title: IL17raDermoCre_pos2_whole lung

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

data_processing:
10x Cellranger V.3.1.0 and V.2.1.0 were used to generate Fastq files, perform alignment,filtering,barcode counting,UMI counting and aggregation.
Seurat V.2.3.1 and V.3.0.0 for scRNA QC and further analysis

source_name: Lung

growth_protocol: All mice were obtained from Jax farm and maintained in specific pathogen-free rooms at Tulane University. Experiment were preformed when mice were at age of six to ten weeks

extract_protocol:
mRNA was extracted from lung single cell suspension using the 10X Genomics Chromium™ Single Cell A Chip Kit
Library construction was performed according to 10x Genomics Chromium™ Single Cell 3' Reagent Kit v2 protocol
single cell gene expression RNA-seq

treatment_protocol: ①immunization with OmpX + LTA1 or heat killed Klebsiella pneumoniae (ATCC 43816) twice 3 weeks apart. ②immunization with OmpX + LTA1 twice 3 weeks apart, and 1 more week later infected with 10e4 CFU K1 strain. Those mice were euthanized for lung tissue extraction 4 hours post infetion.

value: IL17raDermoCre mice

tag: time point of infection

value: K1 KP396_4hours post infection


title: IL17raDermoCre_pos3_whole lung

status: Public on Oct 21 2020

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain


title: IL17raDermoCre_neg1_whole lung


title: IL17raDermoCre_neg3_whole lung


title: WT input

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: fragmented DNA

library_source: genomic

data_processing:
Basecalls were performed using  bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC mm9 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC mm9 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

molecule: genomic DNA

source_name: embryonic stem cell

growth_protocol: ESCs were grown in N2B27 media supplemented with MEK inhibitor, GSK3 inhibitor, and LIF (2i/LIF).

extract_protocol:
RNA was extracted using Trizol reagent (Life technologies). RNAse free DNaseI (Sigma) was used to eliminate DNA contamination and the treated RNA was purified with RNeasy mini kit (Qiagen).
For ChIP, ESCs were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin were sonicated using a E220 focused-ultrasonicator (Covaris). 100 µg sheared chromatin, 5 µg antibody, and 50 µl protein A/G beads (Santa Cruz) were used for each immunoprecipitation. Immunoprecipitated DNA were purified after washing, eluting, reverse-crosslinking, and submitted for library preparation.
PRO-seq was performed following a published protocol (Mahat et al., 2016a) with minor modifications. All 4 biotinylated nucleotides were used at 25 μM each final concentration for the run-on reaction. RPPH (NEB) was used to remove the 5’ RNA cap. Libraries were size selected using a 2% agarose gel on a Pippin HT programmed to elute 140–350 bp.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-seq libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg of total RNA was used as starting material. Libraries were validated using the Agilent DNA 1000 Kit.

treatment_protocol: EB differentiation was performed using the hanging drop method. For NPC differentiation, cells were seeded on gelatinized dish in 2i/LIF media for a day. The two inhibitors and LIF were then withdrawn from the media and cells were kept in plain N2B27 media for 7 days. Cells were then dissociated and seeded in ultra-low attachment plates (Sigma) in N2B27 media containing 10ng/ml EGF (Peprotech) and 10ng/ml FGF2 (Peprotech) for 3 days to form neurospheres. Floating aggregates (neurospheres) were then seeded on gelatinized plates in N2B27 containing 10ng/ml EGF and 10ng/ml FGF2 for 2-4 days. Attached cells were dissociated and seeded again on gelatinized plates in N2B27 containing 10ng/ml EGF and 10ng/ml FGF2. Cells were passaged one more time and harvested for different assays.

tag: cell type

value: embryonic stem cell

tag: cell line

tag: genotype/variation

value: Wildtype/WT


title: IL17raDermoCre_neg2_whole lung


title: DMSO_AF10

description: fragmented DNA

tag: treatment

value: DMSO

tag: chip antibody

value: AF10 (Santa Cruz 53156)


title: DOT1LCI_DMSO_PRO

description: nuclear RNA

data_processing:
Library strategy: PRO-seq
Basecalls were performed using  bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC mm9 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC mm9 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

value: DOT1L catalytic inactive/DOT1LCI


title: DOT1LKO_KL2_PRO

description: nuclear RNA

value: DOT1L knockout/DOT1LKO


title: DOT1LCI_KL2_PRO

description: nuclear RNA


title: IL17raDermoCre_pos1_whole lung


title: B6_OMPxvac_Lung_CD4pos_2

value: without infection


title: B6_OMPxvac_Lung_CD4pos_1


title: WT_KL2_PRO

description: nuclear RNA


title: DOT1LCI_KL2_Pol2

description: fragmented DNA

value: RNA Pol II (Cell signaling Technology 14958)


title: DOT1LKO_KL2_Pol2

description: fragmented DNA


title: DOT1LKO_DMSO_Pol2

description: fragmented DNA


title: LSEC_H3K4me3

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

country: Germany

institute: Medical Faculty Mannheim/University of Heidelberg

data_processing:
Visualization of raw reads was done using FastQC, trimmed of the raw reads using Trimmomatic (Bolger et al. 2014), for the  min length 9 bp , maximun length 71 bp and from the start of the read 13 bp
After sequencing, high quality (Q>30) trimmed fastq files were mapped to the mouse reference genome mm10 (UCSC assembly) using the default settings of STAR
The MarkDuplicates.jar from Picard 1.136 was used to remove PCR artefacts
Peaks overlapping black list defined by ENCODE were discarded by the help of Bedtools v2.15 (intersect -wa)
Mapped bam files were merged by using bamtools merge. Merged bam files were converted to bigwig format by BamCoverage function of deepTools2 (-b 20 -smooth 40 -e 150 --normalizeUsing RPGC --effectiveGenomeSize 2150570000).

source_name: Liver Sinusoidal Endothelial Cell (LSEC)

extract_protocol:
Livers were perfused in situ via the portal vein with a 0.05% collagenase/amino acid/saccharide solution, dissected, mechanically disrupted, pooled from three mice, digested at 38 °C in collagenase/Gey’s balanced salt solution and filtered through a 250 µm mesh. Non-parenchymal cells were separated by a 19.3 % Nycodenz  gradient. Afterwards, LSEC were isolated by magnetic-activated cell sorting (MACS) using anti-CD146 MicroBeads according to the manufacturers’ instructions (Miltenyi Biotech). Purity of LSEC isolates was confirmed by flow cytometry and showed at least 95 % positivity for CD31 and/or Stabilin-2.
Chromatin of 1 million LSEC (approx. 1 millions) was immunoprecipitated with anti-H3K4me3 (ab8580) or anti-H3K27Ac (ab4729) according to the protocol described in (PMID:31024170) After DNA purification, NGS libraries were constructed using the TruSeq ChIP library preparation kit (#IP-202-1024) according to manufacturer’s recommendation. Libraries were sequenced in NextSeq550 platform using V2.5 chemistry

value: wt

tag: antibody

value: anti-H3K4me3 (ab8580)


