title: CBMS1_rep1_d3_EpiLC_EB_d1

description: Biological replicate 1 of 2.


title: dZEB.TGFb_rep3

status: Public on Jun 26 2019

type: SRA

city: Yokohama

first: Kazuhide

last: Watanabe

state: Kanagawa

address: 1-7-22 Suehiro-cho Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: Riken

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using BWA
mapped CAGE tags were counted with respect to the FANTOM5-CAT TSSs (Hon et al., Nature 2017) to give a unit of CAGE tag start site (CTSS).
Genome_build: hg38
Supplementary_files_format_and_content: DEG_summary.txt contains result from edgeR.

molecule: total RNA

organism: Homo sapiens

growth_protocol: MCF10A cells were grown in DMEM/F12(1:1) medium with 5% horse serum, epidermal growth factor (10 ng/mL), cholera toxin (100 ng/mL) and insulin (0.023 IU/mL)

extract_protocol:
Total RNA was extracted by Qiagen miRNeasy Mini Kit (QIAGEN Inc.) according to the manufacturer’s instructions.
CAGE libraries were prepared as previously described (Murata et al., Methods Mol Biol 2014). Briefly, 3 μg of total RNA from each sample was subjected to reverse transcription using SuperScript III Reverse Transcriptase (Life Technologies, Carlsbad, CA, USA) with random primers. The 5-end cap structure were biotinylated by sequential oxidation with NaIO4 and biotinylation with biotin hydrazide (Vector Laboratories, Burlingame, CA, USA). After RNase I treatment (Promega, Madison, WI, USA), the biotinylated cap structure was captured with streptavidin-coated magnetic beads (Life Technologies). After ligation of 5’ and 3’ adaptors, second-strand cDNAs were synthesized with DeepVent (exo−) DNA polymerase (New England BioLabs, Ipswich, MA, USA). The double-stranded cDNAs were treated with exonuclease I (New England BioLabs) and purified.

treatment_protocol: MCF10A cells were treated by combinations of perturbations as follows: recombinant TGF-beta (200 nM) for 4 weeks, CRISPR/Cas9-mediated ZEB1 knockout, doxycycline-inducible expression of exogenous ZEB1, and TGF-beta type1 receptor inhibiotr (SB-431542, 10microM) treatment

tag: cell line

tag: cell type

value: mammary epithelial cells

tag: transgene

value: ZEB1 knockout

tag: passages

tag: treatment

value: recombinant TGF-beta


title: ILC3-PBS-rep-1

city: Shanghai

first: Ju

last: Qiu

address: 320 Yueyang Road

country: China

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
Reads were mapped to Mouse Genome Assembly GRCm38.p5 by STAR v2.5.
Gene and isoform expression quantification was called by RSEM v1.2 with default parameters on GENCODE mouse M16 gene annotation file.
Differential expression analysis was performed by Bioconductor package edgeR v3.18.1.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Csv file indicates ratios of differential gene expression in a-DR3 treated versus wild-type group.

organism: Mus musculus

source_name: lamina proprial lymphocytes

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen).Total RNA sample is digested by DNaseІ (NEB), and purified by oligo-dT beads (Dynabeads   mRNA purification kit, Invitrogen)
Poly (A)-containing mRNA were fragmented into 130bp   with First Strand buffer. First-strand cDNA is generated by N6 primer, First Strand Master Mix and   Super Script II reverse transcription(Invitrogen) (Reaction condition：25℃ for 10 min；42℃ for 40   min；70℃for 15 min). Then add Second Strand Master Mix to synthesize the second-strand cDNA   (16℃ for 1h). Purified the cDNA with Ampure XP Beads (AGENCOURT), then combine with End   Repair Mix, incubate at 20℃for 30min. Purified and add A-Tailing Mix, incubate at 37℃ for 30   min. Then combine the Adenylate 3'Ends DNA, Adapter and Ligation Mix, incubate the ligate   reaction at 20℃for 20 min. Several rounds of PCR amplification with PCR Primer Cocktail and   PCR Master Mix were performed to enrich the cDNA fragments. Then the PCR products are   purified with Ampure XP Beads (AGENCOURT).

tag: genotype/variation

value: PBS


title: CBMS1_rep1_d2_EpiLC

city: Kobe

first: Ichiro

last: Hiratani

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

institute: RIKEN

description: Biological replicate 1 of 2.

library_source: genomic

data_processing:
Read pairs were individually mapped to the mouse genome (UCSC mm9) using the hiclib pipeline (Imakaev et al., 2012) with iterative mapping method.
After read mapping, each side of the mapped reads was also applied to the hiclib pipeline. First, uniquely mapped paired-reads were assigned to HindIII fragments. Only those with correct orientations were considered valid pairs, and non-ligated and self-ligated read pairs were filtered out. Fragment-level filters were next applied to remove invalid reads: reads that started within 5 bp from the restriction sites, duplicated read pairs, extremely large and small restriction fragments (> 100 kbp and < 100 bp, respectively), and extremely high and low count restriction fragments (top 0.5% of all counts and zero counts, respectively).
Biological replicates were merged, and Hi-C contact heatmaps were generated in 200-kb or 40-kb non-overlapping genomic bins for both merged samples (mainly used for visualization) and for single biological replicates.
To correct the bias of the contact heatmaps, iterative correction was performed with the following steps: diagonal removal was applied to only the first diagonal (“removeDiagonal(0)”), bin removal was done by the sequence fraction (0.5), and finally high trans contacts (the fraction of the top 0.05% trans contacts) were removed. The bias-corrected contact heatmaps were used to generate the A/B compartment profiles (200-kb bins or 200-kb sliding windows at 40-kb interval) in each chromosome as previously described (Lieberman-Aiden et al., 2009) by the hiclib pipeline with a small modification in the ∆“doCisPCADomains(domaidunction=”lieverman-”)” function including observed / expected analysis, covariance matrix generation from the Pearson correlation matrix and principal component analysis. The first eigenvalues were used to identify A/B compartments (i.e. Hi-C PC1). Because positive and negative eigenvalues are arbitrary, correlation with the GC content was used to assign positive eigenvalues as ‘A compartment’ and negative eigenvalues as ‘B compartment’. After obtaining A/B compartment profile, quantile normalization was performed using the limma package (Ritchie et al., 2015).
Genome_build: UCSC mm9 (MGSCv37)
Supplementary_files_format_and_content: bedGraph

molecule: genomic DNA

growth_protocol: MEFs (mouse embryonic fibroblasts) were isolated from 12.5-day-old embryos from C57BL6 mice and cultured in D-MEM supplemented with 10% FBS and penicillin/streptomycin. CBMS1 mESCs have been described (Murakami et al. Development, 2011) and were grown in 2i/LIF medium as described (Hayashi K et al., Nat. Protoc., 2013). EpiSCs (female) and their culture protocol have been described and were grown in Activin/FGF medium as described (Tesar et al. 2007).

extract_protocol:
Hi-C experiments were performed as previously reported with some modifications (Sofueva et al., 2013). Cells were fixed with 1% formaldehyde for 10 min at room temperature. Glycine was added to 0.125 M final concentration and incubated for 5 min at room temperature. Tubes were placed on ice for 15 min. Cells were washed in ice-cold PBS by centrifuging at 400 g at 4°C. Then, 1–2 x 10^6 fixed cell pellets were used for the following steps. Cell pellets were resuspended in 500 µl of 3C lysis buffer (10 mM Tris-HCl (pH 8.0), 10 mM NaCl, 0.2% NP-40) with 1x protease inhibitor cocktail (Roche, 1873580), transferred to 1.5 ml Protein LoBind Tubes (Eppendorf) and incubated on ice for 20 min. The samples were spun down for 5 min at 1000 g at 4℃. After removing the supernatants carefully, pellets were resuspended in 212.5 µl of 1.2x NEBuffer 2 with 0.3% SDS and incubated for 1 h at 37°C in the Thermomixer C3 at 950 rpm (Eppendorf). Then, 25.5 µl of 20% Triton X-100 were added to 2% final concentration and the samples were incubated for 1 h at 37°C. Next, 400 U of HindIII (NEB, R0104S) was added and the samples were incubated overnight at 37°C in the Thermomixer C3 at 950 rpm. The next day, the samples were spun down for 5 min at 4°C. After removing the supernatants carefully, pellets were resuspended in 200 µl of 1x NEBuffer 2 with 300 U of HindIII and incubated for at least 8 h at 37°C in the ThermoMixer C3 at 950 rpm. The samples were spun down for 5 min at 4°C. After removing the supernatants carefully, pellets were resuspended in 200 µl of “Fill-in Mix” (1 x NEBuffer 2, 15 µM each of dATP, dGTP, dTTP and 15 µM of Biotin-14-dCTP (Invitrogen, 19518018), 25 U of Klenow (NEB, M0210S)) and incubated for 45 min at 37°C. After spinning down for 5 min at 4°C and removing the supernatants carefully, the pellets were resuspended in 100 µl of “Ligation Mix” (1x T4 DNA ligase buffer (NEB), 6 µl of T4 DNA ligase (1 U/µl, Invitrogen, 15224017)) and incubated overnight at 16°C. The sample volumes were brought up to ~300 µl by adding 10 mM Tris-HCl (pH 7.5) and RNaseA-treated for 30 min at 37°C by adding 3 µl of 10 mg/ml RNaseA. Reverse-crosslinking and proteinase K treatment were performed overnight at 65°C by adding 6.25 µl of 20 mg/ml Proteinase K. The next day, 6.25 µl of 20 mg/ml Proteinase K was added and incubated for 2 h at 65°C. Samples were then extracted twice with phenol/chloroform and once with chloroform. After this, 30 µl of 3 M sodium acetate (pH 5.2) was added and 825 µl of ice-cold EtOH was added. The samples were incubated overnight at –80°C and spun down for 30 min at 20,000 g at 4°C for DNA precipitation. After two 70% EtOH washes (add 1 ml, cfg for 20 min at 20,000 g at 4°C), the DNA pellets were resuspended in 30 µl of 10 mM Tris-HCl (pH 7.5).
For generating next-generation sequencing libraries, 2.5 µg of Hi-C DNA was used per library. To remove biotin from unligated ends, Hi-C DNA was mixed with 50 µl of “T4 DNA pol mix” (1x NEBuffer 2, 1x BSA, 100 µM dATP, 100 µM dGTP, 2.5 U of T4 DNA polymerase (NEB, M0203S)) and incubated for 2 h at 12°C. The sample volumes were brought up to 100 µl by adding 10 mM Tris-HCl (pH 7.5). Samples were extracted once each with phenol/chloroform and chloroform. After EtOH precipitation, the DNA pellets were resuspended in 130 µl of nuclease-free water. DNA samples were sheared (300–500 bp) using the following settings in Covaris S220 (Duty Factor: 5.0, Peak incident power: 175 W, Cycles per burst: 200, Treatment time: 120 sec) using microTUBE with snap cap (Covaris, 520045). After DNA shearing, DNA size selection was performed using AMPure XP beads (Beckman Coulter). Using the size-selected DNA samples, biotin pull-down and sequencing library preparations were performed using 30 µl of Dynabeads MyOne Streptavidin C1 (Invitrogen, 65001) and a part of Nextera Mate Pair Sample Preparation kit (Illumina, FC-132-1001) following the kit’s protocol at half scale. For library amplification, KAPA Real-Time Amplification Kits (KAPA BIOSYSTEMS, KK2701) were used to determine the optimal PCR cycles (9–12 cycles) and the final PCR products were purified by AMPure XP beads.

treatment_protocol: For differentiation, CBMS1 mESCs were differentiated to EpiLCs for 2 days and then switched to aggregation culture (EB/embryoid body culture) in Nunclon Sphera 96U-well plates (ThermoFisher, #174925), starting from 2,000 EpiLCs per well exactly as described (Hayashi K et al. Nat. Protoc., 2013), except for the use of plain GK15 medium (Hayashi K et al. Nat. Protoc., 2013) without any additional factors added during the aggregation culture. This process is practically identical to the SFEBq neural method of mESC differentiation (serum-free floating culture of EB-like aggregates with quick reaggregation) (Eiraku et al. Nat. Protoc., 2012) except that we started from EpiLCs instead of mESCs. In our hands, this resulted in efficient formation of neurectoderm cells based on gene expression after 7 days of differentiation (2 days to EpiLCs and then 5 additional days of EB culture).

