title: HEC1A_EZH2_SiRNA2

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

description:
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.
5457296046_K.AVG_Signal

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V3.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

growth_protocol: Hec-1A was maintained with RPMI1640 supplemented with 15% fetal bovine serum and 0.1% gentamicin sulfate.

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

treatment_protocol: EZH2 siRNA and control siRNA were purchased in Qiagen. siRNA was transfected using N-TERTM Nanoparticle siRNA Transfection System (Sigma-Aldrich) in accordance with the manufacturer’s recommendations.

tag: cell type

value: Endometrial adenocarcinoma

tag: sirna


title: HEC1A_CONTROL-3

status: Public on May 01 2019

type: RNA

country: USA

description:
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.
5457296046_I.AVG_Signal

label: Biotin

molecule: total RNA

organism: Homo sapiens

tag: cell line


title: HEC1A_EZH2_SiRNA1

description:
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.
5457296046_J.AVG_Signal


title: HEC1A_EZH2_SiRNA3

description:
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.
5457296046_L.AVG_Signal


title: 12/238_PBC

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

description: RNA expression levels in the blood of patient diagnosed with primary biliary cholangitis.

hyb_protocol: Standard Illumina hybridization protocol. Hybridization performed in AROS (Denmark) http://arosab.com/services/microarrays/gene-expression/ .

scan_protocol: Standard Illumina scanning protocol.

data_processing: Quantile normalised using lumi library in R 2.15.

label: biotin

source_name: Primary biliary cholangitis, adult

label_protocol: Standard Illumina labeling protocol.

extract_protocol: For RNA extraction, whole blood was collected and total RNA was isolated using the Tempus RNA Isolation Kit (Thermo Fisher Scientific), according to the manufacturer’s instructions. RNA quality and quantity were analyzed using a NanoDrop spectrophotometer, and samples with A260/A280 ratios of 1.8–2.1 were further assessed using an Agilent 2100 Bioanalyzer. Samples used for microarray analysis had RNA integrity numbers in the range 7.6–9.6.

tag: condition

value: primary biliary cholangitis

tag: age group

value: adult

tag: tissue

value: whole blood


title: 25m bio-rep2 tech-rep1

type: SRA

city: Austin

first: Claus

last: Wilke

state: Texas

address: 2500 Speedway, A4800

department: Integrative Biology

institute: University of Texas at Austin

library_source: transcriptomic

data_processing:
alignment with hisat2
counting with bedtools multicov
computation of TPMs with R script
Genome_build: U00096.3 (E. coli K12) and NC_001604.1 (T7), excluding ribosomal genes
Supplementary_files_format_and_content: tab-delimitted text files contain raw counts for each sample, outputted from bedtools multicov

organism:
Escherichia coli
Escherichia phage T7

source_name: cell culture

extract_protocol:
RNA was isolated using Trizol reagent (Thermo Fisher Scientific)
Fragmentation and reverse transcription of RNA with random primers was carried out using the NEB First Strand Synthesis Module (New England Biolabs). Second strand synthesis was done with the NEBNext Ultra Directional RNA Second Strand Synthesis Module (New England Biolabs), then purified with 1.7x AMPURE Bead XP (Beckman Coulter). DNA end repair was carried out with the NEBNext end repair module, dA-tailing used the NEBNext dA-Tailing Module and adapter ligation used the NEBNext Quick Ligation module (New England Biolabs). PCR amplification was carried out for 10 rounds of synthesis using the NEBNext High-Fidelity PCR Master Mix with NEBNext USER Enzyme (New England Biolabs), samples were purified with 1.0x AMPURE Bead XP (Beckman Coulter). Library quality was verified on a Bio-Analyzer DNA chip (Agilent).

tag: t7 strain

value: wild type

tag: time


title: Ex3_IRES_IL-4

city: Bangkok

first: Tanapat

last: Palaga

address: Payathai Road, Pathumwan

department: Microbiology

country: Thailand

institute: Chulalongkorn University

data_processing:
Quality check of the raw reads data files using FASTQC software.
Adapter and poor quality reads were removed using Trimmomatic.
The filtered reads were aligned to Human reference genome (EnsembleXX) using HISAT2 aligner software.
HTSeq program was implemented to obtain raw counts for all human genes.
T+B52he gene counts were used for differential expression analysis with the DESeq2 package.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: counts

source_name: THP-1 cell line

growth_protocol: THP-1 cell line was cultured in RPMI1640 medium supplemented with 10%FBS, HEPES, sodium pyruvate and antibiotics (penicillin and streptomycin)

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (QIAGEN). 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

treatment_protocol: THP-1 cell line was retrovirally transduced with IRES (MSCV-GFP-IRES), NIC1 (MSCV-GFP-MYC-NIC1) or DNMAML (MSCV-GFP-DNMAML) overexpressing construct. GFP+ cells were sorted using cell sorter. For RNASeq, IRES, NIC1 and DNMAML overexpressing THP-1 cell were pretreated with PMA (5 ng/ml) for 48 h before stimulating with IL-4 (20 ng/ml) for 3 h.

tag: transduction

value: IRES

tag: agent


title: 12/295_PBC


title: Ex1_NIC1_IL-4


title: 20m bio-rep2 tech-rep2


title: 10m bio-rep3 tech-rep2


title: Ex2_IRES_IL-4


title: Ex1_IRES_IL-4


title: 20m bio-rep2 tech-rep1


title: WT mouse on high fat diet for 8 wks, 2

city: Concord

first: Eirini

last: Vagena

state: CA

address: 2331 Saint George Dr

institute: UCSF

description: Gene expression data from hypothalamus of WT mice on 8 wks on high fat diet.

hyb_protocol: Hybridization was performed to Rat and Mouse Gene 1.0 ST GeneChip arrays (Affymetrix)

scan_protocol: Arrays were scanned using an Affymetrix GCS3000 scanner and Affymetrix Command Console software.

data_processing: Data were normalized using the RMA algorithm in Affymetrix Expression Console. Microarrays were normalized for array-specific effects using Affymetrix's “Robust Multi-Array” (RMA) normalization.

organism: Mus musculus

source_name: hypothalamic sample of WT mouse for 8 wks on high fat diet

label_protocol: Probes were prepared using NuGEN Ovation Pico WTA V2 kit and NuGEN Encore Biotin Module.

growth_protocol: Mice were maintained either on normal chow or high fat diet.

extract_protocol: RNA isolated with Rneasy Lipid Tissue Mini Kit.

treatment_protocol: Mice were given high fat diet either for 4 or 8 wks and compared to normal chow fed mice.

tag: diet

value: high fat diet

value: brain tissue

tag: genotype

value: WT

tag: age


title: HEC1A_CONTROL-1

description:
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.
5457296046_G.AVG_Signal


title: WT mouse on high fat diet for 8 wks, 1


title: WT mouse on high fat diet for 8 wks, 3


title: 15m bio-rep2 tech-rep1


title: Ex3_DNMAML_un

value: DNMAML

value: unstimulated


title: WT mouse on high fat diet for 4 wks, 3

description: Gene expression data from hypothalamus of WT mice on 4 wks on high fat diet.

source_name: hypothalamic sample of WT mouse for 4 wks on high fat diet


title: HEC1A_CONTROL-2

description:
To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software.
5457296046_H.AVG_Signal


title: Ex2_DNMAML_un


title: 10m bio-rep2 tech-rep2


title: Ex1_DNMAML_un


title: 5m bio-rep2 tech-rep2


title: Ex3_NIC1_un


title: 5m bio-rep2 tech-rep1


title: WT mouse on high fat diet for 4 wks, 2


title: WT mouse on normal chow, 3

description: Gene expression data from hypothalamus of WT mice on normal chow.

source_name: hypothalamic sample of WT mouse on normal chow

value: normal chow


title: Ex2_NIC1_un


title: WT mouse on high fat diet for 4 wks, 1


title: WT mouse on normal chow, 2


title: Ex1_NIC1_un


title: 25m bio-rep1 tech-rep2


title: 15m bio-rep2 tech-rep2


title: Ex3_IRES_un


title: 25m bio-rep1 tech-rep1


title: 20m bio-rep1 tech-rep1


title: 10m bio-rep2 tech-rep1


title: Ex1_IRES_un


title: 15m bio-rep1 tech-rep1


title: 10m bio-rep1 tech-rep2


title: rapamycin_rep2

city: London

first: Manuela

last: Plate

state: Greater London

address: 5, University Street, Rayne Institute

department: UCL Respiratory

country: United Kingdom

institute: UCL

data_processing:
Data analysis was performed with the Illumina Basespace platform.
Reads pre-processing and alignment to the genome (Homo sapiens UCSC hg19) were performed using the Illumina BaseSpace RNA-Seq alignment application STAR aligner.
Counts files for each individual sample were generated with Featurecounts.
Genome_build: hg19
Supplementary_files_format_and_content: All processed data files are in txt format and contain gene counts for each sample. The first column contains Ensembl gene IDs and the second colums contains gene counts.

source_name: primary human lung fibroblasts - rapamycin - 24h

growth_protocol: Primary human lung fibroblasts were grown in Dulbecco Modified Eagle Medium (DMEM) supplemented with 10% Fetal bovine serum (FBS), 1% Penicillin/Streptomycin and 1% L-glutamine. They were maintained at 37 degC and at 10% CO2. Cells were passaged when 80% confluent.

extract_protocol:
mRNA was extracted with the miRCURY RNA Isolation kit - Cell and Plant (Exiqon), following the manufacturer's instructions.
Poly(A)-taled RNA enrichment and library preparation were performed using the KAPA Stranded mRNA-Seq Kit with KAPA mRNA Capture Beads (KAPABiosystems), following the manufacturer's instructions.

treatment_protocol: 90% confluent cells were serum starved for 24h before treatment. Cells were treated with DMSO vehicle, AZD8055 1µM or rapamycin 100nM for 1h in the absence fo FBS. 1ng/mL TGFβ1 diluited in DMEM was spiked in the wells and the cells were incubated for 24h.

value: primary human lung fibroblasts

tag: cell passage

tag: gender

value: Male

tag: smoking history

value: former smoker


title: 10m bio-rep1 tech-rep1


title: Ex2_IRES_un


title: Phaeobacter inhibens ∆65kb+191kb_2

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

data_processing:
The demultiplexed raw fastq-files were quality-controlled using the FASTQ-mcf suite (https://github.com/ExpressionAnalysis/ea-utils). Low quality bases (Phred-score < 30) and Illumina adaptors were clipped. Reads were mapped to the reference genome using bowtie2 (Langmead et al., 2012) with default parameters for single end reads. Ambiguously mapping reads were randomly distributed between all regions to which they could be assigned. The resulting sam-files were converted to indexed binary format and pile-up format using samtools (Li et al., 2009). The program featureCounts (Liao et al., 2014) was used to count the reads mapping to genes.
Genome_build: strain specific (indicated for each sample): NC_009952.1, NC_009955.1 NC_009956.1, NC_009957.1, NC_009958.1, NC_009959.1, NC_018290.1, NC_018291.1, NC_018287.1, NC_018288.1
Supplementary_files_format_and_content: tab-delimited text file contains reads per gene

organism: Phaeobacter inhibens

source_name: strain grown in Marine broth

extract_protocol:
The pestled bacterial cell powder was covered with 1 ml TRIzol reagent (ThermoFisher Scientific, Waltham, MA, USA) and incubated for 5 min at room temperature. The further steps for total RNA isolation starting with the centrifugation at 12,000g for 10 min at 4°C were performed with the RNeasy mini kit (Qiagen, Hilden, Germany) as previously described (Wang et al. 2014). After DNase treatment, the total RNA was resolved in 50 µl ultrapure DEPC-treated H2O. Successful removal of genomic DNA was verified via PCR with specific primers against the 78 kb chromid (P737: 5´-GCTCTGCACCATTTCTTTTCG-3´,  P738: 5´-CGAGGCGGTTTGGTGTGTAGT-3´) using 1 µl of total RNA as a template. Depletion of ribosomal RNA was performed with the mRNA Ribo-Zero Magnetic Kit (Epicentre, Madison, WI, USA) according to the manufacturer´s instructions.
Single end, strand specific cDNA libraries were prepared using the Scriptseq v2 RNA-Seq Library Preparation Kit (Illumina, San Diego, CA, USA) following the manufacturers protocol. For sequencing equal volumes of libraries (12 pM) were multiplexed on a single lane. Sequencing was done on the HiSeq 2500 (Illumina, San Diego, CA, USA) using TruSeq SBS Kit v3 - HS (Illumina, San Diego, CA, USA) for 50 cycles resulting in 50 bp reads. Image analysis and base calling were performed using the Illumina pipeline v 1.8 (Illumina, San Diego, CA, USA).