title: WT_DMSO_PRO

description: nuclear RNA


title: DOT1LKO_DMSO_PRO

description: nuclear RNA


title: LSEC_input


title: DOT1LCI_DMSO_Pol2

description: fragmented DNA


title: B6_Naive_Spleen_CD4pos_1

source_name: Spleen


title: LSEC_AT_GATA4_KO3

data_processing:
Visualization of raw reads was done using FastQC, trimmed of the raw reads using Trimmomatic (Bolger et al. 2014), for the  min length 15 bp , maximun length 70 bp and from the start of the read 17 bp
ATAC-Seq reads were mapped with bowtie2 to mm10 mouse genome. Samtools view (-F 1804 -f2) was used to remove unmapped, mate unmapped, not primary aligned reads.
The MarkDuplicates.jar from Picard 1.136 was used to remove PCR artefacts.
Peak calling was performed with MACS14 (p1e5 --nomodel and --shiftsize 100).
Peaks overlapping black list defined by ENCODE were discarded by the help of Bedtools v2.15 (intersect -wa)
Mapped bam files were merged by using bamtools merge. Merged bam files were converted to bigwig format by BamCoverage function of deepTools2 (-b 20 -smooth 40 -e 150 --normalizeUsing RPGC --effectiveGenomeSize 2150570000).
Genome_build: mm10
Supplementary_files_format_and_content: BigWig

extract_protocol:
Livers were perfused in situ via the portal vein with a 0.05% collagenase/amino acid/saccharide solution, dissected, mechanically disrupted, pooled from three mice, digested at 38 °C in collagenase/Gey’s balanced salt solution and filtered through a 250 µm mesh. Non-parenchymal cells were separated by a 19.3 % Nycodenz  gradient. Afterwards, LSEC were isolated by magnetic-activated cell sorting (MACS) using anti-CD146 MicroBeads according to the manufacturers’ instructions (Miltenyi Biotech). Purity of LSEC isolates was confirmed by flow cytometry and showed at least 95 % positivity for CD31 and/or Stabilin-2.
LSEC cells were isolated from three 1 year old control and GATA4 knockout mice, followed by ATAC-seq, using a modified protocol from (PMID:28846090). Briefly, 50.000 fresh-isolated LSEC were incubated in 50 μL cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal CA-630) for 3 minutes. The lysis was stopped by adding with 1 ml resuspension buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) and the nuclei were pelleted by 10 minute centrifugation (500 x g, 4°C). Isolated nuclei were incubated in transposition reaction mix containing 2.5 µl Nextera Tagment DNA Enzyme TDE (Illumina #15027916) in 47.5 µl 2x transposition buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2, 20% Dimethylformamide) for 30 min at 37 °C. Immediately following the transposition reaction, purification was carried out using ChIP DNA Clean and Concentrator Kit (Zymo #D5205). Sequencing libraries were performing using NEB Next High-Fidelity 2x PCR Master Mix (New England Biolabs #M0541S) and Nextera Index Kit (Illumina #15055290). Magnetic bead purification with two-sided size selection using undiluted Agencourt AMPure XP Beads (Beckman Coulter #A63881) ensured library sizes between 150 and 1000 bp. The quality of the libraries was analyzed by Bioanalyzer High Sensitivity DNA analysis kit (Agilent #5067-4626).


title: LSEC_H3K27ac

value: anti-H3K27Ac (ab4729)


title: B6_HKdKPvac_Lung_CD4pos_1


title: LSEC_AT_GATA4_ctr3


title: LSEC_AT_GATA4_KO1


title: LSEC_AT_GATA4_ctr2


title: LSEC_AT_GATA4_ctr1


title: B6_Naive_Spleen_CD4pos_2


title: B6_HKdKPvac_Lung_CD4pos_2


title: DO1LKO_NPC_RNA2

description: total RNA


title: DO1LKO_NPC_RNA1

description: total RNA


title: DO1LCI_NPC_RNA2

description: total RNA


title: DO1LCI_NPC_RNA1

description: total RNA


title: DOT1LKO_NPC_Pol2

description: fragmented DNA


title: WT_NPC_Pol2

description: fragmented DNA


title: WT_KL2_Pol2

description: fragmented DNA


title: WT_DMSO_Pol2

description: fragmented DNA


title: P1 SC3

type: RNA

city: Palo Alto

first: Suzanne

last: Tharin

state: CA

address: 453 Quarry Road

department: Neurosurgery

institute: Stanford University School of Medicine

description:
test
total microRNA
replicate 3

data_processing:
qPCR data were analyzed using the comparative CT method. Ct values were normalized to the mean of endogenous controls. Normalized Ct values were averaged across replicates for each subtype, and then RQ was calculated using the mean of the normalized Ct values
Relative Quantity (RQ) was calculated for each of the miRNAs, with RQ = 2-ΔΔCt; RQs are given for those microRNAs for which there were triplicate detectable values available

source_name: subcerebral projection neurons

extract_protocol: microRNA was extracted from purified projection neuron cell bodies using the Ambion miRVana microRNA isolation kit (Ambion, Austin, TX) according to the manufacturer’s instructions

tag: tissue

value: subcerebral projection neurons

tag: age

value: postnatal day 1


title: P1 SC1

description:
test
total microRNA
replicate 1


title: P1 SC2

description:
test
total microRNA
replicate 2


title: P1 CPN3

description:
control
total microRNA
replicate 3

source_name: callosal projection neurons

value: callosal projection neurons


title: WT_NPC_RNA2

description: total RNA


title: P1 CPN2

description:
control
total microRNA
replicate 2


title: WT_NPC_RNA1

description: total RNA


title: LSEC_AT_GATA4_KO2


title: DO1LKO_EB_RNA2

description: total RNA


title: DO1LCI_EB_RNA2

description: total RNA


title: DO1LCI_EB_RNA1

description: total RNA


title: P1 CPN1

description:
control
total microRNA
replicate 1


title: Tonsil 71

city: Durham

first: Micah

middle: A

last: Luftig

state: NC

address: 213 Research Dr, DUMC Box 3054

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

data_processing:
Illumina HiSeq 3000/4000
cellranger v.2.0.0 (mkfastq); alignment was performed against the human genome (hg38)
Seurat v.3.1.5 (R); filtered out cells with <200 or >65000 unique RNA molecules and cells with >5% mitochondrial gene expression.
TAR of TSV, MTX

molecule: polyA RNA

organism: Homo sapiens

source_name: Tonsillar cells

growth_protocol: Tonsillar B cells were isolated from discarded, anonymized tonsillectomies from the Duke Biospecimen Repository and Processing Core (BRPC; Durham, NC). Tonsil tissue samples were manually disaggregated, filtered through a cell strainer, and isolated by layering over a cushion made from Histopaque-1077 (H8889; Sigma-Aldrich). Harvested lymphocytes were washed three times with FACS buffer (5% FBS in PBS) and stained for surface markers using: CD19-PE (363003, Biolegend, RRID: AB_2564125), IgD-FITC (348206, Biolegend, RRID: AB_10612567), CD38-APC (303510, Biolegend, RRID: AB_314362), CD83-BV421 (305324, Biolegend, RRID: AB_2561829), CXCR4-PeCy7 (560669, BD Biosciences, RRID: AB_1727435).

