title: Macrophages, without stimulation + S. sendtneri, donor 858-3


title: Macrophages, without stimulation + EtOH 70%, donor 858-2

status: Public on Oct 20 2020

type: RNA

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: Gene expression data from human unstimulated macrophages cultured for 6 days with 70% EtOH

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of human Hugene-2_0-type from Affymetrix. A Custom CDF Version 19 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Buffy coat, donor 858-2

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

growth_protocol: Macrophages were cultured in Macrophage Serum Free Medium at a concentration of 1x10^6 cells/ml, supplemented with 5ng/ml M-CSF, 10^-8M Dexamethasone for 6 days

extract_protocol: RNA was extracted using E.Z.N.A. total RNA Kit I according to manufacturer´s instructions.

treatment_protocol: Macrophages were stimulated at day 0 either with  IFNgamma (100ng/ml) or left untreated as control and cultured with extracts of either S. roemeri (1:500) or S. sendtneri (1:500) or with 70% EtOH (1:500) as control.

tag: tissue

value: PBMC derived monocytes

tag: sample

tag: stimulation

value: Ns

tag: plant extract

value: Ctrl


title: Macrophages, without stimulation + S. roemeri, donor 858-5

description: Gene expression data from human unstimulated macrophages cultured for 6 days with S. roemeri

source_name: Buffy coat, donor 858-5

value: Sr


title: Macrophages, without stimulation + S. roemeri, donor 858-4

source_name: Buffy coat, donor 858-4


title: Macrophages, IFNgamma stimulation + S. sendtneri, donor 858-2

description: Gene expression data from human macrophages stimulated with IFNgamma cultured for 6 days with S. sendtneri

value: IFN

value: Ss


title: Macrophages, without stimulation + EtOH 70%, donor 858-3

source_name: Buffy coat, donor 858-3


title: Macrophages, IFNgamma stimulation + S. sendtneri, donor 858-4


title: Macrophages, without stimulation + S. roemeri, donor 858-2


title: Macrophages, IFNgamma stimulation + S. roemeri, donor 858-3

description: Gene expression data from human macrophages stimulated with IFNgamma cultured for 6 days with S. roemeri


title: Macrophages, IFNgamma stimulation + S. sendtneri, donor 858-3


title: n-3_PUFA_sufficient_MG_1

city: Bordeaux

first: Charlotte

last: Madore

address: 146 rue Leo Saignat

department: Alimentation Humaine

country: France

institute: INRAE

hyb_protocol: not provided

scan_protocol: not provided

data_processing: The raw data were normalized using 6 housekeeping genes.

label: not provided

organism: Mus musculus

source_name: FACS sorted MG cells

label_protocol: not provided

extract_protocol: not provided

tag: maternal state

value: n-3 PUFAs dietary sufficiency

tag: cell type

value: Microglia

tag: developmental stage


title: n-3_PUFA_sufficient_MG_2


title: n-3_PUFA_sufficient_MG_3


title: testis-sheep

type: SRA

city: Nanjing

first: Hua

last: Yang

state: 请选择

address: Weigang No.1

country: China

institute: Nnanjing Agricultural University

library_source: transcriptomic

data_processing:
Testicular cells and Gel Bead were wrapped by "oil droplets" to form GEM (Gel Bead in Emulsion)
Testicular cells were dissolved, and the full-length cDNA sequences were synthesized. After the oil droplets were broken and purified, the cDNA library was amplified using PCR methods. The qualified cDNA libraries were sequenced using the Illumina HiSeq X Ten platform
CellRanger software was used for gene expression quantification and cell type identification based on the cell barcode and UMI information of reads1 in each single cell.
The corresponding read2 was mapped to the reference genome by STAR software to determine the source genes of reads that completed the gene expression quantification.
The DEG analysis was performed by Seurat software, and the functional enrichment of marker genes was investigated by GO and KEGG analysis.
Genome_build: Ovis aries, Oar_rambouillet_v1.0, the file testis_genes.fa includes transcript
Supplementary_files_format_and_content: tab-delimited text files include FPKM values, gene type,chromosome, and strand information for each Sample.

organism: Ovis aries

source_name: testis

extract_protocol:
The sheep testis tissue was obtained and digested by two-step enzyme digestion, then the single cell suspension was used for sequencing.
Single testicular cell RNA-seq was performed with a 10X Genomics system using the Illumina HiSeq X Ten platform

tag: strain

value: Hu

value: testis

value: Sexual maturity

tag: age

value: 1.5 years


title: Macrophages, IFNgamma stimulation + S. sendtneri, donor 858-5


title: A549 - Pol II CTD4HD - Fixed(1)

city: Hong Kong

first: Michi

last: Miura

address: 21 Sassoon Road

country: Hong Kong

institute: The University of Hong Kong

library_source: genomic

data_processing:
Library strategy: CUT&RUN
Basecalling was performed using bcl2fastq2 Conversion Software v2.20 with the default parameters.
The initial 50 bases of each read were aligned to a concatenation of human reference genome (GRCh38) and S. cerevisiae (sacCer3) using BWA (version 0.7.17).
A subset of aligned reads was selected using Samtools (version 1.9) with the following commands: SAM flag 3 (read paired; read mapped in proper pair) (samtools view -f 3); mapping quality greater than 20 (samtools view -q 2 0); without tags ‘XA:Z:’ and ‘SA:Z:’ (grep -v -e ‘XA:Z:’ -e ‘SA:Z:’); and aligned in either one of the chromosomes chr1 to chr22, chrX or chrY (samtools view chr1 chr2 … chrY).
Coverage was computed using deepTools (version 3.1.3 or 3.3.2) including the following settings: --binsize 10 --extendReads.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files (read coverage)

molecule: genomic DNA

growth_protocol: A549 was grown in Dulbecco’s Modified Eagle Medium (Gibco, 11965-092) supplemented with 10% FBS (Gibco, 16140-071), 100 U/ml penicillin and 100 μg/ml streptomycin (Gibco, 15140-122).

extract_protocol:
Released DNA fragments by CUT&RUN were collected and purified with DNeasy Blood & Tissue Kit (Qiagen, 69504) or QIAquick PCR Purification Kit (Qiagen, 28104).
Libraries were constructed using NEBNext Ultra II DNA Library Prep Kit (NEB, E7645).

tag: cell line

value: Lung carcinoma cell line

tag: antibody

value: Pol II CTD4HD (Millipore, 05-623)

tag: treatment

value: Fixed (1)


title: A549 - H3 - Unfixed

value: Histone H3 (Abcam, ab1791)

value: Unfixed


title: A549 - Pol II S2p - Fixed(2)

value: Pol II S2p (Abcam, ab5095)

value: Fixed (2)


title: A549 - Pol II S5p - Fixed(2)

value: Pol II S5p (Abcam, ab5131)


title: A549 - Pol II S2p - Unfixed - rep2


title: A549 - Pol II S5p - Fixed(1)


title: A549 - Pol II CTD4HD - Fixed(2)


title: A549 - Pol II CTD4HD - Unfixed - rep2


title: A549 - Pol II S2p - Fixed(1)


title: n-3_PUFA_deficient_MG_2

value: n-3 PUFAs dietary deficiency


title: n-3_PUFA_deficient_MG_1


title: n-3_PUFA_deficient_MG_4


title: n-3_PUFA_deficient_MG_6


title: n-3_PUFA_deficient_MG_3


title: n-3_PUFA_deficient_MG_5


title: A549 - Pol II S5p - Unfixed - rep2


title: Macrophages, IFNgamma stimulation + S. roemeri, donor 858-4

value: PBMC derived monocytes

value: IFN

value: Sr


title: Macrophages, IFNgamma stimulation + EtOH 70%, donor 858-5

description: Gene expression data from human macrophages stimulated with IFNgamma cultured for 6 days with 70% EtOH

value: Ctrl


title: A549 - Pol II S5p - Unfixed - rep1


title: A549 - Pol II S2p - Unfixed - rep1


title: H3K4me3_M2

city: Paris

first: Violaine

last: Saint-Andre

address: 26 rue d'Ulm

institute: Institut Curie

data_processing:
Reads were mapped with Bowtie2 version 2.1.0, with a tolerance of 1 mismatch in seed alignment
Only unique mapped reads were kept
BigWig files were generated from bam files using genomeCoverageBed followed by bedGraphToBigWig
Genome_build: hg19
Supplementary_files_format_and_content: BigWig

source_name: HEK-based cell line

growth_protocol: For each cell-line, cells were grown up to 90% confluence in 600 cm² square dishes in MEM-alpha medium supplemented with non-essential amino-acids and sodium pyruvate, at 37°C, 5% CO2.

extract_protocol:
First, cells were fixed for 5 min at 37°C by adding room temperature Crosslinking Buffer to culture medium (to final concentrations of 50 mM TrisHCl pH 8, 100 mM NaCl, 1 mM EDTA, 1% formaldehyde). Fixation was topped by adding Glycine to a final concentration of 250 mM and incubates 5 min at room temperature. After two washes of ice-cold PBS, cells were scraped twice in 30 ml and 15 ml PBS. Cells were pelleted for 10 min at 4000 rpm 4°C, washed in ice-cold PBS and resuspended in 10 ml Cell Lysis Buffer (10 mM TrisHCl pH 8, 25 mM KCl, 0.5% NP-40) supplemented with AEBSF. After incubating 10 min on ice, lysate was passed 10 times through a 20G needle and incubated again for 10 min on ice. Nuclei were pelleted for 15 min at 3500 rpm 4°C and resuspended in 3.4 ml Sonication Buffer (50 mM TrisHCl pH 8, 10 mM EDTA, 0.1% SDS) supplemented with AEBSF. Nuclei were then divided in 2 tubes and sonicated for 20 min at 4°C on the Diagenode Bioruptor Pico according to manufacturer’s instructions. Finally, poorly sonicated chromatin was pelleted for 10 min at 16 000g and supernatant was recovered and added to blocked Protein A Dynabeads IP beads for pre-clearing of chromatin. After incubating for 3 hours at 4°C on a rotating wheel, 200 µl were taken as Input. The rest of the chromatin was incubated overnight at 4°C on a rotating wheel with IP antibodies: H3(pan) (Abcam ab1791), H3K36me3 (Abcam ab9050-100), H3K4me3 (Diagenode pAb-003-050), H3K27me3 (Active Motif 39155) or H3K27ac (Abcam ab4729). The next day, 50µl blocked IP beads were added to the chromatin and incubated 4 hours at 4°C on a rotating wheel. They were then washed twice in FA150 buffer (50 mM HEPES pH 7.4, 1 mM EDTA, 1% Triton X-100, 150 mM NaCl, 0.1% NA-Deoxycholate, 0.1% SDS), twice in FA500 (50 mM HEPES pH 7.4, 1 mM EDTA, 1% Triton X-100, 500 mM NaCl, 0.1% Na-Deoxycholate, 0.1% SDS) and once in TE (10 mM TrisHCl pH 8, 1 mM EDTA). To elute chromatin, beads were resuspended in 100 µl ChIP Elution Buffer (50 mM TrisHCl pH 7.4, 10 mM EDTAs 1% SDS) and incubated for 1 hour at 65°C with 650 rpm shaking. Supernatant was then recovered, NaCl was added to a final concentration of 200 mM and incubated overnight in a 65°C waterbath to remove crosslinks. The next day, samples were treated with RNase for one hour at 37°C and with proteinase K for one hour at 45°C. DNA was then purified using Qiagen PCR Purification columns and quantified using Qubit dsDNA HS kit.
ChIP-seq libraries were prepared with TruSeq ChIP Sample Prep Kit (IP-202-1012, Illumina)

value: Mes

tag: chip antibody

value: H3K4me3 (Diagenode pAb-003-050)

tag: fraction

value: IP DNA


title: A549 - Pol II CTD4HD - Unfixed - rep1


title: H3K4me3_M1


title: H3K4me3_E2

value: Epi


title: Macrophages, IFNgamma stimulation + EtOH 70%, donor 858-4


title: Macrophages, IFNgamma stimulation + S. roemeri, donor 858-2


title: H3K4me3_E1


title: H3K27ac_M2

value: H3K27ac (Abcam ab4729)


title: Macrophages, IFNgamma stimulation + S. roemeri, donor 858-5


title: Macrophages, IFNgamma stimulation + EtOH 70%, donor 858-2


title: H3_M2

value: H3(pan) (Abcam ab1791)


title: H3_M1


title: H3_E2


title: H3K36me3_E1


title: H3K27ac_E1


title: H3K27me3_M1

value: H3K27me3 (Active Motif 39155)


title: H3K27me3_M2


title: H3K27me3_E2


title: H3K27ac_E2


title: H3_E1


title: Macrophages, IFNgamma stimulation + EtOH 70%, donor 858-3


title: H3K36me3_M2


title: H3K36me3_E2


title: H3K27ac_M1


title: Input_M2

value: Input DNA


title: H3K36me3_M1


title: Input_E2


title: Input_M1


title: H3K27me3_E1


title: Dex 2

city: Valencia

first: Vicente

last: Balanzà

state: Valencia

address: Campus de la Univ. Politécnica de Valencia. CPI Edif. 8E. Av de los Naranjos s/n

country: Spain

institute: Instututo de Biologia Molecular y Celular de Plantas (CSIC-UPV)

data_processing:
Paired-end sequencing (2 × 300 bp) was performed on a MiSeq (Illumina).
Reads were aligned to the reference genome of Arabidopsis thaliana available at the TAIR database (Lamesch et al., 2012) using TopHat (Trapnell et al., 2009) and Bowtie (Langmead et al., 2009) software.
The abundance estimation of the transcripts was performed using the RSEM package (Li and Dewey, 2011) and the differentially expressed transcripts (FPKM value) were estimated using Cufflinks (Trapnell et al., 2010)
Genome_build: Arabidopsis Thaliana
Supplementary_files_format_and_content: tab-delimited text file include counts values for each sample

organism: Arabidopsis thaliana

source_name: shoot apical meristem

growth_protocol: Plants were grown at 21°C under long day conditions (16 h light, 8h night), in a 2:1:1 by vol. mixture of peat:perlite:vermiculite.

