title: HFD-PFSR

city: Columbia

first: Prakash

last: Nagarkatti

state: SC

address: 6439 Garners Ferry Road

institute: University of South Carolina School of Medicine

hyb_protocol: Labeled samples were hybridized to miRNA 4.0 chips overnight (16h, 48°C, 60 RPM) then washed and stained on an Affymetrix GCS 3000 system Fluidics station using the FS450_0002 protocol.

scan_protocol: Chips were scanned on a Affymetrix GCS 3000 system scanner.

data_processing: Affymetrix Expression Console Version 1.4.1.46 was used for quality control, data summarization, and normalization. The processing algorithm used was RMA-DABG. Affymetrix Transcriptome Analysis Console Version 3.1.0.5 was used to perform differential expression analyses. MicroRNAs were considered differentially expressed between the two groups if linear fold change was greater than ±2 and the ANOVA p-value was less than 0.05

label: Biotin

organism: Mus musculus

source_name: Epididymal fat macrophages

label_protocol: 500ng total RNA was used as starting material for labeling according to the Affymetrix FlashTag Biotin HSR RNA Labeling Kit manufacturer protocol.

growth_protocol: Mice were fed a control 10% low-fat diet (LFD) or 60% high fat diet (HFD) for 16 weeks starting at 6 weeks of age. Mice were then treated with vehicle (Veh) or CB1 antagonist (SR141716A "SR", AM251), daily for 4 weeks. Pair-fed controls are denoted as "PF".

extract_protocol: Total RNA was isolated with Qiagen miRNeasy micro kit.

treatment_protocol: Epididymal fat stromal vascular fractions (SVF) were isolated by collagenase digestion. F4/80+ cells (ATMs) were purified by labeling SVF cells with anti-F4/80-PE (clone: BM8) followed by immunomagnetic selection with StemCell EasySep PE Positive Selection Kit. Each biological replicate is pools of ATMs isolated from either 20 NCD-fed mice or 10 HFD-fed mice.

value: Male

value: 22 weeks

tag: weeks of diet

value: 16 weeks

tag: treatment duration

value: 4 weeks

tag: diet

value: high fat + CB1 antagonist (SR141716A "SR", AM251)


title: HFD+Veh

status: Public on Apr 04 2019

type: RNA

country: USA

molecule: total RNA

tag: gender

tag: strain

tag: age

value: high fat + vehicle


title: S2R+ cells_T20min_S3

type: SRA

city: Boston

first: Yanhui

last: Hu

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

library_source: transcriptomic

data_processing:
Sequencing reads in fastq  files obtained from the genome center were first filtered and trimmed and then  were mapped back to the Drosophila genome using TopHat.
sequence reads  were mapped back to the Drosophila genome using TopHat.
FPKM values were obtained with Cufflinks
Readcounts values were obtained using Htseq
Genome_build: Drosphila genome BDGP6
Supplementary_files_format_and_content: text files with FPKM values and read counts of all samples for each gene at each time point

organism: Drosophila melanogaster

growth_protocol: Drosophila S2R+ cells were incubated 12 hrs in serum-free Schneider’s Drosophila medium (Thermo Fisher Scientific, #21720-024).

extract_protocol:
RNA was harvested using Trizol reagent.
After assessing RNA quality with an Agilent Bioanalyzer, libraries constructed with an Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold.

treatment_protocol: Cells were treated with 25 mg/ml insulin, then lysed at 10 different time points at 20 min intervals (3 biological replicates per time point) after stimulation.

tag: cell type

value: S2R+ cells

tag: treatment

value: insulin

tag: time

value: 20 min

tag: replicate


title: D2_domain_Rep2

city: Planegg-Martinsried

first: Nicolas

last: Gompel

address: Grosshaderner Strasse 2

department: Faculty of Biology, Biozentrum

country: Germany

institute: Ludwig Maximilian University of Munich (LMU)

library_source: genomic

data_processing:
After demultiplexing and removal of adaptor sequences, ATAC-seq reads were aligned to a reference genome (UCSC: dm3) using Bowtie2 v.2.2.9, with the following settings: bowtie2 --local --very-sensitive-local.
Mapped reads were filtered for mapping quality (q > 10) and proper pairing (read paired & read mapped in proper pair) using SAMtools v.1.3.1, with the following settings: samtools view –f 0x3 – q 10.
ATAC-seq signal was defined as a number of Tn5 transposase cuts mapping to each base-pair. The cuts corresponded to 5' ends of ATAC-seq reads, with additional shifting by +4 bp for reads on the plus strand and -5 bp for reads on the minus strand.
Additionally, ATAC-seq signal was defined as coverage of short 1-100 bp fragmentation products (with in silico size selection) that corresponded to nucleosome-free regions (Schep et al., Genome Research, 2015).
ATAC-seq peaks were called with MACS2 v.2.1.1.2, based on the enrichment of Tn5 transposase cuts (smoothed by +/- 100 bp extension). ATAC-seq library from genomic DNA was used as a common control sample. Peak calling was performed separately for each replicate, with the q-value cut-off = 0.01 and the following non-default parameters: macs2 callpeak --keep-dup all -q 0.01 --nomodel --shift -100 --extsize 200 -f BAM -g dm -B.
Genome_build: UCSC dm3
processed data files format and content: BigWig files represent distribution of Tn5 transposase cuts after normalization to sequencing depth (CUTS_Normalized) and normalized coverage of 1-100 bp ATAC-seq fragments (COVERAGE_1-100-bp_Normalized). GFF3 files contain coordinates of ATAC-seq peaks called with MACS2.

molecule: genomic DNA

source_name: Blastoderm (stage-5 embryo)

growth_protocol: Transgenic strains were expanded into population cages. After pre-clearing, embryos were collected on yeasted juice plates for 20 min and aged for additional 150 min, followed by harvesting and dechorionation (50% bleach, 2 min) for 20 min. The embryos were flash-frozen in liquid nitrogen exactly 190 min after the beginning of collections (2:50 – 3:10 h after egg laying). All collections were performed at controlled temperature of 25°C.

extract_protocol: Staged embryos were homogenized on ice with Dounce homogenizer. Tagged nuclei were isolated by antibody pull-down with Dynabeads protein G (ThermoFisher: 10009D) adsorbed to monoclonal anti-FLAG M2 antibody (Sigma-Aldrich: F1804). Fragmentation and amplification of ATAC-seq libraries were performed according to the standard protocol (Buenrostro et al., Current Protocols in Molecular Biology, 2015). Nuclei pellet corresponding to 340 ng of genomic DNA was resuspended in Nextera Tagment DNA Buffer and combined with 6 μl of Nextera Tn5 transposase (Illumina) to the final volume of 25 μl. After 12 PCR amplification cycles, ATAC-seq libraries were purified with Agencourt AMPure XP beads (Beckman Coulter: A63881), using double size selection (left ratio: 2.0x, right ratio: 0.5x). Whole-embryo control samples were generated according to the same protocol, but with exclusion of the step of antibody pull-down.

tag: developmental stage

value: 2:50 - 3:10 h after egg laying

tag: assayed nuclei

value: D2 tagged domain

tag: genetic background

value: wild-type

tag: expression construct

tag: transgenic strain

value: D2 line B


title: ChIP-seq in HAP1 cell line for MTHFD1, replicate 1

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
Base calls provided by the Illumina Realtime Analysis software were converted into BAM format using Illumina2bam and demultiplexed using BamIndexDecoder (https://github.com/wtsi-npg/illumina2bam)
Sequenced reads were trimmed for adaptor sequences
Reads were mapped to hg19 whole genome using bowtie2 v2.2.4 with the –very-sensitive parameter
Duplicate reads were marked and removed with picard tools version 1.118
Library quality was assessed with the phantomPeakQualtools scripts (Landt SG, Genome Research 2012).
Peaks for ATAC-seq samples were called with MACS2 version 2.1.1.20160309 using the “–nomodel” and “–extsize 147” parameters
Transcriptome analysis was performed using the Tuxedo suite. TopHat2 was supplied with reads passing vendor quality filtering (PF reads) and the Ensembl transcript set (Homo sapiens, e75, February 2014) as reference. TopHat2 analyses were run independently for each replicate.
Cufflinks (v2.2.1) was used to assemble transcripts from spliced read alignments, using the Ensembl e73 transcriptome as the reference as well as de novo assembly of transcript models.
Differential expression was assessed with Cuffdiff v2.2.1. Transcriptome sets of all replicates for each sample group were combined with Cuffmerge. Finally, cummeRbund and biomaRt were used to perform quality assessment and refine analysis results.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files contain counts of reads per basepair; tsv file contains FPKM values for each sample at gene level

organism: Homo sapiens

source_name: HAP1 cell line

growth_protocol: HAP1 cell lines were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM, Gibco), supplemented with 10% Fetal Bovine Serum (FBS; Gibco) and incubated in 5% CO2 atmosphere at 37°C.

extract_protocol:
For each immunoprecipitation 30 million nuclei were isolated. Cells were fixed with 1% paraformaldehyde for 10 min at room temperature. The fixation was stopped by addition of glycine. The collected pellet was sonicated using a Covaris S220 sonicator for 43 minutes to fragment the DNA to 200-700 bp. For immunoprecipitation, the sonicated chromatin was added to antibody-conjugated Protein A or G beads (Life Technologies) and incubated rotating at 4°C overnight. Used antibodies were: anti-MTHFD1 (C3, Santa Cruz), anti-BRD4 ((A301‐985A, Bethyl Labs), anti-H3K27Ac (ab4729, Abcam) and mouse IgG (sc-2025, Santa Cruz).
RNA extraction was performed with Qiagen RNeasy Mini Kit (Cat No. 74106) according to the manufacturer's instructions.
Tagmentation was performed by resuspending the magnetic beads in 100 μl tagmentation reaction mix (10 mM Tris pH 8.0, 5 mM MgCl2, 10 % v/v dimethylformamide) containing 2 μl Tagment DNA Enzyme from the Nextera DNA Sample Prep Kit (Illumina) followed by an incubation for 3 min at 37°C. Subsequently, formaldehyde crosslinks were reverted by incubation in elution buffer (0.5% SDS, 300 mM NaCl, 5 mM EDTA and 10 mM Tris-HCl pH 8.0) containing 2 µl of Proteinase K for 1 h at 55°C, and then at 65°C overnight. The DNA was purified using the QIAquick PCR Purification kit (Qiagen). The enrichment of the libraries was performed in a 50 µl-reaction using Kapa HiFi HotStart ReadyMix (Kapa Biosystems) and 0.75 μM primers. Each DNA library was purified and size selected for a fragment length of 200-400 bp using SPRI AMPure XP beads (Beckman Coulter).
Total RNA was quantified using Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the RNA integrity number (RIN) was determined using Experion Automated Electrophoresis System (Bio-Rad). RNA-seq libraries were prepared with TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amount was quantified using Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using Experion Automated Electrophoresis System (Bio-Rad). For sequencing libraries were pooled, diluted and sequenced on Illumina HiSeq 3000 using 50 bp single-read chemistry.