extract_protocol:
Each of the samples were prepared separately using the 10x Genomics Chromium controller
Standard library construction as specified by the manufacturer's protocols (v2 chemistry)
capture and single-cell indexing of total polyA mRNA

treatment_protocol: No additional treatments were applied after primary cell isolation

value: Tonsillar cells

tag: donor


title: WT_EB_RNA2

description: total RNA


title: Tonsil 70


title: Plasma B cells - Tonsil 100

data_processing:
Adaptor sequences were trimmed and mapped to hg38 using Bowtie2.
Reads were then filtered for duplicates.
The filtered reads for each sample were merged, and peak calling was performed by MACS2.
Genome_build: hg38

source_name: Tonsillar B cells

growth_protocol: Tonsillar B cells were isolated from discarded, anonymized tonsillectomies from the Duke Biospecimen Repository and Processing Core (BRPC; Durham, NC). Tonsil tissue samples were manually disaggregated, filtered through a cell strainer, and isolated by layering over a cushion made from Histopaque-1077 (H8889; Sigma-Aldrich). Harvested lymphocytes were washed three times with FACS buffer (5% FBS in PBS) and stained for surface markers using: CD19-PE (363003, Biolegend, RRID: AB_2564125), IgD-FITC (348206, Biolegend, RRID: AB_10612567), CD38-APC (303510, Biolegend, RRID: AB_314362), CD83-BV421 (305324, Biolegend, RRID: AB_2561829), CXCR4-PeCy7 (560669, BD Biosciences, RRID: AB_1727435). For flow cytometry analysis, stained cells were analyzed on a BD FACS Canto II and sorted on a MoFlo Astrios Cell Sorter at the Duke Cancer Institute Flow Cytometry Shared Resource (Durham, NC) using the scheme described above in the summary.

extract_protocol: Three biological replicates of sorted CD19+ B cells (naïve, memory, GC DZ, GC LZ, and plasma cells) were isolated and processed for ATAC–seq as described in Buenrostro JD, Wu B, Chang HY, Greenleaf WJ. 2015. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biol 109:21 29 1-21 29 9. Samples were run on 2 lanes of the Illumina 4000 HiSeq. ATAC-seq data was processed as previously described.

value: tonsillar plasma B cell


title: DO1LKO_EB_RNA1

description: total RNA


title: WT_EB_RNA1

description: total RNA


title: DOT1LKO2_ESC_Pol2

description: fragmented DNA


title: DOT1LKO1_ESC_Pol2

description: fragmented DNA


title: Plasma B cells - Tonsil 90


title: Plasma B cells - Tonsil 89


title: Dark Zone GC B cells - Tonsil 100

value: tonsillar dark zone germinal center B cells


title: Dark Zone GC B cells - Tonsil 89


title: Dark Zone GC B cells - Tonsil 90


title: Light Zone GC B cells - Tonsil 100

value: tonsillar light zone germinal center B cells


title: DOT1LCI2_ESC_Pol2

description: fragmented DNA

value: embryonic stem cell


title: DOT1LKO2_ESC_RNA4

description: total RNA


title: WT_ESC_Pol2_1

description: fragmented DNA

value: Wildtype/WT


title: DOT1LCI1_ESC_Pol2

description: fragmented DNA


title: DOT1LKO1_ESC_RNA4

description: total RNA


title: Light Zone GC B cells - Tonsil 90


title: Light Zone GC B cells - Tonsil 89


title: DOT1LKO1_ESC_RNA3

description: total RNA


title: Memory B cells - Tonsil 90

value: tonsillar memory B cell


title: DOT1LKO2_ESC_RNA3

description: total RNA


title: DOT1LCI1_ESC_RNA2

description: total RNA

value: DOT1L catalytic inactive/DOT1LCI


title: Naïve B cells - Tonsil 100

value: tonsillar naive B cell


title: Memory B cells - Tonsil 89


title: DOT1LCI2_ESC_RNA1

description: total RNA


title: Naïve B cells - Tonsil 90


title: DOT1LCI1_ESC_RNA1

description: total RNA


title: WT_ESC_RNA4

description: total RNA


title: WT_ESC_RNA3

description: total RNA


title: WT_ESC_Pol2_2

description: fragmented DNA


title: RNA_R1881_24h, rep2

first: Zhong

last: Chen

address: 905 S. LaSalle Street

department: Pathology

institute: Duke University

description: Biological replicate 2

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie-2.1 with default parameters. And only uniquely mapped reads were remained for further analysis.
RNA-seq process: The RNA-seq data was aligned by TopHat 2.0. Reads were mapped to the reference genome build (hg19). Read counts were calculated using Partek 7.0 with default parameters. The reads count in exon regions was used to estimate the expression level of the genes.
peaks were called using Homer (v4.10.4) with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: For ChIP-seq, bedgraph files were generated using bedtools, scores represent peaks genomic coverage.
For RNA-seq, tab-delimited text files include read counts of all genes for each Sample.

source_name: human esophagus

growth_protocol: The human ESCC cell lines (KYSE series) were maintained in RPMI 1640 supplemented with 10% fetal bovine serum.

extract_protocol:
For ChIP-seq, cells were crosslinked with 1% formaldehyde for 10 min on horizontal rotator at room temperature and cell pellets were collected and subjected to sonication. The sheared chromatin was then diluted and immunoprecipitated with 4 µg of specific antibodies at 4°C overnight. After washing, chromatin complexes were eluted with elution buffer and crosslinking was reversed at 65°C overnight. DNA fragments were purified with the QIAquick PCR purification kit. For RNA-seq, total RNA was isolated using an RNeasy kit (QIAGEN). Next, mRNA was enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module. After two rounds of processes, the  mRNA was recovered for library generation.
For ChIP-seq, the eluted ChIP DNA was used for library preparation with NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina according to the manufacturer’s protocol. The library was ampliﬁed with 12 PCR cycles and prepared with gel-based size selection. For RNA-seq, the library preparation was performed with NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina following the manufacturer’s instructions. The cDNA molecules were amplified by 8 cycles of PCR. Non-size selection libraries were then sequenced for using Illumina HiSeq 4000 at the Duke sequencing core.

treatment_protocol: For ChIP or RNA-seq experiments, ESCC cells were maintained in phenol red-free RPMI 1640 medium with 5% charcoal-stripped FBS for 3 days, and then treated with vehicle and AR ligands for the indicated time.

value: ESCC cell line KYSE410

tag: disease state

value: esophageal squamous cell carcinoma


title: RNA_R1881_24h, rep1

description: Biological replicate 1


title: Memory B cells - Tonsil 100


title: RNA_vehicle, rep1

description: Biological replicate 1

value: Vehicle


title: DOT1LKO2_ESC_RNA1

description: total RNA

value: DOT1L knockout/DOT1LKO


title: WT_ESC_RNA1

description: total RNA


title: DOT1LKO1_ESC_RNA1

description: total RNA


title: AR_ChIP_R1881, rep3

description:
Biological replicate 3
410_N20_r1881.ucsc.bedGraph.gz

value: AR (N20) from Santa Cruz Biotechnology (Santa Cruz, CA)


title: AR_ChIP_R1881, rep4

description:
Biological replicate 4
410_N20_r1881.ucsc.bedGraph.gz


title: RNA_vehicle, rep2

description: Biological replicate 2


title: DOT1LKO_H3K79me3

description: fragmented DNA


title: AR_ChIP_R1881, rep2

description:
Biological replicate 2
410_N20_r1881.ucsc.bedGraph.gz


title: WT_H3K79me3

description: fragmented DNA


title: DOT1LCI2_ESC_RNA2

description: total RNA


title: Naïve B cells - Tonsil 89


title: AR_ChIP_R1881, rep1

description:
Biological replicate 1
410_N20_r1881.ucsc.bedGraph.gz


title: WT_ESC_RNA2

description: total RNA


title: AR_ChIP_vehicle, rep4

description:
Biological replicate 4
410_N20_v.ucsc.bedGraph.gz


title: RNA_R1881_4h, rep1

description: Biological replicate 1


title: AR_ChIP_vehicle, rep3

description:
Biological replicate 3
410_N20_v.ucsc.bedGraph.gz


title: DOT1LKO2_H3K79me2

description: fragmented DNA

value: H3K79me2 (Homemade, #38)