extract_protocol:
RNA for RNA-seq was obtained with NucleoSpin® RNA Plant kit (MACHEREY-NAGEL)
The cDNA libraries were built using the TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina)

treatment_protocol: Two weeks after bolting, SAM of Arabidopsis plants were treated with dexamethasone, that allows the AP2m3 expression, or mock. 6-8 hours after treatment SAM were collected removing all visible flower primordia.

value: Inflorescence meristem

tag: developmetal stage

value: two weeks after bolting

value: dexamethasone


title: mock 3

value: mock


title: mock 2


title: Dex 1


title: Input_E1


title: SD96hr1_S22: w303 Spores incubated for 96 hours in SC with 0.002% glucose, replicate no.1

city: Delft

first: Theo

last: Maire

address: Van der Maasweg 9

department: Bionanoscience

country: Netherlands

institute: Delft University of Technology

data_processing:
We analyzed the resulting RNA-Seq data (.fastq files) as previously described (Trapnell et al., Nat Protoc 2012).
We removed the adapter contamination, polyA read through, and low quality tails for each sample by using BBDuk (JGI, version 36.85) with following settings: k=13, ktrim=r, forcetrimleft=11, useshortkmers=t, mink=5, qtrim=t, trimq=10, minlength=20.
We performed read aligment using TopHat (version 2.1.1) with Bowtie (version 2.2.9.0).
We performed read assembly and analysis of differential gene expression data using Cufflinks (version 2.2.1).
We optionally used R package called CummeRbund (version 2.7.2) from Bioconductor (version 3.11) to analyze and visualize RNA-seq data. We used the transcriptional modules listed in “transcriptional_modules_list.txt” for grouping the relevant genes into transcriptional modules.
Genome_build: Saccharomyces cerevisiae, Ensembl R64-1-1
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values per condition per gene.

organism: Saccharomyces cerevisiae W303

source_name: w303 Spores

growth_protocol: We collected un-germinated spores by first collecting 1 ml samples of spores that were incubated in a 0.002%-glucose at 0, 16, 48, and 96 hours after the incubation began.

extract_protocol:
We then extracted the RNA from the leftover, un-germinated spores RiboPure Yeast Kit (Ambion, Life Technologies) as described by its protocol. Next, we prepared the cDNA library with the 3' mRNA-Seq library preparation kit (Quant-Seq, Lexogen) as described by its protocol.
Next, we prepared the cDNA library with the 3' mRNA-Seq library preparation kit (Quant-Seq, Lexogen) as described by its protocol. Afterwards, we loaded the cDNA library on an Illumina MiSeq with the MiSeq Reagent Kit c2 (Illumina) as described by its protocol.

treatment_protocol: To isolate the un-germinated spores, we treated the 1-mL samples with zymolyase (786-036, G-Biosciences). Zymolyase lysed vegetative cells that formed from germinated spores, thus ensuring that we only collected RNA from un-germinated spores for sequencing.

tag: genotype

value: spores


title: SD48hr2_S17: w303 Spores incubated for 48 hours in SC with 0.002% glucose, replicate no.2


title: SD48hr3_S18: w303 Spores incubated for 48 hour in SC with 0.002% glucose, replicate no.3


title: SD48hr1_S16: w303 Spores incubated for 48 hours in SC with 0.002% glucose, replicate no.1


title: SD16hr3_S12: w303 Spores incubated for 16 hours in SC with 0.002% glucose, replicate no.3


title: Dex 3


title: SD96hr2_S23: w303 Spores incubated for 96 hours in SC with 0.002% glucose, replicate no.2


title: SD96hr3_S24: w303 Spores incubated for 96 hour in SC with 0.002% glucose, replicate no.3


title: SD16hr2_S11: w303 Spores incubated for 16 hours in SC with 0.002% glucose, replicate no.2


title: Liver tissue, 'Fed-Fed-Fast' intervention, replicate 7

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

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

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

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.52.1).

source_name: Liver tissue, obtained from a mouse that was subjected to a 'Fed-Fed-Fast' intervention

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

growth_protocol: Animal studies were performed using 3 to 4-month-old pure-bred male mice on a C57Bl/6 background. The study was approved by the Local Animal Ethics Committee of Wageningen University.

extract_protocol: RNA was isolated using Qiagen RNeasy Mini Kit (Qiagen), quantified using NanoDrop, and quality was checked with the Agilent 2100 bioanalyzer (Agilent Technologies). Samples were only included for further analyses in case of intact bands corresponding to 18S and 28S ribosomal subunits and absence of chromosomal peaks or RNA degradation products.

treatment_protocol: Mice were exposed to two 16h fasts over a 8 week period, each time being allowed to return to their normal growth trajectory, while another group of 24 mice was fed ad libitum throughout. Of each group, half of the mice were euthanized after a 16h fast, whereas the other half was euthanized in the ab libitum fed state. Livers were collected after sacrifice

tag: gender

value: male

tag: sequence of applied metabolic states

tag: metabolic state at moment of sampling

value: Fast

tag: time of tissue sampling

value: Morning

value: liver


title: n-3_PUFA_sufficient_MG_4

value: n-3 PUFAs dietary sufficiency

value: Microglia


title: SD16hr1_S10: w303 Spores incubated for 16 hours in SC with 0.002% glucose, replicate no.1

tag: tissue


title: Liver tissue, 'Fast-Fast-Fast' intervention, replicate 5

source_name: Liver tissue, obtained from a mouse that was subjected to a 'Fast-Fast-Fast' intervention


title: Liver tissue, 'Fed-Fed-Fast' intervention, replicate 6


title: Liver tissue, 'Fast-Fast-Fed' intervention, replicate 8

source_name: Liver tissue, obtained from a mouse that was subjected to a 'Fast-Fast-Fed' intervention

value: Fed


title: Liver tissue, 'Fast-Fast-Fed' intervention, replicate 5


title: Liver tissue, 'Fast-Fast-Fast' intervention, replicate 7


title: Liver tissue, 'Fed-Fed-Fed' intervention, replicate 7

source_name: Liver tissue, obtained from a mouse that was subjected to a 'Fed-Fed-Fed' intervention


title: SD0hr2_S8: w303 Spores incubated for 0 hour in SC with 0.002% glucose, replicate no.2


title: Liver tissue, 'Fed-Fed-Fast' intervention, replicate 8


title: Liver tissue, 'Fast-Fast-Fed' intervention, replicate 4


title: Liver tissue, 'Fed-Fed-Fed' intervention, replicate 8


title: Liver tissue, 'Fast-Fast-Fed' intervention, replicate 7


title: Liver tissue, 'Fast-Fast-Fast' intervention, replicate 4


title: Liver tissue, 'Fast-Fast-Fast' intervention, replicate 6


title: Liver tissue, 'Fast-Fast-Fed' intervention, replicate 6


title: SD0hr3_S9: w303 Spores incubated for 0 hour in SC with 0.002% glucose, replicate no.3


title: Liver tissue, 'Fed-Fed-Fast' intervention, replicate 5


title: SD0hr1_S7: w303 Spores incubated for 0 hour in SC with 0.002% glucose, replicate no.1


title: SC96hr2_S20: w303 Spores incubated for 96 hours in SC with 0% glucose, replicate no.2


title: SC96hr3_S21: w303 Spores incubated for 96 hour in SC with 0% glucose, replicate no.3


title: SC48hr2_S14: w303 Spores incubated for 48 hours in SC with 0% glucose, replicate no.2


title: Liver tissue, 'Fed-Fed-Fast' intervention, replicate 4


title: Liver tissue, 'Fast-Fast-Fed' intervention, replicate 3


title: SC48hr3_S15: w303 Spores incubated for 48 hour in SC with 0% glucose, replicate no.3


title: SC96hr1_S19: w303 Spores incubated for 96 hours in SC with 0% glucose, replicate no.1


title: SC16hr3_S6: w303 Spores incubated for 16 hours in SC with 0% glucose, replicate no.3


title: SC16hr1_S4: w303 Spores incubated for 16 hours in SC with 0% glucose, replicate no.1


title: SC0hr3_S3: w303 Spores incubated for 0 hour in SC with 0% glucose, replicate no.3


title: Liver tissue, 'Fed-Fed-Fed' intervention, replicate 6


title: SC16hr2_S5: w303 Spores incubated for 16 hours in SC with 0% glucose, replicate no.2


title: Liver tissue, 'Fast-Fast-Fast' intervention, replicate 3


title: SC0hr1_S1: w303 Spores incubated for 0 hour in SC with 0% glucose, replicate no.1


title: Liver tissue, 'Fast-Fast-Fed' intervention, replicate 2


title: SC48hr1_S13: w303 Spores incubated for 48 hours in SC with 0% glucose, replicate no.1


title: Liver tissue, 'Fed-Fed-Fed' intervention, replicate 4


title: Liver tissue, 'Fed-Fed-Fast' intervention, replicate 2


title: Liver tissue, 'Fed-Fed-Fast' intervention, replicate 3


title: Liver tissue, 'Fed-Fed-Fed' intervention, replicate 5


title: Liver tissue, 'Fast-Fast-Fast' intervention, replicate 2


title: Liver tissue, 'Fast-Fast-Fast' intervention, replicate 1


title: Liver tissue, 'Fed-Fed-Fed' intervention, replicate 3


title: Liver tissue, 'Fed-Fed-Fed' intervention, replicate 2


title: Liver tissue, 'Fast-Fast-Fed' intervention, replicate 1


title: Liver tissue, 'Fed-Fed-Fast' intervention, replicate 1


title: NM-AS_ST5_E-2

city: Worcester

first: Néva

last: Meyer

state: MA

address: 950 Main Street

department: Biology

country: USA

institute: Clark University

description: single-cell RNAseq using the 10X genomics platform

data_processing:
Read alignment, UMI counting, and secondary analysis (dimensionality reduction, clustering, and visualization) using CellRanger 2.1.0
Data normalization, variable feature selection, PCA, dimensionality reduction, clustering, t-SNE and UMAP analysis, differential gene expression analysis using Seurat 3.1.0
similarly weighted non-negative embedding (SWNE) analysis using parameters alpha.exp = 1.25, snn.exp = 0.25 and n_pull = 3
Lineage construction and trajectory inference using Monocle3
RNA velocity estimation using velocyto
Genome_build: (Ensembl) Capitella_teleta.Capitella_teleta_v1.0.dna_sm.toplevel.fa
Supplementary_files_format_and_content: Filtered feature barcodes. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column). It also contains gzipped TSV files with feature and barcode sequences corresponding to row and column indices respectively. Features correspond to row indices. For each feature, its feature ID and name are stored in the first and second column of the (unzipped) features.tsv.gz file.

organism: Capitella teleta

source_name: whole-body dissociation

growth_protocol: Healthy males and females were mated under controlled conditions and their offspring collected at the gastrula stage (stage 3). Stage 4 and stage 5 larvae were collected from two different sets of parents, each from a single mother. Capitella teleta embryos and larvae were incubated in artificial seawater (ASW) with 50 ug/mL penicillin and 60 ug/mL streptomycin at 19 °C for 1–2 days until they reached stage 4 prototroch or stage 5.