tag: strain/background

value: CBA/MsM

value: day2 differentiated ESCs


title: dZEB.TGFb_rep4


title: FVB_MMTV_Wnt1_182352_Perou

type: RNA

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

country: USA

institute: University of North Carolina at Chapel Hill

description: Agilent Feature Extractor Software

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software

data_processing: Data for both channels were Lowess-normalized and then the log(2) ratio was taken

source_name: Whole Mouse Reference RNA

label_protocol: not provided

extract_protocol: Total RNA isolated using Qiagen RNeasy Kit

tag: tissue

value: common reference RNA sample for these experiments consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female Day1 pups

value: FVB/n MMTV-Wnt1 mammary tumor


title: FBs RNA-Seq RP10114

city: Cleveland

first: Emina

last: Huang

state: OH

address: 9500 Euclid Ave

department: Stem Cell

institute: Lerner Research Institute/Cleveland Clinic

data_processing:
FastQC (version 0.9.5) was used to check the quality of reads (*.Fastq) --> no need of trimming
TopHat (version 2.0.10) was used to align (*.bam) files
Cufflinks to generate assembled transcripts (*.gtf)
Cuffmerge to merge (*.gtf)+ (*.bam) files
Cuffdiff to generate differentially expressed genes(*.diff)
produce edgeR files
Supplementary_files_format_and_content: CPM

source_name: Primary adult intestinal FBs

growth_protocol: Carpentino JE et al Cancer Research 2009 10.1158/0008-5472.CAN-09-1132

extract_protocol:
Isolated fibrobllasts in passages 3-5 (NL n=5 CT n=8 and CA n=5) were isolated/propagated and harvested prior to RNA extraction and standard sequencing/processing
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

tag: tissue origin

value: FBs cultivated from patient-derived colitic colon mucosa

value: 3-5 passages


title: FBs RNA-Seq AA92014


title: FBs RNA-Seq CM9314


title: FVB_MMTV_Wnt1_174861_Perou

description: Agilent Feature Extractor Software


title: CBMS1_rep1_d0_Undiff

description: Biological replicate 1 of 3.

value: embryonic stem cell


title: FBs RNA-Seq RM82514


title: dZEB.TGFb_rep1


title: dZEB_rep3

value: control


title: FVB_MMTV_Wnt1_172215_Perou

description: Agilent Feature Extractor Software


title: dZEB_rep4


title: FBs RNA-Seq CH9314


title: DMSO_rep1

value: inducible ZEB1

value: DMSO


title: FBs RNA-Seq BB8614


title: dZEB_rep2


title: FVB_MMTV_Wnt1_182281_Perou

description: Agilent Feature Extractor Software


title: FBs RNA-Seq KD8114


title: dZEB.TGFb_rep2


title: dZEB_rep1


title: FBs RNA-Seq CR72514

value: Fibroblast Cell line


title: tm3603 control_3: tm3603 L1, no drug, rep3

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

description: Gene expression data from manf-1(tm3603) L1 in vehicle

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip™ C. elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Caenorhabditis elegans

source_name: C.elegans L1 larvae treated with vehicle (DMSO)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Eggs were harvested from worms growing on MYOB media and OP50 bacteria using alkaline hypochlorite procedure, eggs were allowed to hatch onto MYOB plates without bacteria and washed off with M9 buffer 24 hours after plating.

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

treatment_protocol: Hatched L1 worms suspended in M9 buffer were treated with vehicle (DMSO) or tunicamycin (5ug/uL in DMSO) for 5 hours with gentle rotation, then pelleted on ice.

value: whole body

tag: genotype

value: vehicle (DMSO)

tag: age

value: synchronized L1 larvae


title: FBs RNA-Seq CR112114

value: Lymphoblast Cell line


title: tm3603 treated_3: tm3603 L1, TM, rep3

description: Gene expression data from manf-1(tm3603) L1 in TM

source_name: C.elegans L1 larvae treated with TM (5ug/uL in DMSO)

value: TM (5ug/mL in DMSO)


title: WT.TGFb_rep4

value: mammary epithelial cells

value: recombinant TGF-beta


title: FVB_MMTV_Wnt1_183983_Perou

description: Agilent Feature Extractor Software


title: WT.TGFb_rep3


title: FVB_MMTV_Wnt1_182348_Perou

description: Agilent Feature Extractor Software


title: Wild-type treated_3: wildtype L1, TM, rep3

description: Gene expression data from wildtype L1 in TM

value: wildtype (N2)


title: Wild-type control_3: wildtype L1, no drug, rep3

description: Gene expression data from wildtype L1 in vehicle


title: tm3603 treated_2: tm3603 L1, TM, rep2


title: FBs RNA-Seq PK82814

value: FBs cultivated from normal colon mucosa


title: FVB_MMTV_Wnt1_168512_Perou

description: Agilent Feature Extractor Software

value: common reference RNA sample for these experiments consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female Day1 pups

value: FVB/n MMTV-Wnt1 mammary tumor


title: WT.TGFb_rep1


title: WT.TGFb_rep2


title: tm3603 control_2: tm3603 L1, no drug, rep2


title: FBs RNA-Seq TM81514

value: 3-5 passages


title: FVB_MMTV_Wnt1_171979_Perou

description: Agilent Feature Extractor Software


title: Wild-type treated_2: wildtype L1, TM, rep2


title: FVB_MMTV_Wnt1_175317_Perou

description: Agilent Feature Extractor Software


title: WT_rep4


title: FVB_MMTV_Wnt1_171984_Perou

description: Agilent Feature Extractor Software


title: FVB_MMTV_Wnt1_182345_Perou

description: Agilent Feature Extractor Software


title: tm3603 treated_1: tm3603 L1, TM, rep1


title: FVB_MMTV_Wnt1_183984_Perou

description: Agilent Feature Extractor Software


title: FBs RNA-Seq PK11315


title: FVB_MMTV_Wnt1_171053_Perou

description: Agilent Feature Extractor Software


title: WT_rep2


title: WT_rep1


title: WT_rep3


title: Wild-type control_2: wildtype L1, no drug, rep2


title: FVB_MMTV_Wnt1_169927.2_Perou

description: Agilent Feature Extractor Software


title: tm3603 control_1: tm3603 L1, no drug, rep1


title: dkfz_ABM_15-0017

type: genomic

city: Boston

first: Volker

last: Hovestadt

state: MA

address: 360 Longwood Avenue

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description:
DNA Methylation data from a brain tumor sample
101231000137_R04C02

hyb_protocol: Illumina

scan_protocol: Illumina iScan System

data_processing: Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package. Signal intensities were normalized per sample by performing a background correction (shifting of mean negative control probe intensity to 0) and a dye-bias correction (scaling of mean normalization control probe intensity to 10,000). Standard beta-values were calculated.

label: biotin/DNP

source_name: ABM

label_protocol: Illumina

extract_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out using a Qiagen Blood & Cell Culture DNA Midi Kit (Qiagen, Hilden, Germany) after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany). Automated DNA purification from formalin-fixed, paraffin-embedded (FFPE) tissue was performed using the Maxwell Rapid Sample Concentrator (Promega, Madison, USA). DNA from FFPE tissue was restored using the Infinium HD FFPE DNA Restore Kit (Illumina, San Diego, USA).

tag: institutional tumor diagnosis

value: ABM

tag: molecular subgroup

tag: gender

value: F

tag: age (years)

tag: tumor location

value: parietal/occipital lobe


title: dkfz_CNS-tumor_15-0002

description:
DNA Methylation data from a brain tumor sample
200091640086_R03C01

source_name: unclear histology

value: unclear histology

value: M

value: frontal/parietal lobe, left


title: dkfz_ABM_15-0016

description:
DNA Methylation data from a brain tumor sample
101231000137_R03C02

value: parietal lobe


title: FVB_MMTV_Wnt1_169926_Perou

description: Agilent Feature Extractor Software


title: dkfz_ABM_15-0015

description:
DNA Methylation data from a brain tumor sample
3998568084_R03C02

value: central region, right


title: CtBP_ChIPSeq_Fulvestrant_rep2

city: Houston

first: Tianpeng

last: Gu

address: Cambridge steet

institute: Baylor College of Medicine

description:
single-end sequence reads
CtBP_Ful_skov3.bw

data_processing:
Read quality was checked for each sample using FastQC v0.11.1.
Sequenced reads were mapped to human genome version hg19 using Bowtie2.
Peaks were called using MACS2 by pooling replicates together. Alignments were pileuped by MACS2.
Genome_build: hg19
Supplementary_files_format_and_content: Pileup Bigwig file and binding peaks determined by MACS2

source_name: Ovarian cancer

growth_protocol: SKOV3 cells were cultured in phenol-red free DMEM medium supplemented with 10% Charcoal filtered FBS in humidified 37C incubator with 5% of CO2.

extract_protocol:
The cells were crosslined by 1% Formaldehyde for 10 minites. After the crosslink was quenched by  125mM Glycine. Then the chromatin was fragmented by sonication. The chromatin was subjected pull down by specific antibodies respectively as indicated. The DNA was eventually extracted after the de-crosslinking and Phenol-choloroform extraction.
ChIP-seq library was constructed according the the protocol provided by the NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® kit.

treatment_protocol: The  reagents were directly added into the culturemedium at given time point.

tag: antibody

value: anti-CtBP

value: 8uM Fulverstrant for 24 hours


title: FVB_MMTV_Wnt1_169927.1_Perou

description: Agilent Feature Extractor Software


title: FVB_MMTV_Wnt1_168508_Perou

description: Agilent Feature Extractor Software


title: CtBP_ChIPSeq_rep2

description:
paired-end sequence reads
CtBP_skov3.bw

tag: cell line


title: dkfz_ABM_15-0014

description:
DNA Methylation data from a brain tumor sample
3999834055_R03C01

value: intraventricular


title: MSC2-28 days of osteoblast differentiation-3

city: Birmingham

first: Qiling

last: He

state: AL

address: 1825 University Blvd, Shelby Building

department: Microbiology

institute: University of Alabama at Birmingham

hyb_protocol: 3.0 µg of RNA at 100ng/µL was used to hybridize ssDNA. Standard Affymetrix protocols were followed for hyb, wash, and stain

scan_protocol: Standard Affmetrix protocol for scanning was performed by using the Affymetrix 3000 7G scanner with autoloader. The acquisition and initial quantification of array images were performed by running Affymetrix GeneChip® Command Console® Software (AGCC)

data_processing: Data analysis was performed using Agilent's GeneSpring GX software with the selection of the Affymetrix Exon Expression. After the normalization using RMA-16 method, data were filtered on expression (20.0 - 100.0)th Percentile and were processed to one-way ANOVA followed by post hoc tests using SNK method. P-value was computed by selection of Asymptotic and corrected by Benjamini-Hochberg FDR method.

label: Biotin

source_name: Bone marrow

label_protocol: Biotin

growth_protocol: MSC2 were maintained in α-MEM without ascorbic acid (Invitrogen, A10490-01) supplemented with 10% MSC-qualified FBS (Invitrogen,12763025), media were changed every 3 to 4 days.

extract_protocol: Total cellular RNA of the MSC2 and Osteoblasts differentiated from MSC2 was isolated using Trizol (invitrogen, 15596026 ) according to the manufacturer’s instructions. Integrity and concentration of RNA was evaluated using an Agilent 2100 Bioanalyzer in combination with the Nano Eukaryotic RNA chip. All RNA samples had an average RNA Integrity Number (RIN) of 9.9.

treatment_protocol: Osteoblasts was induced from confluent MSC2 for 14 days or 28 days in DMEM with 10% FBS, 1mM sodium pyruvate, 0.1 μM dexamethasone, 0.2 mM L-Ascorbic acid-2 phosphate, 10mM β-glycerophosphate. Media were changed every 3 to 4 days.