tag: replicons present

tag: biological replicate

tag: technical replicate


title: 20m bio-rep1 tech-rep2


title: rapamycin_rep1


title: rapamycin_rep3


title: Phaeobacter inhibens ∆65kb+191kb_1


title: 5m bio-rep1 tech-rep2


title: AZD8055_rep4

source_name: primary human lung fibroblasts - AZD8055 - 24h


title: 15m bio-rep1 tech-rep2


title: WT mouse on normal chow, 1


title: Phaeobacter inhibens ∆65kb+191kb_3


title: AZD8055_rep3


title: 5m bio-rep1 tech-rep1


title: TBI+Zoloft 470: Whole hippocampus, 24hr post fluid percussion injury+Zoloft drug treatment, rep2

city: Northbrook

first: Michael

last: Falduto

state: IL

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

description: Gene expression of whole hippocampus 24hr post-injury

hyb_protocol: For mRNA: 1 µg of purified cRNA was fragmented to uniform size and applied to Agilent Whole Rat Genome microarrays (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, washed at 37° C for 1 min, and stained with Streptavidin-Alexa555.  For miRNA: Labeled target was applied to Agilent miRNA 8x60K v21 arrays (Design ID# 070154) and hybridized overnight.

scan_protocol: Slides were washed and scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

organism: Rattus norvegicus

label_protocol: For mRNA: Labeled cRNA was prepared by linear amplification of the Poly(A)+ RNA population within the Total RNA sample.  Briefly, Total RNA was reverse transcribed after priming with a DNA oligonucleotide containing the T7 RNA polymerase promoter 5’ to a d(T)24 sequence.  After second-strand cDNA synthesis and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase.  The quantity and quality of the cRNA was assayed by spectrophotometry and on the Agilent Bioanalyzer.  For miRNA: Total RNA samples were dephosphorylated, denatured, and end-labeled according to Agilent's protocols.

growth_protocol: Adult male Sprague-Dawley rats (350 g–400 g) from vendor Charles Rivers were housed 2 per cage with food and water ad libitum in a vivarium with these constant conditions: light cycle (6∶00–18∶00) temperature (21°C–23°C), and humidity (40%–50%).

extract_protocol: RNA was extracted and purified using Ribopure (Ambion) RNA isolation

treatment_protocol: Rats were subjected to experimental severe fluid percussion brain injury (with and without drug treatments), or sham injury and brains were removed 24 hours later, stored in RNA later and total RNA isolated at GenUs Biosystems.

tag: strain

value: Sprague-Dawley

tag: Sex

value: male

value: hippocampus


title: TBI+Zoloft 471: Whole hippocampus, 24hr post fluid percussion injury+Zoloft drug treatment, rep3


title: Phaeobacter inhibens ∆65kb+126kb_3


title: Phaeobacter inhibens ∆65kb+126kb_2


title: Ctrl_6mo_rep1

city: Gifu

first: Akihiro

last: Moriyama

address: 1-1, Yanagido

country: Japan

institute: Gifu University

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 min in a reaction volume of 25 μl containing 1x Blocking Agent and 1x Fragmentation Buffer. On completion of the fragmentation reaction, 2x Hybridization Buffer HI-RPM solution was added to the fragmentation mixture containing 0.6 μg of Cy3-labelled cRNA and hybridized for 17 h, at 65C and 10 rpm. After hybridization, microarrays were washed according to Quick Amp Labeling Kit Protocol (Agilent).

scan_protocol: The hybridized microarray slides were washed according to the manufacturer’s instructions and were scanned with an Agilent DNA Microarray Scanner (#G2565CA, Agilent Technologies, CA, USA) at a resolution of 5 μm.

data_processing: These data were normalized by the percentile shift 75% using GeneSpring GX version 11.5.1 software (Agilent Technologies).

label_protocol: The cDNA was synthesized by Quick Amp Labeling Kit (Agilent) using 0.5 μg total RNA as a template. Cyanine-3 (Cy3) labeled cRNA was prepared from cDNA using the T7 RNA polymerase. Cy3-labeled cRNA was purified by RNeasy Mini Kit (QIAGEN, Hilden, Germany), and checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from the lung by phenol-chloroform method using a Fast RNA Pro Red Kit (MP Biomedicals, California, USA) following the manufacturer's instructions. Total RNA was purified using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer instructions. The concentration and purity of the resulting RNA were evaluated by absorbance at 260 nm using an Agilent 2100 BioanalyzerTM (Agilent Technologies, California, USA).

treatment_protocol: After the mice were sacrificed, their lungs were rapidly removed and processed for DNA microarray analysis.

value: lung


title: AZD8055_rep2


title: TBI+Zoloft 469: Whole hippocampus, 24hr post fluid percussion injury+Zoloft drug treatment, rep1


title: AZD8055_rep1


title: rapamycin_rep4


title: TGFβ1_+_rapamycin_rep4

source_name: primary human lung fibroblasts - TGFβ1 + rapamycin - 24h


title: Phaeobacter inhibens ∆65kb_2B


title: TBI+Prozac 459: Whole hippocampus, 24hr post fluid percussion injury+Prozac drug treatment, rep3


title: TGFβ1_+_rapamycin_rep3


title: Phaeobacter inhibens ∆65kb+126kb_1


title: TGFβ1_+_rapamycin_rep2


title: TBI+Imipramine 466: Whole hippocampus, 24hr post fluid percussion injury+Imipramine, rep3


title: Phaeobacter inhibens ∆65kb_1B


title: NB2

type: genomic

city: beijing

first: zhao

last: mengxin

address: Haidian District Zhongguancun Street

country: China

institute: tsinghua university

description: replicate 2

hyb_protocol: Functional gene arrays (FGAs; GeoChip 4.2) was used for this study. It contains approximately 28 000 probes covering approximately 57 000 gene variants from 292 functional gene families involved in carbon, nitrogen, phosphorus and sulfur cycles, energy metabolism, antibiotic resistance, metal resistance and organic contaminant degradation (Tu et al. 2014). Dried label products were resuspended in 130 uL hybridization solution (40 uL; 50% formamide, 3× SSC, 0.3% SDS, 0.7 ug uL-1 herrring sperm DNA, 0.86 mM DTT) and incubated ant 95℃ for 5 min then maintained at 60℃ until hybridization. Hybridization to microarray was performed on HS4800 Hybridization Station (TECAN US, Durham, NC) at 42℃ for 10 h.

scan_protocol: After hybridization, the arrays were imaged by a ScanArray 5000® Microarray Analysis System (Perkin Elmer, Wellesley, MA) at 95% laser power and 68% PMT (photomultiplier tube gain).

data_processing: Signal intensities were quantified and processed using the data analysis pipeline as previously described (He et al 2010). Then processed GeoChip data were analyzed using the following steps: (i) remove the poor quality spots, which were flagged as 1 or 3 by ImaGene or with a signal to noise ratio (SNR) of less than 2.0; (ii) remove genes detected in only one out of three samples from the same elevation; (iii) the data were diveided by the mean value of each slide and then pultiplied the mean value of all slides; and (iv) the data were then logarithmically transformed.

molecule: genomic DNA

organism: uncultured soil microorganism

source_name: Soil microbes in exotic Ageratina adenophora soils

label_protocol: For each sample, 1.5 ug purified DNA was used to make microarray hybridization. DNA was denatured and then fluorescently labeled with cyanine-5 using random primer and purified as described previously (Wu et al. 2008). Briefly, DNA was mixed with 20 uL random primers (Octamers, 2.5×; Invitrogen BioPrime DNA labeling kit), and denatured in 99℃ for 5 min following by cooling on ice immediately. The labeling master mix (8 uL (2.5 uL of dNTP (5mM dAGC-TP, 2.5 mM dTTP), 1uL of Cy-5 dUTP (25 nM; Amersham), 2uL of Klenow (40 U uL-1), 2.5 uL of water)) was added and samples were incubated at 37℃ for 6 h in a thermocycler. Labeled DNA was using a QIAquick purification kit (Qiagen) according to the instructions, and then dried down in a SpeedVac (45℃, 45 min; ThermoSavant). All previous steps should be protected from the light as much as possible.

extract_protocol: DNA was extracted from 5 g soil using freeze-grinding and sodium dodecyl sulfate (SDS) for cell lysis method (Zhou et al. 1996). The extracted DNA was purified by low melting agarose gel electrophoresis, and followed by phenol-chloroform-butanol extraction. DNA quality was assessed by the ratios of 260/280 nm and 260/230 nm with ND-1000 spectrophotometer (Nanodrop Inc.). The final concentrations were quantified with a Qaunt-ItTM PicoGreen® kit (Invitrogen, Carlsbad, CA).

treatment_protocol: The study area was located in southwestern Yunnan Province, China. Soil samples from 5 A. adenophora expansion plots were collected in December 2010. For each plot, soil samples were collected as follows: after removal of 1 cm of litter from the soil surface and loosening of soil within a 30-cm radius of each plant with a shovel, plants were pulled up and shaken vigorously in situ until approximately 80% of the soil was removed. All soil remaining was then collected as a rhizosphere sample. Bulk soil samples were collected from the soil left in the hole.

tag: rhizosphere, bulk soils

value: bulk

tag: plant type

value: native plant


title: TGFβ1_+_rapamycin_rep1

tag: tissue


title: TBI+Prozac 456: Whole hippocampus, 24hr post fluid percussion injury+Prozac drug treatment, rep1


title: NB3

description: replicate 3


title: TBI+Imipramine 464: Whole hippocampus, 24hr post fluid percussion injury+Imipramine, rep1


title: NB1

description: replicate 1


title: Phaeobacter inhibens ∆65kb_1A


title: TBI+Prozac 458: Whole hippocampus, 24hr post fluid percussion injury+Prozac drug treatment, rep2


title: TGFβ1_+_AZD8055_rep4

source_name: primary human lung fibroblasts - TGFβ1 + AZD8055 - 24h


title: AXB3

description: replicate 3

value: multiculture of Ageratina adenophora and native plants


title: TBI 454: Whole hippocampus, 24hr post fluid percussion injury, rep2


title: TGFβ1_+_AZD8055_rep3


title: AXB1

description: replicate 1


title: TBI 460: Whole hippocampus, 24hr post fluid percussion injury, rep3


title: Phaeobacter inhibens DSM17395_3A


title: TBI 453: Whole hippocampus, 24hr post fluid percussion injury, rep1


title: TBI+Imipramine 465: Whole hippocampus, 24hr post fluid percussion injury+Imipramine, rep2


title: AXB2

description: replicate 2


title: Phaeobacter inhibens DSM17395_2B


title: TGFβ1_+_AZD8055_rep2


title: AB3

description: replicate 3

value: monoculture Ageratina adenophora


title: Phaeobacter inhibens DSM17395_2A


title: Second-round cell sort, library rep 5

city: Ann Arbor

first: Jacob

last: Kitzman

state: MI

address: 4811 Med Sci II, 1241 E Catherine St

department: Department of Human Genetics

institute: University of Michigan

library_source: genomic

source_name: Human HAP1 cells

growth_protocol: HAP1 and HAP1-derived cell lines and pools were maintained in Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 10% FBS and 100 units/mL penicillin, 100 µg/mL streptomycin (Invitrogen).

extract_protocol:
Genomic DNA was prepared using the Gentra Puregene kit (Qiagen #158767)
Integrated sgRNAs were amplified by PCR for 24 cycles. For sgRNA sequencing, 2 ug of gDNA per PCR reaction was used as template, and four reactions were pooled per sample to ensure sufficient representation of integrated sgRNAs. The resulting amplicon was diluted and further amplified in a second-round PCR to add Illumina adaptor sequences and sample-specific index barcodes.