tag: cell linw

tag: knockout

value: WT


title: D1_domain_Rep1

value: D1 tagged domain

value: D1 line A


title: S2R+ cells_T180min_S2

value: 180 min


title: S2R+ cells_T60min_S3

value: 60 min


title: S2R+ cells_T160min_S2

value: 160 min


title: S2R+ cells_T0min_S3

value: baseline control


title: HFD+SR

value: Male

value: 22 weeks

tag: weeks of diet

value: 16 weeks

value: 4 weeks


title: LFD+Veh

tag: treatment duration

value: low fat + vehicle


title: S2R+ cells_T140min_S2

value: S2R+ cells

value: insulin

value: 140 min


title: S2R+ cells_T120min_S2

value: 120 min


title: ChIP-seq in HAP1 cell line for Input, replicate 1


title: S2R+ cells_T100min_S2

value: 100 min


title: ChIP-seq in HAP1 cell line for IgG, replicate 2

value: WT


title: S2R+ cells_T60min_S2


title: T1460_PT

type: genomic

city: San Francisco

first: Mark

last: Magbanua

state: CA

address: 1450 3rd Street, PO Box 589001

department: HemOnc

institute: UCSF/Helen Diller Familiy Comprehensive Cancer Center

description: Promega Human Genomic DNA  cat#G147A

hyb_protocol: We combined and precipitated 30 µL Cy3 labeled test DNA, 30 µL Cy5 labeled reference DNA and 100 µg human Cot-1 DNA by adding 0.1 volumes of 3 M sodium acetate (pH 5.2) and 2.5 volumes of ice-cold ethanol. We collected the precipitate by centrifugation  at 14000 rpm for 45 minutes at 4°C. We the final hybridization mixture containing 7ul dH20, 14µL  20% SDS, and 49 µL or Master Mix (5 mL ultra pure formamide from Invitrogen, 1g 500000MW Dextran Sulfate, 1mL 20xSSC, 1mL H20). We denatured the hybridization mixture at 73°C for 15 min and then incubated the samples at 37°C for 2hours to allow the Cot 1 DNA to anneal to repetitive DNA sequeces on both the sample and reference DNA. We exposed our printed arrays to 260000uJoules of UV using StrataLinker and applied a rubber cement ring around each array to form a well. After air drying the rubber cement we added our combined sample/reference hybridization solution onto the array. We placed a silicone gasket around the edge of the wells and laid a clean glass microscope slide on top of the gasket. We clamped the assembly together using binder clips to create an air tight environment. The arrays were incubated or 48-68 hours at 37°C on a slowly rocking table (1rpm). After disassembling the hybridization chamber, we rinsed off the excess hybridization fluid with PN buffer (PN: 0.1 M sodium phosphate, 0.1% nonidet P40, pH 8), then washed the arrays once in a solution containing 50% formamide in 2xSSC for 15 min. at 45°C and finally in PN buffer at room temperature for 15 min. We removed the ring of rubber cement, drained excess liquid from the arrays, mounted them in a solution containing 90% glycerol, 10% PBS and 1 mM DAPI, and sealed them with a cover slip.

scan_protocol: Arrays were imaged using a custom built CCD array imaging system  and analyzed using the UCSF Spot Program to calculate Cy3/Cy5 ratios.

data_processing: Raw test/ref log2 ratios per spot have been observed in general to exhibit systematic variations of unknown origin across the array. To remove these, an in-house R package ('SpotCorrection'; publication in preparation) was employed. The observed log2 ratios are modeled as the sum of a genomic component (i.e. the desired signal) and a two-dimensional (2D) array component. The genomic and 2D components are iteratively estimated. The estimate of the 2D component after three iterations is then subtracted from the raw ratios. SpotCorrection also includes a relatively subtle correction based on clone GC content. No drastic changes in profiles are observed after correction. The resultant log2 ratios were analyzed by UCSF Sproc to yield the mean and standard deviation of the log2 ratios over replicate spots. The May 2004 freeze of the human genome sequence (hg17) was used to map the array CGH data.

source_name: Primary tumor tissue from early breast cancer patient

label_protocol: BioPrime Array CGH Labeling System (Invitrogen) was used to enzymatically label approximately 600ng of test or reference DNA with Cyanine 3-dCTP or Cyanine 5-dCTP (Amersham), respectively.Briefly, DNA suspended in 11µL of water and 10µL of random prime mix was heated for 10mins at 100°C and snap cooled on ice. 2.5uL of 10x-dNTP mix (8µL of 100mM dATP, 8µL of 100mM dGTP, 8µL of 100mM dTTP, 4µL of 100mM dCTP, 2µL 1M Tris, 0.4µL of 0.5M EDTA, and water), 1µL of Cy3 or Cy5 labeled dCTP( 1mM) and 0.6µL Exo-Klenow (40 U/µL) were added to the denatured DNA and incubated for 12 -20 hours at 37°C. Unincorporated nucleotides were removed using a Sephadex G-50 spin-columns.

extract_protocol: Magnetic beads coated with EpCAM mAb are used to enrich for tumor cells and then subjected to FACS analysis using differentially labeled mAbs to distinguish tumor cells (EpCAM+) from leukocytes (CD45+) during sorting. Using this protocol, we isolated small pools of highly purified CTCs from breast cancer patients. DNA from Tumor cells sorted in 10µL of TE was amplified using the GenomePlex® Single Cell Whole Genome Amplification Kit (Sigma-Aldrich) according to manufacturer’s protocol. The approach was evaluated using breast tumor cell model systems, BT474 and MCF7, and CTCs metastatic breast cancer (MBC) patients. Microdissection and DNA extraction of archival formalin-fixed paraffin-embedded (FFPE) primary tumor were done as previously described in Waldman FM, DeVries S, Chew KL, Moore DH, 2nd, Kerlikowske K, Ljung BM. Chromosomal alterations in ductal carcinomas in situ and their in situ recurrences. J Natl Cancer Inst 2000;92(4):313-20.

treatment_protocol: Array CGH experiments of Circulating Tumor, Primary Tumor, or cell line genomic DNA as test samples and normal human genomic DNA as reference sample.

tag: cancer type

value: Breast cancer

tag: tumor stage

value: Early Breast Cancer

value: Female

tag: source tissue

value: Breast

tag: source cell type

value: Primary Tumor

source_name: Promega reference Male genomic DNA

tag: sample type

value: Whole genome amplified reference male genomic DNA


title: T1448_PT

description: Promega Human Genomic DNA  cat#G147A

tag: gender


title: T1661_PT

description: Promega Human Genomic DNA  cat#G147A


title: ChIP-seq in HAP1 cell line for Input, replicate 2


title: ChIP-seq in HAP1 cell line for IgG, replicate 1


title: S2R+ cells_T40min_S2

tag: cell type

tag: treatment

tag: time

value: 40 min


title: S2R+ cells_T20min_S2

value: 20 min

tag: replicate


title: S2R+ cells_T0min_S2

value: baseline control


title: S2R+ cells_T180min_S1

value: 180 min


title: T1425_PT

description: Promega Human Genomic DNA  cat#G147A


title: S2R+ cells_T80min_S2

value: 80 min


title: ChIP-seq in HAP1 cell line for BRD4, antibody 2, replicate 1


title: T1310_PT

description: Promega Human Genomic DNA  cat#G147A


title: T1362_PT

description: Promega Human Genomic DNA  cat#G147A


title: S2R+ cells_T160min_S1

value: S2R+ cells

value: 160 min


title: S2R+ cells_T140min_S1

value: insulin

value: 140 min


title: S2R+ cells_T100min_S1

value: 100 min


title: S2R+ cells_T120min_S1

value: 120 min


title: S2R+ cells_T60min_S1

value: 60 min


title: T1485_LN

description: Promega Human Genomic DNA  cat#G147A

value: Breast cancer

value: Early Breast Cancer

value: Lymph Node


title: T1487_PT

description: Promega Human Genomic DNA  cat#G147A

value: Female

value: Breast

value: Primary Tumor


title: T1424_PT

description: Promega Human Genomic DNA  cat#G147A

value: Whole genome amplified reference male genomic DNA


title: S2R+ cells_T40min_S1

value: 40 min


title: S2R+ cells_T80min_S1


title: ChIP-seq in HAP1 cell line with MTHFD1KO, clone F5 for IgG

value: MTHFD1, clone F5


title: ChIP-seq in HAP1 cell line with MTHFD1KO, clone F5 for BRD4, antibody 2

description: WY10_HAP1_ChIP-seq_MTHFD1KO_F5_BRD4_new-ab_1


title: S2R+ cells_T0min_S1

value: baseline control


title: ChIP-seq in HAP1 cell line with MTHFD1KO, clone F5 for Input


title: S2R+ cells_T20min_S1

value: S2R+ cells

value: 20 min


title: ChIP-seq in HAP1 cell line with MTHFD1KO, clone C8 for MTHFD1

value: MTHFD1, clone C8


title: ChIP-seq in HAP1 cell line for BRD4, antibody 2, replicate 2

value: WT


title: LSC-Favorable CD34_P12

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

description:
Gene expression data
Well-defined cell populations were FACS-purified from BM of newly diagnosed AML patients and also control subjects.

hyb_protocol: The labelled products were hybridized using GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix Inc.) for 48 hours at 45°C and 60rpm.

scan_protocol: The arrays were scanned on GeneChip Scanner 3000 7G (Affymetrix Inc.).

data_processing: The expression signals were acquired using the Affymetrix GeneChip Command Console Software (AGCC). The system was used to generate the numerical values of the probe intensity (Signal). The differentially expressed mRNAs were defined using Partek Genomics Suite software (Partek Incorporated, Missouri, USA) and and RMA normalization.

label: biotin

source_name: LSC-Favorable

label_protocol: Biotinylated mRNAs were prepared according to the GeneChip® Human Transcriptome Pico Assay 2.0  protocol (Affymetrix Inc.) using 50ng total RNA.

extract_protocol: Total RNA was extracted using RNeasiy micro kit (QIAGEN AG) according to the manufacturer's instructions.

tag: patient id

value: M


title: ChIP-seq in HAP1 cell line with MTHFD1KO, clone C8 for IgG


title: ChIP-seq in HAP1 cell line with MTHFD1KO, clone C8 for BRD4, antibody 2

description: WY10_HAP1_ChIP-seq_MTHFD1KO_C8_BRD4_new-ab_1


title: T1320_PT

description: Promega Human Genomic DNA  cat#G147A


title: T1339_PT

description: Promega Human Genomic DNA  cat#G147A


title: ChIP-seq in HAP1 cell line with MTHFD1KO, clone C8 for Input


title: ChIP-seq in HAP1 cell line with MTHFD1KO, clone F5 for MTHFD1


title: T1260_PT

description: Promega Human Genomic DNA  cat#G147A


title: T1599_PT

description: Promega Human Genomic DNA  cat#G147A


title: T1579_PT

description: Promega Human Genomic DNA  cat#G147A


title: HepG2_IRb_starve_rep2

first: John

middle: G

last: Flanagan

address: 200 Longwood Ave, Building C2, Room 523

department: Cell Biology

data_processing:
ChIP-seq data quality was evaluated by using FASTQC (Andrews, 2010), and if required, reads were trimmed with Cutadapt (v1.4.2) (Martin, 2011).
High quality sequencing reads were mapped to the human genome UCSC build hg19 using Bowtie2 2.2.8 (Langmead and Salzberg, 2012). Alignments (BAM files) were filtered to retain only reads with a unique mapping to the genome.
Peaks were called with MACS2 2.1.1 (Zhang et al., 2008) using default parameters, and a narrow peak cutoff of P<0.001.
To assess the reproducibility of peaks across replicates, samples were run through the IDR pipeline (Babu et al., 2011), in which peak consistency was validated by use of pooled pseudo-replicates.
Genome_build: hg19
Supplementary_files_format_and_content: BED files contain genomic coordinates for peaks that were identified as reproducible, per the IDR analysis. BigWig files were generated from BAM files using Deeptools within the Galaxy platform (v1.0.4).

growth_protocol: For ChIP-seq, two biological replicates from independent experiments were used for each condition. HepG2 and SH-SY5Y cells were maintained in EMEM or a 1:1 mixture of EMEM and F-12 medium, respectively. Medium was supplemented with 10% final concentration of fetal bovine serum (FBS) and 1% penicillin-streptomycin in a humidified incubator with 5% CO2 at 37˚C.

extract_protocol:
Lysates were clarified from sonicated nuclei and IR-DNA or Pol2-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed using Thruplex DNAseq kit (Rubicon) according to manufacturer’s instruction.

treatment_protocol: For serum starvation, medium was removed, cells were washed three times with PBS, and medium supplemented with 0.1% BSA was added to cells for 16h. Cells were stimulated with 10 nM insulin for 20min.

tag: cell line

value: serum starvation

tag: chip antibody

value: rabbit, anti-IR_beta, sc-711


title: drh-3 input_rep_2

first: Ekaterina

last: Gushchanskaia

address: 72 East Conconrd, K425

institute: Boston University School of Medicine

data_processing:
Reads were aligned to the WS220/ce10 assembly of the C. elegans genome using Bowtie for Illumina (Galaxy Version 1.1.2) (Langmead et al., 2009) with default settings.
Read counting at specific loci (either genes, annotated regions or genomic bins) was performed with package GenomicAlignments (Lawrence et al., 2013); only reads with mapping quality 20 or higher were included in subsequent analyses. Regions without reads across the sample set were removed.
Counts were then normalized using the TMM method, which takes RNA composition bias into account (Robinson and Oshlack, 2010), using the edgeR package (Robinson et al., 2010).
Genome_build: WS220/ce10
Supplementary_files_format_and_content: *.bedGraph: Coverage files.