tag: strain

tag: cell type

value: Osteoblasts differentiated from MSC2 after 28 days of osteoblast induction


title: CtBP_ChIPSeq_rep1

description:
single-end sequence reads
CtBP_skov3.bw


title: FVB_MMTV_Wnt1_167213_Perou

description: Agilent Feature Extractor Software


title: dkfz_ABM_15-0013

description:
DNA Methylation data from a brain tumor sample
9855358031_R06C01


title: FVB_MMTV_Wnt1_169918_Perou

description: Agilent Feature Extractor Software


title: ERα_ChIPSeq_EtOH_rep2

description:
single-end sequence reads
ERa_Etoh_skov3.bw

value: anti-ERα

value: EtOH for 24 hours


title: FVB_MMTV_Wnt1_167209_Perou

description: Agilent Feature Extractor Software

value: common reference RNA sample for these experiments consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female Day1 pups


title: dkfz_ABM_15-0011

description:
DNA Methylation data from a brain tumor sample
3998568070_R05C02

value: temporal lobe


title: ERα_ChIPSeq_EtOH_rep1


title: dkfz_ABM_15-0012

description:
DNA Methylation data from a brain tumor sample
3998568070_R06C02

value: frontal lobe


title: CtBP_ChIPSeq_Fulvestrant_rep1


title: FVB_MMTV_Wnt1_172499_Perou

description: Agilent Feature Extractor Software

value: FVB/n MMTV-Wnt1 mammary tumor


title: ERα_ChIPSeq_E2_rep2

description:
paired-end sequence reads
ERa_E2_skov3.bw

value: 10 nm E2 for 24 hours


title: FVB_MMTV_Wnt1_126355_Perou

description: Agilent Feature Extractor Software


title: Gab3-KO RNAseq 3

city: Spring House

first: Kasper

last: Hoebe

state: PA

address: 1400 McKean rd

department: Immunology

institute: J&J

data_processing:
sequences were aligned to mm10 mouse genome assembly (UCSC) by using CSBB-v3.0.
Differential expression analysis and interactive heatmap generation were performed with CSBB-v3.0.
Genome_build: mm10

source_name: Uterine NK cells

extract_protocol:
For gd8.5 uNK cells, total RNA isolated from 1 X 104 cells was amplified with the Ovation RNA-Seq System v2 (NuGEN) and  Libraries were sequenced with Illumina HiSeq2500 (DNA sequencing core, University of Cincinnati).
RNA-seq libraries were generated from 300 ng total RNA with an RNA Sample Prep Kit (Illumina).

treatment_protocol: C57BL/6 and Gab3KO males were mated with C57BL/6 and Gab3KO females respectively. The morning of detection of a copulation plug was designated gestational day (gd) 0.5. Pregnant females were dissected at gd8.5, gd12.5 or gd18.5. Gd8.5 implantation sites and gd12.5 placentas were removed from the pregnant uterus by scrapping and collected in media for flow cytometry. Gd8.5 implantation sites per mouse were pooled, minced and digested with Liberase (Sigma-Aldrich) and Dnase (Life Technologies) at 37o C for 1 hour. Digested tissues were processed through a 70 μM filter and washed with complete RPMI media, followed by RBC lysis. Subsequently, hematopoietic cells were isolated using biotinylated anti-CD45.2 antibody, MojoSort™ Streptavidin Nanobeads (BioLegend).  Cells were stained with anti-NK1.1, anti-CD122, DBA and a live/dead marker for flow sorting. Single, live, CD45.2+ CD3-, CD122+ cells were collected using the MoFlo XPD (Beckman Coulter) for subsequent RNA isolation.

value: Purified uterine NK cells

tag: gestational day


title: FVB_MMTV_Wnt1_124328_Perou

description: Agilent Feature Extractor Software


title: ERα_ChIPSeq_E2_rep1

description:
single-end sequence reads
ERa_E2_skov3.bw

tag: treatment

value: 10 nm E2 for 24  hours


title: Gab3-KO RNAseq 1


title: Gab3-KO RNAseq 2


title: Input_rep2

description:
single-end sequence reads
Input_skov3.bw


title: Adherent replicate 2

city: Media

first: Megan

last: Povelones

address: 25 Yearsley Mill Road

department: Sciences

institute: Penn State Brandywine

description: Cells were grown in brain heart infusion medium supplemented with 20 ug/ml hemin at 27 degrees C. 1 x 10^7 cells/ml in 20 ml were allowed to adhere for 2 h followed by media removal and 3 washes in media. 20 ml of media was then added back to the flask and adherent cells were allowed to grow for 24 h prior to RNA isolation.

data_processing:
fastq files were aligned to the C. fasciculata transcriptome (version 28) and the Aedes aegypti Liverpool strain transcriptome (version AGWG AaegL5.1) using Kallisto, version 0.43.0
abundance data were read into the R/bioconductor environment using the TxImport package, version 1.0.2
transcripts with low/no read counts across all samples were eliminated, for analysis of Cf transcripts from infected mosquitoes, transcripts with low/no read counts in three of the cultured samples or any of the mosquito samples were eliminated
data was normalized using the calcNormFactors function from Limma (3.34.4), using the TMM method
for Ae. aegypti transcripts the SVA package ComBat function was used to correct for variation introduced by the batch experimental design
precision weights were applied to expression data using the Limma/VOOM function
differentially expressed genes (0.01 adjusted Pval and 2 fold change for C. fasciculata transcripts and 0.05 adjusted Pval and 1.5 fold change for Ae. aegypti transcripts) were identified using linear modeling and Bayesian statistics using the Limma package

organism: Crithidia fasciculata

source_name: Adherent

extract_protocol:
Total RNA was extracted using Trizol.
1 microgram of total RNA was subjected to library synthesis using the TruSeq mRNA kit.

tag: form

value: adherent haptomonad


title: Adherent replicate 3


title: MSC2-28 days of osteoblast differentiation-2


title: FVB_MMTV_Wnt1_121993_Perou

description: Agilent Feature Extractor Software


title: MSC2-14 days of osteoblast differentiation-3

value: Osteoblasts differentiated from MSC2 after 14 days of osteoblast induction


title: Adherent replicate 1


title: Input_rep1


title: MSC2-28 days of osteoblast differentiation-1


title: FVB_MMTV_Wnt1_134413_Perou

description: Agilent Feature Extractor Software


title: WT RNAseq 3


title: MSC2-14 days of osteoblast differentiation-2


title: MSC2-14 days of osteoblast differentiation-1


title: MSC2-undifferentiated-3

value: Bone marrow-derived clonal mesenchymal stromal cells (named as MSC2)


title: Swimming replicate 3

description: Cells were grown in brain heart infusion medium supplemented with 20 ug/ml hemin at 27 degrees C. Cells were diluted to 1 x 10^7 cells/ml and then allowed to grow on a rocking platform for 24 hours prior to RNA isolation.

source_name: Swimming

value: swimming nectomonad


title: SKOV3_CtBP_OE2

description: 2x150 paired-end sequence reads

data_processing:
Sequenced reads were trimmed by Trimmomatic with parameters HEADCROP:12 CROP:80 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
Read quality was checked for each sample using FastQC v0.11.1.
Sequenced reads were mapped to human genome version hg19 using Tophat2.
Read counts of genes were calculated using FeatureCounts with parameters "-p" "-T" "3" "-s" "2" "-t" "exon" "-g" "gene_id" "-a"
Differentially expressed genes were determined by the R package EdgeR. Only genes with CPM > 0.2 in at least two samples were analyzed.
Genome_build: hg19
Supplementary_files_format_and_content: Read Counts in a TXT file, and differentially expressed genes in CSV files.

growth_protocol: SKOV3 cells were cultured in Phenol-red free DMEM supplemented with Charcoal filtered FBS (10%). Cells were confirmed to be mycoplasma negative.

extract_protocol:
Total RNA was extracted using RNeasy (Qiagen) as per manufacturer’s protocol.
Libraries were made using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: SKOV3 cells were treated by 20nM 17b-Estrodiol for 24 hours.

tag: genotype/variation

value: CtBP overexpression


title: FVB_MMTV_Wnt1_124326_Perou

description: Agilent Feature Extractor Software

tag: tissue


title: WT RNAseq 2


title: Wild-type control_1: wildtype L1, no drug, rep1

value: whole body

value: wildtype (N2)

value: vehicle (DMSO)

value: synchronized L1 larvae


title: Swimming replicate 2


title: WT RNAseq 1


title: MSC2-undifferentiated-1


title: Wild-type treated_1: wildtype L1, TM, rep1

description: Gene expression data from wildtype L1 in TM

value: TM (5ug/mL in DMSO)


title: SKOV3_CtBP_OE1

description: 2x150 paired-end sequence reads


title: FVB_MMTV_Wnt1_125673_Perou

description: Agilent Feature Extractor Software

value: common reference RNA sample for these experiments consisted of total RNA harvested from equal numbers of C57Bl6/J and 129 male and female Day1 pups


title: SKOV3_ERα_OE2

description: 2x150 paired-end sequence reads

value: ERalpha overexpression


title: Swimming replicate 1


title: LIP3

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

description: processed data file: counts.txt

data_processing:
Sequencing information was extracted using bcl2fastq v1.8.3 (Illumina).
Reads were mapped using TopHat v1.4.1.
Reads per gene were counted using HTSeq count v0.5.4.
Genome_build: genome: GRCh38/mm10; annotation: RefSeq 2012-05-17
Supplementary_files_format_and_content: counts.txt: Tab-delimited text file contains gene counts per gene for each sample.

source_name: fibroblasts, CEBPB-LIP overexpression

extract_protocol:
Extraction of total RNA was done using RNeasy Plus Mini Kit (QIAGEN).
Library preparation was done using Illumina's TruSeq RNA library preparation kit v2 following the manufacturer's instruction.

tag: strain/background

tag: construct

value: CEBPB-LIP

value: fibroblasts


title: FVB_MMTV_Wnt1_125285_Perou

description: Agilent Feature Extractor Software

value: FVB/n MMTV-Wnt1 mammary tumor


title: LIP2

description: processed data file: counts.txt


title: SKOV3_ERα_OE1

description: 2x150 paired-end sequence reads


title: FVB_MMTV_Wnt1_123738_Perou

description: Agilent Feature Extractor Software


title: LIP1

description: processed data file: counts.txt


title: SKOV3_Control

description: 2x150 paired-end sequence reads

value: control


title: LAP3

description: processed data file: counts.txt

source_name: fibroblasts, CEBPB-LAP overexpression

value: CEBPB-LAP


title: Infected mosquito replicate 3

description: For each replicate, 50 female mosquitoes 3-6 days post eclosion were starved overnight and then allowed to feed on 10% sucrose (uninfected) or 10% sucrose mixed with mid-log phase (3-5E7 cells/ml) C. fasciculata culture that had been washed with PBS. Mosquitoes were allowed to feed for 24 h before being switched back to regular sugar. 7 days later, hindguts were dissected and processed for RNA isolation.

organism:
Crithidia fasciculata
Aedes aegypti

source_name: Infected mosquito

value: Liverpool Blackeye/CfC1

value: adherent haptomonad (mosquito)


title: FVB_MMTV_Wnt1_121796_Perou

description: Agilent Feature Extractor Software


title: LAP2

description: processed data file: counts.txt


title: FVB_MMTV_Wnt1_123420_Perou

description: Agilent Feature Extractor Software


title: LAP1

description: processed data file: counts.txt


title: Infected mosquito replicate 1


title: FVB_MMTV_Wnt1_124504_Perou

description: Agilent Feature Extractor Software


title: FVB_MMTV_Wnt1_123114_Perou

description: Agilent Feature Extractor Software


title: Infected mosquito replicate 2


title: Uninfected mosquito replicate 3

organism: Aedes aegypti

source_name: Uninfected mosquito

value: Liverpool Blackeye


title: EV3

description: processed data file: counts.txt

source_name: fibroblasts, empty vector control CEBPB k/o

value: empty vector control CEBPB k/o


title: EV2

description: processed data file: counts.txt


title: FVB_MMTV_Wnt1_123070_Perou

description: Agilent Feature Extractor Software


title: FVB_MMTV_Wnt1_122016_Perou

description: Agilent Feature Extractor Software


title: EV1

description: processed data file: counts.txt


title: Uninfected mosquito replicate 1


title: MSC2-undifferentiated-2

tag: age

value: Bone marrow-derived clonal mesenchymal stromal cells (named as MSC2)


title: RNA_ILC2_IL33_cAMP_4h_rep2

status: Public on Jun 25 2019

first: Yuka

last: Kanno

address: 10 Center Drive, Rm13C120

department: NIAMS

institute: NIH

data_processing:
ATAC-seq: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads were mapped to the mouse genome (mm9 assembly) using Bowtie 0.12.8. In all cases, redundant reads were removed using FastUniq (Xu et al., 2012), and customized Python scripts were used to calculate the fragment length of each pair of uniquely mapped paired-end (PE) reads. Only one mapped read to each unique region of the genome that was less than 175 bp was kept and used in peak calling.
ATAC-seq: Regions of open chromatin were identified by MACS (version 1.4.2) using a p-value threshold of 1 × 10−5.
RNA-seq: Sequence reads from all samples were processed and aggregated using Cell Ranger.
RNA-seq: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads of 50 bases were mapped to mouse genome mm9 using TopHat 2.1.0.
Gene expression values (FPKM; fragments per kilobase exon per million mapped reads) were calculated with Cufflinks 2.2.1
Genome_build: ATAC-seq: mm9
Genome_build: RNA-seq: mm10
Supplementary_files_format_and_content: bw for ATAC-seq and mRNA-seq peak files

