title: Pooled_Input [microglia]

data_processing:
Illumina v1.8 software used for basecalling.
Raw reads were aligned to the mouse reference (GRCm38-mm10) using GSNAP (with parameters -M 2 -n 10 -B 2 -i 1 --pairmax-dna=1000 --terminal-threshold=1000 --gmap-mode=none --clip-overlap). Reads were filtered to include only uniquely mapped reads.
ChIP-seq peaks were called for each dataset with matched input using MACS2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Peak files are in tab-delimited text format.

source_name: Primary microglia

extract_protocol:
Primary microglia were isolated from newborn mouse brains (P0-P2) as described (Lian et al., 2016). Briefly, hippocampi and cortices were mechanically dissociated and meninges removed with a 70 µm filter. Single cell suspensions from 4-5 brains were pooled in T-225 flasks (Corning) in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% heat inactivated fetal bovine serum, 2 mM glutamine, 100 U/mL penicillin, and 100 μg/mL streptomycin (Gibco). The culture media was changed the next day to remove cell debris. After 10-14 days of culture, microglia were collected by shaking the flask at 110 rpm for 1 h. Microglia were plated on non-treated plates. The next day they were treated with 0.1 μM 4-hydroxytamoxifen (4-OHT, Sigma-Aldrich) for 48 h. Active Motif Epigenetic services performed ChIP assays. Cells fixed with 1% formaldehyde for 11 min were quenched with 0.25 M glycine and then were swollen in lysis buffer for 30 min on ice. Chromatin was isolated after sonication to shear the DNA to an average length of 300–500 bp. Input and immunoprecipitated DNAs were treated with RNase, proteinase K, and heat for de-crosslinking, followed by ethanol precipitation. Antibodies used for immunoprecipitation were c/EBPß (Santa Cruz H-7), H3K4me3 (Abcam ab8580) and H2K27ac (Abcam ab4729).
Libraries were prepared using standard protocols for the Ovation Ultralow System. Briefly, samples were PCR-amplified and sized using the Agilent 2100Bioanalyzer. Barcoded libraries were sequenced 75 bp single end on HiSeq 2500 (Illumina).

tag: background

tag: age

value: Mixed

tag: cell type

value: Microglia

tag: chip antibody


title: N_deltaXrn1_42C_16min_RNAseq

status: Public on Aug 14 2020

type: SRA

city: Edinburgh

first: Stefan

last: Bresson

state: Scotland

address: Max Born Crescent, Swann 5.1

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

library_source: transcriptomic

data_processing:
Demultiplexing. Command: pyBarcodeFilter.py -f raw_file.fastq -b barcodes_file.txt
Adapter stripping and quality control. Command: flexbar -r file.fastq -a adapters.txt -ao 4 -m 11 -at RIGHT -u 2 -q TAIL -qf i1.8
Collapsing. Command: pyFastqDuplicateRemover.py -f file.fastq (Note that this step was used only for the CRAC analysis. RNAseq files were not collapsed)
Removal of low-complexity reads. Command: bbduk.sh in=file.fasta entropy=0.5 entropywindow=10 entropyk=6
Alignment. Command: novoalign -f file.fasta -r Random -o SAM -d genome.novoindex
samtools view -bS file.sam
samtools sort file.bam
Bedgraph files (+ strand). Command: bedtools genomecov -split -strand + -ibam sorted_file.bam -bg -scale variable > file_plus_strand.bedgraph
Bedgraph files (- strand). Command: bedtools genomecov -split -strand - -ibam sorted_file.bam -bg -scale variable > file_minus_strand.bedgraph
Read counting. Command: pyReadCounters.py -f file.bam --file_type=bam --sense --gtf=annotation_file.gtf
Genome_build: Saccharomyces cerevisiae EF4.74 with the introns artificially removed to improve mapping
Supplementary_files_format_and_content: The .txt files (generated using pyReadCounters.py) contain information on the number of reads mapping to each transcript. The bedgraph files show the distribution of reads across the genome. Individual replicates were merged into a single file to generate the bedgraph files.

molecule: total RNA

organism: Saccharomyces cerevisiae

growth_protocol: For CRAC experiments (07-99), cells were cultured in SC -TRP medium containing 2% glucose to 0.4 OD. For the 'control', cells were then subjected to 100 mJ of 254nm UV-crosslinking (4-6 seconds), collected by filtration, resuspended in 50 mL of ice cold PBS, centrifuged to pellet, and frozen at -80°C. For all other conditions,  cells at 0.4 OD were first collected by filtration,  then transferred to the appropriate medium and cultured for either 30 seconds or 16 minutes prior to UV-crosslinking. All subsequent harvesting steps were identical to the control. For RNAseq experiments (A-S), we used the same approach as for CRAC but without the crosslinking step.

extract_protocol: The CRAC protocol is based on Tuck and Tollervey, 2013. Modifications are described in Bresson and Tollervey, 2020.

tag: genotype/variation

tag: cell/ploidy type

value: haploid cells

tag: treatment


title: KO1_CEBPb [microglia]

city: South San Francisco

first: Rohit

last: Reja

state: CA

address: 1 DNA Way

country: USA

institute: Genentech

description: c/EBPß (Santa Cruz H-7)

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: genotype

value: Cop1 KO

value: c/EBP<beta> (Santa Cruz H-7)


title: S_deltaXrn1_42C_16min_RNAseq


title: WT2_CEBPb [microglia]

description: c/EBPß (Santa Cruz H-7)

value: Cop1 WT


title: Total_small_RNA_N2

city: Hefei

first: Shouhong

last: Guang

state: Anhui

address: 443 HuangShan Road

department: School of Life Sciences

country: China

institute: University of Science & Technology of China

data_processing:
The Illumina-generated raw reads were first filtered to remove adaptors, low quality tags as well as contaminants to get clean reads at BGI Shenzhen. Clean reads ranging from 17 to 30 nt were mapped to the C. elegans genome and the transcriptome assembly WS243, respectively, using Bowtie2 with default parameters (Langmead and Salzberg Nat Methods 9: 357-359. (2012)). The number of reads targeting each gene was counted by custom Perl scripts and displayed by IGV (Thorvaldsdottir et al. Brief Bioinform 14: 178-192. (2013)). Total mappable reads excluding sense rRNA were used for normalization.
gel purified and then deep sequenced using an Illumina platform, according to the manufacturer′s instructions, by Novogene (Beijing, China). The number of reads with distinct 3′ -end modifications were counted by custom Perl scripts.
Genome_build: WS243
Supplementary_files_format_and_content: .txt files.located in /count content. Basically, the reads were aligned to C. elegans transcriptome WS243 version by Bowtie2 and counted the number of reads targeting each transcript by Perl script.

organism: Caenorhabditis elegans

source_name: young adult stage

growth_protocol: C. elegans strains were cultured on NGM plates with E. coli OP50 as the food source in a temperature controlled incubator. Worms were maintained at 20°C prior to the experiment. Worms were synchronized by using the standard egg-prep protocol. L1s were released onto 10 cm NGM concentrated OP50 plate (approximately 3000 L1s per plate).

extract_protocol:
Total small RNAs were isolated from young adult stage worms. Briefly, worms were harvested and dounced on ice with pestle B in TRIzol reagent (Invitrogen) followed by isopropanol precipitation. The precipitates were treated with calf intestinal alkaline phosphatase (CIAP, Invitrogen), re-extracted with TRIzol, and treated with T4 polynucleotide kinase (T4 PNK, New England Biolabs) in the presence of 1 mM ATP.
Small RNAs were cloned and deep sequenced using an Illumina platform, according to the manufacturer's instructions, by  Novogene (Beijing, China). sRNAs ranging from 17 to 30 nt were gel-purified and ligated to a 3’ adaptor (5’-pUCGUAUGCCGUCUUCUGCUUGidT-3’; p, phosphate; idT, inverted deoxythymidine) and a 5’ adaptor (5’-GUUCAGAGUUCUACAGUCCGACGAUC-3’). The ligation products were gel-purified, reverse transcribed, and amplified using Illumina’s sRNA primer set (5’-CAAGCAGAAGACG GCATACGA-3’; 5’-AATGATACGGCGACCACCGA-3’). The samples were sequenced using an Illumina Hiseq platform.

tag: temperature

value: 20oC on OP50

tag: antibody

tag: molecule subtype

value: total small RNA


title: M_deltaXrn1_control_RNAseq

value: control


title: L_deltaSki2_42C_16min_RNAseq


title: I_wt_42C_16min_RNAseq

value: wt


title: WT1_CEBPb [microglia]

description: c/EBPß (Santa Cruz H-7)


title: KO2_H3K4me3 [microglia]

value: Histone H3K4me3 antibody (Abcam ab8580)


title: KO1_H3K4me3 [microglia]


title: J_wt_42C_CHX_16min_RNAseq


title: K_deltaSki2_control_RNAseq


title: KO1_H3K27ac [microglia]

value: Histone H3K27ac antibody (Abcam ab4729)


title: WT2_H3K4me3 [microglia]


title: H_wt_control_RNAseq


title: WT1_H3K4me3 [microglia]


title: HBL-52 shKLF4 #3

city: Leuven

first: Peihua

last: Zhao

address: Herestraat 49

country: Belgium

institute: KU Leuven

data_processing:
Reads were mapped on GRCh38 human transcriptome with GENCODE reference annotation, version 22 and quantified using RSEM v1.3.1
Read counts were normalized by calculating TPM (Transcripts Per Kilobase Million)
DESeq2 was used for differential expression analysis
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for each sample

organism: Homo sapiens

source_name: Human Brain Meningioma Cell Line

growth_protocol:
Human Meningeal Cells (HMCs) were cultured in Meningeal cell medium supplemented with 2% FBS, 1% meningeal cells growth supplements (MCGS) and 1% Pen/Strep.
HBL-52 cells were cultured in McCoy5a medium supplemented with 10% FBS and 1% Pen/Strep

extract_protocol:
Cells were trypsinized, peletted, and RNA was harvested using Nucleospin (Macherey). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HMCs and HBL-52 cells were infected with Lentiviral vectors expressing the indicated constructs, and kept in culture until harvest.

tag: cell line


title: B6 training 2 Blood BBA-seq

city: Changchun

first: Yang

last: Han

address: Xi'an road 5333, Jilin University Heping Campus, Changchun, China

institute: Jilin University

data_processing:
Library strategy: barcoded bisulfite amplicon sequencing (BBA-seq)
Fastq files were subjected to adaptor trimming by TrimGalore
FastQC were subsequently applied for quality checking of Fastq files.
To estimate DNAm levels for each CpG based on BBA-seq data we used the Bismark tool
Genome_build: hg19
Supplementary_files_format_and_content: Text files list the beta values for all the targeted CpGs

source_name: Peripheral  blood

extract_protocol:
Genomic DNA was isolated from peripheral blood with the QIAamp DNA Mini Kit (Qiagen),or from buccal swab with NucleoSpin Tissue Kit (Macherey-Nagel). Then was bisulfite converted by the EZ DNA Methylation Kit (Zymo)
10 pM DNA library was diluted with 15% PhiX spike-in control and eventually subjected to 250 bp pair-end sequencing on a MiSeq lane (Illunima, CA, USA) using Miseq reagent V2 Nano kit (Illumina).

tag: tissue

value: Peripheral  blood

tag: age (week)

tag: gender

value: f

tag: disease state

value: Healthy


title: KO2_CEBPb [microglia]

description: c/EBPß (Santa Cruz H-7)


title: HBL-52 shKLF4 #1


title: WT1_H3K27ac [microglia]


title: HBL-52 shKLF4 #2


title: WT2_H3K27ac [microglia]


title: HBL-52 shGFP #3

value: shGFP


title: Pooled_Input (Cop1 control)

data_processing:
Illumina v1.8 software used for basecalling
Raw reads were aligned to the mouse reference (GRCm38-mm10) using GSNAP (with parameters -M 2 -n 10 -B 2 -i 1 --pairmax-dna=1000 --terminal-threshold=1000 --gmap-mode=none --clip-overlap). Reads were filtered to include only uniquely mapped reads.
ChIP-seq peaks were called for each dataset with matched input using MACS2.
Genome_build: mm10
Supplementary_files_format_and_content: Peak files are in XLS format

source_name: Bone Marrow Derived Macrophages

extract_protocol:
BMDMs were derived as previously described (Trouplin et al., 2013) from Copwt/wt Rosa26-CreERT2 and Copfl/fl Rosa26-CreERT2 mice. Cop1 deletion was achieved by treatment with 4-OHT (0.1 µM) for 48 h in culture. Activ Motif Epigenetic services performed ChIP assays. Cells fixed with 1% formaldehyde for 11 min were quenched with 0.25 M glycine and then were swollen in lysis buffer for 30 min on ice. Chromatin was isolated after sonication to shear the DNA to an average length of 300–500 bp. Input and immunoprecipitated DNAs were treated with RNase, proteinase K, and heat for de-crosslinking, followed by ethanol precipitation. Antibodies used for immunoprecipitation were c/EBPß (Santa Cruz H-7), H3K4me3 (Abcam ab8580) and H2K27ac (Abcam ab4729).
Libraries were prepared using standard protocols for the Ovation Ultralow System. Briefly, samples were PCR-amplified and sized using the Agilent 2100Bioanalyzer. Barcoded libraries were sequenced 75 bp single end on HiSeq 2500 (Illumina).

