title: FFA3

city: Lincoln

first: Matthew

last: Moran

state: NE

address: 1901 Vine St.

department: Biochemistry

institute: University of Nebraska-Lincoln

data_processing:
Reads were trimmed of adaptor sequences by Flexbar v. 2.4, and then aligned to the GRCh38 Ensembl genome by Tophat2 2.0.1 together with Bowtie v. 1. Reads that did not map to the transcriptome were mapped to the genome.
Cufflinks 2.1.1 was used to determine transcripts and Cuffdiff v. 2.1.1 was used to determine FPKM values.
edgeR was used for differential expression analysis, using the easyRNAseq R package to generate counts.
Genome_build: human Ensembl Genome build 38
Supplementary_files_format_and_content: The format of processed_data_full.csv is a csv file containing CPM, logCPM, FPKM, gene name, log2 Fold Change from EdgeR, pValue, FDR, Ensembl biotype and Ensembl gene and transcript IDs.

source_name: HUVEC treated with palmitic acid/BSA

growth_protocol: HUVECs were grown in Lonza EGM-2 Media (Cat. No. CC-3162) in a 37C incubator, 5% CO2.

extract_protocol:
HUVECs were lysed and RNA extracted using TRIzol Reagent (Thermo Fisher).
RNA was ribodepleted and the library was constructed with Standard Construction and run on Illumina HiSeq 2500 (Beckman Coulter Genomics, California, USA).

treatment_protocol: HUVECs were treated with palmitic acid conjugated to fatty acid free BSA in a 3:1 molar ratio or BSA as a control. Treatment was continued for 8 hours and then RNA was harvested.

value: Human Umbilical Vein Endothelial Cells


title: M_36

status: Public on Dec 20 2019

type: SRA

city: Kunming

first: Zunxi

last: Huang

state: Yunnan

address: 768 Ju Xian Street

country: China

institute: Yunnan Normal University

library_source: transcriptomic

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GS115 whole genome using Hisat2 v2.0.5
Expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were calculated using a protocol from Trapnell, Cole, et al., 2010.The effect of sequencing depth and gene length on fragments count was also considered.
Genome_build: GS115
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

molecule: total RNA

organism: Komagataella phaffii

source_name: Fermentation mixture

growth_protocol: High-cell-density fed-batch cultivation encompassing four stages, namely, bench-scale batch fermentation, glycerol feed, GM phase, and methanol induction phases is used for Pichia pastoris to analysis the synthesis of recombinant proteins and investigating responses to various carbon sources

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Komagataella phaffii GS118

tag: fermentation stage

value: Methanol growth at 36 h


title: Paraffin embedded tissue of ESCC patient 17

type: RNA

city: Shantou

first: Yang

last: Chen

address: Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou

institute: Shantou University Medical College

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-017T

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings.

label: biotin

organism: Homo sapiens

source_name: Paraffin embedded tissue of ESCC patients

label_protocol: Total RNA were amplified, labeled and purified by using Ovation FFPE WTA System (Cat#3403， NuGEN, San Carlos, CA, US) and FL-Ovation™ cDNA Biotin Module V2(Cat#4200，NuGEN, San Carlos, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

extract_protocol: Total RNA was extracted and purified using RecoverAllTM  Total Nucleic Acid Isolation (Cat#AM1975, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

tag: patient diagnosis

value: Esophageal squamous cell carcinoma (ESCC)

tag: tissue

value: Esophagus


title: FFA2

country: USA

tag: cell type


title: Myofiber MyHC-1_8(S10)

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description: Gene expression of single mouse myofiber. Biological replicates of the same myofiber type were numbered from 1 to 10 and marked with the muscle of origin (S for soleus, and E for EDL) and the number of the animal.

hyb_protocol: 800 ng of labeled cDNA were mixed with 5 µl of 10X Blocking Agent (Agilent Technologies) and water to a final volume of 25 µl. Samples were denatured at 95°C for 2 min. and added to 25 µl of 2X GEx Hybridization Buffer HI-RPM (Agilent Technologies). 40 µl of mix was dispensed onto one array of the SurePrint G3 Mouse Gene Expression 8x60K microarray. Slides were loaded into the Agilent SureHyb chambers and hybridization was performed in a hybridization oven at 65°C for 17 hours with 10 rpm rotation. Finally, slides were washed using Wash Buffer Kit (Agilent Technologies) and dried at room temperature.

scan_protocol: Microarrays were scanned using the Agilent Technologies Scanner G2505C US22502723 (ChipScan software version A.8.5.1), scan region 61 x 21.6 mm, scan resolution 3 micron single pass, Green PTM 100%, no extended dynamic range (NO XDR).

data_processing: Data was extracted from the scanned image using the Agilent Feature Extraction Software version 10.7.3.1 (protocol GE1_107_Sep09). Quantile inter-arrays normalization was performed with the Expander software (Bioinformatics 2003; 19:1787-99) on the gProcessedSignal column of the result table and normalized data is reported in the VALUE column. Only characterized lincRNAs (with the “accession string” field of platform defined with a symbol) was used in the normalization process. The other lincRNAs (with the “accession string” field of platform defined with the chromosomal location) was not used in the normalization process and marked as “null”. Probes with Found or Well Above Background value of zero were disregarded and labeled as “null”. Mean values were calculated for multiple probes with the same Agilent Probe ID.

organism: Mus musculus

source_name: Individual pure type 1 myofiber from soleus muscle.

label_protocol: RNA was exponentially amplified using the TransPlex WholeTranscriptome Amplification 2 Kit (Sigma-Aldrich) in accordance with the manufacturer’s instructions, using 18 cycles of amplification. Amplification product was purified with the GenElute PCR Clean-up columns (Sigma-Aldrich). Resulting cDNA was quantified with Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific). 2 µg of amplified-purified cDNA were labeled using the Genomic DNA Enzymatic Labeling Kit (Agilent Technologies), as suggested by manufacturer, and purified using the Amicon 30kDa filters (Millipore). On average, cDNA yield was about 4 µg and the specific activity of 30 pmol Cy3 per µg cDNA.

growth_protocol: CD1 male mice were housed in a normal environment provided with ad libitum food and water and were killed by rapid cervical dislocation to minimize suffering.

extract_protocol: A single myofiber was lysed in 250 µl of TRIzol Reagent (Thermo Fisher Scientific) following the manufacturer’s instructions. After phases separation the upper aqueous phase containing RNA was added with 70% ethanol before column purification with RNeasy Micro Kit (Qiagen). Total RNA quality was monitored using the RNA Pico LabChip on a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Muscles from both hind limbs of the same mouse were immediately removed by microdissection, taking care to handle them only by their tendons to minimize mechanical damage to the fibers. Digestion proceeded for 40 - 45 min. at 37°C in 1 ml high-glucose DMEM (Thermo Fisher Scientific) containing 10 mg type I collagenase (220 U mg-1, Sigma-Aldrich). The collagenase-treated muscles were sequentially rinsed for 2 min. in 3 ml of DMEM, 3 ml DMEM supplemented with 10% fetal bovine serum (FBS) and 3 ml of DMEM and finally transferred into 50 mm x 18 mm well containing 3 ml of DMEM with 10% FBS. Single myofibers were liberated by gentle physical trituration with a wide-mouth plastic Pasteur pipette (about 4 mm diameter). Quickly, intact, not contracted, and well-isolated fibers were picked under stereomicroscope and washed first in DMEM and then in phosphate buffered saline. About one-third of each fiber was clipped and placed in Laemmli buffer for fiber typing by SDS-PAGE; the remaining part of the fiber was dissolved TRIzol Reagent (Thermo Fisher Scientific) for RNA extraction. All samples were collected within 45 min. from the last trituration step.

tag: age

value: 3 months

tag: gender

value: Male

value: Soleus muscle

tag: myofiber type

value: Individual pure type 1 myofiber


title: iTreg input

city: London

first: Richard

last: Jenner

address: 72 Huntley Street

department: Cancer Biology

country: United Kingdom

institute: UCL Cancer Institute

library_source: genomic

data_processing:
Basecalls performed using CASAVA
Reads were filtered to remove adapters using fastq-mcf and for quality using seqkt
Reads were then aligned to the mouse genome (mm9) with Bowtie2 (default settings)
Regions of significant enrichment (10^-7) were identified using MACS version 1.4 (Zhang et al., 2008) using input as background, with the setting –keep-dup=1
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing peaks derived from analyses

molecule: genomic DNA

source_name: iTreg

growth_protocol: CD4+ T cells from spleens and lymph nodes of 4- to 10-wk-old Balb/c mice were purified by CD4 positive selection (Miltenyi Biotec) followed by sorting of naive CD4+CD25-CD62LhighCD44low cells using a FACSAria II (BD Biosciences).

extract_protocol:
Cells were crosslinked by the addition of one-tenth volume of fresh 11% formaldehyde solution for 20 minutes at room temperature before the reaction was quenched by addition of glycine. Cells were rinsed twice with 1xPBS and flash frozen in liquid nitrogen. Cells were lysed with non-ionic detergent, nuclei washed and then lysed with ionic detergent.  Cells were sonicated on ice to solubilize and shear crosslinked DNA (24W for 10 x 30 second pulses using a Misonix Sonicator 3000). The resulting whole cell extract was cleared by centrifugation and then incubated overnight at 4°C with 100 µl of Dynal Protein G magnetic beads that had been pre-incubated with 5 µg each of 2 Foxp3 antibodies, Santa Cruz S-31738 and eBioscience FJK-16. Beads were washed 6 times with RIPA buffer and 1 time with TE containing 50 mM NaCl. Bound complexes were eluted from the beads by heating at 65°C with occasional vortexing and crosslinks then reversed in IP and input DNA by overnight incubation at 65°C. IP and input DNA were then purified by treatment with RNase A, proteinase K and phenol:chloroform extraction followed by ethanol precipitation.
Libraries were constructed from ChIP and input DNA by standard Illumina protocols, except that DNA in the range 150-350bp was gel-purified after PCR-amplification. The libraries were quantified using a Qubit and Agilent bioanalyzer, pooled and subjected to 35 or 50 bp single-end read sequencing with an Illumina GAIIx or HiSeq 2000 sequencer

treatment_protocol: Cells were activated for 72 hours by plate-bound anti-CD3 and anti-CD28 (both 10 ug/ml; clones 145-2C11 and 37.51, respectively; Bio X Cell). iTreg cells were generated by culturing in recombinant human TGF-β1 (33 ng/ml) and IL-2 (20 ng/ml; R & D Systems) for 7 days. Th1 cells were polarized with 20 ng/ml IL-2 (Biolegend) and polarized with 20 ng/ml IL-12 (eBioscience) and 10 μg/ml anti-IL-4 (BioXCell).

value: iTreg

value: Balb/c


title: Myofiber MyHC-1_2(S4)


title: Paraffin embedded tissue of ESCC patient 18

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-018T


title: Myofiber MyHC-1_1(S2)


title: FFA1


title: Paraffin embedded tissue of ESCC patient 13

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-013T


title: iTreg Foxp3 ChIP

tag: chip antibody

value: anti-Foxp3 (Santa Cruz S-31738 and eBioscience FJK-16)


title: Paraffin embedded tissue of ESCC patient 14

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-014T


title: CRC ≥ 70 years. Sample 2

type: genomic

city: Salamanca

first: Juan Luis

last: Garcia

state: Salamanca

address: Campus Miguel de Unamuno

country: Spain

institute: Centro de Investigación del Cáncer IBMCC-CIC

hyb_protocol: Hybridization was carried out in a Roche NimbleGen Hybridisation Chamber (Roche NimbleGen, Inc.) for 48 h.