extract_protocol:
For single-cell dissociation, 300 larvae from a single brood (i.e. from one male and female) for each stage were then collected into 1.5 mL centrifuge tubes and equilibrated in Ca2+/Mg2+-free ASW (CMFSW). Most of the CMFSW was removed from the tubes, and larvae were mechanically homogenized using separate, clean and sterile pestles as well as a hand-held homogenizer (Cole Parmer, LabGEN 7B) for 5–10 seconds. Homogenized larvae from each stage were then incubated in 1% Trypsin (SigmaAldrich, Cat# T4799-5G) in CMFSW for 30 minutes at room temperature with constant rocking. During incubation, dissociated tissues were periodically triturated using both wide-mouthed and narrow-mouthed Pasteur pipettes. After 30 minutes of incubation, the tissue lysate was passed through a 40 µm nylon cell-strainer (Fisherbrand, Cat# 22-363-547) to get rid of undissociated cell-clumps. The resultant cell-suspension was then centrifuged at 1100 x g for 7 minutes with slow-braking and washed twice in cell media that was developed originally for marine hemichordate cell-cultures (3.3X Dulbecco’s PBS and 20 mM HEPES, pH = 7.4). Dissociated cells were then resuspended in the cell media and checked under an inverted phase-contrast microscope to ensure a single-cell suspension was obtained.
RNA libraries were prepared for sequencing using standard Illumina protocols for NextSeq-500
paired-end RNAseq

tag: Stage

value: Stage 5

value: untreated

value: wild-type


title: NM-AS_ST4_PT-1

value: Stage 4 prototroch


title: Input_WT_0h_rep1

city: Iowa City

first: Anna

last: Malkova

state: Iowa

address: 29 E. Jefferson St.

department: iBio

institute: University of Iowa

data_processing:
Raw reads were first trimmed using fastp version 0.20.1 to remove adaptors and low-quality reads
mapp to the genome using bowtie2 version 2.2.4 with default parameters
Duplicates reads were removed by samtools version 1.10 markdup function with -r parameter
Peaks were called using macs2 version 2.2.7.1 callpeak function with -B -g 1.2e7 -q 0.01 parameters using input as background control
Signal tracks were generated using mac2 bdgcmp function with -m ppois parameter using input as background control
Genome_build: AM1003 - custom genome with truncated chrIII (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2516063/)
Supplementary_files_format_and_content: normalized signal tracks in bigwig format
peak files in bed format

organism: Saccharomyces cerevisiae

source_name: budding yeast

growth_protocol: Yeast cells are firstly grown in YEP-raffino media for overnight to reach a concentration of 0.5x10^7 cells/ml.

extract_protocol:
Yeasts were break down by beads beater for 6 minutes, then cell lysate was sonicated to DNA size at 100 bp to 1000 bp, RPB1 antibody and dynabeads were used for ChIP, DNA is first purified by phenol:chloroform and further purified by AMPure XP (Beckman Coulter)
Takara ThruPLEX Plasma-seq Kit (Takara Bio)

treatment_protocol: 2% galactose was added to induce DSB by GAL::HO. 50ml cultures are collected before and after galactose addition.


title: Input_Rad51_0h


title: Input_WT_6h_rep2

value: treat with 2% galactose for 6 hours


title: Input_WT_0h_rep2


title: RNA_ASFV_12H_3

city: Beijing

first: Jingrui

last: Li

address: Yuanmingyuan West Road No.2

institute: China Agricultural Universtiy

description:
12 h post ASFV infection
mRNA_expression_profile.txt

data_processing:
Basecalls performed using CASAVA
For RNA-seq, Illumina sequencing reads were mapped to pig (Sus scrofa v11.1) and ASFV (MK333180.1) genome by using Hisat2.1.0 with default settings for parameters. Kallisto_0.45.1 was used for quantifying abundance of each transcript. TPM values were calculated to measure the expression levels of gene’s transcripts. Differential expression analysis of genes was performed by Sleuth_0.30.0. Differentially expressed genes were filtered by the following parameters: TPM ≧ 20, fold-changed (FC) ≧ 2 and p-value < 0.05.
For small RNA-seq, sequencing adapters (AGATCGGAAGAGCACACGTCT) was removed by using cutadpt1.18. Reads were mapped to pig genome by using Bowtie2.2.5. The unmapped reads were collected and then mapped to ASFV genome. A brief annotation of PAMs encoded small RNAs were performed by using unitas_1.7.0. FeatureCount_1.6.4 was used for quantifying abundance of each miRNA. RPM values were calculated to measure the expression levels of each miRNA. Differential expression analysis of miRNAs was performed by DESeq2_1.22.2. Differentially expressed miRNAs were filtered by the following parameters: fold-changed (FC) ≧ 2 and p-value < 0.05.
Genome_build: Sus_scrofa_v11.1
Supplementary_files_format_and_content: Tab-delimited text file includes TPM values for each RNA-seq samples. Tab-delimited text file includes reads_count for each small RNA-seq samples.

organism: Sus scrofa

source_name: porcine alveolar macrophages

growth_protocol: Porcine alveolar macrophages (PAMs) were collected from 4-week-old SPF pigs as previously described. PAMs were maintained in RPMI1640 medium supplemented with 10% FBS at 37°C with 5% CO2.

extract_protocol:
The RNA was extracted from the infected cells at 0-, 6-, 12- and 24-hpi.
For strand specific RNA-seq, depletion of ribosomal RNA (rRNA) and RNA-seq libraries were constructed according to the manufacturer’s protocol of the Illumina kit. For small RNA-seq, small RNA-seq libraries were constructed according to the manufacturer’s protocol of the Illumina kit.

treatment_protocol: Cells were infected with ASFV Chinese isolates (Pig/HLJ/18) at a multiplicity of infection (MOI) of 1 and incubated for 1 h at 37°C. The infected cells were then cultured at 37°C with fresh RPMI 1640 medium supplemented with 10% FBS.

tag: cell type

value: porcine alveolar macrophages

tag: breed

value: SPF

tag: infection

value: ASFV infection

tag: time point (hour post infection)


title: IP_Rad51_0h

tag: strain

value: RPB1 (BioLegend, 664912 lot B281694)


title: SC0hr2_S2: w303 Spores incubated for 0 hour in SC with 0% glucose, replicate no.2

value: spores


title: Liver tissue, 'Fed-Fed-Fed' intervention, replicate 1

value: male

tag: age


title: IP_Rad51_6h

tag: treatment


title: IP_WT_6h_rep2

tag: chip antibody


title: RNA_ASFV_12H_1


title: RNA_ASFV_24H_2

description:
24 h post ASFV infection
mRNA_expression_profile.txt


title: RNA_ASFV_24H_3


title: Input_WT_6h_rep1


title: RNA_ASFV_24H_1


title: RNA_ASFV_6H_3

description:
6 h post ASFV infection
mRNA_expression_profile.txt

value: 6 h


title: IFN_Vero_SARS-CoV-2

city: New York

first: Adolfo

last: Garcia-Sastre

state: NY

address: 1 Gustave Levy Pl

department: Microbiology and Immunology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
raw bcl files were converted into fastq format using the cellranger suite's mkfastq function
gene expression fastq files were aligned to a custom host-virus genome reference containing African Green Monkey (Chlorocebus sabaeus; ENSEMBL version 100) genome concatenated with the SARS-CoV-2 genome  (USA-WA1/2020; NCBI GenBank: MN985325.1) using the count function in the cellranger suite (10X Genomics, v3.0.1)
MULTIseq fastq files were quantified using cellranger v3.1.0 count with settings for 'Antibody Capture'
Feature x cell counts matrices (gene expression and MULTIseq) were loaded into R v.4.0.2 and demultiplexed with deMULTIplex v1.0.2 (https://github.com/chris-mcginnis-ucsf/MULTI-seq). Sample identities were supplied as metadata for associated cell barcodes (Sample-cell barcode assignment table).
Genome_build: custom genome; African Green Monkey (Chlorocebus sabaeus; ENSEMBL version 100) genome concatenated with the SARS-CoV-2 genome  (USA-WA1/2020; NCBI GenBank: MN985325.1)
Supplementary_files_format_and_content: The feature-gene-cell barcode count matrix is the standard output provided by the CellRanger count command
Supplementary_files_format_and_content: The MULTIseq sample metadata maps MULTIseq hashing barcodes to corresponding experimental conditions
Supplementary_files_format_and_content: Sample-cell barcode assignment indicates demultiplexed sample membership for each cell barcode (post-filter, "negative" and "multiplet" cell barcodes excluded)

organism: Chlorocebus sabaeus

source_name: Vero E6 African Green Monkey kidney cell line

growth_protocol: Vero E6 African green monkey kidney cells were seeded in 6-well plates at a 500,000 cells/well in viral growth media (Dulbecco's Modified Eagle Medium with 2% fetal bovine serum, 1% penicillin-streptomycin, 5% non-essential amino acids and 5% HEPES) and grown at 37oC (5% CO2) for 24 hours.

extract_protocol:
After stimulation, cells were dissociated into single cell suspension, labelled with MULTIseq lipid-modified oligos for multiplexing and pooled equivalently. The prepared mixture was loaded into the 10X Chromium controller.
Sequencing library was prepared in accordance to the 10X Genomics 5'-end single cell RNA sequencing protocol (Chromium Next GEM Single Cell 5’ v1.1)

treatment_protocol: Cells were either mock (Dulbecco's Modified Eagle Medium with 2% fetal bovine serum, 1% penicillin-streptomycin, 5% NEAA and 5% HEPES) treated or infected with SARS-CoV-2 (MOI 0.05) for 8 hours at 37oC (5% CO2). After 8 hour infection, cells were mock treated or treated with Type I (100 IU/ml) , Type II (10 ng/ml) or Type III IFN (100 IU/ml) for 6 hours at 37C (5% CO2).

tag: cell line

value: Vero E6

tag: agent

value: mixed sample (non-demultiplexed)


title: RNA_ASFV_6H_2


title: RNA_ASFV_0H_3

description:
0 h post ASFV infection
mRNA_expression_profile.txt

value: 0 h


title: Neuroblastoma cells - SK-N-BE(2) siNC_rep2

city: Shanghai

first: Yaoyao

last: Gu

state: State...

address: No. 1665 Kongjiang Road

institute: Xinhua Hospital

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were filtered using Cutadapt version 2.10. Sequenced reads with 3' adaptor-trimming and whose average quality score is lower than Q20 were removed.
Tophat Version 2.1.1 was used to align the filtered high quality sequence (Clean Data) to the reference genome GRCh38. According to the comparison results, the expression of each gene is calculated.
The  difference expression analysis, enrichment analysis and cluster analysis were further performed. The reads on the alignment were spliced to restore the transcript sequence. In order to make the gene expression levels of different genes and different samples comparable, we use FPKM (Fragments Per Kilo bases per Million fragments) to normalize the expression level.
HTSeq version 0.12.4 was used to statistically compare the read count value of each gene as the original expression level of the gene. For pair-end sequencing, each fragments will have two reads, and FPKM only counts the number of fragments that can be compared to the same transcript by the two reads. In the participating transcriptome, we generally think that genes with FPKM>1 are expressed. RSeQC version 3.0.1 was used to analyze the expression saturation.
Genome_build: GRCh38
Supplementary_files_format_and_content: FPKM expression values

molecule: polyA RNA

source_name: Human neuroblastoma cells

growth_protocol: Cells were routinely maintained in a 1:1 mixture of Eagle’s Minimum Essential Medium and Ham’s nutrient mixture F-12 Medium supplemented with 10% fetal bovine serum (Gibco, USA) at 37 °C with 5% CO2.

extract_protocol:
TRIzol reagent (Invitrogen, USA) was used to extract total RNA from cells. Enrichment of mRNA with polyA structure in total RNA by Oligo(dT) magnetic beads.
The RNA was broken to a length of about 300bp by means of ion interruption. Synthesize cDNA with 6-base random primers and reverse transcriptase.The first strand of cDNA was synthesized using RNA as template, and the second strand of cDNA was synthesized using the first strand of cDNA as the template.

treatment_protocol: The cells were transfected with siRNA at a final concentration of 60 nM for 24 h performing in Lipofectamine™ RNAimax(Invitrogen, USA). To be specific, cultured the cells in a 6-well plate and performed transfection when the cell density was about 30%. In 200ul Opti MEM I medium, mixed 0.12nmol siRNA with 8ul transfection reagent and incubated for 5min, added to one well of a 6-well plate, and then add 2ml complete medium. After 24 h of incubation, the medium was replaced with a standard medium and the cells were ready for further experiments.