treatment_protocol: HAP1 cells were transduced with the GECKOv2 lentiviral library, and at 24-hours post infection, puromycin (2.5 ug/ml final concentration) was added to the media to select for transduced cells.

tag: cell line


title: Phaeobacter inhibens DSM17395_3B


title: Sham 457: Whole hippocampus, 24hr post sham treatment, rep1


title: Phaeobacter inhibens DSM17395_1B


title: 200932680194_R06C01: CAFs shCtrl Replicate 2

city: Chicago

first: Mark

middle: Adam

last: Eckert

address: 929 East 57th St, W107

department: OB/GYN

institute: University of Chicago

description: cancer-associated fibroblast shCtrl

hyb_protocol: Standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: cancer-associated fibroblasts expressing shCtrl

label_protocol: Standard Illumina protocol

growth_protocol: Cells were grown in DMEM with 10 micromolar methionine for 21 days.

extract_protocol: DNA was extracted with the Qiagen AllPrep DNA/RNA Mini Kit per manufacturer's instructions.

treatment_protocol: No treatments applied.

tag: genotype/variation

value: shCtrl


title: Sham 461: Whole hippocampus, 24hr post sham treatment, rep2


title: 200932680194_R05C01: CAFs shCtrl Replicate 1

description: cancer-associated fibroblast shCtrl

value: cancer-associated fibroblasts expressing shCtrl


title: Second-round cell sort, library rep 4


title: 200932680194_R08C01: CAFs shNNMT Replicate 2

description: cancer-associated fibroblast shNNMT

source_name: cancer-associated fibroblasts expressing shNNMT

value: shNNMT


title: TGFβ1_rep3

source_name: primary human lung fibroblasts - TGFβ1 - 24h


title: NR3

description: replicate 3

value: rhizosphere


title: 200932680194_R02C01: WI-38 fibroblasts Ctrl Replicate 2

description: fibroblast control

source_name: fibroblasts expressing control

value: WI-38 fibroblasts expressing control

value: control


title: TGFβ1_rep4

value: primary human lung fibroblasts


title: AB2

description: replicate 2


title: AB1

description: replicate 1


title: Phaeobacter inhibens DSM17395_1A


title: TGFβ1_rep2

value: Male


title: Second-round cell sort, library rep 3


title: NR2

description: replicate 2


title: Second-round cell sort, library rep 2


title: 200932680194_R01C01: WI-38 fibroblasts Ctrl Replicate 1

description: fibroblast control


title: 200932680194_R03C01: WI-38 fibroblasts NNMT Replicate 1

description: fibroblast NNMT overexpression

source_name: fibroblasts overexpressing NNMT

value: WI-38 fibroblasts overexpressing NNMT

value: NNMT overexpression


title: Cntrl-FLAG-R1_miseq

city: Sheffield

first: Ian

last: Sudbery

address: Firth Court, Western Bank

department: Molecular Biology and Biotechnology

institute: University of Sheffield

description: Control iCLIP Replicate 1

data_processing:
Library strategy: iCLIP
Reads from complete lanes mapping to spiked in PhiX were removed by mapping the PhiX genome using bowtie v1.1.2 with paramteres ‘-v 2 --best --strata -a’
UMI sequences were removed from 5' end of reads using the extract command from UMI-tools v0.5.3 with the parameters '--bc-pattern=NNNXXXXNN'
Reads were adaptor trimmed and demultiplexed using repear version 15-065 keeping only reads longer than 15nt.
Reads were mapped to hg19 using STAR 2.4.2a and a junction database built from ensembl 75. The options to STAR were ‘--outFilterMultimapNmax 1 --outFilterType BySJout --outFilterMismatchNoverLmax 0.2 --outFilterScoreMin 0.8 --alignSJDBoverhangMin 1’
Alignments from different sequencing lanes for the same sample were merged and deduplicated using the dedup command from UMI-tools v0.5.3 with parameters `--method=directional`
Bed files of per base tag counts were produced by taking either the 5' most deletion in an alignment or the base immediately 5' of the 5' end of the alignment, accounting for alignement strand using iCLIP2BigWig from iCLIPlib (www.github.com/sudlab/iCLIPlib)
Genome_build: hg19
Supplementary_files_format_and_content: Bed files containing the tag count for each base in the genome. Union files contain counts from the sum of all replicates.

source_name: FlipIn HEK293T cells

growth_protocol: FlpIn-293 cells expressing the FLAG-tagged proteins were generated as described previously (Hautbergue et al., 2009, PMID: 19836239 ) and maintained in DMEM with 10% FBS, 15 µg/mL Blasticidin, and 0.1 mg/mL Hygromycin.

extract_protocol: iCLIP was then performed exactly as described previously (König et al., 2011 PMID: 21559008 ) but using 10 µg of anti-FLAG antibodies (Sigma) and performing the high salt washes of the immunoprecipitation part of the protocol at room temperature (22°C) on a rotating wheel for 5 minutes per wash. Additionally, the following modifications from (Broughton et al., 2013 PMID: 23583680) were used. All nucleic acid pellets were air dry for a maximum of 10 minutes to ease resuspension. Nucleic acids centrifugations after each overnight precipitation were done at 4°C, 16000 x g for 20 minutes and 5 minutes for the EtOH 80% washes. During the cDNA gel purification step, each gel piece was transferred to a 0.5 mL microcentrifuge tube pierced with 3-4 holes made with a 19-gauge needle. The gel-containing 0.5 mL tube was itself inserted inside a 1.5 mL microfuge tube and the assembly was centrifuged at 16000 x g for 2 minutes to efficiently shred the gel piece. After circularisation of the cDNAs, the Circligase was inactivated by heating the samples for 15 minutes at 80°C. To linearize the cDNAs, the standard iCLIP cut_oligo was replaced by a cut_oligo bearing a 3’ dideoxycytosine instead of four adenosines. Libraries for each sample were mixed and the mixture split across multiple sequencing lanes.

treatment_protocol: FLAG-tagged protein expression was induced for 48h in the stable cell lines by addition of tetracycline at 5 ng/mL for Nxf1, and 10 ng/mL for Chtop, and Alyref.

value: Expresses empty FLAG construct

tag: antibody

value: anti-FLAG (Sigma)


title: No_treatment_rep3

source_name: primary human lung fibroblasts -vehicle - 24h

value: former smoker


title: NR1

description: replicate 1


title: Nxf1-FLAG-R2_miseq

description: Nxf1-FLAG iCLIP Replicate 2

value: Expresses Nxf1-FLAG


title: TGFβ1_rep1


title: No_treatment_rep2


title: AXR2

description: replicate 2


title: 200932680194_R04C01: WI-38 fibroblasts NNMT Replicate 2

description: fibroblast NNMT overexpression


title: Cntrl-FLAG-R2_miseq

description: Control iCLIP Replicate 2


title: Phaeobacter inhibens ∆65kb_2A


title: Second-round cell sort, library rep 1


title: No_treatment_rep4


title: Weight-stable (ID155_098E)

city: Huddinge

first: Ingrid

last: Dahlman

address: Hälsovägen

department: Medicine

country: Sweden

institute: Karolinska Institutet

hyb_protocol: From non-degraded high-quality total RNA we prepared and hybridized biotinylated complementary RNA to Affymetrix Human Clariom D Assay, and then washed and stained slides using standardized protocols (Affymetrix Inc., Santa Clara, CA).

scan_protocol: We used standardized Affymetrix protocols (Affymetrix Inc., Santa Clara, CA).

data_processing: These arrays were pre-processed with RMA, which includes normalization, summarization of probes to probesets, and background correction. Prior to further analysis, collapseRows R function (Miller et al., 2011) was used to convert and collapse the transcript abundance quantification detected by Affymetrix probe sets to mapped FANTOM-CAT IDs. 48368 probe sets annoated as locus type coding or multiple complex were filtered for in order to include only protein-coding genes. Subsequently, probe sets with gene name absent, indicated as miRNA, transcript identified by AceView, uncharacterized LOC or uncharacterized protein were excluded, leaving 26064 transcripts for further analysis.

source_name: Subcutaneous adipose tissue

label_protocol: Total RNA were amplified and biotin labeled using the Whole Transcript (WT) Sense Target Labeling Protocol.

growth_protocol: Not relevant.

extract_protocol: Total RNA was isolated using the RNeasy kit (cat no. 217004, Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Biopsies from the abdominal subcutaneous adipose tissue depot were obtained from the surgical incision. Samples were immediately frozen in liquid nitrogen and kept at -70C for subsequent DNA and RNA preparation.

value: White adipose tissue

value: female

tag: weight change

value: Weight-stable

tag: time point

value: Follow-up

tag: subject id


title: AXR3

description: replicate 3

value: multiculture of Ageratina adenophora and native plants


title: Weight-losing (ID152_068F)

tag: age

value: Weight-losing

value: Baseline


title: Chtop-FLAG-R2_miseq

description: Chtop-FLAG iCLIP Replicate 2

value: Expresses Chtop-FLAG


title: AXR1

description: replicate 1

value: rhizosphere


title: AR2

description: replicate 2

value: monoculture Ageratina adenophora


title: AR3

description: replicate 3


title: Weight-losing (ID154_109E)

tag: gender


title: No_treatment_rep1

value: primary human lung fibroblasts

tag: cell passage

value: Male

tag: smoking history


title: Chtop-FLAG-R1_miseq

description: Chtop-FLAG iCLIP Replicate 1


title: Normal-2

city: Seoul

first: Minwoo

last: Park

address: 25, Seonyu-ro 13-gil, youngdeungpo-gu

department: Research & Development

country: South Korea

institute: ebiogen

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Liver

growth_protocol: Male C57BL/6 mice (4 weeks of age, 18 to 20 g of weight) purchased from Central Lab. Animal Inc. (Seoul, Republic of Korea) were used in all experiments. Mice were housed in a temperature-controlled room in the animal facility of the Chung-Ang University (Seoul, Republic of Korea) with a half day light/dark cycle and fed a standard laboratory diet. Mice were acclimated to the environment for at least seven days before being used for experiments.

extract_protocol:
RNA was extracted using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: We injected LPS (25mg/kg, i.p.) in Control group mice and the same volume of saline was injected into the Normal group mice.