scan_protocol: Slides were washed and scanned using a NimbleGenMS 200 Microarray Scanner (Roche NimbleGen, Inc.).

data_processing: Array image ﬁles produced by the MS 200 Data Collection Software were imported into DEVA v1.2.1(Roche NimbleGen Inc.) for analysis. In addition,segmentation analysis was performed in all cases byusing circular binary segmentation (CBS) available in waviCGH software (http://wavi.bioinfo.cnio.es/).

source_name: Rectum

label_protocol: One microgram of genomic DNA(gDNA) from each test and reference sample(Human Genomic DNA [Male G1471/FemaleG1521] from Promega Corporation, Madison, WI) was labeled using the NimbleGen Dual-C olor DNALabeling Kit.

extract_protocol: DNA was extracted using proteinase K digestion, phenol/chloroform extraction, Phase Lock Gel Light (Eppendorf AG, Hamburg, Germany), and ethanol precipitation.

tag: Sex

value: Female

tag: molecular classification

value: MSS y CIMP-High

tag: sample type

value: reference


title: Paraffin embedded tissue of ESCC patient 12

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-012T


title: Myofiber MyHC-2A_4(S5)

source_name: Individual pure type 2A myofiber from soleus muscle.

value: Individual pure type 2A myofiber


title: M_12

value: Komagataella phaffii GS116

value: Methanol growth at 12 h


title: Paraffin embedded tissue of ESCC patient 11

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-011T


title: BSA3

source_name: HUVEC treated with BSA only

value: Human Umbilical Vein Endothelial Cells


title: S3: Buffalo3

city: nanning

first: kongwei

last: huang

address: 100, Daxue Road Nanning,Guangxi P.R.CHINA

institute: Guangxi University

data_processing:
From the raw FASTQ files, adapter was removed using Trim Galore and filtered data were aligned to the Bos taurus reference genome (bosTau7) from UCSC (http://genome.ucsc.edu/) with TopHat2 (version 2.0.14).
Select transcripts with length ≥ 200 bp and Exon ≥ 2; calculate reads ≥ 3 by cufflinks.
Coding potential screening: CPC analysis, CNCI analysis, pfam protein domain analysis and phyloCSF analysis take the intersection to screen for unencoding lncRNA.
Then screening lncRNA-mRNA relationship pairs to construct lncRNA-mRNA co-expression network.
LncRNAs were normalized as the number of uniquely mapped fragments per kilobase of exon per million fragments mapped (FPKM).
Supplementary_files_format_and_content: Additional file 1: Primers designed for quantitative real time PCR.
Supplementary_files_format_and_content: Additional file 2: Four predictive software(CNCI,CPAT,CPC,Pfam) prediction results to plot the result list file of Venn diagram in bovine muscle tissues.
Supplementary_files_format_and_content: Additional file 3: All sample lncRNA expression distribution box line graph
Supplementary_files_format_and_content: Additional file 4: LncRNA cis target gene prediction result in skeletal muscle, using LncTar soft the prediction results based on the principle of sequence complementation.
Supplementary_files_format_and_content: Additional file 5: LncRNA trans target gene prediction result file, using LncTar soft the prediction results based on the principle of sequence complementation.
Supplementary_files_format_and_content: Additional file 6: Comparative analysis of lncRNA and mRNA expression.
Supplementary_files_format_and_content: Additional file 7: Differential expression lncRNA target gene protein interaction on the list of details, based on the STRING database

organism: Bubalus kerabau

source_name: adult longissimus muscle

growth_protocol: Six longissimus muscle samples from Guangxi native cattles and swamp buffalo ( adult, 12 M old) were collected from nanning meat factory abattoir, a local slaughterhouse of Nanning, P.R. China. Tissue samples were snap-frozen in liquid nitrogen and stored at –80°C freezer until use.

extract_protocol:
Total RNA was assessed by electrophoresis on a denaturing agarose gel and quantified by NanoDrop spectrophotometer (NanoDrop, USA) and Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA). The total RNA samples (3 mg) were treated with the epicentre Ribo-ZeroTM Kit to remove rRNA before constructing the RNA-seq libraries. For RNase R treatment, ribosome-depleted RNA was incubated for 15 min at 37°C with 5 units μg−1 of RNase R (Epicentre Technologies, Madison, WI).
Then the rRNA depleted RNA samples or circRNAs samples were fragmented and used to synthesize first- and second-strand complementary DNA (cDNA) with random hexamer primers, dNTPs and DNA Polymerase I. The cDNA fragments were cleaned and concentrated using AMPure XP beads, then the ends were repaired and modified with T4 DNA polymerase Klenow DNA polymerase to add A and adapter at the 3’ end of the DNA fragments. The ligated cDNA products were purified with AMPure XP beads and treated with uracil DNA glycosylase to remove the second-strand cDNA.
Purified first-strand cDNA was subjected to PCR amplification, and the libraries were quality controlled with an Agilent 2100 Bioanalyzer and sequenced by HiSeq 2500 (Illumina, San Diego, CA) on a 150 bp paired-end (PE) run.

value: longissimus muscle

tag: developmental stage

value: Adult

value: 12 M old

tag: molecule subtype

value: lncRNA


title: S2: Buffalo2


title: GM_2

value: Komagataella phaffii GS115

value: Glycerol and methanol mixture feed culture at 2 h


title: BSA2


title: Paraffin embedded tissue of ESCC patient 10

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-010T

value: Esophageal squamous cell carcinoma (ESCC)

value: Esophagus


title: BSA1


title: G_3

value: Glycerol growth at 3 h


title: M_24

value: Komagataella phaffii GS117

value: Methanol growth at 24 h


title: S1: Buffalo1


title: Human_Cerebellum_H3K27ac_2

city: Utrecht

first: Menno

middle: P

last: Creyghton

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
ChIP-seq: Illumina sequencing reads were aligned using bowtie version 1.1.2 ((http://bowtie-bio.sourceforge.net) excluding reads with more than 1 mismatch (seed length of 36 base pairs (bp)) or with multiple alignment. Duplicate reads were discarded using Samtools version 1.3.1. Peak-calling was done using MACS2 version 2.1.1.20160309 (pvalue < 10-5, extsize 300, local lambda 100,000). Reads in peaks were counted using Bedtools version 2.26.
RNA-seq:  Sequencing reads were aligned using HISAT2 version 2.0.5. Reads that mapped to multiple locations and duplicate reads were removed using Samtools version 1.3.1. Reads in genes were counted using the featureCount function of the Rsubread package in R.  The GTF file of Marmoset genes was obtained here: ftp://ftp.ensembl.org/pub/release-91/gtf/callithrix_jacchus.
Genome_build: Homo sapiens: hg38, Pan troglodytes: panTro5, Macaca mulatta: rheMac8, Callithrix jacchus: calJac3
Supplementary_files_format_and_content: ChIP-seq peaks called by MACS2 are in _peaks.narrowPeak; H3K27ac bigwig files are in .bw; RNA-seq count values are in _RNAseq.txt;

source_name: Human Cerebellum

extract_protocol: TruSeq DNA sample preparation kit (Illumina)

value: anti-H3K27ac (Abcam, catalog#:ab4729)

value: Cerebellum


title: tae1 expressed A. baylyi vs E. coli-replicate 3

city: Basel

first: Marek

last: Basler

address: Klingelbergstr. 50/70

country: Switzerland

institute: Biozentrum, University of Basel

description:
A. baylyi & E. coli
PR353vsPR17_F_III

data_processing:
SPARTA pipeline (Johnson et al., BMC Bioinformatics, 2016)
using Bowtie (Langmead et al., Genome Biology, 2009) to remove any sequences mapping to E. coli for the analysis of the ADP1 transcriptome
statistical analysis of the data and generation of the processed data file were performed using edgeR (Robinson et al., Bioinformatics, 2010)
Genome_build: GCA_000046845.1
Supplementary_files_format_and_content: CPM values for each Sample as well as Log2FC, P value and FDR

organism:
Escherichia coli
Acinetobacter baylyi

source_name: tae1 expressed A. baylyi vs E. coli

growth_protocol: The predator (tae1-single effector strain or ΔtssM in the vipA-sfGFP clpV-mCherry background) and prey strains (E. coli MG1655) were diluted from overnight cultures and regrown to OD600 of approximately 1 at 30 °C without antibiotics.

extract_protocol:
The filters were directly transferred into 650 µL of TRI Reagent (Sigma). The RNA was then extracted using the Zyppy Direct-zol Mini Plus Kit (Zymo).
Illumina TruSeq Stranded mRNA Library Kit after rRNA depletion.

treatment_protocol: Cells from these cultures were then concentrated to an OD600 of 10 and mixed in a 1:1 ratio. 100 µl of the mixtures were spotted on hydrophilic Omnipore PTFE 0.45 µm filters and the competition was incubated for 10-30 min at 30 °C.

tag: genotype

value: rpsL-K88R vipA-sfGFP clpV-mCherry2 {delta}ACIAD0053 {delta}ACIAD1790 {delta}ACIAD3114 {delta}ACIAD3425


title: B_10

value: Bench-scale batch growth fermentation at 10 h


title: tae1 expressed A. baylyi vs E. coli-replicate 2

description:
A. baylyi & E. coli
PR353vsPR17_F_II


title: DMSO-control-2

city: Kannapolis

first: Robert

last: Reid

state: NC

address: 150 Research Campus Drive, Suite 3333

department: Bioinformatics and Genomics

institute: UNC Charlotte

data_processing:
Bowtie2 Alignment
Parameters: -p 10 -q --no-unal -k 20
Version 2.10
DESeq2
default
DE_genes.csv
Genome_build: ASSEMBLY ACCESSION: GCF_000002235.5
name: sea urchin Strongylocentrotus purpuratus (TAXID: 7668)
Supplementary_files_format_and_content: counts

organism: Ophioderma brevispina

source_name: arm tissue at the level of the 15th segment (counting from the disk)

growth_protocol: Adult individuals of the brittle star Ophioderma brevispina (Say, 1825) were purchased from the Marine Biological Laboratory (Woods Hole, MA) and were allowed to acclimate overnight in aerated sea water

extract_protocol:
The tissue samples for RNA extraction included the most distal segment of the stump and entire outgrowth (regenerate). The samples from three arms of each individual were pooled together and quickly homogenized in 500 μl of ice-cold TRI reagent (Sigma-Adlrich, 93289) using a disposable Micro Tissue Homogenizer (Kimble, K7496250030). The homogenized samples were briefly vortexed, additional 500 μl of the TRI reagent were added to each tube, and the subsequent steps of RNA purification were performed as directed by the manufac- turer’s protocol.
Illumina HiSeq 2000/2500 platform. The libraries were barcoded, pooled and sequenced in a single flow cell in the Rapid Mode (2 × 100 bp).