value: scrambled NC siRNA

value: neuroblastoma cell line


title: IP_WT_6h_rep1


title: IP_WT_0h_rep1


title: Neuroblastoma cells - SK-N-BE(2) siNC_rep3


title: RNA_ASFV_0H_2


title: Input_Rad51_6h


title: Neuroblastoma cells - SK-N-BE(2) siMCM6_rep3


title: RNA_ASFV_0H_1


title: RNA_ASFV_12H_2


title: Neuroblastoma cells - SK-N-BE(2) siNC_rep1


title: Neuroblastoma cells - SK-N-BE(2) siMCM6_rep2


title: Neuroblastoma cells - SK-N-BE(2) siMCM6_rep1


title: IP_WT_0h_rep2


title: s3A

city: Longyan

first: YAN

middle: MING

last: HUANG

state: Fujian

address: 105 Jiuyi North Road, Xinluo

department: Neurosurgery

institute: Longyan First Hospital Affiliated to Fujian Medical University

description:
circRNA
Q30=91.75%

data_processing:
All of the reads were mapped to human reference genome using Hisat2. The transcription abundance was estimated using StringTie software. FPKM value of each gene was calculated by Ballgown.
All of the reads were mapped to human reference genome using STAR. The Reads count of circRNA was estimated using CIRCexplorer2 software.
Genome_build: hg19
Supplementary_files_format_and_content: Reads count  text file

source_name: mononuclear cell

extract_protocol:
Blood samples of three pairs of matched patients with primary MIA and healthy individuals were collected.To ensure the quality of samples, the present study excluded those factors that could affect the state of peripheral blood, including pregnancy, chemotherapy and fever (≥37.3˚C). Individuals in the MIA and matched groups were matched based on age, sex and past medical history, such as hypertension and smoking. Total RNA was extracted from peripheral blood mononuclear cell samples using TRlzol reagent (Takara, USA) according to the kit’s instructions. RNase R (Epicentre; Illumina, Inc.) was used to degrade linear RNA and enrich circRNAs in total RNA.
The circRNA library was constructed according to the manufacturer’s protocols (NEBNext Ultra Directional RNA Library Prep kit; New England BioLabs, Inc.).
circRNA-Seq

tag: group

value: Primary multiple intracranial aneurysms

value: female

tag: hypertension

value: yes


title: s2A

description:
circRNA
Q30=92.82%

tag: gender


title: s3B

description:
circRNA
Q30=92.16%

value: Healthy individual


title: s2B

description:
circRNA
Q30=91.84%


title: RNA_ASFV_6H_1


title: s1B

description:
circRNA
Q30=92.65%


title: A1

description:
circRNA
Q30=68.46%


title: CD151KO_4

city: Suita-city

first: Yoshito

last: Takeda

state: Osaka

address: Yamada-oka, 2-2

department: Department of Respiratory Medicine and Clinical Immunology

country: Japan

institute: Osaka University Graduate School of Medicine

hyb_protocol: Hybridisations were carried out using Hybridisation, Wash and Stain Kit (Affymetrix), with washing and staining of arrays on Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned using Scanner 3000 7G (Affymetrix).

data_processing: Microarray signal intensities were normalized using the Expression Console software (Microarray Suite 5) (Affymetrix).

label_protocol: cDNA synthesized from 500ng of total RNA was labeled with GeneChip IVT Express Kit (Affymetrix).

growth_protocol: The lungs were transferred into QIAzol lysis reagent (Qiagen) and disrupted and homogenized using a TissueLyser homogenizer (Qiagen).

extract_protocol: Total RNA was extracted from the lung lysates using the RNeasy mini kits (Qiagen).

tag: strain background

value: 20 wks of age

tag: genotype/variation

value: lung


title: CD9KO_2

tag: tissue


title: CD151KO_2


title: CD151KO_3


title: CD9KO_1


title: CD9KO_3


title: CD9KO_5


title: CD151KO_5


title: wild type_5

source_name: wild type_lung

value: wild type


title: wild type_1


title: CD9KO_4


title: CD151KO_1


title: wild type_4


title: wild type_3


title: BRD4_DMSO_ChIP_Input_Rep2

city: Chapel Hill

first: Austin

middle: J

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
For H4ac ChIP, single end 50-bp reads were filtered using TagDust (Lassmann et al. 2009). ChIP-Rx normalization was performed as described in (Orlando et al. 2014). Briefly, reads were first aligned to the Drosophila dm3 genome using Bowtie (Langmead et al. 2009). Unmapped reads were then aligned to the human hg19 genome using Bowtie and reads were normalized to Drosophila mapped read counts.
To generate differential windows, input signal was subtracted from ChIP signal. Signal was then averaged across 300bp sliding windows offset by 100 bp. Differential windows were identified using DESEQ2 (Love et al. 2014). Windows with significant enrichment were merged and identified as a peak.
For BRD4 ChIP, single end 50-bp reads were filtered using TagDust (Lassmann et al. 2009) and aligned to hg19 using Bowtie (Langmead et al. 2009). Peaks were called with MACS2 (Zhang et al. 2008).
Sequencing reads were aligned to hg19 (STAR v2.5.2b, (Dobin et al. 2013). Differential genes were identified by DESEQ2 (Love et al. 2014) and count data was used to generate the MAplot using RStudio.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files represent spike-in normalized read depth genomic coverage
Excel files contain peak calls as determined by MACS2
DESeq2 differential gene files contain relevant data necessary to determine differential genes via DESeq2
ROSE super-enhancer files lists enhancer, super-enhancers, and signal associated with called enhancers
Differential window files contain differential H4ac peaks as determined by DESeq2
The combined expression matrix contains the TPMs (as calculated by Salmon) for each RefSeq isoform across all samples.

growth_protocol: Cells were grown in RPMI-1640 plus 20% FBS

extract_protocol:
RNA was extracted using TRIzol reagent. For H4ac ChIP, HL60 cells were cultured to a density of 7x10^5 cell/mL and treated with 1 µM SAHA or 0.01% DMSO for 1 h prior to ChIP protocol.
Sequencing libraries were generated from DNA enriched by ChIP following the manufacturer’s specification for the Tru-Seq library preparation kit (Illumina)

treatment_protocol: HL60 cells were treated with either DMSO or SAHA for 1hr or 2hr prior to collection

value: leukemia cell line HL60

value: DMSO

tag: spike-in genome


title: DMSO_H4ac_Rep2_and_H3K27ac_ChIP_Input


title: H3K27ac_SAHA_ChIP

value: SAHA


title: BRD4_SAHA_ChIP_Input_Rep2


title: H3K27ac_DMSO_ChIP


title: H4ac_DMSO_ChIP_Input_Rep1


title: BRD4_SAHA_ChIP_Rep1


title: BRD4_DMSO_ChIP_Input_Rep1


title: BRD4_DMSO_ChIP_Rep1


title: BRD4_SAHA_ChIP_Input_Rep1


title: BRD4_SAHA_ChIP_Rep2


title: H4ac_SAHA_ChIP_Input_Rep1


title: H4ac_SAHA_ChIP_Rep2


title: SAHA_H4ac_Rep2_and_H3K27ac_ChIP_Input


title: H4ac_SAHA_ChIP_Rep1


title: H4ac_DMSO_ChIP_Rep2


title: Mac_SSc_Arm_F_1183

city: Stanford

first: Kun

last: Qu

state: CA

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

data_processing:
Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie2, duplicate fragments were then removed using Picard. Peaks were called using the MACS2 algorithm, which was first applied to each dataset independently. Mapped reads from each group of samples were merged to call peaks using MACS2, and highquality peaks were filtered using FDR < 10E-7. The peak sets from each sample group were then merged using ZIMBA to generate a merged peak list.
Number of Raw reads in each peak was calculated using in house generated script, and data matrix was normalized using R
Genome_build: hg19
Supplementary_files_format_and_content: Peak files are in tab seperated format, which includes the following columns: chromosome, start, stop, name, number of reads in peak, strand, arbitary score

source_name: human macrophage cell

growth_protocol: Donors were recruited under a Stanford University IRB-approved protocol. Volunteer patients with Systemic Sclerosis were recruited from Stanford Hospital. Informed consent was obtained. Standard skin biopsy were obtained for each donor. Healthy human donors provided 5 mm punch skin sample and each sample was digested to single cell suspension. Patients’ samples were obtained from clinically affected skin of the arm and clinically unaffected skin of the back of patients with SSc. From each skin biopsy, we isolated CD4+ and CD8+ T cells, fibroblasts, melanocytes, macrophages, endothelial and dendritic cells using flow cytometry. For each cell type we then performed ATAC-seq to map the location and accessibility of regulatory elements genome-wide from 50,000 cells.

extract_protocol:
9 cell types, CD4+ and CD8+ T cell, pericyte, dendritic, langerhan, CD31 cell, macrophage, fibroblast and keratinocyte cells were isolated from skin biopsy using flow cytometry. Around 50,000 cells were used for each transposition reaction. Nuclei were prepared prior to transposition.
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit.

tag: cell type

value: human macrophage cell

value: disease cell from Systemic Sclerosis patient

value: Female


title: Mac_SSc_Back_F_1183

value: normal cell from Systemic Sclerosis patient


title: H4ac_DMSO_ChIP_Rep1


title: Fib_SSc_Arm_M_29

source_name: human fibroblast cell

value: human fibroblast cell

value: Male


title: Mac_SSc_Arm_F_1181


title: Fib_SSc_Back_F_1205


title: Fib_SSc_Back_M_29


title: DC_SSc_Back_F_1183

source_name: human denditic cell

value: human denditic cell


title: Fib_SSc_Arm_F_1202


title: DC_SSc_Arm_M_25_rep2


title: CD8_SSc_Back_M_29_rep1

source_name: human CD8+ T cell

value: human CD8+ T cell


title: CD8_SSc_Back_M_25


title: DC_SSc_Arm_F_1181


title: CD8_SSc_Back_M_29_rep2


title: CD8_SSc_Arm_F_28_rep2


title: CD8_SSc_Back_F_1183


title: CD8_SSc_Arm_M_25_rep2


title: Fib_SSc_Arm_F_1205


title: DC_SSc_Arm_F_28


title: DC_SSc_Arm_M_25_rep1


title: CD8_SSc_Arm_F_28_rep1


title: CD8_SSc_Arm_M_25_rep1


title: CD8_SSc_Arm_F_1181


title: CD4_SSc_Back_M_29_rep2

source_name: human CD4+ T cell

value: human CD4+ T cell


title: Fib_SSc_Arm_M_25


title: CD4_SSc_Back_F_1183


title: DC_SSc_Back_F_1181


title: CD4_SSc_Arm_M_25_rep2


title: CD4_SSc_Arm_M_25_rep1


title: CD4_SSc_Arm_F_28_rep2


title: sRNA_ASFV_24H_2

description:
24 h post ASFV infection
miRNA_reads_count.txt

value: porcine alveolar macrophages

tag: breed

value: SPF

value: ASFV infection


title: CD4_SSc_Back_F_1181


title: CD4_SSc_Back_M_29_rep1


title: sRNA_ASFV_12H_3

description:
12 h post ASFV infection
miRNA_reads_count.txt

tag: infection


title: sRNA_ASFV_24H_3

tag: time point (hour post infection)


title: CD4_SSc_Arm_F_28_rep1

tag: strain


title: CD4_SSc_Arm_F_1181


title: EC_SSc_Back_F_1205

source_name: human endotheliocyte

extract_protocol:
9 cell types, CD4+ and CD8+ T cell, pericyte, dendritic, langerhan, endotheliocyte, macrophage, fibroblast and keratinocyte cells were isolated from skin biopsy using flow cytometry. Around 50,000 cells were used for each transposition reaction. Nuclei were prepared prior to transposition.
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit.

value: human endotheliocyte


title: EC_SSc_Arm_F_1205


title: sRNA_ASFV_6H_1

description:
6 h post ASFV infection
miRNA_reads_count.txt

tag: age

value: 6 h


title: Pericyte_NormSkin_M_27

source_name: human pericyte cell

value: human pericyte cell

value: Normal Donor


title: sRNA_ASFV_12H_1


title: sRNA_ASFV_6H_3


title: LC_NormSkin_54

source_name: human langerhans cell

value: human langerhans cell


title: sRNA_ASFV_6H_2


title: sRNA_ASFV_0H_3

description:
0 h post ASFV infection
miRNA_reads_count.txt

value: 0 h


title: sRNA_ASFV_0H_2


title: LC_NormSkin_51


title: KC_NormSkin_54

source_name: human keratinocyte cell

value: human keratinocyte cell


title: KC_NormSkin_47


title: KC_NormSkin_48


title: CD4_SSc_Arm_M_25_rep3

value: disease cell from Systemic Sclerosis patient


title: sRNA_ASFV_0H_1


title: Fib_NormSkin_M_43


title: sRNA_ASFV_24H_1


title: Fib_NormSkin_M_24


title: DC_NormSkin_M_34

source_name: human dendritic cell

value: human dendritic cell


title: Fib_NormSkin_F_44

value: human fibroblast cell

value: Female


title: DC_NormSkin_M_21

value: Male


title: DC_NormSkin_M_24


title: CD8_NormSkin_M_34

value: human CD8+ T cell


title: CD8_NormSkin_M_43


title: CD4_NormSkin_M_43

value: human CD4+ T cell


title: CD4_NormSkin_M_34


title: C6: in utero oxycodone exposure

city: OMAHA

first: Sowmya

middle: V

last: Yelamanchili

state: Nebraska

address: 984455 Nebraska Medical Center

department: Anesthesiology

institute: UNIVERSITY OF NEBRASKA MEDICAL CENTER

data_processing:
RNAseq libraries were generated by the UNMC NGS Core beginning with 1 ug of total RNA from each sample using the TruSeq V2 RNA sequencing library kit from Illumina following recommended procedures
Resultant libraries were assessed for size of insert by analysis of an aliquot of each library on a BioAnalyzer instrument
Multiplexed libraries (18 samples per pool) were sequenced on a single flow cell of the NextSeq550 DNA Analyzer (Illumina) to generate a total of approximately 28 million 75 bp single reads for each sample.
Genome_build: GCA_000001895.4

organism: Rattus norvegicus

source_name: Prefrontal Cortex

extract_protocol:
The prefrontal cortex was removed from the brains of P14 rats. Tissues were frozen on dry ice. Total RNA was isolated from each sample using the Zymo Direct-Zol RNA kit according to manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For the in utero exposure animals (IUO), an ascending dosing procedure was used wherein doses of 10 mg/kg/day oxycodone (oxy) were orally gavaged for 5 days followed by 0.5 mg/kg/day escalation for 10 days to a final dose of 15 mg/kg/day, after which F0 females were mated with proven male breeders, and the treatment regimen continued throughout mating, gestation, and parturition until weaning. For post-natal exposure (PNO), F0 dams were orally gavaged with 15 mg/kg/day of oxy after parturition until weaning.