organism: Caenorhabditis elegans

source_name: L3 larvae

growth_protocol: Strains were maintained at 20 °C using standard methods (Brenner, 1974). For the ChIP-seq experiments, worm populations were synchronized and grown for approximately 40 h after hatching at 20 °C on OP-50 E. coli at a density of ~50,000 animals per 15-cm Petri dish until they reached L3 stage.

extract_protocol:
Chromatin immunoprecipitation was performed following the modENCODE Protocol from the Lieb Lab (modENCODE Consortium et al., 2009) with some modifications. The worm pellet fixed with 2% PFA for 30 minutes at 20°C was washed in M9 3 times and resuspended in RIPA buffer supplemented with Protease inhibitors (Thermo Scientific, 78443). DNA fragmentation was performed using sonication with Covaris (Peak power 240, Duty factor 20, Cycles/burst 200, 8 min). Then, 1.5–2mg of cross-linked chromatin extract was incubated at 4°C ON with a specific antibody and the immune complexes were then incubated with 50 µl IgG Dynabeads (Invitrogen) for 3h at 4°C. DNA was cleaned up with the Qiagen PCR purification kit.
ChIP-seq libraries were prepared using TruSeq Illumina kit (set A – 15034288, set B - 15034289) according to manufacturer’s instructions. Sequencing was performed on Illumina NextSeq500. The 75-bp single-end Illumina sequencing reads were preprocessed by trimming the adapter sequences with Cutadapt (Didion et al., 2017). After that, reads were aligned to the WS220/ce10 assembly of the C. elegans genome using Bowtie for Illumina (Galaxy Version 1.1.2) (Langmead et al., 2009) with default settings. The SAMtools (Galaxy Version 1.1.2) (Li et al., 2009; Li, 2011) utility was used to convert the alignments to BAM format. A table containing the number of reads aligned to genome is included in supplementary data (Table 1).

tag: strain

tag: antibody

value: no antibody


title: DTC_T1810_20DTC

description: Promega Human Genomic DNA  cat#G147A

source_name: Disseminated tumor cells Isolated from bone marrow of early breast cancer patient

value: Breast cancer

value: Early Breast Cancer

value: Bone Marrow

value: Disseminated Tumor Cells


title: drh-3 input_rep_1


title: T1317_PT

description: Promega Human Genomic DNA  cat#G147A

value: Female

value: Breast

value: Primary Tumor


title: DTC_T1798_20DTC

description: Promega Human Genomic DNA  cat#G147A

value: Whole genome amplified reference male genomic DNA


title: DTC_T1757_20DTC

description: Promega Human Genomic DNA  cat#G147A


title: N2 input_rep_1

value: N2 (Bristol)


title: N2 input_rep_2


title: DTC_T1802_20DTC

description: Promega Human Genomic DNA  cat#G147A


title: drh-3 H3K36me3_ChIPseq_rep_2

value: H3K36me3 (Abcam, ab9050)


title: DTC_T1617_18DTC

description: Promega Human Genomic DNA  cat#G147A


title: DTC_T1661_20DTC

description: Promega Human Genomic DNA  cat#G147A


title: DTC_T1742_20DTC

description: Promega Human Genomic DNA  cat#G147A


title: DTC_T1717_20DTC

description: Promega Human Genomic DNA  cat#G147A


title: DTC_T1605_20DTC

description: Promega Human Genomic DNA  cat#G147A


title: DTC_T1707_20DTC

description: Promega Human Genomic DNA  cat#G147A


title: DTC_T1744_20DTC

description: Promega Human Genomic DNA  cat#G147A


title: DTC_T1599_20DTC

description: Promega Human Genomic DNA  cat#G147A


title: DTC_T1586_20DTC

description: Promega Human Genomic DNA  cat#G147A


title: DTC_T1714_20DTC

description: Promega Human Genomic DNA  cat#G147A


title: WM193 H3K36me3_ChIPseq_rep_2

value: WM193 (csr-1, partial lof)


title: WM193 H3K36me3_ChIPseq_rep_1


title: drh-3 H3K36me3_ChIPseq_rep_1


title: WM193 input_rep_2


title: Sample 6_CD200R-/- rep3

city: Manchester

first: Stefano

last: Rossi

address: Grafton Street

country: United Kingdom

institute: Univeristy of Manchester

data_processing:
Read trimming was carried out with Trimmomatic v0.36 and then quality control was validated with FastQC software v0.11.3.
Pseudoalignment was performed with Kallisto v0.9. Tximport v1.6.0 was applied to create a gene-level count matrix that was further analysed with DESeq2 package v1.18.1 to perform differential expression analysis (i.e. comparing CD200R KO versus Wildtype condition).
Unsupervised gene clustering analysis was applied with pheatmap package v1.0.12 using a mean centering scaling.
Genome_build: Mus Musculus GRCm38
Supplementary_files_format_and_content: Spreadsheet including gene counts, lengths and adundances (i.e. txi.abundance.tsv, in sheet 1) and output of the DESeq2 tool (in sheet 2).

growth_protocol: Primary neutrophils were isolated from WT and CD200R-/- mouse bone marrow with Neutrophil Isolation Kit (Miltenyi Biotec, #130-097-658)

extract_protocol:
RNA was extracted from neutrophils using RNeasy Micro Kit (Qiagn, #74004) according to the manufacturers protocol.
Libraries were generated using the TruSeq® Stranded mRNA assay (Illumina, Inc.) according to the manufacturer’s protocol. Briefly, total RNA (0.1-4 µg) was used as input material from which polyadenylated mRNA was purified using poly-T, oligo-attached, magnetic beads.

tag: strain background

tag: genotype/variation

value: CD200R KO

tag: tissue

value: bone marrow

value: Neutrophils


title: Sample 5_CD200R-/- rep2


title: WM193 input_rep_1


title: N2 H3K36me3_ChIPseq_rep_2


title: DTC_T1490_20DTC

description: Promega Human Genomic DNA  cat#G147A

tag: cancer type

tag: tumor stage


title: DTC_T1553_20DTC

description: Promega Human Genomic DNA  cat#G147A

tag: source tissue

tag: source cell type


title: DTC_T1487_20DTC

description: Promega Human Genomic DNA  cat#G147A

tag: gender

tag: sample type


title: DTC_T1579_20DTC

description: Promega Human Genomic DNA  cat#G147A


title: DTC_T1485_20DTC

description: Promega Human Genomic DNA  cat#G147A


title: Sample 3_Wildtype rep3

value: Wild type

tag: cell type


title: DTC_T1478_20DTC

description: Promega Human Genomic DNA  cat#G147A


title: Sample 2_Wildtype rep2


title: Sample 1_Wildtype rep1


title: drh-3 H3K27me3_ChIPseq_rep_1


title: drh-3 H3K27me3_ChIPseq_rep_2


title: WM193 H3K27me3_ChIPseq_rep_2


title: DTC_T1823_20DTC

description: Promega Human Genomic DNA  cat#G147A


title: DTC_T1460_20DTC

description: Promega Human Genomic DNA  cat#G147A


title: Sample 4_CD200R-/- rep1


title: MNase_seq B6CASTF1 PRDM9hc

city: Oxford

first: Anjali

middle: Gupta

last: Hinch

address: Roosevelt Drive

department: WCHG

institute: Oxford University

data_processing:
Alignment with bwa-0.7.15
Peaks were called using an in-house algorithm R code available at https://github.com/anjali-hinch/hybrid-rescue
Alleles were called using an in-house algorithm (described in Hinch et al)
[Third-party reanalysis] H3K4me3 calls were made using an in-house algorithm (Hinch et al) using raw data from GSE119727
Filtering of false-positive hotspots and overlap with PRDM9-independent H3K4me3 were performed using in-house algorithm (Hinch et al)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with column descriptions in commented header; each line corresponds to one DMC1 peak

source_name: whole adult testis

growth_protocol: Data were generated from in vivo tissue samples from an adult male mouse - no culturing was performed.

extract_protocol:
Testes samples were stripped of the tunica and processed as described in accompanying manuscript (Hinch et al).
Libraries were prepared according to Illumina's instructions

value: testis

tag: prdm9 genotype

value: HUM/CAST


title: WM193 H3K27me3_ChIPseq_rep_1


title: MNase H3K4me3 ChIPseq B6CASTF1 PRDM9hc


title: DTC_T1427_20DTC

description: Promega Human Genomic DNA  cat#G147A

value: Breast cancer


title: N2 H3K27me3_ChIPseq_rep_2


title: N2 H3K27me3_ChIPseq_rep_1


title: DTC_T1425_20DTC

description: Promega Human Genomic DNA  cat#G147A

value: Early Breast Cancer


title: M_TDLN

first: Joshua

last: Pollack

address: 2 Tower Pl.  Ste 800

institute: Pionyr Immunotherapeutics

data_processing:
Data were processed according to the 10x Cellranger pipeline.
BAM files were generated with v2.1 10X Genomics Cellranger software using default parameters.
Gene-barcode matrices were generated from Cellranger v2.1 using default parameteres.
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger outputs a .mtx file with the gene-barcode matrix. This matrix contains the counts of molecules per cell (UMI/cell) as determined after filtering and counting by Cellranger. The matrix is in market exchange format while the row (gene names) and columns (cell barcodes) are provided as TSV files. File formats are documented in Cellranger software manual.

source_name: sorted myeloid cells (CD90.2- B220- NK1.1- and CD11c+ or CD11b+)

extract_protocol:
Sorted cells were processed using standard protocols associated with 10X Genomics Chromium Single Cell 3' Library and Gel Bead Kit V2
Libraries were constructed using standard protocols associated with 10X Genomics Chromium Single Cell 3' Library and Gel Bead Kit V2

value: B16-F10 tumor-draining lymph node

tag: genetic model

tag: treatment

value: day 5 post-DTx


title: N2 H3K36me3_ChIPseq_rep_1


title: DTC_T1416_50DTC

description: Promega Human Genomic DNA  cat#G147A

value: Female

value: Bone Marrow

value: Disseminated Tumor Cells


title: DTC_T1424_20DTC

description: Promega Human Genomic DNA  cat#G147A

value: Whole genome amplified reference male genomic DNA


title: DTC_T1399_20DTC

description: Promega Human Genomic DNA  cat#G147A


title: DTC_T1397_14DTC

description: Promega Human Genomic DNA  cat#G147A


title: drh-3 H3K9me3_ChIPseq_rep_1

value: H3K9me3(Abcam, ab8898)


title: p2606_7: NrasQ61K_rep2

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

institute: ETH/University of Zurich

description:
in vivo tdTomato labeled
FACS isolated
pre-tumorigenic

data_processing:
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR  v2.5.4b, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Mus_musculus/Ensembl/GRCm38.PatchesSkipped
Supplementary_files_format_and_content: tad-delimited, raw counts

source_name: dermal hyperplasia cells

extract_protocol:
Rneasy Micro Kit, Qiagen
Clontech SMRTer Stranded total RNA-Seq Kit-Pico Input Mammalian
Clontech, built-in rRNA removal

treatment_protocol: in vivo Tamoxifen induced tdTomato labeling of melanocytic dermal hyperplasia cells in Tyr::NrasQ61K (ColA1-LSL-Ezh2Y646N) Tyr::CreERT2 R26R-LSL-tdTomato mice and FACS isolation of tdTomato positive cells.

value: dermal hyperplasia cells

tag: genotype


title: p2606_5: Ezh2Y646N_rep2


title: p2606_6: NrasQ61K_rep1


title: DTC_T1382_38DTC

description: Promega Human Genomic DNA  cat#G147A


title: WM193 H3K9me3_ChIPseq_rep_2

value: WM193 (csr-1, partial lof)


title: WM193 H3K9me3_ChIPseq_rep_1


title: N2 H3K9me3_ChIPseq_rep_2

value: N2 (Bristol)


title: M_TDLN_FOXP3DTR

description: Raw data file provided by sequencing facility was corrupt and failed upload to NCBI/SRA.