treatment_protocol: DAPT reagent, N-[N-(3,5-Difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl es- ter, was purchased from Sigma-Aldrich (catalog number D5942) and dissolved in DMSO (Dimethyl sulfoxide) to make a 20 mM stock solution.

tag: chemical treatment

value: DMSO (Dimethyl sulfoxide)


title: DMSO-control-3


title: tae1 expressed A. baylyi vs E. coli-replicate 1

description:
A. baylyi & E. coli
PR353vsPR17_F_I


title: DMSO-control-1


title: EV3 RNAseq

city: Helsinki

first: pirkko

middle: maria

last: mattila

address: Tukholmankatu 8

department: FIMM TC

country: Finland

institute: University of Helsinki

description:
EV3
Poly-A RNA
processed data file: EV.xlsx

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. STAR –aligner was used to map the trimmed reads to GRCh37r72 version of human genome. Only reads uniquely mapped to genome and not mapped to ribosomal RNA -species were utilized for HTseq –tool to count reads mapping to genes.
Estimates for transcript abundances, reported as transcripts per million (TPM), were produced by Kallisto algorithm and further analysed by Sleuth software to calculate and visualize the differences between conditions.
Genome_build: GRCh37r72
Supplementary_files_format_and_content: *.xlsx: Excel files include TPM values and HT-seq counts for each sample.

source_name: Red blood cell extracellular vesicles

extract_protocol:
Total RNA was isolated by Qiagen miRNeasy micro kit and RNAseq sample preparation was performed by using Clontech SmartSeqv4 kit with 10 ng of starting material.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Red blood cell extracellular vesicles


title: EV2 RNAseq

description:
EV2
Poly-A RNA
processed data file: EV.xlsx


title: EV4 RNAseq

description:
EV4
Poly-A RNA
processed data file: EV.xlsx


title: T6SS- A. baylyi vs E. coli-replicate 3

description:
A. baylyi & E. coli
DH044vsPR17_F_III

source_name: T6SS- A. baylyi vs E. coli


title: EV1 RNAseq

description:
EV1
Poly-A RNA
processed data file: EV.xlsx


title: Paraffin embedded tissue of ESCC patient 6

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-006T


title: T6SS- A. baylyi vs E. coli-replicate 2

description:
A. baylyi & E. coli
DH044vsPR17_F_II


title: Paraffin embedded tissue of ESCC patient 7

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-007T


title: Paraffin embedded tissue of ESCC patient 8

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-008T


title: DAPT-treated-2

value: DAPT reagent, N-[N-(3,5-Difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester


title: Paraffin embedded tissue of ESCC patient 27

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-027T


title: Paraffin embedded tissue of ESCC patient 9

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-009T


title: DAPT-treated-3


title: Paraffin embedded tissue of ESCC patient 5

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-005T


title: RBC4 RNAseq

description:
RBC4
Poly-A RNA
processed data file: RBC.xlsx

source_name: Red blood cells

value: Red blood cells


title: T6SS- A. baylyi vs E. coli-replicate 1

description:
A. baylyi & E. coli
DH044vsPR17_F_I


title: Paraffin embedded tissue of ESCC patient 4

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-004T


title: DAPT-treated-1


title: RBC3 RNAseq

description:
RBC3
Poly-A RNA
processed data file: RBC.xlsx


title: mixed monocytes (U937 cell line) and macrophages rep2

city: Boston

first: Nikolai

last: Slavov

state: MA

address: 360 Huntington Avenue

institute: Northeastern University

data_processing:
Demultiplexing and count matrix estimation was carried out using CellRanger software.
Upon QC and manual inspection, the cells containing less than 1e4 UMI barcodes were determined to be amplifying empty or background droplets and discarded.
The scRNA-seq datasets were pre-processed using pagoda2 package to normalize for cell size and gene variance distributions.
Joint alignment of proteome and scRNA-seq data was performed using Conos package29, using CCA space.
Supplementary_files_format_and_content: txt, gene expression matrix, genes x cells

source_name: mixed monocytes and macrophages

growth_protocol: U-937 (monocytes) cells were grown as suspension cultures in RPMI medium (HyClone 16777-145) supplemented with 10% fetal bovine serum (FBS, Millipore Sigma F4135) and 1% penicillin-streptomycin (pen/strep, ThermoFisher 15140122). Cells were passaged when a density of 106 cells/ml was reached, approximately every two days. Monocytes were differentiated to macrophage-like cells by first adding phorbol 12-myristate 13-acetate (PMA) to the culture medium at final concentration of 5nM for 24 hours. Then, these newly-adherent cells were washed with fresh PMA-free medium and allowed to recover in PMA-free medium for an additional 48 hours before harvest. Mock-treated U-937 cells were passaged with fresh PMA-free media at 24 hours and harvested along with the treated cells at 72 hours.

extract_protocol:
10x Genomics Chromium platform and the Single Cell 3’ Library & Gel Bead Kit (v2). Two biological replicates of the cell suspension (stock concentration: 1200 cells/μl) were loaded into independent lanes of the device. An average number of about 10,000 cells/lane were recovered.
Following the library preparation and sample QC by Agilent BioAnalyzer High Sensitivity chip, the two libraries were pooled together, quantified by KAPA Library Quantification kit and sequenced using the Illumina Novaseq 6000 system (Nova S1 100 flow cell) with the following run parameters: Read1: 26 cycles, i7 index: 8 cycles, Read2: 93 cycles.
10x Genomics Chromium platform

value: monocyte and macrophage


title: Paraffin embedded tissue of ESCC patient 3

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-003T


title: PA23_Erf_chlo_3

city: Zurich

first: Julian

last: Trouillon

address: Otto-Stern-Weg 3

department: Institute of Molecular Systems Biology

institute: ETH Zurich

description:
adaptor-ligated sheared genomic DNA
PA23_E_chlo_processed.xlsx

data_processing:
Library strategy: DAP-seq
Read trimming using Trimmomatic
Alignment using Bowtie2
Peak calling using MACS2
closest features called with BEDtools
Genome_build: IHMA879472, PAO1b, PA23, CHA0, KT2440
Supplementary_files_format_and_content: excel table, MACS2 analysis results with closest features

organism: Pseudomonas chlororaphis

source_name: purified genomic DNA from liquid cultures

extract_protocol:
Purified proteins bound to magnetic beads were incubated with adaptor-ligated sheared genomic DNA. After washes and isolation of bead-protein-DNA complexes, the bound DNA regions were eluted by heating and then used for library preparation.
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: erfa origin

value: P. chlororaphis


title: RBC2 RNAseq

description:
RBC2
Poly-A RNA
processed data file: RBC.xlsx


title: Marmoset_PrefrontalCortex_NeuNpositive_ATAC_2

data_processing:
ChIP-seq: Illumina sequencing reads were aligned using bowtie version 1.1.2 ((http://bowtie-bio.sourceforge.net) excluding reads with more than 1 mismatch (seed length of 36 base pairs (bp)) or with multiple alignment. Duplicate reads were discarded using Samtools version 1.3.1. Peak-calling was done using MACS2 version 2.1.1.20160309 (pvalue < 10-5, extsize 300, local lambda 100,000). Reads in peaks were counted using Bedtools version 2.26.
ATAC-seq: Illumina sequencing reads were trimmed to remove Nextera adapters using cutadapt (1.13). Reads were mapped using bowtie version 1.1.2 (http://bowtie-bio.sourceforge.net) excluding reads with more than 1 mismatch (seed length 36 base pairs) or with multiple aligment. Duplicate reads were discarded using Samtools verions 1.3.1. Peak-calling was done using MACS2 version 2.1.1.20160309 (pvalue < 10-5, extsize 300, local lambda 100,000). Reads in peaks were counted using Bedtools version 2.26
Genome_build: Homo sapiens: hg38, Pan troglodytes: panTro5, Macaca mulatta: rheMac8, Callithrix jacchus: calJac3
Supplementary_files_format_and_content: ChIP-seq and ATAC-seq peaks called by MACS2 are in _peaks.narrowPeak; H3K27ac and ATAC bigwig files are in .bw

organism: Callithrix jacchus

source_name: Marmoset Prefrontal Cortex

extract_protocol: NEBNext High-Fidelity PCR (NEB)

value: Marmoset Prefrontal Cortex


title: Paraffin embedded tissue of ESCC patient 29

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-029T


title: PA23_Erf_chlo_2

tag: strain


title: CHA0_Erf_I_3

description:
adaptor-ligated sheared genomic DNA
CHA0_processed.xlsx

organism: Pseudomonas protegens

value: P. aeruginosa


title: PA23_Erf_chlo_1


title: RBC1 RNAseq

description:
RBC1
Poly-A RNA
processed data file: RBC.xlsx


title: Paraffin embedded tissue of ESCC patient 1

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-001T

value: Esophageal squamous cell carcinoma (ESCC)


title: Marmoset_PrefrontalCortex_NeuNnegative_ATAC_2


title: Marmoset_PrefrontalCortex_NeuNpositive_ATAC_1


title: KT2440_Erf_I_3

description:
adaptor-ligated sheared genomic DNA
KT2440_processed.xlsx

organism: Pseudomonas putida


title: CHA0_Erf_I_2


title: PA23_Erf_I_3

description:
adaptor-ligated sheared genomic DNA
PA23_E_I_processed.xlsx


title: KT2440_Erf_I_2


title: PA23_Erf_I_2


title: Marmoset_WhiteMatter_H3K27ac_3

source_name: Marmoset White Matter

tag: antibody

value: Marmoset White Matter


title: CHA0_Erf_I_1


title: KT2440_Erf_I_1


title: CHA0_neg_3

description: adaptor-ligated sheared genomic DNA


title: Marmoset_PrefrontalCortex_NeuNnegative_ATAC_1


title: PA23_Erf_I_1


title: Marmoset_WhiteMatter_H3K27ac_2


title: KT2440_neg_3

description: adaptor-ligated sheared genomic DNA


title: PA23_neg_3

description: adaptor-ligated sheared genomic DNA


title: Paraffin embedded tissue of ESCC patient 2

description:
Raw data were normalized by RMA algorithm, Affy packages in R.
ESCC-002T

source_name: Paraffin embedded tissue of ESCC patients

tag: patient diagnosis

value: Esophagus


title: KT2440_neg_2

description: adaptor-ligated sheared genomic DNA


title: CHA0_neg_1

description: adaptor-ligated sheared genomic DNA


title: PA23_neg_2

description: adaptor-ligated sheared genomic DNA


title: mixed monocytes (U937 cell line) and macrophages rep1

treatment_protocol: Monocytes were differentiated to macrophage-like cells by first adding phorbol 12-myristate 13-acetate (PMA) to the culture medium at final concentration of 5nM for 24 hours. Then, these newly-adherent cells were washed with fresh PMA-free medium and allowed to recover in PMA-free medium for an additional 48 hours before harvest. Mock-treated U-937 cells were passaged with fresh PMA-free media at 24 hours and harvested along with the treated cells at 72 hours.


title: Marmoset_WhiteMatter_RNAseq_2

extract_protocol: TruSeq Stranded mRNA Library Preparation (Illumina)

tag: tissue

value: White Matter


title: Marmoset_WhiteMatter_H3K27ac_1


title: Myofiber MyHC-1_9(S11)

description: Gene expression of single mouse myofiber. Biological replicates of the same myofiber type were numbered from 1 to 10 and marked with the muscle of origin (S for soleus, and E for EDL) and the number of the animal.