value: Liver

tag: agent

value: saline


title: LGK974-2


title: LGK974-1


title: Nxf1-FLAG-R1_miseq

description: Nxf1-FLAG iCLIP Replicate 1

value: anti-FLAG (Sigma)


title: Normal-1


title: AR1

description: replicate 1


title: Alyref-FLAG-R1_miseq

description: Alyref-FLAG iCLIP Replicate 1

value: Expresses Alyref-FLAG


title: LPS 25mg//kg -3

value: LPS 25mg/kg


title: Alyref-FLAG-R2_miseq

description: Alyref-FLAG iCLIP Replicate 2


title: LPS 25mg//kg -4


title: Weight-stable (ID145_085E)

value: White adipose tissue


title: TGFβ1_+_AZD8055_rep1

value: former smoker


title: LPS 25mg//kg -2


title: LPS 25mg//kg -1


title: dbp2∆3-untreated

city: West Lafayette

first: Elizabeth

middle: J

last: Tran

state: IN

address: 175 S. University Street

department: Biochemistry

institute: Purdue University

description:
YPD1154
020936_115-3-YPD_TGACCA_run469_L004

data_processing:
Illumina adaptors were removed using Trimmomatic (version 0.36)
The random trimers were trimmed from the 5’ end of forward reads using cutadapt (version 1.9.1).
The processed reads were mapped to the S288C reference genome (R64-2-1, from Saccharomyces Genome Database) using STAR (version 2.5.2b) and only uniquely mapped reads (MAPQ = 255 after STAR alignment) were kept for the following analysis.
After ignoring genes with sequence overlaps with at least one other gene on the same strand, we retained 4861 genes for differential structure analysis. Reads were grouped according to their source mRNA, and the start and end indices from genomic alignment of each read were converted to the mRNA coordinates with the start of 5’ UTR as position +1.
The number of reads starting 1 nt downstream of each nucleotide were tallied to get the detection counts (detection of modification/noise in (+) DMS samples and noise in (-) DMS samples) for the nucleotide. In addition, the number of reads starting anywhere upstream of, at or 1 nt downstream of each nucleotide, and ending anywhere downstream of the nucleotide were tallied as its local coverage. Detection rates were calculated as ratio of detection counts to local coverage for each nucleotide. Raw reactivities were calculated by combining the information from (+) DMS and (-) DMS samples of the same biological replicate.
Raw reactivities in each replicate were normalized using 2-8% approach (ref), i.e., top 2% of reactivities were filtered as outliers and mean of the next 8% reactivities was used to normalize all reactivities in that replicate.
For each mRNA, reads from untreated (i.e., no DMS) Structure-seq libraries that were mapped to the ORF or 150 nt downstream of the 3’ UTR (referred as extended region below) were counted using the summarizeOverlaps function (IntersectionNotEmpty mode) in the Bioconductor package “GenomicAlignments” (version 1.8.4). Only transcripts (1) of which the extended region does not overlap with the downstream transcript, (2) with more than 0.97 counts per million, and (3) detected in at least two libraries, were analyzed. The differential expression of ORFs and extended regions between WT and dbp2∆ was analyzed using the Bioconductor edgeR package (version 3.14.0, (Robinson et al., 2010)). ORFs or extended regions with a false discovery rate (FDR) equal to or less than 0.05 were considered differentially expressed in dbp2∆ compared to the WT. For each transcript, if the ORF was not changed or down-regulated, but the extended region was up-regulated in dbp2∆, then it was regarded as a read-through mRNA in dbp2∆. If the ORF is up-regulated in dbp2∆, the extended region in dbp2∆ should be up-regulated and have a fold change twice higher than the fold change in the ORF to be considered as a read-through defect in dbp2∆ compared to the WT.
Genome_build: S288C reference genome (R64-2-1, from Saccharomyces Genome Database)
Supplementary_files_format_and_content: tab-delimited text files with normalized reactivity values in each transcript
Supplementary_files_format_and_content: tab-delimited text files with read counts of each transcript in each sample

molecule: polyA RNA

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were grown in YP with 2% glucose at 30 °C to an O.D. of 0.5~0.7

extract_protocol:
Total RNA was isolated using acid phenol/chloroform extraction. Polyadenylated RNAs were enriched with the Poly(A)Purist MAG kit (ThermoFisher Scientific). The poly(A) RNAs were treated with TURBO DNase and extracted using acid phenol/chloroform.
The procedure for library construction is as described by Ding et al. (Nat. Protocol 2015)

treatment_protocol: 50 mL of cells were incubated with 10 mM dimethyl sulfate (DMS) for 10 min at 30 °C with vigorous shaking. The reaction was quenched with 75 mL of 4.8 M 2-mercaptoethanol (BME) and 25 mL of isoamyl alcohol.

value: BY4741 (dbp2{delta})

value: MATa dbp2::KanMx6 his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0

tag: culture condition

value: liquid culture at mid-log phase

tag: treatment


title: dbp2∆1-DMS treated

source_name: dbp2∆-DMS treated

tag: strain

value: 10 mM dimethyl sulfate for 10 min


title: 200932680194_R07C01: CAFs shNNMT Replicate 1

description: cancer-associated fibroblast shNNMT

value: cancer-associated fibroblasts expressing shNNMT

value: shNNMT


title: Weight-stable (ID149_020F)

value: female

value: Weight-stable

value: Baseline


title: Weight-gaining (ID142_070F)

value: Weight-gaining


title: 6SBR_91_1

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

country: Italy

institute: University of Padova

description: Biological replicate 50

hyb_protocol: Oligo aCGH analysis was performed following the manufacturer’s recommendations, using  Oligo aCGH/ChIP-on-chip Hybridization Kit (Agilent Technologies)

scan_protocol: Arrays were scanned at 3 µm resolution using an Agilent G2565CA scanner, and image data were processed using Feature Extraction version 11.5

data_processing: Genomic Workbench version 7.0.4 fwas employed for data analysis, raw data were normalized using the centralization algorithm with a threshold of eight.

organism: Canis lupus familiaris

source_name: DLBCL

label_protocol: Tumor and reference DNA samples were labelled independently with cyanine 5-deoxyuridine triphosphate (dUTP) and cyanine 3-dUTP, respectively, using SureTag Complete DNA Labeling Kit.

extract_protocol: Genomic DNA was extracted from lymph nodes and skin punches using the DNeasy Blood & Tissue Kit (QIAGEN, Valencia, CA, USA) according to the manufacturer's instructions.

value: tumor

source_name: normal

value: skin biopsy


title: Weight-gaining (ID140_067F)


title: 61RAP_97_4

description: Biological replicate 49


title: dbp2∆3-DMS treated


title: dbp2∆1-untreated

description:
YPD1152
020932_115-1-YPD_ATCACG_run469_L002


title: Weight-gaining (ID147_092E)

value: Follow-up


title: Weight-gaining (ID139_123E)


title: Weight-stable (ID144_151E)


title: DKO 3

city: Brookings

first: Adam

middle: David

last: Hoppe

state: SD

address: Avera Health and Sciences Building RM 131, Box 2202

department: Chemistry and Biochemistry

institute: South Dakota State University

description: DKO replicate 3

data_processing:
The libraries were sequenced on an Illumina NextSeq 500 using a NextSeq 500/550 High Output Reagent Cartridge v2 (San Diego, CA) at 151 cycles. Fastq files were generated and demultiplexed on Illumina’s BaseSpace cloud network (San Diego, CA). Total read lengths are 150 nt.
Sequence reads were trimmed for adaptor sequence, low quality score reads were filtered, and reads pass filter were mapped to mouse genome GRCm38.p5) in CLC genomic workbench 9.0.1
Reads after trimming less than 15 nt were discarded
Reads Per Kilobase of exon per Megabase of library size (RPKM)  and total exon count were calculated by CLC genomic workbench 9.0.1
Supplementary_files_format_and_content: counts

source_name: Bone marrow drived macrophages

growth_protocol: Bone marrow derived Macrophages were differentiated from mouse bone marrow in DMEM+10%FBS+L-cell super natant(containing CSF-1) in uncoated culture plates until Day9

extract_protocol:
Adherent Cells were detached from plate and spun down, and RNA were extracted using GeneJET RNA purification kit( K0731, ThermoFisher scientific) and Turbofree DNA free Kit (# AM1907, ThermoFisher Scientific)  were used to remove genomic DNA from total RNA
The total RNA was quantified by QuBit dsDNA HS Assay (Life Technologies, Carlsbad, CA) and pooled in equimolar concentrations.
Library was prepped through TruSeq Stranded mRNA Library Prep for NeoPrep protocol(Illumina)

tag: genotype

value: Cbl-/- and Cbl-b -/-

value: Day 9


title: Weight-stable (ID148_135E)

value: White adipose tissue


title: Weight-stable (ID138_084E)


title: 60MAG_605_3

description: Biological replicate 48


title: 5MAN_283_3

description: Biological replicate 47


title: WT3-DMS treated

source_name: WT-DMS treated

value: BY4741 (Wild type)

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0


title: DKO 2

description: DKO replicate 2


title: Weight-stable (ID137_149E)


title: Weight-stable (ID136_142E)


title: 59PIO_603_4

description: Biological replicate 46


title: WT2-DMS treated


title: 58RIS_606_4

description: Biological replicate 45


title: DKO 1

description: DKO replicate 1


title: Cbl-b 3

description: Cbl-b -/- replicate 3

value: Cbl-b -/-


title: WT1-DMS treated

value: liquid culture at mid-log phase


title: Weight-losing (ID135_025F)

value: Weight-losing


title: Weight-gaining (ID134_024F)


title: WT3-untreated

description:
WT4YPD
020934_WT3-YPD_CAGATC_run469_L003

source_name: WT-untreated


title: Cbl-b 2

description: Cbl-b -/- replicate 2


title: WT2-untreated

description:
WT3YPD
020938_WT2-YPD_ATCACG_run469_L004


title: Weight-losing (ID132_108E)


title: Cbl 3

description: Cbl -/- replicate 3

value: Cbl -/-


title: Cbl-b 1

description: Cbl-b -/- replicate 1


title: 57DIL_92_4

description: Biological replicate 44


title: 56GAL_99_4

description: Biological replicate 43


title: WT1-untreated

description:
WT2YPD
020930_WT1-YPD_TGACCA_run469_L002


title: 53GUE_603_3

description: Biological replicate 41


title: 55DIA_92_1

description: Biological replicate 42


title: 52SOL_605_2

description: Biological replicate 40


title: Cbl 2

description: Cbl -/- replicate 2


title: Set1-2

data_processing:
library strategy: iCLIP-seq
The Solexa adaptors were removed from the reads using Trimmomatic (version 0.36)
To separate the reads from each library, the fastq files were de-multiplexed using the script from the Chang lab (splitFastq.pl, https://github.com/qczhang/icSHAPE/tree/master/scripts)
PCR duplicates were removed based on the random barcodes incorporated in the RT primers using the script provided by the Chang lab (readCollapse.pl, https://github.com/qczhang/icSHAPE/tree/master/scripts)
Barcode sequences (13 nt) were trimmed from the 5’ end of kept forward reads using cutadapt (version 1.9.1)
Reads were mapped to the S288C reference genome (R64-2-1, from Saccharomyces Genome Database) using STAR (version 2.5.2b), and only uniquely mapped reads (MAPQ = 255 after STAR alignment) were kept for the following analysis.
For each of the three Dbp2-iCLIP replicates, reads that are not overlapped with any reads in the other two replicates were regarded as background and were discarded. The number of reads mapping to each mRNA was counted using the summarizeOverlaps function. Transcripts that had less than 5 counts in each library were filtered from the analysis. Only transcripts that were identified in all three replicates were regarded as binding targets. The same filtering was applied to the three replicates of our control Set1-iCLIP experiment. The nucleotide position before the start of each read was extracted from the forward reads as the crosslinking sites in each replicate. Crosslinking sites found in the Set1-iCLIP samples were removed from Dbp2-iCLIP data as background.
Genome_build: S288C reference genome (R64-2-1, from Saccharomyces Genome Database)
Supplementary_files_format_and_content: Bedgraph files with data values showing the relative level of Dbp2 binding at each nucelotide. The positive and negative value indicate the strandeness. The binding counts in each replicate were normalized to the library size. The normalized values were then summed from all three replicates.

source_name: total RNA pulled down with Set1

growth_protocol: yeast cells expressing DBP2-3XFLAG or 3XFLAG-SET1 were grown in 250 mL of YP with 2% glucose at 30 °C to an O.D. of 0.5~0.7.

extract_protocol:
Cells were harvested, frozen in liquid nitrogen, and lysed cryogenically using a Retsch Oscillating Mill MM400. 3XFLAG tagged Dbp2 or Set1 and bound RNAs were immunoprecipitated using M2 anti-FLAG antibody. After immunoprecipitation, samples were ligated with a biotinylated 3' adaptor, size-selected by SDS-PAGE, digested with proteinase K, and RNAs  were extracted using acid phenol/chloroform.
cDNAs were generated using TGIRT-III enzyme and circularized using CircLigase II (epicentre). After purified using MyOne Streptavidin C1 Dynabeads, cDNAs were amplified using SYBR master mix (Applied Biosystems) and gel-purified.

treatment_protocol: Cells were harvested and washed in 10 mL ice-cold TBS (20 mM Tris, 150 mM NaCl, pH 7.4) with 2% glucose. After centrifugation at 5000 rpm for 5 min, pellets were resuspended in 12.5 mL ice-cold TBS with 2% glucose and placed in a 15-cm2 petri dish. Cells were irradiated on ice by UV-C (254 nm) at 180 mJ/cm2 twice, with a 45-second rest between irradiations.