source_name: mouse primary lung ILC2s

growth_protocol:
growth protocol 1: FastATACseq in vitro: Lin- CD3- TCRβ- Thy1+ CD127+ KLRG1+ ILC2s were purified from lungs of mice by cell sorting (>98% purity; FACSAria III or FACSAria Fusion; Becton Dickinson) and cultured 2-4 weeks in the presence of recombinant mouse IL-7 (10 ng/ml; R&D) and recombinant human IL-2 (100 U/ml). Then, IL-2 and IL-7 were removed from ILC2 culture and additionally cultured for 4 hr before in vitro stimulation.1 x 10^4 cells were cultured with various stimulants including IL-33 (10 ng/ml), NMU (10 ng/ml), CGRP (10 ng/ml) for 4hr. These were then collected and processed for subsequent ATAC-seq. Cells were maintained in supplemented tissue culture medium (RPMI-1640 with 10% fetal calf serum, 50µM β-Mercaptoethanol, 100 U/ml penicillin, 100 mg/ml streptomycin; Life Technologies) and cultured at a density of 5 x 10^4 cells/ml in U bottomed, 96 well tissue culture-treated plates (CoStar).
growth protocol 2: scRNAseq ex vivo: 1.3 x 10^4 Lin- CD3- TCRβ- Thy1+ ILCs or CD3+ TCRb+ CD4+ Th cells were purified from lungs of mice by cell sorting (>98% purity; FACSAria III or FACSAria Fusion; Becton Dickinson) and immediately pocessed for subsequent scRNA-seq (10X Genomics).
growth protocol 3: mRNAseq ex vivo: 2-5 x 10^4 CD3+ TCRβ+ CD4+ CD62L+ CD44low CD25- naive Th cells were purified from mediastinal lymph nodes (mLNs) of mice by cell sorting (>98% purity; FACSAria III or FACSAria Fusion; Becton Dickinson) and stored in Trizol reagent (Invitrogen) for subsequent RNA isolation.
growth protocol 4: mRNAseq ex vivo: 2-5 x 10^4 Lin- CD3- CD4- TCRβ- Thy1+ CD127+ KLRG1+ ILC2s or CD3+ TCRb+ CD4+ ST2+ Th2 cells were purified from lungs of mice by cell sorting (>98% purity; FACSAria III or FACSAria Fusion; Becton Dickinson) and stored in Trizol reagent (Invitrogen) for subsequent RNA isolation.
growth protocol 5: mRNAseq in vitro: Lin- CD3- TCRβ- Thy1+ CD127+ KLRG1+ ILC2s were purified from lungs of mice by cell sorting (>98% purity; FACSAria III or FACSAria Fusion; Becton Dickinson) and cultured 2-4 weeks in the presence of recombinant mouse IL-7 (10 ng/ml; R&D) and recombinant human IL-2 (100 U/ml). Then, IL-2 and IL-7 were removed from ILC2 culture and additionally cultured for 4 hr before in vitro stimulation.3 x 10^4 cells were cultured with various stimulants or inhibitor, including IL-33 (10 ng/ml), NMU (10 ng/ml), CGRP (10 ng/ml), Dibutyryl-cAMP (100 μM), and Gaq inhibitor (10 μM) for 4hr. These were then collected and resuspended in Trizol ragent (Invitrogen) for subsequent RNA isolation. Cells were maintained in supplemented tissue culture medium (RPMI-1640 with 10% fetal calf serum, 50µM β-Mercaptoethanol, 100 U/ml penicillin, 100 mg/ml streptomycin; Life Technologies) and cultured at a density of 1.5 x 10^5 cells/ml in U bottomed, 96 well tissue culture-treated plates (CoStar).

extract_protocol:
FastATAC-seq: 1 X 10^4 cells were pelleted and washed with 50 μl 1× PBS. After pelleting the nuclei by centrifuging at 500 × g for 10 min, the pellets were re-suspended in 50 μl transposase mixture (25 µl of 2x TD buffer, 2.5 µl of TDE1, 0.5 µl of 1% digitonin, 22 µl of nuclease-free water) (#FC-121-1030, Illumina; #G9441, Promega). The reaction was incubated at 37°C with shaking at 300 rpm for 30 min. The fragmentalized DNAs were then purified using a QIAGEN MinElute kit and amplified with 10 or 11 cycles of PCR based on the amplification curve, and the paired-end libraries were purified using a QIAGEN PCR cleanup kit
scRNA-seq: Freshly sorted ILCs and Th cells (13,000 cells each) were encapsulated into droplets, and libraries were prepared using Chromium Single Cell 3’ Reagent Kits v2 according to manufacturer’s protocol (10X Genomics).
RNA-seq: Total RNA was extracted from 2-5 x 10^4 cells by Direct-zol™ RNA MicroPrep (Zymo Research). Single-end libraries were prepared from 0.1-0.5 μg of total RNA using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, E7530S)

tag: Sex

value: female

value: 6-12 weeks

tag: culture condition

value: 4 hour in vitro culture (growth protocol 5)

tag: genotype

value: WT

tag: lab  data id


title: RNA_ILC2_cAMP_4h_rep2


title: RNA_ILC2_IL33_cAMP_4h_rep1


title: RNA_ILC2_IL33_NMU_Gaqi_4h_rep2


title: case3 adjacent normal lung tissue

first: Ming

last: Xu

address: 280 Mohe Road

department: Oncology

institute: Shanghai 9th People's Hospital, Shanghai Jiao Tong University School of Medicine

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65℃ in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 4 out of 8 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses.Differentially expressed circRNAs with statistical significance between two samples or two groups were identified using fold change cutoff or through Volcano Plot filtering respectively.

source_name: inferior lobe of left lung

label_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA. The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

tag: case

tag: disease state

value: Early stage lung adenocarcinoma

value: 70 years

tag: smoking story

value: no

tag: gender

tag: differentiation

value: well-moderately

tag: Stage

value: T1bN0M0 IA

value: adjacent normal


title: Uninfected mosquito replicate 2

tag: strain


title: RNA_ILC2_IL33_CGRP_Gaqi_4h_rep2


title: case4 lung adenocarcinoma tissue

source_name: superior lobe of left lung

value: 68 years

value: moderately

value: T1aN1M0 IIA

value: tumor


title: case3 lung adenocarcinoma tissue

value: T1bN0M1 IA


title: case4 adjacent normal lung tissue


title: case1 adjacent normal lung tissue

source_name: inferior lobe of right lung

value: 58 years

value: male

value: poorly


title: RNA_ILC2_IL33_CGRP_Gaqi_4h_rep1

value: female

value: 6-12 weeks


title: RNA_ILC2_IL33_NMU_4h_rep2

value: 4 hour in vitro culture (growth protocol 5)

value: WT


title: case2 lung adenocarcinoma tissue

value: Early stage lung adenocarcinoma

value: 66 years

value: well


title: RNA_ILC2_IL33_NMU_CGRP_4h_rep1


title: case1 lung adenocarcinoma tissue

value: no

value: T1bN0M0 IA


title: RNA_ILC2_IL33_CGRP_4h_rep2


title: RNA_ILC2_IL33_CGRP_4h_rep1


title: case2 adjacent normal lung tissue

value: adjacent normal


title: RNA_ILC2_IL33_4h_rep1


title: RNA_ILC2_cAMP_4h_rep1


title: RNA_ILC2_IL33_4h_rep2


title: RNA_ILC2_IL33_NMU_Gaqi_4h_rep1


title: RNA_ILC2_CGRP_4h_rep1


title: RNA_ILC2_nostim_4h_rep2


title: RNA_ILC2_nostim_4h_rep1


title: RNA_ILC2_lung_nippo_day14

value: ex vivo (growth protocol 4)


title: RNA_ILC2_lung_nippo_day5


title: RNA_ILC2_IL33_NMU_4h_rep1


title: RNA_ILC2_lung_nippo_day9


title: RNA_ILC2_IL33_NMU_CGRP_4h_rep2


title: RNA_ILC2_lung_nippo_day2


title: RNA_ILC2_NMU_4h_rep1


title: RNA_ILC2_NMU_4h_rep2


title: RNA_ILC2_lung_steady


title: RNA_Th2_lung_nippo_day14

source_name: mouse primary lung Th2 cells


title: RNA_Th2_lung_nippo_day9


title: RNA_ILC2_CGRP_4h_rep2


title: FastATAC_ILC2_IL33_NMU_CGRP_4h_rep2

value: 4 hour in vitro culture (growth protocol 1)


title: RNA_naïve_CD4_T_mLNs

source_name: mouse primary mLNs naïve Th cells

value: ex vivo (growth protocol 3)


title: FastATAC_ILC2_IL33_NMU_CGRP_4h_rep1


title: FastATAC_ILC2_IL33_NMU_4h_rep1


title: FastATAC_ILC2_IL33_NMU_4h_rep2


title: FastATAC_ILC2_IL33_4h_rep1


title: FastATAC_ILC2_IL33_CGRP_4h_rep2


title: FastATAC_ILC2_IL33_CGRP_4h_rep1


title: FastATAC_ILC2_IL33_4h_rep2


title: FastATAC_ILC2_CGRP_4h_rep1


title: FastATAC_ILC2_nostim_4h_rep2


title: FastATAC_ILC2_CGRP_4h_rep2


title: FastATAC_ILC2_NMU_4h_rep2


title: FastATAC_ILC2_nostim_4h_rep1


title: FastATAC_ILC2_NMU_4h_rep1


title: WT mono+GMCSF/IL4 day 1 sample 1

city: Montréal

first: Salix

last: Boulet

state: Québec

address: 5415 rue de l'assomption

country: Canada

institute: Centre de recherche de l'hôpital Maisonneuve-Rosemont

data_processing:
Basecalls performed using Illumina RTA 1.17.21.3
Sequenced reads were trimmed for sequencing adapters using Trimmomatic 0.35 and mapped to the mouse reference genome GRCm38 using STAR version 2.5.1b. Gene annotations included were provided by gencode release M9.
RNA expression levels were obtained as readcounts from the STAR alignment pipeline (2nd strand).
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include readcout values for each sample. Columns are: Ensembl gene id, counts for unstranded RNA-seq, counts for the 1st read strand, counts for the 2nd read strand.

molecule: polyA RNA

source_name: WT mono+GMCSF/IL4 day 1

extract_protocol:
Total RNA from sorted monocytes and from monocytes cultured with GM-CSF and IL-4 for 1 and 2 days (2 samples per group from 2 independent experiments) was isolated using Trizol as recommended by the manufacturer (Invitrogen), and then further purified using RNeasy columns (Qiagen). Presence of contamination with chemicals was assessed by Nanodrop spectrophotomer using 260/280 and 260/230 ratios. Quantification of total RNA was made by QuBIT (Life Technologies).
Library preparation was done with the KAPA mRNAseq stranded library preparation kit (Roche, after mRNA capture with Dynabeads® mRNA DIRECT™ Purification Kit). 20 ng of total RNA were used as input for library preparation. Ligation was made with 0.5µl (final concentration 1.8 nM) of NEBNext Index primer for Illumina and 16 PCR cycles were required to amplify cDNA libraries. Libraries were then quantified by QuBit and the quality assessed with BioAnalyzer DNA 1000 and/or DNa High sensitivity chip. All librairies were diluted to 10nM and normalized by qPCR using the KAPA library quantification kit (KAPA). Libraries were pooled to equimolar concentration.

value: C57BL/6 background

value: bone marrow

tag: treatment

value: culture with GMCSF+IL4, 1 day


title: WT mono+GMCSF/IL4 day 1 sample 2


title: KO mono+GMCSF/IL4 day 1 sample 1

source_name: KO mono+GMCSF/IL4 day 1

value: Nr4a3 KO


title: implantation failure_IF 5

city: Mumbai

first: Indira

last: Hinduja

address: 15, Dr. G. Deshmukh Marg

country: India

institute: Jaslok Hospital and Research centre

description: endometrial biopsy during implantation window undergoing long protocol of ovarian stimulation from an implantation failure patient having previous 2 IVF failures with unexplained infertility.