value: 6-8 weeks


title: HBL-52 shGFP #2


title: HBL-52 shGFP #1


title: HMCs KLF4-K409Q #4

source_name: Human Meningeal Cell Line

value: HMC


title: KO2_CEBPb

value: c/EBPß (Santa Cruz H-7)


title: WT2_CEBPb


title: KO2_H3K27ac [microglia]

value: Microglia


title: HMCs KLF4-K409Q #3


title: KO1_CEBPb


title: WT1_CEBPb


title: KO2_H3K4me3


title: HMCs wt-KLF4 #4


title: HMCs KLF4-K409Q #1


title: HMCs wt-KLF4 #2


title: KO2_H3K27ac


title: WT2_H3K4me3 (Cop1 control)


title: HMCs wt-KLF4 #1


title: WT1_H3K4me3 (Cop1 control)


title: HMCs GFP #2

value: GFP


title: HMCs GFP #3


title: HMCs GFP #4


title: WT2_H3K27ac (Cop1 control)

value: Histone H3K27ac antibody(Abcam ab4729)


title: Cop1-ko-rep3

data_processing:
Illumina v1.8 software used for basecalling
Raw paired-end FASTQ files were aligned to the mouse reference genome (GRCm38/mm10) using GNAP (-M 2 -n 10 -B 2 -i 1 --pairmax-dna=1000 --terminal-threshold=1000 --gmap-mode=none --clip-overlap). For downstream analysis, reads mapping to the mitochondrial genome and blacklisted regions were removed from the analysis. ENCODE ATACseq pipeline (https://www.encodeproject.org/atac-seq/#standards) with minor modification was used to process the data further. Peaks were called using Macs (version 2) (Zhang et al., 2008),first at sample level and then at group level by pooling samples together. Peaks from pooled samples that were also called in the biological replicates were retained for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Peak files are in XLS format

extract_protocol:
BMDMs were derived as previously described (Trouplin et al., 2013) from Copwt/wt Rosa26-CreERT2 and Copfl/fl Rosa26-CreERT2 mice. Cop1 deletion was achieved by treatment with 4-OHT (0.1 µM) for 48 h.
Libraries were prepared using standard protocols for the Ovation Ultralow System. Briefly, samples were PCR-amplified and sized using the Agilent 2100Bioanalyzer. Barcoded libraries were sequenced 50 bp single end on HiSeq 2500 (Illumina).


title: WT1_H3K27ac (Cop1 control)


title: HMCs GFP #1


title: HMCs shTRAF7-2 #3


title: Cop1-ko-rep1


title: Cop1-wt-rep3


title: Cop1-ko-rep2


title: HMCs shTRAF7-2 #1


title: HMCs shGFP #3


title: Cop1-wt-rep1


title: Cop1-wt-rep2


title: HMCs wt-KLF4 #3


title: KO1_H3K4me3


title: KO1_H3K27ac


title: HMCs KLF4-K409Q #2


title: HMCs shTRAF7-2 #2


title: HMCs shGFP #2


title: HMCs shGFP #1


title: NSCs, ShOgt-6

city: Stanford

first: Julien

last: Couthouis

address: 279 Campus Dr

department: Genetics

institute: Stanford University

description:
ShOgt treated replicate 6
ShLuc_vs_ShOgt-ExpDiff.csv

data_processing:
RNAseq analysis
illumina basecalling
STAR alignment
RSEM counts
DESeq2 normalization and analyzis
Full pipeline with settings used available on https://github.com/emc2cube/Bioinformatics/blob/master/sh_RNAseq.sh
Genome_build: hg38
Supplementary_files_format_and_content: comma separated value text files with normalized abundance measurements and differential expression (output from DESeq2)

source_name: Primary Adult Hippocampal Neural Stem Cells

growth_protocol: Primary adult hippocampal neural stem cells (NSCs) were cultured growth medium (Neurobasal A medium supplemented with 2% B27 without Vitamin A, 1% Glutamax, 1% Penicillin Streptomycin, 10ng/ml EGF, 10ng/ml bFGF) at a density of 10,000 cells/well on a PDL/laminin-coated 24-well tissue culture plate.

extract_protocol:
RNA extracted using TRIzol (Thermo FIsher)
polyA enriched mRNA libraries (SureSelect Automated Strand-Specific RNA Library Prep, mRNA Library Prep for Illumina Paired-End Multiplexed Sequencing)

treatment_protocol: For vehicle and OSMI-1 treatment, growth media was supplemented with either 12.5μM OSMI-1 (Sigma-Aldrich) or an equal volume of DMSO 24 hours prior to RNA extraction. Acute knockdown of Ogt was induced by treating plated NSCs with shRNA -encoding lentiviruses (10 viral particles per cell) for three days prior to RNA extraction.

value: Neural Stem Cells

value: ShRNA Ogt


title: NSCs, ShOgt-5

description:
ShOgt treated replicate 5
ShLuc_vs_ShOgt-ExpDiff.csv


title: Sample25: Human peripheral blood mononuclear cells RNA-seq

city: Rochester

first: Mrinal

middle: M.

last: Patnaik

state: MN

address: 200 First Street SW

department: Division of Hematology

institute: Mayo Clinic

data_processing:
MAPRSeq v2.0. bionformatics pipeline (Kalari et al. MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing. BMC Bioinformatics 2014;(15):224)
Genome_build: GRCh37 / hg19
Supplementary_files_format_and_content: Raw feature counts for the transcripts annotated in GRCh37 / hg19 in tab-delimited TXT file generated by Subread/featureCounts v1.6.2 (http://subread.sourceforge.net)

source_name: Peripheral blood mononuclear cells

extract_protocol: Illumina TruSeq Stranded Total RNA

value: Peripheral blood

tag: cell selection

value: Ficoll-gradient selected mononuclear cells

value: Dysplastic CML


title: NSCs, ShOgt-2

description:
ShOgt treated replicate 2
ShLuc_vs_ShOgt-ExpDiff.csv


title: NSCs, ShOgt-3

description:
ShOgt treated replicate 3
ShLuc_vs_ShOgt-ExpDiff.csv


title: Sample23: Human peripheral blood mononuclear cells RNA-seq

value: Proliferative CML


title: NSCs, ShOgt-1

description:
ShOgt treated replicate 1
ShLuc_vs_ShOgt-ExpDiff.csv


title: Sample22: Human peripheral blood mononuclear cells RNA-seq


title: G422-shVec_3

city: Wuhan

first: Liu

last: Feng

state: Hubei

address: 13 Hangkong Road, Hankou

department: School of Basic Medicine

institute: Huazhong University of Science and Technology

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: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: glioblastoma cell line G422

growth_protocol: G422-shNgb or G422-shVec were inoculated subcutaneously into Kunming mice.

extract_protocol:
The subcutaneous G422 glioma was subject to the RNA-seq. Total RNA were extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: untreated

value: glioblastoma cell

tag: strain

value: Kunming

value: untreated

tag: shRNA

value: shVec


title: NSCs, ShLuc-6

description:
ShLuc control replicate 6
ShLuc_vs_ShOgt-ExpDiff.csv

tag: cell type

value: ShRNA control


title: G422-shNgb_2

value: shNgb


title: G422-shNgb_3


title: G422-shVec_2


title: G422-shNgb_1


title: B6 validation 24 Blood BBA-seq

value: Peripheral  blood

value: m

value: Healthy


title: NSCs, ShLuc-3

description:
ShLuc control replicate 3
ShLuc_vs_ShOgt-ExpDiff.csv


title: Sample21: Human peripheral blood mononuclear cells RNA-seq


title: G422-shVec_1


title: Sample18: Human peripheral blood mononuclear cells RNA-seq


title: Sample20: Human peripheral blood mononuclear cells RNA-seq


title: Sample24: Human peripheral blood mononuclear cells RNA-seq


title: NSCs, ShLuc-4

description:
ShLuc control replicate 4
ShLuc_vs_ShOgt-ExpDiff.csv


title: B6 validation 13 Blood BBA-seq


title: Larp7-/- rep3

city: Minhang

first: bing

last: zhang

state: Shanghai

address: 800 Dong Chuan Road

department: Shanghai Center for Systems Biomedicine

institute: Shanghai Jiao Tong University

data_processing:
RNA-seq reads were aligned to mm10 genome assembly using hisat2.
Count  per Million mapped reads (CPM) were calculated using HTseq
Genome_build: mm10
Supplementary_files_format_and_content: BAM

source_name: Mouse embryonic heart tissue

extract_protocol:
Hearts were removed from chests, whole hearts of embryonic mice or 20-30mg apex tissue from adult mice hearts were flash frozen. Total RNA were extracted using a RNeasy RNA isolation Kit (Qiagen) coupled with an on-column DNase I digestion to eliminate residual DNA and 1ug total RNA was used for sequencing library  construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Heart

tag: age


title: CTR rep2

source_name: Adult mouse heart apex tissue

value: Heart apex


title: mCKO rep2


title: Sample19: Human peripheral blood mononuclear cells RNA-seq


title: mCKO rep1


title: NSCs, ShLuc-2

description:
ShLuc control replicate 2
ShLuc_vs_ShOgt-ExpDiff.csv

value: Neural Stem Cells


title: NSCs, ShLuc-5

description:
ShLuc control replicate 5
ShLuc_vs_ShOgt-ExpDiff.csv


title: CTR rep1


title: Larp7-/- rep2


title: Sample16: Human peripheral blood mononuclear cells RNA-seq


title: Sample15: Human peripheral blood mononuclear cells RNA-seq


title: Larp7+/+ rep3


title: Larp7+/+ rep1


title: Larp7+/+ rep2


title: NSCs, Vehicle_OSMI_6

description:
Vehicle treated replicate 6
Vehicle_OSMI_vs_12p5uM_OSMI-ExpDiff.csv

value: Vehicle control


title: NSCs, Vehicle_OSMI_5

description:
Vehicle treated replicate 5
Vehicle_OSMI_vs_12p5uM_OSMI-ExpDiff.csv


title: Sample14: Human peripheral blood mononuclear cells RNA-seq

value: Peripheral blood


title: NSCs, Vehicle_OSMI_4

description:
Vehicle treated replicate 4
Vehicle_OSMI_vs_12p5uM_OSMI-ExpDiff.csv


title: Sample17: Human peripheral blood mononuclear cells RNA-seq

value: Ficoll-gradient selected mononuclear cells


title: Sample13: Human peripheral blood mononuclear cells RNA-seq


title: NSCs, Vehicle_OSMI_3

description:
Vehicle treated replicate 3
Vehicle_OSMI_vs_12p5uM_OSMI-ExpDiff.csv


title: Sample12: Human peripheral blood mononuclear cells RNA-seq

value: Dysplastic CML


title: NSCs, Vehicle_OSMI_2

description:
Vehicle treated replicate 2
Vehicle_OSMI_vs_12p5uM_OSMI-ExpDiff.csv


title: JIBRV1

city: Beijing

first: shimeng

last: Huang

address: No. 2 Yuanmingyuan West Road, Haidian District

department: College of Animal Science and Technology

institute: China Agricultural University

description: JIBRVvsDMSORV.xls

data_processing:
Illumina Casava1.8 software used for basecalling.
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 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: kidney

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext® UltraTM NA Library Prep Kit for Illumina® (NEB, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RNA-sequencing data from HEK293A cells were pre-treated with JIB-04 (10 μM) for 12 hr, and then uninfected and infected with porcine rotavirus (PoRV) (MOI=0.01) for the 12 hpi. Total RNA recovered from four separate group include DMSO, JIB(10 μm), DMSORV and JIBRV.