value: BY4741 (3XFLAG-SET1)

value: 3XFLAG-SET1:MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 3XFLAG-SET1

tag: culture stage


title: Cbl 1

description: Cbl -/- replicate 1


title: Set1-3


title: Weight-gaining (ID130_144E)

tag: tissue

value: female


title: WT 3

description: WT replicate 3

value: Wild type


title: Weight-gaining (ID127_052F)

value: Weight-gaining

value: Baseline


title: Set1-1


title: Dbp2-3

source_name: total RNA pulled down with Dbp2

value: BY4741 (DBP2-3XFLAG)

value: DBP2-3XFLAG:MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 DBP2-3XFLAG


title: Weight-stable (ID126_072F)

value: Weight-stable


title: WT 2

description: WT replicate 2

value: Day 9


title: 50RUZ_603_2

description: Biological replicate 39

value: tumor

value: skin biopsy


title: Dbp2-2


title: 48CAS_91_3

description: Biological replicate 36


title: 4DIG_282_4

description: Biological replicate 38


title: 49CAV_99_2

description: Biological replicate 37


title: WT 1

description: WT replicate 1


title: Weight-stable (ID128_017F)

value: White adipose tissue


title: Dbp2-1


title: Weight-gaining (ID125_045F)


title: DRG_WT_PSP_3

city: St Lucia

first: Alexander

last: Mueller

state: Queensland

address: 306 Carmody Rd

department: Institute for Molecular Bioscience

country: Australia

institute: University of Queensland

data_processing:
Alignment: STAR aligner (version star/2.3.0e) and samtools
Mapping: Mapped to Ensembl Mus musculus mm10 genome (version GRCm38)
Counts: Generated using HTSeq_count in the HTSeq package
Genome_build: mm10
Supplementary_files_format_and_content: .txt files, tab-delimited.

source_name: Dorsal root ganglia from levels L3, L4 and L5

extract_protocol:
Whole dorsal root ganglia (DRG) from levels L3, L4 and L5 (ipsilateral to the injured paws) were removed and immediately put into RNALater and cut into pieces in RNA later. DRGs from four animals were collected and pooled to obtain one biological replicate. RNA was extracted using the Rneasy Mini kit (Qiagen).
RNA libraries were prepared using TruSeq stranded total RNA library preparation.

value: male

value: 8 weeks

value: 24h post surgery


title: DRG_WT_PSP_2


title: 46MAR_97_3

description: Biological replicate 34


title: DRG_WT_PSP_1


title: Weight-stable (ID123_083E)

value: Follow-up


title: Weight-losing (ID121_056F)

value: Weight-losing


title: DRG_WT_sham_3

value: naïve


title: 45FON_91_4

description: Biological replicate 33


title: DRG_WT_sham_2


title: Weight-stable (ID120_064F)

value: female


title: Weight-stable (ID118_154E)


title: 47GIA_93_1

description: Biological replicate 35


title: 44GHE_605_1

description: Biological replicate 32


title: Weight-stable (ID117_107E)


title: 42TAD_601_1

description: Biological replicate 30


title: Weight-gaining (ID119_050F)


title: macrophage_bb94 treated_on plastic_bio rep2

first: Stephen

middle: J.

last: Weiss

address: 210 Washtenaw Avenue

department: Life Sciences Institute

description: Gene expression data from LPS-stimulated macrophages in the presence of MMP inhibitors on plastic

hyb_protocol: Following labeling procedure, 2.75 ug of cDNA were hybridized at 48C on [Array], and were washed and stained using the Affymetrix GeneTitan system (software version 4.3.0.1592)

scan_protocol: Arrays were scanned using the Affymetrix GeneTitan system (software version 4.3.0.1592).

data_processing: Data was analyzed using the oligo and limma Bioconductor package implemented in the R-statistical language version 3.4.3. RMA was used to fit log2 transformed expression values.

source_name: macrophages, with BB94 inhibitor, on plastic

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix WT Pico kit protocol (GeneChip® WT Pico Reagent Kit Manual P/N 703262 Rev. 1) from 5 ng total RNA

growth_protocol: Macrophages were differentiated and maintained in RPMI 1640 with 1% penicillin-streptomycin solution and 20% autologous serum for 5-7 days. Autologous serum was prepared by incubating non-heparinized whole blood at 37 °C for 1 h followed by centrifugation at 2,850 g for 15 minutes, and sterile filtration of the serum fraction.

extract_protocol: RNA was isolated from macrophages using the NucleoSpin RNA kit (Macherey Nagel) according to manufacturer's instructions

treatment_protocol: Macrophages were treated with 1ug/ml LPS in the presence or absence of 5um BB-94 for 72h then rinsed with PBS twice before the addition of extraction buffer (NucleoSpin RNA kit--Macerey Nagel)

tag: cell type

value: primary human peripheral blood monocyte derived macrophage

tag: substrate

value: TC-treated plastic


title: macrophage_untreated_on plastic_bio rep2

description: Gene expression data from LPS-stimulated macrophages on plastic

source_name: macrophages, no inhibitor, on plastic


title: Weight-losing (ID115_057F)

value: Baseline


title: Weight-stable (ID116_019F)


title: DRG_WT_sham_1


title: 41RAI_90_2

description: Biological replicate 29


title: macrophage_untreated_on plastic_bio rep1


title: macrophage_bb94 treated_on plastic_bio rep1


title: 43GIA_604_4

description: Biological replicate 31


title: 40PIN_97_2

description: Biological replicate 28


title: Weight-stable (ID113_002F)


title: 3GIAN_281_2

description: Biological replicate 27


title: macrophage_bb94 treated_on mesentery_bio rep2

description: Gene expression data from LPS-stimulated macrophages in the presence of MMP inhibitors on tissue

source_name: macrophages, with BB94 inhibitor, on mesentery tissue

value: decellularized rat mesentery tissue


title: PBS006_S2

city: Paris

first: Felipe

middle: Leal

last: Valentim

state: Île-de-France

address: Bâtiment Cervi, 4ème étage, pièce 052

country: France

institute: INSERM/UPMC

description: control

data_processing:
Nextera adaptor removal: Trimmomatic (Bolger et al., 2014)
Reads alignment : hisat2 (Kim et al., 2015)
Read counts: featureCounts (Liao et al., 2014)
Read counts normalization: DESeq2 (Anders and Huber, 2010)
SAM to BAM conversion: samtools (Li et al., 2009)
Genome_build: Ensembl genome (Yates et al., 2016) version GRCm38:
Supplementary_files_format_and_content: reads_count.gene_level.txt: Raw read counts as outputed by featureCounts

source_name: Uterus

extract_protocol:
Females (4 diphtheria toxin treated and 4 PBS1X) were scarified at day E8 of pregnancy and the entire uterus (with fetal tissues) was collected and samples were incubated overnight in RNAlater (Qiagen) at 4°C and then transferred to -80°C for storage. Samples were then lysed and homogenized using the tissue lyser (Qiagen) and total RNA was purified using Trizol (Invitrogen) according to the manufacturer’s instructions. RNA yield was assessed using a NanoDrop 1000 spectrophotometer (NanoDrop Products, Thermo Fisher Scientific). RNA integrity was assessed using an Agilent Bioanalyzer showing a quality RNA integrity number of 8–10 (Agilent Technologies).
The RNA was processed using the Illumina TotalPrep RNA Amplification Kit Protocol according to the manufacturer's protocol. High quality libraries were prepared using the Kapa mRNA hyperprep kit (ROCHE). The quality control was done in Tapestation and Quantifluor. Illumina sequencing of the 8 samples in 100 million reads/sample was done with the NextSeq 500 High Output Kit v2 (300 cycles) sequencer (Illumina Inc) generating paired end reads of approximately 2 x 75 bp in length.

treatment_protocol: Foxp3DTR females were allogenic matted with BALB/c males and treated with daily intraperitoneal injections of 1ug of diphtheria toxin or PBS1X at E1, E3, E5, and E7 days of pregnancy. That treatment regimen allowed the depletion of 85% of total Tregs after four injections and was based on the study done for the Foxp3DTR  mouse line.

tag: treatement

value: Control PBS1X

tag: pregnancy stage

value: Day 8


title: 39BER_99_1

description: Biological replicate 26


title: PBS002_S1

description: control


title: PBS004_S2

description: control


title: PBS001_S1

description: control


title: DT005_S4

description: regulatory T cells depleted

value: Diphteria toxin


title: DT004_S4

description: regulatory T cells depleted


title: Weight-losing (ID112_145E)

tag: weight change

tag: time point


title: macrophage_bb94 treated_on mesentery_bio rep1


title: DT003_S3

description: regulatory T cells depleted


title: macrophage_untreated_on mesentery_bio rep2

description: Gene expression data from LPS-stimulated macrophages on tissue

source_name: macrophages, no inhibitor, on mesentery tissue


title: 37BEG_601_4

description: Biological replicate 24

value: tumor


title: Weight-gaining (ID108_076F)

tag: age

value: Weight-gaining

tag: subject id


title: 38GOV_93_4

description: Biological replicate 25

value: skin biopsy


title: 36REI_601_3

description: Biological replicate 23


title: LSF-LC-

city: Shanghai

first: Yiqing

last: Zhu

address: 800 Xiang Yin Road

department: department of medical genetics

institute: Second military medical university

hyb_protocol: Hybridyzation was performed in Agilent's SureHyb Hybridization Chambers.

scan_protocol: After washing, slides were scanned with the Agilent DNA Microarray Sacnner. Data was extracted using Agilent Feature Extraction software.

data_processing: Further data analysis was performed using Agilent GeneScring GX v11.5.1 software.

source_name: LSF-normal lung tissue

label_protocol: 1 ug of total RNA was reverse-transcribed (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of Cyanine-3-CTP  according to the instructions for the Gene

extract_protocol: Total RNA was extracted from tissues with TRIzol reagent (Invitrogen) according to the instructioiins.

value: normal lung


title: DT001_S3

description: regulatory T cells depleted


title: ZGC-LC-

source_name: ZGC-normal lung tissue


title: macrophage_untreated_on mesentery_bio rep1


title: WT_e12point5_2

city: Boston

first: Edroaldo

last: Lummertz da Rocha

state: MA

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

description:
DR9_WT_e12point5_2
Wild type

data_processing:
Alignments were performed with STAR aligner (version 2.3.1z4)
Counts were generated using featureCounts
Normalization was performed with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated text file containing gene expression counts

source_name: Microdissected Tail Bud

extract_protocol:
RNA was isolated using the Qiagen Micro RNeasy kit and assayed for quality using the Agilent Bioanalyzer. RNA-seq libraries were prepared by The Center for Cancer Computational Biology (CCCB), Dana-Farber Cancer Institute, Boston MA using NEB Ultra Directional RNA library prep kit for Illumina and sequenced using Illumina NextSeq 500 Single Read 75.
RNA libraries were prepared for sequencing using NEB Ultra Directional RNA library prep kit for Illumina and sequenced using Illumina NextSeq 500 Single Read 75.
RNA-seq libraries were prepared by The Center for Cancer Computational Biology (CCCB), Dana-Farber Cancer Institute, Boston MA using NEB Ultra Directional RNA library prep kit for Illumina and sequenced using Illumina NextSeq 500 Single Read 75

value: tail bud


title: 35ANG_98_4

description: Biological replicate 22


title: Weight-losing (ID111_063F)

source_name: Subcutaneous adipose tissue

value: White adipose tissue

tag: gender


title: 34BOR_604_3

description: Biological replicate 21

source_name: DLBCL


title: CHN-LC-

source_name: CHN-normal lung tissue


title: CWL-LC-

source_name: CWL-normal lung tissue


title: Weight-losing (ID105_111E)

value: Follow-up


title: 32TEB_97_1

description: Biological replicate 19

source_name: normal


title: WT_e12point5_1

description:
DR8_WT_e12point5_1
Wild type


title: Weight-stable (ID107_029F)

value: Weight-stable


title: 33DIG_92_2

description: Biological replicate 20


title: Weight-stable (ID106_065F)


title: Weight-gaining (ID109_127E)


title: iLin28a_e12point5_8noCre

description:
DR7_iLin28a_e12point5_8noCre
Dox-treated TRE-Lin28a; RLSL-rtTA (control, no Cre)


title: WT_e12point5_3

description:
DR10_WT_e12point5_3
Wild type


title: 30CER_96_4

description: Biological replicate 18


title: phosphorus_3

city: Udine

first: Fabio

last: Marroni

address: Via delle Scienze 208

institute: Università di Udine

description:
PolyA RNA
Processed data file: cuffdiff_control_phosphorus.diff
Processed data file: cuffdiff_iron_phosphorus.diff

data_processing:
Adapter Removal, Cutadapt v.1.11, Default parameters.
Trimming, ERNE-filter v.1.4.6, default parameters.
Alignment to Transcriptome Reference, TopHat V.2.0.5, default parameters.
Transcript Quantification, Cufflinks V2.0.2, default parameters.
Differential Expression analysis, Cuffdiff V2.0.2, default parameters.
Genome_build: GDDH13_1-1, available for download at: ftp://ftp.bioinfo.wsu.edu/www.rosaceae.org/Malus_x_domestica/Malus_x_domestica-genome_GDDH13_v1.1/assembly/GDDH13_1-1_formatted.fasta.gz
Supplementary_files_format_and_content: *.diff: Three standard cuffdiff output files, one for each of the pairwise comparisons (control VS Fe, Control VS P, Fe VS P); DE files.