title: DOT1LKO1_H3K79me2

description: fragmented DNA


title: DOT1LCI_H3K79me3

description: fragmented DNA


title: DOT1LCI2_H3K79me2

description: fragmented DNA


title: AR_ChIP_vehicle, rep2

description:
Biological replicate 2
410_N20_v.ucsc.bedGraph.gz


title: DOT1LKO2_RNA2

description: total RNA


title: AR_ChIP_vehicle, rep1

description:
Biological replicate 1
410_N20_v.ucsc.bedGraph.gz


title: RNA_R1881_4h, rep2

description: Biological replicate 2


title: DOT1LKO1_ESC_RNA2

description: total RNA


title: 0144-V05

city: Oxford

first: Daniel

last: O'Connor

state: Oxfordshire

address: Churchill Hospital

department: Paediatrics

country: United Kingdom

institute: University of Oxford

description:
Human infant whole blood RNA-sequencing data
ribosomal and globin RNA depleted

data_processing:
Human RNA-sequencing alignment against Homo sapiens genome build GRCh38 (https://ccb.jhu.edu/software/hisat2/index.shtml), using HISAT2 version 2.0.5.
Gene counting was conducted using the HTSeq version 0.9.1, utilizing human gene annotation gtf (General Transfer Format) version GRCh38.88 (www.ensembl.org).
Computational depletion of ribosomal RNA using SortMeRNA (version 2.1).
The R (version 3.4.4) software environment for statistical computing was used. R packages: edgeR, used TMM  (version 3.20.9), limma used voom function (version 3.34.9)

source_name: Whole blood

extract_protocol:
Total RNA was extracted using the Blood RNA Kit (PreAnalytiX, Switzerland), using the automated protocol (QIAcube instrument, QIAGEN, Germany).
The ribodepleted and globin depleted fraction was selected from the total RNA using Ribo-ZeroTM Gold rRNA removal Kit (Illumina, USA). RNA was converted to cDNA, second-strand cDNA synthesis incorporated dUTP. The cDNA was end-repaired, A-tailed and adapter-ligated and prior to amplification, samples underwent uridine digestion (to ensure strand-specific sequencing)
The prepared libraries were size selected, multiplexed and quality controlled before 100bp paired-end sequencing (HiSeq4000). Sequencing was conducted at the Wellcome Trust Centre for Human Genetics (Oxford, UK).

treatment_protocol: Peripheral blood (up to 1.5ml) was collected into a reduced volume PAXgeneTM RNA stabilisation reagent (ratio of blood to PAXgene equivalent to manufacturer’s specifications).

value: Whole blood

tag: vaccination status

tag: study group

value: Test

tag: Sex

value: Male

tag: post-vaccination log10 (menb sba titres)

tag: post-vaccination fever

value: Fever


title: 0107-V05


title: 0073-V05


title: 0087-V04

value: Pre-vaccination

value: Female


title: 0131-V05

value: Control


title: WT_H3K79me2_2

description: fragmented DNA

value: embryonic stem cell

value: Wildtype/WT


title: Breast_n3

city: Sherbrooke

first: Michelle

middle: S

last: Scott

state: Quebec

address: 3201 Jean Mignault

department: Biochemistry

country: Canada

institute: University of Sherbrooke

description: cDNA library generated with TGIRT

data_processing:
Fastq files were checked for quality using FastQC and trimmed using Trimmomatic (Bolger et al. 2014) (parameters: TRAILING:30, LEADING:30, MINLEN:20) to remove Illumina sequencing adapters and portions of reads of low quality.
Reads were aligned using STAR (v2.6.1a) with parameters optimized for the alignment of multi-mapped reads (parameters: --outFilterScoreMinOverLread 0.3, --outFilterMatchNminOverLread 0.3, --outFilterMultimapNmax 100, --winAnchorMultimapNmax 100, --alignEndsProtrude 5, ConcordantPair). The reference genome used was hg38 and the reference annotation to build the STAR alignment index was taken from Ensembl (v87).
Gene expression estimation in transcript per million (TPM) was produced with CoCo (v 0.2.1p4) to optimize the quantification of small non-coding RNAs (parameters: -c both). The annotation provided to CoCo was the Ensembl (v87) annotation bonified with the 115 new sncRNA gene entries as well as the tRNAs from GtRNAdb (PMID: 26673694) and modified through the use of the CoCo correct annotation module (default parameters).
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated value (.csv) file containing the gene id and abundance in the sample (in TPM) for all the genes detected in the TGIRT-Seq.

source_name: Breast tissue

extract_protocol:
Total RNA was extracted using Qiagen’s RNEasy minikit according to their protocol with on-column DNAse 1 digestion then evaluated on an Agilent Bioanalyser.
5 µg of the RNA sample, to which a 1ul spike-in of ERCC EXfold mix 1 was added (Thermofisher Scientific) were ribo-depleted by using a RiboZero Gold (Human/Mouse/Rat) kit (Illumina). 50ng of the resulting sample were then fragmented using an NEBNext Magnesium RNA Fragmentation Module (New England Biolabs) at 94°C for 2 or 3min (depending on RIN) and treated with T4 polynucleotide kinase (Epicentre) to remove 3′ phosphates and 2′, 3′ cyclic monophosphates, which impede TGIRT template switching (Mohr et al. 2013). RNAs were purified after ribo-depletion, fragmentation, and dephosphorylation by using a modified version of the Zymo RNA Clean & Concentrator protocol (addition of eight sample volumes of ethanol to increase retention of very small RNA species). The recovered RNA was used for cDNA synthesis via TGIRT template switching with 1 μM TGIRT-III RT (InGex, LLC) for 15 min at 60°C, as previously described (Qin et al. 2016). The template-switching reaction seamlessly links the complement of an Illumina Read 2 sequencing primer-binding site (R2R DNA) to the 5′ end of the cDNA during cDNA synthesis, after which a DNA oligonucleotide containing the complement of an Illumina Read 1 sequencing primer-binding site (R1R DNA) is ligated to the cDNA 3′ end by using Thermostable 5′ AppDNA/RNA Ligase (New England Biolabs). Ligated cDNAs with R1R and R2R sequencing adapters on either end were then amplified for 12 cycles of PCR (Qin et al. 2016; initial denaturation at 98°C for 5 sec, followed by cycles of 98°C for 5 sec, 65°C for 10 sec, 72°C for 10 sec), during which Illumina capture and index sequences were added. Libraries were size-selected by using Ampure XP beads (Beckman-Coulter), evaluated on an Agilent 2100 Bioanalyzer, and quantified using Qubit 2.0 fluorometer (Invitrogen) as was the final equimolar pool of the TGIRT-seq libraries. They were then sequenced using the Illumina NextSeq 500 instrument (75-nt paired-end reads) with the Illumina NextSeq 500/550 High Output Kit v2 (150 Cycles).