value: the human embryonic kidney 293 cells

tag: infection

value: porcine rotavirus (PoRV)


title: JIB3

description: JIBvsDMSO.xls


title: JIBRV3

description: JIBRVvsDMSORV.xls


title: JIBRV2

description: JIBRVvsDMSORV.xls


title: Larp7-/- rep1


title: JIB1

description: JIBvsDMSO.xls


title: NSCs, ShLuc-1

description:
ShLuc control replicate 1
ShLuc_vs_ShOgt-ExpDiff.csv


title: DMSORV3

description: JIBRVvsDMSORV.xls


title: JIB2

description: JIBvsDMSO.xls


title: Sample11: Human peripheral blood mononuclear cells RNA-seq


title: NSCs, Vehicle_OSMI_1

description:
Vehicle treated replicate 1
Vehicle_OSMI_vs_12p5uM_OSMI-ExpDiff.csv


title: Sample10: Human peripheral blood mononuclear cells RNA-seq


title: DMSORV2

description: JIBRVvsDMSORV.xls


title: DMSO3

description: JIBvsDMSO.xls


title: DMSORV1

description: JIBRVvsDMSORV.xls


title: NSCs, 12p5uM_OSMI_6

description:
12.5µM OSMI treated replicate 6
Vehicle_OSMI_vs_12p5uM_OSMI-ExpDiff.csv

value: 12.5µM OSMI


title: Sample09: Human peripheral blood mononuclear cells RNA-seq


title: Sample08: Human peripheral blood mononuclear cells RNA-seq


title: DMSO1

description: JIBvsDMSO.xls


title: NSCs, 12p5uM_OSMI_5

description:
12.5µM OSMI treated replicate 5
Vehicle_OSMI_vs_12p5uM_OSMI-ExpDiff.csv


title: NSCs, 12p5uM_OSMI_4

description:
12.5µM OSMI treated replicate 4
Vehicle_OSMI_vs_12p5uM_OSMI-ExpDiff.csv


title: Sample07: Human peripheral blood mononuclear cells RNA-seq

value: Proliferative CML


title: S42 anti-IgM 72h donorE

city: Clayton

first: Ferdinando

last: Bonfiglio

address: Rainforest Walk

country: Australia

institute: Monash University

data_processing:
The raw RNAseq reads were quality assessed using FastQC v0.11.7 and sequencing adaptors trimmed with fastp v0.19.6
STAR v2.6.0c was used to align fastq files to the human primary assembly (GRCh37 release 92), and to produce counts of mapped reads per gene.
Genome_build: GRCh37 release 92
Supplementary_files_format_and_content: text files with raw gene counts (STAR ReadsPerGene output) for every gene and every sample

source_name: B cells

growth_protocol: PBMCs were isolated from buffy-coats or from whole blood by a ficoll density gradient centrifugation method. B-cells were then purified from the PBMC fraction using a negative selection Easysep human B-cell enrichment kit (STEMCELL Technologies).

extract_protocol:
The total RNA was isolated using the RNeasy micro kit (Qiagen). The quality of the isolated RNA was determined with a Fragment Analyzer (Agilent, Santa Clara, California, USA).
The TruSeq Stranded mRNA kit (Illumina, Inc, California, USA) was used in the subsequent steps. Briefly, total RNA samples (60 ng) were polyA enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired and adenylated before ligation of TruSeq adapters containing unique dual indices (UDI) for multiplexing.

treatment_protocol: 1E6 isolated B-cells were used per condition, stimulated with IFN-l3 (100 ng/mL) or α-IgM (0.5 μg/mL) or with a combination of α-IgM and IFN-lambda.

tag: stimulation

value: anti-IgM 72h

tag: donor

value: E


title: S43 anti-IgM+IFN-lambda 72h donorE

value: anti-IgM+IFN-lambda 72h


title: S46 anti-IgM+IFN-lambda 72h donorF

value: F


title: Sample06: Human peripheral blood mononuclear cells RNA-seq


title: S45 anti-IgM 72h donorF


title: NSCs, 12p5uM_OSMI_2

description:
12.5µM OSMI treated replicate 2
Vehicle_OSMI_vs_12p5uM_OSMI-ExpDiff.csv

tag: treatment


title: NSCs, 12p5uM_OSMI_1

description:
12.5µM OSMI treated replicate 1
Vehicle_OSMI_vs_12p5uM_OSMI-ExpDiff.csv


title: Sample05: Human peripheral blood mononuclear cells RNA-seq


title: S39 anti-IgM 72h donorD

value: D


title: Sample_S20

city: Newcastle

first: John

last: Casement

address: Framlington Place

department: Bioinformatics Support Unit

institute: Newcastle University

data_processing:
Quality assessment with FastQC Version 0.11.2
Gene-level read counts calculated using Kallisto, with index created from Gencode realease 24 (GRCh38) transcripts
Genome_build: Gencode release 24 (GRCh38)
Supplementary_files_format_and_content: A matrix of gene-level counts for each sample in a tab delimited text file. Counts in the matrix are not normalized.

source_name: oral squamous cell carcinoma

extract_protocol:
10 μm sections were cut from the FFPE blocks and collected in 2 ml microcentrifuge tubes. The number of sections per sample was dependent on the size of the tissue; 4 sections for small sized samples, 3 - 4 sections for medium sized samples, 2 - 3 sections for large sized samples and 1 – 2 sections for very large sized samples. RNA extraction and purification were performed using the QIAGEN RNeasy FFPE kit following the manufacturer's protocol.
Whole transcriptome sequencing was performed using Illumina’s Next Generation Sequencing RNA-Seq platform following established protocols. RNA samples were assessed for quantity and integrity using the NanoDrop 8000 spectrophotometer V2.0 and Agilent 2100 Bioanalyser. From each sample, 100 ng of total RNA was used to prepare RNA libraries using the KAPA Stranded RNASeq Kit with RiboErase. Prior to first strand cDNA synthesis, fragmentation was carried out using incubation conditions recommended by the manufacturer for degraded samples (65°C for 1 minute), and 14 cycles of PCR were performed for final library amplification. The libraries produced were quantified using the Qubit 2.0 spectrophotometer and assessment of the average fragment size was performed using the Agilent 2200 TapeStation. The Illumina NextSeq®500 was used to generate 75 bp paired-end reads for each library.

tag: condition

value: malignant


title: S31 unstimulated donorD

value: unstimulated


title: Sample_S19


title: S40 anti-IgM+IFN-lambda 72h donorD


title: S41 unstimulated donorE


title: S36 IFN-lambda 72h donorD

value: IFN-lambda 72h


title: S30 anti-IgM+IFN-lambda 72h donorC

value: C


title: Sample04: Human peripheral blood mononuclear cells RNA-seq


title: Sample03: Human peripheral blood mononuclear cells RNA-seq


title: Sample_S18


title: DMSO2

description: JIBvsDMSO.xls


title: S29 anti-IgM 72h donorC


title: Sample02: Human peripheral blood mononuclear cells RNA-seq


title: S26 IFN-lambda 72h donorC


title: Sample_S17


title: S21 unstimulated donorC


title: S20 anti-IgM+IFN-lambda 72h donorB

value: B


title: Sample01: Human peripheral blood mononuclear cells RNA-seq

value: Peripheral blood


title: Sample_S16


title: S19 anti-IgM 72h donorB


title: S16 IFN-lambda 72h donorB


title: S11 unstimulated donorB


title: S10 anti-IgM+IFN-lambda 72h donorA

value: A


title: RKO_200_HCT116_200_SW480_200

city: Ann Arbor

first: Jun Hee

last: Lee

state: MI

address: 109 Zina Pitcher Pl

institute: University of Michigan

data_processing:
Sequencing by Illumina HiSeq-4000 High-Output system, with asymmetrical reads of 26 bp × 110 bp
Raw reads were processed using DropSeqTools (v1.13) and aligned to hg19 genome using STAR (v.2.6.0a).
The aligned reads were further processed using popscle dsc-pileup to produce the profiles of UMI and pileups of reads overlapping with polymorphic variants with minor allele frequency from 1000 Genomes Phase 3 panel.
The deconvolution of cell types was performed using popscle freemuxlet using variant-overlapping reads.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include counts of the transcript for each barcode

source_name: Human Colon Cancer Cell Line

growth_protocol: Cells were seeded at 100 cells/mL in DMEM with FBS until the cells were treated with 5FU when the cells reached 70% confluence.

extract_protocol: single cell RNA libraries were prepared by Drop-seq method for sequencing using Hiseq4000 Illumina protocols

treatment_protocol: DNA damage was induced by treatments with 5-fluorouracil (10µM, 50µM and 200µM)

value: RKO, HCT116, SW480 (multiplexed)

tag: dna damage to each cell line


title: RKO_50_HCT116_50_SW480_50


title: S6 IFN-lambda 72h donorA


title: RKO_0_HCT116_0_SW480_0 3


title: Sample_S15


title: S1 unstimulated donorA


title: Sample_S14


title: S9 anti-IgM 72h donorA


title: Sample_S13


title: RKO_50_HCT116_200_SW480_0


title: Sample_S11


title: Sample_S10

value: non-transformed


title: Sample_S12


title: RKO_10_HCT116_10_SW480_10 2


title: RKO_0_HCT116_50_SW480_200


title: Sample_S9


title: RKO_0_HCT116_0_SW480_0 2


title: Sample_S8


title: RKO_10_HCT116_10_SW480_10 1


title: RKO_200_HCT116_0_SW480_50


title: Sample_S7


title: set-2/qC1 P0 replicate 2

city: Santa Cruz

first: Susan

last: Strome

address: 1156 High St

department: MCD Biology

institute: UC Santa Cruz

data_processing:
TopHat2 was used to align the RNA-seq reads to the C. elegans transcriptome (WS220). Only reads with one unique mapping were allowed, otherwise default arguments were used. Reads mapping to ribosomal RNAs were then removed.
HTSeq was used to obtain read counts per transcript.
Normalization of read counts per transcript and differential expression analysis with no consideration for lineage-dependent relations were done with DESeq2 in R using HTSeq counts. P-values were adjusted for multiple testing using the Benjamini–Hochberg method as implemented in DESeq2.
Genome_build: WS220
Supplementary_files_format_and_content: Text files for each sample with HTSeq counts per transcript (tab delimited). And one text file with DESeq output for normalized read counts per gene for each sample and the differential expression analyses performed (comma delimited).

source_name: dissected gonads from young adults day 1

growth_protocol: C. elegans strains were maintained at 15° or 20° C on OP50 bacteria as described (Brenner 1974). For experiments, set-2 worms were upshifted to 25° C.

extract_protocol:
Total RNA was extracted using Trizol reagent and ribosomal RNA was depleted using the NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (Cat. #E6310).
Libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina sequencing (Cat. #E7530). Libraries were sequenced at the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley using the Illumina HiSeq 2500 or 4000 platforms.

treatment_protocol: Each lineage was initially started from twenty five set-2(bn129)/+ animals grown at 25° C . Subsequent generations of set-2 animals resulting from these 25 worms were assessed for sterility and gonads were isolated at F2 and F4 generations on Day 1 of adulthood. Fertility/sterility was assessed by the presence of progeny and/or eggs in the uterus. Each lineage contains 1 sample of gonads from P0 set-2(bn129)/+ animals, 1 sample of gonads from fertile F2 set-2(bn129) animals, 1 sample of gonads from fertile F4 set-2(bn129) animals and 1 sample of  gonads from sterile F4 set-2 (bn129) animals.

tag: genotype

tag: temperature


title: set-2/qC1 P0 replicate 3


title: set-2/qC1 P0 replicate 1


title: Sample_S6


title: set-2 F4 sterile replicate 3


title: Sample_S5


title: set-2 F4 sterile replicate 2


title: Sample_S4


title: ADWST11

city: Irvine

first: Scott

last: Atwood

state: California

address: 4340 McGaugh Hall, Ring Rd

department: Department of Developmental & Cell Biology

institute: University of California, Irvine

description: mRNA from single cells

data_processing:
Transcripts from human donors were mapped to the reference genome (GRCh38) using Cell Ranger Version 2.1.0
Quality control of all data sets was performed using Seurat (Version 3.0.0)
Processed files were analyzed with Seurat V3.1.0 and Velocyto.R V0.6.
Genome_build: GRCh38
Supplementary_files_format_and_content: Cell Ranger output

source_name: Peri-tumor primary skin tissue

extract_protocol:
Human basal cell carcinoma (BCC) subtypes (n=4) and peri-tumor skin (n=2; peri-tumor skin constitutes site adjacent to BCC lesion). Samples were surgically excised and placed in DMEM + 10% FBS overnight at 4C. The tissue was finely minced, incubated with collagenase at 37C overnight, and trypsinized for 10 min. Cells were incubated with DNAse for 5 min, filtered over 40um cell strainer, and flow sorted for live cells for library preparation.
Single cells were captured using the Chromium Platform (10X Genomics) and libraries were generated using Single Cell 3’ v2 chemistry. Cell capture, library preparation, quality control, and sequencing was performed at UCI Genomics High Throughput Facility at the University of California, Irvine.

tag: tissue

value: Peri-tumor skin

value: Skin adjacent to BCC

tag: sample type

value: Primary tissue


title: ADWST10

description: mRNA from single cells


title: paracancerous tissue of BC 6

type: RNA

city: Shanghai

first: Zhanghan

last: Chen

address: 180 Fenglin Road, Xuhui District

institute: Fudan University

hyb_protocol: The microarray hybridization was performed following the manufacturer’s standard protocols using a Gene Expression Hybridization Kit (Santa Clara, CA, US) in a Hybridization Oven (Santa Clara, CA, US).