hyb_protocol: 750ng of normalized cRNA (aRNA) was hybridized to 'Illumina Human HT-12' bead chip as per Standard Illumina hybridization protocol

scan_protocol: Hybridized bead chip was scanned by 'I Scan' using Standard Illumina scanning protocol

data_processing: The data was analysed using Genome studio software 2011. Quantile normalization method was used to normalize the raw data.  The file sample probe profile.txt (available on the series record) contains the normalized data with gene annotation.

source_name: endometrial tissue during implantation window

label_protocol: Biotinylated aRNA was prepared by using Epicentre TargetAmp Nano-g Biotin-aRNA Labelling Kit for the Illumina System. In this, 500ng total RNA was reverse transcribed to obtain first and second strand of cDNA and subjected to in-vitro transcription of biotin labelled amplified RNA (aRNA) as described in the manufacturer's instruction.

extract_protocol: Total RNA was extracted using trizol method as per manufacture's instruction. It was followed by Dnase treatment using DNase enzyme. Quality control of RNA was performed by Agilent 2100 bioanalyzer and RNA was quantified using Qubit Ribogreen quantitation @ SPPL. RNA integrity number (RIN) in the range of 7.5-10 was considered to have good quality

treatment_protocol: After collection of endometrial tissue with the help of endometrial suction curette by Gynetics in sterile environment, it was washed with phosphate buffer saline at pH7.0, homogenized in liquid nitrogen and dissolved in trizol solution.

value: endometrium

tag: sample group and identifier

tag: sample collection day

tag: stimulation protocol

value: GnRH agonist long protocol


title: implantation failure_IF 13

tag: tissue


title: implantation failure_IF 8

tag: age


title: KO mono+GMCSF/IL4 day 2 sample 1

source_name: KO mono+GMCSF/IL4 day 2

value: culture with GMCSF+IL4, 2 days


title: KO monocytes 1

source_name: KO monocytes

value: undifferentiated


title: WT monocytes 1

source_name: WT monocytes

value: WT


title: WT mono+GMCSF/IL4 day 2 sample 2

source_name: WT mono+GMCSF/IL4 day 2


title: WT monocytes 2


title: WT mono+GMCSF/IL4 day 2 sample 1


title: oocyte donor_OD 21

description: endometrial biopsy during implantation window from oocyte donor with healthy proven fertility undergoing long protocol of ovarian stimulation


title: oocyte donor_OD 12


title: implantation failure_IF 6

description: endometrial biopsy during implantation window undergoing long protocol of ovarian stimulation from an implantation failure patient having previous 7 IVF failures with unexplained infertility.


title: oocyte donor_OD 22


title: KO monocytes 2


title: oocyte donor_OD 5


title: oocyte donor_OD 7


title: implantation failure_IF 3

description: endometrial biopsy during implantation window undergoing long protocol of ovarian stimulation from an implantation failure patient having previous 3 IVF failures with unexplained infertility.


title: implantation failure_IF 10

description: endometrial biopsy during implantation window undergoing long protocol of ovarian stimulation from an implantation failure patient having previous 4 IVF failures with unexplained infertility.


title: implantation failure_IF 2


title: implantation failure_IF 12


title: oocyte donor_OD 20


title: oocyte donor_OD 24


title: implantation failure_IF 1


title: implantation failure_IF 4

description: endometrial biopsy during implantation window undergoing long protocol of ovarian stimulation from an implantation failure patient having previous 5 IVF failures with unexplained infertility.


title: oocyte donor_OD 23


title: KO mono+GMCSF/IL4 day 2 sample 2


title: KO mono+GMCSF/IL4 day 1 sample 2


title: M3125 CZX-2

city: Athens

first: Anthony

middle: E.

last: Glenn

state: GA

address: 950 College Station Rd

department: Toxicology & Mycotoxin Research Unit

institute: USDA, ARS, USNPRC, R.B. Russell Research Center

description: PDB liquid culture

data_processing:
Remove Adapter, Cutadapt 1.9.dev1, Trimmomatic 0.32
Tophat 2.0.13
Samtools 1.2
HTseq 0.6.1p1
DESeq2
Genome_build: Fusarium verticillioides 7600 RefSeq Genome
Supplementary_files_format_and_content: raw counts of sequencing reads for the genes of interest in .txt format. Gene identifiers correspond to FVEG locus tags (e.g., gene11400 is equivalent to  FVEG_11400).

organism: Fusarium verticillioides

source_name: Chlorzoxazone treatment Rep2

growth_protocol: Two milliliters of PDB (potato dextrose broth; Neogen Food Safety, Lansing, MI, USA) cultures in sterile snap-cap tubes, with caps loose, were seeded with 10000  FRC M-3125 wild-type F. verticillioides conidia and grown at 27 °C, 250 rpm for 47 hours

extract_protocol:
After the final hour, 1 mL liquid culture from each tube was pelleted by centrifugation at 8000 g for 5 min at 4 °C, resuspended in 1 mL lysis buffer, and transferred to lysing matrix D tubes (MP Biomedicals, LLC, Santa Ana, CA, USA). The tubes were homogenized with a FastPrep-24TM 5G instrument (MP Biomedicals) at 6 m/s with 2 pulses of 30 s and a 1 min intervening pause at room temperature. Total RNA was extracted from the homogenized samples with a PureLink® RNA Mini Kit (Thermo Fisher Scientific Inc., MA, USA) following the manufacturer’s protocol.
Sequencing libraries were constructed with Illumina Truseq DNA LT sample prep kit (Illumina Inc., San Diego, CA, USA) following the manufacturer’s protocol.

treatment_protocol: At the final hour, 10 μL DMSO containing 100 μg of BOA, OXD, CMN, or CZX, or 10 μg of PA, or 40 μg of PB were was added to the respective treatments. Ten microliters of DMSO was added to control samples. All culture tubes were incubated for a final one-hour induction.

value: Wild-type FRC M-3125

tag: hours growth

value: 47 before induction + 1 after

value: Chlorzoxazone


title: M3125 CZX-1

description: PDB liquid culture

source_name: Chlorzoxazone treatment Rep1


title: M3125 CMN-3

description: PDB liquid culture

source_name: 2-Coumaranone treatment Rep3


title: M3125 CMN-2

description: PDB liquid culture

source_name: 2-Coumaranone treatment Rep2


title: M3125 OXD-3

description: PDB liquid culture

source_name: 2-Oxindole treatement Rep3


title: M3125 CMN-1

description: PDB liquid culture

source_name: 2-Coumaranone treatment Rep1


title: M3125 OXD-1

description: PDB liquid culture

source_name: 2-Oxindole treatement Rep1


title: M3125 OXD-2

description: PDB liquid culture

source_name: 2-Oxindole treatement Rep2


title: M3125 BOA-3

description: PDB liquid culture

source_name: 2-Benzoxazolinone treatment Rep3


title: M3125 Ctr-2

description: PDB liquid culture

source_name: Control Rep2

value: Control


title: M3125 PB-1

description: PDB liquid culture

source_name: Pyrrocidine B treatment Rep1

value: Pyrrocidine B


title: M3125 PB-2

description: PDB liquid culture

source_name: Pyrrocidine B treatment Rep2


title: M3125 PB-3

description: PDB liquid culture

source_name: Pyrrocidine B treatment Rep3


title: M3125 PA-3

description: PDB liquid culture

source_name: Pyrrocidine A treatment Rep3

value: Pyrrocidine A


title: M3125 PA-2

description: PDB liquid culture

source_name: Pyrrocidine A treatment Rep2


title: M3125 Ctr-1

description: PDB liquid culture

source_name: Control Rep1


title: Liver_MO_110d_female_4

city: Mexico

first: CONSUELO

last: LOMAS

state: MEXICO

address: Vasco de Quiroga 15, Belisario Domínguez Sección XVI,

department: REPRODUCTIVE BIOLOGY

country: Mexico

institute: INCMNSZ

description:
processed data file: PROCESSED DATA FEMALE.txt
rat_liver_obese_RNA_seq_60
MO 4 female

data_processing:
Libraries were normalized to 10 nM and were diluted/denatured to 20 pM before loading on the cBot 2X100 Paired end sequencing was performed on the Illumina HiSeq 2500 sequencer.
Output demultiplexed reads were exported to Partek Flow for analysis.
Read FASTQ files were quality trimmed to Phred 30 at each end.
Trimmed reads were aligned to the Rattus norvegicus genomic reference (RGSC 5.0/rn5) with STAR aligner v2.3.1j.
Gene and transcript abundance were quantified against rn5 RefSeq annotation and normalized for transcript abundance for all samples as a dataset using RPKM.
Genome_build: RGSC 5.0/rn5
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample .

organism: Rattus norvegicus

extract_protocol:
F1 liver tissue samples (10-20 mg) were homogenized with the BioSpec BeadBeater and RNA was extracted using the QIagen miRNeasy mini kit (Qiagen), according to the manufacturer’s instructions for n= 6 controls and n= 5 MO for each sex. RNA isolated quantity and quality were determined by using a Nanodrop spectrophotometer (Nanodrop Technologies, DE, USA) and stored at -80°C until use.
cDNA libraries were prepared from 1 μg total RNA using an Illumina TruSeq RNA LS Sample Preparation kit v2 according to the manufacturer’s instructions (Illumina, San Diego, CA, USA). Final individual cDNA libraries were assessed for quality and fragment size using the Agilent DNA 1000. Sequencing libraries were quantified with KAPA Library Quantification kit for Illumina platforms.

value: Wistar

tag: maternal diet

value: obesogenic (MO) diet

value: post natal day 110

tag: Sex

value: female

value: liver


title: Liver_MO_110d_female_5

description:
processed data file: PROCESSED DATA FEMALE.txt
rat_liver_obese_RNA_seq_61
MO 5 female


title: Liver_MO_110d_female_3

description:
processed data file: PROCESSED DATA FEMALE.txt
rat_liver_obese_RNA_seq_59
MO 3 female


title: Liver_MO_110d_female_1

description:
processed data file: PROCESSED DATA FEMALE.txt
rat_liver_obese_RNA_seq_57
MO 1 female


title: Liver_MO_110d_male_5

description:
processed data file: PROCESSED DATA MALE.txt
rat_liver_obese_RNA_seq_8
MO 5 male

value: male


title: Liver_MO_110d_female_2

description:
processed data file: PROCESSED DATA FEMALE.txt
rat_liver_obese_RNA_seq_58
MO 2 female


title: Liver_MO_110d_male_2

description:
processed data file: PROCESSED DATA MALE.txt
rat_liver_obese_RNA_seq_5
MO 2 male


title: Liver_MO_110d_male_3

description:
processed data file: PROCESSED DATA MALE.txt
rat_liver_obese_RNA_seq_6
MO 3 male


title: Liver_MO_110d_male_4

description:
processed data file: PROCESSED DATA MALE.txt
rat_liver_obese_RNA_seq_7
MO 4 male


title: Liver_MO_110d_male_1

description:
processed data file: PROCESSED DATA MALE.txt
rat_liver_obese_RNA_seq_4
MO 1 male


title: M3125 BOA-1

description: PDB liquid culture

source_name: 2-Benzoxazolinone treatment Rep1


title: M3125 BOA-2

description: PDB liquid culture

source_name: 2-Benzoxazolinone treatment Rep2


title: M3125 PA-1

description: PDB liquid culture

source_name: Pyrrocidine A treatment Rep1


title: slh1ski2_rep2

city: Frederick

first: Colin

last: Wu

department: RNA Biology Laboratory

institute: NCI

data_processing:
Base calling was performed at Johns Hopkins core facilities with CASAVA 1.8
Adapter sequence (NNNNNNCACTCGGGCACCAAGGA) removed with Skewer
4 random nucleotides included in RT primer (RNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC/iSP18/TTCAGACGTGTGCTCTTCCGATCTGTCCTTGGTGCCCGAGTG) were removed from the 5’ end of reads. Trimmed reads longer than 15 nt were aligned to yeast ribosomal and non-coding RNA sequences using STAR with ‘--outFilterMismatchNoverLmax 0.3’.
Genome_build: Unmapped reads were then mapped to genome using the following options ‘--outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.1’.
Supplementary_files_format_and_content: SacCer3 R64-1-1 with NGD-CGA reporter; RFP normalized count table

organism: Saccharomyces cerevisiae

source_name: Whole Cells

growth_protocol: Yeast cells were grown to OD ~0.5.