organism: Malus domestica

source_name: Root

extract_protocol:
Total RNA was extracted from root samples of control plants and treated plants using the Spectrum™ Plant Total RNA Kit (Sigma Aldrich).
cDNA library preparation and sequencing reactions were performed by IGA Technology Services s.r.l. (Udine, Italy). An amount of 2 μg of total RNA was used for library preparation following the Illumina protocol TruSeq 2.0. Briefly, RNA was fragmented into fragment with an average of 500 bp. Then, mRNA was purified using poly-T beads. The first- and second-strand cDNAs were synthesized and end repaired. Adaptors were ligated after adenylation at the 3’ ends and cDNA templates were enriched by PCR. The 50 bp single end reads were obtained using an Illumina Hiseq2000 platform.

value: Root

value: P deficiency


title: ZGC-LC+

source_name: ZGC-lung adenocarcinoma tissue

value: lung adenocarcinoma


title: Weight-losing (ID103_086E)

value: female

value: Weight-losing


title: HJP-LC-

source_name: HJP-normal lung tissue


title: Weight-stable (ID101_054F)

value: Baseline


title: iLin28a_e12point5_6noCre

description:
DR5_iLin28a_e12point5_6noCre
Dox-treated TRE-Lin28a; RLSL-rtTA (control, no Cre)


title: Weight-losing (ID104_021F)


title: CWL-LC+

source_name: CWL-lung adenocarcinoma tissue


title: 2VOL_283_4

description: Biological replicate 17


title: 29PED_602_4

description: Biological replicate 16


title: Weight-stable (ID096_141E)


title: phosphorus_2


title: iLin28a_e12point5_5Cre

description:
DR4_iLin28a_e12point5_5Cre
Dox-treated TRE-Lin28a; RLSL-rtTA; FoxD1-Cre


title: HJP-LC+

source_name: HJP-lung adenocarcinoma tissue


title: CHN-LC+

source_name: CHN-lung adenocarcinoma tissue


title: Weight-gaining (ID094_014F)


title: Weight-stable (ID100_143E)


title: Weight-stable (ID097_001F)


title: LSF-LC+

source_name: LSF-lung adenocarcinoma tissue


title: phosphorus_1


title: iLin28a_e12point5_7noCre

description:
DR6_iLin28a_e12point5_7noCre
Dox-treated TRE-Lin28a; RLSL-rtTA (control, no Cre)


title: iLin28a_e12point5_4Cre

description:
DR3_iLin28a_e12point5_4Cre
Dox-treated TRE-Lin28a; RLSL-rtTA; FoxD1-Cre


title: 28MAN_600_4

description: Biological replicate 15


title: 26PAS_604_2

description: Biological replicate 13


title: 24ERM_s_600_3

description: Biological replicate 12


title: iron_3

description:
PolyA RNA
Processed data file: cuffdiff_control_iron.diff
Processed data file: cuffdiff_iron_phosphorus.diff

value: Fe deficiency


title: iron_2


title: 27GAR_603_1

description: Biological replicate 14


title: iLin28a_e12point5_3Cre

description:
DR2_iLin28a_e12point5_3Cre
Dox-treated TRE-Lin28a; RLSL-rtTA; FoxD1-Cre


title: iLin28a_e12point5_2Cre

description:
DR1_iLin28a_e12point5_2Cre
Dox-treated TRE-Lin28a; RLSL-rtTA; FoxD1-Cre


title: KO-4-liver

city: Helsinki

first: Juho

last: Väänänen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

data_processing:
bcl2fastq2 Conversion Software was used to convert BCL files to FASTQ file format and demultiplex samples.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic. Parameters used: :2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed reads were mapped to GRCm38.p5 whole genome using STAR aligner (2.5.0c) with parameters  --runThreadN 20 --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJstitchMismatchNmax 5 -1 5 5 --outFilterType BySJout --outFilterMismatchNmax 999 --outSAMattributes NH HI NM MD AS nM jM jI XS --outSAMtype BAM SortedByCoordinate --outSAMmapqUnique 60 --quantMode GeneCounts --twopassMode Basic
Counts per gene were calculated using featureCounts software. Parameters used: -s 2 -T 20 -t exon -g gene_id -a /data/bioinfo/alignment/GENOMES/mm_M12/gencode.vM12.primary_assembly.annotation.gtf
Differential expression analysis used the DESeq2 software in R environment. Procedures included: Normalization of count values between samples using a geometric mean, estimation of samples-wise factors to correct for library size variability (for example), estimation of dispersion (i.e. variance, scatter) of gene-wise values between conditions, negative binomial linear model and Wald test to produce p-values, removal of low-expression outliers (using Cook's distance) results to optimize for p-value adjustment and finally, multiple testing adjustment of p-values with Benjamini-Hochberg procedure.
Genome_build: GRCm38.p5 from GENCODE Mus musculus Release M12
Supplementary_files_format_and_content: Raw count matrix of sequencing reads (featureCounts meta-feature level) as .xlsx

source_name: liver

growth_protocol: Mice were grown and housed in standard conditions for 6 months

extract_protocol:
RNAeasy mini kit using mouse liver tissue
NEBNext Ultra Directional RNA library prep after purifying mRNA with polyA-binding beads

treatment_protocol: KO mouse done as escribed in Lee at (1992) Cell 69,737-749.

value: p75NTR KO

value: Bulk liver tissue

value: B6.1129S4-Ngfr/J -Jackson lab


title: KO-2-liver


title: iron_1


title: control_3

description:
PolyA RNA
Processed data file: cuffdiff_control_iron.diff
Processed data file: cuffdiff_control_phosphorus.diff

value: Control


title: Weight-stable (ID092_100E)


title: control_2


title: Weight-gaining (ID089_055F)

value: Weight-gaining


title: Weight-stable (ID093_081E)


title: 21STA_90_4

description: Biological replicate 10

value: tumor

value: skin biopsy


title: 1ZON_283_1

description: Biological replicate 9


title: Weight-gaining (ID091_116E)

value: White adipose tissue


title: 23RAI_91_2

description: Biological replicate 11


title: WT-3-liver

value: wild type


title: Weight-losing (ID090_060F)


title: WT-2-liver


title: Weight-stable (ID087_146E)

value: Weight-stable

value: Follow-up


title: Weight-gaining (ID088_147E)


title: Weight-stable (ID085_074F)


title: 19DON_98_3

description: Biological replicate 8


title: 18COR_604_1

description: Biological replicate 7


title: KO-1-liver


title: Weight-stable (ID084_077F)


title: PAO1RpoN(DK2)_mRNA_replicate 1

city: Braunschweig

first: Denitsa

last: Eckweiler

state: Lower Saxony

address: Spielmannstr. 7

department: Institute of Microbiology

country: Germany

institute: Technische Universität Braunschweig

description: mRNA-seq RpoN-DK2 rep 1

data_processing:
Sequenced ChIP-seq reads were trimmed for adaptor sequence allowing for a minimal quality of 10 at their ends, then mapped to the PAO1 genome using stampy with default parameters
RNA-seq reads were mapped to the PAO1 genome using the stampy aligner with default settings.
ChIP-seq peaks were called using the MACS algorithm with the following options: -g 5200000 –nomodel --shiftsize=30 -p 0.05
Differential expression was estimated using the DESeq2 R library.
For detection of the differentially expressed genes, both replicates for each condition were used, thus the corresponding processed data files were generated on the basis of 4 samples each. The ChIP-seq peaks were detected superposing the treated against the control sample.
Genome_build: gi|110645304|ref|NC_002516|
Supplementary_files_format_and_content: Artemis browser files containing the read pileup at each genomic position covered in the ChIP-seq experiments. Processed RNA-seq data includes the raw read counts for each gene.

organism: Pseudomonas aeruginosa

growth_protocol: PAO1RpoN(WT) and PAO1rpoN(DK2) strains in LB medium at 37°C and 180 r.p.m. Sigma factor expression induced with l-arabinose at OD600 = 0.1, cells harvested at OD600=2.0.

extract_protocol:
Isolation of total RNA performed with the RNeasy Mini Kit (Qiagen) and enrichment of mRNA was performed using the ScriptSeq Complete Kit (Bacteria) (Illumina).
Library preparation was performed with the ScriptSeq Complete Kit (Bacteria) (Illumina).

treatment_protocol: Cells from 1.5 mL of culture, sampled before ChIP crosslinking were harvested and used for RNA isolation and rRNA depletion.

tag: strain background

tag: genotype/variation


title: 17CAN_602_3

description: Biological replicate 6


title: WT-1-liver


title: 16RIG_602_2

description: Biological replicate 5


title: 13ZOP_98_2

description: Biological replicate 4


title: Weight-gaining (ID082_038F)


title: control_1

value: Root


title: PAO1RpoN(WT)_mRNA_replicate 2

description: mRNA-seq RpoN-WT rep 2

value: RpoN(WT)


title: Lifelong Cl-13 infection at day >200 post-infection [Late_Infection_12]

first: Pablo

last: Penaloza-Macmaster

state: Illinois

address: 303 E. Chicago Avenue

department: Microbiology-Immunology

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file with read counts per gene

growth_protocol: Splenocytes were harvested in RPMI containing 10% FBS, L-glutamine and pen/strep. After FACS-sorting, cells were resuspended in Trizol.

extract_protocol:
Spleen cells were MACS sorted to isolate CD8 T cells by MACS negative selection (STEMCELL kit). Then, DbGP276+ cells were FACS-sorted and resuspended in Trizol. RNA extraction was performed using the Agecourt RNA extraction kit as per the manufacter instructions, and extracted RNA was delivered to the NUSeq Core at Northwestern University in downtown Chicago.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CD4 T cells were depleted and mice were infected intravenously with LCMV Cl-13

tag: infection

value: LCMV Cl-13

value: at day >200 post-infection

value: CD8 T cells


title: Lifelong Cl-13 infection at day >200 post-infection [Late_Infection_11]


title: CON_2

city: Beijing

first: Fei

last: Chen

address: NO.1 Beichen West Road, Chaoyang District

institute: Beijing Institute of Genomics

data_processing:
The quality of raw sequence data was assessed using FastQC,and the reads with quality below 30 were discarded using samtools (version 1.0).
The clean data were aligned to the UCSC rat reference genome (rn6) using Tophat (version 2.0.9) with default parameters. The aligned reads were further subjected to Cufflinks (version 2.2.1) software for assembling transcripts.
Differentially expressed genes (DEGs) were generated using Cuffdiff (version 2.2.1).
Genome_build: rn6
Supplementary_files_format_and_content: txt files include the expression values (FPKM) for each gene of the related statistical test.

