics pipeline, available at https://github.com/indrops/indrops, using library version "v3".
The cDNA read was trimmed using Trimomatic (5) (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:30).
Barcodes for each read were matched against a list of the pre-determined barcodes, and errors of up to two nucleotides mismatch were corrected. Reads with a barcode separated by more than two nucleotides from the reference list were discarded. The reads were then split into barcode-specific files for mapping and UMI filtering.  All files were submitted to SRA. R1 = 61 nt, R2 & R3 = 8 nt, R4 = 14. A file with the original raw file name and associated SRR is available on the series record.
The trimmed reads were aligned using Bowtie (version 1.1.1, parameters: -n 1 -l 15 -e 100 -m 200 -best -strata -a) to the mouse transcriptome. The reference transcriptome was built using annotations from ENSEMBL (GRCm38.81) including all annotations with ""Transcript Support Levels"" of 1, 2, or NA (only accepted for protein coding genes).
A custom Python and PySAM script to process mapped reads into counts of UMI-filtered transcripts per gene, as previously described (Zilionis et al., Nature Protocols 2017).
Genome_build: GRCm38
Supplementary_files_format_and_content: Column 1 contains the sample ID. Column 2 contains the library ID. Column 3 contains the cell barcode sequence. Columns 4 and 5 contain the total number of sequencing reads and transcript counts, respectively, for each barcode. Column 6 contains a flag for whether the cell barcode passed our total counts filter (1=pass, 0=fail). Column 7 contains the fraction of each barcode's total counts coming from mitochondrial genes, a sign of cell stress. Column 8 contains a flag for whether the cell barcode passed our mitochondrial gene fraction filter (1=pass, 0=fail). Column 9 contains a flag for whether a cell passed both filters (1=pass, 0=fail) and was used in downstream analyses. Columns 10+ contain counts for each gene.

source_name: Bone marrow hematopoietic progenitors

extract_protocol:
Using inDrops, cells were encapsulated into 4-nL droplets on ice and lysed using a final concentration of 0.4% NP-40. Single-cell lysates were subject to reverse transcription at 50°C without purification of RNA (as previously described in Klein et al., Cell 2015).
Libraries were prepared as in Zilionis et al., Nat. Protoc. 2017, with modifications summarized in Supplementary Table 7 of this manuscript (Khoramian Tusi et al., Nature 2018).

treatment_protocol: A detailed protocol of this procedure can be found at the Protocol Exchange (Khoramian Tusi and Socolovsky, 2018). Bone marrow cells from adult BALB/cJ male or female mice (aged 8-12 weeks) were lineage-depleted using the Mouse Streptavidin RapidSpheres Isolation Kit (STEMCELL Technologies 19860A), with the following biotinylated antibodies: anti-CD11B (clone M1/70, BD Biosciences 557395), anti-LY-6G and LY-6C (clone RB6-8C5, BD Biosciences 553125), anti-CD4 (clone RM4-5, BD Biosciences 553045), anti-CD8A (Ly-2) (clone 53-6.7, BD Bioscience 553029), anti-CD19 (clone 1D3, BD Biosciences 553784), anti-TER119 (clone TER119, BD Biosciences 553672). Lineage-depleted cells were then labelled with the following antibodies in the presence of 1% rat serum: streptavidin Alexa Fluor 488 (Molecular Probes) to mark lineage-positive cells, CD117-APC Cy7 (clone 2B8, Biolegend 105826), TER119-BUV395 (clone TER-119, BD Biosciences 563827), CD71-PE Cy7 (clone RI7217, Biolegend 113812), CD55-AF647 (clone RIKO-3, Biolegend 131806), CD105-PE (clone MJ7/18, Biolegend 120408), CD150-BV650 (clone TC15-12F12.2, Biolegend 115931), CD41-BV605 (clone MWReg30, Biolegend 133921), CD49F (also known as ITGA6)-BV421 (clone GoH3, Biolegend 313624). After washes, cells were re-suspended in DAPI-containing buffer and sorting was performed using a BD FACSAria II with a 100-um nozzle. Sorted populations were defined as in Fig. 2a of Khoramian Tusi et al., Nature 2018. Cells were then centrifuged and resuspended in PBS with 15% Optiprep for input into the inDrops platform.

value: BALB/cJ

value: bone marrow

value: 8-week old adult

tag: purification


title: FACS population P5


title: FACS population P2


title: FACS population P1


title: FACS population P1-CD71hi


title: IMpTB1

data_processing:
The Tophat program (v2.1) was used to align the reads, and the Cufflinks program (v2.2) was used for the measurements of transcript abundance represented by Fragments Per Kilobase of transcript per Million mapped reads (FPKM) and statistical analysis of differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Cuffdiff2 output files:
4comparisons_gene_exp.diff
4comparisons_genes.read_group_tracking (IMP 0)


title: IMmTB1

data_processing:
The Tophat program (v2.1) was used to align the reads, and the Cufflinks program (v2.2) was used for the measurements of transcript abundance represented by Fragments Per Kilobase of transcript per Million mapped reads (FPKM) and statistical analysis of differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Cuffdiff2 output files:
4comparisons_gene_exp.diff
4comparisons_genes.read_group_tracking (IMM 0)


title: Al2O3 nanoparticle treated A549_No3


title: AMpTB3

data_processing:
The Tophat program (v2.1) was used to align the reads, and the Cufflinks program (v2.2) was used for the measurements of transcript abundance represented by Fragments Per Kilobase of transcript per Million mapped reads (FPKM) and statistical analysis of differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Cuffdiff2 output files:
4comparisons_gene_exp.diff
4comparisons_genes.read_group_tracking (AMP 2)

source_name: Alveolar macrophages with Mtb

value: Alveolar macrophages


title: wild type A549_No2


title: AMpTB2

data_processing:
The Tophat program (v2.1) was used to align the reads, and the Cufflinks program (v2.2) was used for the measurements of transcript abundance represented by Fragments Per Kilobase of transcript per Million mapped reads (FPKM) and statistical analysis of differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Cuffdiff2 output files:
4comparisons_gene_exp.diff
4comparisons_genes.read_group_tracking (AMP 1)


title: wild type A549_No1


title: AMmTB1

data_processing:
The Tophat program (v2.1) was used to align the reads, and the Cufflinks program (v2.2) was used for the measurements of transcript abundance represented by Fragments Per Kilobase of transcript per Million mapped reads (FPKM) and statistical analysis of differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Cuffdiff2 output files:
4comparisons_gene_exp.diff
4comparisons_genes.read_group_tracking (AMM 0)

source_name: Alveolar macrophages without Mtb


title: AMpTB1

data_processing:
The Tophat program (v2.1) was used to align the reads, and the Cufflinks program (v2.2) was used for the measurements of transcript abundance represented by Fragments Per Kilobase of transcript per Million mapped reads (FPKM) and statistical analysis of differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Cuffdiff2 output files:
4comparisons_gene_exp.diff
4comparisons_genes.read_group_tracking (AMP 0)


title: AMmTB3

data_processing:
The Tophat program (v2.1) was used to align the reads, and the Cufflinks program (v2.2) was used for the measurements of transcript abundance represented by Fragments Per Kilobase of transcript per Million mapped reads (FPKM) and statistical analysis of differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Cuffdiff2 output files:
4comparisons_gene_exp.diff
4comparisons_genes.read_group_tracking (AMM 2)


title: FACS population P3


title: AMmTB2

data_processing:
The Tophat program (v2.1) was used to align the reads, and the Cufflinks program (v2.2) was used for the measurements of transcript abundance represented by Fragments Per Kilobase of transcript per Million mapped reads (FPKM) and statistical analysis of differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Cuffdiff2 output files:
4comparisons_gene_exp.diff
4comparisons_genes.read_group_tracking (AMM 1)


title: wt cisplatin, biological rep 3

city: A Coruña

first: Angel

last: Vizoso-Vázquez

address: Púa da Fraga, 10

department: Cellular and Molecular Biology Department

country: Spain

institute: University of A Coruña

description: gene expression data from W303 cells grown in complete synthetic medium and treated with 600 microM cisplatin in DMSO

hyb_protocol: Hybridization, washes and staining were done with the GeneChip® HT Hybridization, Wash and Stain Kit. (Manufactured for Affymetrix, Inc. by Ambion, Inc.Affymetrix)

scan_protocol: Image caption and preliminary data analysis were carried out with Affymetrix® Expression Console™ software (v.1.1)

data_processing:
Array data were normalized and summarized using the RMA algorithm from Affymetrix. The data were analyzed using the web suite Babelomics (version 4.3) (Medina et al., 2010). Statistical analysis to identify DEGs were made by using the LIMMA (Linear models for microarray data) test (Smyth, 2005).
The FDR (False Discovery Rate) was estimated to correct values for multiple comparison (Benjamini and Hochberg, 1995), using a adjusted p-value of 0.05.