scan_protocol: The hybridized slides were washed, fixed and finally scanned to obtain images by an Agilent Microarray Scanner (Santa Clara, CA, US).

data_processing: The data were extracted with Feature Extraction software 12.0 (CA, US), and the raw data were normalized by the Quantile algorithm in the limma package in R.

source_name: paracancerous tissue of BC

label_protocol: The total RNA was amplified and labeled by a Low Input Quick Amp WT Labeling Kit (Santa Clara, CA, US), and the labeled cRNAs were purified by an RNeasy mini kit.

extract_protocol: The total RNA was extracted and purified using TRIzol reagent (Invitrogen) and an RNeasy Mini Kit (Qiagen, USA) following the manufacturer’s instructions. The total RNA was quantified by a NanoDrop-2000 spectrophotometer (NanoDrop, USA). The selected RNA samples were assessed by an Agilent Bioanalyzer 2100 (CA, US) to inspect the RNA integrity.

value: paracancerous tissue

tag: gender

value: female


title: tumor tissue of BC 6

source_name: tumor tissue of BC

value: tumor tissue of BC


title: set-2 F4 fertile replicate 2


title: BCC10

description: mRNA from single cells

source_name: Basal cell carcinoma primary skin tissue

value: Basal cell carcinoma

tag: disease state

value: Infiltrative with peineural invasion


title: set-2 F2 fertile replicate 3


title: paracancerous tissue of BC 2


title: RKO_0_HCT116_0_SW480_0 1


title: Sample_S3


title: tumor tissue of BC 1


title: RF2CD4_MicroC

city: Ithaca

first: Charles

middle: Grahe

last: Danko

state: NY

address: 235 Hungerford Hill Road

department: Baker Institute for Animal Health

institute: Cornell University

data_processing:
library strategy: MicroC
Data was processed using the Juicer pipeline (Durand et al. Cell.Syst, 2016 [PMID: 27467249])
Genome_build: hg19
Supplementary_files_format_and_content: Hi-C and MicroC contact with mapping quality for each fragment are provided in the merged_nodup.txt suffixed filles. Contact frequancy matrices with resolution ranging from 5Kbp to 2.5Mbp are provided as hic files.

organism: Macaca mulatta

source_name: Primery CD4+ T-cells from PBMCs

growth_protocol: CD4+ T-cells isolated from peripheral blood using positive selection for the CD4 antigen.

extract_protocol:
Nuclei were extracted as described (Danko et. al. (2015) Nature Methods).
Hi-C libraries were prepered according to Rho et al. 2018, cell (PMID: 25497547). MicroC was performed according to Krietenstein et al. Mol. Cell, 2020 (PMID:32213324)

tag: individual

tag: Sex

value: Female

value: blood-deriven CD4+ T-cells


title: tumor tissue of BC 2


title: paracancerous tissue of BC 5


title: Sample_S2


title: BCC8

description: mRNA from single cells

value: Unknown subtype


title: paracancerous tissue of BC 4


title: set-2 F2 fertile replicate 2

tag: strain


title: BCC3

description: mRNA from single cells

value: Superficial and nodular


title: tumor tissue of BC 4


title: tumor tissue of BC 5


title: Sample_S1


title: tumor tissue of BC 3


title: set-2 F4 fertile replicate 3


title: RM1CD4_HiC

data_processing:
Data was processed using the Juicer pipeline (Durand et al. Cell.Syst, 2016 [PMID: 27467249])
Genome_build: hg19
Supplementary_files_format_and_content: Hi-C and MicroC contact with mapping quality for each fragment are provided in the merged_nodup.txt suffixed filles. Contact frequancy matrices with resolution ranging from 5Kbp to 2.5Mbp are provided as hic files.

value: Male

tag: cell type


title: set-2 F2 fertile replicate 1


title: Osx- Cd45- cKO rep2

status: Public on Aug 13 2020

city: St. Louis

first: Roberto

last: Civitelli

state: Missouri

address: 660 S. Euclid Ave.

department: Bone and Mineral Diseases

institute: Washington University St. Louis

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with custom demultiplexer written in python
Technical replicate fastq files were combined and aligned with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45 and annotated with Ensembl Biomart.  RPKM calculated from gene counts with standard RPKM transformation with custom R scripting.
Genome_build: Ensembl GRCm38.76
Supplementary_files_format_and_content: Gene counts in tab-delimited text format

source_name: Stromal cells from orthotopic MMTV-BO1 tumors

extract_protocol:
We inoculated 6 Cdh2-cKO;Ai9 and 4 Osx-cre;Ai9 (wild type) mice and selected, from these cell preparations, those samples that met the quality control test for RNA integrity (average RIN=8.95).  Based on this protocol, we submitted 2-3 biological replicates per group of cells, per each genotype to RNAseq analysis.
Clontech SMARTer v1

tag: age

value: Postnatal day 56

tag: phenotype

value: Osx- Cd45-


title: Osx- Cd45- cKO rep1

value: Stromal cells from orthotopic MMTV-BO1 tumors


title: paracancerous tissue of BC 3


title: BCC2

description: mRNA from single cells

value: Superficial, nodular and infiltrative


title: Osx- Cd45+ cKO rep3

value: Osx- Cd45+


title: Osx- Cd45+ cKO rep2


title: Osx- Cd45- cKO rep3


title: paracancerous tissue of BC 1

source_name: paracancerousl tissue of BC


title: RF2CD4_HiC


title: Osx+ CD45+ Cko rep3

value: Osx+ CD45+


title: Osx+ CD45+ Cko rep2


title: Osx+ CD45+ Cko rep1


title: Osx- Cd45+ cKO rep1


title: Osx+ CD45- cKO rep1

value: Osx+ CD45-


title: Osx+ CD45- cKO rep2


title: Osx- Cd45- WT rep3

value: wild type


title: Osx- Cd45+ WT rep3


title: Osx- Cd45+ WT rep1


title: Osx- Cd45- WT rep2


title: Osx+ CD45+ WT rep3


title: Osx+ CD45+ WT rep1


title: Osx+ CD45- WT rep2


title: Osx+ CD45- WT rep1


title: WT-P39-2

city: Los Angeles

first: Wenlin

last: Zhang

address: 200 Stein Plaza, Dserc 3-143

institute: UCLA, Jules Stein Eye Institute

description:
Slc4a11+/+
MCEC-WT-P39-2_S27_L004_R1_001

data_processing:
Alignment - HISAT2, --no-unal
Assemble and Quantify - HTSeq-count
DGE analysis - LIMMA and VOOM
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: txt - list of DGE

source_name: corneal endothelium

growth_protocol: All MCEnC lines were cultured on flasks coated with a mixture of 40 µg/cm2  chondroitin sulfate (Sigma-Aldrich) and 40 ng/ cm2 laminin (Sigma-Aldrich). The cells were grown at 33°C in OptiMEM-I medium (Thermo Fisher Scientific) supplemented with 8% fetal bovine serum (Atlanta Biologicals), 10 ng/mL recombinant human FGF, pituitary extract 50 μg/mL (Sigma-Aldrich), CaCl2 200 mg/L, 0.08% chondroitin sulfate (G6737, Sigma-Aldrich), gentamicin 50 μg/mL (Thermo Fisher Scientific), 100 µg/mL penicillin (Thermo Fisher Scientific), and 100 µg/mL streptomycin (Thermo Fisher Scientific).

extract_protocol:
Total RNA from cultured MCEnC was isolated and purified using the RNeasy Plus Mini Kit (Qiagen).
UCLA TCGB protocol

value: immortalized mouse corneal endothelial cells

tag: passage


title: KO-P40-3

description:
Slc4a11-/-
MCEC-KO-P40-3_S31_L004_R1_001


title: WT-P6-2

description:
Slc4a11+/+
MCEC-WT-P6-2_S33_L004_R1_001


title: WT-P6-1

description:
Slc4a11+/+
MCEC-WT-P6-1_S32_L004_R1_001


title: WT-P39-1

description:
Slc4a11+/+
MCEC-WT-P39-1_S26_L004_R1_001


title: WT-P6-3

description:
Slc4a11+/+
MCEC-WT-P6-3_S33_L004_R1_001


title: KO-P7-3

description:
Slc4a11-/-
MCEC-KO-P7-3_S37_L004_R1_001


title: KO-P7-2

description:
Slc4a11-/-
MCEC-KO-P7-2_S36_L004_R1_001


title: Osx- Cd45- WT rep1


title: KO-P7-1

description:
Slc4a11-/-
MCEC-KO-P7-1_S35_L004_R1_001


title: ECHi-C Osteoblast D1 Experiment #1

city: Odense M

first: Susanne

last: Mandrup

state: Fyn

address: Campusvej 55

department: Department of Biochemistry and Molecular Biologi

country: Denmark

institute: University of Southern Denmark

data_processing:
Base calling for all sequencing runs was performed using bcl2fastq (v2.20.0.422).
ChIP-seq: Reads were aligned using STAR (v2.3.1, --outSJfilterIntronMaxVsReadN 0 --outFilterMatchNmin 25 --outFilterMismatchNmax 2 --alignIntronMax 1). Duplicated reads/fragments were removed using Picard (v2.5.0). Reads/fragments were counted using HOMER (v4.10.3) in DNase I hypersensitive regions identified in a previous study (Rauch et al., 2019)
scATAC-seq: Reads (R1 and R2) were trimmed using TrimGalore (v. 0.6.0) and aligned aligned using STAR (v2.3.1, --outSJfilterIntronMaxVsReadN 0 --outFilterMatchNmin 25 --outFilterMismatchNmax 2 --alignIntronMax 1). Only short fragments (< 140bp) were kept , the short fragments were deduplicated using Picard (v2.5.0) and peaks were detected using MACS2 (v. 2.1.2). The cell barcodes (Index1) were quality filtered using FASTX toolkit (v. 0.0.13, -q 30 -p 80). The quality filtered barcodes were matched to the barcode white list (10X Genomics) and only barcodes with more than 10000 reads were kept. The raw aligned reads were split into cell-specific files using the filtered barcodes and individually deduplicated. Count matrices were generated by counting fragments for each cell using featureCounts (v.2.0.0) in peak detected regions. Cells and peaks were quality filtered and co-accessible peaks were identified using Cicero.
CUT&RUN: Reads trimmed with cutadpt and aligned using STAR (v2.3.1, --outSJfilterIntronMaxVsReadN 0 --outFilterMatchNmin 25 --outFilterMismatchNmax 2 --alignIntronMax 1).
RNA-seq: Reads were aligned using STAR (v2.3.1). Reads were counted using iRNA-seq (v1.0).
HiC: Reads were aligned and quality controlled using Hicup (v0.6.1). TADs were identified using HiTAD from TADlib (v0.3.1).
ECHiC: Reads were aligned and quality controlled using Hicup (v0.6.1). Interactions between virtual restriction fragments were detected using Chicago (v1.6.0) using custom weights calculated from high confidence interactions in the data.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq: Tab-delimited txt files containing normalized tag counts for each replicate in DNase I hypersensitive regions identified in a previous study (Rauch et al., 2019). For each replicate, read depth normalized bedGraph files are also supplied for filtered and deduplicated alignments.
Supplementary_files_format_and_content: scATAC-seq: Tab-deliminted txt file containing the peak co-accessibility (estimated with Cicero).
Supplementary_files_format_and_content: CUT&RUN: Tab-delimited txt files containing raw tag counts for each replicate in DNase I hypersensitive regions identified in a previous study (Rauch et al., 2019). For each replicate, read depth normalized bedGraph files are also supplied.
Supplementary_files_format_and_content: RNA-seq: Tab-delimited txt file containing raw tag counts for each replicate for all RefSeq genes . For each replicate, read depth normalized bedGraph files are also supplied.
Supplementary_files_format_and_content: Hi-C: The BED file contains all detected TADs and subTADs (identified using HiTAD).
Supplementary_files_format_and_content: ECHi-C: All interactions identified (using Chicago), as well as counts in all samples and annotation is also supplied in a tab-delimited txt file.

growth_protocol: Telomerase-immortalized human mesenchymal stromal cells of bone marrow (BM-hMSC-TERT4) were grown under standard cell culture conditions in α-MEM supplemented with 10 % fetal calf serum (FCS) and 1 % penicillin/streptomycin (P/S).

extract_protocol:
Capture Hi-C of enhancers was performed on 500 ng Hi-C libraries using the custom-designed biotinylated RNA bait library and custom blockers according to the manufacturer’s instructions (SureSelect, Agilent). Post-capture PCR amplification using universal primer and 6 bp-index primers (New England Biolabs) were performed.
ECHi-C libraries were constructed from genomic DNA according to the manufacturer's instructions (Illumina).