extract_protocol:
Total RNA was extracted using TRIzol Reagent following the manufacturer’s instructions and the RNA integrity was assessed using RIN (RNA Integrity Number) with an Agilent Bioanalyzer 2100. Qualified RNA samples were further purified with a RNeasy Micro kit and a RNase-Free DNase Set. For RNA-seq analysis, mRNA samples were prepared by using the TruSeq RNA Sample Preparation Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: healthy control

value: liver

value: 22 weeks


title: WT 3

city: Columbus

first: Jelena

last: Brkljacic

address: 1060 Carmack Rd

institute: The Ohio State University

data_processing:
Reads were trimmed to remove adapters and low-quality ends using trim-galore
Alignment: Paired-end FASTQ data was aligned to Araport11 genome using STAR version 2.5.2a (Dobin 2013) with maximum intron size of 10 kb
Filtering: Duplicates were removed from alignments using samtools
Deduplicated alignments were converted to counts per genomic feature with featureCounts from the subread package (Liao 2014)
Differential expression analysis was conducted using the R package DESeq2 (Love 2014)
filtering: genes with log2 fold change > 0.6 and adjusted p-value < 0.05 were selected for further analysis
Genome_build: Araport 11
Supplementary_files_format_and_content: tab-separated DESeq2 normalized count data for all samples and DESeq2 output.

organism: Arabidopsis thaliana

source_name: self-pollinated siliques

extract_protocol:
Total RNA extracted from WT and eml1-2 eml3-4 siliques (1-5 DAP) were treated with DNase I (Life Tecnologies) twice to ensure no genomic DNA contamination. Two micrograms of total RNA was subjected to two rounds of hybridization to oligo(dT) beads (Illumina). The poly(A)-enriched mRNA was fragmented by heating at 94°C for 5 min in fragmentation buffer supplied by Illumina, followed by ethanol precipitation. The fragmented mRNA was added to 1× first-strand buffer (2.5 mM deoxynucleotide triphosphate, 10 mM DTT, RNaseOUT, and random primers mix). After adding Superscript II, first-strand cDNA synthesis was performed at 25°C for 10 min, 42°C for 50 min, and 70°C for 15 min. The second-strand cDNA synthesis was performed in GEX Second Strand Buffer (25 mM deoxynucleotide triphosphate, 1 μL RNase H, and 5 μL DNA Pol I for 2.5 h at 16°C) and purified by a PCR purification kit (Qiagen).
After end repair and A-base addition, adapter ligation was performed using NEBNext system according to the manufacturer’s instructions (NEB). We used Index 25, 27 and 4 or Index 6, 7 and 12 for WT or eml1-2 eml3-4, respectively. Ligated fragments were subjected for selection of fragments of ∼300 bp in length, followed by PCR amplification (10 cycles). PCR products were purified with Agencourt AMPure (Beckman Coulter). Library DNA was checked for concentration and size distribution in an Agilent Bioanalyzer before being subjected to Illumina sequencing using the OSUCCC Nucleic Acid Shared Resource (The Ohio State University).

tag: developmental stage

value: 1-5 days after pollination

value: silique

value: WT


title: PAO1RpoN(DK2)_mRNA_replicate 2

description: mRNA-seq RpoN-DK2 rep 2


title: Lifelong Cl-13 infection at day >200 post-infection [Late_Infection_10]

tag: strain


title: WT 2

tag: genotype


title: CON_1

tag: tissue


title: WT 1


title: PAO1RpoN(WT)_mRNA_replicate 1

description: mRNA-seq RpoN-WT rep 1


title: Weight-stable (ID081_022F)

data_processing: These arrays were pre-processed with RMA, which includes normalization, summarization of probes to probesets, and background correction. Prior to further analysis, collapseRows R function (Miller et al., 2011) was used to convert and collapse the transcript abundance quantification detected by Affymetrix probe sets to mapped FANTOM-CAT IDs. 48368 probe sets annoated as locus type coding or multiple complex were filtered for in order to include only protein-coding genes. Subsequently, probe sets with gene name absent, indicated as miRNA, transcript identified by AceView, uncharacterized LOC or uncharacterized protein were excluded, leaving 26064 transcripts for further analysis.

extract_protocol: Total RNA was isolated using the RNeasy kit (cat no. 217004, Qiagen) according to the manufacturer’s instructions.

value: female

value: Baseline


title: Weight-stable (ID075_069F)

value: White adipose tissue


title: eml dm 3

value: eml1,eml3 double mutant


title: Weight-losing (ID080_134E)

value: Weight-losing


title: Weight-losing (ID078_152E)

value: Follow-up


title: ZDF_2

value: diabetic


title: Lifelong Cl-13 infection at day ~40 post-infection [Early_Infection_8]

value: at day ~40 post-infection

tag: cell type


title: Lifelong Cl-13 infection at day ~40 post-infection [Early_Infection_7]

value: LCMV Cl-13


title: 12CAN_98_1

description: Biological replicate 3

value: tumor

value: skin biopsy


title: 11DES_606_3

description: Biological replicate 2


title: 10BIN_606_2

description: Biological replicate 1


title: eml dm 2


title: eml dm 1


title: ZDF_1


title: pitr1_rep2

city: Eugene

first: Amy

middle: K

last: Webster

state: Oregon

address: Institute of Ecology and Evolution

institute: University of Oregon

data_processing:
Bowtie version 1.2.2 was used to map reads to the WS210 version of the genome using the commands --best --chunkmbs 256 -k 1 -m 2 -S -p 2
Count files were generated with HTSeq using the GTF file used in Maxwell et al., 2012. This file includes features of the WS210 genome in addition to features of WS220 mapped back to WS210.
Batch correction and differential expression analysis were performed in edgeR using the GLM method as described in section 4.2 of the edgeR manual (Robinson, McCarthy, and Smyth 2010).
Count tables were subsetted to include 12,395 reliably-expressed genes and only the libraries of interest, including empty vector and daf-2 RNAi samples, or empty vector and pitr-1 RNAi samples.
The “calcNormFactors” function was used to normalize libraries. The GLM model was set up using the command model.matrix(~condition + replicate), where condition denotes the RNAi condition, and replicate denotes biological replicate (or batch). The dispersion was estimated, then the model was fit using the “glmQLFit” function and differential expression was determined using “glmQLFTest”.
Genome_build: WS210
Supplementary_files_format_and_content: Count files include the sequence identifier for each gene and the number of counts mapping to that gene (not normalized across libraries). Excel file includes results of differential expression analysis.

organism: Caenorhabditis elegans

source_name: L1 larvae

growth_protocol: hrde-1(tm1200) animals were bleached and embryos were plated on empty vector, daf-2, or pitr-1 RNAi (HT115). Animals were allowed to develop for 72 hr, after which embryos were released via bleaching and allowed to hatch in the absence of food.

extract_protocol:
Total RNA was extracted using TRIzol with minor modifications to the manufacturer's protocol. 1mL of TRIzol was used per sample. Samples were homogenized using 100uL of acid-washed sand.
Libraries were prepared using the NEB Next Ultra Non-directional mRNA-seq Kit.

treatment_protocol: Arrested L1 larvae were snap frozen in liquid nitrogen ~24 hr after bleaching.

tag: biological replicate

tag: maternal rnai

value: Arrested L1 larvae


title: slmp P5 - 2

city: Rehovot

first: Idan

last: Efroni

address: POB 12

department: Plant Sciences

country: Israel

institute: Hebrew University

data_processing:
Expression calling was performed by aligning to the tomato genome ITAG3.2 using bowtie2, followed by expression calling using htseq-count. As the library is 3’ biased, we extended all genes to cover 500 additional base pairs downstream.
Expression data were normalized using Deseq2 and genes induced at False Discovery Rate (FDR )<0.01 were selected
Genome_build: Solanum lycopersicum ITAG3.2
Supplementary_files_format_and_content: Normalized expression reads for all samples

organism: Solanum lycopersicum

source_name: young leaf primordia

growth_protocol: Tomato slmp-1 plants were grown in a controlled growth chamber under fluorescent bulbs providing ;300 mmol m22 s21 at an 18 h/6-h light/dark regimen. Young plants were genotyped and the indicated tissue was collected for furthur analysis.

extract_protocol:
15 young leaf primordia (Leaf number 5 at the P5 stage) were collected and flash frozen. RNA-extraction was performed using Qiagen RNAEasy Microkit
sequencing libraries prepared using Lexigen 3’ Quant-Seq kit, according to the manufacturer instructions.

treatment_protocol: Seedlings were sprayed one time with DDW, 1 hour before collecting the tissue.

tag: treatment

value: mock

value: leaf primordia

value: slmp


title: pitr1_rep4


title: CD4+Foxp3+CD25- uTregs E6-E11

data_processing:
Nextera adaptor removal: Trimmomatic (Bolger et al., 2014)
Reads alignment : hisat2 (Kim et al., 2015)
Read counts: featureCounts (Liao et al., 2014)
Read counts normalization: DESeq2 (Anders and Huber, 2010)
SAM to BAM conversion: samtools (Li et al., 2009)
Genome_build: Ensembl genome (Yates et al., 2016) version GRCm38
Supplementary_files_format_and_content: reads_count.gene_level.txt: Raw read counts as outputed by featureCounts

source_name: Tregs Pregnant uterus day 6, 7 and 8 of pregnancy

extract_protocol:
Uterine and uDLN Tregs and uterine CD4conv were isolated by cell sorting using FACS ARIA (BD Biosciences) after enrichment in CD4+ cells was performed using the EasySep Mouse APC Positive Selection Kit (Stemcell 18452). Groups of 20 mice per non-pregnant sample and 3 to 8 mice per pregnant sample were made and 4 samples were collected per cell type.
RNA was purified with the RNAqueous®-Micro Total RNA Isolation Kit (Invitrogen AM1931). cDNA was prepared with the SMART-Seq v4 Ultra Low Input RNA Kit. Indexed paired-end libraries were done with the Nextera® XT Library Prep Kit and the Nextera XT Index Kit. The quality control was done in Tapestation and Quantifluor. Illumina sequencing of the 16 samples in 2x150, 50 million reads/sample was done with the NextSeq 500 High Output Kit v2 (300 cycles) sequencer (Illumina Inc) generating paired end reads of approximately 2 x 150 bp in length. The samples were sequenced in two batches; CD4conv and uTreg E6-E8 samples in the first batch, and uDLN Treg NP and uTreg NP samples in the second batch.

value: BALB/c background Foxp3IRES-GFP (Bettelli et al. 2006)

value: Uterus

value: Treg

tag: pregnancy stage

value: Pregnant day 6, 7 and 8 of pregnancy


title: pitr1_rep3


title: Weight-stable (ID073_124E)

first: Ingrid

last: Dahlman

address: Hälsovägen

institute: Karolinska Institutet

source_name: Subcutaneous adipose tissue

value: White adipose tissue

value: female

tag: weight change

value: Weight-stable

tag: time point


title: CD4+Foxp3+CD25- uTregs E6-E9


title: CD4+Foxp3+CD25- uTregs E6-E10


title: Weight-losing (ID066_075F)

tag: age

value: Weight-losing

value: Baseline

tag: subject id


title: Weight-gaining (ID067_02F)

tag: gender

value: Weight-gaining


title: pitr1_rep1


title: CD4+Foxp3+CD25- uTregs E6-E8


title: Lifelong Cl-13 infection at day ~40 post-infection [Early_Infection_6]

city: Chicago

value: LCMV Cl-13

value: at day ~40 post-infection

value: CD8 T cells


title: CD4+Foxp3+CD25- uTregs NP-5

source_name: Tregs Non-pregnant uterus

value: Non-pregnant


title: daf2_rep4

value: Arrested L1 larvae


title: slmp P5 - 1

value: mock

value: leaf primordia


title: Weight-gaining (ID074_132E)

city: Huddinge

value: Follow-up


title: Weight-stable (ID065_121E)


title: slmp P5 - 3

value: slmp


title: CD4+Foxp3+CD25- uTregs NP-3

value: BALB/c background Foxp3IRES-GFP (Bettelli et al. 2006)

value: Uterus

value: Treg


title: Weight-losing (ID064_030F)

value: White adipose tissue

value: female


title: daf2_rep3


title: CD4+Foxp3+CD25- uTregs NP-2


title: daf2_rep2


title: daf2_rep1


title: Weight-stable (ID058_095E)

value: Weight-stable


title: Weight-losing (ID059_140E)

value: Weight-losing


title: ev_rep4

value: empty vector


title: CD4+Foxp3+CD25- uTregs NP-1


title: NNMT-3: Normal WI-38 fibroblasts expressing NNMT overexpression construct, biological replicate 3

first: Mark

last: Eckert

address: 929 East 57th St, W107

institute: University of Chicago

description: Gene expression data from human normal lung fibroblasts expressing NNMT overexpression construct, biological replicate 3

hyb_protocol: 5.5 ug of the fragmented and labeled cDNA was hybridized to Mouse Clariom S  array for 16 h at 45°C and 60 rpm in an Affymetrix Hybridization Oven 640. Arrays were washed and stained with Streptavidin Phycoerythrin in an Affymetrix Fluidics Station 450 according to Affymetrix  GeneChip  Pico Reagent Kit guide (Thermo Fisher Scientific, Inc).