value: post-natal day 14

value: Sprague Dawley Rat

value: Prefrontal Cortex

tag: treatment

value: in utero oxycodone exposure


title: EC_NormSkin_M_43

value: human endotheliocyte


title: C5: in utero oxycodone exposure


title: C4: in utero oxycodone exposure


title: EC_NormSkin_F_44

source_name: human endotheliocyte cell

value: human endotheliocyte cell


title: Fib_NormSkin_F_42

value: Normal Donor


title: C3: in utero oxycodone exposure


title: EC_NormSkin_F_42

extract_protocol:
9 cell types, CD4+ and CD8+ T cell, pericyte, dendritic, langerhan,endotheliocyte, macrophage, fibroblast and keratinocyte cells were isolated from skin biopsy using flow cytometry. Around 50,000 cells were used for each transposition reaction. Nuclei were prepared prior to transposition.
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit.


title: C2: in utero oxycodone exposure


title: 705 DMSO rep 2

city: Heidelberg

first: Obada

middle: Taleb

last: Alhalabi

address: Im Neuenheimer Feld 580 - TP3

department: Brain Tumor Translational Targets

institute: German Cancer Research Center DKFZ

description: Gene expression after 72 hr DMSO treatment

hyb_protocol: 0,6 ug of Cy3 labelled cRNA were hybridized for 17 hr at 65°C on Agilent SurePrint G3 Human Gene Expression v3 8x60K Microarray.

scan_protocol: Gene Expression Microarrays were scanned using the Agilent Scanner G2505C . The scanned images were analyzed with Feature Extraction Software (Agilent technologies) using default settings.

data_processing: Data processing followed using ChipYard (developed in-house, www.dkfz.de/genetics/ChipYard). US22502683_257236318062_S01_GE1_107_Sep09_2_4.txt was excluded for poor sample quality

source_name: Glioblastoma stem-like cells (GSCs)

label_protocol: The Agilent Low Input Quick Amp Labeling Kit (One-Color) is used to generate single-stranded cRNA from input amounts of 50ng total RNA.

growth_protocol: Tissues were enzymatically dissociated and cells were cultivated as floating neurospheres in serum-free DMEM/F-12:Ham medium, supplemented with 2% B27-admixture (PeloBiotech) and basal fibroblast growth factor (Biomol), epidermal growth factor (Life Technologies) at 20 ng/ml each and heparin at 5 ng/ml, in addition to 1% penicillin/streptomycin. Passaging and seeding was carried out by dissociation with accutase (Sigma-Aldrich). Cells were regularly checked for mycoplasma contamination as per the recommendations of the German Collection of Microorganisms and Cells (Germany). Glioblastoma cell lines were authenticated using single nucleotide polymorphism profiling.

extract_protocol: RNA was extracted from GSCs using the RNAeasy MiniKit (Qiagen) according to the manufacturer’s protocol and examined for integrity using an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: 1µM Dasatinib for 72 hours with a DMSO control

value: Brain

value: 72 hr DMSO treatment


title: C1: in utero oxycodone exposure


title: 705 Dasa 1µM rep 1

description: Gene expression after 72 hr dasatinib treatment

value: 72 hr dasatinib treatment


title: 711 Dasa 1µM rep 3


title: 705 DMSO rep 3


title: B6: post-natal oxycodone exposure

value: post-natal oxycodone exposure


title: 711 DMSO rep 3


title: 711 Dasa 1µM rep 2


title: 705 Dasa 1µM rep 2


title: B5: post-natal oxycodone exposure


title: B3: post-natal oxycodone exposure


title: B4: post-natal oxycodone exposure


title: B2: post-natal oxycodone exposure


title: B1: post-natal oxycodone exposure


title: 711 Dasa 1µM rep 1


title: mock 1

source_name: shoot apical meristem

value: Inflorescence meristem

tag: developmetal stage

value: two weeks after bolting

value: mock


title: A6: saline control

value: saline control


title: 711 DMSO rep 1

tag: cell line


title: 711 DMSO rep 2

tag: agent


title: BRD4_DMSO_ChIP_Rep2

value: leukemia cell line HL60

tag: chip antibody

value: DMSO


title: A4: saline control

value: post-natal day 14


title: A5: saline control

value: Sprague Dawley Rat


title: A3: saline control

value: Prefrontal Cortex


title: A2: saline control


title: A1: saline control


title: CPX treatment Day 6, biological rep 3

city: Lund

first: Mehrnaz

last: Safaee Talkhoncheh

address: Sölvegatan 17

country: Sweden

institute: Lund University

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Data normalized with Affymetrix GeneChip Expression v1.4 Software

label: Biotin

source_name: CB HSC, CPX, day6, Biological 3

label_protocol: cRNA (20 µg) was purified and reverse transcribed into sense-strand (ss) cDNA.Next, we incorporated the unnatural dUTP residues relative to dTT and cDNA was fragmented and finally  labeled with biotin.

growth_protocol: CB-CD34+CD90+ cells were sorted from total mononuclear cell derived from umbilical cord blood.

extract_protocol: Total RNA extraction was done using Qiagen RNeasy Micro kit (#74126).

treatment_protocol: Sorted CD34+CD90+ cells were treated with either CPX or DMSO control for 24 hours or 6 days. For 24 hours, cells were collected after treatment period and processd furhter for RNA extraction. For 6 days samples, we again sorted cells after collection for CD34+CD90+ cells. RNA isolation and further sample preparation was performed by the KFB institute in Germany.

value: Cord Blood

value: CPX 6 days

value: Sorted CD34+CD90+ cells


title: CPX treatment Day 6, biological rep 2

source_name: CB HSC, CPX, day6, Biological 2


title: DMSO treatment Day 6, biological rep 2

source_name: CB HSC, DMSO, day6, Biological 2

value: DMSO 6 days


title: DMSO treatment Day 6, biological rep 1

source_name: CB HSC, DMSO, day6, Biological 1


title: CPX treatment 24 hours, biological rep 3

source_name: CB HSC, CPX, 24hrs, Biological 3

value: CPX 24 hours


title: CPX treatment 24 hours, biological rep 2

source_name: CB HSC, CPX, 24hrs, Biological 2


title: CPX treatment Day 6, biological rep 1

source_name: CB HSC, CPX, day6, Biological 1


title: DMSO treatment 24 hours, biological rep 2

source_name: CB HSC, DMSO, 24hrs, Biological 2

value: DMSO 24 hours


title: P50 Braf MT rep 3

city: Irvine

first: Arthur

last: Lander

address: 2300 Biological Science

institute: University of California Irvine

data_processing:
FASTQ files were generated from Illumina’s binary base call raw output with Cell Ranger’s (v2.1.0) `cellranger mkfastq` command.
Alignment and count matrix for each sample was produced with `cellranger count` (v2.1.0) using the standard options (`--id=[UNIQUE ID], --fastq=[PATH TO FASTQ FILES], --sample=[SAMPLE NAME FROM FASTQ FILE], --transcriptome =[PATH TO REFERENCE]`). Transcripts were aligned to the mm10 reference genome.
Samples were aggregated together with `cellranger aggr` using the following options --id=[UNIQUE ID], --csv=[PATH TO CSV FILE CONTAINING LIST OF CELLRANGER COUNT OUTPUTS], --normalize=[mapped].
Genome_build: mm10
Supplementary_files_format_and_content: TSV and MTX. Files will be a list of cell barcodes; a list of genes, and the matrix data.

source_name: skin

extract_protocol:
Procedure was conducted at either post natal day 30 (P30) or post natal day 50 (P50). Mice were euthanized at the appropriate age and the hair on the dorasal skin was removed by shaving and depilation. A 2x3 cm section of the dorsal skin was removed, and the fat scraped off from the underside. The piece was then diced into smaller pieces and suspended in dissociation buffer (RPMI, liberase, Hepes, Sodium Pyruvate, Collagenase:Dispase) for 50 minutes at 37°C with gentle agitation. After incubation, DNaseI was added for 10 minutes and then inactivated with fetal bovine serum and EDTA.  The tissue suspension was further dissociated mechanically with the GentleMACS.  Single cell suspensions were filtered twice through a 70µm strainer and dead cells removed by centrifugation.  The live cells were washed with 0.04% UltraPure BSA:PBS buffer, gently re-suspended in the same buffer. Samples were loaded onto the 10X Chromium platform.
Libraries were prepared using the Chromium Single Cell 3’ v2 protocol (10X Genomics).  Briefly, individual cells and gel beads were encapsulated in oil droplets where cells were lysed and mRNA was reverse transcribed to 10X barcoded cDNA.  Adapters were ligated to the cDNA followed by the addition of the sample index.  Prepared libraries were sequenced using paired end 100 cycles chemistry for the Illumina HiSeq 4000.

treatment_protocol: Mice were treated with 4-hydroxytamoxifen at P2, P3, and P4 to indcue Braf V600E mutation.

value: skin

tag: genotype

value: Braf CA/+; Cre +

value: Post natal day 50


title: P50 Braf MT rep 2


title: DMSO treatment 24 hours, biological rep 1

source_name: CB HSC, DMSO, 24hrs, Biological 1


title: P50 Braf MT rep 1


title: Input_HIF1b_ChIP

city: Cleveland

first: Paul

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

description: CRISPR-Control OPCs

data_processing:
Reads were quality and adapter trimmed using Trim Galore! Version 0.4.1.
Trimmed reads were alighed to mm10 with Bowtie2 version 2.3.2.
Duplicate reads (potential artifacts of PCR in library preparation) were removed using Picard MarkDuplicates.
Genome_build: mm10
Supplementary_files_format_and_content: bigWIG files were generated using Deeptools bamCoverage with reads per genome coverage normalization. BED files in a narrowPeaks format from MACS2.

source_name: Oligodendrocyte progenitor cells (OPCs)

growth_protocol: OPCs were grown in DMEM F12 supplemented with N2max and B27 and Fgf2 and Pdgfa.

extract_protocol: Nuclei isolation and chromatin shearing were performed using the Covaris TruChIP protocol following manufacturer’s instructions for the “high-cell” format. In brief, 5-20 million cells were crosslinked in “Fixing buffer A” supplemented with 1% fresh formaldehyde for 10 minutes at room temperature with oscillation and quenched for 5 minutes with “Quench buffer E.” These cells were then washed with PBS and either snap frozen and stored at -80, or immediately continued to nuclei extraction and shearing per the manufacturer protocol. The samples were sonicated with the Covaris S2 using the following settings: 5% Duty factor 4 intensity for four 60-second cycles. Sheared chromatin was cleared and incubated overnight at 4 degrees with antibody that was pre-incubated with protein G magnetic DynaBeads (ThermoFisher). Protein G dynabeads were then washed, eluted, reverse cross-linked and treated with RNase A followed by proteinase K. ChIP DNA was purified using Ampure XP beads (Aline Biosciences, C-1003-5) and then used to prepare illumina sequencing libraries.

treatment_protocol: Comparison between control and Vhl knockout OPCs.

value: epiblast stem cell derived oligodendrocyte progenitor cells (OPCs)

tag: antibody

tag: number of cells per chip


title: Control_HIF1a_ChIP_B

description: CRISPR-Control OPCs

value: HIF1a (abcam2185, 25ug)

value: 80 million OPCs


title: Vhl_HIF1a_ChIP_B

description: CRISPR-Vhl OPCs


title: CPX treatment 24 hours, biological rep 1

source_name: CB HSC, CPX, 24hrs, Biological 1


title: Control_Olig2_ChIP_A

description: CRISPR-Control OPCs

value: Olig2 (Millipore ab9610, 15ug per ChIP)

value: 20 million OPCs


title: Vhl_Olig2_ChIP_A

description: CRISPR-Vhl OPCs


title: WT_OPC_ATAC_A

description: WT OPCs

data_processing:
Reads were quality and adapter trimmed using Trim Galore! Version 0.4.1.
Trimmed reads were alighed to mm10 with Bowtie2 version 2.3.2.
Duplicate reads (potential artifacts of PCR in library preparation) were removed using Picard MarkDuplicates.
Genome_build: mm10
Supplementary_files_format_and_content: bigWIG files were generated using Deeptools bamCoverage with reads per genome coverage normalization. BED files were generated using the narrowPeaks functions of MACS2.