value: sorted myeloid cells (CD90.2- B220- NK1.1- and CD11c+ or CD11b+)


title: N2 H3K9me3_ChIPseq_rep_1


title: DTC_T1362_50DTC

description: Promega Human Genomic DNA  cat#G147A


title: drh-3 H3K9me3_ChIPseq_rep_2


title: DTC.T1859.50CD45

description:
Control
Preamplified cDNA from total RNA

scan_protocol: ABI Prism 7900 HT Sequence Detection System (Applied Biosystems, Foster City, CA, USA).

data_processing:
Amplification curves were processed using SDS 2.4 and analyzed using RQ Manager 1.2.1 to obtain mean cycle threshold (Ct) of the triplicate measurements for each gene.
The mean Ct for ACTB and RPS18 was used to calculate for the ∆Cts

label: FAM

source_name: Bone Marrow Leukocytes

label_protocol:
Reverse transcription (RT) and preamplification were performed using Taqman® PreAmp Cells-to-CT™ kit (Ambion, Texas) following manufacturer’s instructions with some modification. These steps were performed in the same tube the cells were sorted into to avoid any loss of nucleic acids.  RT was performed on total RNA in the whole cell lysate (11µL) by adding 12.5µL of 2X RT buffer, 1.25µL of 20X RT enzyme and 0.25µL of nuclease free water and incubated in a thermal cycler for 60 min at 37°C and 5 min at 95°C to inactivate the RT enzyme. Specific transcript preamplification was performed by adding 50µL of Taqman® PreAmp Master and 25µL of the Custom PreAmp Pool to the RT reaction mix (25µL) and incubated in a thermal cycler for 10 min at 95°C followed by 14 cycles at 95°C for 15 sec and 60°C for 4 min. The Custom PreAmp Pool contained 63 Taqman® assays. The same set of Taqman® assays were also printed onto the TLDA card and used for subsequent RT-PCR. The primers for RPS18 were not included in the custom pool due to the already high expression level of this gene. Note that each assay contained specific primers for transcript specific preamplification.
Preamplified cDNA was diluted to 1/32 by adding 12.5µL of cDNA from the completed RT reaction to 187.5µL of nuclease free water and 200µL of Taqman® Universal PCR Master Mix (no UNG). Two samples were loaded in each TLDA card (100 µL per port; 4 ports per sample). RT-PCR was performed using the ABI PRISM 7900HT.

extract_protocol: Cells were sorted into reaction tubes containing 9.5µL of lysis buffer and 0.5 µL of DNAse. Lysis reaction was carried out for 5 min at room temperature and 1µL of Stop solution was added and incubated for 2 min and immediately placed on ice. Whole cell lysates were then stored in -80°C until further use.

treatment_protocol: Cell isolation via IE/FACS: If a patient had ≥1 DTC/mL via Immunomagnetic Enrichment/Flow Cytometry (IE/FC) the remaining volume of bone marrow was subjected to immunomagnetic enrichment and fluorescence activated cell sorting (IE/FACS) within 24-32 hr after bone marrow draw. In the initial step, magnetic beads coated with EpCAM mAb are used to enrich for tumor cells. Enriched samples are then subjected to FACS analysis using differentially labeled mAbs to distinguish tumor cells (EpCAM+/CD45-) from leukocytes (CD45+/EpCAM-) during sorting. This procedure allows for the isolation of small pools of cells, which can be subjected to downstream molecular analyses.

value: Early

tag: matched leukocyte sample


title: p2606_3: Ezh2Y646N_rep1


title: DTC_T1448_20DTC

description: Promega Human Genomic DNA  cat#G147A


title: DTC.T1856.20DTC.1

description:
Test
Preamplified cDNA from total RNA

source_name: Disseminated Tumor Cells

value: no pair


title: DTC_T1344_100DTC

description: Promega Human Genomic DNA  cat#G147A


title: DTC.T1852.50CD45


title: DTC.T1852.20DTC

description:
Test
Preamplified cDNA from total RNA


title: DTC_T1340_75DTC

description: Promega Human Genomic DNA  cat#G147A


title: DTC_T1347_50DTC

description: Promega Human Genomic DNA  cat#G147A


title: DTC_T1320_400DTC

description: Promega Human Genomic DNA  cat#G147A


title: DTC_T1335_80DTC

description: Promega Human Genomic DNA  cat#G147A


title: DTC_T1342_13DTC

description: Promega Human Genomic DNA  cat#G147A


title: DTC_T1339_93DTC

description: Promega Human Genomic DNA  cat#G147A


title: DTC_T1329_204DTC

description: Promega Human Genomic DNA  cat#G147A


title: DTC.T1850.20DTC.1

description:
Test
Preamplified cDNA from total RNA


title: DTC_T1317_28DTC

description: Promega Human Genomic DNA  cat#G147A


title: DTC_T1310_117DTC

description: Promega Human Genomic DNA  cat#G147A


title: DTC.T1841.20DTC.1

description:
Test
Preamplified cDNA from total RNA


title: NTM_156, Baseline

city: London

first: Steven

last: Cowman

address: Dovehouse Lane

department: National Heart and Lung Institute

institute: Imperial College London

hyb_protocol: Samples were hybridized using the GeneTitan Hybridization, Wash and Stain Kit for WT Array Plates (Affymetrix).

scan_protocol: Microarrays were scanned using the Affymetrix GeneTitan instrument.

data_processing: Data were processed using Affymetrix Power Tools. Background correction was applied to probe intensities using the RMA algorithm, quantile normalisation was performed, gene level expression were summarised from the intensities using the median polish method and finally values were log2 transformed.

source_name: whole blood

label_protocol: RNA was amplified to cDNA using the Ovation Pico WTA System V2 (NuGEN) and samples were fragmented and labelled using the Encore® Biotin Module Kit (NuGEN)

extract_protocol: RNA was extracted from whole blood using the PAXgene Blood RNA Kit (PreAnalytiX) according to the manufacturer’s protocol.

tag: fvc

tag: tlc

tag: tlco

tag: kco

tag: ctscore

tag: albumin

tag: crp

tag: neutrophils

tag: death


title: NTM_156, Follow-up

description: Not analysed in current study


title: Healthy_51, Baseline

description: Not analysed in current study


title: Control_61, Baseline


title: Control_124, Baseline


title: DTC_T1300_200DTC

description: Promega Human Genomic DNA  cat#G147A

tag: cancer type

tag: tumor stage

tag: gender

tag: source tissue

tag: source cell type


title: NTM_133, Follow-up

description: Not analysed in current study


title: Healthy_47, Baseline

description: Not analysed in current study


title: Control_137, Baseline


title: DTC.T1850.50CD45


title: Control_78, Baseline


title: DTC.T1838.10DTC

description:
Test
Preamplified cDNA from total RNA


title: DTC.T1830.50CD45.1


title: NTM_133, Baseline


title: DTC_T1294_103DTC

description: Promega Human Genomic DNA  cat#G147A

tag: sample type


title: DTC.T1859.20DTC.1

description:
Test
Preamplified cDNA from total RNA


title: DTC_T1249_250DTC

description: Promega Human Genomic DNA  cat#G147A


title: DTC.T1824.50CD45.1


title: control 1

city: Shanghai

first: Zhiyong

last: Liu

state: China

address: changhai road 168

country: China

institute: Changhai Hospital

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with Trimmomatic ( 0.36 ), then mapped to GR38p7 whole genome using Hisat2 ( 2.0.5 ) with parameters ( --rna-strandness RF --fr  )
FPKM value of each gene was calculated using cufflinks ( 2.2.1 ),and the read counts of each gene were obtained by htseq-count (  0.9.1 )
Genome_build: GR38p7
Supplementary_files_format_and_content: counts, fpkm and differential expression statistics

source_name: Hepatocellular carcinoma cell line

extract_protocol:
The RNAs from Huh7 cells stably knockdown LINC00998 (sh-LINC00998) and control (sh-control) were isolated, quantified and purified. The sequencing libraries were generated using the TruSeq Stranded Total RNA Library Prep Kit from Illumina according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: cell type

value: Hepatocellular carcinoma

tag: genotype

value: sh-control


title: control 2


title: NTM_120, Follow-up

description: Not analysed in current study

tag: fvc

tag: tlc


title: NTM_163, Baseline

tag: tlco

tag: kco


title: case 2

value: linc00998 knockdown


title: DTC.T1824.20DTC.1

description:
Test
Preamplified cDNA from total RNA

value: Breast cancer

tag: matched leukocyte sample


title: case 1


title: DTC.T1830.20DTC.1

description:
Test
Preamplified cDNA from total RNA


title: DTC.T1823.50CD45.1


title: Healthy_57, Baseline

description: Not analysed in current study

tag: ctscore

tag: albumin

tag: crp


title: Dami-DEL

city: Guangzhou

first: Fei

last: Li

address: Xingang West Road

department: School of Life Science

institute: Sun Yat-sen university

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Tophat2 tools soft were used to map with reference genome.
Gene function was annotated based on the following databases:Nr (NCBI non-redundant protein sequences)；Nt (NCBI non-redundant nucleotide sequences)；Pfam (Protein family)；KOG/COG (Clusters of Orthologous Groups of proteins)；Swiss-Prot (A manually annotated and reviewed protein sequence database)；KO (KEGG Ortholog database)；GO (Gene Ontology).
Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample. GATK2 or Samtools software was used to perform SNP calling. Raw vcffiles were filtered with GATK standard filter method and other parameters ( clusterWindowSize: 10; MQ0 >= 4 and (MQ0/(1.0*DP)) > 0.1; QUAL < 10; QUAL < 30.0 or QD < 5.0 or HRun > 5), and only SNPs with distance > 5 were retained.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.

source_name: AMKL cells (T01)

growth_protocol: AMKL cell Dami stably expressing GFP or Mpl-del-GFP were established by transduction with GFP or Mpl-del-GFP lentiviruses and cultured in 10%FBS IMDM medium

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen, Part#15596206) according to the manufacturer’s instructions.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H-）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: 20ng/ml TPO treament for 48h

tag: disease state

value: AML (M7)

value: DAMI

value: Mpl-del overexpression


title: NTM_120, Baseline

tag: neutrophils

tag: death


title: Control_18, Baseline


title: DTC.T1822.20DTC

description:
Test
Preamplified cDNA from total RNA

tag: cancer type

tag: tumor stage

tag: gender

value: Female

tag: source tissue

value: Bone Marrow


title: DTC.T1823.20DTC.1

description:
Test
Preamplified cDNA from total RNA


title: Dami-GFP

source_name: AMKL cells (T02)

tag: cell line

value: control


title: DTC_T1260_173DTC

description: Promega Human Genomic DNA  cat#G147A

value: Early Breast Cancer

tag: source cell type

value: Disseminated Tumor Cells

tag: sample type

value: Whole genome amplified reference male genomic DNA


title: Control Input DNA 72h

city: RTP

first: Raja

last: Jothi

state: NC

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

description: Input DNA from cells transitioning from naïve ground state (ESCs) to primed state (EpiLCs)

data_processing:
ChIP-Seq reads were aligned to the mouse genome (mm9) using the Bowtie algorithm. Those reads that mapped to unique locations were retained for further analysis.
RNA-Seq reads were mapped to the mouse (mm9) genome using the STAR (version 2.5.2a) algorithm, allowing up to three mismatches, retaining only reads that align to unique locations, and permitting a maximum intron length of 100,000
Genome_build: mm9

source_name: mouse Embryonic Stem Cells (ESCs)

growth_protocol: Mouse ES cells (E14Tg2a, ATCC) were grown in serum free N2B27-based medium, supplemented with 2i (MEK inhibitor PD0325901, 1.0 μM and Gsk3b inhibitor CHIR99021, 3.0 μM) and LIF (1000u/ml) in tissue culture (TC) plates coated with poly L-ornithine and  laminin.