scan_protocol: The arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G and CEL intensity files were generated by GeneChip Command Console Software (AGCC, Thermo Fisher Scientific, Inc)

data_processing: Transcriptome Analysis Software 4.0 (TAS 4.0) Signal Space Transformation-Robust Multi-Chip Analysis (SST-RMA)

label_protocol: 700 pg of total RNA was used to generate double strand cDNA and the Ds cDNA was fragmented and biotin labeled according to Affymetrix  GeneChip  Pico Reagent Kit manual (Thermo Fisher Scientific, Inc).

growth_protocol: All cell lines were grown in methionine-free DMEM supplemented with 10% dialyzed fetal bovine serum and 10 micromolar methionine for 21 days before collection.

extract_protocol: RNA was extracted with the Qiagen AllPrep DNA/RNA Mini Kit per manufacturer's instructions. RNA integrity was checked on a bioanalyzer (Agilent,Inc). High-quality RNA (RNA integrity number >8.5) was used for expression microarray analysis

treatment_protocol: All cell lines were stably infected with the indicated constructs and no additional treatment was performed.

value: Normal WI-38 fibroblasts

tag: expression construct

value: NNMT


title: CD4+Foxp3+CD25+ uDLN Tregs-5

source_name: Tregs Non-pregnant paraaortic lymph nodes

value: Paraaortic lymph nodes


title: ev_rep3


title: CD4+Foxp3+CD25+ uDLN Tregs-3

value: Non-pregnant


title: ev_rep2

value: Arrested L1 larvae


title: NNMT-1: Normal WI-38 fibroblasts expressing NNMT overexpression construct, biological replicate 1

description: Gene expression data from human normal lung fibroblasts expressing NNMT overexpression construct, biological replicate 1


title: Weight-losing (ID055_138E)


title: CD4+Foxp3+CD25+ uDLN Tregs-2


title: Weight-gaining (ID062_102E)

value: Weight-gaining


title: ev_rep1


title: CD4+Foxp3+CD25+ uDLN Tregs-1


title: kidney cortex A2 rep 3

city: Biberach a.d. Riss

first: Eric

last: Simon

address: Birkendorfer Str. 65

institute: Boehringer Ingelheim Pharma GmbH & Co KG

data_processing:
Sequenced read quality was checked with FastQC v0.11.2
RNA-Seq reads from all samples were aligned to the genome using the STAR Aligner v2.5.2a11
Duplication rates of the RNA-Seq samples were computed with bamUtil v1.0.11 to mark duplicate reads and the dupRadar v1.4 Bioconductor R package for assessment
The gene expression profiles were quantified using Cufflinks software version 2.2.114 to get the Reads Per Kilobase of transcript per Million mapped reads (RPKM) as well as read counts from the feature counts software package
Genome_build: Macaca_fascicularis_5.0
Supplementary_files_format_and_content: tab-delimited text files contain RPKM values for each sample

organism: Macaca fascicularis

source_name: kidney cortex

extract_protocol:
Total RNAs were individually extracted using the Ambion Magmax™-96 total RNA isolation kit (Life Sciences) according to the manufacturer’s instructions. Briefly, 5 mg of tissue was placed in the lysis solution and homogenised in Qiagen Tissuelyzer™ for a period of 30 sec. Nucleic acids were captured onto magnetic beads, washed and treated with DNase. Total RNA was then eluted in 50 μl elution buffer. RNA quality and concentration was measured using an RNA Pico chip on an Agilent Bioanalyzer.
The Sequencing library preparation has been done using 200 ng of total RNA input with the TrueSeq RNA Sample Prep Kit v2-Set B (RS-122-2002, Illumina Inc, San Diego, CA) producing a 275bp fragment including adapters in average size. In the final step before sequencing, eight individual libraries were normalised and pooled together using the adapter indices supplied by the manufacturer. Pooled libraries have then been clustered on the cBot Instrument from Illumina using the TruSeq SR Cluster Kit v3 - cBot - HS(GD-401-3001, Illumina Inc, San Diego, CA)  sequencing was then performed as 2x85bp, paired reads and 7 bases index read on an Illumina HiSeq3000 instrument using the TruSeq SBS Kit HS- v3  (50-cycle) (FC-401-3002, Illumina Inc, San Diego, CA).

value: kidney cortex

tag: animal

tag: Sex


title: Weight-stable (ID057_090E)

value: Follow-up


title: Ctrl-3: Normal WI-38 fibroblasts expressing Ctrl construct, biological replicate 3

description: Gene expression data from human normal lung fibroblasts expressing Ctrl construct, biological replicate 3

value: Ctrl


title: NNMT-2: Normal WI-38 fibroblasts expressing NNMT overexpression construct, biological replicate 2

description: Gene expression data from human normal lung fibroblasts expressing NNMT overexpression construct, biological replicate 2


title: CD4+Foxp3- CD4conv-5

source_name: CD4conv Non-pregnant uterus

value: BALB/c background Foxp3IRES-GFP (Bettelli et al. 2006)


title: kidney cortex A2 rep 1


title: kidney cortex A2 rep 2


title: CD4+Foxp3- CD4conv-3

value: Uterus


title: Weight-stable (ID054_047F)

value: Baseline


title: Weight-losing (ID053_101E)

value: White adipose tissue


title: Ctrl-1: Normal WI-38 fibroblasts expressing Ctrl construct, biological replicate 1

description: Gene expression data from human normal lung fibroblasts expressing Ctrl construct, biological replicate 1


title: liver A2 rep 3

value: liver

value: female


title: CD4+Foxp3- CD4conv-1


title: Weight-stable (ID052_097E)

value: Weight-stable


title: liver A2 rep 2


title: Donor_3_d2

city: Toulouse

first: Jean Jacques

last: FOURNIE

address: 2 av Hubert Curien

department: oncology

institute: INSERM

data_processing:
Raw data were firstly demultiplexed using mkfastq application (Cell Ranger v1.2.1).
Fastq files were then run with count application (Cell Ranger v1.2.1) using default settings, which performs alignment (using STAR aligner), filtering and UMI counting. The UMI count table was used for further analysis.
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include UMI numbers for all genes and single cells that passed filtering

source_name: purified Vgd2

extract_protocol: Sequencing library was prepared following the manufacturer’s instructions (10X Genomics), with 14 cycles used for cDNA amplification and 12 cycles for library amplification

value: purified TCRVdelta 2 gammadelta T lymphocytes

tag: cmv status

value: CMV-


title: Weight-losing (ID051_105E)

value: Weight-losing


title: Ctrl-2: Normal WI-38 fibroblasts expressing Ctrl construct, biological replicate 2

description: Gene expression data from human normal lung fibroblasts expressing Ctrl construct, biological replicate 2

value: Normal WI-38 fibroblasts


title: liver A2 rep 1


title: shNNMT-1: Cancer associated fibroblasts expressing shNNMT construct, biological replicate 1

description: Gene expression data from human CAFs expressing shNNMT construct, biological replicate 1

source_name: CAFs expressing shNNMT construct

value: Cancer associated fibroblasts (CAFs)

value: shNNMT


title: Donor_3_d1

source_name: purified Vgd1

value: purified TCRVdelta 1 gammadelta T lymphocytes


title: shNNMT-2: Cancer associated fibroblasts expressing shNNMT construct, biological replicate 2

description: Gene expression data from human CAFs expressing shNNMT construct, biological replicate 2


title: Weight-losing (ID046_027F)


title: shNNMT-3: Cancer associated fibroblasts expressing shNNMT construct, biological replicate 3

description: Gene expression data from human CAFs expressing shNNMT construct, biological replicate 3


title: Weight-gaining (ID047_110E)

value: Weight-gaining


title: Weight-losing (ID050_082E)

value: Follow-up


title: DAPK1 ko clone 21/9 1

city: Erlangen

first: Regine

last: Schneider-Stock

state: Bavaria

address: Universitaetsstrasse 22

department: Department of Pathology

institute: University Hospital Erlangen

description: DAPK1 ko cancer cell line

hyb_protocol: The Nanostring hybridization reaction containing 3 µl Reporter CodeSet, 5 µl hybridization buffer, 2 µl Capture ProbeSet and 5 µl total RNA (100 ng) was conducted for 16 h at 65°C. After hybridization, labelled RNA was processed automatedly according to the manufacturer's instructions for approximately 2.5 to 3 h through the NanoString nCounter Prep Station, where mRNA specific magnetic beads separation and mRNA immobilization on the cartridge surface takes place.

scan_protocol: Automated counting and tabulating of signals of the reporter probes was performed using the nCounter Digital Analyzer (Nanostring), a multi-channel epifluorescence scanner specifically configured for use with Nanostring's nCounter cartridges, and standard settings.

data_processing:
Data were processed internally using the nCounter Digital Analyzer (Nanostring). The number of mRNA specific reporter signals counted corresponds to number of respective mRNA molecules counted and present in the sample. For each sample, one Reported Code Count (RCC) file is generated, which contains the gene expression raw data. RCC files were downloaded from the nCounter Digital Analyzer and imported into the nSolver Analysis Software 3.0 (Nanostring) for data processing, quality control and analysis. Finally, housekeeping gene (geometric mean of 40 genes) normalization for quantitating gene expression levels, positive control normalization for background noise correction and data analysis was performed using nSolver™ Analysis Software 3.0 (NanoString Technologies, Hamburg, Germany) and standard settings. The fold-change of counts was determined by averaging results per DAPK1 ko cell line and comparing them to average counts of HCT116 cells.
Matrix tables contain normalized counts, raw data and fold change (FC) data of nine samples (see samples list above) obtained from the nSolver Analysis Software 3.0. Fold changes of counts were determined by averaging results per DAPK1 ko cell line (n = 1-3) and by comparing them to the average counts of HCT116 cells (n = 3) and are given in excel sheet Grouped FC all ko clones. Two further sheets present individual fold change data of all replicates (HCT116: n = 3, clone 7/6: n = 2, clone 10/8: n = 3, clone 21/9: n=1) and fold changes grouped per ko clone.

label: Reporter CodeSet & Capture ProbeSet (PanCancer Progression Panel, Nanostring)

source_name: HCT116_DAPK1 ko clone 21/9

label_protocol: 100 ng (contaied in 5 µl) of total RNA per sample was labeled with the Reporter CodeSet & Capture ProbeSet included in the following kit: XT_PGX_HuV1_CancerProg_CSO XT-CSO-PROG1-12(Cat. no. 115000152, Nanostring).

growth_protocol: All cell lines HCT116 and DAPK1 ko clones 7/6, 10/8 and 21/9  were cultured in a 100 cm cell culture dish and maintained in RPMI medium supplemented with 1% penicillin/streptomycin and 10% FBS.

extract_protocol: Cell harvesting was performed on ice. Cells were scraped off from the cell culture plates and cell pellets were prepared by centrifugation at 5000 rpm fr 5 min at 4 °C. Cells were washed with PBS, centrifugation was repeated, supernatants were discarded and dry cell pellets were frozen in liquid nitrogen and stred at -80°C. RNA was isolated from frozen cell pellets using the QIAzol Lysis Reagent (Qiagen) and RNeasy Mini Kit (Qiagen) according to the manufacturer's protocols.

treatment_protocol: No treatment was applied.

tag: cell line

value: HCT116 DAPK1 ko clone 21/9

value: colorectal carcinoma