extract_protocol:
Monosomes or disomes were isolated by sucrose gradient centrifugation after RNaseI treatment. RNA was extracted using SDS/hot phenol/chloroform.
Fragments ranging from 15-34 nt or 15-90 nt were gel purified for monosome or disome footprints, respectively. rRNA was depleted from this pool through Ribo-Zero Gold treatment. Upon dephosphorylation of sample RNA, linker was ligated and this product was once again gel purified. This was followed by reverse transcription as well as circularization of cDNAs. PCR amplification of this library was then sent for sequencing.

treatment_protocol: Yeast cells were harvested by vacuum filtration and flash frozen. Samples were homogenized and lysed with lysis buffer using a freezer mill.

tag: genotype/variation

tag: plasmid(s)

tag: molecule subtype

value: Ribosome Protected mRNA (15-34 nt)


title: SMRtrisome

source_name: isolated tirsome fractions

value: Ribosome Protected mRNA (15-90 nt)


title: hel2dom34ski2_rep2


title: slh1dom34ski2_rep2

value: Ribosome Protected mRNA (40-80 nt)


title: noEtrisome


title: M3125 Ctr-3

description: PDB liquid culture

source_name: Control Rep3


title: dom34ski2_rep2


title: cue2slh1dom34ski2_rep4


title: M3125 CZX-3

description: PDB liquid culture

source_name: Chlorzoxazone treatment Rep3


title: slh1ski2_rep1

data_processing:
Library strategy: ribosome profiling
Base calling was performed at Johns Hopkins core facilities with CASAVA 1.8
Adapter sequence (NNNNNNCACTCGGGCACCAAGGA) removed with Skewer
4 random nucleotides included in RT primer (RNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC/iSP18/TTCAGACGTGTGCTCTTCCGATCTGTCCTTGGTGCCCGAGTG) were removed from the 5’ end of reads. Trimmed reads longer than 15 nt were aligned to yeast ribosomal and non-coding RNA sequences using STAR with ‘--outFilterMismatchNoverLmax 0.3’.
Unmapped reads were then mapped to genome using the following options ‘--outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.1’.
Genome_build: SacCer3 R64-1-1 with NGD-CGA reporter
Supplementary_files_format_and_content: csv file includes raw counts of each position of CGA reporter. The 'seq' column includes the base of the position.

extract_protocol:
Monosomes or disomes were isolated by sucrose gradient centrifugation after RNaseI treatment. RNA was extracted using SDS/hot phenol/chloroform.
Fragments ranging from 15-34 nt or 40-80 nt were gel purified for monosome or disome footprints, respectively. rRNA was depleted from this pool through Ribo-Zero Gold treatment. Upon dephosphorylation of sample RNA, linker was ligated and this product was once again gel purified. This was followed by reverse transcription as well as circularization of cDNAs. PCR amplification of this library was then sent for sequencing.

tag: rna source

tag: genotype

value: slh1 ski2


title: ski2_rep1


title: dom34ski2_rep1_disome

value: dom34 ski2


title: hel2dom34ski2_rep1

value: hel2 dom34 ski2


title: slh1dom34ski2_rep1_disome

value: slh1 dom34 ski2


title: cue2dom34ski2_rep1

value: cue2 dom34 ski2


title: cue2slh1dom34ski2_rep2_disome

value: cue2 slh1 dom34 ski2e


title: cue2slh1dom34ski2_rep3

value: cue2 slh1 dom34 ski2


title: dom34ski2_rep1


title: R402Atrisome


title: Donor HU1020 (AKA BD405A) HBV/HDV co-infected, 28 days, sample 1

city: Princeton

first: Alexander

last: Ploss

state: NJ

address: Washington Road

department: Molecular Biology

institute: Princeton University

data_processing:
The samples were run on two HiSeq 2500 Rapid Run mode flowcells. Basecalling was performed by Illumina RTA version 1.18.64.0. BCL files were then converted to fastq format using Illumina’s bcl2fastq version 1.8.4. Reads that aligned to phiX using Bowtie 1.1.1 (Langmead et al., 2009) were removed as well as reads that failed Illumina’s default chastity filter. The fastq files from each lane were then combined before splitting the reads from each sample using the barcode sequences allowing 1 mismatch, using the barcode_splitter program, version 0.18.2 (Leach and Parsons, 2017).
A reference genome was created using the NCBI GRCh38 human reference (iGenomes), the NCBI GRCm38 mouse reference (iGenomes), the NCBI U95551.1 Hepatitis B virus subtype ayw, complete genome, and the NCBI M21012.1 Hepatitis delta virus RNA, complete genome. The reference sequences (fasta) and gene annotations (gtf) were combined to form a single unified reference. The read alignment, quantification, and differential expression analysis was done using a locally installed instance of the Galaxy workflow platform (Afgan et al., 2016). The reads for each sample were then aligned to the combined reference using STAR (Galaxy Version 2.5.2b-1) with default parameters (Dobin et al., 2013). Quantification for each gene was then done using featurecounts (Galaxy Version 1.6.0.1) with default settings (Liao et al., 2014).
Genome_build: A reference genome was created using the NCBI GRCh38 human reference (iGenomes), the NCBI GRCm38 mouse reference (iGenomes), the NCBI U95551.1 Hepatitis B virus subtype ayw, complete genome, and the NCBI M21012.1 Hepatitis delta virus RNA, complete genome.
Supplementary_files_format_and_content: Tabular files of ENSEMBL gene ID and counts

organism:
Homo sapiens
Mus musculus

source_name: SACC-PHHs

growth_protocol: All SACC-PHHs were grown in Hurel Maintenance media containing 5% fetal bovine serum (FBS) and 1% v/v penicillin/streptomycin.

extract_protocol:
Total RNA extracted using Qiagen Rneasy Mini Kit per manufacturer's directions.
The integrity of total RNA samples were assessed on Bioanalyzer 2100 using RNA 6000 Nano chip (Agilent Technologies, CA); only samples with RNA Integrity Number (RIN) greater than 9.0 were used for RNA-seq.  The poly-A containing RNA transcripts were enriched from 1μg of total RNA for each sample using oligo-dT bead, and further converted to cDNA then Illumina sequencing library using PrepX RNA-seq library kit on the automated Apollo 324TM NGS Library Prep System (Wafergen Biosystems, CA) according to the manufacturer's protocol.  Different DNA barcodes were added to each RNA-seq library.  The libraries were examined on Agilent Bioanalyzer DNA High Sensitivity chips for size distribution, and quantified by Qubit fluorometer (Invitrogen, CA).  The RNA-seq libraries were pooled at equal molar amount and sequenced on Illumina HiSeq 2500 Rapid flowcells as single-end 75 nucleotide reads following the standard protocol.  Raw sequencing reads were filtered by Illumina HiSeq Control Software, and only the Pass-Filter (PF) reads were used for further analysis.

treatment_protocol: PHHs (188,000 cells/well) were seeded along with 3T3 J mouse (30,000 cells/well) in a 24 well format.  Seven to ten days after seeding, SACC-PHHs were challenged with respective viruses.

tag: cell type

value: Primary human hepatocytes co-cultured with mouse 3T3J non-parenchymal cells

value: Co-infected with HBV (MOI = 4,000) and HDV (MOI = 1,000)


title: Donor HU1016 HBV uninfected, 8 days

value: Uninfected


title: Donor HU1020 (AKA BD405A) HBV/HDV co-infected, 28 days, sample 3


title: Donor HU1016 HBV uninfected, 28 days


title: hel2slh1dom34ski2_rep2


title: Donor HU1020 (AKA BD405A) HBV/HDV co-infected, 28 days, sample 2


title: Donor HU1020 (AKA BD405A) HBV/HDV co-infected, 8 days, sample 3


title: Donor HU1020 (AKA BD405A) HBV/HDV co-infected, 8 days, sample 1


title: cue2dom34ski2_rep2


title: Donor HU1019 (AKA BD330) HBV/HDV co-infected for 28 days, sample 3


title: Donor HU1019 (AKA BD330) HBV/HDV co-infected for 8 days, sample 2


title: Donor HU1019 (AKA BD330) HBV/HDV co-infected for 28 days, sample 2


title: Donor HU1019 (AKA BD330) HBV/HDV co-infected for 28 days, sample 1


title: Donor HU1019 (AKA BD330) HBV/HDV co-infected for 8 days, sample 3


title: Donor HU1020 (AKA BD405A) HBV/HDV co-infected, 8 days, sample 2


title: Donor HU1019 (AKA BD330) HBV/HDV co-infected for 8 days, sample 1


title: slh1dom34ski2_rep1


title: hel2slh1dom34ski2_rep1

value: hel2 slh1 dom34 ski2


title: SW620

city: Orlando

first: WEI

last: ZHANG

state: FL

address: 4000 central florida blvd

department: Computer Science

institute: UNIVERSITY OF CENTRAL FLORIDA

hyb_protocol: Hybridization of NanoString probes was conducted according to the manufacturer's protocol.

data_processing: The  geometric  mean  of  the  ten  house  keeping  genes  (TAF5L,  HPS6,  DNTTIP2, GNRHR, ZNF407, KCNK7, KIAA1539, RBM12, DGCR14, and KHDRBS1) was applied to normalized the NanoString signal in each cell line. Then, the expressions of isoforms in one gene can be estimated by minimizing the differences between the predicted and observed intensities for all probes in the gene.

label: NanoString labeling

source_name: cancer cell line

label_protocol: NanoString probe labeling was conducted accoding to the manufacturer's protocol.

growth_protocol: Cells were grown in DMEM media supplemented with 10% FBS and antibiotics. Cell were harvested when they were around 70% confluency.

extract_protocol: A standard TriZol RNA extraction method was used for toal RNA extraction from harvested cells.

treatment_protocol: No treatments

value: Colon

value: colon cancer cell line

tag: cell line


title: T47D

value: Breast

value: breast cancer cell line


title: SW480


title: TOV21G

value: Ovary

value: ovarian cancer cell line


title: WI38

value: Lung

value: lung cancer cell line


title: RMG1


title: OVSAHO

value: OVSAHO


title: PANC1

value: Pancreas

value: pancreas cancer cell line


title: SKOV3


title: PC3

value: Prostate

value: prostate cancer cell line


title: SKMES1


title: OVCAR8


title: OVCAR4


title: OVCAR3


title: NCI_H460


title: SKBR3


title: SNU484

value: Stomach

value: stomach cancer cell line


title: hESC WT hN - 2

city: Guelph

first: Scott

last: Ryan

state: ON

address: 50 Stone Rd E

institute: University of Guelph

hyb_protocol: The slides were hybridized at 45ºC for at least 16 hr according to manufacturer's protocol.

scan_protocol: The slides were subsequently washed and scanned with an Illumina DNA Microarray Scanner according to manufacturer's protocol.

data_processing: After scanning, the intensities of the spots were extracted using Feature Extraction Version 10.1.1.

label: Biotin Allonamide Triphosphate

source_name: hESC

label_protocol: 400 ng of RNA was labeled and used for each microarray according to manufacturers protocol.

growth_protocol: hPSC colonies were dissociated into a single cell suspension using accutase. To purify PSCs and remove fibroblast feeders, medium containing dissociated fibroblasts and PSCs was placed in gelatin-coated dishes. After adherence of the dissociated fibroblasts, supernatant containing purified PSCs was collected and re-plated at 4x104 cells/cm2 on Matrigel (BD)-coated tissue culture dishes for differentiation. Floor-plate induction was carried out using medium containing knockout serum replacement (KSR), LDN193189 (100 nM), SB431542 (10 μM), Sonic Hedgehog (SHH) C25II (100 ng/ml), Purmorphamine (2 μM), Fibroblast growth factor 8 (FGF8; 100 ng ml−1), and CHIR99021 (3 μM). On day 5 of differentiation, KSR medium was incrementally shifted to N2 medium (25%, 50%, 75%) every 2 days. On day 11, the medium was changed to Neurobasal/B27/Glutamax supplemented with CHIR. On day 13, CHIR was replaced with Brain Derived Neurotrophic Factor (BDNF; 20 ng ml−1), ascorbic acid (0.2 mM), Glial Derived Neurotrophic Factor (GDNF; 20 ng ml−1), transforming growth factor beta 3 (TGFβ3; 1 ng ml−1), dibutyryl cAMP (db cAMP; 0.5 mM), and DAPT (10 μM) for 9 days. On day 20, cells were dissociated using accutase and re-plated under high cell density 400x103 cells/cm2 in terminal differentiation medium (NB/B27 + BDNF, ascorbic acid, GDNF, db cAMP, TGFβ3 and DAPT) or DAN Medium (DA Neuron) on dishes pre-coated with poly-ornithine(15 μg/ml)/laminin (1 μg ml−1)/fibronectin (2 μg ml−1).