source_name: Individual pure type 1 myofiber from soleus muscle.

value: 3 months

value: Male

value: Soleus muscle

value: Individual pure type 1 myofiber


title: KT2440_neg_1

description: adaptor-ligated sheared genomic DNA


title: Lib10:H2228_H1975_A549_H838_HCC827_Mixture_10X_RNASeq

status: Public on Dec 19 2019

city: Clayton

first: Shanika

last: Amarasinghe

state: VIC

address: 15 Innovation Walk

department: Monash Biomedicine Discovery Institute

country: Australia

institute: Monash Unviersity

data_processing:
Fastq files were generated using Cellranger. All R1 files were concatenated and all R2 files were concatenated for processing with scPipe.
Sample filtered gene count matrix was generated using scPipe with ENSEMBL GRCh38p10 gene annotation. With scPipe, we processed the 5000 most enriched cell barcodes, with comp=2 used for quality control to remove poor quality cells.
Genome_build: GRCh38 patch 10
Supplementary_files_format_and_content: RNAseq_samplesheet.csv: Samplesheet output from the sequencing
Supplementary_files_format_and_content: Lib10.csv: Barcodes for Lib10
Supplementary_files_format_and_content: Lib10_gene_count.csv: Counts matrix with samples along the columns and genes along the rows for Lib10
Supplementary_files_format_and_content: Lib90.csv: Barcodes for Lib90
Supplementary_files_format_and_content: Lib90_gene_count.csv: Counts matrix with samples along the columns and genes along the rows for Lib90

molecule: polyA RNA

source_name: lung adenocarcinoma

growth_protocol: The human lung adenocarcinoma cell lines H2228, H1975, A549, H838 and HCC827 were retrieved from ATCC (https://www.atcc.org/) and cultured in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% fetal calf serum (FCS) and 1% Penicillin-Streptomycin.  The cells were grown independently at 37C  with 5% carbon dioxide until near 100% confluency.

extract_protocol:
The cells were counted using Chamber Slide and rounghly 2 million cells from each cell line were mixed and processed by 10X.
following the standard 10X single cell RNA-seq document, using v3 chemistry.

value: mixture of 5 human lung adenocarcinoma cell lines:H2228, H1975, A549, H838 and HCC827

tag: barcode coordinate

value: bases 1 to 16 on R1

tag: umi coordinate

value: bases 17 to 26 on R1


title: Lib90:H2228_H1975_A549_H838_HCC827_Mixture_10X_RNASeq


title: Lib90:H2228_H1975_A549_H838_HCC827_Mixture_10X_ATACSeq

data_processing:
Fastq files were generated using Cellranger.
Sample filtered gene count matrix was generated using scPipe with ENSEMBL GRCh38p10 gene annotation. With scPipe, we processed the 5000 most enriched cell barcodes, with comp=2 used for quality control to remove poor quality cells.
The aligned BAMs from both Lib10 and Lib90 were merged together and demuxlet was run on it using known variants for the same data to identify the cell types based on their natural generic variations
Genome_build: GRCh38 patch 10
Supplementary_files_format_and_content: ATACseq_samplesheet.csv: Samplesheet output from the sequencing
Supplementary_files_format_and_content: ATACLib10_barcodes.csv: Barcodes for Lib10
Supplementary_files_format_and_content: ATACLib10_matrix.mtx: Cellranger output for Lib10 data
Supplementary_files_format_and_content: ATACLib10_peaks.bed: Cellranger predicted peaks for Lib10 data
Supplementary_files_format_and_content: ATACLib90_barcodes.csv: Barcodes for Lib90
Supplementary_files_format_and_content: ATACLib90_matrix.mtx: Cellranger output for Lib90 data
Supplementary_files_format_and_content: ATACLib90_peaks.bed: Cellranger predicted peaks for Lib90 data
Supplementary_files_format_and_content: cell_identitiy_allbarcodes.csv: Processed demxlet results for merged (Lib10 and Lib90) dataset

extract_protocol:
The cells were counted using Chamber Slide and rounghly 2 million cells from each cell line were mixed and processed by 10X.
following the standard 10X single cell ATAC-seq document, using v3 chemistry.


title: CL2

city: Monrovia

first: Jianjun

state: CA

department: Systems Biology

institute: Beckman Research Institute of City of Hope

data_processing:
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
the RPKM were calculated using RSEM 1.2.31 with default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: .xls file containing the expression and p value

extract_protocol:
RNA was extracted by using TRIzol reagent (Invitrogen, Carlsbad, CA). NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA) was used for polyA RNA purification.
Library was prepared by or NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs, Ipswich, MA).

tag: tumor

value: acute myeloid leukemia

tag: treatment

value: HHT 5ng/ml


title: CL4

value: PBS


title: CL3

value: HHT 10ng/ml


title: CL6


title: Lib10:H2228_H1975_A549_H838_HCC827_Mixture_10X_ATACSeq


title: CL1


title: mm_ESE14_ADD21_PPARg_rep2

city: Debrecen

first: Gergely

last: Nagy

address: Egyetem ter 1.

department: Department of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

description: PPARg ChIP-Seq analysis of mouse E14 embryonic stem cells differentiated to adipocytes (day 21, rep2)

data_processing:
alignment with bwa v0.7.10 using default parameters
bam generation with samtools v0.1.19 using default parameters
tag directory generation with homer v4.2 makeTagDirectory using -checkGC parameter
bedgraph generation with homer v4.2 makeUCSCfile using -fsize 1e50 -norm parameters
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph

source_name: embryonic stem cell

extract_protocol:
Immunoprecipitation was carried out with antibodies for RXR (sc-774) and PPARγ (Perseus #PP-A3409A). Protein antibody complexes were washed six times and eluted from Protein A coated paramagnetic beads. DNA was purified with the Qiagen Minelute kit.
Libraries were prepared with the Ovation Ultralow Library Systems (Nugen) according to the manufacturer protocol.

value: embryonic stem cell

tag: differentiation stage

value: adipocyte (day 21)

tag: chip antibody

value: PPARg (Perseus #PP-A3409A)


title: mm_ESE14_ADD30_RXR_rep1

description: RXR ChIP-Seq analysis of mouse E14 embryonic stem cells differentiated to adipocytes (day 30, rep1)

value: adipocyte (day 30)


title: mm_BMDM_24hIL4_RXR_rep1

description: RXR ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4, rep1)

source_name: bone marrow-derived macrophage

extract_protocol:
Cells were double crosslinked and lysed. Immunoprecipitation was carried out with an antibody for RXR (sc-774). Protein antibody complexes were washed six times and eluted from Protein A coated paramagnetic beads. DNA was purified with the Qiagen Minelute kit.
Libraries were prepared with the Ovation Ultralow Library Systems (Nugen) according to the manufacturer protocol.

value: bone marrow-derived macrophage

tag: age

tag: Sex

value: male


title: Adipose_MNR_F2

first: Victor

middle: KM

last: Han

state: Ontario

address: 1151 Richmond St

country: Canada

institute: University of Western Ontario

description:
MNR pregnancy, impaired fasting blood glucose (IFBG) MNR
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_MNR_F2

data_processing:
Hiseq 2500 was used at McGill University and Genome Innovation Centre (muscle and liver) or National Research Council (NRC) (adipose tissue)
Fastqc was used to ensure all samples obtained good quality reads, then reads were aligned to the mm9 transcriptome using bowtie2 (default settings)
Sample tables were merged into a master count table for each tissue in the R console. Samples with single-end reads that were run in two lanes were aggregated.
Transcripts were collapsed to the gene level in the R console using Biomart "ensembl_transcript_id" and "ensembl_gene_id" from the may 2012 mm9 archived version (see supplementary files)
Data was normalized and differential expression was determined using DESeq2, ALDex2 and EdgeR tools
Genome_build: mm9
Supplementary_files_format_and_content: counts.txt files (for individual samples); count_table.txt files (master count tables; liver and muscle have lanes aggregated so that each column represents a mouse)

source_name: Perigonadal adipose tissue

extract_protocol:
Frozen tissue was pulverized then homogenized. Total RNA was isolated with TRIzol the PureLink Mini RNA kit (Invitrogen, USA) using the manufactuer's on-column DNAseI protocol.
Liver and muscle libraries were created at McGill University and Genome Quebec Innovation Center (Quebec, CA) and adipose libraries at National Research Council Canada (Saskatoon, SK).For all tissues, Illumina TruSeqTM mRNA stranded library kit (Illumina) was used according to the manufacter's protocol.

tag: animal number

value: CD-1 IGS

tag: pregnancy

value: MNR

tag: glucose tolerance

value: Adipose

tag: developmental stage

value: 6 months


title: Adipose_Control_C8

description:
control pregnancy, control glucose tolerance
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_Control_C8

value: control

value: control glucose tolerance


title: Adipose_Control_C2

description:
control pregnancy, control glucose tolerance
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_Control_C2


title: mm_ESE14_ADD21_PPARg_rep1

description: PPARg ChIP-Seq analysis of mouse E14 embryonic stem cells differentiated to adipocytes (day 21, rep1)


title: Adipose_MNR_I6

description:
MNR pregnancy, intolerant MNR
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_MNR_I6

value: intolerant MNR


title: Adipose_MNR_I1

description:
MNR pregnancy, intolerant MNR
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_MNR_I1


title: Adipose_MNR_T8

description:
MNR pregnancy, tolerant MNR
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_MNR_T8

value: tolerant MNR


title: bigfile-brittle

description: Illumina MiSeq platform

source_name: (Pooled from 42 tissues) arm tissue at the level of the 15th segment (counting from the disk)

tag: chemical treatment

tag: pooling strategy for de novo assembly

value: 42 RNA samples (6 conditions × 7 individuals) were mixed in equimolar quantities and sequenced on the Illumina MiSeq platform (2 × 250 bp).