label: biotin

source_name: wild-type S. cerevisiae treated with cisplatin in DMSO

label_protocol: not provided

extract_protocol: RNA was extracted from a number of cells corresponding to OD600 of 3 with the AurumTM Total RNA Mini Kit (Bio-Rad) and following the manufacturer’s instructions. The RIN parameter (RNA Integrity Number) evaluated with the 2100 was near to the value 9 in all the samples.

tag: background strain

tag: genotype

value: wild-type


title: Dixr1 cisplatin, biological rep2

description: gene expression data from W303-Dixr1 cells grown in complete synthetic medium and treated with 600 microM cisplatin in DMSO

source_name: Dixr1  mutant treated with cisplatin in DMSO

value: ixr1  mutant


title: wt cisplatin, biological rep 1


title: Dixr1 non treated, biological rep3

description: gene expression data from W303-Dixr1 cells grown in complete synthetic medium suplemented with DMSO

source_name: control, Dixr1  mutant treated with DMSO


title: Dixr1 cisplatin, biological rep1


title: wt cisplatin, biological rep 2


title: Dixr1 non treated, biological rep1


title: wt non treated, biological rep 2

description: gene expression data from W303 cells grown in complete synthetic medium suplemented with DMSO

source_name: control, wild-type S. cerevisiae treated with DMSO


title: wt non treated, biological rep 1


title: PC9GR

city: Shanghai

last: Xu

address: 280 South Chongqing Rd

department: Pharmacology

institute: Shanghai Jiao Tong University, School of Medicine

description: miRNA expression

hyb_protocol: Agilent miRNA expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies Scanner G2505C at 3 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol miRNA_107_Sep09 and Grid: 046064_D_F_20121223) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: gefitinib-resistant PC9 cells

label_protocol: 100 ng of total RNA was used by AgilentÒ miRNA Complete Labeling and Hybridization Kit

growth_protocol: Gefitinib-resistant sub-cell lines were generated by growing gefitinib-sensitive EGFR-mutant NSCLC cell lines (PC9 and HCC827) in increasing concentrations of gefitinib to a final concentration of 10uM up to 6 months.

extract_protocol: Total RNA was extracted using the QIAzol reagent and the miRNeasy Mini Kit (Qiagen)

value: non-small cell lung cancer (NSCLC)

value: gefitinib-resistant PC9 cells


title: 150000_CNS_nuclei

city: Seattle, WA 98195

first: Alexander

middle: B

last: Rosenberg

state: WA

address: 4000 15th Ave NE

department: Electrical Engineering

institute: University of Washington

data_processing:
Fastq files were aligned to either a combined mm10-hg19 genome or a mm10 genome using STAR/2.4.1d
Single cell/nuclei transcriptomes were assembled by combining aligned reads with the same combination of barcodes using a custom script (see Supplementary Materials for more details).
Genome_build: mm10 or mm10-hg19 combined genome
Supplementary_files_format_and_content: .mat with digital gene expression, genes, barcodes, sample type, cluster assignment (if applicable), and spinal cord cluster assignment (if applicable)

source_name: Brain and Spinal Cord

growth_protocol: HEK293 and Hela-S3 cells were cultured in DMEM + 10% FBS, while NIH/3T3 cells were cultured in DMEM + 10% FCS. Cells were rinsed twice with 1x PBS, then detached by incubating 2-5 min at room temperature with 1ml of TrypLE. Once cells were detached, they were added to 2mL of media with 10% FBS. In mouse-human species mixing experiments, cells were combined at the desired concentrations at this step

extract_protocol:
Nuclei were extracted using a modified version of the protocol described in Krishnaswami et al (PMID: 26890679).
scRNA-seq libraries were prepared using the SPLiT-seq protocol

value: C57BL/6 x DBA/2

value: wild type

value: post natal day 2 and 11

value: brain and spinal cord


title: Dixr1 cisplatin, biological rep3


title: Dixr1 non treated, biological rep2


title: 100_CNS_nuclei


title: PC9

description: miRNA expression

source_name: PC9 cells

value: PC9 cells


title: ∆cpdA 3

description: Gene expession in ∆cpdA

hyb_protocol: For each array, 19 µL of the purified Cy3-labeled cRNA (600 ng) was mixed with 5 µL of 10× Blocking Agent, 1 µL of 25× Fragmentation Buffer, and 25 µL of 2× GE Hybridization Buffer HI-RPM. The resultant mixtures were hybridized to the arrays at 65ºC for 17 h. After hybridization, each microarray slide was washed with Gene Expression wash buffer 1 at room temperature for 1 min, followed by Gene Expression wash buffer 2 at 37ºC for 1min.

scan_protocol: Slides were air dried for 1 min and scanned using an Agilent DNA Microarray Scanner at 5-µm resolution.

data_processing: Gene expression data (fluorescent intensities) were extracted from the scanned image using the Feature Extraction Software version 8.1 (Agilent Technologies) and normalized and statistically analyzed using GeneSpring GX version 11.5 (Agilent Technologies).

source_name: ∆cpdA replicate 3

label_protocol: Cyanine3 (Cy3)-labeled cRNA was synthesized from 50 ng of total RNA using the Low Input Quick Amp WT Labeling Kit (Agilent Technologies) and purified using a RNeasy Mini Kit (Qiagen). The labeled cRNA was quantified using NanoDrop ND-1000 Spectrophotometer (Thermo Scientific).

growth_protocol: Shewanella cells were aerobically grown in lactate minimal medium until logrithmic growth phase.

extract_protocol: Total RNA was extracted using a Trizol reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s instructions and subsequently purified using an RNeasy Mini Kit and an RNase-Free DNase Set (Qiagen, Valencia, CA). The quality of total RNA was evaluated using an Agilent 2100 Bioanalyzer with RNA 6000 Pico reagents and RNA Pico Chips (Agilent Technologies) according to the manufacture’s instruction.

treatment_protocol: Cells were harvested by centrifugation at 7,000 g for 10 min and stored at -80°C

value: delta cpdA


title: HCC827

description: miRNA expression

source_name: HCC827 cells

value: HCC827 cells


title: HCC827GR

description: miRNA expression

source_name: gefitinib-resistant HCC827 cells

value: gefitinib-resistant HCC827 cells


title: ∆cpdA 4

description: Gene expession in ∆cpdA

source_name: ∆cpdA replicate 4


title: ∆cpdA 1

description: Gene expession in ∆cpdA

source_name: ∆cpdA replicate 1


title: wt non treated, biological rep 3


title: WT 3

description: Gene expession in the wild-type strain MR-1

source_name: Wild type replicate 3

value: Wild type


title: ∆cpdA 2

description: Gene expession in ∆cpdA

source_name: ∆cpdA replicate 2


title: WT 1

source_name: Wild type replicate 1


title: WT 4

source_name: Wild type replicate 4


title: WT 2

source_name: Wild type replicate 2


title: pituitary_PrlrKO_2months_array2_dup2

city: le Kremlin-Bicêtre

first: Nadine

last: Binart

address: 63 rue Gabriel Péri

department: Faculté de médecine Paris Sud

country: France

institute: INSERM 1185

description:
Gene expression in Prlr KO 2-months old mouse pituitary
ar2_PrlrKO_2mo_dup2

hyb_protocol: Labeled cDNA was then fragmented and hybridized over 1 Sureprint G3 Mm9 8×60K array (Agilent technologies), allowing the study of the 8 samples in parallel and interrogating over 40K annotated transcripts of Mm9 assembly. Hybridization was performed according to manufacturer's instructions.

scan_protocol: Raw fluorescence data were extracted using Genespring software v12 (Agilent technologies).