extract_protocol: RNA was harvested from hPSC-derived neuro9ns (n = 3 experiments) using the RNeasy Kit (Qiagin) according to manufacturer’s protocol.  Samples were prepped with Affymetrix WT PLUS Kit according to manufacturers protocol.

value: Dopaminergic Neuron


title: hESC A53T hN - 3


title: hESC A53T hN - 1


title: hESC WT hN - 3


title: hipsc A53T hN - 1

source_name: hiPSC


title: hipsc A53T hN - 2


title: hipsc corr hN - 1


title: hESC A53T hN - 2


title: hESC WT hN - 1


title: hipsc corr hN - 2


title: hipsc A53T hN - 3


title: NCI_H358


title: NCI_H1299


title: MRC5


title: MDA_MB436


title: CKO2_brain

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include count, normalized data, fold-change values etc.

extract_protocol:
Total RNA was extracted by using Trizol reagent. Total 2ug RNA for the construction of sequencing libraries
mRNA were enriched by Oligo(dT) bread and then fragmented by fragmentation buffer. cDNA was synthesized by reverse transcription using 6bp random primers and purified by QIAQuick PCR kit. After adapter ligation, DNA was PCR amplified sequences and band isolated from an agarose gel.

tag: strain background

tag: developmental stage

value: brain


title: WT2_brain

value: WT; Wt1fl/fl


title: M1A_Paca2


title: MDA_MB231


title: MCF7


title: MCF10A

source_name: Immortalized normal breast cell line

value: Immortalized normal breast cell line


title: LoVo

value: Colon

value: colon cancer cell line

value: LoVo


title: LS174T


title: ATAC-SEQ DCA

city: PHILADELPHIA

first: Arndt

last: Siekmann

state: Pennsylvania

address: 421 Curie Boulevard, 1114 Biomedical Research Building II/III

department: Perelman School of Medicine

institute: UNIVERSITY OF PENNSYLVANIA

data_processing:
Basecalls performed using CASAVA version 1.7
data were aligned against the Mus musculus mm10 genome using BWA (Li,2010)
MACS2 (Zhang, 2008) was used for peak calling
ATAC-seq peaks were further refined as +/–75bp regions of peak summits identified by MACS2.
Common satellite repeat regions were removed against the UCSC Repeatmasker track.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig (.bw)

source_name: mouse primary muscle myoblasts

growth_protocol: Myoblasts were isolated from hindlimb muscles from young adult (6-9week) old C57/BL6 animals, then expanded for ~8 passages prior to experiments.Subconfluent myoblasts (50%) were grown in 15% FBS + DMEM (5mM glucose, 1mM pyruvate, 2mM glutamine) for 24 hours, followed by 24h control or drug treatment

extract_protocol:
For ATACSeq 50,000 primary myoblasts were prepared according to Buenrostro, et al (Nature Methods, 2013) using the Nextera DNA Library Preparation Kit
Cells were trypsinized and then washed in PBS before downstream processing steps
Sequencing libraries were constructed according to Illumina protocols.

treatment_protocol: Cells were treated for 24 hours either with PBS or 5mM DCA

tag: passage

value: 9-12 passages

value: young adult (6-9week)

tag: strain

tag: agent

value: 5mM DCA


title: H3K9|14ac ChipSEQ PBS

extract_protocol:
For ChIP-SEQ  ~1 x 10^7 primary myoblasts were cross-linked in 1% formadehyde for 15 min, with constant agitation, and quenched with 150mM glycine for 5 min. Micrococcal nuclease (New England Biolabs, Inc.) was used to fragment chromatin to a range of 200-400 bp. Chromatin was incubated with H3ac antibody (Millipore, 06-599) overnight at 4°C with constant agitation. Protein A Dynabeads was incubated with antibody-protein complexes for 2 hr at 4°C with constant agitation. After de-crosslinking, DNA was isolated using a MinElute column (Qiagen).
Cells were trypsinized and then washed in PBS before downstream processing steps
Sequencing libraries were constructed according to Illumina protocols.

value: PBS


title: H3K9|14ac ChipSEQ DCA


title: KURAMOCHI

tag: tissue

value: Ovary

value: ovarian cancer cell line

value: KURAMOCHI


title: KM125M


title: MHV68_3T12_18h [Illumina RNA-Seq]

city: Gainesville

last: Tibbetts

department: Molecular Genetics & Microbiology

institute: University of Florida

description: poly(A)-selected RNA

data_processing:
Illumina 1.9 basecalling
Alignment to the MHV68.ORF73bla genome using STAR version 2.3.0.1 with default parameters
Generation of wig files using IGVTools
Genome_build: The MHV68.ORF73bla genome is a modified version of GCF_000845665.1 genome assembly, with a b-lactamase insert.
Supplementary_files_format_and_content: plus and minus strand wig files for the MHV68.ORF73bla genome

growth_protocol: Cells were maintained in Dulbecco's Modified Eagle's Medium (DMEM) with L-glutamine, 4.5g/L glucose and sodium pyruvate supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin

extract_protocol:
Total RNA was extracted using TRIzol reagent
RNA libraries were prepared for sequencing using stranded Illumina TruSeq protocols

treatment_protocol: Cells were plated at a density of 2 x 10^5 cells/well in a flat-bottom 6-well TC-treated cell culture plate. Twenty four hours later, cells were infected at MOI 5 with a floxed, BAC-derived wild-type MHV68 which carries a β-lactamase marker fused to ORF73 (MHV68.ORF73bla). RNA was harvested after 18 hours.

value: NIH 3T12

tag: hpi

tag: virus strain


title: 48hr cultured MuSC - Run 2 (C3)

description: Freshly isolated A7/CD34+ stem cells from 8-12wk female BL6 were cultured for 48hr on hydrogel. Samples run on Sequencing Run #2 along with samples MuSC 4 and MuSC 5

data_processing:
Sickle, end trimming
STAR read mapping
RSEM transcript quantification
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file reports counts per transcript for each Sample

source_name: 48hr cultured MuSC

growth_protocol: 20% FBS/40% Low Glucose DMD/40% F-10

extract_protocol:
[Isolation protocol] CD45-Sca1-CD31-CD11b-alpha7Integrin+CD34+ stem cells were isolated by FACS from hindlimb muscles of 8-12wk old BL6 female mice
Qiagen RNAeasy Micro Kit
NuGEN Ovation v2 cDNA amplification, Illumina RNASeq v2 Library construction

value: WT

value: hindlimb muscle

value: muscle stem cells

tag: protocol

value: cultured 48hr on 12kPA hydrogel


title: 48hr cultured MuSC - Run 2 (C2)


title: 48hr cultured MuSC - Run 2 (C1)


title: KM12C


title: ATAC-SEQ PBS

tag: age


title: J82

value: Urinary bladder

value: urinary bladder cancer cell line


title: hipsc corr hN - 3

value: Dopaminergic Neuron


title: IMR90

source_name: Normal fibroblast cells from lung

value: Lung

value: lung normal fibroblast cell line


title: Fresh MuSC - Run 1 (F3)

description: Freshly isolated A7/CD34+ stem cells from 8-12wk female BL6.

source_name: Fresh MuSC

value: fresh


title: Fresh MuSC - Run 2 (F4)

description: Freshly isolated A7/CD34+ stem cells from 8-12wk female . Samples run on Sequencing Run #2 with samples Cul-1-3


title: Fresh MuSC - Run 1 (F2)


title: Fresh MuSC - Run 1 (F1)


title: HT29

value: Colon

value: colon cancer cell line


title: HT1080

value: connective tissue

value: human fibrosarcoma cell line


title: HsS78T

value: Breast

value: breast cancer cell line


title: Hey_A8

value: Ovary

value: ovarian cancer cell line


title: Fresh MuSC - Run 2 (F5)

value: WT

value: hindlimb muscle


title: HepG2

value: Liver

value: liver cancer cell line


title: Isthmus-2

city: Tokyo

first: Yoku

last: Hayakawa

state: TOKYO

address: 7-3-1, Hongo, Bunkyo-ku, Clinical Research Center 4F, Room 425

institute: University of Tokyo

description: TCW-Mouse430_2-12972.mas5.chp Signal

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Mist1+Tomato+ cells in gastric corpus after Lgr5+ cell ablation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

extract_protocol: Ambion RNA extraction kit

tag: treatment

value: Lgr5+ cell ablation

value: stomach

value: Mist1+Tomato+ cells


title: Isthmus-1

description: TCW-Mouse430_2-12971.mas5.chp Signal


title: Isthmus-3

description: TCW-Mouse430_2-12973.mas5.chp Signal


title: 375

city: Honolulu

first: Christian

middle: Ka'ikekuponoaloha

last: Dye

state: HI

address: 641 Ilalo St. BSB 222K

department: Native Hawaiian Health

institute: University of Hawaii at Manoa

description:
genomic DNA from monocytes
insulin sensitive monocyte

hyb_protocol: bisulfite DNA was amplified, fragmented and hybridised to Illumina HumanMethylation 450K Beadchip following Illumina's standard protocol

scan_protocol: arrays were imaged using iScan SQ instrument (Illumina) following recommended settings

data_processing: RnBeads 0.99.10

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from monocytes using the Qiagen AllPrep DNA/RNA mini kit (ThermoScientific) following manufacturer's recommendations

tag: gender

value: female

tag: sample type

value: monocyte

tag: disease state

value: insulin sensitive

tag: condition

value: HIV seronegative


title: Parietal cell-3

description: TCW-Mouse430_2-12970.mas5.chp Signal

source_name: Gastric parietal cells

value: Parietal cells


title: Parietal cell-2

description: TCW-Mouse430_2-12969.mas5.chp Signal


title: PID 02 M1

description:
genomic DNA from classical monocytes (CD14++CD16-)
healthy control

source_name: PID 02 M1

value: male

value: healthy control


title: Parietal cell-1

description: TCW-Mouse430_2-12968.mas5.chp Signal


title: 294

description:
genomic DNA from monocytes
insulin resistant monocyte

value: insulin resistant


title: PID 02 M2

description:
genomic DNA from intermediate monocytes (CD14++CD16+)
healthy control

source_name: PID 02 M2


title: HCT15

value: Colon

tag: cell type

value: colon cancer cell line


title: Chief-3

description: TCW-Mouse430_2-12967.mas5.chp Signal

source_name: Mist1+Tomato+ cells in gastric corpus


title: L3 M1

source_name: L3 M1


title: Chief-2

description: TCW-Mouse430_2-12966.mas5.chp Signal


title: Chief-1

description: TCW-Mouse430_2-12965.mas5.chp Signal


title: 399


title: mHGG_EGFRvIII_3: EGFRvIII driven glioma; biological rep 3

city: Genoa

first: Paolo

last: Malatesta

address: Largo Rosanna Benzi 10

country: Italy

institute: IRCCS Ospedale Policlinico San Martino

description: Gene expression data from high-grade murine glioma cells

hyb_protocol: cDNA was hybridized at 45°C for 16 hours by using the affymetrix hybridization, wash and stain kit.

scan_protocol: Scanned using an Affymetrix GeneChip scanner following manufacturer's instructions on Affymetrix GeneChip Scanner 3000 7G

data_processing: Expression values were extracted by using the RMA function from the Bioconductor package affy 3.4.2 (Gautier et al. 2004) in R (R Core Team 2017; https://www.R-project.org/). RMA and further analysis were run on a larger dataset including rowdata from GSE9566; GSE37516; GSE58260

source_name: Primary cultured cells derived by dissociation of mouse glioma

label_protocol: 5ug of cDNA was fragmented and botin labelled by using the Encore® Biotin Module (NuGEN)

growth_protocol: Neural progenitor cells derived from E14 mouse embryos from the specified strain where in vitro transduced with retroviral vectors expressing DsRed and either PDGF-B or EGFRvIII and transplanted in brain parecyma of BALBc adult mice. The animals were sacrificed at the onset of glioma symptoms. Tumor masses were then dissociated and cultured

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. cDNA was obtained from 30 ng of RNA by using the Ovation® Pico WTA System V2 kit (NuGEN).