title: Adipose_MNR_I9

description:
MNR pregnancy, intolerant MNR
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_MNR_I9

tag: strain


title: Adipose_MNR_T2

description:
MNR pregnancy, tolerant MNR
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_MNR_T2


title: CHA0_neg_2

description: adaptor-ligated sheared genomic DNA

tag: erfa origin


title: PA23_neg_1

description: adaptor-ligated sheared genomic DNA


title: Adipose_MNR_T5

description:
MNR pregnancy, tolerant MNR
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_MNR_T5

tag: tissue


title: Marmoset_WhiteMatter_RNAseq_1

value: White Matter


title: Adipose_Control_C5

description:
control pregnancy, control glucose tolerance
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_Control_C5


title: Adipose_MNR_F1

description:
MNR pregnancy, impaired fasting blood glucose (IFBG) MNR
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_MNR_F1


title: CL5

value: acute myeloid leukemia

value: HHT 5ng/ml


title: Adipose_MNR_I4

description:
MNR pregnancy, intolerant MNR
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_MNR_I4


title: Adipose_MNR_T4

description:
MNR pregnancy, tolerant MNR
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_MNR_T4


title: Adipose_Control_C7

description:
control pregnancy, control glucose tolerance
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_Control_C7


title: Adipose_MNR_I3

description:
MNR pregnancy, intolerant MNR
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_MNR_I3


title: Adipose_MNR_T3

description:
MNR pregnancy, tolerant MNR
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_MNR_T3


title: Adipose_MNR_F3

description:
MNR pregnancy, impaired fasting blood glucose (IFBG) MNR
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_MNR_F3


title: Adipose_Control_C1

description:
control pregnancy, control glucose tolerance
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_Control_C1


title: Adipose_Control_C4

description:
control pregnancy, control glucose tolerance
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_Control_C4


title: Adipose_MNR_I5

description:
MNR pregnancy, intolerant MNR
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_MNR_I5


title: Adipose_MNR_T1

description:
MNR pregnancy, tolerant MNR
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_MNR_T1


title: Adipose_MNR_I2

description:
MNR pregnancy, intolerant MNR
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_MNR_I2


title: Adipose_MNR_F4

description:
MNR pregnancy, impaired fasting blood glucose (IFBG) MNR
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_MNR_F4


title: Adipose_Control_C6

description:
control pregnancy, control glucose tolerance
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_Control_C6


title: Muscle_MNR_I9_1

description:
MNR pregnancy, intolerant MNR, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_I9

source_name: Quadriceps femoris

value: Muscle


title: Muscle_MNR_I9_2

description:
MNR pregnancy, intolerant MNR, lane 2
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_I9


title: Muscle_MNR_I8_1

description:
MNR pregnancy, intolerant MNR, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_I8


title: Muscle_MNR_T8_1

description:
MNR pregnancy, tolerant MNR, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_T8


title: Muscle_MNR_T7_2

description:
MNR pregnancy, tolerant MNR, lane 2
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_T7


title: Muscle_MNR_I8_2

description:
MNR pregnancy, intolerant MNR, lane 2
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_I8


title: Muscle_MNR_T7_1

description:
MNR pregnancy, tolerant MNR, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_T7


title: Muscle_MNR_T8_2

description:
MNR pregnancy, tolerant MNR, lane 2
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_T8


title: Adipose_MNR_I7

description:
MNR pregnancy, intolerant MNR
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_MNR_I7


title: Muscle_MNR_I7_2

description:
MNR pregnancy, intolerant MNR, lane 2
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_I7


title: Muscle_MNR_F4_2

description:
MNR pregnancy,impaired fasting blood glucose (IFBG) MNR, lane 2
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_F4


title: Muscle_MNR_F4_1

description:
MNR pregnancy,impaired fasting blood glucose (IFBG) MNR, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_F4


title: Muscle_MNR_I7_1

description:
MNR pregnancy, intolerant MNR, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_I7


title: Muscle_MNR_F3_1

description:
MNR pregnancy,impaired fasting blood glucose (IFBG) MNR, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_F3


title: Adipose_Control_C3

description:
control pregnancy, control glucose tolerance
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_Control_C3


title: Adipose_MNR_T7

description:
MNR pregnancy, tolerant MNR
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_MNR_T7


title: Muscle_MNR_F3_2

description:
MNR pregnancy,impaired fasting blood glucose (IFBG) MNR, lane 2
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_F3


title: Muscle_MNR_I6_2

description:
MNR pregnancy, intolerant MNR, lane 2
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_I6


title: Adipose_MNR_I8

description:
MNR pregnancy, intolerant MNR
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_MNR_I8


title: Muscle_MNR_I5_2

description:
MNR pregnancy, intolerant MNR, lane 2
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_I5


title: Muscle_MNR_I5_1

description:
MNR pregnancy, intolerant MNR, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_I5


title: Adipose_MNR_T6

description:
MNR pregnancy, tolerant MNR
Processed data file:  Adipose_count_table.txt
Column header:  Adipose_MNR_T6


title: Muscle_MNR_I4_2

description:
MNR pregnancy, intolerant MNR, lane 2
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_I4


title: Muscle_MNR_I4_1

description:
MNR pregnancy, intolerant MNR, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_I4


title: Muscle_MNR_T6_2

description:
MNR pregnancy, tolerant MNR, lane 2
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_T6


title: Muscle_MNR_T5_2

description:
MNR pregnancy, tolerant MNR, lane 2
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_T5


title: Muscle_MNR_I3_2

description:
MNR pregnancy, intolerant MNR, lane 2
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_I3


title: Muscle_MNR_T4_1

description:
MNR pregnancy, tolerant MNR, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_T4


title: Muscle_MNR_T4_2

description:
MNR pregnancy, tolerant MNR, lane 2
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_T4


title: Muscle_MNR_T6_1

description:
MNR pregnancy, tolerant MNR, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_T6


title: Muscle_MNR_I3_1

description:
MNR pregnancy, intolerant MNR, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_I3


title: Muscle_MNR_T5_1

description:
MNR pregnancy, tolerant MNR, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_T5


title: Muscle_MNR_T2_1

description:
MNR pregnancy, tolerant MNR
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_T2


title: Muscle_MNR_I2_2

description:
MNR pregnancy, intolerant MNR, lane 2
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_I2


title: Muscle_MNR_I2_1

description:
MNR pregnancy, intolerant MNR, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_I2


title: Muscle_MNR_T1_2

description:
MNR pregnancy, tolerant MNR, lane 2
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_T1


title: Muscle_MNR_T3_2

description:
MNR pregnancy, tolerant MNR, lane 2
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_T3


title: Muscle_MNR_F2_2

description:
MNR pregnancy,impaired fasting blood glucose (IFBG) MNR, lane 2
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_F2


title: Muscle_MNR_T3_1

description:
MNR pregnancy, tolerant MNR, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_T3


title: Muscle_MNR_T1_1

description:
MNR pregnancy, tolerant MNR, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_T1


title: Muscle_MNR_I1_2

description:
MNR pregnancy, intolerant MNR, lane 2
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_I1


title: Muscle_MNR_F1_1

description:
MNR pregnancy,impaired fasting blood glucose (IFBG) MNR, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_F1


title: Muscle_MNR_F1_2

description:
MNR pregnancy,impaired fasting blood glucose (IFBG) MNR, lane 2
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_F1


title: Muscle_MNR_I6_1

description:
MNR pregnancy, intolerant MNR, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_I6


title: Muscle_Control_C8_1

description:
control pregnancy, control glucose tolerance, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_Control_C8


title: Muscle_Control_C7_2

description:
control pregnancy, control glucose tolerance, lane 2
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_Control_C7


title: Muscle_Control_C6_2

description:
control pregnancy, control glucose tolerance, lane 2
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_Control_C6


title: Muscle_Control_C6_1

description:
control pregnancy, control glucose tolerance, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_Control_C6


title: Muscle_Control_C7_1

description:
control pregnancy, control glucose tolerance, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_Control_C7


title: Muscle_Control_C5_2

description:
control pregnancy, control glucose tolerance, lane 2
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_Control_C5


title: Muscle_Control_C4_2

description:
control pregnancy, control glucose tolerance, lane 2
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_Control_C4


title: Muscle_Control_C4_1

description:
control pregnancy, control glucose tolerance, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_Control_C4


title: Muscle_Control_C3_1

description:
control pregnancy, control glucose tolerance, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_Control_C3


title: Muscle_Control_C2_2

description:
control pregnancy, control glucose tolerance, lane 2
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_Control_C2


title: Muscle_Control_C1_1

description:
control pregnancy, control glucose tolerance, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_Control_C1


title: Muscle_Control_C1_2

description:
control pregnancy, control glucose tolerance, lane 2
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_Control_C1


title: Liver_MNR_T8_2

description:
MNR pregnancy, tolerant MNR, lane 2
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_T8

source_name: Right medial liver lobe

value: Liver


title: Muscle_MNR_F2_1

description:
MNR pregnancy,impaired fasting blood glucose (IFBG) MNR, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_F2


title: Liver_MNR_T7_1

description:
MNR pregnancy, tolerant MNR
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_T7


title: Muscle_MNR_I1_1

description:
MNR pregnancy, intolerant MNR, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_MNR_I1


title: Liver_MNR_F4_1

description:
MNR pregnancy,impaired fasting blood glucose (IFBG) MNR, lane 1
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_F4


title: Liver_MNR_T8_1

description:
MNR pregnancy, tolerant MNR, lane 1
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_T8


title: Muscle_Control_C8_2

description:
control pregnancy, control glucose tolerance, lane 2
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_Control_C8


title: Liver_MNR_I7_2

description:
MNR pregnancy, intolerant MNR, lane 2
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_I7


title: Liver_MNR_I6_4

description:
MNR pregnancy, intolerant MNR, lane 2
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_I6


title: Liver_MNR_I6_1

description:
MNR pregnancy, intolerant MNR, lane 1
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_I6


title: Liver_MNR_F4_2

description:
MNR pregnancy,impaired fasting blood glucose (IFBG) MNR, lane 2
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_F4


title: Liver_MNR_I7_1

description:
MNR pregnancy, intolerant MNR, lane 1
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_I7


title: Liver_MNR_F3_1

description:
MNR pregnancy,impaired fasting blood glucose (IFBG) MNR, lane 1
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_F3


title: Liver_MNR_I5_2

description:
MNR pregnancy, intolerant MNR, lane 2
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_I5


title: Liver_MNR_F3_2

description:
MNR pregnancy,impaired fasting blood glucose (IFBG) MNR, lane 2
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_F3


title: Liver_MNR_I4_2

description:
MNR pregnancy, intolerant MNR, lane 2
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_I4


title: Liver_MNR_I4_1

description:
MNR pregnancy, intolerant MNR, lane 1
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_I4


title: Liver_MNR_I5_1

description:
MNR pregnancy, intolerant MNR, lane 1
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_I5


title: Liver_MNR_T6_2

description:
MNR pregnancy, tolerant MNR, lane 2
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_T6


title: Muscle_Control_C5_1

description:
control pregnancy, control glucose tolerance, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_Control_C5


title: Liver_MNR_T6_1

description:
MNR pregnancy, tolerant MNR, lane 1
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_T6


title: Liver_MNR_I3_2

description:
MNR pregnancy, intolerant MNR, lane 2
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_I3


title: Liver_MNR_T5_2

description:
MNR pregnancy, tolerant MNR, lane 2
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_T5


title: Muscle_Control_C2_1

description:
control pregnancy, control glucose tolerance, lane 1
Processed data file:  Muscle_count_table.txt
Column header:  Muscle_Control_C2


title: Liver_MNR_T5_1

description:
MNR pregnancy, tolerant MNR, lane 1
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_T5


title: Liver_MNR_I3_1

description:
MNR pregnancy, intolerant MNR, lane 1
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_I3


title: Liver_MNR_T4_2

description:
MNR pregnancy, tolerant MNR, lane 2
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_T4


title: Liver_MNR_I2_2

description:
MNR pregnancy, intolerant MNR, lane 2
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_I2


title: Liver_MNR_T4_1

description:
MNR pregnancy, tolerant MNR, lane 1
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_T4


title: Liver_MNR_T3_2

description:
MNR pregnancy, tolerant MNR, lane 2
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_T3


title: Liver_MNR_I2_1

description:
MNR pregnancy, intolerant MNR, lane 1
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_I2