value: Breast tissue


title: WT_H3K79me1_1

description: fragmented DNA

value: H3K79me1 (Homemade, #36)


title: 0066-V05


title: DOT1LKO2_H3K79me1

description: fragmented DNA


title: 0052-V05


title: WT_H3K79me2_1

description: fragmented DNA


title: DOT1LCI1_H3K79me2

description: fragmented DNA

value: DOT1L catalytic inactive/DOT1LCI


title: 0060-V05


title: 0016-V05


title: DOT1LCI1_H3K79me1

description: fragmented DNA


title: WT_H3K79me1_2

description: fragmented DNA


title: 8963-V04


title: 0027-V03


title: 0139-V05


title: 8955-V05


title: DOT1LKO1_H3K79me1

description: fragmented DNA


title: DOT1LCI2_H3K79me1

description: fragmented DNA


title: 6-14A-Young [RNA-seq]

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
RNA-seq tags reads were aligned to the human reference genome (assembly GRCh37.75/hg19) using STAR with default parameters. Alignments with a mapping score <10 were discarded using SAMtools and alignments mapped to mitochondria and chrUn (contigs that cannot be confidently placed on a specific chromosome) were removed using BEDtools.
FeatureCounts was used to generate a matrix of mapped fragments per RefSeq annotated gene, from which genes annotated by RefSeq as rRNA were discarded. Analysis for differential gene expression was performed using the DESeq2 R package with FDR <0.05.
Genome_build: hg19
Supplementary_files_format_and_content: read count per gene

source_name: CNDR brain bank (Penn)

extract_protocol:
Total RNA was isolated from 20 mg frozen brain tissue using the RNAeasy Mini kit (Qiagen) coupled to an RNase-free DNase step (Qiagen).
Ribosomal RNA was removed using the rRNA Depletion kit (NEB) and the resulting RNA was used to construct sequencing libraries using the NEBNext Ultra Directional RNA library Prep Kit for Illumina (NEB). Libraries were multiplexed using NEBNext Multiplex Oligos for Illumina (dual index primers) and single-ended sequenced (75 bp) on the NextSeq 500 platform (Illumina) in accordance with the manufacturer’s protocol.

value: Lateral temporal lobe from Frozen postmortem brain tissue

value: young


title: 7-19T-Young [RNA-seq]


title: 8-15A-Young [RNA-seq]


title: 4-13A-Young [RNA-seq]


title: 5-18T-Young [RNA-seq]


title: 9-16A-Young [RNA-seq]


title: 8955-V03


title: 3-17T-Young [RNA-seq]


title: 8963-V05


title: 8942-V04


title: 31-7T-AD [RNA-seq]


title: 8899-V05


title: 30-9T-AD [RNA-seq]


title: 29-6T-AD [RNA-seq]


title: 8942-V05


title: 8892-V05


title: 26-3A-AD [RNA-seq]


title: 8892-V03


title: 25-5T-AD [RNA-seq]


title: 8856-V04


title: 24-3T-AD [RNA-seq]


title: 28-8T-AD [RNA-seq]


title: 8899-V04


title: 8767-V05


title: 8767-V04


title: 23-2A-AD [RNA-seq]


title: 2-12A-Young [RNA-seq]


title: 8636-V04


title: 8636-V05


title: 21-1A-AD [RNA-seq]


title: 20-1T-AD [RNA-seq]


title: 22-2T-AD [RNA-seq]


title: 8617-V04


title: 8617-V05


title: 8856-V05


title: 8593-V05


title: 19-11A-Old [RNA-seq]

value: old


title: 18-10A-Old [RNA-seq]


title: 17-9A-Old [RNA-seq]


title: 8593-V04


title: 8494-V05


title: 16-14T-Old [RNA-seq]


title: 8494-V04


title: 15-13T-Old [RNA-seq]


title: 12-6A-Old [RNA-seq]


title: 11-10T-Old [RNA-seq]


title: 8403-V04


title: 8325-V05


title: 8325-V04


title: 8321-V05


title: 8274-V05


title: 8321-V04


title: 8165-V05


title: 10-8A-Old [RNA-seq]


title: 8274-V03


title: 8165-V03


title: 14-7A-Old [RNA-seq]


title: RD-8-IVT11-R-D1-3

city: Hinxton

first: Rik

last: Lindeboom

address: Wellcome Trust Genome Campus

department: Cellular Genetics

institute: Wellcome Sanger Institute

description: rnaseq_trainedMonocytes.normalizedReadcounts.tsv

data_processing:
RNA-sequencing reads were aligned with Hisat2 version 2.0.4 to the provided and pre-indexed hg38 transcript assembly from UCSC, with alignment tailoring for transcript assemblersenabled. Samtools was used to filter reads with a quality score lower than 20, and PCRduplicates were removed with Picard. Reads per gene were counted with the htseq-countscript from the Hisat2 software suite using the GTF file corresponding to the transcriptassembly, with reverse strandness enabled and identification attribute set to gene_id.Differential gene expression analysis was performed with the DESeq2 package version1.18.1. Genes with no reads mapped in any of the samples were filtered prior to differentialexpression analysis. The ‘rlogTransformation’ function in DESeq2 was used to normalize,transform and noise-stabilize the expression data for visualization purposes.
ChIP sequencing data was aligned to human genome hg19 with BWA. Samtools was usedto filter reads with a quality score lower than 20, and PCR duplicates were removed with Picard. Peaks were identified with MACS 2.2.6 in paired-end mode and ‘call-summits’enabled at a false discovery rate of 0.01. A union of all identified peaks was generated with BEDTools, which was used to count reads per peak in each sample. Read counts wereanalyzed with DESeq2 to identify significant dynamics, as described for the RNA-seq analysis.
Genome_build: RNA-seq: hg38, ChIP-seq: hg19
Supplementary_files_format_and_content: RNA-seq: read counts per transcript, ChIP-seq: read counts per called peak. Both normalized and stabilized with the rlogTransform function in DESeq2,

source_name: monocytes from healthy donor

growth_protocol: PBMCs were isolated by differential centrifugation over Ficoll-Paque (Lymphoprep, Stemcell Technologies). Cells were washed three times in PBS. PBMCs and monocytes were resuspended in RPMI culture medium supplemented with 2mM glutamax, 1mM pyruvate and penicillin/streptomycin (all from Thermo Fisher Scientific) and counted on a Casy counter. Monocytes were isolated using negative MACS isolation with the Pan monocyte isolation kit (Miltenyi Biotech). Briefly, stimulated PBMCs were washed with PBS and incubated with versene solution (0.48mM EDTA, Sigma Aldrich) for 30 minutes at 37 °C. Cells were scraped from the plates, counted, spun down and resuspended in MACS isolation buffer (PBS with 0.5% BSA and 2mM EDTA). Monocytes from COVID-19 patients were isolated directly after isolation of PBMCs. PBMCs were counted, spun down and resuspended in MACS isolation buffer. Monocyte isolation was performed according to manufacturer’s instructions