treatment_protocol: Gliomas were visualized under a fluorescence microscope thanks to the EGFP expression and dissected in HBSS medium. Tumor cells were dissociated with enzymatic digestion in Trypsin/EDTA and mechanical dissociation with a Pasteur pipette in 10% FBS and after centrifugation at 500xg for 5 minutes, the pellet was suspended in PBS supplemented with 1% FBS and 1.5mM EDTA and EGFP expressing cells were sorted with a FACSAria II cell sorter.

value: BALBc INK4a -/-

value: dsRed-positive glioma cells

tag: tumor stage

value: high-grade


title: 238


title: mHGG_EGFRvIII_2: EGFRvIII driven glioma; biological rep 2


title: L3 M2

source_name: L3 M2


title: 310


title: 401


title: PID237

value: HIV


title: L3 M3

description:
genomic DNA from non-classical monocytes (CD14-/lowCD16++)
healthy control

source_name: L3 M3


title: PID231


title: 393


title: 333


title: PID245


title: PID228


title: PID226


title: mHGG_EGFRvIII_4: EGFRvIII driven glioma; biological rep 4


title: mHGG_EGFRvIII_1: EGFRvIII driven glioma; biological rep 1


title: HCC827

source_name: cancer cell line

value: Lung

value: lung cancer cell line

tag: cell line


title: mHGG_PDGF_2: PDGF-B driven glioma; biological rep 2

value: BALBc


title: 293

value: female


title: HCC1937

value: Breast

value: breast cancer cell line


title: mHGG_PDGF_1: PDGF-B driven glioma; biological rep 1


title: HeLa

value: Cervix

value: cervix cancer cell line

value: HeLa


title: PID221

value: male

value: monocyte

value: insulin sensitive


title: PID 02 M3

source_name: PID 02 M3

value: healthy control


title: Control Pl_med: Control cells with plain medium

city: Hidaka

first: Akihiko

last: Okuda

state: Saitama

address: 1397-1 Yamane

department: Research Center for Genomic Medicine

institute: Saitama Medical University

description: Reference sample of SACCs with ES medium

hyb_protocol: Labelled samples were hybridized to the microarrays according to the manufacturer’s protocol with Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneArray Scanner 3000. Scanning was preformed as described elsewhere. (Irizarry et al, Nucleic Acids Res 31, e15, 2003)

data_processing: The data were background-subtracted and normalized using the Transcriptome Analysis Console Software (ThermoFisher).

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol. (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: One spleen tissue was divided into 6 pieces and each spleen piece was placed into a single well of 12 (or 24) well dish. Then, each spleen piece was provided with RPMI 1640 medium containing 5% fetal bovine serum (0.5 ml per well) and then placed in regular CO2 incubator. The medium was changed every 2 to 3 days. For isolating SACCs, the medium was replaced by StemMedium®, serum-free medium for mouse ESCs (ES medium; DS Pharma Biomedical, Japan) once initiation of colony formation was evident (approximately 7 to 14 days post initiation of culture).

extract_protocol: Total RNAs were prepared using RNeasy Kit from Qiagen.

value: spleen

tag: cell state

value: monolayered cells


title: Hacat

value: Epithelial keratinocyte

value: epithelial keratinocyte cell line

value: Hacat


title: SACCs Es_med: SACCs with ES medium

source_name: SACCs

value: compact colony


title: Control Pl_med_v2: Control cells with plain medium Ver.2

description: Reference sample of SACCs with plain medium


title: SNT15

city: New Orleans

first: Erik

last: Flemington

state: LA

address: 1430 Tulane Ave

institute: Tulane University

data_processing:
Gene expression levels were computed based on human (Ensembl v85) and EBV Akata (Genbank KC207813.1) transcriptomes.
Quantification was performed using Salmon (v. 0.8.2) run with default parameters.
Genome_build: GRCh38 + EBV Akata (Genbank KC207813.1)
Supplementary_files_format_and_content: RNA-seq counts (reads per gene and transcripts per million per gene)

source_name: SNT15 cells

extract_protocol: Total RNA was extracted from cultured cells with TRIzol reagent (Life Technologies, catalog no. 15596-018) according to the manufacturer’s protocol. Library preparations of polyadenylated RNAs were generated using the Illumina TruSeq stranded mRNA library preparation kit and 100 base single-end sequencing was performed using an Illumina HiSeq 2000 sequencer (University of Wisconsin Biotechnology Center).

value: extranodal NK/T-cell lymphoma (ENKTL)-derived cell line


title: SNK6

source_name: SNK6 cells


title: SNT16

source_name: SNT16 cells


title: SNK9

source_name: SNK9 cells


title: SNK10

source_name: SNK10 cells


title: PID213

value: HIV


title: B_plus_640.7_tube.33

city: Saint Louis

first: Bo

last: Zhang

state: MO

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine

data_processing:
The RNA-seq reads were aligned to the mm10 mouse genome (STAR version 2.4.2a). Gene counts were derived from the number of uniquely aligned unambiguous reads (Subread:featureCount, version 1.4.6) and annotated (GENCODE). Only non-redundant uniquely aligned reads were used to estimate the expression level of genes. All gene-level transcript counts were then normalized for library size (R/Bioconductor DEseq2).
Genome_build: mm10
Supplementary_files_format_and_content: gene level reads count table

source_name: cortical bone from tibia

extract_protocol:
Four hours after the last loading bout, right and left tibiae were stripped of all muscle tissue and flushed by centrifugation (10,000g x 2 min) at room temperature to remove bone marrow.  The flushed tibiae were then cut 2 mm from the articular surface and again at the distal TFJ to isolate the area of peak strain.  Tissue samples were flash-frozen in liquid nitrogen and stored at -80C°.  Frozen tibiae were pulverized in liquid nitrogen using a Mikro Dismembrator (Mikro-Dismembrator S; B. Braun Biotech International, Melsungen, Germany), resuspended in TRIzol (15596026; Invitrogen, USA), and stored at -80C°.  Total RNA was isolated using a Direct-zol kit per manufacturer instructions (R2072; Zymo Research, USA).  RNA concentration was determined using a Nanodrop (ND-2000; ThermoFisher, USA).  RIN values were used to determine RNA quality (Bioanalyzer 2100; Agilent Technologies, USA), and the average RIN score was 5.4.
RNA sequencing was performed on the Total RNAble platform (Cofactor Genomics, http://cofactorgenomics.com, St. Louis, MO, USA).  Briefly, species-specific rRNA-probes were hybridized to total RNA to remove nuclear-encoded and mitochondrial contaminating ribosomal RNA from the sample.  The resulting ribo-depleted RNA was then fragmented.  First-strand cDNA synthesis was performed using reverse transcriptase and random primers in the presence of Actinomycin D, followed by second-strand cDNA synthesis with DNA polymerase I and RNase H.  Double-stranded cDNA was end-repaired and A-tailed for subsequent adaptor ligation.  Indexed adaptors were ligated to the A-tailed c-DNA.  Enrichment by PCR was performed to generate the final cDNA sequencing library.  Libraries were sequenced as single-end 75 base pair reads on an Illumina NextSeq500 following the manufacturer’s protocols.

treatment_protocol: Unilateral axial tibial compression was performed on the right tibiae of 16-week-old, male animals.  The left tibia served as a non-loaded control.   A force of 8.7N or 10.0N was used to generate a -2000 microstrain deformation in Ctrl and NT3-Cre+ animals, respectively.  Mice were subjected to 1 loading bout per day   (1200 cycles, 4 Hz triangle waveform with 0.1 s rest-insertion after each cycle) for a total of 9 days (Tuesday-Friday, week 1; Monday-Friday, week 2) using an Electropulse 1000 materials testing apparatus (Instron, Norwood, MA, USA).  Mice were anesthetized with isoflurane/oxygen before the procedure and their level of sedation monitored by hind paw reflex.  After loading, mice received either buprenorphine (0.1 mg/kg, SQ) or buprenorphine SR (1.0 mg/kg, SQ) for pain control and were monitored until they could ambulate normally.

value: cortical bone from tibia

tag: Sex

tag: genotype

tag: loading condition

value: loaded R side

tag: group designation

value: B plus


title: B_plus_637.1_tube.29.637.1.R.tibia

tag: tissue


title: B_plus_608.1_tube.21.608.1.R.tibia


title: DMS53

value: Lung

value: lung cancer cell line


title: ES2

value: Ovary

value: ovarian cancer cell line


title: DLD1

value: Colon

value: colon cancer cell line


title: Du145

value: Prostate

value: prostate cancer cell line


title: PID155

value: male

value: monocyte

value: insulin sensitive


title: B_minus_640.7_tube.34

value: non-loaded L side

value: B minus


title: B_minus_637.1_tube.30.637.1.L.tibia


title: Capan1

value: Pancreas

value: pancreas cancer cell line


title: A_plus_586.7_tube.15.586.7.R.tibia

value: cortical bone from tibia

value: Ctrl

value: loaded R side

value: A plus


title: B_plus_526.3_tube.11.526.3.R.tibia

value: B plus


title: B_minus_526.3_tube.12.526.3.L.tibia


title: PID125

value: HIV


title: A_plus_524.1_tube.9.524.1.R.tibia


title: A_plus_510.3_tube.3.510.3.R.tibia


title: B_minus_608.1_tube.22.608.1.L.tibia


title: CAOV3

value: Ovary

value: ovarian cancer cell line


title: A_minus_586.7_tube.16.586.7.L.tibia

value: A minus


title: A_plus_509.2_tube.1.509.2.R.tibia


title: Calu1

value: Lung

value: lung cancer cell line


title: Calu3


title: PID023

value: male

value: monocyte


title: Caco2

value: Colon

value: colon cancer cell line


title: A_minus_524.1_tube.10.524.1.L.tibia

value: non-loaded L side


title: PID014

value: insulin sensitive


title: PID012


title: A_minus_509.2_tube.2.509.2.L.tibia

value: cortical bone from tibia


title: A_minus_510.3_tube.4.510.3.L.tibia

value: Ctrl


title: BxPC3

value: Pancreas

value: pancreas cancer cell line


title: BT549

value: Breast

value: breast cancer cell line


title: AGS

value: Stomach

value: stomach cancer cell line

value: AGS


title: A549

value: Lung


title: PID104

value: HIV


title: TLR5 FliC 4

city: Gold Coast

first: Glen

middle: C

last: Ulett

state: QLD

address: Parklands Drive

department: School of Medical Science

country: Australia

institute: Griffith University

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used for basecalling
STAR version 2.5.3 was used to align the raw reads to the reference genome using parameters --ouReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
HTSeq-count version 0.9.1 was used to create raw counts from aligned STAR file using parameters -m union -r pos -t exon -i gene_id -a 10 -s no -f bam
DESeq2 was used to normalize the counts and identify differentially expressed genes.
Genome_build: Gencode GRCm38 p4 Release M11
Supplementary_files_format_and_content: tab delimited Excel file containing raw count values for each gene for each sample

growth_protocol: FliC of CFT073delta4 or CFT073delta4deltaFliC (for Control) UPEC was prepared in PBS

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions
We used the Illumina NextSeq 500 and the latest versions of sequencing reagents and flow cells. Total RNA was subjected to 2 rounds of poly(A)+ selection and converted to cDNA. We used TruSeq library generation kits, as per the manufacturer’s instructions (Illumina, San Diego, California). Library construction consisted of random fragmentation of the poly(A) mRNA, followed by cDNA production using random primers. The ends of the cDNA were repaired and A-tailed, and adaptors were ligated for indexing (with up to 12 different barcodes per lane) during the sequencing runs. The cDNA libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit (Kapa Biosystems, Woburn, Massachusetts) prior to cluster generation. Clusters were generated to yield approximately 725K–825K clusters/mm2. Cluster density and quality was determined during the run after the first base addition parameters were assessed. We ran paired-end 2 × 75–bp sequencing runs to align the cDNA sequences to the reference genome

treatment_protocol: Mice were catheterized using a sterile Teflon catheter and 50 microlitres of PBS containing 30 micrograms of FliC was instilled transurethrally into the bladder (Controls received 50 microlitres of carrier). Whole bladders collected at 2h following challenge

tag: strain/genotype

value: TLR5-deficient B6.129S1-Tlr5tm1Flv/J

value: FliC-treated

value: bladder


title: TLR5 FliC 5


title: PID055

value: male

value: monocyte


title: TLR5 FliC 3


title: A431

value: Skin

value: skin cancer cell line


title: PID149

value: insulin sensitive


title: TLR5 FliC 2


title: TLR5 Ctrl 5

value: control


title: PID094


title: A2780

value: Ovary

value: ovarian cancer cell line


title: TLR5 FliC 1