extract_protocol:
Omni ATAC-Seq was performed on 50,000 OPCs from two independent biological replicates following the protocol outlined in (Corces et al., 2017). In brief, nuclei were extracted from cells and treated with transposition mixture containing Nextera Tn5 Transposase for (Illumina, FC-121-1030). Transposed fragments were then purified using Qiagen MinElute columns (Qiagen, 28004), PCR amplified, and libraries were purified with Agencourt AMPure XP magnetic beads (Beckman Coulter) with a sample to bead ratio of 1:1.2.
Libraries were amplified by low cycle number PCR utilizing illumina compatible indexed primers.

value: Omni ATAC-seq


title: WT_OPC_ATAC_B

description: WT OPCs


title: P50 Braf WT rep 3

value: Braf +/+; Cre +


title: P50 Braf WT rep 2


title: P50 Braf WT rep 1


title: P30 Braf MT rep 2

value: Post natal day 30


title: DMSO treatment 24 hours, biological rep 3

source_name: CB HSC, DMSO, 24hrs, Biological 3

value: Cord Blood


title: P30 Braf WT rep 2


title: cDCs.Eµ.3 [Emu-Myc]

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

institute: University of Münster

description: Eµ-Myc lymphoma exposed

hyb_protocol: Hybridization was performed with GeneChip™ WT PLUS Reagent Kit according to manufacturer's protocol (Affymetrix, Thermo Fisher Scientific).

scan_protocol: Scanning was performed according to manufacturer's protocol (Affymetrix, Thermo Fisher Scientific).

data_processing: For each comparison (5*Eµ-Myc lymphoma exposed cDC samples or 3*C/EBPβ-/- samples versus 6*naive cDC samples), we imported raw CEL data and quantile-normalized single probe intensities separately. The background normal distribution was fitted based on common quantile-normalized measurement values and corrected by computation of expected measurement signals (cf. RMA). Too dim probes (intensities lower than the background mode minus 0.8 times the half width of the background mode) were excluded via spot filtering. Probe intensities were transformed to log scale with base 2 for handling of gene expression ratios. All single-probe-level log2(intensities) were then grouped to probesets according to manufacturer annotations and aggregated via median polishing. Probe sets with more than 50% of NaNs probes (by spot filtering) were excluded.

source_name: Dendritic cells from spleen

label_protocol: RNA was transcribed and labeled by GeneChip™ WT PLUS Reagent Kit according to manufacturer's protocol (Affymetrix, Thermo Fisher Scientific).

growth_protocol: Dendritic cells were derived from spleens of C57BL/6, CD11c.Cre and CD11c.Cre x C/EBPβflox/flox mice, or from Eµ-Myc transfer mice.

extract_protocol: Isolation of RNA from cell lysate samples was performed using the RNeasy Micro or Mini Kit (Qiagen) with the RNase-free DNase Set (Qiagen), following the instructions provided.

treatment_protocol: Splenic DCs (CD11c+MHCclassII+) were derived from C57BL/6, CD11c.Cre and CD11c.Cre x C/EBPβflox/flox mice, or from Eµ-Myc transfer mice with an average splenic tumor load of 10-36% of all lymphocytes. DC purity after sorting was >95%.

tag: strain/background

value: Splenic dendritic cells

tag: microenvironment

value: Emu-Myc lymphoma exposed

tag: replicate


title: cDCs.Naiv.6 [Emu-Myc]

tag: cell type

value: Naive


title: cDCs.Naiv.2 [Emu-Myc]


title: cDCs.Eµ.4 [Emu-Myc]

description: Eµ-Myc lymphoma exposed


title: cDCs.Naiv.5 [Emu-Myc]


title: cDCs.Naiv.1 [Emu-Myc]


title: C_EBPbetaKO.3 [CEBPbetaKO]

description: C/EBPβ-/-

tag: genotype/variation

value: C/EBPbeta-/-


title: P30 Braf WT rep 1

tag: tissue


title: cDCs.Naiv.4 [Emu-Myc]


title: cDCs.Eµ.2 [Emu-Myc]

description: Eµ-Myc lymphoma exposed


title: C_EBPbetaKO.1 [CEBPbetaKO]

description: C/EBPβ-/-


title: C_EBPbetaKO.2 [CEBPbetaKO]

description: C/EBPβ-/-


title: P30 Braf MT rep 1


title: cDCs.Naiv.3 [Emu-Myc]


title: cDCs.Naiv.6 [CEBPbetaKO]

description: C/EBPβ+/+

value: C/EBPbeta+/+


title: cDCs.Eµ.1 [Emu-Myc]

description: Eµ-Myc lymphoma exposed


title: SAC26-8

city: Albuquerque

first: Nikolaos

last: Mellios

state: NM

address: 915 Camino De Salud NE

department: Neuroscience

institute: University of New Mexico

data_processing:
Image analysis and base calling were performed using solexa platform v1.8, Sequence quality was examined using FastQC software.
Adapter trimming and filtering by cutadapt software. Reads were then aligned to mouse genome using HiSat 2 Software.
Transcript abundance for each for each sample was estimated using StringTie, and the FPKM value for gene and transcript levels were caluclated using R package Ballgown.
Genome_build: GRCm28
Supplementary_files_format_and_content: fastq, xlsx

source_name: Whole Brain

extract_protocol:
RNA was extracted from E18 whole brains by Qiagen miRNeasy kit according to manufacturer supplied protocol. 1ug of Total RNA was used for library construction.
Libraries were constructed using Kapa Stranded RNA-seq Library Kit

treatment_protocol: PAE vs SAC

value: Brain

value: sacharin control

tag: Sex

value: Male


title: cDCs.Eµ.6 [Emu-Myc]

description: Eµ-Myc lymphoma exposed


title: SAC26-5

tag: strain

value: Female


title: cDCs.Naiv.4 [CEBPbetaKO]

description: C/EBPβ+/+


title: cDCs.Naiv.5 [CEBPbetaKO]

description: C/EBPβ+/+


title: SAC12-7

tag: age


title: SAC12-6

tag: treatment


title: Mac_NormSkin_M_34

source_name: human macrophage cell

value: human macrophage cell

value: Normal Donor

tag: gender


title: L9.23P

city: NEWCASTLE UPON TYNE

first: David

last: Young

address: Centre For Life

country: United Kingdom

institute: Newcastle University

data_processing:
Quality control of reads was performed using FastQC and Cutadapt. Trimmed Fastq wiles were aligned against known bos taurus miR sequences from miRBase using Bowtie2. Quantification was determined by counting aligned reads against a reference, using a combination of RSamTools and ShortRead bioconductor packages. Differential expression was assessed using DESeq2
Genome_build: N/A
Supplementary_files_format_and_content: Normalised gene counts in tab-delimited text

organism: Bos taurus

growth_protocol: Full depth articular cartilage explants were removed (5mm biopsy punch; Selles Medical Limited, Hull, UK) from the metacarpophalangeal joint of <3-week old bovine calves within 6hrs of slaughter Cartilage explants were equilibrated in culture medium for 3-days prior to mechanical load. All cultures were maintained at 37oC, 5% CO2, 20% O2. Each experiment utilised tissue from between 2-3 animals, and repeat experiments utilised tissue from independent animals.

extract_protocol:
Total RNA was extracted from cartilage explants using 500µl Trizol® reagent
Library preparation was conducted on 450ng total RNA using the NEB Next® Small RNA Library Prep Set for Illumina®, and amplified cDNA purified using a QIAquick PCR Purification Kit (Qiagen, West Sussex, UK). miR libraries were selected by running purified cDNA samples on 8% (v/v) polyacrylamide gels and excising bands located at ~140bp. A Multiplex Compatible kit (NEB Next® Small RNA Library Prep Set for Illumina®) was used to elute and purify the miRs, and the concentration of miR libraries assessed prior to analysis on a HiSeq™ Sequencing System.

treatment_protocol: Cartilage explants were subjected to either a ‘physiological’ (2.5MPa, 1Hz) or a ‘non-physiological’ load (7MPa, 1Hz) for 15mins using the ElectroForce® 3200 (TA Instruments, Delaware, USA) (Al-Sabah et al., 2016) and gene expression analysed at 2, 6 and 24-hours post-load; unloaded explants served as controls. Explants were immediately snap frozen and remained in liquid nitrogen (< 48hrs) until RNA extraction. Loading regimes were selected based on articular cartilage literature demonstrating that ≤5MPa is generally accepted as a ‘physiological’ load (Grodzinsky et al., 2000; Fehrenbacher et al., 2003), while peak loads >5MPa are considered degradative i.e. ‘non-physiological’ (Fehrenbacher et al., 2003); frequency was set at 1Hz which has been demonstrated to resemble a human fast walking speed (Bader et al., 2011).

value: cartilage

tag: timepoint

tag: molecule subtype

value: Small RNA


title: L6.24P


title: L9.22P


title: L6.23P


title: SAC12-5


title: 705 DMSO rep 1

source_name: Glioblastoma stem-like cells (GSCs)

tag: cell line

tag: agent

value: 72 hr DMSO treatment


title: ES27-4

value: Prenatal alcohol exposure


title: L6.22P


title: cDCs.Naiv.3 [CEBPbetaKO]

description: C/EBPβ+/+


title: cDCs.Naiv.2 [CEBPbetaKO]

description: C/EBPβ+/+


title: cDCs.Naiv.1 [CEBPbetaKO]

description: C/EBPβ+/+


title: SAC26-7


title: L5.24P


title: ES27-1


title: ES23-4


title: ES19-4


title: ES23-7


title: L5.22P


title: ES19-8


title: L8.24P


title: L8.23P


title: L3.23P


title: L8.22P


title: CD34_Pos_Basophil_10

city: Solna

first: Joakim

middle: S

last: Dahlin

address: CMM, Visionsgatan 18

department: Department of Medicine, Solna

institute: Karolinska Institutet

data_processing:
RNA-seq reads were aligned to mm10 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: mm10
Supplementary_files_format_and_content: HTSeq counts(.txt)

source_name: Bone marrow

extract_protocol:
94 single cells were index-sorted into a 96-well PCR plate containing 2.3 µl lysis buffer (2.3 U SUPERase In™ RNase Inhibitor (ThermoFisher Scientific, AM2696) in 0.2 % Triton) per well, vortexed and frozen at -70 °C. Sample preparation for RNA sequencing was performed following Picelli et al (Nature Protocols 9, 171-181 (2014)) and GSE128003 with modifications. Following brief centrifugation at 2000 rpm to thaw cells, oligo-dT was annealed to polyA-mRNA at 72 °C for 3 minutes. cDNA was reverse transcribed with 20 U/reaction Maxima H Minus Reverse Transcriptase (ThermoFisher) in the presence of PEG8000 (Sigma), and amplified using 19 PCR cycles with 1.25 U Terra PCR Direct Polymerase per reaction (Takara). ERCC Spike-In Mix (Invitrogen, 4456740) was included in each single cell reaction. PCR products were cleaned using 1:0.6 ratio of cDNA: AMPure XP beads (Beckman Coulter, A63882). Single cell cDNA library was eluted in 26 µl volume of EB Buffer (Qiagen, 19086) and 25 µl volume collected to ensure minimal bead carryover.
Libraries for scRNA-sequencing were prepared using Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1096) and Nextera Index Kit v2 Set D (FC-121-2004), following the manufacturer’s protocol using ¼ of the recommended volumes and 1.25 µl cDNA library. Single cell libraries were pooled and cleaned with AMPure XP beads; first with 1:0.5 ratio of cDNA: beads then the supernatant cleaned with 1:0.3 ratio of cDNA: beads. Pooled libraries were eluted in 25 µl EB Buffer and 23 µl collected to ensure minimal bead carryover. The libraries were sequenced on the Illumina HiSeq4000 system (50 bp single-end reads).

tag: cell population

value: CD34 Pos Basophil

tag: sorting strategy

value: Live Lin- Sca1- FcεRI+ CD34+ cells

value: female


title: CD34_Pos_Basophil_8


title: L2.24P


title: L4.22P


title: L3.22P


title: Control_H3K27Ac_ChIP_B

description: CRISPR-Control-OPCs

data_processing:
Reads were quality and adapter trimmed using Trim Galore! Version 0.4.1.
Trimmed reads were alighed to mm10 with Bowtie2 version 2.3.2.
Duplicate reads (potential artifacts of PCR in library preparation) were removed using Picard MarkDuplicates.
Genome_build: mm10
Supplementary_files_format_and_content: bigWIG files were generated using Deeptools bamCoverage with reads per genome coverage normalization. BED files in a broadPeaks format from MACS2.