treatment_protocol: Two days post confluency (day 0), cells were induced to undergo adipocyte differentiation by exposing them to a adipogenic differentiation cocktail (DMEM supplemented with 10% fetal calf serum, 10ug/mL insulin, 1µM rosiglitazone, 100 mM dexamethasone, and 500 µM isobutylmethylxanthine). Medium was replaced on days 2, 4, 7 and 9.

value: Osteoblast

tag: Stage

value: Day 1


title: Osx- Cd45+ WT rep2


title: ECHi-C Adipocyte D1 Experiment #2

description:
ECHiC_Lineages.counts.txt.gz
ECHiC_Adipogenesis.counts.txt.gz

value: Adipocyte


title: ECHi-C Adipocyte D10 Experiment #2

value: Day 10


title: ECHi-C Adipocyte D10 Experiment #1


title: ECHi-C Osteoblast D1 Experiment #2


title: Hi-C Msc Experiment #2

extract_protocol:
Hi-C was performed using in-nucleus ligation following a modified version of a previously described protocol (Nagano et al., 2015). Chromatin was digested using MboI restriction enzyme. The digested ends were filled in using biotinylated d-ATP and ligated. Chromatin was de-crosslinked and purified by phenol-chloroform extraction. Purified DNA (50 µg) was sheared to an average size of 400 bp by sonication (Covaris). The sheared DNA was end-repaired, adenine-tailed and double size-selected using AMPure XP beads to isolate DNA ranging from 250 to 550 bp. Ligation fragments marked by biotin were immobilized using MyOne Streptavidin C1 DynaBeads (Invitrogen) and ligated to NEBNext hairpin adaptors (New England Biolabs) followed by U excision by USER Enzyme (New England Biolabs). The resulting Hi-C libraries were amplified using universal primer and 6bp-index primers (New England Biolabs).
Hi-C libraries were constructed from genomic DNA according to the manufacturer's instructions (Illumina).

value: Stem cell

value: Day 0


title: Hi-C Msc Experiment #1


title: Osx+ CD45+ WT rep2


title: WT-P39-3

description:
Slc4a11+/+
MCEC-WT-P39-3_S28_L004_R1_001


title: ECHi-C Msc Experiment #2


title: ECHi-C Msc Experiment #1


title: RNA-seq Adipocyte D10 Experiment #3

extract_protocol:
RNA was extracted from 6-well dishes using TRI Reagent (Sigma) followed by chloroform extraction and purification of RNA using Econo Spin columns (Epoch Life Sciences).
RNA-seq libraries were constructed from 2 µg of RNA according to manufacturer’s instructions (TruSeq 2, Illumina).


title: RNA-seq Adipocyte D10 Experiment #2


title: ECHi-C Adipocyte D1 Experiment #1


title: RNA-seq Adipocyte D10 Experiment #1


title: KO-P40-2

description:
Slc4a11-/-
MCEC-KO-P40-2_S30_L004_R1_001


title: KO-P40-1

description:
Slc4a11-/-
MCEC-KO-P40-1_S29_L004_R1_001


title: TEAD1 ChIP-seq Adipocyte D1 Experiment #2

extract_protocol:
Chromatin was prepared from 150 mm culture dishes by in 1% formaldehyde in PBS (10 minutes, RT). Cross-linking was stopped by adding glycine to a final concentration of 0.125 M (10 minutes, RT). The cells were washed twice in ice-cold PBS, and harvested in ice-cold lysis buffer (0.1% SDS, 1% Triton X-100, 0.15 M NaCl, 1 mM EDTA, 20 mM Tris pH=8) and sonicated at high setting in a Bioruptor-Twin (Diagenode) at a volume of 1.5 ml in 15-mL tubes for 40 cycles of 30 seconds on and 30 seconds off. The chromatin IPs were performed as described in (Nielsen R, et al. 2014. Methods in Enzymology 537: 261-279).
ChIP-seq libraries were constructed from 10 to 20 ng of genomic DNA according to the manufacturer's instructions (Illumina) as described in (Nielsen R, et al. 2014. Methods in Enzymology 537: 261-279).

tag: antibody

value: TEAD1 (BD Biosciences, 610923)


title: MED1 ChIP-seq Adipocyte D10 Experiment #1

extract_protocol:
Chromatin was prepared from 150 mm culture dishes by cross-linking in 2 mM disuccinimidyl glutarate (20 minutes, RT) and subsequently, in 1% formaldehyde in PBS (10 minutes, RT). Cross-linking was stopped by adding glycine to a final concentration of 0.125 M (10 minutes, RT). The cells were washed twice in ice-cold PBS, and harvested in ice-cold lysis buffer (0.1% SDS, 1% Triton X-100, 0.15 M NaCl, 1 mM EDTA, 20 mM Tris pH=8) and sonicated at high setting in a Bioruptor-Twin (Diagenode) at a volume of 1.5 ml in 15-mL tubes for 40 cycles of 30 seconds on and 30 seconds off. The chromatin IPs were performed as described in (Nielsen R, et al. 2014. Methods in Enzymology 537: 261-279).
ChIP-seq libraries were constructed from 10 to 20 ng of genomic DNA according to the manufacturer's instructions (Illumina) as described in (Nielsen R, et al. 2014. Methods in Enzymology 537: 261-279).

value: MED1 (Santa Cruz:sc-8998)


title: TEAD1 ChIP-seq Msc Experiment #2


title: MED1 ChIP-seq Adipocyte D10 Experiment #2


title: TEAD4 ChIP-seq Msc Experiment #2

value: TEAD4 (Santa Cruz, sc-101184)


title: 11559_alone-1

first: Olga

last: Lastovetsky

address: 334 Plant Science Building, 236 Tower Rd, Cornell University

description:
processed data file: pre-contact_fungal_atcc11559.count
processed data file: pre-contact_fungal_atcc11559_results

data_processing:
Reads were quality controlled using FASTQ and trimmed with Trimmomatic to eliminate low quality reads and Illumina adapters
reads were aligned to the fungal genomes of R. microsporus ATCC 52813 (GenBank accession JOSV00000000) and R. microsporus ATCC 11559 (GenBank MCOJ00000000) using TopHat with following parameters tophat -p 11 -o outputdirectory -G genome.gff3 --transcriptome-index xxx --no-novel-juncs genomefile xxx_R1_paired.fq xxx_R2_paired.fq. Bacterial reads were aligned to genome of Burkholderia sp. B13 (FTPM01000001-FTPM01000002) using bwa with the following parameters: bwa mem -t 8 GENOME.fa -t 8 xxx.fq > xxx.sam
Fungal transcript abundances were quantified with CuffDiff, bacterial transcript abundances measured with RSEM, and the counts files used for differential expression analysis with EdgeR
Genome_build: R. microsporus ATCC 52813 NCBI accession number: JOSV00000000
Genome_build: R. microsporus ATCC 11559 NCBI accession number: MCOJ00000000
Genome_build: Burkholderia sp. B13 European Nucleotide Archive (ENA) accession FTPM01000001-FTPM01000002
Supplementary_files_format_and_content: tab-delimeted text file with read counts generated by CuffDiff  or RSEM which was then used for differential expression analysis with EdgeR. EdgeR-generated tab-delimited text file with fold change, p- and and false discovery rate-values for all the genes .

organism: Rhizopus microsporus ATCC 52813

source_name: vegetative mycelium

extract_protocol:
Total RNA was extracted with the Ambion ToTALLY Total RNA Isolation Kit (Life Technologies, Grand Island, NY) and rRNA was removed with RiboZero Magnetic Gold Kit (Epicentre, Madison, WI)
RNA sequencing libraries were prepared using the NEBNext® mRNA Library Prep Reagent Set for Illumina®

value: vegetative mycelium

tag: growth stage

value: 50h post inoculation


title: 13f_alone-3

description:
processed data file: pre-contact_fungal_atcc52813.count
processed data file: pre-contact_fungal_atcc52813_results


title: 13f_alone-2


title: 13f_alone-1


title: 11559_alone-2

value: 56h post inoculation


title: Embryonic Stem Cell [methylation]

city: Cleveland

first: Ryan

middle: C.

last: Gimple

state: OH

address: 10900 EUCLID AVENUE

institute: CASE WESTERN RESERVE UNIVERSITY

description: Methyl Capture Sequencing

data_processing:
Reads were aligned to the reference genome using Bismark.
MethylKit was used for differential methylation as described in the methods.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig

source_name: embryonic stem cell

growth_protocol: The cells were cultured in RPMI 1640 medium (Invitrogen) supplemented with 10% FBS (Hyclone, Cat# SV30014.03), 1% Anti-Anti (Life Technologies, Cat# 15240-062), 1% GlutaMAX (Gibco, Ref: 35050-061) at 37oC in a 5% CO2-air incubator. hESC line H1 (NIH catalogue # WA01) was cultured (as previously described in Lee et al., 2007) in mTeSRTM media (Stem Cell Technologies, Cat# 85870) with 0.1mg/ml Matrigel (Corning, Cat# 356231) coated plates at 37oC in a 5% CO2-air incubator. Cells were passaged with Accutase solution (Millipore sigma, Cat# SCR005) and media was changed on a daily basis.

extract_protocol:
DNeasy Blood and Tissue Kit (Qiagen, Cat #69504).
TruSeq Methyl Capture EPIC Library Prep Kit and KAPA HiFi HotStart Uracil ReadyMix PCR Kit.

treatment_protocol: Sendai virus (SeV) vectors encoding reprogramming factors OCT4, SOX2, c-MYC and KLF4 were purchased from Invitrogen (Cat# A16518). The viral transduction was performed based on manufacturer’s instructions. The expression level of the stemness genes in cancer cell lines was determined by quantitative polymerase chain reaction (qPCR). Thyroid tumor cells were plated at a density of 2x10^5 cells/well of a six-well plate in cancer cell culture medium and kept overnight before the transduction. The conventional hiPSC generation SeV vector cocktail (containing polycistronic-KLF4, OCT4, and SOX2; monocistronic-c-MYC, and monocistronic-KLF4 was transduced to the cells at multiplicity of infection (MOI) of 5:5:3, respectively. After transduction, the cells were maintained in the same culture condition and morphology change was observed every day. 5 days after transduction, the cells were transferred to Matrigel-coated plates with half RPMI medium and half mTeSR medium. The next day the medium was changed to mTeSR. The cells were grown in mTeSR for 30-45 days. hiPSCs were maintained as previously described by us in Tobe et al., 2017. After 4-6 weeks post-induction, clones with hESC/hiPSC morphology were visualized microscopically. Live staining was performed with TRA-1-60 mouse anti-human mAb, AlexaFluor 488 Conjugate Kit for live Cell Imaging (Life technology, Cat. no. A25618) according to the manufacturer's instruction. Then hiPSC-like colonies were manually transferred into 24 well plates. Reprogramming efficiency was determined by the percentage of the cells that were triple positive for stem cell markers Tri1- 81, SSEA-4 and Tri-1-60 using the flow cytometry analysis.

value: embryonic stem cell


title: CTCF ChIP-seq Msc Experiment #1

value: CTCF (Active Motif, 61312)


title: CTCF ChIP-seq Adipocyte D1 Experiment #2


title: CTCF ChIP-seq Msc Experiment #2


title: SW1736 [methylation]

description: Methyl Capture Sequencing

source_name: Thyroid cancer cell line

value: Thyroid cancer cell line


title: TEAD4 ChIP-seq Msc Experiment #1


title: CTCF ChIP-seq Adipocyte D1 Experiment #1


title: snATAC-seq Msc

extract_protocol:
Nuclei were prepared by trypsinating the cells, passing them through a 40 µm cell strainer and washing twice in PBS. The cells were resuspended in buffer A (15 mM Tris-HCL pH 8.0, 15 mM NaCl, 60 mM KCl, 0.5 mM Spermidin) and counted. Cell concentration was adjusted to 2 ∙ 10^6 cells/ml in buffer A and diluted 1:1 in buffer A containing 0.04% IGEPAL-CA630 and 0.02% Digiton-in. Cells were transferred to a precooled 2 ml douncer, incubated 10 min on ice with 5 strokes with a loose pestle after 3 and 8 min. Nuclei were pelleted at 1200 g for 5 min at 4°C, washed twice in 400 µl cold buffer A supplemented with 1% BSA and resuspended in 30 µl nuclease free H2O.
scATAC-seq libraries were constructed using 10.000 nucleic according to the manudacturer's instructions (10X Genomics).