data_processing: Raw fluorescence data were normalized using the 75th percentile method. Values were then log2 normalized and subtracted of the median value for each replicate.

source_name: pituitary, PrlrKO, 2 months

label_protocol: Fifty ng total RNA was amplified and labeled with Cy3 using Low input Quick Amp labeling Kit (Agilent technologies, Santa Clara, California) according to manufacturer's instructions.

extract_protocol: Total RNA was extracted from pituitaries using TRIreagent solution (Ambion, Saint-Aubin, France). RNA was quantified using a NanoDrop-1000 spectrophotometer

treatment_protocol: Two and four months-old wild-type (n=6 and 6 respectively) and Prlr KO (n=6 and 6 respectively) mice were sacrified by decapitation. Pituitaries were removed, pooled three by three to form duplicates for each genotype, and frozen at -80°C before RNA extraction. The whole experiment was replicated with another set of animals (12 wild-type and 12 Prlr -/-  mice).  (Note : in the replication experiment (array2), the second duplicate for 4 months-old mice did not hybridize correctly and therefore was removed before analysis, both in the WT and the Prlr KO conditions)

tag: Sex

value: female

value: pituitary

value: 2 months

value: Prlr KO


title: pituitary_PrlrWT_4months_array2

description:
Gene expression in WT 4-months old mouse pituitary
ar2_PrlrWT_4mo

source_name: pituitary, WT, 4 months

value: 4 months

value: WT


title: pituitary_PrlrKO_4months_array2

description:
Gene expression in Prlr KO 4-months old mouse pituitary
ar2_PrlrKO_4mo

source_name: pituitary, PrlrKO, 4 months


title: pituitary_PrlrWT_2months_array2_dup2

description:
Gene expression in WT 2-months old mouse pituitary
ar2_PrlrWT_2mo_dup2

source_name: pituitary, WT, 2 months


title: pituitary_PrlrKO_4months_array1_dup2

description:
Gene expression in Prlr KO 4-months old mouse pituitary
ar1_PrlrKO_4mo_dup2


title: pituitary_PrlrKO_2months_array2_dup1

description:
Gene expression in Prlr KO 2-months old mouse pituitary
ar2_PrlrKO_2mo_dup1


title: LNCaP-DMSO-48h-rep2

city: Ann Arbor

first: Marcin

middle: Piotr

last: Cieslik

state: Michigan

address: 500 S State St

department: Pathology

institute: University of Michigan

description: LNCaP cell treated with DMSO

data_processing:
Alignment using STAR to GRCh38
Read quantification using featureCounts
genoce V23 and MiTranscriptome uses as reference transcriptomes
additional steps: adapter timming, read quality filtering
Genome_build: GRCh38
Supplementary_files_format_and_content: featureCounts output files gzipped (raw counts of reads)

source_name: LNCAP

growth_protocol: VCaP cells were maintained in DMEM (Invitrogen) supplemented with 10% fetal bovine serum (FBS). LNCaP cells were maintained in RPMI 1640 (Invitrogen) supplemented with 10% FBS. MDA-PCa-2b cells were maintained in ATCC-formulated F-12K medium, supplemented with 20% FBS, 25 ng/ml cholera toxin, 10 ng/ml mouse epidermal growth factor, 100 pg/ml hydrocortisone, 0.005 mM phosphoethanolamine, 45nM selenous acid, and 0.005 mg/ml bovine insulin.

extract_protocol:
Total RNA was isolated using miRNeasy Kit (Invitrogen) following the manufacturer’s instructions.
polaA-selected stranded RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Specifically, for DHT treatment LNCaP cells or VCaP cells were grown in charcoal-stripped serum containing media for 48hrs (starvation), followed by treatment with vehicle or 10nM DHT for indicated times. For the other experiments cells were not starved. Non-targeting SI (siNT) are used as controls for knock-down experiments, DMSO is used as control for Enzalutamide treatment.

value: LNCAP

value: prostate cancer

tag: treatment time (h)

tag: treatment

value: DMSO


title: MDA-PCA-2B-siNT-rep1

description: MDA-PCA-2B treated with non-targeting si

value: siNT


title: MDA-PCA-2B-siARlnc1-rep2

description: MDA-PCA-2B treated with siARlnc1


title: MDA-PCA-2B-siARlnc1-rep1

description: MDA-PCA-2B treated with siARlnc1


title: MDA-PCA-2B-siNT-rep3

description: MDA-PCA-2B treated with siNT


title: MDA-PCA-2B-siAR-rep2

description: MDA-PCA-2B treated with siAR

value: siAR


title: MDA-PCA-2B-siAR-rep1

description: MDA-PCA-2B treated with siAR


title: LNCaP-DMSO-48h-rep1

description: LNCaP cell treated with DMSO


title: MDA-PCA-2B-siNT-rep2


title: VCaP-DHT-0h

description: LNCAP cells treated with DHT at 0h

source_name: VCAP

value: VCAP

value: DHT


title: pituitary_PrlrWT_2months_array2_dup1

description:
Gene expression in WT 2-months old mouse pituitary
ar2_PrlrWT_2mo_dup1

tag: tissue


title: LNCaP-Enza-48h-rep1

description: LNCaP cell treated with Enzalutamide

value: Enza


title: pituitary_PrlrKO_2months_array1_dup2

description:
Gene expression in Prlr KO 2-months old mouse pituitary
ar1_PrlrKO_2mo_dup2


title: pituitary_PrlrWT_4months_array1_dup2

description:
Gene expression in WT 4-months old mouse pituitary
ar1_PrlrWT_4mo_dup2


title: LNCaP-Enza-48h-rep2

description: LNCaP cell treated with Enzalutamide


title: pituitary_PrlrKO_4months_array1_dup1

description:
Gene expression in Prlr KO 4-months old mouse pituitary
ar1_PrlrKO_4mo_dup1


title: pituitary_PrlrWT_4months_array1_dup1

description:
Gene expression in WT 4-months old mouse pituitary
ar1_PrlrWT_4mo_dup1


title: pituitary_PrlrWT_2months_array1_dup2

description:
Gene expression in WT 2-months old mouse pituitary
ar1_PrlrWT_2mo_dup2


title: pituitary_PrlrWT_2months_array1_dup1

description:
Gene expression in WT 2-months old mouse pituitary
ar1_PrlrWT_2mo_dup1


title: pituitary_PrlrKO_2months_array1_dup1

description:
Gene expression in Prlr KO 2-months old mouse pituitary
ar1_PrlrKO_2mo_dup1


title: VCaP-DHT-6h

description: LNCAP cells treated with DHT at 6h


title: LNCaP-DHT-24h

description: LNCAP cells treated with DHT at 24h


title: V0980U-x2 input

city: York

first: Andrew

middle: Nicholas

last: Holding

address: Wentwork Way

department: Biology

country: United Kingdom

institute: University of York

library_source: genomic

data_processing:
Aligment with Bowitie
Blacklisting against DAC blacklist
Peak calling with MACS2
Genome_build: hg19
Supplementary_files_format_and_content: peak files

molecule: genomic DNA

extract_protocol: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Libraries were prepared according to the Thruplex DNA-seq Kit Manual.