title: Liver_MNR_T2_2

description:
MNR pregnancy, tolerant MNR, lane 2
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_T2


title: Liver_MNR_T1_2

description:
MNR pregnancy, tolerant MNR, lane 2
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_T1


title: Liver_MNR_T3_1

description:
MNR pregnancy, tolerant MNR, lane 1
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_T3


title: Liver_MNR_F2_1

description:
MNR pregnancy,impaired fasting blood glucose (IFBG) MNR, lane 1
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_F2


title: Liver_Control_C7_2

description:
control pregnancy, control glucose tolerance, lane 2
Processed data file:  Liver_count_table.txt
Column header:  Liver_Control_C7


title: Liver_Control_C6_2

description:
control pregnancy, control glucose tolerance, lane 2
Processed data file:  Liver_count_table.txt
Column header:  Liver_Control_C6


title: Liver_MNR_F1_1

description:
MNR pregnancy,impaired fasting blood glucose (IFBG) MNR, lane 1
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_F1


title: Liver_MNR_F2_2

description:
MNR pregnancy,impaired fasting blood glucose (IFBG) MNR, lane 2
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_F2


title: Liver_MNR_T2_1

description:
MNR pregnancy, tolerant MNR, lane 1
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_T2


title: Liver_Control_C5_1

description:
control pregnancy, control glucose tolerance, lane 1
Processed data file:  Liver_count_table.txt
Column header:  Liver_Control_C5


title: Liver_Control_C4_2

description:
control pregnancy, control glucose tolerance, lane 2
Processed data file:  Liver_count_table.txt
Column header:  Liver_Control_C4


title: Liver_MNR_I1_2

description:
MNR pregnancy, intolerant MNR, lane 2
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_I1


title: Liver_MNR_F1_2

description:
MNR pregnancy,impaired fasting blood glucose (IFBG) MNR, lane 2
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_F1


title: Liver_MNR_I1_1

description:
MNR pregnancy, intolerant MNR, lane 1
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_I1


title: Liver_Control_C8_2

description:
control pregnancy, control glucose tolerance, lane 2
Processed data file:  Liver_count_table.txt
Column header:  Liver_Control_C8


title: Liver_Control_C8_1

description:
control pregnancy, control glucose tolerance, lane 1
Processed data file:  Liver_count_table.txt
Column header:  Liver_Control_C8


title: Liver_Control_C1_1

description:
control pregnancy, control glucose tolerance, lane 1
Processed data file:  Liver_count_table.txt
Column header:  Liver_Control_C1


title: Liver_Control_C6_1

description:
control pregnancy, control glucose tolerance, lane 1
Processed data file:  Liver_count_table.txt
Column header:  Liver_Control_C6


title: Liver_Control_C7_1

description:
control pregnancy, control glucose tolerance, lane 1
Processed data file:  Liver_count_table.txt
Column header:  Liver_Control_C7


title: Liver_Control_C3_2

description:
control pregnancy, control glucose tolerance, lane 2
Processed data file:  Liver_count_table.txt
Column header:  Liver_Control_C3


title: Liver_Control_C2_1

description:
control pregnancy, control glucose tolerance, lane 1
Processed data file:  Liver_count_table.txt
Column header:  Liver_Control_C2


title: Liver_Control_C5_2

description:
control pregnancy, control glucose tolerance, lane 2
Processed data file:  Liver_count_table.txt
Column header:  Liver_Control_C5


title: Liver_MNR_T1_1

description:
MNR pregnancy, tolerant MNR, lane 1
Processed data file:  Liver_count_table.txt
Column header:  Liver_MNR_T1


title: Liver_Control_C3_1

description:
control pregnancy, control glucose tolerance, lane 1
Processed data file:  Liver_count_table.txt
Column header:  Liver_Control_C3


title: 21-5hmC Seq

data_processing:
Library strategy: 5hmC-Seq
Reads were aligned using BWA
The identification of 5hmC peaks in each sample was performed using MACS2
IGV was used to visualize the sequencing signals
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig files were generated by MACS2 and bedGraphToBigWig. BedWig files can be uploaded to UCSC Genome Browser for visualization

extract_protocol:
“Preparing Samples for ChIP Sequencing of DNA” (Part# 111257047 Rev. A).
DNA libraries were generated following the Illumina protocol for “Preparing Samples for ChIP Sequencing of DNA” (Part# 111257047 Rev. A).

value: HHT 10ng/ml


title: Liver_Control_C4_1

description:
control pregnancy, control glucose tolerance, lane 1
Processed data file:  Liver_count_table.txt
Column header:  Liver_Control_C4


title: 20-5hmC Seq

value: PBS


title: Liver_Control_C2_2

description:
control pregnancy, control glucose tolerance, lane 2
Processed data file:  Liver_count_table.txt
Column header:  Liver_Control_C2


title: Liver_Control_C1_2

description:
control pregnancy, control glucose tolerance, lane 2
Processed data file:  Liver_count_table.txt
Column header:  Liver_Control_C1


title: SL237159

city: Huntsville

first: Brian

middle: Scott

last: Roberts

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description: small RNA-seq library

data_processing:
bowtie2 aligned to human genome(hg19)
reads with multiple mapping assigned fractionally
known small RNAs annotated in R script
read normlaization and differential expression calculated with DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: raw count table CSV

source_name: breast tumor biopsy

extract_protocol:
Norgen Total RNA Purification Kit
see PMID:26209131

treatment_protocol: tumor tissue micro-dissected from normal adjacent

value: breast tumor biopsy

tag: patient treatment

value: letrozole + bevacizumab

tag: clinical response

value: PR

tag: letrozole + bevacizumab binary responder

value: responder

tag: letrozole only binary responder

tag: cdna conc

tag: frac mrna


title: SL237158

description: small RNA-seq library


title: SL237154

description: small RNA-seq library


title: SL237156

description: small RNA-seq library

value: letrozole

value: SD


title: Control 35

first: Eduard

middle: Iosifovich

last: Drizik

address: 72 East Concord Street

department: Computational Biomedicine

institute: Boston University

description: Gene expression data from nasal epithelium of DEE unexposed factory worker

hyb_protocol: The labeled, fragmented DNA was hybridized to the GeneChip Human Gene 1.0 ST Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven at 640 at 45 deg. C with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450 with streptavidin-R-phycoerythrin (SAPE) and the signal was amplified using a biotinylated goat anti-streptavidin antibody followed by another SAPE staining (Hybridization, Washing and Staining Kit, Affymetrix, Santa Clara, CA).

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray hugene10sthsentrezgcdf R package (version 17.0.0).

source_name: nasal epithelium

label_protocol: Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA from brushings of nasal epithelium was isolated using the miRNeasy Mini Kit (Qiagen, Valencia, CA)

tag: exposure

value: control

tag: rin

tag: batch

tag: cell type

value: nasal epithelium


title: Control 36


title: SL237153

description: small RNA-seq library


title: Control 29


title: Control 28


title: Control 33


title: Control 38


title: Control 34


title: SL237186

description: small RNA-seq library


title: Control 27


title: Control 31


title: Control 37


title: Control 26


title: Control 30


title: BMDM, WT, 24hrs

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.50.0).

source_name: Pool of bone marrow-derived macrophages, wild type, incubated with fatty acids for 24 hrs

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: To isolate bone marrow-derived macrophages (BMDM), 8-12 week old HilpdaΔMΦ mice and their wild-type Hilpdaflox/flox littermates were killed by cervical dislocation. Both femurs and hind legs were isolated at the hip joint, keeping the femur and tibia intact. Bone marrow was extracted from the femur and tibia and differentiated in DMEM, supplemented with 10% FCS, 1% P/S and 15% L929 conditioned medium. After seven days of differentiation, BMDM were scraped, plated and used for experiments.

extract_protocol: Total RNA was isolated from samples using the RNeasy kit (Qiagen) according to the manufacturer’s protocol. RNA quality was verified on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands) using 6000 Nano Chips according to manufacturer’s instructions. RNA was considered suitable for array hybridization only if RNA integrity number exceeded 8.0. RNA from 3 samples per group was pooled for microarray analysis.

treatment_protocol: Bone marrow-derived macrophages were incubated with 600uM final concentrations of fatty acids (mixture of palmitate and oleate in a ratio of 1:2) for 12 or 24 hours. All fatty acid stocks were initially reconstituted in absolute ethanol. Sub-stocks of fatty acids at 25 mM were prepared in sterile water containing filter-sterilised KOH. Complete DMEM medium supplemented with fatty acid-free BSA (Sigma-Aldrich, St. Louis, MO) was filter sterilised, and incubated for 30 min with fatty acids to complex BSA to fatty acids. Ratio of BSA to fatty acids were approximately 1:2.

value: bone marrow-derived macrophages

tag: genotype

value: wild type

tag: incubation time (hrs)


title: BMDM, KO, 24hrs

source_name: Pool of bone marrow-derived macrophages, Hilpda knockout, incubated with fatty acids for 24 hrs

value: Hilpda knockout


title: BMDM, KO, 12hrs

source_name: Pool of bone marrow-derived macrophages, Hilpda knockout, incubated with fatty acids for 12 hrs


title: Control 22


title: Control 23


title: BMDM, WT, 12hrs

source_name: Pool of bone marrow-derived macrophages, wild type, incubated with fatty acids for 12 hrs


title: Control 24


title: Control 32


title: Control 21


title: SL237184

description: small RNA-seq library


title: SL237182

description: small RNA-seq library


title: SL237183

description: small RNA-seq library

value: PD


title: SL237181

description: small RNA-seq library


title: SL237152

description: small RNA-seq library


title: SL237230

description: small RNA-seq library


title: SL237180

description: small RNA-seq library


title: SL237174

description: small RNA-seq library

value: DS


title: SL237228

description: small RNA-seq library


title: SL237176

description: small RNA-seq library


title: Control 20


title: SL237124

description: small RNA-seq library


title: Control 25


title: Control 17


title: SL237123

description: small RNA-seq library


title: Control 16


title: SL237173

description: small RNA-seq library


title: Control 9


title: Control 12


title: SL237171

description: small RNA-seq library


title: Control 11


title: Control 10


title: Control 13


title: Control 19


title: Control 14


title: SL237145

description: small RNA-seq library


title: Control 7


title: SL237168

description: small RNA-seq library


title: Control 15


title: SL237169

description: small RNA-seq library


title: SL237178

description: small RNA-seq library


title: Control 8


title: SL237120

description: small RNA-seq library


title: Control 18


title: SL237143

description: small RNA-seq library


title: Control 4


title: Control 3


title: SL237137

description: small RNA-seq library


title: Control 5


title: SL237142

description: small RNA-seq library


title: SL237141

description: small RNA-seq library


title: SL237140

description: small RNA-seq library


title: Control 2


title: Control 1


title: SL237148

description: small RNA-seq library


title: SL237136

description: small RNA-seq library


title: Control 6


title: SL237128

description: small RNA-seq library


title: SL237132

description: small RNA-seq library


title: Diesel 40

description: Gene expression data from nasal epithelium of DEE exposed factory worker