title: 8505C [methylation]

description: Methyl Capture Sequencing


title: IPS-8505C [methylation]

description: Methyl Capture Sequencing


title: CEBPb ChIP-seq Adipocyte D1 Experiment #2

value: CEBPb (Santa Cruz, sc-150)


title: IPS-SW1736 [methylation]

description: Methyl Capture Sequencing


title: 11559_alone-3


title: TEAD1 ChIP-seq Adipocyte D1 Experiment #1


title: TEAD1 ChIP-seq Msc Experiment #1


title: CEBPb ChIP-seq Msc Experiment #1


title: CEBPb ChIP-seq Msc Experiment #2


title: CEBPb ChIP-seq Adipocyte D1 Experiment #1


title: IPS-8505C [8i-RNA_S4]

data_processing:
FASTQ files were concatenated and quality control performed with FASTQC. Reads were trimmed using Trim Galore
Salmon was used for generation of counts tables and DESEQ2 was used for differential expression analysis.
Genome_build: hg38. Gencodev29
Supplementary_files_format_and_content: counts; DESEQ2

growth_protocol: The cells were cultured in RPMI 1640 medium (Invitrogen) supplemented with 10 % FBS (Hyclone, Cat# SV30014.03), 1% Anti-Anti ((Life Technologies, Cat# 15240-062), 1% GlutaMAX (Gibco, Ref: 35050-061) at 37oC in a 5% CO2-air incubator. hESC line H1 (NIH catalogue # WA01) was cultured (as previously described in Lee et al, 2007) in mTeSRTM media (Stem Cell technologies, Cat# 85870) with 0.1mg/ml Matrigel (Corning, Cat# 356231) coated plates at 37oC in a 5% CO2-air incubator. Cells were passaged with Accutase solution (Millipore sigma, Cat# SCR005) and media was changed on a daily basis.

extract_protocol:
Total RNA was extracted from cells with RNeasy Mini Kit (Qiagen, Cat# 74104).
RNA-free DNA was isolated from cells with DNeasy Blood & Tissue Kit (Qiagen, Cat# 69504). The quality of DNA was tested by Qubit Fluorometer. Next Generation Sequencing was performed using an Illumina NextSeq 500 with TruSeq Methyl Capture EPIC Library Prep Kit and KAPA HiFi HotStart Uracil ReadyMix PCR Kit. Then the sequencing data was analyzed via Integrative Genomics Viewer (http://software.broadinstitute.org/software/igv/).

treatment_protocol: Sendai virus (SeV) vectors encoding reprogramming factors OCT4, SOX2, c-MYC and KLF4 were purchased from Invitrogen (Cat# A16518). The viral transduction was performed based on manufacturer’s instructions. The expression level of the stemness genes in cancer cell lines was determined by quantitative polymerase chain reaction (qPCR) [. Thyroid tumor cells were plated at a density of 2x105 cells/well of a six-well plate in cancer cell culture medium and kept overnight before the transduction. The conventional hiPSC generation SeV vector cocktail (containing polycistronic-KLF4, OCT4, and SOX2; monocistronic-c-MYC, and monocistronic-KLF4 was transduced to the cells at multiplicity of infection (MOI) of 5:5:3, respectively. After transduction, the cells were maintained in the same culture condition and morphology change was observed every day. 5 days after transduction, the cells were transferred to Matrigel-coated plates with half RPMI medium and half mTeSR medium. The next day the medium was changed to mTeSR. The cells were grown in mTeSR for 30-45 days. hiPSCs were maintained as previously described by us in Tobe et al, 2017. After 4-6 weeks post-induction, clones with hESC/hiPSC morphology were visualized microscopically. Live staining was performed with TRA-1-60 mouse anti-human mAb, AlexaFluor 488 Conjugate Kit for live Cell Imaging (Life technology, Cat. no. A25618) according to the manufacture instruction. Then hiPSC-like colonies were manually transferred into 24 well plates. Reprogramming efficiency was determined by the percentage of the cells that were triple positive for stem cell markers Tri1- 81, SSEA-4 and Tri-1-60 using the flow cytometry analysis.

tag: cell line background

value: ATC lines C643, Hth74, 8505C and SW1736 purchased from Univ. of Colorado Cancer Center (Univ. of Colorado Anschutz Medical Campus, USA).


title: SW1736 [S-RNA_S3]


title: Embryonic Stem Cell [ES-RNA_S2]


title: IPS-SW1736 [Si-RNA_S5]


title: 8505C [01-8-RNA_S1]


title: BC3 H3K27ac

city: Chicago

first: Eva

middle: Henriette

last: Gottwein

state: IL

address: 320 E Superior St., Tarry building, Room 6-752

department: Microbiology-Immunology

institute: Northwestern University

data_processing:
ChIP-Seq reads were aligned to hg19 and KSHV BAC16 genomes using Bowtie v1.1.2. Peak calling was performed using MACS v1.4.2 and compared to respective inputs as indicated.
Genome_build: hg19, KSHV (BAC16 reference)
Supplementary_files_format_and_content: BigWig

growth_protocol: All cells were grown in RPMI-1640 containing 10 µg/mL gentamycin, 0.05 mM β-mercaptoethanol and 20% Serum Plus-II media. Cells were maintained at densities between 2E5 and 1E6 cells/mL

extract_protocol:
Cells were crosslinked with 1% formaldehyde in PBS for 10 min and quenched with 0.125 M glycine for 5 min at room temperature. All buffers were supplemented with 1X protease inhibitor cocktail (Roche) and 1 mM phenylmethylsulfonyl fluoride. Cells were incubated in 1 mL buffer 1 (50 mM HEPES-KOH, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) for 10 min on ice. Nuclei were then pelleted at 1,350 g,  for  5 min, and resuspended in 1 mL buffer 2 (10 mM Tris-HCl, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA). Pelleted nuclei were lysed in 1 mL buffer 3 (1% SDS, 10 mM EDTA, 50 mM Tris-HCl) by multiple pipetting.  and cChromatin was sheared by sonication using a BioruptorTM (Diagenode). 100 µl 10% Triton X-100 was added to each sample, samples were mixed, and cell debris was removed by centifugation at 20,000 g and, 4°C, , for 10 min.   For each ChIP, chromatin from 1x106 cells was diluted 1:10 in ChIP dilution buffer (0.01 % SDS, 1.1 % Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, 167 mM NaCl) and incubated with 4 µg of the respective antibody for 16 h rotating at 4°C. Chromatin immunocomplexes were bound to 50 µl BSA-blocked Pierce ChIP-grade Protein A/G Magnetic Beads (Thermo Fisher Scientific, Cat.# 26162) for 1 hr at 4°C.   Beads were washed using increasing salt concentrations: low-salt buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, 150 mM NaCl); high-salt buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, 500 mM NaCl); LiCl-wash buffer (0.25 M LiCl, 1 % Nonidet P-40, 1 % sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl); with the final two washes with TE buffer without protease inhibitors.   Chromatin was eluted in 210 µl elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1 % SDS) for 30 min at 65°C. De-crosslinking was performed by adding 8 µl 5M NaCl at 65°C overnight. Chromatin was diluted in with 200 µl TE buffer and treated with 8 µl RNAse A (10 mg/ml) for 2 h at 37°C. After the addition of 7µl CaCl2 solution (300 mM CaCl2 in 10 mM Tris-HCl), remaining protein was degraded using 4 µl Proteinase K (40 mg/ml) for 1h at 55°C. DNA was purified by standard phenol/chloroform extraction followed by ethanol precipitation. Samples were resuspended in 55µl 10 mM Tris-HCl. Input DNA from 2.5X105 cells was de-crosslinked and purified similarly to ChIP samples.
Sequencing libraries were generated from 2-10 ng ChIP DNA or input using the NEXTflex Illumina ChIP-Seq Library Prep Kit (Bioo Scientific, Cat#5143-02) as per the manufacturer´s instructions.

tag: chip antibody

value: H3K27ac (Abcam #ab4729)


title: BC3 H3K4me1

value: H3K4me1 (Cell Signaling #5326)


title: BC3 Input for H3K4me1, H3K27ac


title: BCBL1 H3K27ac


title: BCBL1 Input


title: BC1 H3K27ac


title: BC1 Input


title: IRF4_1: IRF4 Rep. 1

data_processing:
ChIP-Seq reads were aligned to hg19 and KSHV BAC16 genomes using Bowtie v1.1.2. Peak calling was performed using MACS v1.4.2 and compared to Input #1.
Genome_build: hg19, KSHV (BAC16 reference)
Supplementary_files_format_and_content: BigWig

value: IRF4 (Cell Signaling #15106S)


title: BATF_1: BATF Rep. 1

value: BATF (CDI Laboratories #m14-108)


title: BATF_2: BATF Rep. 2


title: BATF_3: BATF Rep. 3


title: IRF4_2: IRF4 Rep. 2


title: IRF4_3: IRF4 Rep. 3


title: stressed for 14 days + Recreation for 7 days [29_ML51_14dSD-7dREC]

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix mouse GeneChip 1.0 ST microarrays.  The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing:
Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = MTA-1_0
program-name = Expression Console
program-version = 1.4.1.46

label: Biotin

label_protocol: Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Mouse HuGene-1_0-st-v1 GeneChips (Affymetrix, Inc).  DNase treatment was included as part of isolation to remove possible contaminating DNA.  Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling.  300 ng of total RNA was used for labeling with theAmbion WT Expression Kit (cat#4411974)  and Affymetrix kit (Cat # 900652).After hybridization,  the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

extract_protocol: Trizol (Invitrogen) and RNaseazy (Qiagen) kits were used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: as described in the paper

tag: genotype

value: WT

tag: diet

value: stress+recreation

tag: tissue/cell type

value: Brain_endothelial cells


title: stressed for 7 days [16_ML19_7dSD-10min]

source_name: stressed for 7 days

value: stressed


title: stressed for 14 days + Recreation for 7 days [30_ML52_14dSD-7dREC]


title: stressed for 14 days + Recreation for 7 days [28_ML50_14dSD-7dREC]


title: stressed for 14 days [15_ML18_14dSD-10min]

source_name: stressed for 14 days


title: stressed for 1 day [18_ML21_1dSD-10min]

source_name: stressed for 1 day


title: stressed for 1 day [19_ML22_1dSD-10min]


title: stressed for 7 days [9_ML12_7dSD-10min]


title: stressed for 14 days [14_ML17_14dSD-10min]


title: stressed for 14 days [13_ML16_14dSD-10min]


title: efl1_rep2

city: Cambridge

first: Francesco Nicola

last: Carelli

address: Henry Wellcome Building of Cancer and Developmental Biology,  Tennis Court Road

institute: University of Cambridge

data_processing:
RNA-seq reads were aligned using STAR (Dobin et al., 2013) with the two-pass mode using the C. elegans gene annotation from Wormbase (version WS260) as a guide (after removing any gene annotation from the mitochondrial DNA).
BigWig tracks were generated using the wigToBigWig tool downloaded from the UCSC website (http://hgdownload.soe.ucsc.edu/).
Genome_build: ce11
Supplementary_files_format_and_content: Forward and reverse-strand genome-wide read coverage in RPM (reads per million of mapped reads)

molecule: polyA RNA

source_name: efl-1 (se1)_whole worm

growth_protocol: Synchronized adults grown in liquid culture using standard S-basal medium with HB101 E. coli at 20°C were bleached to isolate embryos, the eggs were hatched at 25°C in M9 buffer, and starved L1s were sucrose floated and collected 20-22 hours following hatching by flash freezing in liquid nitrogen. The efl-1 mutants were hatched at 26°C to ensure that the gene was inactivated post early-embryogenesis.

extract_protocol:
Total RNA was extracted using TriPure (Roche) and further purified using an RNeasy column (Qiagen).
RNA-seq libraries were prepared from 100-1000 ng of total RNA using the Illumina TruSeq RNA kit according to the manufacturers’ instructions.

value: efl-1 (se1)

tag: developmental stage

value: starved L1

tag: growth temperature

tag: tissue

value: whole worm

tag: sample id


title: stressed for 14 days + Recreation for 7 days [31_ML53_14dSD-7dREC]

tag: strain


title: Home Caged [6_ML08_HC]

source_name: Home Caged

value: Control


title: efl1_rep1


title: stressed for 7 days [17_ML20_7dSD-10min]


title: Home Caged [2_ML03_HC]


title: met2_rep2

source_name: met-2 (n4256)_whole worm


title: Home Caged [1_ML02_HC]


title: stressed for 7 days [25_ML29_7dSD-10min]


title: BMDM_ko_LPS_c

city: Schlieren

first: Marc

last: Pfefferle

state: Schweiz

address: Wagistrasse 12

country: Switzerland

institute: University hospital Zürich (USZ)

description: Nrf2-/- Bone marrow derived macrophages treated LPS for 4 hours

hyb_protocol: After purification of amplified cRNA according to the QIAgen RNeasy purification protocol (QIAGEN) 825 ng of Cy3 and Cy5 labeled cRNA were competitively hybridized for 17 hours at 65° C in a hybridization oven (Agilent G2545A) set to 10 rpm in GEx Hybridization buffer HI-RPM according to the manufacturer's protocol (Agilent’s Two-Color Microarray-Based Gene Expression Analysis). Washing was performed according to the recommended protocol including the Stabilization and Drying Solution step.