value: epiblast stem cell derived OPCs

tag: antibody

value: H3K27Ac (abcam4729, 9ug per ChIP

tag: number of cells per chip

value: 5-20 million OPCs


title: Vhl_H3K27Ac_ChIP_B

description: CRISPR-Vhl OPCs


title: Vhl_HIF1a_ChIP_A

description: CRISPR-Vhl OPCs

value: HIF1a (abcam2185, 25ug)

value: 100 million OPCs


title: Control_HIF1a_ChIP_A

description: CRISPR-Control-OPCs


title: L2.22P


title: Input_HIF1a_ChIP

description: CRISPR-Control OPCs


title: L7.22P


title: CD34_Pos_Basophil_9


title: L7.23P


title: Input_Olig2_ChIP

description: CRISPR-Control OPCs

value: epiblast stem cell derived oligodendrocyte progenitor cells (OPCs)


title: CD34_Pos_Basophil_5


title: PA15

city: Barcelona

first: Anna

last: PLANAS

state: - If in U.S, Select a State -

address: Rossello 161 planta 6

institute: Spanish Research Council (CSIC)

data_processing:
Raw reads were analyzed for data quality using FastQC v0.11.5
and filtered using skewer (v0.2.2) for removing the low quality reads and trimming the Illumina adapter if necessary.
Reads were then aligned to the reference genome  using the annotation from Ensembl (version 88) with STAR aligner (v2.5.3a) using the option "--quantMode GeneCounts" for retrieving the gene counts.
Differential gene expression analysis was performed using DESEQ2 package
Genome_build: GRCm38
Supplementary_files_format_and_content: csv file with raw read counts (only unique mapping reads)

source_name: Brain Ipsilateral hemisphere (ischemic)

extract_protocol:
CD11c-eYFP+ cells and microglia were isolated from the brain of adult CD11c-eYFP mice, parabiotic WT/CD11c-eYFP mice or CX3CR1CreERT2-ROSA26 tdTomato mice respectively (13-16 weeks old) using Fluorescence Activated Cell Sorting. Brains were collected in cold HBSS buffer (w/o Ca2+ and Mg2+, Thermo Fisher Scientific #14175-053). The brain tissue was enzymatically dissociated using the Neural Tissue Dissociation Kit (P) (Miltenyi Biotec #130-092-628). The gentleMACS™ Dissociator with Heaters (Miltenyi Biotec #130-096-427) was used for mechanical dissociation steps following the Neural Tissue Dissociation Kit (P) for dissociation without heaters. The digested tissue was filtered twice with 70 µm and 40 µm filters washing with HBSS (w/ Ca2+ and Mg2+, Thermo Fisher Scientific #14025-092). Cells were separated from myelin and debris by 30% isotonic percoll gradient (GE Healthcare #17-0891-01) in Myelin Gradient Buffer (MGB). Samples were centrifuged at 950g for 30 min without acceleration nor brake. Cells were collected from the interface, washed once with FACS Stain Buffer (BD Biosciences #554656), and processed for FACS (no staining required) in a FACSAriaII sorter (BD Biosciences)
Libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA kit (#634890, Clontech) and NEBNext Ultra DNA Library Prep kit (#E7370, New England) according to the manufacturer's protocol. Briefly, 1 or 5 ng of total RNA were converted to cDNA using the SMART-seq kit. Long distance PCR was performed for 9 (5 ng) or 11 (1 ng) cycles. Agilent 2100 Bioanalyzer (High Sensitivity DNA Chip) was used for quantification and validation of the obtained cDNA. Ten ng of the resultant cDNA was fragmented using the Covaris S2 instrument in a final volume of 55 l and adjusting the settings as follows: 10% duty cycle, intensity 5, and 200 cycles per burst for 5 minutes. The resultant fragments were used for the library synthesis using the NEBNext Ultra kit. Briefly, fragments were subjected to end repair and addition of “A” bases to 3′ ends, ligation of adapters and USER excision. Library amplification was performed through 10 cycles of PCR using different indexed primers for multiplexing. All purification steps were performed using AgenCourt AMPure XP beads.
Final libraries were analyzed using Agilent DNA High Sensitivity chip to estimate the quantity and to check the size distribution and were then quantified by qPCR using the KAPA Library Quantification Kit (#KK4835, KapaBiosystems). Sequencing was carried out using the Illumina HiSeq 2500, Single Reads, 50nts.

value: Brain Ipsilateral hemisphere (ischemic)

value: 15-16 week old


title: L7.24P


title: CD34_Pos_Basophil_7


title: CD34_Pos_Basophil_6


title: CD34_Pos_Basophil_47


title: HG-podo-EVs-3

city: Guangzhou

first: Ying

last: Huang

state: Guangdong

address: 106 Zhongshan 2 Road

department: Division of Nephrology

institute: Guangdong Provincial People's hospital

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Clean reads were obtained after remove of low quality reads and removing reads with 5' linker sequence, reads without 3' linker sequence, reads without the insert tag, reads with poly (A), and reads shorter than 17 nt.
The clean reads were compared to the miRbase21 and Rfam database  to identify known miRNA and other non-coding RNAs.
The raw count for known miRNAs  were summarized and then normalized using reads per million mapped reads (RPM).
Total clean reads were  also mapped to the mouse reference genome using the bwa aligner.The mapped reads were further annotated to the repeats and exon regions based on the genome annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

source_name: HG-podo-EVs

growth_protocol: Podocytes were grown in RPMI1640 medium supplemented with 10% fetal bovine serum (FBS) and interferon-γ under an atmosphere of 5% CO2/95% air at 33℃. Once confluence reached 70%–80%, the podocytes were subcultured at 37℃ in DMEM medium supplemented with 5% FBS on collagen-coated dishes for 10 days in the absence of interferon-γ to promote differentiation.

extract_protocol:
Extracellular vesicles were isolated from the cell culture supernatants using ExoQuick-TC Exosome Precipitation Solution (System Biosciences) in accordance with the manufacturer's recommendations, and the RNA of extracellular vesicles was extracted by the MagZol (Magen) according to the manufacturer's protocol. The quantity and integrity of RNA yield was assessed by using the Agilent 2200 TapeStation (Agilent Technologies, USA).
RNAs were ligated with 3'RNA adapter, and followed by 5'adapter ligation. Subsequently, the adapter-ligated RNAs were subjected to RT-PCR and amplified with a low-cycle. Then the PCR products were size selected by PAGE gel according to instructions of NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Illumina, USA).

treatment_protocol: Podocytes were divided into three groups: a normal glucose group (NG,5.3 mM glucose), high glucose group (HG,30 mM glucose), and  mannitol group (MA,5.3 mM glucose + 24.7 mM mannitol;iso-osmolality control). After 48 h of continuous treatment, the cell culture supernatants were collected for extracellular vesicles isolation.

value: Conditionally immortalized mouse podocyte cell line

value: high glucose

tag: sample type

value: extracellular vesicles from podocytes culture supernatants


title: L1.23P

value: cartilage

value: Small RNA


title: DMSO treatment Day 6, biological rep 3

source_name: CB HSC, DMSO, day6, Biological 3

value: Cord Blood

value: DMSO 6 days

tag: cell type

value: Sorted CD34+CD90+ cells


title: L1.24P


title: L2.23P


title: CD34_Pos_Basophil_45

value: CD34 Pos Basophil

value: Live Lin- Sca1- FcεRI+ CD34+ cells

value: female


title: HG-podo-EVs-2


title: CD34_Pos_Basophil_46


title: CD34_Pos_Basophil_4


title: CD34_Pos_Basophil_41


title: CD34_Pos_Basophil_43


title: CD34_Pos_Basophil_42


title: MA-podo-EVs-2

source_name: MA-podo-EVs

value: mannitol


title: HG-podo-EVs


title: NG-podo-EVs-3

source_name: NG-podo-EVs

value: normal glucose


title: MA-podo-EVs-3


title: CD34_Pos_Basophil_40


title: NG-podo-EVs-2


title: NG-podo-EVs


title: CD34_Pos_Basophil_3


title: CD34_Pos_Basophil_38


title: CD34_Pos_Basophil_36


title: CD34_Pos_Basophil_37


title: CD34_Pos_Basophil_35


title: arid4b∆ Mesoderm H3K27me3

city: Boston

first: Jialiang

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

data_processing:
ChIP-seq reads were aligned to the mm10 reference genome by using Bowtie2 with default parameters.
Duplicate reads were removed using PICARD tools (http://picard.sourceforge.net).
MACS2 was used for ChIP-seq peaks calling MACS2 with following parameters (--nomodel --keep-dup 1 --extsize=146 -q 0.01).
Peaks were filtered using the consensus excludable ENCODE blacklist (The ENCODE Project Consortium, 2012).
MAnorm was used for determining differential ChIP-seq peaks between WT and KO as previously described100 the threshold of M-value 1 and FDR 0.01.
Genome_build: mm10

source_name: Mesoderm differentiated mouse ESCs

growth_protocol: mESCs were grown and directed to endoderm/mesoderm for 5 days.

extract_protocol:
Formaldehyde fixed lysates were clarified from sonicated cells and histone-DNA complexes were isolated with antibody. Chromatin Immunoprecipitation (ChIP) was performed as described previously (Kim et al., 2009; Das et al., 2014).
ChIP-seq libraries were prepared using NEBnext ChIP-seq library kit (E6240S) and NEBnext multiplex oligos fo Illumina sequencing (E7335S) according to manufacturer’s protocol. The concentrations of library cDNA samples were analyzed using Qubit. Sequencing was performed using Illumina HiSeq2000.

treatment_protocol: mESCs were crosslinked with 37% formaldehyde solution to a final concentration of 1% for 8 min at room temperature with gentle shaking; the reaction was quenched by adding 2.5M glycine to a final concentration of 0.125M

tag: genotype


title: arid4b∆ Mesoderm H3K27Ac


title: arid4b∆ Mesoderm H3K4me3


title: CD34_Pos_Basophil_34


title: WT Mesoderm H3K27Ac

value: WT


title: CD34_Pos_Basophil_32


title: arid4b∆ Mesoderm Input DNA


title: CD34_Pos_Basophil_39


title: CD34_Pos_Basophil_31


title: WT Mesoderm H3K27me3


title: WT Mesoderm Input DNA


title: arid4b∆ Endoderm H3K4me3

source_name: Endoderm differentiated mouse ESCs


title: MA-podo-EVs


title: WT Mesoderm H3K4me3


title: arid4b∆ Endoderm Input DNA


title: CD34_Pos_Basophil_44


title: CD34_Pos_Basophil_30


title: WT Endoderm H3K27Ac


title: CD34_Pos_Basophil_29


title: WT Endoderm H3K27me3


title: CD34_Pos_Basophil_2


title: CD34_Pos_Basophil_28


title: arid4b∆ Endoderm H3K27Ac


title: CD34_Pos_Basophil_26


title: CD34_Pos_Basophil_27


title: CD34_Pos_Basophil_33


title: L4.23P

tag: tissue


title: CD34_Pos_Basophil_24

tag: Sex


title: sRNA_ASFV_12H_2

city: Beijing

first: Jingrui

last: Li

address: Yuanmingyuan West Road No.2

institute: China Agricultural Universtiy

data_processing:
Basecalls performed using CASAVA
For RNA-seq, Illumina sequencing reads were mapped to pig (Sus scrofa v11.1) and ASFV (MK333180.1) genome by using Hisat2.1.0 with default settings for parameters. Kallisto_0.45.1 was used for quantifying abundance of each transcript. TPM values were calculated to measure the expression levels of gene’s transcripts. Differential expression analysis of genes was performed by Sleuth_0.30.0. Differentially expressed genes were filtered by the following parameters: TPM ≧ 20, fold-changed (FC) ≧ 2 and p-value < 0.05.
For small RNA-seq, sequencing adapters (AGATCGGAAGAGCACACGTCT) was removed by using cutadpt1.18. Reads were mapped to pig genome by using Bowtie2.2.5. The unmapped reads were collected and then mapped to ASFV genome. A brief annotation of PAMs encoded small RNAs were performed by using unitas_1.7.0. FeatureCount_1.6.4 was used for quantifying abundance of each miRNA. RPM values were calculated to measure the expression levels of each miRNA. Differential expression analysis of miRNAs was performed by DESeq2_1.22.2. Differentially expressed miRNAs were filtered by the following parameters: fold-changed (FC) ≧ 2 and p-value < 0.05.
Genome_build: Sus_scrofa_v11.1
Supplementary_files_format_and_content: Tab-delimited text file includes TPM values for each RNA-seq samples. Tab-delimited text file includes reads_count for each small RNA-seq samples.