tag: tissue id

value: Breast Cancer patient-derived xenograft (PDX)

tag: chip antibody

value: none (input)


title: AB580-x1 input


title: LNCaP-DHT-6h

description: LNCAP cells treated with DHT at 6h

tag: cell line

value: DTH


title: STG195-x4 input


title: LNCaP-DHT-0h

description: LNCAP cells treated with DHT at 0h


title: AB555B-x2 input


title: VHI0244o2-x4 ChIP-seq

tag: parallel chip antibody

value: CTCF (D31H2)


title: AB580-x1 ChIP-seq


title: VHI0244o2-x4 input


title: STG195-x4 ChIP-seq


title: V0980U-x2 ChIP-seq


title: TGFb_Rock_8Br-cAMP_BMP4_d15_1

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

department: A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine

country: Finland

institute: University of Eastern Finland

description: TGFb_Rock_8Br-cAMP_BMP4_d15_1__hg19 reads FPKM

data_processing:
Libraries were sequenced for 50 cycles on an Illumina HiSeq 2000 according to the manufacturer’s instructions.
RNA-Seq results were trimmed to remove 3' A-stretches originating from the library preparation and poor quality reads were filtered out (minimum 97% of bp over quality cutoff 10).
Reads were aligned to the hg19 genome using Tophat.
Data analysis was performed using HOMER (http://homer.ucsd.edu/homer/) and the differential gene expression usign edgeR
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression values (RPKM) and UCSC Bedgraphs are provided

growth_protocol: HiPSC colonies were cut from Matrigel-coated dishes under a microscope with a scalpel and pieces of hiPSC were washed with phosphate buffered saline (PBS). Cells were dissociated with Accutase (Sigma-Aldrich) and approximately 0,7 x 104 cells per cm2 were plated on a fibronectin-gelatin (10 µg/ml, 0.05%; Sigma-Aldrich) coated dish. Cells were cultured in serum-free EBM™-2 Endothelial basal medium-2 (Lonza CC-3156) with EGMTM-2 SingleQuots medium supplement including human epidermal growth factor (hEGF), recombinant human long R3 insulin like growth factor-1 (R3-IGF-1), ascorbic acid, hydrocortisone, human FGF-2, heparin and antibiotics GA-1000 (Lonza CC-4176).  From this supplement, fetal bovine serum (FBS) and vascular endothelial growth factor (VEGF) was discarded to obtain serum free and VEGF-controlled cell culture conditions.  Knockout serum replacement (GIBCO) was used in final concentration of 20 μl/ml and recombinant human VEGF-A 165 (R&D Systems) was used in final concentration of 200 ng/ml.

extract_protocol:
RNA was purified using RNeasy Mini Kit (Qiagen) and depleted from rRNAs using  Ribo-Zero Gold Kit (Illumina).
Strand-specific RNA-Seq: The RNA was base-hydrolyzed, dephosphorylated with PNK and purified using RNA Clean & Concentrator kit (Zymo). Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers containing Illumina adapter sequences. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified using ChIP DNA Clean & Concentrator kit. The recovered cDNA was RNaseH treated and circularized (CircLigase) and amplified for 11 cycles. The final product was ran on 10% TBE gel, gel purified (180-350 bp) and cleaned-up using ChIP DNA clean & Concentrator Kit.

treatment_protocol: Following small molecules and growth factors were used in different combinations and time courses: 10 uM TGFβ-inhibitor SB431542 (Tocris Bioscience), 10 uM ROCK-inhibitor Y-27632 (Sigma-Aldrich), 20 ng/ml recombinant human BMP-4 (R&D Systems) and 0,25 mM 8-Br-cAMP (SB 431542, Sigma-Aldrich). Different cell culture conditions are described in table 1. In all groups without TGFβ-inhibitor at day 1 in the differentiation, it was added at day 4. In those groups with BMP-4 at day 1, it was removed at day 4. Differentiating ECs were passaged every 4-6 days using Accutase (Sigma-Aldrich).

tag: source cell type

value: induced pluripotent stem cell (IPSCs)

tag: culture condition

tag: molecule subtype

value: rRNA-depleted RNA


title: TGFb_Rock_8Br-cAMP_BMP4_d5

description: TGFb_Rock_8Br-cAMP_BMP4_d5__hg19 reads FPKM


title: Rock_8Br-cAMP_d15_2

description: Rock_8Br-cAMP_d15_2__hg19 reads FPKM


title: Rock_8Br-cAMP_d5

description: Rock_8Br-cAMP_d5__hg19 reads FPKM


title: TGFb_Rock_BMP4_d5

description: TGFb_Rock_BMP4_d5__hg19 reads FPKM


title: TGFb_Rock_8Br-cAMP_BMP4_d15_2

description: TGFb_Rock_8Br-cAMP_BMP4_d15_2__hg19 reads FPKM


title: Rock_BMP4_d15_1

description: Rock_BMP4_d15_1__hg19 reads FPKM


title: RNA-Seq_HUVEC_rep2

growth_protocol: HiPSC colonies were cut from Matrigel-coated dishes under a microscope with a scalpel and pieces of hiPSC were washed with phosphate buffered saline (PBS). Cells were dissociated with Accutase (Sigma-Aldrich) and approximately 0,7 x 104 cells per  cm2 were plated on a fibronectin-gelatin (10 µg/ml, 0.05%; Sigma-Aldrich) coated dish. Cells were cultured in serum-free EBM™-2 Endothelial basal medium-2 (Lonza CC-3156) with EGMTM-2 SingleQuots medium supplement including human epidermal growth factor (hEGF), recombinant human long R3 insulin like growth factor-1 (R3-IGF-1), ascorbic acid, hydrocortisone, human FGF-2, heparin and antibiotics GA-1000 (Lonza CC-4176).  From this supplement, fetal bovine serum (FBS) and vascular endothelial growth factor (VEGF) was discarded to obtain serum free and VEGF-controlled cell culture conditions.  Knockout serum replacement (GIBCO) was used in final concentration of 20 μl/ml and recombinant human VEGF-A 165 (R&D Systems) was used in final concentration of 200 ng/ml.

extract_protocol:
RNA was purified using RNeasy Mini Kit (Qiagen) and depleted from rRNAs using  Ribo-Zero Gold Kit (Illumina).
The RNA was base-hydrolyzed, dephosphorylated with PNK and purified using RNA Clean & Concentrator kit (Zymo). Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers containing Illumina adapter sequences. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified using ChIP DNA Clean & Concentrator kit. The recovered cDNA was RNaseH treated and circularized (CircLigase) and amplified for 11 cycles. The final product was ran on 10% TBE gel, gel purified (180-350 bp) and cleaned-up using ChIP DNA clean & Concentrator Kit.
Strand-specific RNA-Seq

value: HUVEC

tag: cell type

value: umbilical vein endothelial cell


title: Rock_8Br-cAMP_d15_1

description: Rock_8Br-cAMP_d15_1__hg19 reads FPKM


title: TGFb_Rock_BMP4_d15_1

description: TGFb_Rock_BMP4_d15_1__hg19 reads FPKM


title: TGFb_Rock_BMP4_d15_2

description: TGFb_Rock_BMP4_d15_2__hg19 reads FPKM


title: Rock_BMP4_d15_2

description: Rock_BMP4_d15_2__hg19 reads FPKM


title: RNA-Seq_HUVEC_rep1


title: RNA-Seq_HAEC_rep1

value: HAEC

value: aortic endothelial cell


title: RNA-Seq_HAEC_rep2


title: TGFb_Rock_8Br-cAMP_d5

description: TGFb_Rock_8Br-cAMP_d5__hg19 reads FPKM


title: TGFb_Rock_8Br-cAMP_d15_1

description: TGFb_Rock_8Br-cAMP_d15_1__hg19 reads FPKM


title: TGFb_Rock_d5

description: TGFb_Rock_d5__hg19 reads FPKM


title: AB555B-x2 ChIP-seq


title: TGFb_Rock_8Br-cAMP_d15_2

description: TGFb_Rock_8Br-cAMP_d15_2__hg19 reads FPKM


title: Rock_d15_2

description: Rock_d15_2__hg19 reads FPKM


title: TGFb_Rock_d15

description: TGFb_Rock_d15__hg19 reads FPKM


title: Rock_d5

description: Rock_d5__hg19 reads FPKM


title: Rock_d15_1

description: Rock_d15_1__hg19 reads FPKM


title: iPSC_2

description: iPSC_2__hg19/ reads FPKM

source_name: iPSC

value: control

tag: passage

value: passage 61


title: iPSC_1

description: iPSC_1__hg19/ reads FPKM

value: passage 58


title: Rock_BMP4_d5

description: Rock_BMP4_d5__hg19 reads FPKM


title: PubertalMale1

city: Boston

first: Lester

last: Kobzik

address: 665 Huntington Ave

department: Environmental Health

institute: Harvard T.H. Chan School of Public Health

hyb_protocol: Standard Affymetrix procedure

scan_protocol: Standard Affymetrix procedure

data_processing: Using Partek Genomics Suite Software, RMA Background Correction with Quantile Normalization, Probeset Summarization using Median Polish

source_name: Male Bl/6 mice

label_protocol: Standard Affymetrix procedure

extract_protocol: RNA was extracted using Qiagen RNAeasy® Micro Kit and hemogloblin RNA was depleted using PAXgene Blood RNA system (Qiagen,Valencia, CA).