scan_protocol: Array slides were XDR scanned at 5 mcm resolution on a Agilent Microarray High-Resolution C Scanner (G2505C) with 100% PMT and 10% for lower intensity.

data_processing:
Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software Version 10.5.1.1. Spot values were normalized using the default linear-lowess normalization. To identify differentially expressed features, calculated log10 ratio values (Cy5/Cy3) were imported into JMP Genomics 8.0 without further normalization and the built-in Basic Expression Workflow (ANOVA, LSMeans Differences) was performed.
We imported the calculated and lowess-normalized log10 ratios of the Feature Extraction result text files directly into JMP Genomis 8.0 and performed the statistical analysis without further normalization.
For the statistical analysis of our array experiments we imported the log10 ratios of the Feature Extraction result text files into JMP Genomis 8.0. As Feature Extraction Software does already a linear-lowess normalization, we didn't perform any further normalization. That means that our normalized data are already included in the Agilent Feature Extraction Files, which have been uploaded with this Metadata Worksheet. Any further data processing, i.e. filtering for x-fold over- or underexpression of significant features, we performed after the ANOVA analysis.

label: Cy3 (green signal)

source_name: BMDM

label_protocol: Fluorescently labeled cRNA was generated from 500 ng total RNA with the Quick Amp Labeling Kit (Agilent) according to Agilent’s Two-Color Microarray-Based Gene Expression Analysis Protocol Version 5.7, March 2008 (Agilent publication number G4140-90050). In short, total RNA was reverse transcripted to cDNA using T7 Promotor Primer and MMLV-RT. Then cDNA was converted to cRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP.

growth_protocol: Bone marrow cells were obtained from the femurs and tibias of 8- to 10-week-old mice. The bone marrow murine stem cells were expanded and differentiated in RPMI medium supplemented with 10% FCS in the presence of recombinant mouse M-CSF (PeproTech 315-02-100UG, lot 0914245) at 10 ng/ml for 7 days

extract_protocol: After washing and lysing the cells with Buffer RLT, total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Basel, Switzerland) according to the manufacturer’s instructions, including an on-column DNA digestion step (RNase-Free DNase Set; QIAGEN). To ensure that only high quality RNA (RIN >7.0) was used for gene expression analysis, each RNA sample was checked on a RNA Nanochip with a Bioanalyzer 2100 (Agilent Technologies, Basel, Switzerland). RNA was quantified spectrophotometrically with a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

treatment_protocol: Macrophages were exposed to heme-albumin complexes or albumin alone (200 mcM) for four hours before challenge with LPS (10 ng/ml)

tag: treatment

value: no treatment

tag: incubation time

label: Cy5 (red signal)

value: LPS (4h)


title: stressed for 14 days [12_ML15_14dSD-10min]


title: BMDM_ko_LPS_d


title: met2_rep1


title: Home Caged [5_ML07_HC]


title: stressed for 1 day [4_ML06_1dSD-10min]


title: BMDM_ko_LPS_b


title: dpl1_rep2

source_name: dpl-1 (n2994)_whole worm


title: BMDM_ko_LPS_a


title: dpl1_rep1


title: BMDM_wt_LPS_c

description: Nrf2+/+ Bone marrow derived macrophages treated LPS for 4 hours


title: lin37_rep2

source_name: lin-37 (n758)_whole worm


title: lin37_rep1


title: BMDM_wt_LPS_b


title: BMDM_ko_HemeAlb200LPS_e

description: Nrf2-/- Bone marrow derived macrophages pretreated with Albumin plus 200 mcM Heme for 4 hours and then with LPS for 4 hours

value: heme-albumin (4h, 200 mcM) + LPS (4h)


title: lin15BTHAPdel_rep2

source_name: lin-15B (we23)_whole worm


title: BMDM_wt_LPS_a


title: lin15B_rep1

source_name: lin-15B (n744)_whole worm


title: lin36THAPdel_rep3

source_name: lin-36 (we31)_whole worm


title: lin36THAPdel_rep2


title: lin36full_rep2

source_name: lin-36 (we36)_whole worm


title: lin36THAPdel_rep1


title: lin15BTHAPdel_rep3


title: lin36full_rep1


title: lin36PM_rep2

source_name: lin-36 (n766)_whole worm


title: BMDM_wt_HemeAlb200LPS_a

description: Nrf2+/+ Bone marrow derived macrophages pretreated with Albumin plus 200 mcM Heme for 4 hours and then with LPS for 4 hours


title: lin36PM_rep3


title: BMDM_ko_HemeAlb200LPS_c


title: lin15BTHAPdel_rep1


title: BMDM_Control_c

description: Nrf2+/+ Bone marrow derived macrophages treated with Albumin (without heme) for 4 hours

value: Albumin (4h)


title: BMDM_ko_HemeAlb200LPS_d


title: BMDM_Control_b


title: BMDM_ko_HemeAlb200LPS_b


title: BMDM_wt_HemeAlb200LPS_b


title: lin36PM_rep1


title: lin15B_rep2


title: BMDM_wt_HemeAlb200LPS_c


title: islet preparation 6 under control condition

city: Bruxelles

first: Anthony

last: Piron

address: Route de Lennik 808 CP618

department: Faculté de Medecine

institute: Université Libre de Bruxelles

data_processing:
The sequencing reads were mapped to the human genome using Tophat v2.0.11 (https://ccb.jhu.edu/software/tophat/index.shtml)
The transcript quantification was done using flux-capacitor v1.2.3  (http://flux.sammeth.net) which deconvolves the reads mapping into mutliple transcripts optimizing a linear equation system.
The paired palmitate vs control differential analysis was done using the Deseq2 bioconductor R package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: deseq2-palmitate.tsv is tab separated deseq2 output ; RPKM VALUES-CTL VS PAL.xlsx is an excel file containing the RPKM converted expression matrix and some statistics.

source_name: islets of Langerhans_control

growth_protocol: Human islet preparations were obtained from heart-beating organ donors with no medical history of diabetes or metabolic disorders. The islets were isolated using collagenase digestion and density gradient purification. They were cultured in M199 culture medium containing 5.5 mM glucose and shipped within 1-5 days following isolation. Upon arrival, the human islet cells were cultured in Ham's F-10 medium containing 6.1 mM glucose, 10% fetal bovine serum (FBS), 2 mM GlutaMAX, 50 μM 3-isobutyl-1-methylxanthine, 1% BSA, 50 U/ml penicillin and 50 μg/ml streptomycin.

extract_protocol:
Total RNA was isolated using the Rneasy Mini Kit (Qiagen, Venlo, The Netherlands), which favors purification of all RNA molecules longer than 200 nucleotides and sample preparation was done as described by the manufacturer (Illumina, Eindhoven, The Netherlands). Briefly, mRNA was purified from two μg total RNA using oligo (dT) beads, before it was fragmented and randomly primed for reverse transcription followed by second-strand synthesis to create ds cDNA fragments. The generated cDNA had undergone paired-end repair to convert overhangs into blunt ends. After 3’-monoadenylation and adaptor ligation, cDNAs were purified on a 2% agarose gel and 200 basepair (bp) products were excised from the gel.
Following gel digestion, purified cDNA was amplified by PCR using primers specific for the ligated adaptors. The generated libraries were submitted to quality control with the Agilent bioanalyzer 2100 (Agilent Technologies, Wokingham, UK) before sequencing. The RNA integrity number (RIN) values for all samples were 7.5 and above. 1 μL cDNA was loaded on an Agilent DNA chip (DNA-1000) to verify cDNA quality and quantity. Only libraries reaching satisfactory conditions were used for sequencing, on one sequencing lane of an Illumina Genome Analyzer II system (GAII, Illumina).

treatment_protocol: The islets were exposed or not to 0.5 mM palmitate in the same medium without FBS for 2 days (8; 13; 31). The serum-free culture conditions have previously been validated (32). Human islet viability, assessed after Hoechst 33342 and propidium iodide staining (see below), was similar in serum-free or 10% FBS-containing medium (respectively 93±1% vs 95±1% viable cells after 72 h, n=8, p=0.3).

value: islets of Langerhans

value: control


title: islet preparation 4 under control condition [re-analysis]

description:
ID4_ctl
re-analysis of GSM1303932
This is duplicated sample record of GSM1303932 for the convenient retrieval of the complete raw data from SRA


title: islet preparation 5 under palmitate exposure [re-analysis]

description:
ID5_pal
re-analysis of GSM1303935
This is duplicated sample record of GSM1303935 for the convenient retrieval of the complete raw data from SRA

source_name: islets of Langerhans_palmitate exposure

value: palmitate exposure


title: islet preparation 6 under palmitate exposure


title: islet preparation 4 under palmitate exposure [re-analysis]

description:
ID4_pal
re-analysis of GSM1303933
This is duplicated sample record of GSM1303933 for the convenient retrieval of the complete raw data from SRA


title: islet preparation 5 under control condition [re-analysis]

description:
ID5_ctl
re-analysis of GSM1303934
This is duplicated sample record of GSM1303934 for the convenient retrieval of the complete raw data from SRA


title: BMDM_ko_HemeAlb200LPS_a


title: BMDM_Control_a


title: lin36full_rep3


title: lin35_rep4

source_name: lin-35 (n745)_whole worm


title: lin35_rep3


title: islet preparation 3 under palmitate exposure [re-analysis]

description:
ID3_pal
re-analysis of GSM1303931
This is duplicated sample record of GSM1303931 for the convenient retrieval of the complete raw data from SRA


title: islet preparation 2 under palmitate exposure [re-analysis]

description:
ID2_pal
re-analysis of GSM1303929
This is duplicated sample record of GSM1303929 for the convenient retrieval of the complete raw data from SRA


title: islet preparation 3 under control condition [re-analysis]

description:
ID3_ctl
re-analysis of GSM1303930
This is duplicated sample record of GSM1303930 for the convenient retrieval of the complete raw data from SRA


title: lin35_rep1


title: lin35_rep2


title: islet preparation 2 under control condition [re-analysis]

description:
ID2_ctl
re-analysis of GSM1303928
This is duplicated sample record of GSM1303928 for the convenient retrieval of the complete raw data from SRA


title: N2_26C_rep2

source_name: N2 (Bristol)_whole worm

value: N2 (Bristol)


title: islet preparation 1 under control condition [re-analysis]

description:
ID1_ctl
re-analysis of GSM1303926
This is duplicated sample record of GSM1303926 for the convenient retrieval of the complete raw data from SRA


title: N2_rep3


title: N2_rep1


title: EFL1.lin35.rep2

data_processing:
ChIP-seq reads were aligned to a concatenated ce11+cb3 assembly of the C. elegans and C. briggsae genomes using BWA v. 0.7.7 with default settings (BWA-backtrack algorithm) (Li and Durbin, 2010).
The SAMtools v. 0.1.19 ‘view’ utility (Li et al., 2009) was used to convert the alignments to BAM format. Normalized mapq10 ChIP-seq coverage tracks were generated using the BEADS algorithm (Cheung et al., 2011).
Genome_build: ce11 + cb3 (concatenated)
Supplementary_files_format_and_content: BEADS-normalized genome-wide linear read coverage (from reads with MAPQ value >= 10)

source_name: EFL1.lin35.whole worm

growth_protocol: Starved L1 animals were collected by bleaching synchronized adults grown in liquid culture using standard S-basal medium with HB101 E. coli at 20°C. Following bleaching, eggs were hatched at 25°C in M9 and starved L1s were sucrose floated and collected 20-22 hours following hatching by flash freezing in liquid nitrogen.

extract_protocol:
Frozen starved L1 worms were ground to a powder, which was incubated in 1.5 mM EGS (Pierce 21565) in PBS for 8 minutes, followed by the addition of formaldehyde to a final concentration of 1%, and incubated for a further 8 minutes. The fixation was quenched for 5 minutes by the addition of 0.125 M glycine. Fixed tissue was washed 2X with PBS with protease inhibitors (Roche EDTA-free protease inhibitor cocktail tablets 05056489001) and once in FA buffer (50 mM Hepes pH7.5, 1 mM EDTA, 1% TritonX-100, 0.1% sodium deoxycholate, and 150 mM NaCl) with protease inhibitors (FA+), then resuspended in 1 ml FA+ buffer per 1 ml of ground worm powder. The extract was sonicated to an average size of ~250 base pairs using a Bioruptor Pico (Diagenode), and 10-20 ug of DNA was used per ChIP reaction.
ChIP DNA is blunt ended, A-tailed, ligated to adaptors, amplified by PCR, then size selected using AMPure beads. Illumina TruSeq adaptors and barcodes were used.