extract_protocol:
For RNA isolation 1*106 isolated monocytes were resuspended in 350 μl of RNA later Buffer (Qiagen). RNA was isolated using RNeasy kit (Qiagen) including DNAseI (Qiagen) digestions. For ChIP-seq, isolated monocytes were resuspended in RPMI culture medium and fixed using formaldehyde (1% final concentration, Sigma Aldrich) for 10 minutes at room temperature. Unreacted formaldehyde was quenched with 125 mM glycine and incubated for 5 minutes at room temperature. Cells were washed twice in PBS containing protease inhibitor cocktail (Roche) and 1 mM PMSF (Roche), and subsequently snap frozen in liquid nitrogen. Cell pellets were stored at -80 °C for further use. Cells were sonicated at a concentration of 15 million cells/ml using a Bioruptor pico sonicator (Diagenode; 10 cycles, 30s on, 30s off, at 4 °C). Immunoprecipitation was performed using the MagnaChIP kit (Merck Millipore) according to manufacturer’s instruction. In short, 500,000 cells were incubated overnight with 1 μg H3K4me3 or H3K27Ac antibody (Diagenode) and protein A magnetic beads at 4 °C. Beads and chromatin/antibody mixture were washed four times for 5 minutes at 4 °C. After washing chromatin was eluted and proteins were degraded using proteinase K. DNA was purified using spin columns and eluted in millliQ.
Total RNA isolated from monocytes was used for the preparation of the RNA sequencing libraries using the KAPA RNA HyperPrep Kit with RiboErase (KAPA Biosystems). In short, oligo hybridization and rRNA depletion, rRNA depletion cleanup, DNase digestion, DNase digestion cleanup, and RNA elution were performed according to protocol. Fragmentation and priming were performed at 94⁰ C for 6 min. First strand synthesis, second strand synthesis and A-tailing was performed according to protocol. For the adapter ligation, a 1.5 μM stock was used (NextFlex DNA barcodes, Bioo Scientific). First and second post-ligation cleanup was performed according protocol. A total of 11 PCR cycles were performed for library amplification. The library amplification cleanup was done using a 0.8x followed by a 1.0x beadbased cleanup. Library size was determined using the High Sensitivity DNA bioanalyzer kit, and the library concentration was measured using the dsDNA High Sensitivity Assay  17 (Denovix). Paired-end sequencing reads of 50 bp were generated using an Illumina NextSeq 500.   ChIP-seq libraries were prepared using the Kapa Hyper Prep Kit according to manufacturer’s protocol, with the following modifications. 2.5 μL of the NEXTflex adapter stock (600 nM, Bioo Scientific) was used for adapter ligation of each sample. Libraries were amplified with 12-15 PCR cycles followed by a double post-amplification clean-up was used to ensure proper removal of adapters. Samples were analyzed for purity using a High Sensitivity DNA Chip on a Bioanalyzer 2100 system (Agilent). Libraries were paired-end sequenced to a read length of 50 bp on an Illumina NextSeq500.

treatment_protocol: Human PBMCs were trained as described before. In short, 500.000 PBMCs were added into 96-well flat bottom plates. Cells were allowed to adhere for 1h at 37°C. Cells were washed three times with PBS prior to stimulations. After washing cells were incubated with culture medium only as negative control, or treated with 100 μM chloroquine (Sigma Aldrich), 100 μM hydroxychloroquine (Sigma Aldrich) or 0.01 μM rapamycin (Selckchem) for 1 hour at 37°C. Subsequently cells were incubated with 105 cells/ml HKCA (Invivogen) for 24 hours together with the respective treatment for 24 hours at 37°C. Subsequently, cells were washed and cells were rested for five days in RPMI culture medium containing 10% FBS. After the resting period cells were stimulated with either RPMI as negative control, 10ng/ml LPS (Sigma Aldrich) or 1ug/ml Pam3CSK4 (Invivogen).

value: monocytes

value: healthy donor

value: HKCA+HCQ

tag: icu admission


title: RD-4-IVT10-R-D1-2

value: HKCA


title: RD-7-IVT10-R-D1-3


title: RD-5-IVT11-R-D1-2


title: RD-9-IVT13-R-D1-3


title: 8403-V05

value: Whole blood

value: Test

value: Male


title: 8131-V05


title: 13-11T-Old [RNA-seq]


title: RD-6-IVT13-R-D1-2


title: RD-3-IVT13-R-D1-1

value: untreated


title: RD-2-IVT11-R-D1-1


title: 8131-V04

value: Pre-vaccination

value: Control


title: 8087-V05

value: Female

value: Fever


title: RD-1-IVT10-R-D1-1


title: CP-IVT13-3-K4-ChIP

description: union_peaks_ChIP.normalizedReadcounts.tsv

value: H3K4me3 ChIP-seq


title: 8087-V03


title: CP-IVT13-3-K27-ChIP

value: H3K27ac ChIP-seq


title: CP-IVT13-2-K4-ChIP


title: CP-IVT13-2-K27-ChIP


title: CP-IVT13-1-K4-ChIP


title: 0160-V05


title: 0160-V04


title: 8123-V05


title: 0159-V05


title: CP-IVT13-1-K27-ChIP


title: CP-IVT11-2-K4-ChIP


title: CP-IVT11-3-K4-ChIP


title: CP-IVT11-3-K27-ChIP


title: 0158-V05


title: 0159-V04


title: 8123-V03


title: 0157-V04


title: CP-IVT11-2-K27-ChIP


title: CP-IVT11-1-K27-ChIP


title: CP-IVT11-1-K4-ChIP


title: CP-IVT10-3-K4-ChIP


title: 8021-V04


title: 0154-V05


title: 8021-V05


title: 0155-V05


title: CP-IVT10-3-K27-ChIP


title: 0154-V04


title: CP-IVT10-2-K27-ChIP


title: 0152-V05


title: 0149-V05


title: CP-IVT10-2-K4-ChIP


title: CP-IVT10-1-K4-ChIP


title: 0152-V03


title: 0158-V04


title: CP-IVT10-1-K27-ChIP


title: 0157-V05


title: 27-5A-AD [RNA-seq]

value: Lateral temporal lobe from Frozen postmortem brain tissue


title: 0149-V03


title: CP-8-1-RNA

description: rnaseq_covidPatients.normalizedReadcounts.tsv

source_name: monocytes from COVID19 patient

value: COVID19 patient

value: 0 days HCQ

value: no ICU admission


title: 0148-V05


title: CP-9-1-RNA

value: monocytes


title: CP-7-1-RNA


title: 0147-V05


title: 0147-V03


title: CP-6-2-RNA

value: 5 days HCQ


title: 0146-V05


title: CP-5-1-RNA


title: CP-6-1-RNA


title: 0146-V03


title: 0145-V05


title: 0144-V04


title: CP-4-2-RNA


title: 0145-V03


title: 0143-V05


title: 0141-V05


title: CP-2-1-RNA

value: ICU admission


title: CP-2-2-RNA


title: 0141-V04

value: Whole blood


title: 0143-V03


title: 0140-V05


title: CP-3-1-RNA


title: CP-12-2-RNA


title: 0139-V03


title: CP-13-2-RNA


title: 0140-V03


title: CP-1-2-RNA


title: CP-4-1-RNA


title: 0138-V03

value: Test


title: CP-11-1-RNA


title: CP-10-1-RNA


title: 0137-V05

value: Male


title: CP-10-2-RNA


title: CP-12-1-RNA


title: 0136-V03


title: T3: BovTick6

city: Pullman

first: Massaro

middle: W

last: Ueti

state: WA

address: 3003 ADBF

department: Animal Disease Research Unit

institute: United States Department of Agriculture

data_processing:
HiSeq control software HCS 2.2.58, RTA 1.18.64
Align reads to reference (STAR v2.5.2a) with 2-pass mapping
Count feature mapping with Subread featureCounts v1.6.0
TMM normalization
edgeR (v3.20.9) significance testing with GLM LRT
significance defined as |logFC| >=1 & FDR 5%
Supplementary_files_format_and_content: read counts, log CPM and normalized values, FDR significance

organism: Babesia bovis

source_name: Tick

extract_protocol:
Trizol Extraction
Illumina TruSeq mRNA - polyA selected

treatment_protocol: Homogenized, cooled and centrifuged to remove large particles