value: diesel


title: Diesel 37


title: Diesel 41


title: Diesel 38


title: SL237131

description: small RNA-seq library


title: Diesel 36


title: SL237130

description: small RNA-seq library


title: Diesel 34


title: SL237139

description: small RNA-seq library


title: Diesel 39


title: RIP input PLC/PRF5

city: Guangzhou

first: Kaiyuan

last: Ji

address: No.9 Jinsui Road, Guangzhou, China

department: Guangzhou Women and Children’s Medical Center

institute: Guangzhou Medical University

description: Co-immunoprecipitated RNAs

data_processing:
The RIP-seq reads were aligned against the hg19 human reference genome with the UCSC known gene transcript annotation using TopHat v2.0.13.
The RIP-seq peaks were identified for + and – strand separately using RIPSeeker.
Genome_build: hg19
Supplementary_files_format_and_content: peaks.bed file

source_name: Hepatocellular Carcinoma Cell Line

growth_protocol: PLC/PRF5 cells were cultured in DMEM medium supplemented with 10% fetal bovine serum (FBS)

extract_protocol:
RNA immunoprecipitation (RIP) was carried out with Magna RIP RNA-Binding Protein immunoprecipitation kit (Millipore; USA) according to the manufacturer’s instruction. Briefly, cells overexpressing MTR4-HA were lysed by RIP lysis buffer containing protease inhibitor cocktail (Thermo fisher, USA) and RNase inhibitor (Invitrogen, USA). Nuclear pellets were collected and lysed by sonication. Nuclear lysates were incubated with anti-HA antibody or control IgG overnight at 4 °C, followed by incubation with protein A/G Dynabeads (Thermo fisher, USA) for 2 hours. After vigorous washing, pellets were resuspended in TRIzol (Invitrogen, USA). Co-immunoprecipitated RNAs were purified by RNAeasy Mini Kit (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: overexpression MTR4

tag: cell line

tag: rip antibody

value: IgG


title: SL237129

description: small RNA-seq library


title: SL237117

description: small RNA-seq library


title: SL237149

description: small RNA-seq library


title: dcl2dcl3dcl4 replicate3

city: Castanet

first: Matthias

last: Zytnicki

address: 24, Chemin de Borde-Rouge

department: Applied Mathematics and Informatics

country: France

institute: INRA

description: T

data_processing:
Mapping with tophat1 on TAIR9 using the TAIR9 annotation as guide.
Clustering of overlapping genes.
Quantification of the genes using S-MART
Genome_build: TAIR9
Supplementary_files_format_and_content: CSV table with clustered genes as first column.

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Seeds were sterilized with bleach and ethanol and grown on S-Medium from Duchefa (http:// www.duchefa-biochemie.com) under 18 h of light and 6 h dark cycles with an average temperature of 22◦C

extract_protocol:
Buffer containing 0.1 M NaCl, 2% SDS, 50 mMTris–HCl (pH 9), 10 mMEDTA (pH 8) and 20 mM ß- mercaptoethanol was added to the frozen powder andRNA was extracted twice with phenol and recovered by ethanol precipitation. For small RNA analysis, total RNA was sep- arated on a 15% denaturing polyacrylamide gel and stained with ethidium bromide.
Library construction has been realized by GATC Biotech
All libraries were pooled together and sequenced on HiSeq 2000 platform

treatment_protocol: Whole seedlings were collected 11 days after germination and grinded in liquid nitrogen.

value: Seedlings

tag: mutation

tag: cultivar


title: Diesel 35


title: Diesel 32


title: Diesel 28


title: Diesel 33


title: Diesel 31


title: 35S-RTL2 in dcl2dcl3dcl4 replicate3

description: S

tag: tissue


title: RIP MTR4 PLC/PRF5

description: Co-immunoprecipitated RNAs

data_processing:
The RIP-seq reads were aligned against the hg19 human reference genome with the UCSC known gene transcript annotation using TopHat v2.0.13.
The RIP-seq peaks were identified for + and – strand separately using RIPSeeker.
Genome_build: hg19
Supplementary_files_format_and_content: sequence of the peak region, peaks.bed file

value: anti-HA


title: 35S -RTL1-Myc in Col-0 replicate1

description: R


title: Diesel 26


title: rtl2-1 replicate3

description: Q


title: Col-0 replicate3

description: L

value: WT


title: Col-0 replicate2

description: N


title: rtl2-1 replicate2

description: M


title: 35S-RTL2 in Col-0 replicate2

description: P


title: SL237135

description: small RNA-seq library

value: breast tumor biopsy

tag: patient treatment

value: letrozole + bevacizumab


title: 35S -RTL1-Myc in Col-0 replicate2

description: K


title: Diesel 29


title: 35S-RTL2 in Col-0 replicate3

description: H


title: rtl2-1 replicate1

description: I


title: Diesel 27


title: Diesel 21


title: Diesel 22


title: Diesel 30


title: Diesel 25


title: Diesel 20


title: Diesel 18


title: Col-0 replicate1

description: G


title: 35S-RTL2 in Col-0 replicate1

description: F


title: Diesel 19


title: Diesel 24


title: Diesel 16


title: Diesel 15


title: Diesel 13


title: Diesel 23


title: Diesel 17


title: Diesel 12


title: Diesel 14


title: dcl2dcl3dcl4 replicate1

description: C


title: dcl2dcl3dcl4 replicate2

description: E


title: 35S-RTL2 in dcl2dcl3dcl4 replicate2

description: D


title: 35S-RTL2 in dcl2dcl3dcl4 replicate1

description: A


title: 35S-truncatedDCL1 in dcl2dcl3dcl4

description: B


title: Diesel 11


title: Teated buds (at 50% bud break) buds

city: Nanjing

first: Muhammad

last: Khalil-Ur-Rehman

address: No.1 Weigang

institute: Nanjing Agricultural university

data_processing:
The primary raw reads obtained by Illumina HiSeqTM2000 were filtered to remove low quality reads which were low complexity or containing adaptor sequence
The cleaned reads were aligned to the reference genome of Vitis using HISAT software version 0.1.6.
GO functional enrichment analysis and KEGG pathway analysis was continued with Blast2Go. KEGG pathway analysis is also used for the target gene candidates. In organisms, genes usually interact with each other to play different roles in certain biological function. The analysis based on pathways could facilitate the understanding of biological functions of genes. KEGG is the major public pathway-related database[8]. KEGG pathway analysis identifies significantly enriched metabolic pathways or signal transduction pathways in target gene candidates comparing with the whole reference gene background. The calculating formula is the same as that in GO analysis. Here N is the number of all genes with KEGG annotation, n is the number of target gene candidates in N, M is the number of all genes annotated to a certain pathway, and m is the number of target gene candidates in M. Genes with FDR<=0.05 are considered as significantly enriched in target gene candidates
DEGseq2 was used for gene expression analysis.
Genome_build: Vitis vinifera (ftp://ftp.ensemblgenomes.org/pub/release-23/plants/gtf/vitis_vinifera/)

organism: Vitis vinifera

source_name: bud

extract_protocol:
Trizol method
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Selected branches were cut in to pieces to prepare single node cuttings. Hydorogen cyanamide was applied @ 5% and water was sprayed as control treatement

tag: treatment

value: at 50 % bud break

value: Shine Muscat


title: CK (0h) buds


title: Diesel 10


title: Diesel 7


title: Diesel 8


title: Diesel 6


title: Diesel 9


title: Diesel 5


title: Diesel 4


title: Diesel 1


title: Diesel 2


title: DU145-miR-221* rep 2

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

institute: IRCCS Ospedale San Raffaele

description:
DU145 cells transfected with miR-221* synthetic mimic
5591989072_B

hyb_protocol: Standard Illumina DASL hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data were log2 transformed and normalized with robust spline normalization using the lumi package from Bioconductor.

source_name: prostate cancer cells

label_protocol: Biotinylated cRNA was prepared with the TotalPrep Amplification kit (Ambion) for Illumina arrays

growth_protocol: DU145 cells were maintained at 37°C/5% CO2 in RPMI medium supplemented with 10% fetal bovine serum

extract_protocol: Trizol (Invitrogen/Life Technologies) according to the manufacturer's protocol

treatment_protocol: Transfection of Ambion® Pre-miR™ miRNA Precursors (Life Technologies) at 20 nM final concentration using Lipofectamine reagent.


title: DU145-miR-1272 rep 3

description:
DU145 cells transfected with miR-1272 synthetic mimic
5591989038_L


title: DU145-miR-1272 rep 2

description:
DU145 cells transfected with miR-1272 synthetic mimic
5591989038_K


title: Diesel 3


title: FACS Sorted cells from the small intestine, KO4

city: New York

first: Dan

last: Littman

state: NY

address: 430 East 29th St Room 403

institute: New York University School of Medicine

description: VIPR2 WT CCR6+ ILC3 Mouse 3

data_processing:
Reads were aligned to Ensemble genome GRCm38 with STAR v 2.6.1d
Read pairs were counted using featurecounts from the Subread package v 1.6.2
DESeq2 was used for normalization and differential expression analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel file of Normalized Counts

growth_protocol: Bone marrow mononuclear cells were isolated from CD45.1 VIPR2+/+ and CD45.2 (or CD45.1/2) VIPR2−/− mice by flushing the long bones. Red blood cells were lysed with ACK Lysing Buffer and the remaining cells were resuspended in PBS for injection in at a 1:1 ratio (WT:VIPR2 KO). 4×10e6 cells were injected intravenously into 6 week old CD45.1/2 (CD45.2) mice that were irradiated 4h before reconstitution using 1000 rads/mouse (2×500rads, at an interval of 3h, at X-RAD 320 X-Ray Irradiator). To deplete intestinal ILC3, one day after the bone marrow transfer, mice were treated with InVivoMAb anti-mouse Thy1.2 (200ug/mice for 4 consecutive days, Clone 30H12, BioXCell). Experiments were performed 6-7 weeks after the last treatment with α-Thy1.2.

extract_protocol:
The ileum (distal 14cm of the small intestine) was dissected from mice. Mesenteric fat tissue and Peyer’s patches were carefully removed from these tissues. Intestinal tissue was opened and extensively cleaned of fecal matter. Following, this tissue was sequentially treated with HBSS 1X (1 mM DTT) at 37°C for 10 min with gentle shaking (200rpm), and twice with 5 mM EDTA at 37°C for 10 min to remove epithelial cells. The remaining tissue was then minced with a scissor and dissociated in RPMI containing 10% FBS, Dispase (0.05 U/ml; Worthington), collagenase (1 mg/ml collagenase II; Roche) and DNase I (100 μg/ml; Sigma) at constant shaking at 37°C for 45 min (175rpm). The digested tissue was then filtered through a 70μm strainer to remove large debris. Viable Lamina Propria Lymphocytes (LPLs) were collected at the interface of a 40%/80% Percoll/RPMI gradient (GE Healthcare). Cells were stained for surface markers. DAPI (ThermoFisher) was used to exclude dead cells. The following monoclonal antibodies were purchased from eBiosciences, BD Pharmingen or BioLegend: CD3, CD45.1, CD45.2, TCRβ, CD11c, CD14, CD19, TCRβ, TCRγ, NK1.1, CD127, CD90.2, CCR6. Sorting was performed on an Aria II (BD Biosciences).
RNA quantity and quality were determined using Agilent's RNA 6000 Pico Chip
RNA-seq libraries were prepared with the Low input Clontech SMART-Seq HT with Nxt HT.
The sequencing was performed using the Nextseq 500 High output kit v2.
RNA-seq libraries were prepared and sequenced by the Genome Technology Core at New York University School of Medicine.