treatment_protocol: Whole blood from mice of both sexes at ages day 24 (prepubertal) and day 36 (pubertal) was collected by cardiac puncture after euthanasia.

tag: strain

value: Male

tag: age at blood sampling

value: 36 days

value: blood


title: Combination_2

city: Seoul

first: Junseong

last: Park

address: 222 Banpo-daero, Seocho-gu

department: Cancer Evolution Research Center

country: South Korea

institute: The Catholic University of Korea

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Mouse 2.0 ST Array at 45°C for 16 h.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: After importing CEL files, the data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Expression Console™ Software (EC).

label: Biotin

source_name: Glioblastoma

label_protocol: The sense cDNA was fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: GL261 cells (mouse glioblastoma cell line) were orthotopically implanted to male 8 wk old C57BL/6 mice. 16 days after injection, mice were sacrificed and their brains were removed.

extract_protocol: Total RNA was extracted from the tumor mass using a Qiagen RNeasy Plus Mini kit.

treatment_protocol: TMZ (30 mg/kg) was intraperitoneally administered to mice; anti-PD-1 (10 mg/kg) was intravenously injected (twice/wk).

value: Brain

tag: histology

value: Glioblastoma

value: Combination


title: Combination_3


title: PubertalMale4


title: TMZ_2

value: TMZ


title: TMZ_1


title: PubertalMale3


title: Anti-PD-1_1


title: PubertalFemale2

source_name: Female Bl/6 mice

value: female


title: PrepubertalMale4

value: 24 days


title: Control_1

value: Control


title: PrepubertalMale3


title: PubertalFemale4


title: Combination_1


title: PrepubertalFemale4


title: PubertalFemale1


title: VCaP-DHT-24h

description: LNCAP cells treated with DHT at 24h

value: VCAP

value: prostate cancer

value: DHT


title: Control_3


title: TMZ_3


title: Control_2


title: Anti-PD-1_2


title: PubertalFemale3


title: PrepubertalMale1


title: PrepubertalMale2


title: PubertalMale2


title: Anti-PD-1_3


title: PrepubertalFemale2


title: PrepubertalFemale3


title: Pubertal Day9 Influenza4

extract_protocol: Whole lungs were isolated after euthanasia on days 3, 6 or 9 after infection or vehicle treatment.

treatment_protocol: Mice received 50 uL of vehicle (PBS) or influenza ( A/Puerto Rico/8/1934 (PR8)) by intranasal insufflation at age 25 or 28.

tag: age at infection

value: 28 days

value: lung

tag: harvest day after infection

value: day 9


title: Pubertal Day9 Influenza3

tag: Sex


title: Pubertal Day9 Influenza2


title: Pubertal Day9 Vehicle2


title: Pubertal Day9 Influenza1


title: Pubertal Day9 Vehicle1


title: Prepubertal Day9 Influenza1

value: 25 days


title: Pubertal Day9 Vehicle3


title: Prepubertal Day6 Influenza3

value: day 6


title: Pubertal Day3 Influenza3

value: day 3


title: Pubertal Day6 Influenza4


title: Prepubertal Day9 Influenza3


title: Pubertal Day9 Vehicle4


title: Prepubertal Day9 Influenza2


title: Pubertal Day3 Influenza4


title: Prepubertal Day3 Influenza2


title: Prepubertal Day6 Influenza2


title: Pubertal Day3 Influenza1


title: Study2_dSaCas9KRAB_Pcsk9gRNA_rep4

city: Durham

first: Charles

last: Gersbach

state: NC

address: 101 Science Dr

department: Biomedical Engineering

institute: Duke University

description: Sample 28

data_processing:
Trim reads to 50 bp using fastx_trimmer (FASTX-Toolkit)
Filter out delivered adeno-associated viral vector sequences using bowtie2
Alignment to reference transcriptome using bowtie2
Reads were converted from .sam to .bam using samtools view -bS
Sort reads using samtools sort
Index reads using samtools index
Duplicate reads were removed using picard-tools MarkDuplicates
Bam files were re-indexed after duplicates were removed using Samtools Index
Reads were counted using samtools idxstats
Differential expression was computed using R version 3.1.2 using the Deseq package  with default settings
Genome_build: RefSeq transcripts from mm10
Supplementary_files_format_and_content: Counts of the number of reads aligned to each RefSeq transcript

extract_protocol:
On day of harvest, mice were perfused with PBS and euthanized by CO2 inhalation. Livers were harvested and stored in RNALater solution (Ambion). Total RNA was extracted using Qiagen RNA Universal kit. mRNA was purified using oligodT Dynabead (Invitrogen).
First-strand cDNA was synthesized using the SuperScript VILO cDNA Synthesis Kit (Invitrogen) and second-strand cDNA was synthesized using DNA polymerase I (New England Biolabs). cDNA was purified using Agencourt AMPure XP beads (Beckman Coulter). Purified cDNA was treated with Nextera transposase (Illumina) for 5 min at 55 °C to simultaneously fragment and insert sequencing primers into the double-stranded cDNA. Transposase activity was halted using QG buffer (Qiagen) and fragmented cDNA was purified on AMPure XP beads.

tag: transduced gene

value: dSaCas9-KRAB and gRNA

tag: grna target

tag: aav dose (total viral genomes/mouse)

value: Liver


title: Prepubertal Day3 Influenza1

tag: tissue


title: Pubertal Day6 Influenza2


title: Prepubertal Day3 Vehicle4


title: Prepubertal Day9 Influenza4


title: Prepubertal Day3 Influenza3


title: Prepubertal Day3 Influenza4


title: Prepubertal Day6 Influenza1


title: Prepubertal Day3 Vehicle3


title: Prepubertal Day3 Vehicle2


title: Pubertal Day3 Influenza2


title: Pubertal Day6 Influenza3


title: Prepubertal Day6 Influenza4


title: Study2_dSaCas9KRAB_Pcsk9gRNA_rep3

description: Sample 27


title: Study2_Pcsk9gRNAonly_rep1

description: Sample 21

value: gRNA


title: Study2_dSaCas9KRABonly_rep4

description: Sample 20


title: Study2_Pcsk9gRNAonly_rep3

description: Sample 23


title: Study2_Pcsk9gRNAonly_rep2

description: Sample 22


title: Study2_dSaCas9KRAB_Pcsk9gRNA_rep2

description: Sample 26


title: Study2_PBS_sham_rep3

description: Sample 15


title: Study2_PBS_sham_rep4

description: Sample 16


title: Study2_PBS_sham_rep1

description: Sample 13


title: Study2_dSaCas9KRAB_Pcsk9gRNA_rep1

description: Sample 25


title: Study2_dSaCas9KRABonly_rep3

description: Sample 19


title: Study2_Pcsk9gRNAonly_rep4

description: Sample 24


title: Study1_dSaCas9KRAB_Pcsk9gRNA_rep1

description: Sample 9


title: Study2_dSaCas9KRABonly_rep1

description: Sample 17


title: Study2_PBS_sham_rep2

description: Sample 14


title: Study1_dSaCas9KRAB_Pcsk9gRNA_rep3

description: Sample 11


title: Study1_PBS_sham_rep4

description: Sample 4


title: Study1_dSaCas9KRABonly_rep3

description: Sample 7


title: Study1_PBS_sham_rep2

description: Sample 2


title: Study1_dSaCas9KRABonly_rep4

description: Sample 8


title: Study1_dSaCas9KRAB_Pcsk9gRNA_rep4

description: Sample 12


title: Study1_dSaCas9KRABonly_rep1

description: Sample 5


title: Study1_dSaCas9KRABonly_rep2

description: Sample 6


title: Study1_PBS_sham_rep3

description: Sample 3


title: Prepubertal Day3 Vehicle1


title: Study1_PBS_sham_rep1

description: Sample 1


title: Study2_dSaCas9KRABonly_rep2

description: Sample 18


title: 1130S5: EarlyDisease8

city: Cambridge

first: Chris

last: Roberts

state: Massachusetts

address: 301 Binney St.

institute: Biogen

data_processing:
Sequence alignments were performed In OmicSoft using OSA4 aligner
Gene expression quantification was performed in OmicSoft using RSEM
Differential gene expression analysis was performed in OmicSoft using DESeq2
Genome_build: mm10 Gencode M6

source_name: Spinal cord

growth_protocol: mice were maintained DOX-ON until 8-12 weeks of age. Then diets were maintained as described in the sample table.