value: Tick

tag: developmental stage

value: Kinete

tag: strain

value: Texas


title: Patient 2 PA scRNA-seq

city: La Jolla

last: Torkamani

address: 3344 North Torrey Pines Court, Suite 300

department: Scripps Research Translational Institute

institute: Scripps Research

data_processing:
Library strategy: scRNA-Seq
10X Genomics cellranger count version 3.0.2 with default parameters was used, processing 4 lanes of paired-end fastq files (8 fastq files per sample) into expression matrix data files. This was repeated for each of the 6 samples. The resulting processed files (tar archives) have names formatted as 0?dat2019???????CARcon???_featurebcmatrixfiltered.tar. Concurrently, an h5 molecule info file was created by the same cellranger count processing step, and this h5 files is used for a further aggregation processing step. The 6 sample molecule info files created have the name format 0?dat2019???????CARcon???_moleculeinfo.h5. The GRCh38 transcriptome was used for mapping and alignment by the cellranger count software.
The 6 samples were aggregated together into a single processed file using 10X Genomics cellranger aggr version 3.0.2. Default parameters were applied, including --normalize mapped.
Genome_build: GRCh38 transcriptome
Supplementary_files_format_and_content: There are two processed file types containing similar information. The tar archive files contain 3 text files each and are embodiments of expression data. These are features.tsv.bz, barcodes.tsv.gz, and matrix.mtx.gz. The features file contains the gene ids (rows), the barcodes file contains the cell ids (columns), and the matrix.mtx file contains a sparse representation of the expression data, in the form of row number, column number, and UMI count, separated by spaces. The other processed file is a molecule_info file.h5 containing compressed molecule information typical of 10X Genomics single cell experiments The h5 processed file and is used for producing the aggregated cell data set (tar file).

source_name: Carotid artery proximal adjacent

extract_protocol:
AC and PA  artery tissue from patients undergoing  endarterectomy and was immediately collected from the operating room and transferred on ice for tissue dissociation. Samples were weighed, minced with surgical blades, then placed in conical tubes with pronase (5000U/ml) and collagenase II (0.1% solution). Tissue was then incubated at 37C for one hour with continuous gentle agitation. 30min into the incubation period, DNase I solution was added, and the entire solution remained incubated for an additional 30min. Pipetting mixture up and down every 10min helped break tissue apart. After one-hour incubation was complete, 10% FBS+Complete EC media (Cell Applications, Inc) was immediately added to dissociated tissue to quench enzymatic activity. The sample was then inverted a few times and then set down for 30sec, allowing all debris to settle at the bottom. The entire solution was carefully transferred, without settled debris, to another conical tube (use pipettor to transfer solution near debris pellet carefully, removing all solution but leaving pellet at bottom of tube). Sample was then centrifuged at 500g for 5min and supernatant discarded. Cell pellet was resuspended in 5mL 1X RBC lysis buffer and incubated at RT for 5min. 30mL 1X PBS was added to stop the reaction and the sample was then spun immediately at 500g for 5min at RT. The supernatant was discarded, and cell pellet resuspended in 10mL FACS buffer composed of: 1X PBS, 2.5mM EDTA, 25mM HEPES, 1% FBS (heat-inactivated), and 1% Pen-Strep. To wash excess reagents, the sample is centrifuged again at 500g for 5min, supernatant discarded, then cell pellet is again resuspended in 2mL FACS buffer. 2ul of 5mM DRAQ5 is added to each tube, and solution is pipetted up and down a few times. Next, solution is triturated with P1000 and entire sample sieved through 100uM cell strainer fitted onto 50mL conical tube. This step is repeated next through a 40uM cell strainer. The solution is placed on ice and immediately transported for FACS. Cells were sorted on a MoFLo Astrios EQ cell sorter (Beckman Coulter) with a 100 µm nozzle tip at a sheath pressure of 20 psi. Cells were distinguished from cellular debris by gating DRAQ5 positive events and doublets excluded using appropriate FSC and SSC gating. (Extended Data Fig. 1a-d). Cells isolated represented <1% of the total particles in the sample which was then transported for evaluation of viability and subsequent sequencing. Cells were then processed on the 10X Genomics Chromium single cell 3’ v3 gene expression platform. Cells were counted and checked for viability using a Countess II Automated Cell Counter (Thermo Fisher).
Sequencing libraries were prepared as recommended in the user manual with cell target numbers ranging between 6,000 – 22,000 cells per sample. Completed sequencing libraries were then sequenced on an Illumina NextSeq500 using 28 x 91 paired-end reads with 8 base i7 index reads to demultiplex different samples. Aggregating our 6 samples (3 patient-matched PA and AC samples) resulted in 51,981 cells, a sequencing depth of 15,549 reads/cell, 1,339 median genes/cell and 3,776 UMI/cell.

value: carotid

tag: location

value: proximal adjacent


title: 0137-V03

value: Pre-vaccination

value: Control


title: Patient 2 AC scRNA-seq

source_name: Carotid artery atherosclerotic core

value: atherosclerotic core


title: Patient 3 AC scRNA-seq


title: T1: BovTick4


title: 0134-V03


title: 0133-V05

value: Female


title: 0136-V05

value: Fever


title: C3: BovBlood6

source_name: Blood

growth_protocol: Cultured in RBC's from defibrinated blood in 3% Oxygen and 5% CO2

value: Blood

value: Merozoite


title: CP-1-1-RNA

tag: cell type

value: monocytes

value: COVID19 patient

value: 0 days HCQ


title: 0134-V05

value: Whole blood

value: Test


title: T2: BovTick5

value: Tick


title: 0138-V05


title: CP-13-1-RNA

tag: treatment

value: ICU admission


title: Patient 1 AC scRNA-seq


title: Input [5hmC]

data_processing:
Raw sequencing reads were first trimmed by Trim Galore! v.0.4.4 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adapter sequences and poor-quality nucleotides. High-quality reads were then mapped to the hg19 reference genome by Bowtie v.1.1.1 with uniquely mapped reads retained for the following analyses. PCR duplicates were removed by Samtools and normalization was performed by deepTools. Reads of samples from the same study group were pooled for 5hmC track visualization.
To compare 5hmC with RNA-seq, fragments per kilobase of transcript per million mapped read values for 5hmC over each RefSeq gene were computed using FeatureCounts and correlation plots with corresponding gene RNA-seq expression levels were plotted in R v.3.3.2. To compare 5hmC with ChIP–seq data, metaplots of 5hmC signal over the ChIP–seq peaks identified across the younger, old and AD samples (distinguishing TSS versus enhancer sites) were plotted using deepTools.
Genome_build: hg19
Supplementary_files_format_and_content: peak for each library

extract_protocol:
Nano-hmC-Seal was performed as described previously in Han et al. Briefly, 100 ng of genomic DNA were fragmented in tagmentation buffer at 55 °C. Fragmented DNA was purified by Zymo DNA Clean and Concentration Kit (Zymo Research). Then, selective 5hmC chemical labeling was performed in glycosylation buffer (50 mM of HEPES buffer, pH 8.0, 25 mM of MgCl2) containing the fragmented DNA, βGT and N3-UDP-Glc, and incubated at 37 °C for 2 h. After DNA purification in double-distilled H2O, DBCO-PEG4-Biotin (Click Chemistry Tools) was added and incubated at 37 °C for 2 h. The biotin-labeled DNA was pulled down by C1 Streptavidin beads (Thermo Fisher Scientific) for 15 min at room temperature.
The captured DNA fragments were subjected to PCR amplification using the Nextera DNA Sample Preparation Kit. The resulting amplified product was purified by 1.0× AMPure XP beads. The input library was made by direct PCR from fragmented DNA directly without labeling and pulldown. The libraries were quantified by a Qubit Fluorometer (Life Technologies Invitrogen Qubit 2.0 DNA RNA Protein Fluorometer, Q32866) and sequenced on a NextSeq 500 Platform in accordance with the manufacturer’s protocol.