value: VIPR2 WT

tag: lineage

value: Lineage negative (CD3, CD11c, CD14, CD19, NK1.1, KLRG1, TCRbeta, TCRgamma), Thy1.2+, CCR6+, CD45.1

tag: strain


title: FACS Sorted cells from the small intestine, WT4

description: VIPR2 KO CCR6+ ILC3 Mouse 1

value: VIPR2 KO

value: Lineage negative (CD3, CD11c, CD14, CD19, NK1.1, KLRG1, TCRbeta, TCRgamma), Thy1.2+, CCR6+, CD45.2


title: FACS Sorted cells from the small intestine, KO3

description: VIPR2 KO CCR6+ ILC3 Mouse 2


title: DU145-miR-205* rep 3

description:
DU145 cells transfected with miR-205* synthetic mimic
5591989038_F


title: DU145-miR-221* rep 3

description:
DU145 cells transfected with miR-221* synthetic mimic
5591989072_C


title: DU145-miR-141 rep 3

description:
DU145 cells transfected with miR-141 synthetic mimic
5591989072_F


title: FACS Sorted cells from the small intestine, WT3

description: VIPR2 WT CCR6+ ILC3 Mouse 1


title: FACS Sorted cells from the small intestine, KO5

description: VIPR2 KO CCR6+ ILC3 Mouse 3


title: DU145-miR-141 rep 1

description:
DU145 cells transfected with miR-141 synthetic mimic
5591989072_D


title: DU145-miR-221* rep 1

description:
DU145 cells transfected with miR-221* synthetic mimic
5591989072_A


title: DU145-miR-141 rep 2

description:
DU145 cells transfected with miR-141 synthetic mimic
5591989072_E


title: DU145-miR-1272 rep 1

description:
DU145 cells transfected with miR-1272 synthetic mimic
5591989038_J


title: FACS Sorted cells from the small intestine, WT5

description: VIPR2 WT CCR6+ ILC3 Mouse 2


title: high-pressure processed whole milk from donor C (exosomal fraction)

city: Lodz

first: Urszula

last: Smyczyńska

address: Mazowiecka 15

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Lodz

description:
mirna_count_table.txt
Milk-Ex-3C

data_processing:
Read adapters were trimmed and UMI sequences were extracted by UMI-tools v1.0.0. Maximum 2bp mismatch in a 19bp-long adapter sequence (AACTGTAGGCACCATCAAT) was allowed. Reads with incomplete UMI sequence (<12nt) and shorter than 15bp after trimming were excluded from the downstream analyses.
Trimmed reads were mapped to miRBase v22 mature human miRNA sequences. Prior to mapping, mature miRNA records with identical sequences were collapsed to allow unique mapping. Bowtie2 v2.3.4.1 local alignment with following parameters was used: “-N1 -L9 --norc -k10 --local --score-min L,4,1.3 --mp 4”. Reads mapping to multiple miRNAs with equal scores were excluded. Uniquely mapped reads were deduplicated based on UMI using the “unique" method in UMI-tools. Next, SAMtools v1.9 idxstats was used to obtain read counts for each miRNA. The counts are in mirna_count_matrix.txt
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited matrix of miRBase mapping read counts

source_name: breast milk

extract_protocol:
miRCURY Exosome Cell/Urine/CSF Kit (Qiagen, Hilden, Germany), according to manufacturers instructions.
Serum/Plasma Advanced Kit (Qiagen), according to manufacturers instructions.
QIAseq miRNA Library Kit (Qiagen), according to manufacturers instructions.

treatment_protocol: HPP samples: subjected to HPP in 62.5°C for 30 minutes in Human Milk Pasteurizer S90 Eco (Sterifeed, Medicare Colgate Ltd, England, Cullompton). HoP samples: HoP using U 4000/65 apparatus (Unipress Equipment, Poland, Celestynow). Control samples: untreated. Storage: frozen at -20°C before further processing.

tag: material

value: exosomes

value: HPP

tag: donor

value: C


title: Holder pasteurized  whole milk from donor C (exosomal fraction)

description:
excluded from expression analysis due to low miRNA read count
mirna_count_table.txt
Milk-Ex-2C

value: HoP


title: DU145-miR-205* rep 1

description:
DU145 cells transfected with miR-205* synthetic mimic
5591989038_D


title: MDA_mut-3

city: Jerusalem

first: Rami

last: Aqeilan

address: Hadassah medical school

department: Immunology and Cancer Research

country: Israel

institute: Hebrew University

hyb_protocol: hybridized using Affymetrix GeneChip® Human Genome U133 Plus 2.0 arrays.

scan_protocol: The quality assurance, calibration, data normalization and principal component analysis for the Affymetrix cell format files were performed by Partek Genomics Suite 6.5 (Partek Genomics, St Louis, MO, USA).

data_processing: Differentially expressed genes were analyzed using the Enricher dataset (http://amp.pharm.mssm.edu/Enrichr/) and the KEGG database.

source_name: metastatic melanoma cancer

label_protocol: standard Affymetrix protocol

growth_protocol: cells were grown in DMEM (Gibco) supplemented with 10% FBS, glutamine and penicillin/streptomycin

extract_protocol: Total RNA was prepared using TRI reagent, BIO TRI (Biolab, Israel) as described by the manufacturer.

treatment_protocol: Stable clones for WWOX overexpression were produced using a lenti-viral vector (pDEST12.2TM destination vector, Gateway Cloning Technology) containing either WT or mutated (WFPA) WWOX. Clones were selected using 2mg/ml G418 (Gibco 11811031).

tag: lenti-viral vector

value: WFPA MUT WWOX protein


title: MDA_wox5-3


title: MDA_wox5-2


title: MDA_wox5-1


title: high-pressure processed whole milk from donor B (exosomal fraction)

description:
mirna_count_table.txt
Milk-Ex-3B

value: B


title: Holder pasteurized  whole milk from donor B (exosomal fraction)

description:
excluded from expression analysis due to low miRNA read count
mirna_count_table.txt
Milk-Ex-2B


title: Holder pasteurized  whole milk from donor A (exosomal fraction)

description:
excluded from expression analysis due to low miRNA read count
mirna_count_table.txt
Milk-Ex-2A

value: A


title: unprocessed whole milk from donor C (exosomal fraction)

description:
mirna_count_table.txt
Milk-Ex-1C

value: untreated


title: high-pressure processed  whole milk from donor C

description:
mirna_count_table.txt
Milk-3C

extract_protocol:
Serum/Plasma Advanced Kit (Qiagen), according to manufacturers instructions.
QIAseq miRNA Library Kit (Qiagen), according to manufacturers instructions.

value: whole milk


title: MDA_mut-2


title: high-pressure processed whole milk from donor A (exosomal fraction)

description:
mirna_count_table.txt
Milk-Ex-3A


title: unprocessed whole milk from donor B (exosomal fraction)

description:
mirna_count_table.txt
Milk-Ex-1B


title: MDA_EV(wox+)-3

value: WT WWOX protein


title: SCLC tumor, sgp130_6697T2

city: Cambridge

first: A

last: Bhutkar

address: 77 Massachusetts Avenue

institute: MIT

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Reads were mapped to the mouse transcriptome (UCSC annotation, genome build mm9) using rsem v1.2.12 and bowtie v1.0.1 with default options. Estimated counts from rsem were upper-quartile normalized where the 75th percentile was set to 1000.
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel files include estimated read counts (from rsem) per gene for each sample and normalized counts per gene for each sample.

source_name: Small cell lung cancer tumor

extract_protocol:
Tumors were dissected from lungs upon necropsy and flash-frozen in liquid nitrogen, followed by storage at -80C. Total RNA was isolated from frozen tumors using the AllPrep DNA/RNA Mini Kit (QIAGEN #80204).
Libraries were prepared using the KAPA mRNA HyperPrep Kit (Roche #08098123702), according to the manufacturer's protocols.

value: mixed C57BL/6;129/Sv

tag: crispr-mediated mutation

value: Small cell lung cancer tumor


title: INPUT_1

city: HERSHEY

first: Guy

last: Townsend

state: PA

address: 500 University Drive, BMR Rm. C6820

department: Biochemistry & Molecular Biology

institute: Penn State College of Medicine

description: Total input DNA 10 minutes following a switch from mid-exponential phase growth in glucose as a sole carbon source to carbon starvation (replicate 1)

data_processing:
files were converted to fastqsanger using FASTQ Groomer
reads were mapped to the B. thetaiotaomicron genome using Bowtie2 (v.2.3.4)
Peaks were called for each sample using bamCoverage (v.2.5.0)
Peaks enriched in IP samples relative to total input DNA were normalized by bamCompare (v.2.5.0))
Genome_build: NC_004.fastq.gz663
Supplementary_files_format_and_content: bigwig files corresponding to regions of the B. thetaiotaomicron genome enriched in IP samples relaltive to total input DNA

organism: Bacteroides thetaiotaomicron

source_name: human gut bacteria

growth_protocol: Cells were grown to mid-exponential phase in minimal media containing 0.5% glucose and switched to carbon starvation for 10 minutes

extract_protocol:
Cross-linked DNA was immunoprecipitated using a rabbit anti-HA antibody (MilliporeSigma Cat# H6908) and the EZ-Magna ChIP A/G Chromatin Immunoprecipitation Kit (MilliporeSigma Cat# 17-10086)
Libraries were prepared using the standard Illumina protocol entitled: Preparing Samples for ChIP  Sequencing of DNA

treatment_protocol: Cells were treated with formaldehyde following by the addition of glycine to quench and ice cold PBS washes as previously described (PMID: 19300486)

tag: condition

value: No C


title: IP_3

description: IP following 10 minutes following a switch from mid-exponential phase growth in glucose as a sole carbon source to carbon starvation (replicate 3)


title: IP_2

description: IP following 10 minutes following a switch from mid-exponential phase growth in glucose as a sole carbon source to carbon starvation (replicate 2)


title: INPUT_2

description: Total input DNA 10 minutes following a switch from mid-exponential phase growth in glucose as a sole carbon source to carbon starvation (replicate 2)


title: high-pressure processed whole milk from donor A

description:
mirna_count_table.txt
Milk-3A


title: SCLC tumor, sgp130_6697T1


title: INPUT_3

description: Total input DNA 10 minutes following a switch from mid-exponential phase growth in glucose as a sole carbon source to carbon starvation (replicate 3)


title: MDA_EV(wox+)-2


title: SCLC tumor, sgp130_6638T3


title: SCLC tumor, sgp130_6638T5


title: Holder pasteurized  whole milk from donor C

description:
excluded from expression analysis due to low miRNA read count
mirna_count_table.txt
Milk-2C


title: SCLC tumor, sgp130_6637T3


title: SCLC tumor, sgp130_6637T2


title: IP_1

description: IP following 10 minutes following a switch from mid-exponential phase growth in glucose as a sole carbon source to carbon starvation (replicate 1)


title: unprocessed whole milk from donor A (exosomal fraction)

description:
mirna_count_table.txt
Milk-Ex-1A