source_name: porcine alveolar macrophages

extract_protocol:
The RNA was extracted from the infected cells at 0-, 6-, 12- and 24-hpi.
For strand specific RNA-seq, depletion of ribosomal RNA (rRNA) and RNA-seq libraries were constructed according to the manufacturer’s protocol of the Illumina kit. For small RNA-seq, small RNA-seq libraries were constructed according to the manufacturer’s protocol of the Illumina kit.

value: porcine alveolar macrophages

tag: breed

value: SPF

tag: infection

value: ASFV infection

tag: time point (hour post infection)


title: WT Endoderm Input DNA


title: WT Endoderm H3K4me3


title: arid4b∆ Endoderm H3K27me3


title: CD34_Pos_Basophil_23

tag: strain


title: CD34_Pos_Basophil_25


title: arid4b∆ Mesoderm Rep 3

data_processing:
RNA-seq reads were aligned to the reference mouse genome mm10 using STAR with default parameters.
Aligned reads were counted in the genomic transcripts annotations from GenomicFeatures, using Rsamtools (Morgan M, 2016).
DESeq2 were used for differentially expressed gene analysis was performed by using, with the threshold at adjusted P-value 0.01 and fold-change 2.
Genome_build: mm10

extract_protocol:
Cells were collected and resuspended in Trizol (Thermo, 15596018). RNA was extracted using Qiagen RNeasy plus kits according to provided protocols. Genomic DNA was eliminated in column during RNA extraction using DNase (Qiagen, 79254). The quality of the RNA samples was tested on Agilent BioAnalyzer.
Libraries were prepared using NEB reagents (NEBnext ultra directional RNA library prep kit (E7420S), NEBnext rRNA depletion kit (E6310S), NEBnext multiplex oligos fo Illumina sequencing (E7335S)). The concentrations of library cDNA samples were analyzed using Qubit. Sequencing was performed using Illumina HiSeq2000.


title: CD34_Pos_Basophil_21


title: CD34_Pos_Basophil_22


title: WT Mesoderm Rep 3


title: CD34_Pos_Basophil_1


title: WT Mesoderm Rep 2


title: CD34_Pos_Basophil_19


title: arid4b∆ Endoderm Rep 3


title: CD34_Pos_Basophil_18


title: CD34_Pos_Basophil_17


title: WT Mesoderm Rep 1


title: CD34_Pos_Basophil_16


title: CD34_Pos_Basophil_15


title: arid4b∆ Endoderm Rep 2


title: WT Endoderm Rep 2


title: arid4b∆ Endoderm Rep 1


title: CD34_Pos_Basophil_13


title: CD34_Pos_Basophil_14


title: WT Endoderm Rep 3


title: WT Endoderm Rep 1


title: naive-L-R3: CX3CR1Low macrophage naive replicate 3

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11. Only sequences at least 25 nt in length were considered for further analysis and the 5 first bases were trimmed following library manufacturer’s instructions.
STAR version 2.5.0a, with default parameters, was used for alignment on the reference genome.
Genes were counted using featureCounts version 1.4.6-p3 [3] from Subreads package (parameters: -t exon -g gene_id -s 1).
Count data were analyzed using R version 3.4.3 and the Bioconductor package DESeq2 version 1.18.1. The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between the four biological conditions. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with an adjusted p-value lower than 0.05 were considered differentially expressed. Count data were transformed using Variance Stabilizing Transformation (VST) to perform samples clustering and PCA plot.
Genome_build: Mus musculus GRCm38_87 from Ensembl version 87
Supplementary_files_format_and_content: Normalized counts from DESeq2

source_name: Bladder macrophage

growth_protocol: Samples were obtained from the bladder of naïve and 6 weeks post-infected (uropathogenic E coli) female C57BL/6J mice. Biological replicates were generated from a pool of 10 mice per sample. Macrophage subsets were FACS-purified into 350 μl of RLT plus buffer (QIAGEN) and β-mercaptoethanol.

extract_protocol:
Total RNA was extracted using the RNAeasy micro kit (QIAGEN) following the manufacturer’s instructions
Directional libraries were prepared using the Smarter Stranded Total RNA-Seq kit- Pico Input Mammalian following manufacturer’s instructions (Clontech, 635005). The quality of all libraries was assessed with the DNA-1000 kit (Agilent) on a 2100 Bioanalyzer and quantification was performed with Quant-It assays on a Qubit 3.0 fluorometer (Invitrogen). Clusters were generated for the resulting libraries, with Illumina HiSeq SR Cluster Kit v4 reagents. Sequencing was performed with the Illumina HiSeq 2500 system and HiSeq SBS kit v4 reagents. Runs were carried out over 65 cycles, including seven indexing cycles, to obtain 65-bp single-end reads. Sequencing data were processed with Illumina Pipeline software (Casava version 1.9).

treatment_protocol: We used the non-fluorescent uropathogenic E coli strain UTI89. To allow expression of type 1 pili, necessary for infection, bacteria cultures were grown statically in Luria-Bertani broth medium for 18 hours at 37°C. Adult female mice were anesthetized by injection of 100 mg/kg ketamine and 5 mg/kg xylazine, and infected via catheterization with 10^7 counting forming units (CFU) of UPEC strain UTI89. 6 weeks post-infection, mice had cleared infection and were  sacrificed by carbon dioxide inhalation.

value: Female

value: Bladder

value: Macrophage


title: naive-L-R4: CX3CR1Low macrophage naive replicate 4


title: arid4b∆ Mesoderm Rep 1


title: CD34_Pos_Basophil_20


title: CD34_Neg_Basophil_9

value: CD34 Neg Basophil

value: Live Lin- Sca1- FcεRI+ CD34- cells


title: CD34_Pos_Basophil_12


title: naive-H-R4: CX3CR1High macrophage naive replicate 4


title: CD34_Pos_Basophil_11


title: naive-L-R1: CX3CR1Low macrophage naive replicate 1


title: CD34_Neg_Basophil_7


title: naive-H-R3: CX3CR1High macrophage naive replicate 3


title: CD34_Neg_Basophil_5


title: CD34_Neg_Basophil_6


title: naive-H-R2: CX3CR1High macrophage naive replicate 2


title: CD34_Neg_Basophil_4


title: CD34_Neg_Basophil_47


title: arid4b∆ Mesoderm Rep 2


title: naive-H-R1: CX3CR1High macrophage naive replicate 1


title: inf-L-R4: CX3CR1Low macrophage post-infection replicate 4


title: inf-L-R3: CX3CR1Low macrophage post-infection replicate 3


title: inf-L-R2: CX3CR1Low macrophage post-infection replicate 2


title: CD34_Neg_Basophil_43


title: CD34_Neg_Basophil_46


title: CD34_Neg_Basophil_44


title: CD34_Neg_Basophil_45


title: inf-L-R1: CX3CR1Low macrophage post-infection replicate 1


title: naive-L-R2: CX3CR1Low macrophage naive replicate 2


title: CD34_Neg_Basophil_8


title: inf-H-R3: CX3CR1High macrophage post-infection replicate 3


title: inf-H-R2: CX3CR1High macrophage post-infection replicate 2


title: CD34_Neg_Basophil_40


title: CD34_Neg_Basophil_42


title: CD34_Neg_Basophil_3


title: Vhl_H3K27Ac_ChIP_A

description: CRISPR-Vhl OPCs

source_name: Oligodendrocyte progenitor cells (OPCs)

value: epiblast stem cell derived OPCs

value: H3K27Ac (abcam4729, 9ug per ChIP

value: 5-20 million OPCs


title: Input_H3K27Ac_ChIP

description: CRISPR-Control OPCs


title: inf-H-R1: CX3CR1High macrophage post-infection replicate 1


title: CD34_Neg_Basophil_38


title: CD34_Neg_Basophil_37


title: CD34_Neg_Basophil_36


title: EYFP 11 Sp

description:
tot_counts.txt.gz
EYFP_11_Sp_19859_ATTCCT

data_processing:
Raw reads were analyzed for data quality using FastQC v0.11.5
Reads were then aligned to the reference genome using the annotation from Ensembl (version 88) with STAR aligner (v2.5.3a) using the option "--quantMode GeneCounts" for retrieving the gene counts.
Genome_build: GRCm38
Supplementary_files_format_and_content: csv file with raw read counts (only unique mapping reads)

source_name: Spleen

extract_protocol:
CD11c-eYFP+ cells and microglia were isolated from the brain of adult CD11c-eYFP mice or CX3CR1CreERT2-ROSA26 tdTomato mice respectively (13-14 weeks old) using Fluorescence Activated Cell Sorting. Brains were collected in cold HBSS buffer (w/o Ca2+ and Mg2+, Thermo Fisher Scientific #14175-053). The brain tissue was enzymatically dissociated using the Neural Tissue Dissociation Kit (P) (Miltenyi Biotec #130-092-628). The gentleMACS™ Dissociator with Heaters (Miltenyi Biotec #130-096-427) was used for mechanical dissociation steps following the Neural Tissue Dissociation Kit (P) for dissociation without heaters. The digested tissue was filtered twice with 70 µm and 40 µm filters washing with HBSS (w/ Ca2+ and Mg2+, Thermo Fisher Scientific #14025-092). Cells were separated from myelin and debris by 30% isotonic percoll gradient (GE Healthcare #17-0891-01) in Myelin Gradient Buffer (MGB). Samples were centrifuged at 950g for 30 min without acceleration nor brake. Cells were collected from the interface, washed once with FACS Stain Buffer (BD Biosciences #554656), and processed for FACS (no staining required) in a FACSAriaII sorter (BD Biosciences)
libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit v2 (Illumina, # RS-122-2101/2) according to the manufacturer's protocol. Briefly, from 2,4 to 147 ng of total RNA were used for poly(A)-mRNA selection using streptavidin-coated magnetic beads and were subsequently fragmented to approximately 300bp. cDNA was synthesized using SuperScript II reverse transcriptase (Invitrogen # 18064-014) and random primers. The second strand of the cDNA incorporated dUTP in place of dTTP. Double-stranded DNA was further used for library preparation. dsDNA was subjected to A-tailing and ligation of the barcoded Truseq adapters. All purification steps were performed with AMPure XP beads and eluted in 20 µl EB. Library amplification was performed by PCR on the size selected fragments using the primer cocktail supplied in the kit.
Final libraries were analyzed using Agilent DNA 1000 chip to estimate the quantity and check size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit (KapaBiosystems #KK4835) prior to amplification with Illumina’s cBot. Libraries were sequenced Single Reads, 50nts on the Illumina HiSeq 2500.

value: Spleen

tag: age

value: 13-14 week old

value: male


title: EYFP 14 Sp

description:
tot_counts.txt.gz
EYFP_14_Sp_19858_CGTACG


title: CD34_Neg_Basophil_34

value: female


title: inf-H-R4: CX3CR1High macrophage post-infection replicate 4


title: EYFP 13 Sp

description:
tot_counts.txt.gz
EYFP_13_Sp_19857_GATCAG


title: CD34_Neg_Basophil_35


title: CD34_Neg_Basophil_32


title: EYFP 11 Ipsi

description:
tot_counts.txt.gz
EYFP_11_Ipsi_19852_ATCACG

value: Brain Ipsilateral hemisphere

tag: disease state

value: ischemic


title: D04

description:
tot_counts.txt.gz
D04_19854_TAGCTT


title: CD34_Neg_Basophil_41


title: CD34_Neg_Basophil_31


title: CD34_Neg_Basophil_30


title: EYFP #19

description:
tot_counts.txt.gz
EYFP_19_19853_ACTTGA


title: CD34_Neg_Basophil_2


title: CD34_Neg_Basophil_39


title: CD34_Neg_Basophil_29


title: CD34_Neg_Basophil_27


title: CD34_Neg_Basophil_26


title: CX3CR1 4 IPSI

description:
tot_counts.txt.gz
CX3CR1_4_IPSI_19851_CCGTCC

value: CX3CR1+ microglia


title: CX3CR1 13 IPSI

description:
tot_counts.txt.gz
CX3CR1_13_IPSI_19849_TGACCA


title: CX3CR1 14 IPSI

description:
tot_counts.txt.gz
CX3CR1_14_IPSI_19850_CAGATC


title: CD34_Neg_Basophil_25


title: CX3CR1 17 CTL

description:
tot_counts.txt.gz
CX3CR1_17_CTL_19847_GTGAAA

source_name: Brain Control

value: Brain

value: control


title: CX3CR1 11 IPSI

description:
tot_counts.txt.gz
CX3CR1_11_IPSI_19848_CGATGT


title: CD34_Neg_Basophil_24


title: CD34_Neg_Basophil_33


title: E05

description:
tot_counts.txt.gz
E05_19855_GGCTAC


title: EYFP 12 Sp

description:
tot_counts.txt.gz
EYFP_12_Sp_19856_TTAGGC


title: CX3CR1 16 CTL

description:
tot_counts.txt.gz
CX3CR1_16_CTL_19846_CTTGTA


title: CD34_Neg_Basophil_22