extract_protocol:
Mice were euthanized with ketamine/xylazine cocktail and perfused with ice-cold PBS. Spinal cords were flushed from the spinal column using PBS and placed in ice-cold HBSS with HEPES. Tissue was homogenized using Wheaton tissue grinders to achieve a single cell suspension. The homogenate was centrifuged through a 30% Percoll gradient to remove myelin and enrich for microglia. After washing with FACS buffer (HBSS, HEPES, BSA, EDTA) cells were Fc-blocked (CD16/32, Cat. #101321, Biolegend, San Diego, CA, USA) and stained with CD11b-PE (Cat. #553311, BD Biosciences, MA, USA) and CD45-BV421 (Cat. #103134, Biolegend). DRAQ7 was used for dead cell exclusion. Cells were sorted on an ARIA Fusion Flow Cytometer and collected directly into RNA lysis buffer. RNA was isolated with the RNeasy Micro Kit Plus from Qiagen.
Libraries were constructed using the SMART-Seq Ultra Low-input (Clontech, Mountain View, CA, USA) and NexteraXT kits (Illumina, San Diego, CA, USA). Libraries were sequenced at an average depth of 20 million paired end reads.

value: mixed C57BL/6J X C3HeJ F1

tag: genotype

tag: gender

value: F

tag: dox treatment

value: 2 WKS OFF

tag: phenotype

value: Early disease

value: Spinal cord


title: 1102S8: EarlyDisease6

value: M


title: 1130S1: LateDisease5

value: 6 WKS OFF

value: Late disease


title: S. pennellii acc. PE47, water stress condition, rep. 3

city: Espinardo - Murcia

first: Francisco

middle: Borja

last: Flores

state: Murcia

address: P.O. Box 164

department: Stress Biology and Plant Pathology

institute: CEBAS-CSIC

hyb_protocol: The biotinylated cRNA targets were cleaned up and 15 microgr were fragmented in order to prepare the hybridization mix, using Hybridization, Wash and Stain Kit (Affymetrix),  according to recommendations of manufacturer. The resulting preparations were hybridized to GeneChip(R) Tomato Genome Array (Affymetrix) interrogating 10209 sequences. After applying hybridization, by using hybridization controls (spike controls) and labeling controls (polyA controls and 3'/5' ratios of housekeeping genes) it was tested that the 12 chips have overcome the quality criteria.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 from Affymetrix with GeneChip Operating Software (GCOS 1.4, Affymetrix®) and Expression Console Software (EC 1.1, Affymetrix®) for image processing

data_processing:
In order to minimize discrepancies due to variables such as sample preparation, hybridization, etc. all the arrays were scaled by defining an arbitrary value of 500 as average intensity and using the Expression ConsoleTM (EC 1.1, Affymetrix®) software. Differences of scaling factor among the different samples did not surpass the value of 3 in any case so results are sufficiently homogenous and feasible. The BioConductor affyPLM package was used to obtain Normalized Unsealed Standard Error (NUSE) plot to study the quality of the chips for each set of probes from intensity values of each probeset.  All samples presented NUSE values within the required ranges.  The intensity value of each probe in the array were processed and normalized according to the Robust Multichip Average (RMA) method to obtain an individual intensity value for each probeset.  First filtering, normalization and second filtering of probes yield a final list of 5050 sequences (working list).  Non-supervised Principal Components Analysis (PCA) and hierarchical clustering were performed and they showed that samples tend to separate according to genotype and condition. A statistical analysis based in multiple test corrections was performed using the FDR on the working list (Benjamini and Hochberg, 1995, Controlling the false discovery rate - A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society, Series B-methodological, 57, 289-300).  Genes with an FDR < 0.05 and a fold change (ratio value) of ≥ 2.0 when comparing genotypes in the same experimental condition were identified as differentially expressed genes. A final list of 535 genes was accomplished with the above conditions.  The annotation of probe sets was obtained from Affymetrix and loaded in the Partek Genomics Suite software (Partek Incorporated, St. Louis, USA).
Robust Multichip Average (RMA) method was used to obtain an individual intensity value for each probeset, data expressed as log2 signal RMA

organism: Solanum pennellii

source_name: S. pennellii leaflets_water stress condition

label_protocol: Biotinylated cRNA was sinthetized from 200 ng of each sample using the GeneChip 3' IVT Express Kit (Affymetrix), according to the protocol supplied by the manufacturer. The amount and quality of biotinylated cRNA was checked by Nanodrop and agarose gel electrophoresis.

growth_protocol: Seeds of Solanum pennellii acc. PE47 and S. lycopersicum cv. P73 were germinated in darkness, in a 2:1:1 (v/v) mixture of peat:perlite:siliceous sand, at 28∘C temperature and 90% relative humidity. Seedlings were maintained in a controlled growth chamber and they were irrigated daily with half-strength Hoagland solution (Hoagland and Arnon, 1950, The Water-Culture Method for Growing Plants Without Soil, Vol. 347. Agricultural Experiment Station Circular, Berkeley, CA, pp 1–32). The environmental conditions applied in the growth chamber were the optimal ones for tomato seedlings growth, varying temperature between 18 and  25∘C and relative humidity between 50 and 80%, with a photoperiod of 16 h light/8 h dark. A photosynthetic photon flux (400–700 nm) of 345 μmolm−2 s−1 at the plant level was provided by fluorescent tubes [Luminux daily light 58W and Fluora 58W (Osram, Madrid, Spain)]. Plantlets with developed true leaves were placed in pots with substrate (same proportion of peat:perlite: siliceous sand as before) by couples (one PE47 and one P73 per pot).

extract_protocol: Total RNA from the 12 biological replicates was extracted by means of Rneasy Mini Kit and QIAshredder (Qiagen) according to instrutions from manufacturer.The amount and quality of the RNA was checked by Bioanalyzer and spectrophotometrically by Nanodrop.

treatment_protocol: 18 pots with plants reaching 2-3 full-developed leaves and 1-2 developing ones for P73, and 3-4 full-developed and 1-2 developing ones for PE47, were selected. Half of the pots with plants in such plant developmental stages were subjected to water stress treatment by withholding water during 4 days, while the rest of pots were maintained in control condition (well-watered) .  Three biological replicates were considered per genotype, PE47 and P73, and treatment, control and water stress, constituted each one by 3 pots, with one PE47 plant and one P73 plant each. At the end of the treatment sampling was fulfilled for each biological replicate; leaflets from P73 and PE47 plants were collected and immediately frozen in liquid nitrogen to be stored at -80ºC.

tag: cultivar/accession

value: acc. PE47

tag: age

value: Plants with 3-4 full-developed leaves and 1-2 developing leaves

tag: condition

value: Water stress treatment by withholding watering during 4 days

value: Leaflets


title: 1130S3: LateDisease7

tag: strain


title: 1102S1: LateDisease2


title: 1102S6: EarlyDisease4


title: 1019S7: EarlyDisease3


title: 1102S7: EarlyDisease5


title: 1102S3: LateDisease4


title: 1019S8: Control13

value: Control


title: 1102S2: LateDisease3


title: Study1_dSaCas9KRAB_Pcsk9gRNA_rep2

description: Sample 10


title: S. pennellii acc. PE47, control condition, rep. 2

source_name: S. pennellii leaflets_control condition

value: Optimal growth condition


title: 1102S4: Control14


title: 1130S4: EarlyDisease7


title: S. pennellii acc. PE47, water stress condition, rep. 2


title: 1130S2: LateDisease6


title: S. pennellii acc. PE47, control condition, rep. 3


title: Tomato (S. lycopersicum) cv. P73, water stress condition, rep. 3

organism: Solanum lycopersicum

source_name: Tomato leaflets_water stress condition

value: cv. P73

value: Plants with 2-3 full-developed leaves and 1-2 developing leaves


title: 1019S3: Control10


title: 1019S6: Control12


title: Tomato (S. lycopersicum) cv. P73, water stress condition, rep. 1


title: 0810S9: Control9

value: Continuously on DOX


title: S. pennellii acc. PE47, water stress condition, rep. 1


title: 1019S2: EarlyDisease1

value: mixed C57BL/6J X C3HeJ F1


title: 1019S1: LateDisease1


title: 0810S8: Control8


title: 0810S7: Control7

value: F


title: Tomato (S. lycopersicum) cv. P73, water stress condition, rep. 2


title: Tomato (S. lycopersicum) cv. P73, control condition, rep. 2

source_name: Tomato leaflets_control condition


title: S. pennellii acc. PE47, control condition, rep. 1


title: Tomato (S. lycopersicum) cv. P73, control condition, rep. 3


title: 1019S4: Control11

value: 2 WKS OFF


title: Tomato (S. lycopersicum) cv. P73, control condition, rep. 1


title: 0810S6: Control6


title: 0810S5: Control5


title: BAL_normal control_rep15

city: London

first: Chih-hsi

middle: Scott

last: Kuo

address: South Kensington Campus

department: Department of Computing

institute: Imperial College London

description: BAL_normal control

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000.