extract_protocol:
RNA-Seq: Total RNA was extracted with Qiazol lysis reagent (Qiagen) treatment and purified using miRNeasy Kit.   ChIP-Seq: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with an antibody.
RNA-Seq libraries were prepared according to the TruSeq Stranded Total RNA Gold Kit (Illumina) using random hexamer priming.  ChIP-Seq libraries were prepared from size-selected ChIP DNA according to the standard Illimina library preparation protocol

treatment_protocol: For EpiLC induction, ESCs, adapted for a minimum of 4 passages in 2i+LIF, were plated on TC dishes coated with human plasma fibronectin (5µg/ml) in N2B27 medium containing activin A (20 ng/ml), bFGF (12µg/ml) and KSR (1%).

tag: treatment

value: N2B27 medium containing activin A, bFGF, and knockout serum replacement (KOSR , 1%)

tag: passages

tag: time point


title: Control Input DNA 48h


title: DTC.T1818.50CD45.2

tag: matched leukocyte sample


title: DTC.T1818.20DTC.1

description:
Test
Preamplified cDNA from total RNA


title: Control Input DNA 36h


title: Control_34, Baseline

tag: fvc

tag: tlc

tag: tlco

tag: kco

tag: ctscore


title: Control_128, Baseline

tag: albumin

tag: crp

tag: neutrophils

tag: death


title: DTC.T1810.20DTC.2

description:
Test
Preamplified cDNA from total RNA

tag: cancer type

tag: tumor stage

tag: gender

tag: source tissue


title: Control Input DNA 24h

tag: treatment

tag: cell line


title: Control Input DNA 12h

tag: passages

tag: time point


title: DTC.T1802.50CD45

tag: matched leukocyte sample


title: NTM_152, Baseline

tag: fvc

tag: tlc


title: NTM_113, Follow-up

description: Not analysed in current study

tag: tlco

tag: kco


title: Control Input DNA 6h


title: NTM_1, Baseline

tag: ctscore

tag: albumin


title: Control Input DNA 1h


title: DTC.T1802.20DTC.1

description:
Test
Preamplified cDNA from total RNA


title: DTC.T1798.20DTC.1

description:
Test
Preamplified cDNA from total RNA


title: DTC.T1810.50CD45


title: DTC.T1796.16DTC

description:
Test
Preamplified cDNA from total RNA


title: Control Input DNA 0h


title: H3K9me2 ChIP-Seq 72h

description: ChIP DNA from cells transitioning from naïve ground state (ESCs) to primed state (EpiLCs)

tag: antibody

value: Anti-H3K9me2 (Abcam ab1220)


title: DTC.T1794.20DTC.1

description:
Test
Preamplified cDNA from total RNA

value: Early


title: DTC.T1780.20DTC.2

description:
Test
Preamplified cDNA from total RNA

value: no pair


title: NTM_111, Follow-up

description: Not analysed in current study

tag: crp

tag: neutrophils

tag: death


title: H3K9me2 ChIP-Seq 36h


title: H3K9me2 ChIP-Seq 48h


title: Control_72, Baseline


title: NTM_111, Baseline


title: DTC.T1777.50CD45

tag: cancer type

tag: tumor stage

tag: gender


title: H3K9me2 ChIP-Seq 24h

tag: treatment

tag: cell line


title: Control_146, Baseline


title: NTM_96, Follow-up

description: Not analysed in current study


title: H3K9me2 ChIP-Seq 12h

tag: passages

tag: time point


title: H3K9me2 ChIP-Seq 6h


title: NTM_113, Baseline

description: Not analysed in current study

tag: fvc


title: NTM_87, Baseline

tag: tlc


title: NTM_96, Baseline

description: Not analysed in current study

tag: tlco


title: DTC.T1744.20DTC.3

description:
Test
Preamplified cDNA from total RNA

tag: source tissue

tag: matched leukocyte sample


title: DTC.T1755.20DTC.1

description:
Test
Preamplified cDNA from total RNA


title: Control_114, Baseline

tag: kco

tag: ctscore

tag: albumin


title: H3K9me2 ChIP-Seq 1h

tag: antibody


title: NTM_87, Follow-up

description: Not analysed in current study

tag: crp

tag: neutrophils

tag: death


title: T1605_PT

description: Promega Human Genomic DNA  cat#G147A

tag: cancer type

tag: tumor stage

tag: gender

value: Breast

tag: source cell type

value: Primary Tumor

tag: sample type


title: DTC.T1777.20DTC.1

description:
Test
Preamplified cDNA from total RNA


title: H3K9me2 ChIP-Seq 0h

tag: treatment

tag: cell line

tag: passages

tag: time point


title: DTC.T1742.50CD45

tag: source tissue

tag: matched leukocyte sample


title: NTM_81, Baseline

tag: fvc

tag: tlc

tag: tlco

tag: kco

tag: ctscore


title: DTC.T1742.20DTC.1

description:
Test
Preamplified cDNA from total RNA


title: RNA Pol II ChIP-Seq 72h

tag: antibody

value: Anti-RNA Polymerase II 8WG16 (Covance MMS-126R)


title: RNA Pol II ChIP-Seq 48h


title: DTC.T1755.50CD45.1

tag: cancer type

value: Breast cancer


title: NTM_81, Follow-up

description: Not analysed in current study

tag: albumin

tag: crp

tag: neutrophils

tag: death


title: scap WT_2@251486836166_S01_GE1_107_Sep09_1_2

city: Wuhan, Hubei Province

first: Song

last: Bao-Liang

address: College of Life Sciences

institute: Wuhan university

description: Total liver RNAs isolated from 8-week-old L-Scap-/- mice and WT littermates (n = 2 mice per group) subjected to microarray analysis

hyb_protocol: Each slide was hybridized with 1.65 μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (5188-5242, Agilent technologies) in Hybridization Oven (G2545A, Agilent technologies).

scan_protocol: Slides were washed in staining dishes (#121, Thermo Shandon) with Gene Expression Wash Buffer Kit (5188-5327, Agilent technologies), and scanned by Agilent Microarray Scanner (G2565CA, Agilent technologies) with default settings (Dye channel: Green, Scan resolution = 5 μm, PMT 100%, 10%, 16bit).

data_processing: Data were extracted with Feature Extraction software 10.7 and normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies).

source_name: 8-week-old WT littermates

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (5190-2305, Agilent technologies).Labeled cRNA were purified by RNeasy mini kit (74106, QIAGEN).

extract_protocol: Total RNA was extracted from the liver tissue of individual mouse using TRIzol (Invitrogen). The RNA concentration was measured by absorbance spectroscopy and RNA integrity was confirmed by nondenaturing agarose gel electrophoresis.

treatment_protocol: Total liver RNAs isolated from 8-week-old chow-diet fed L-Scap-/- mice and WT littermates subjected to microarray analysis

tag: strain background

tag: gender

value: male

tag: genotype/variation

value: wild type

tag: age

value: 8 weeks

tag: tissue

value: Liver


title: Microdissected Rat Renal cTAL, Lithium_72h, RNA-Seq, Transcriptome 10

city: Bethesda

first: Lihe

last: Chen

state: MD

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

data_processing:
Sequenced reads were mapped to Ensembl rat gene set (Rnor_6.0) using STAR v2.5.2b
Transcript abundances in TPM were caculated by RSEM/1.2.31
Genome_build: Rnor_6.0 (Ensembl)
Supplementary_files_format_and_content: tab-delimited text file includes TPM  for each sample

molecule: polyA RNA

organism: Rattus norvegicus

growth_protocol: Pathogen-free male Sprague-Dawley rats weighing 120-160 g had free access to ad libitum drinking water and normal rodent chow before experiment. The rats were housed one per cage, maintained on a 12:12-h light-dark cycle, and acclimated to the housing conditions for 2 days before the experimental procedures.

extract_protocol:
After microdissecting cortical collecting duct and cortical collecting duct,  Total RNA were extracted using the Direct-zol™ RNA Kits (Zymo Research) and cDNA was synthesized by SMARTer V4 Ultra Low RNA kit (Clontech). The cDNA was then amplified for 15 PCR cycles, purified by AmPure XP magnetic beads (Beckman Coulter Genomics), and eluted with 15 μL Elution Buffer. The purified cDNA was further quantified by Qubit. Library size distribution was determined using the Agilent 2100 bioanalyzer using High-Sensitive DNA kit. The Nextera XT DNA Library Preparation Kits (Illumina) was used to generate the libraries with input of 1 ng.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Rats are exposed to food without (Control) or with 40mM lithium chloride (LiCl) /kg food for 0, 12, 24, 36, and 72 hrs

tag: strain

value: Sprague-Dawley

value: Kidney

tag: tissue sample

value: Microdissected Renal cTAL

tag: agent

value: Lithium

tag: time


title: NTM_95, Baseline

description: Not analysed in current study

tag: fvc

tag: tlc

tag: tlco

tag: kco


title: RNA Pol II ChIP-Seq 36h

tag: treatment

tag: cell line

tag: passages

tag: time point

tag: antibody


title: Microdissected Rat Renal cTAL, Lithium_72h, RNA-Seq, Transcriptome 09

tag: gender


title: DTC.T1710.20DTC

description:
Test
Preamplified cDNA from total RNA

tag: cancer type

tag: tumor stage

value: Female

tag: source tissue

value: Bone Marrow

tag: matched leukocyte sample


title: DTC.T1707.20DTC.1

description:
Test
Preamplified cDNA from total RNA


title: DTC.T1702.20DTC.1

description:
Test
Preamplified cDNA from total RNA


title: NTM_76, Follow-up

description: Not analysed in current study

tag: ctscore

tag: albumin

tag: crp

tag: neutrophils

tag: death


title: scap K0_2@251486836166_S01_GE1_107_Sep09_1_4

source_name: 8-week-old L-Scap-/- mice

tag: strain background

tag: genotype/variation

value: L-Scap-/-

tag: age

tag: tissue


title: Control_119, Baseline

tag: fvc

tag: tlc

tag: tlco

tag: kco


title: scap K0_1@251486836166_S01_GE1_107_Sep09_1_3

tag: gender


title: Microdissected Rat Renal cTAL, Lithium_72h, RNA-Seq, Transcriptome 08

tag: strain

tag: tissue sample

tag: agent

tag: time


title: Microdissected Rat Renal cTAL, Lithium_72h, RNA-Seq, Transcriptome 07


title: DTC.T1698.20DTC.1

description:
Test
Preamplified cDNA from total RNA

tag: cancer type

tag: tumor stage

value: Early

tag: source tissue

tag: matched leukocyte sample


title: scap WT_1@251486836166_S01_GE1_107_Sep09_1_1

tag: strain background


title: RNA Pol II ChIP-Seq 6h

tag: treatment

value: N2B27 medium containing activin A, bFGF, and knockout serum replacement (KOSR , 1%)

tag: cell line

tag: passages

tag: time point

tag: antibody


title: DTC.T1717.20DTC.1

description:
Test
Preamplified cDNA from total RNA

value: no pair


title: RNA Pol II ChIP-Seq 1h


title: RNA Pol II ChIP-Seq 24h


title: NTM_66, Baseline

tag: fvc

tag: tlc

tag: tlco

tag: ctscore

tag: albumin

tag: crp

tag: neutrophils

tag: death


title: RNA Pol II ChIP-Seq 12h


title: Microdissected Rat Renal cTAL, Lithium_72h, RNA-Seq, Transcriptome 06

tag: strain

tag: gender

tag: tissue

tag: tissue sample

tag: agent

tag: time


title: DTC.T1605.20DTC.1

description:
Test
Preamplified cDNA from total RNA

tag: cancer type

tag: tumor stage

tag: source tissue

tag: matched leukocyte sample


title: RNA Pol II ChIP-Seq 0h

tag: treatment

tag: cell line

tag: passages

tag: time point

tag: antibody


title: Microdissected Rat Renal cTAL, Lithium_72h, RNA-Seq, Transcriptome 05


title: H3K4me1 ChIP-Seq 72h

value: Anti-H3K4me1 (Abcam ab8895)