title: EFL1.lin35.rep1


title: EFL1.lin15B.rep2

source_name: EFL1.lin15B.whole worm


title: EFL1.lin15B.rep1


title: EFL1.lin36.rep1

source_name: EFL1.lin36.whole worm


title: N2_26C_rep1


title: N2_rep2


title: EFL1.N2.rep1

source_name: EFL1.N2.whole worm


title: LIN36.lin15B.rep2

source_name: LIN36.lin15B.whole worm


title: LIN36.lin35.rep1

source_name: LIN36.lin35.whole worm


title: LIN36.lin15B.rep1


title: LIN36.lin35.rep2


title: EFL1.lin36.rep2


title: EFL1.lin36::eGFP.rep2

source_name: EFL1.lin36::eGFP.whole worm

value: lin-36::eGFP (we30)


title: LIN36.lin36::eGFP.rep1

source_name: LIN36.lin36::eGFP.whole worm


title: LIN15B.lin15BTHAPdel.rep1

source_name: LIN15B.lin15BTHAPdel.whole worm


title: LIN15B.lin35.rep2

source_name: LIN15B.lin35.whole worm


title: BC3 H3K4me3

value: H3K4me3 (Millipore #04-745)


title: LIN15B.lin15BTHAPdel.rep2


title: LIN36.lin36::eGFP.rep2


title: BC3 CTCF

value: CTCF (Cell Signaling #3418)


title: LIN15B.lin36.rep2

source_name: LIN15B.lin36.whole worm


title: islet preparation 1 under palmitate exposure [re-analysis]

description:
ID1_pal
re-analysis of GSM1303927
This is duplicated sample record of GSM1303927 for the convenient retrieval of the complete raw data from SRA


title: LIN15B.lin35.rep1


title: EFL1.N2.rep2


title: EFL1.lin36::eGFP.rep1


title: BC3 Input for CTCF, H3K4me3


title: VIRF3_3: vIRF3 Rep. 3

tag: cell type

value: vIRF3 (Novus #NB200-167SS)


title: LIN15B.lin36::eGFP.rep2

source_name: LIN15B.lin36::eGFP.whole worm


title: WSNdelNS1-3

city: Hong Kong

first: Honglin

address: Rm 5-19, 5/F, Lab block, 21 Sassoon Road, Pokfulam

department: Department of Microbiology

country: Hong Kong

institute: The University of Hong Kong

description: Infected with mutant WSNdelNS1

data_processing:
Using software from Illumina (bcl2fastq), sequencing reads were assigned into individual samples with adapter trimming and demultiplexing.
Fastq reads were subsequently aligned to the human genome (hg38, GENCODE V29 ). STAR (V2.7.2a) was used to align RNA-Seq samples and counts were generated with its in-built htseq-count algorithm. Genes with counts below 10 across all RNA-Seq samples were excluded for differential expression analysis. DESeq2 was used to assess for differential expression and generation of normalized expression values.
Genome_build: hg38
Supplementary_files_format_and_content: Raw and normalized counts are in csv file format with genes across rows and samples across columns.

source_name: 293T Cells

growth_protocol: 293T cells were infected with influenza A/WSN/33 (H1N1) wildtype strain (WSNWT) or a NS1-defective mutant virus; WSNdelNS1 at an designated MOI for 6 hours.

extract_protocol:
Total RNA was extracted using NucleoSpin® RNA Plus kit (Macherey-nagel) according to the manufacture’s instruction, including an on-column genomic DNA digestion step.  Quality and quantity of RNA was checked with Qubit and Bioanalyzer.
Ribosomal RNA (rRNA) depletion was performed using Ribo-Zero Manetic Gold Kit. cDNA libraries were prepared by NEBNext® Ultra II Directional RNA Library Prep Kit.  The purified rRNA-depleted RNA was fragmented to 200 – 500 bp. The fragmented rRNA-depleted RNA was then applied as template to synthesize the first-strand cDNA by using random hexamer-primer and reverse transcriptase. In the second strand cDNA synthesis, the mRNA template was removed, and a replacement strand was generated to form the blunt-end double-stranded (ds) cDNA. The ds cDNA underwent, 3’ adenylation and indexed adaptor ligation, followed by treatment with User Enzyme. The adaptor-ligated libraries were enriched and indexed by polymerase chain reaction (PCR). Illumina HiSeq 4000 was used for Pair-End 101bp sequencing.

tag: replicate

tag: viral strain

tag: moi

value: 6 hours


title: WSNdelNS1-2

description: Infected with mutant WSNdelNS1


title: LIN15B.N2.rep1

source_name: LIN15B.N2.whole worm


title: LIN35.lin15B.rep2

source_name: LIN35.lin15B.whole worm


title: LIN15B.N2.rep2


title: LIN15B.lin36::eGFP.rep1


title: WSNdelNS1-1

description: Infected with mutant WSNdelNS1


title: VIRF3_1: vIRF3 Rep. 1


title: INPUT_1: Input Rep. 1


title: WSNWT-3

description: Infected with wildtype (H1N1)

value: Wildtype (H1N1)


title: LIN35.lin36.rep1

source_name: LIN35.lin36.whole worm

value: starved L1


title: LIN35.lin36.rep2

value: whole worm


title: LIN35.lin15B.rep1


title: LIN35.lin36::eGFP.rep2

source_name: LIN35.lin36::eGFP.whole worm


title: LIN35.lin36::eGFP.rep1


title: colon_Snap25_cre-pos_ip_GF_2

city: New York

first: Paul

middle: Andrew

last: Muller

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Library strategy: Ribo-Seq
Kallisto alignment
Genome_build: Ensembl Mus musculus release 91: GRCm38.p5 (GCA_000001635.7)

source_name: Immunoprecipitated ribosome-bound mRNA from colon myenteric plexus of germ free Snap25:RiboTag Cre-positive mice

extract_protocol: Duodenum, ileum, and colon myenteric plexus was dissected into PBS with cycloheximide (0.2 mg/mL) (PBS/CHX). The RiboTag immunoprecipitation protocol (http://depts.washington.edu/mcklab/RiboTagIPprotocol2014.pdf)  was then followed with the following modifications: All samples were homogenized by hand with a dounce homogenizer in 2.5 mL supplemented homogenization buffer (changes per 2.5 mL: 50 µl Protease Inhibitor, 75 µl heparin (100 mg/mL stock), 25 µl SUPERase In RNase Inhibitor). Samples were then centrifuged for 10 minutes at 10,000 G, after which 800 µl of supernatant was removed and 5µL of anti-HA antibody (Abcam, ab9110) was added. For input samples, 40uL of supernatant was removed and 60uL of PicoPure lysis buffer was added. These input samples were then put at -80°C. Immunoprecipitated samples were kept rotating at 4°C with antibody for 1 hour. 200 µl of Thermo Protein magnetic A/G beads were washed with homogenization buffer, added to the sample, and kept rotating for 30 minutes at 4°C. The beads were washed four times with high-salt buffer and samples were eluted with 100 µl of PicoPure lysis buffer.  RNA was extracted using the Arcturus PicoPure RNA isolation kit (Applied Biosystems) according to the manufacturer’s instructions.

value: Colon myenteric plexus


title: WSNWT-2

description: Infected with wildtype (H1N1)


title: WSNWT-1

description: Infected with wildtype (H1N1)


title: Mock-3

description: Uninfected

value: Uninfected


title: LIN35.N2.rep2

source_name: LIN35.N2.whole worm


title: H3K9me2.lin15B.rep2

source_name: H3K9me2.lin15B.whole worm


title: colon_Snap25_cre-pos_ip_GF_1


title: H3K9me2.lin36.rep1

source_name: H3K9me2.lin36.whole worm


title: LIN15B.lin36.rep1


title: H3K9me2.lin36.rep2


title: LIN35.N2.rep1


title: colon_Snap25_cre-neg_ip_GF_2

source_name: Immunoprecipitated ribosome-bound mRNA from colon myenteric plexus of germ free Snap25:RiboTag Cre-negative mice


title: colon_Snap25_cre-neg_ip_GF_1


title: H3K9me2.lin35.rep2

source_name: H3K9me2.lin35.whole worm


title: Mock-1

description: Uninfected


title: Mock-2

description: Uninfected


title: H3K9me2.lin35.rep1


title: colon_Snap25_cre-pos_ip_SPF_3

source_name: Immunoprecipitated ribosome-bound mRNA from colon myenteric plexus of specific pathogen free Snap25:RiboTag Cre-positive mice


title: H3K9me2.N2.rep2

source_name: H3K9me2.N2.whole worm


title: colon_Snap25_cre-pos_ip_SPF_2


title: H3K9me2.N2.rep1


title: HTZ1.lin15B.rep1

source_name: HTZ1.lin15B.whole worm


title: HTZ1.lin15B.rep2


title: VIRF3_2: vIRF3 Rep. 2


title: PCOS-day12-rep3

city: Portland

first: Brett

last: Davis

state: Oregon

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

description:
Day 12-3006-PCOS
Pair-match 3-PCOS

data_processing:
Sequencing reads were trimmed for adapter sequence with Trimmomatic v0.39, and to a max length of 50bp
Trimmed reads were aligned to the human hg19 (GRCh37) reference genome with bowtie2 v2.3.5, specifying the -x 2000 parameter
Alignments were filtered to remove reads mapping to mitochondrial chromosome, reads with mapq score < 30, improperly paired reads as specified by samtools 0x02 flag, and duplicate reads determined by Picard Tools
Peaks were called on each sample with MACS2 v2.1.2 with a significance threshold of p-value < 0.05. Peaks on canonical chromosomes were retained.
Differential analysis of peak regions was performed using DiffBind v2.12.0
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files output from MACS2, contain peak regions surpassing p-value < 0.05 threshold in each sample
Supplementary_files_format_and_content: diffPeak.bed files contain the genomic coordinates of the significant differential peaks (FDR < 0.05) for each comparison

source_name: subcutaneous adipose tissue

growth_protocol: Adipose stem cells were plated in 10 cm dish containing DMEM/10% FCS, 0.05 U/ml penicillin, 0.05 mg/ml streptomycin, 1.25 mg/ml fungizone and cultured at 37°C until confluency and expanded for 2 additional generations. Subsequently, generation 4 ASCs were cultured in adipocyte differentiation medium consisting of DMEM/Ham's F-12 (1:1, v/v), HEPES, pH 7.4, fetal bovine serum, biotin, pantothenate, human insulin, dexamethasone, 3-isobutyl-1-methylxanthine (IBMX), PPARg agonist, penicillin, streptomycin, and amphotericin B (Zen-bio) at 37°C for 3-12 days to allow for differentiation into mature adipocytes.

extract_protocol:
At days 0, 3, and 12, cells were trypsinized and 100,000 cells were subject to nuclei preparation for ATAC-Seq.
ATAC-seq libraries were generated according to Berostro et al. (doi: 10.1002/0471142727.mb2129s109) with minor modifications. Nuclei were treated with Tn5 transposon TDE1 (Nextera DNA Library Prep kit, Illumina, San Diego, CA) for 35 min at 37°C. The transposition reaction was then purified using Zymo DCC-5 columns (Zymo Research, Irvine, CA). Following, Polymerase Chain Reaction (PCR) was performed using 25 μl NEBNext High-Fidelity 2x PCR Master Mix (NEB, MA, Boston) 4 µl of each Index 1 (i7) and index 2 (i5) (Nextera XT Index kit, Illumina, San Diego, CA), 2 µl of PPC (Illumina, San Diego, CA) and 15 µl of purified tagmentation reaction. After performing the initial extension and 5 PCR cycles, quantitative PCR was performed on 5 µl of the previous PCR reaction by adding 1 µl of SYBR Green (15x), 1 µl of PPC, 5 μl NEBNext High-Fidelity 2x PCR Master Mix and 3 µl of H2O in a final volume of 15 µl for 20 cycles. The number of additional cycles was determined as the cycle number corresponding to ¼ of maximum fluorescent intensity. Final libraries were purified using 45 µl (1:1 ratio) of SPRI beads (Beckman and Coulter, Indianapolis, Indiana) cat# B23318). Final libraries were visualized on a TapeStation 2200 using a D1000 ScreenTape. Libraries were pooled and paired-end sequenced (PE 2X100) on the Illumina HiSeq4000.

tag: female type

value: Polycystic Ovary Syndrome (PCOS)

value: subcutaneous adipose


title: PCOS-day12-rep2

description:
Day 12-3019-PCOS
Pair-match 2-PCOS


title: colon_Snap25_cre-pos_ip_SPF_1


title: HTZ1.lin36.rep2

source_name: HTZ1.lin36.whole worm


title: colon_Snap25_cre-neg_ip_SPF_2

source_name: Immunoprecipitated ribosome-bound mRNA from colon myenteric plexus of specific pathogen free Snap25:RiboTag Cre-negative mice


title: HTZ1.lin36.rep1