data_processing: The data were quality controlled and pre-processed using R code of Affymetric Analysis QC workflow from ArrayAnalysis.org with Robust Multichip Average (RMA) as normalization method.

source_name: BAL_normal control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (GeneChip Expression Analysis Technical Manual, Copyright 2005-2009, Affymetrix)

extract_protocol: column-based extraction of total RNA was performed according to the manufacturer's instructions

value: female

tag: smoking history

value: non-smoker

tag: technical batches

value: B


title: BAL_normal control_rep17

description: BAL_normal control

value: C


title: BAL_normal control_rep18

description: BAL_normal control

value: male

value: A


title: BAL_normal control_rep14

description: BAL_normal control


title: BAL_normal control_rep19

description: BAL_normal control


title: 0810S4: Control4

value: Spinal cord


title: 0810S3: Control3

value: M

value: 6 WKS OFF, 1 WK ON


title: BAL_adenoCA_stage4_rep11


title: 0810S2: Control2

value: Control


title: 0810S1: Control1


title: 0803S9: Recovery9

value: Recovery


title: 0803S5: Recovery5


title: 0803S8: Recovery8


title: 0803S7: Recovery7


title: BAL_adenoCA_stage4_rep13

value: smoker


title: BAL_adenoCA_stage4_rep8


title: BAL_squamousCA_stage4_rep7


title: BAL_squamousCA_stage3b_rep9


title: BAL_adenoCA_stage4_rep5


title: BAL_adenoCA_stage4_rep10


title: 0803S3: Recovery3


title: BAL_adenoCA_stage4_rep4


title: BAL_adenoCA_stage3b_rep6


title: BAL_squamousCA_stage4_rep12


title: 0803S4: Recovery4


title: 0803S2: Recovery2


title: control group vs. cells treated with 3.2 mg/L sanguinarine replication 3

first: Hua

last: Zhong

address: No. 325, Guohe Road

institute: Second Military Medical University

description: 10709P_3 v 4

hyb_protocol: Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer. Labeled controls and test samples were quantitatively adjusted based on the efficiency of Cy5-dCTP or Cy3-dCTP incorporation and dissolved in 80 μl hybridization solution containing 3 × SSC, 0.2% SDS, 5 × Denhardt's solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a CapitalBio BioMixerTM II Hybridization Station overnight at a rotation speed of 8 rpm and a temperature of 42℃ and washed in a CapitalBio SlideWasher TM (CapitalBio) with two consecutive solutions (0.2% SDS, 2 × SSC at 42℃ for 5 min, and 0.2 × SSC for 5 min at room temperature).

scan_protocol: Luxscan 10K (CapitalBio)

data_processing:
A spatial and intensity dependent normalization based on the LOWESS program was employed , which is prevalent in microarray expression profiling. Each gene was represented in triplicate on each slide and the hybridization experiments were performed by dye-swap strategy.
The geometric mean of lowess normalized log2 ratio (control/test) for the independent experiments was calculated.

organism: Candida albicans

source_name: control C. albicans cells treated with DMSO

label_protocol: cDNA labeled with a fluorescent dye (Cy5-dCTP) was produced by Eberwine's linear RNA amplification method and subsequent enzymatic reaction. This procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA. In detail, double-stranded cDNAs (containing the T7 RNA polymerase promoter sequence) were synthesized from 1 μg total RNA using the CbcScript reverse transcriptase with cDNA synthesis system according to the manufacturer's protocol (CapitalBio) with the T7 Oligo (dT). The T7-oligo (dT) primer was provided in the kit with sequence of (5'-AAACGACGGCCAGTGAATTGTAATACGACTCACTATAGGCGCTTTTTTTTTTTTTTTTT-3'). After completion of double-stranded cDNA (dsDNA) synthesis using DNA polymerase and RNase H, the dsDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and eluted with 30 μl elution buffer. The eluted double-stranded cDNA products were vacuum evaporated to 16 μl and subjected to 40 μl in vitro transcription reactions at 37℃ for 4-144 h using a T7 Enzyme Mix. The amplified cRNA was purified using the RNA Clean-up Kit (MN). Klenow enzyme labeling strategy was adopted after reverse transcription using CbcScript II reverse transcriptase. Briefly, 2 μg amplified RNA was mixed with 4 μg random nanomer, denatured at 65℃ for 5 min, and cooled on ice. Then, 5 μl of 4 × first-strand buffer, 2 μl of 0.1 M DTT, and 1.5 μl CbcScript II reverse transcriptase were added. The mixtures were incubated at 25℃ for 10 min, then at 37℃ for 90 min. The cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and vacuum evaporated to 14 μl. The cDNA was mixed with 4 μg random nanomer, heated to 95℃ for 3 min, and snap cooled on ice for 5 min. Then, 5 μl Klenow buffer, dNTP, and Cy5-dCTP (GE Healthcare) were added to final concentrations of 240 μM dATP, 240 μM dGTP, 240 μM dTTP, 120 μM dCTP, and 40 μM Cy5-dCTP. 1.2 μl Klenow enzyme was then added, and the reaction was performed at 37℃ for 90 min.

growth_protocol: C. albicans cells were incubated in RPMI 1640 medium.

extract_protocol: Total RNA was isolated by the hot phenol method.

treatment_protocol: 1×10^6 cells/mL C. albicans in RPMI 1640 medium were prepared. After 6 hours' incubation, SAN was added to the suspension and maintained under the concentration of 3.2 mg/L. The drug treatment went on for 20 min until the suspension was centrifuged and washed with PBS. The C. albicans cells were then stored in liquid nitrogen as the sample of the microarrays assay.

tag: genotype/variation

value: wild type

tag: treated with

value: DMSO (control)

source_name: C. albicans treated with  3.2 mg/L sanguinarine

value: 3.2 mg/L sanguinarine


title: control group vs. cells treated with 3.2 mg/L sanguinarine replication 1

description: 10709P_1 v 2


title: control group vs. cells treated with 3.2 mg/L sanguinarine replication 2

description: 10709P_5 v 6


title: BAL_adenoCA_stage4_rep2


title: BAL_squamousCA_stage3b_rep3


title: HEC-TM-KCL24h_R2

city: Lyon

first: jean-michel

last: flaman

address: 28 rue Laennec

department: CRCL

institute: Inserm 1052

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. After fragmentation 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent GE Whole Human Genome Oligo Microarrays (Agilent-026652) 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 briefly in acetonitrile.

scan_protocol: Microarrays were scanned with an Agilent DNA microarray scanner G2565CA (Agilent Technologies).Fluorescent signals were extracted and normalized with the Feature Extraction software version 10.5.1.1 (Agilent Technologies),

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

source_name: Mammary epithelial cells immortalized with hTERT treated with KCL during 24 hours

label_protocol: cRNAs were synthesized and labeled with the Cy3 dye from 100 ng of total RNA using the one-color Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's recommandations, followed by RNeasy Mini column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human mammary epithelial cells (HECs; Lonza) were cultured in mammary epithelial cell growth medium (Promocell) with penicillin/ streptomycin 100 U/ml (Life Technologies). The cells were maintained in a humidified atmosphere at 37°C under 5% CO2.