title: Microdissected Rat Renal cTAL, Lithium_72h, RNA-Seq, Transcriptome 04


title: DTC.T1599.20CD45


title: NTM_155, Baseline

tag: fvc

tag: tlc

tag: tlco

tag: kco

tag: ctscore

tag: albumin

tag: crp

tag: neutrophils


title: NTM_76, Baseline

tag: death


title: Healthy_43, Baseline

description: Not analysed in current study


title: DTC.T1586.20DTC.1

description:
Test
Preamplified cDNA from total RNA

tag: cancer type

tag: tumor stage

tag: gender


title: Microdissected Rat Renal cTAL, Lithium_72h, RNA-Seq, Transcriptome 03

tag: strain

tag: tissue

tag: tissue sample

tag: agent

tag: time


title: Control_48, Baseline

tag: fvc


title: H3K4me1 ChIP-Seq 48h

tag: treatment

tag: cell line

tag: passages

tag: time point

tag: antibody


title: NTM_41, Baseline

tag: tlc

tag: tlco

tag: kco

tag: ctscore

tag: albumin

tag: crp


title: DTC.T1586.20CD45

tag: cancer type

tag: tumor stage

tag: gender

tag: source tissue

tag: matched leukocyte sample


title: NTM_50, Baseline

description: Not analysed in current study

tag: fvc

tag: neutrophils

tag: death


title: Microdissected Rat Renal cTAL, Lithium_72h, RNA-Seq, Transcriptome 02

tag: strain

tag: tissue

tag: tissue sample

tag: agent

tag: time


title: NTM_41, Follow-up

description: Not analysed in current study

tag: tlc

tag: tlco

tag: kco


title: Microdissected Rat Renal cTAL, Lithium_72h, RNA-Seq, Transcriptome 01


title: H3K4me1 ChIP-Seq 36h

tag: treatment

tag: cell line

tag: passages

tag: time point

tag: antibody


title: DTC.T1579.20DTC.1

description:
Test
Preamplified cDNA from total RNA

tag: cancer type

tag: tumor stage

tag: gender

tag: source tissue

tag: matched leukocyte sample


title: Combined_input

city: cambridge

first: Eric

last: Miska

address: tennis court road

department: The Gurdon Institute

institute: University of Cambridge

data_processing:
read trimming
mapping to genome with BWA
removal of blacklisted areas
MACS2 peak calling with a summed input, p value cutoff 0.01
preparation of normalized signal tracks with BEADs algorithm.
Genome_build: ce10
Supplementary_files_format_and_content: bw, narrowpeak

source_name: Young adults

growth_protocol: 20 C, in NGM plates.

extract_protocol:
Animals were frozen in liquid nitogen and crushed in metallic grinder. Animal extracts were lysed in FA Buffer and sonicated in BIORUPTOR at 4C.
NEB-NEXT Ultra II DNA Prep

tag: tissue

value: whole animal extract

tag: developmental stage

value: Young adults


title: DTC.T1599.20DTC.1

description:
Test
Preamplified cDNA from total RNA

value: Breast cancer


title: Microdissected Rat Renal cTAL, Control_72h, RNA-Seq, Transcriptome 12

tag: strain

value: male

tag: tissue sample

tag: agent

value: Control


title: DTC.T1579.20CD45


title: Microdissected Rat Renal cTAL, Control_72h, RNA-Seq, Transcriptome 11

tag: time


title: H3K4me1 ChIP-Seq 12h


title: H3K4me1 ChIP-Seq 24h


title: TOFU-5 ChIP-seq


title: Microdissected Rat Renal cTAL, Control_72h, RNA-Seq, Transcriptome 10


title: H3K4me1 ChIP-Seq 1h


title: H3K4me1 ChIP-Seq 6h


title: TOFU-4 ChIP-seq


title: Microdissected Rat Renal cTAL, Control_72h, RNA-Seq, Transcriptome 09


title: Control_46, Baseline

tag: fvc

tag: tlc

tag: tlco

tag: kco

tag: ctscore

tag: albumin

tag: crp

tag: neutrophils

tag: death


title: NTM_50, Follow-up

description: Not analysed in current study


title: Control_131, Baseline


title: SNPC-4 ChIP-seq


title: Control_115, Baseline


title: H3K4me1 ChIP-Seq 0h

tag: treatment

tag: cell line

tag: passages

tag: time point

tag: antibody


title: NTM_37, Baseline


title: H3K27me3 ChIP-Seq 72h

value: Anti-H3K27me3 (Millipore 07-449)


title: PRDE-1 ChIP-seq

tag: tissue

tag: developmental stage


title: NTM_36, Follow-up

description: Not analysed in current study


title: NTM_36, Baseline


title: Microdissected Rat Renal cTAL, Control_72h, RNA-Seq, Transcriptome 07

tag: strain

value: Sprague-Dawley

tag: gender

tag: tissue sample

tag: agent

tag: time


title: Microdissected Rat Renal cTAL, Control_72h, RNA-Seq, Transcriptome 06

value: Kidney


title: Microdissected Rat Renal cTAL, Control_72h, RNA-Seq, Transcriptome 05

value: Microdissected Renal cTAL


title: H3K27me3 ChIP-Seq 36h


title: Microdissected Rat Renal cTAL, Control_72h, RNA-Seq, Transcriptome 04


title: NTM_25, Baseline

tag: fvc

tag: tlc

tag: tlco

tag: kco

tag: ctscore


title: H3K27me3 ChIP-Seq 48h

tag: treatment


title: H3K27me3 ChIP-Seq 12h

tag: cell line


title: H3K27me3 ChIP-Seq 24h

tag: passages


title: Microdissected Rat Renal cTAL, Control_72h, RNA-Seq, Transcriptome 03


title: Microdissected Rat Renal cTAL, Control_72h, RNA-Seq, Transcriptome 08


title: Microdissected Rat Renal cTAL, Control_72h, RNA-Seq, Transcriptome 02


title: H3K27me3 ChIP-Seq 6h

tag: time point


title: H3K27me3 ChIP-Seq 1h

tag: antibody


title: ASCs from perigonadal adipose tissue pool 3

city: toulouse

first: Amandine

last: GIROUSSE

address: 4 bis avenue Hubert Curien, Bâtiment INCERE stromalab

country: France

institute: CNRS

description:
primary cell
Gene expression data from ASCs isolated from murine perigonadal adipose tissue.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mo Gene 1.1 ST Array Strip; Affymetrix. Array hybridization, washing and staining were performed as described by the manufacturer (GeneAtlas Hybridization, Wash and Stain Kit for WT Array Strips; Affymetrix) with the GeneAtlas System

scan_protocol: Arrays were then then scanned (GeneAtlas Imaging Station; Affymetrix) and analyzed by using Command Consol

data_processing: The CEL files were imported into Partek Genomic Suite v6.4 (Partek, Inc., MO, USA). Genes with expression  > 1.5-fold difference between ScAT and perigonadal (PG) AT (PGAT) originating from ASCs and p<0.05. Cluster analyses and principal component analysis were conducted with Partek default settings

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2,5 ug total RNA (Encore Biotin Module (NuGEN)).

growth_protocol: Primary cells: cells  are not grown. They are processed just after tissue isolation

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

treatment_protocol: After mouse sacrifice, adipose tissues were dissected and the stroma vascular fraction was isolated via mechanical and enzymatic digestion. Adipose stromal cells were sorted by Automacs (Miltenyi) according to the immunophenotype CD45-CD31-Sca1+

tag: cell type

value: Adipose stromal cells

tag: tissue

value: perigonadal adipose tissue


title: ASCs from perigonadal adipose tissue pool 2

source_name: isolated from murine perigonadal adipose tissue


title: BLD_SNI_rep3

city: Montreal

first: Marc

last: Parisien

state: Quebec

address: 740 Dr. Penfield Avenue

department: Dentistry

country: Canada

institute: McGill University

description: Parisien_Suppl_Table_08_gene_BLD_CTRvsSNI.xlsx

data_processing:
RNA-Seq data has been trimmed with Trimmomatic version v0.32.
Trimmed reads were aligned using tophat version v2.0.11 and bowtie version v1.0.0 on the reference mouse genome version mm10.
Differential gene expression was estimated with cuffdiff version v2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include fpkM values, fold changes, and associated fold change P-values, for paired CFA versus CTR, or SNI versus CTR.

source_name: blood

extract_protocol:
Total RNA was isolated using RNeasy Lipid Tissue Mini Kit, while RNA from blood cells was isolated using the RNeasy Mini Kit, including DNase I treatment (all Qiagen), all according to the manufacturer’s instructions. Total RNA was quantified using the NanoDrop 2000 (Thermo Scientific), while RNA quality was assessed with the 2100 Bioanalyzer (Agilent Technologies).
All RNA-sequencing procedures were performed by Genomics Platform facility at Institute for Research in Immunology and Cancer, Montreal, Canada. Transcriptome libraries were generated from 1 μg of total RNA using the Kapa RNA stranded Sample Prep Kit (KK8400, KAPABiosystems) following the manufacturer’s protocols. Briefly, poly-A mRNA was purified using poly-T oligo-attached magnetic beads using two rounds of purification. During the second elution of the poly-A RNA, the RNA was fragmented and primed for cDNA synthesis. During cDNA synthesis, dUTP is incorporated in the second-strand synthesis, where dUTP-containing strand is selectively degraded. Adenylation of the 3’ ends and ligation of adapters were done following the manufacturer protocol. Enrichment of DNA fragments that have adapter molecules on both ends was done using 10 cycles of PCR amplification using the KAPA PCR mix and Illumina-adapted primers cocktail.

treatment_protocol: Complete Freund’s adjuvant (CFA): (CFA; 50%; Sigma) was injected subcutaneously in a volume of 20 μl into the left and right plantar hind paws using a 100-μl microsyringe with a 30-gauge needle. 3 days post-CFA mice were sacrificed. Spared nerve injury (SNI): performed under isoflurane/oxygen anesthesia using an operating microscope (x40), the three terminal branches of the sciatic nerve (tibial, sural and common peroneal) are exposed. The tibial and common peroneal nerve are cut, after tight ligation with 6.0 silk, “sparing” the sural nerve. The incisions are closed in layers using interrupted sutures (6-0 Vicryl) and wound clips. The animal recovers on a thermostatically-controlled heating pad (carefully monitored to prevent over-heating) until ambulatory as per standard operating procedures. To reduce the overall number of mice required, the SNI surgery was performed in a bilaterally fashion (i.e. left and right side). 7 days after the surgery the mice were sacrificed.

tag: strain

value: BALB/c

value: blood

tag: age

value: 18 weeks

tag: pain model

value: SNI


title: H3K27me3 ChIP-Seq 0h

value: N2B27 medium containing activin A, bFGF, and knockout serum replacement (KOSR , 1%)


title: H3K27ac ChIP-Seq 72h

value: Anti-H3K27ac (Abcam ab4729)


title: Microdissected Rat Renal cTAL, Control_72h, RNA-Seq, Transcriptome 01

tag: gender

tag: tissue sample

tag: agent


title: H3K27ac ChIP-Seq 48h


title: NTM_122, Baseline

tag: fvc

tag: tlc

tag: albumin

tag: crp

tag: neutrophils

tag: death


title: ASCs from subcutaneous adipose tissue pool 2

description:
primary cell
Gene expression data from ASCs isolated from murine subcutaneous adipose tissue.

value: subcutaneous adipose tissue


title: BLD_SNI_rep2


title: BLD_SNI_rep1


title: ASCs from perigonadal adipose tissue pool 1


title: ASCs from subcutaneous adipose tissue pool 1

source_name: isolated from murine subcutaneous adipose tissue


title: H3K27ac ChIP-Seq 36h

tag: treatment

tag: cell line

tag: passages


title: BLD_CFA_rep3

description: Parisien_Suppl_Table_07_gene_BLD_CTRvsCFA.xlsx

value: CFA


title: Control_118, Baseline

tag: tlco

tag: kco

tag: ctscore


title: Control_139, Baseline


title: NTM_25, Follow-up

description: Not analysed in current study


title: NTM_150, Baseline


title: NTM_35, Baseline

description: Not analysed in current study


title: Healthy_80, Baseline

description: Not analysed in current study


title: ASCs from subcutaneous adipose tissue pool 3

tag: cell type

tag: tissue


title: Microdissected Rat Renal CCD, Lithium_72h, RNA-Seq, Transcriptome 16

tag: strain

tag: gender

value: Microdissected Renal CCD

value: Lithium

tag: time


title: Microdissected Rat Renal CCD, Lithium_72h, RNA-Seq, Transcriptome 18

value: male

tag: tissue sample

tag: agent


title: Microdissected Rat Renal CCD, Lithium_72h, RNA-Seq, Transcriptome 17


title: BLD_CFA_rep2

tag: age

tag: pain model


title: Microdissected Rat Renal CCD, Lithium_72h, RNA-Seq, Transcriptome 19


title: Healthy_98, Baseline

description: Not analysed in current study

tag: fvc

tag: tlc

tag: albumin

tag: crp

tag: neutrophils


title: Control_26, Baseline

tag: tlco

tag: death


title: NTM_23, Follow-up

description: Not analysed in current study

tag: kco

tag: ctscore


title: H3K27ac ChIP-Seq 12h

tag: treatment

tag: cell line

tag: passages

tag: time point

tag: antibody


title: H3K27ac ChIP-Seq 24h


title: Microdissected Rat Renal CCD, Lithium_72h, RNA-Seq, Transcriptome 14

tag: strain

tag: gender

tag: tissue

tag: tissue sample

tag: agent

tag: time


title: Control_13, Baseline

tag: fvc

tag: tlc

tag: albumin

tag: crp


title: Microdissected Rat Renal CCD, Lithium_72h, RNA-Seq, Transcriptome 12


title: BLD_CTR_rep2

tag: age

tag: pain model

value: CTR


title: BLD_CTR_rep1


title: H3K27ac ChIP-Seq 0h

tag: treatment


title: H3K4me3 ChIP-Seq 48h

tag: cell line

value: Anti-H3K4me3 (Abcam ab8580)


title: Microdissected Rat Renal CCD, Lithium_72h, RNA-Seq, Transcriptome 13

value: Sprague-Dawley

value: Kidney


title: NTM_22, Follow-up

description: Not analysed in current study

tag: tlco

tag: kco

tag: ctscore

tag: neutrophils

tag: death


title: H3K27ac ChIP-Seq 1h

tag: passages

tag: time point

tag: antibody


title: DRG_SNI_rep1

description: Parisien_Suppl_Table_06_gene_DRG_CTRvsSNI.xlsx

source_name: dorsal root ganglia

tag: strain

tag: tissue

value: dorsal root ganglia


title: DRG_SNI_rep3


title: H3K4me3 ChIP-Seq 72h


title: Microdissected Rat Renal CCD, Lithium_72h, RNA-Seq, Transcriptome 11

tag: gender

tag: tissue sample

tag: agent

tag: time


title: Microdissected Rat Renal CCD, Lithium_72h, RNA-Seq, Transcriptome 15


title: H3K4me3 ChIP-Seq 36h


title: DRG_SNI_rep2

tag: age

tag: pain model


title: BLD_CFA_rep1


title: Healthy_62, Baseline

description: Not analysed in current study

tag: fvc

tag: tlc

tag: albumin

tag: crp


title: NTM_12, Baseline

description: Not analysed in current study

tag: tlco

tag: kco

tag: ctscore

tag: neutrophils


title: NTM_17, Baseline

tag: death


title: Control_29, Baseline


title: H3K27ac ChIP-Seq 6h

tag: treatment

tag: cell line

tag: passages

tag: time point

tag: antibody


title: BLD_CTR_rep3

tag: strain

tag: tissue


title: Microdissected Rat Renal CCD, Lithium_72h, RNA-Seq, Transcriptome 09

tag: gender

tag: tissue sample

tag: agent

tag: time


title: Microdissected Rat Renal CCD, Lithium_72h, RNA-Seq, Transcriptome 10


title: DRG_CFA_rep3

description: Parisien_Suppl_Table_05_gene_DRG_CTRvsCFA.xlsx

tag: age

tag: pain model


title: Microdissected Rat Renal CCD, Lithium_72h, RNA-Seq, Transcriptome 08


title: NTM_23, Baseline

tag: fvc

tag: tlc

tag: tlco

tag: kco

tag: albumin

tag: crp


title: NTM_17, Follow-up

description: Not analysed in current study

tag: ctscore

tag: neutrophils

tag: death


title: Microdissected Rat Renal CCD, Lithium_72h, RNA-Seq, Transcriptome 07

tag: strain


title: H3K4me3 ChIP-Seq 12h

tag: treatment

tag: cell line

tag: passages

tag: time point

tag: antibody


title: NTM_12, Follow-up

description: Not analysed in current study


title: DRG_CFA_rep2

tag: tissue

tag: age


title: NTM_11, Baseline

tag: fvc


title: Microdissected Rat Renal CCD, Lithium_72h, RNA-Seq, Transcriptome 06

tag: gender

tag: tissue sample

tag: agent

tag: time


title: Microdissected Rat Renal CCD, Lithium_72h, RNA-Seq, Transcriptome 05


title: H3K4me3 ChIP-Seq 1h


title: H3K4me3 ChIP-Seq 6h


title: DRG_CFA_rep1

tag: pain model


title: DRG_CTR_rep2


title: DRG_CTR_rep3


title: Microdissected Rat Renal CCD, Lithium_72h, RNA-Seq, Transcriptome 03


title: H3K4me3 ChIP-Seq 0h


title: Microdissected Rat Renal CCD, Lithium_72h, RNA-Seq, Transcriptome 04


title: NTM_10, Baseline

tag: tlc

tag: tlco

tag: kco

tag: ctscore

tag: albumin

tag: crp


title: DRG_CTR_rep1

tag: strain


title: NTM_11, Follow-up

description: Not analysed in current study

tag: neutrophils

tag: death


title: RNA-Seq 72h, Rep 1

description: RNA from cells transitioning from naive ground state (ESCs) to primed state (EpiLCs)

tag: treatment

tag: cell line

tag: passages

tag: time point


title: H3K4me3 ChIP-Seq 24h

tag: antibody


title: Microdissected Rat Renal CCD, Lithium_72h, RNA-Seq, Transcriptome 02

tag: gender

tag: tissue

tag: tissue sample

tag: agent


title: SC_SNI_rep3

description: Parisien_Suppl_Table_04_gene_SC_CTRvsSNI.xlsx

source_name: spinal cord

value: spinal cord

tag: age

tag: pain model


title: Microdissected Rat Renal CCD, Lithium_72h, RNA-Seq, Transcriptome 01

tag: time


title: RNA-Seq 48h, Rep 2


title: NTM_10, Follow-up

description: Not analysed in current study

tag: fvc

tag: tlc

tag: tlco

tag: kco

tag: ctscore

tag: albumin


title: SC_SNI_rep2

tag: strain

value: BALB/c


title: Microdissected Rat Renal CCD, Lithium_36h, RNA-Seq, Transcriptome 03


title: NTM_84, Baseline

tag: crp

tag: neutrophils

tag: death


title: RNA-Seq 48h, Rep 1

tag: treatment

tag: cell line

tag: passages

tag: time point


title: SC_SNI_rep1

tag: tissue

tag: age


title: Microdissected Rat Renal CCD, Lithium_36h, RNA-Seq, Transcriptome 02

tag: gender

tag: tissue sample

tag: agent

tag: time


title: SC_CFA_rep3

description: Parisien_Suppl_Table_03_gene_SC_CTRvsCFA.xlsx

tag: pain model


title: RNA-Seq 36h, Rep 2


title: Control_135, Baseline

tag: fvc

tag: tlc

tag: tlco

tag: kco

tag: ctscore


title: NTM_147, Baseline

description: Not analysed in current study

tag: albumin

tag: crp

tag: neutrophils

tag: death


title: Microdissected Rat Renal CCD, Lithium_36h, RNA-Seq, Transcriptome 01

tag: strain


title: RNA-Seq 72h, Rep 2

tag: treatment

tag: cell line

tag: passages

tag: time point


title: RNA-Seq 36h, Rep 1


title: Microdissected Rat Renal CCD, Lithium_24h, RNA-Seq, Transcriptome 03

tag: gender

tag: tissue

tag: tissue sample

tag: agent


title: NTM_5, Baseline

tag: fvc

tag: tlc


title: RNA-Seq 24h, Rep 2


title: RNA-Seq 24h, Rep 1


title: SC_CTR_rep3

tag: age

tag: pain model


title: NTM_5, Follow-up

description: Not analysed in current study

tag: tlco

tag: kco

tag: ctscore

tag: albumin


title: Control_27, Baseline

tag: crp

tag: neutrophils

tag: death


title: RNA-Seq 12h, Rep 2

tag: treatment

tag: cell line

tag: passages


title: Control_148, Baseline


title: Healthy_55, Baseline

description: Not analysed in current study


title: SC_CTR_rep2

tag: strain

tag: tissue


title: SC_CTR_rep1


title: Microdissected Rat Renal CCD, Lithium_12h, RNA-Seq, Transcriptome 02

tag: gender

tag: tissue sample

tag: agent

tag: time


title: RNA-Seq 6h, Rep 2

tag: time point


title: SC_CFA_rep1

tag: age

tag: pain model


title: Microdissected Rat Renal CCD, Control_72h, RNA-Seq, Transcriptome 17

value: Control


title: BRN_SNI_rep3

description: Parisien_Suppl_Table_02_gene_BRN_CTRvsSNI.xlsx

source_name: brain

value: brain

value: 18 weeks


title: SC_CFA_rep2


title: Microdissected Rat Renal CCD, Control_72h, RNA-Seq, Transcriptome 16


title: RNA-Seq 6h, Rep 1

value: N2B27 medium containing activin A, bFGF, and knockout serum replacement (KOSR , 1%)


title: RNA-Seq 12h, Rep 1


title: RNA-Seq 1h, Rep 2


title: Control_21, Baseline

tag: fvc

tag: tlc

tag: tlco

tag: kco

tag: ctscore


title: Microdissected Rat Renal CCD, Lithium_24h, RNA-Seq, Transcriptome 02


title: Microdissected Rat Renal CCD, Lithium_24h, RNA-Seq, Transcriptome 01


title: BRN_SNI_rep1

value: SNI


title: BRN_CFA_rep3

description: Parisien_Suppl_Table_01_gene_BRN_CTRvsCFA.xlsx


title: RNA-Seq 1h, Rep 1

tag: treatment


title: NTM_4, Baseline

tag: albumin

tag: crp

tag: neutrophils

tag: death


title: Microdissected Rat Renal CCD, Control_72h, RNA-Seq, Transcriptome 14

tag: strain

tag: gender

tag: tissue


title: RNA-Seq 0h, Rep 2

tag: cell line

tag: passages


title: Microdissected Rat Renal CCD, Control_72h, RNA-Seq, Transcriptome 15

tag: tissue sample

tag: agent

tag: time


title: Control_65, Baseline

tag: fvc

tag: tlc


title: Microdissected Rat Renal CCD, Control_72h, RNA-Seq, Transcriptome 13


title: NTM_4, Follow-up

description: Not analysed in current study

tag: tlco

tag: kco


title: Control_33, Baseline

tag: ctscore


title: BRN_CFA_rep2

tag: age

tag: pain model


title: Healthy_59, Baseline

description: Not analysed in current study

tag: albumin

tag: crp

tag: neutrophils


title: BRN_SNI_rep2

tag: strain


title: RNA-Seq 0h, Rep 1

tag: treatment

tag: time point


title: BRN_CFA_rep1

tag: tissue


title: Microdissected Rat Renal CCD, Control_72h, RNA-Seq, Transcriptome 12

tag: gender

tag: tissue sample


title: BRN_CTR_rep3


title: Microdissected Rat Renal CCD, Control_72h, RNA-Seq, Transcriptome 11

tag: agent

tag: time


title: Control_121, Baseline

tag: fvc

tag: tlc

tag: death


title: Microdissected Rat Renal CCD, Control_72h, RNA-Seq, Transcriptome 10


title: BRN_CTR_rep2


title: BRN_CTR_rep1


title: Microdissected Rat Renal CCD, Control_72h, RNA-Seq, Transcriptome 09


title: Microdissected Rat Renal CCD, Control_72h, RNA-Seq, Transcriptome 07


title: Microdissected Rat Renal CCD, Control_72h, RNA-Seq, Transcriptome 08


title: SH-SY5Y-NOTCH3IC_on_336 hrs_tumor2

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

description: Tumors from cell line SH-SY5Y transfected with human NOTCH3-IC. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate mRNA expression profiles.

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix).