extract_protocol: Total RNA was extracted from HEC-TM cells using NucleoSpin® RNA (Macherey Nalgen) following the manufacturer's recommendations

treatment_protocol: HECs were treated daily for 24 or 96 hours with 4-OHT (Sigma-Aldrich) at 250 nM, or with 65 mM KCl (Sigma-Aldrich),for 24 hours

tag: cell type

tag: treatment

value: treated with KCL during 24 hours


title: HEC-TM-OHT24h_R2

source_name: Mammary epithelial cells immortalized with hTERT treated with 4-OHT during 24 hours

value: Human mammary epithelial cells (HECs; Lonza)

value: treated with 4-OHT during 24 hours


title: HEC-TM-OHT96h-shSCN9A_R3

source_name: Mammary epithelial cells immortalized with hTERT expressing anti SCN9A shRNA treated with 4-OHT during 96 hours


title: HEC-TM-OHT96h-shSCN9A_R2

value: expressing anti SCN9A shRNA treated with 4-OHT during 96 hours


title: HEC-TM-KCL24h_R1


title: HEC-TM-OHT96h_R1

source_name: Mammary epithelial cells immortalized with hTERT treated with 4-OHT during 96 hours

value: treated with 4-OHT during 96 hours


title: HEC-TM_R1

source_name: Mammary epithelial cells immortalized with hTERT


title: HEC-TM-KCL24h_R3


title: HEC-TM_R2


title: HEC-TM-OHT24h_R3


title: HEC-TM-OHT96h_R3


title: HEC-TM-OHT96h-shSCN9A_R1


title: NDE4

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description:
raw data file: NDE34_US83300186_252644110809_S01_GE2_1105_Oct12_1_4.txt
Gene expression in 11d chicken embryo liver injected with NDELA

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two biological replicas were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) mouse (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing:
The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction vs.11 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas, Biological Theory, 11(3):123-137, 2016..
We used the multiple yellow hybridization design in which differently labeled biological replicates are co-hybridized with microarray. Gene expressions in samples that were similarly labeled but exposed to distinct conditions are compared and results averaged over the two types of fluorescent labels.
Data table contains normalized ratio of the background subtracted signal of that feature and the median of the background subtracted signals of all valid features in the green or red channel of the array. A NULL indicates that the feature was not considered because it is a control fetarure, OR is locally corrupted, OR has saturated pixels, OR the median of the foreground signal is less than 2x median of the background signal.

organism: Gallus gallus

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: Fertilized specific pathogen free premium white leghorn chicken (Gallus gallus) eggs of undetermined sex were purchased from Charles River (North Franklin, CT). Upon arrival, eggs were numbered, weighed and randomly divided into control and dosed groups (at least 10 eggs per group). The first day of incubation was designated as Day 0. Eggs were incubated in GQF Manufacturing Company Hova Bator Model 2362N styrofoam incubators (Murray McMurray Hatchery, Webster City, IA) with automatic egg turners at 37 ± 0.5 °C and 60 ± 5 % humidity. Viability was assessed on day 8 by transillumination, eggs that did not developed were eliminated. Control and dosed eggs were separated to avoid cross contamination.

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a Thermo Scientific NanoDrop ND-2000 and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: Four eggs (labelled as DEN1-4) were injected with 4mg DEN in 0.15 ml/egg deionized water in days 9, 10 an 11 post incubation while four eggs (labeled NDE1-4) were injected with 4mg NDELA in 0.15ml/egg deioized water.

value: embryo liver

tag: developmental stage

value: 11th day of incubation

value: injected with NDELA


title: HEC-TM-OHT24h_R1


title: NDE1

description:
raw data file: NDE12_US83300186_252644110809_S01_GE2_1105_Oct12_1_3.txt
Gene expression in 11d chicken embryo liver injected with NDELA


title: NDE2

source_name: 11d chicken embryo liver injected with NDELA


title: HEC-TM-OHT96h_R2


title: NDE3


title: DEN2

description:
raw data file: DEN12_US83300186_252644110823_S01_GE2_1105_Oct12_1_3.txt
Gene expression in 11d chicken embryo liver injected with DEN

value: injected with DEN


title: HEC-TM_R3


title: DEN3

description:
raw data file: DEN34_US83300186_252644110823_S01_GE2_1105_Oct12_1_4.txt
Gene expression in 11d chicken embryo liver injected with DEN


title: DEN4

source_name: 11d chicken embryo liver injected with DEN


title: DEN1


title: BAL_adenoCA_stage3a_rep1

value: male

value: non-smoker

value: A


title: WAT2

description:
raw data file: WAT12_US83300186_252644110852_S01_GE2_1105_Oct12_1_4.txt
Gene expression in 11d chicken embryo liver injected with distilled water

data_processing:
The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction vs.11 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas, Biological Theory, 11(3):123-137, 2016.
We used the multiple yellow hybridization design in which differently labeled biological replicates are cohybridized with the microarray, expression levels of similarly labled samples from the two conditions are compared and results averaged over the two fluorescent labels. Therefore, this is like a one-color experiment.
Data table contains normalized ratio of the background subtracted signal of that feature and the median of the background subtracted signals of all valid features in the green or red channel of the array. A NULL indicates that the feature was not considered because it is a control feature, OR is locally corrupted, OR has saturated pixels, OR the median of the foreground signal is less than 2x median of the background signal.

treatment_protocol: Four eggs (labelled as WAT1-4) were injected with 0.15 ml/egg deionized water in days 9, 10 an 11 post incubation while four eggs (labeled CTR1-4) were kept as environmental controls. We found that water injections had a very small effect, regulating less than 1% of the genes. Both WAT and CTR data sets were used as refernces in further experiments for eggs expossed to various water-soluble carcinogenic compounds.

value: injected with distilled water


title: CTR4

description:
raw data file: CTR34_US83300186_252644110852_S01_GE2_1105_Oct12_1_1.txt
Gene expression in Control 11d chicken embryo liver

source_name: Control 11d chicken embryo liver

value: control


title: WAT4

description:
raw data file: WAT34_US83300186_252644110852_S01_GE2_1105_Oct12_1_3.txt
Gene expression in 11d chicken embryo liver injected with distilled water


title: CTR2

description:
raw data file: CTR12_US83300186_252644110852_S01_GE2_1105_Oct12_1_2.txt
Gene expression in Control 11d chicken embryo liver


title: WAT1

source_name: 11d chicken embryo liver injected with distilled water


title: KHT3

city: Barcelona

first: Eva

middle: C

last: Vaquero

address: Carrer Villarroel 170

institute: Hospital Clínic

description: Neoplastic cells treated with Pancreatic Stellate Cells heterozygous, replicate 3

hyb_protocol: 600ng of Cy3 labeled cDNA was directly mix with hybridization buffer and Agilent blocking agent incubated at 95ºC for 3 minutes and immediately transfer on ice. Then, it was hybridized toAgilent-074809 SurePrint G3 Mouse GE v2 8x60K Microarray for 40h at 65ºC in a rotating Agilent hybridization oven

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

source_name: Neoplastic cells

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 500ng of double stranded cDNA using the SureTag Complete DNA Labeling kit (Agilent 5190-4240) according to manufacturer’s instructions

extract_protocol: total RNA extraction

value: Neoplastic cells


title: MA (A 2015.11.17)

city: Gifu

first: Kazuo

last: Kajita

address: Yanagido 1-1

department: General Internal Medicine

institute: Gifu University Graduate School of Medicine

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers 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 SurePrint G3 Mouse Gene Expression v2 8x60K Microarray (Agilent, G4852B) 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).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 074809_D_F_20150624) to obtain background subtracted and spatially detrended Processed Signal intensities. The 75th percentile shift normalization was performed using Agilent GeneSpring GX.

source_name: mature adipocytes

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng Total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Epididymal fat from 20-weeks-old male C57/BL mice were digested with collagenase, and then centrifuged at 9 xg for 1 sec. The floating cells were separated from the lower phase (SVC). The floating cell fraction was centrifugazed at 226 xg for 3 min. The resultant floating cells and sediment cells were regarded as mature adipocytes (MA) and SPA, respectively. SVC and SPA were cultured in DMEM. When the cultured cells reached 90% confluency, they were harvested, and total RNA was extracted.

extract_protocol: Total RNA was extracted using TRIzol(Thermo Fisher Scientific), followed by DNase I (TaKaRa) digestion and repurified with phenol/chloroform.

value: Epididymal fat


title: KHT2

description: Neoplastic cells treated with Pancreatic Stellate Cells heterozygous, replicate 2