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: SH-SY5Y-NOTCH3IC cells were subcutaneously injected, allowed to generate tumors of 200-250 mm3 and treated with doxycycline to induce NOTCH3-IC expression and compared to non-induced control tumors.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.

treatment_protocol: The NOTCH3-IC transgene in SH-SY5Y-NOTCH3IC cells was induced with 200 µg/ml doxycycline in the drinking water.

tag: cell type

value: Tumor from neuroblastoma cell line SH-SY5Y with doxycycline inducible expression of human NOTCH3-IC


title: Il10-/- 7 Gy rep 3

city: New York

first: Sanjay

last: Mukherjee

state: NY

address: 630 W 168th street

institute: Columbia University

description: Gene expression in 7Gy X-ray irradiated Il10-/- mice whole blood

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60○C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65┬░C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37○C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan setting with eXtended dynamic range, Scan area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended green Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers or Features not Positive and significant were excluded.  Data were filtered to exclude features not positive and significant in 25% of the samples, or those without at least a 1.5-fold change in expression values across the samples.

source_name: Whole blood from  Il10-/- 24h post 7Gy X-ray irradiation, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labeling Kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mice were housed under standard vivarium conditions, and all procedures were conducted under an approved IACUC protocol.

extract_protocol: RNA was purified following the PAXgene RNA kit recommendations with on-column DNase I treatment, followed by globin reduction using GLOBINclear-Mouse/Rat.

treatment_protocol: Blood was collected by cardiac puncture at the time of euthanasia at 24 hours post-irradiation. Each sample was added to a 15 ml centrifuge tube that contained of PAXgene Blood RNA stabilization and lysis solution and mixed thoroughly

value: Whole Blood

value: Male


title: Il10-/- 7 Gy rep 4

source_name: Whole blood from  Il10-/- 24h post 7Gy X-ray irradiation, replicate 4


title: SH-SY5Y-NOTCH3IC_on_336 hrs_tumor1


title: SH-SY5Y-NOTCH3IC_on_168 hrs_tumor2


title: Microdissected Rat Renal CCD, Control_72h, RNA-Seq, Transcriptome 06

value: Microdissected Renal CCD


title: SH-SY5Y-NOTCH3IC_off_336 hrs_tumor2


title: Il10-/- 7 Gy rep 5

source_name: Whole blood from  Il10-/- 24h post 7Gy X-ray irradiation, replicate 5


title: SH-SY5Y-NOTCH3IC_off_168 hrs_tumor2


title: Il10-/- 7 Gy rep 2

source_name: Whole blood from  Il10-/- 24h post 7Gy X-ray irradiation, replicate 2


title: control/PortoTorres(PT) 3

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

hyb_protocol: 43°C, 16/20 h, hybridization buffer Northern Max (Ambion). Pre-hybridization for 1h in same conditions.

scan_protocol: Scanned on Chip Reader (Applied biosystems Laboratories) at 5 µm resolution

data_processing: Offset background subtracted, global mean normalisation across microarray surfaces and local mean normalisation across element signal intensity. Data obtained from log2 of processed Ch2 signal / processed Ch1 signal.

organism: Mytilus galloprovincialis

source_name: pooled samples of digestive gland tissue

label_protocol: 5 µg of total RNA were primed with 0.5 µg oligodT(19)VN primer at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 400 U ReverseAid MuLV H minus  RTase (Fermentas), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labeled dCTP or Cy5-label dCTP

extract_protocol: Total RNA extracted from the digestive gland of a single individual mussel using Trizol following manufacturer's instructions

value: caged for 30 days in Formelli (control)

value: female

value: caged for 30 days in Porto Tores


title: control/PortoTorres(PT) 2


title: control/PortoTorres(PT) 4


title: control/CalaReale(CR) 4

value: caged for 30 days in Cala Real


title: control/PortoTorres(PT) 1


title: Microdissected Rat Renal CCD, Control_72h, RNA-Seq, Transcriptome 05

value: Sprague-Dawley

value: male

value: Kidney


title: Il10-/- 7 Gy rep 1

source_name: Whole blood from  Il10-/- 24h post 7Gy X-ray irradiation, replicate 1


title: SH-SY5Y-NOTCH3IC_on_168 hrs_tumor1


title: SH-SY5Y-NOTCH3IC_off_168 hrs_tumor1


title: SH-SY5Y-NOTCH3IC_off_336 hrs_tumor1


title: SH-SY5Y-NOTCH3IC_on_168 hrs_followed by_off_168 hrs

description: Cell lines were transfected with human NOTCH3-IC. Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate mRNA expression profiles.

growth_protocol: SH-SY5Y-NOTCH3IC cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum.

treatment_protocol: The NOTCH3-IC transgene in SH-SY5Y-NOTCH3IC cells was induced with 100 ng/ml doxycycline in the culture medium. Switching-off the NOTCH3-IC transgene was performed by wash-out of doxycycline from the culture medium.

value: Neuroblastoma cell line SH-SY5Y with doxycycline inducible expression of human NOTCH3-IC


title: Il10-/- 0 Gy rep 5

description: Gene expression in mock irradiated Il10-/- mice whole blood

source_name: Whole blood from  Il10-/- 24h post mock irradiation, replicate 5


title: Microdissected Rat Renal CCD, Control_72h, RNA-Seq, Transcriptome 03

value: Control


title: control/CalaReale(CR) 3


title: Microdissected Rat Renal CCD, Control_72h, RNA-Seq, Transcriptome 04


title: Il10-/- 0 Gy rep 4

source_name: Whole blood from  Il10-/- 24h post mock irradiation, replicate 4


title: Microdissected Rat Renal CCD, Control_72h, RNA-Seq, Transcriptome 02


title: Il10-/- 0 Gy rep 2

source_name: Whole blood from  Il10-/- 24h post mock irradiation, replicate 2


title: DLS396_UNC-62_3E6_IP

city: Chapel Hill

first: Robert

middle: Houston

last: Dowen

address: 321 Fordham Hall, CB7100

department: Cell Biology and Physiology

institute: University of North Carolina at Chapel Hill

data_processing:
The adapter-trimmed ChIP-Seq reads were mapped to the WS260 genome with bowtie2 using the default parameters.
Low quality reads (view -bS -q 10) and duplicate reads (rmdup -s) were removed using the SAMtools package (Li et al., Bioinformatics, 2009).
ChIP-Seq peaks were identified from the filtered sequencing read files using MACS2 (Zhang et al., Genome Biology, 2008) with the following parameters: -g ce --nomodel --extsize 175 --SPMR --keep-dup all -q 0.01.
ChIP-Seq enrichment calculations were performed using the bamCompare module within the deepTools suite (Ramirez et al., Nucleic Acids Research, 2016).  The enrichment was calculated for 10 bp bins as the log2 ratio relative to input (--extendReads 175 --scaleFactorsMethod readCount).
Genome_build: WS260
Supplementary_files_format_and_content: BigWig ChIP enrichment files were generated from the processed alignment files using the bamCompare module within the deepTools suite (Ramirez et al., Nucleic Acids Research, 2016).  The ChIP enrichment was calculated for 10 bp bins as the log2 ratio relative to input (--extendReads 175 --scaleFactorsMethod readCount).
Supplementary_files_format_and_content: NarrowPeak files were generated from the processed alignment files using MACS2 (Zhang et al., Genome Biology, 2008) with the following parameters: -g ce --nomodel --extsize 175 --SPMR --keep-dup all -q 0.01.

source_name: Whole animals

growth_protocol: C. elegans L1 animals were synchronized by egg prep and grown at 20°C on E. coli OP50 for ~72 hours until they reached day 1 of adulthood.

extract_protocol:
Animals were harvested in M9 buffer, washed, and ground to a find powder with a mortar and pestle in liquid Nitrogen.  Whole animal lysates were crosslinked with 2% formaldehyde for 30 minutes, and the genomic DNA was sheared using a Bioruptor Plus (Diagenode).  The resulting chromatin was immunoprecipitated with anti-HA or anti-GFP antibodies.
ChIP-Seq libraries were prepared for sequencing using the KAPA Hyper Prep Kit (Kapa Biosystems) according to the manufacturer’s instructions.

tag: developmental stage

value: Day 1 adults

tag: genotype

tag: chip antibody

value: anti-GFP (3E6, Thermo Fisher, A-11120)


title: control/CalaReale(CR) 1


title: Microdissected Rat Renal CCD, Control_36h, RNA-Seq, Transcriptome 03


title: control/CalaReale(CR) 2


title: SH-SY5Y-NOTCH3IC_on_168 hrs nb2228


title: DLS395_CEH-60_mIgG1_IP

value: anti-HA (mIgG1, Pierce, 26181)


title: DLS396_CEH-60_3F10_IP


title: Microdissected Rat Renal CCD, Control_36h, RNA-Seq, Transcriptome 02


title: Microdissected Rat Renal CCD, Control_36h, RNA-Seq, Transcriptome 01


title: DLS395_CEH-60_3F10_IP


title: Il10-/- 0 Gy rep 3

source_name: Whole blood from  Il10-/- 24h post mock irradiation, replicate 3


title: WT 7 Gy rep 4

description: Gene expression in 7 Gy X-ray irradiated WT mice whole blood

source_name: Whole blood from Wild-type 24h post 7Gy x-ray irradiation, replicate 4


title: Il10-/- 0 Gy rep 1

source_name: Whole blood from  Il10-/- 24h post mock irradiation, replicate 1


title: WT 7 Gy rep 5

source_name: Whole blood from Wild-type 24h post 7Gy x-ray irradiation, replicate 5


title: WT 7 Gy rep 3

source_name: Whole blood from Wild-type 24h post 7Gy x-ray irradiation, replicate 3


title: SH-SY5Y-NOTCH3IC_off_168 hrs nb2227


title: SH-SY5Y-NOTCH3IC_on_504 hrs

treatment_protocol: The NOTCH3-IC transgene in SH-SY5Y-NOTCH3IC cells was induced with 100 ng/ml doxycycline in the culture medium.


title: SH-SY5Y-NOTCH3IC_off_0 hrs nb2226


title: WT 7 Gy rep 2

source_name: Whole blood from Wild-type 24h post 7Gy x-ray irradiation, replicate 2


title: Microdissected Rat Renal CCD, Control_24h, RNA-Seq, Transcriptome 03


title: SH-SY5Y-NOTCH3IC_on_168 hrs nb2155


title: Microdissected Rat Renal CCD, Control_72h, RNA-Seq, Transcriptome 01


title: Microdissected Rat Renal CCD, Control_24h, RNA-Seq, Transcriptome 02


title: MoPRMT1KO2

city: BEIJING

first: zhiqiang

last: li

address: NO. 2 yuanmingyuan west road

department: Institute of plant protection

institute: Chinese academy of agricultural sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Pyricularia oryzae

source_name: hypha

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

value: hypha

tag: age

value: post natal day 21


title: WT 7 Gy rep 1

source_name: Whole blood from Wild-type 24h post 7Gy x-ray irradiation, replicate 1

value: Whole Blood


title: MoPRMT1KO1


title: SH-SY5Y-NOTCH3IC_on_336 hrs nb2157


title: SH-SY5Y-NOTCH3IC_on_24 hrs


title: Microdissected Rat Renal CCD, Control_12h, RNA-Seq, Transcriptome 03


title: SH-SY5Y-NOTCH3IC_off_504 hrs


title: DLS395_input


title: WTGuy11-2


title: WT 0 Gy rep 4

description: Gene expression in mock irradiated WT mice whole blood

source_name: Whole blood from Wild-type 24h post mock irradiation, replicate 4

value: Male


title: SH-SY5Y-NOTCH3IC_off_168 hrs nb2154


title: Microdissected Rat Renal CCD, Control_12h, RNA-Seq, Transcriptome 02

value: Microdissected Renal CCD


title: Microdissected Rat Renal CCD, Control_12h, RNA-Seq, Transcriptome 01


title: WTGuy11-1


title: WT 0 Gy rep 3

source_name: Whole blood from Wild-type 24h post mock irradiation, replicate 3


title: WT 0 Gy rep 5

source_name: Whole blood from Wild-type 24h post mock irradiation, replicate 5


title: Microdissected Rat Renal CCD, Control_24h, RNA-Seq, Transcriptome 01