value: Lateral temporal lobe from Frozen postmortem brain tissue


title: C1: BovBlood4

value: Texas


title: C2: BovBlood5


title: 0133-V03


title: 0131-V04

value: Male


title: 0130-V05


title: GTT31_T

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

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

description: Thymic Tregs; mice ID GTT31: Pregnant RANK FOXN1 WT

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 and 3.3.52 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.3 and 2.7.7.
BCL to BAM file conversion and demultiplexing with Illumina2bam 1.17 (http://wtsi-npg.github.io/illumina2bam/) and custom programmes based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Spliced genome alignments to GRCm38 (UCSC Genome Browser mm10) and Ensembl reference transcriptome e100 (April 2020) with STAR 2.7.1a and options recommended by the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Differential expression modelling with Bioconductor 3.11 package DESeq2 1.28.1, running under R 4.0.2.
Genome_build: UCSC mm10 based on GRCm38
Supplementary_files_format_and_content: Per gene and sample raw (integer) counts and DESeq2-calculated FPKMs in tab-separated value (TSV) format

source_name: thymus

extract_protocol:
Equal numbers of Tregs (280 cells) were sorted from the thymus and placenta of E17.5 pregnant Bl6 females, mated with syngeneic Bl6 males. To increase robustness, the 280 placental Tregs were purified from 5 individual placentas per pregnant female (56 Tregs/placenta). Cells were sorted directly into a cell lysis buffer consisting of a 0.2% (vol/vol) Triton X-100 solution and an RNase inhibitor.
For the generation of full-length cDNA, the Smart-seq2 protocol (Picelli, S. et al, Nat Protoc. 2014 Jan;9(1):171-81. doi:10.1038/nprot.2014.006) was used.
The subsequent library preparation from the amplified cDNA was performed using the Nextera XT DNA library prep kit (Illumina).
For sequencing, libraries were pooled, diluted and sequenced on Illumina HiSeq 3000 using 50 bp single-read chemistry.

value: thymus

value: regulatory T-cell

tag: gender

value: female

tag: genotype

value: Tnfrsf11a (Rank) Foxn1 wild-type

tag: pregnancy status

value: pregnant


title: GTT31_P

description: Placenta Tregs; mice ID GTT 31: Pregnant RANK FOXN1 WT

source_name: placenta

tag: tissue

value: placenta

tag: quality

value: low quality (this sample was not reflected in the expression matrices)


title: 9-16A-Young [5hmC]

tag: age

value: young


title: GTT17_T

description: Thymic Tregs; mice ID GTT17: Pregnant RANK FOXN1 KO

value: Tnfrsf11a (Rank) Foxn1 knock-out


title: Patient 1 PA scRNA-seq

value: carotid

value: proximal adjacent


title: 0130-V04

value: Whole blood

tag: vaccination status

value: Pre-vaccination

value: Control


title: GTT16_T

description: Thymic Tregs; mice ID GTT16: Pregnant RANK FOXN1 KO


title: 7-19T-Young [5hmC]

value: Lateral temporal lobe from Frozen postmortem brain tissue


title: GTT17_P

description: Placenta Tregs; mice ID GTT17: Pregnant RANK FOXN1 KO


title: 0129-V05

tag: study group

value: Female


title: GTT14_T

description: Thymic Tregs; mice ID GTT14: Pregnant RANK FOXN1 WT


title: 6-14A-Young [5hmC]


title: GTT14_P

description: Placental Tregs; mice ID GTT14: Pregnant RANK FOXN1 WT


title: GTT15_T

description: Thymic Tregs; mice ID GTT15: Pregnant RANK FOXN1 WT


title: GTT16_P

description: Placenta Tregs; mice ID GTT16: Pregnant RANK FOXN1 KO


title: GTT15_P

description: Placental Tregs; mice ID GTT15: Pregnant RANK FOXN1 WT


title: GTT13_T

description: Thymic Tregs; mice ID GTT13: Pregnant RANK FOXN1 WT


title: 3-17T-Young [5hmC]


title: 0127-V05

tag: Sex


title: GTT13_P

description: Placental Tregs; mice ID GTT13: Pregnant RANK FOXN1 WT


title: 0129-V04

tag: post-vaccination log10 (menb sba titres)


title: 31-7T-AD [5hmC]


title: GTT12_T

description: Thymic Tregs; mice ID GTT12: Pregnant RANK FOXN1 KO


title: 0127-V03

description:
Human infant whole blood RNA-sequencing data
ribosomal and globin RNA depleted

tag: post-vaccination fever


title: 0125-V05

value: Male


title: GTT12_P

description: Placental Tregs; mice ID GTT12: Pregnant RANK FOXN1 KO


title: GTT11_T

description: Thymic Tregs; mice ID GTT11: Pregnant RANK FOXN1 KO

value: thymus


title: 4-13A-Young [5hmC]


title: GTT11_P

description: Placental Tregs; mice ID GTT11: Pregnant RANK FOXN1 KO

value: regulatory T-cell


title: 0125-V04


title: 28-8T-AD [5hmC]


title: 27-5A-AD [5hmC]


title: NCF ALI Polyps cells - healthy donor PNCF4

city: Montpellier

first: Magali

last: Taulan-Cadars

address: 641 avenue du Doyen Gaston Giraud

country: France

institute: EA7402 Laboratoire de génétique de maladies rares

description:
Polyps cells obtained from nasal brushings of healthy donor and differenciated about 40 days on 1 cm2 transwell inserts
NCF-CF-ALI-Polyps-miRNA.xlsx
NCF4-Po-PNCF4

data_processing:
Basecalls were generated through Illumina on a MiSeq DX
Reads were aligned to hg19 and miRbase (v21) using sRNAbench (web tool server included in sRNAtoolbox)
Reads used were trimmed and readcount filtered (readcount >10 reads)
Using sRNAde based on EdgeR algorithm, differential expression of miRNA between healthy and CF donors were calculated for each model
Excel files summarizing EdgeR expression for each miRNA in each sample and models were generated
Genome_build: hg19
Supplementary_files_format_and_content: excel files

source_name: ALI Polyps cells

growth_protocol: Bronchial, Polyps and Nasal cells were obtained from surgery or nasal brushing and grown in transwell permeable inserts about 30-40 days in air-liquid interface to constitute 3D epithelium

extract_protocol:
Total RNA were extracted using TRIzol according to manufacturer's instructions
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Small RNA kit (part# RS-200-0012). One μg of total RNA with a RIN>7 was used for library construction. After ligation of adapters to the 3’- and 5’-ends, RNA were reverse transcribed using Superscript II and amplified with barcoded primers. Correct enrichment of cDNA containing miRNA sequences was controlled by running each sample on a High Sensitivity DNA Chip on a Bioanalyzer 2100. cDNA derived from microRNAs were selected by purification through a 6% TBE-polyacrylamide gel. After validation of the size using a Bioanalyzer 2100, 12 small-RNA libraries were pooled together at equal molarity to create a unique pool and sequenced on a MiSeq

treatment_protocol: untreated

value: Polyps cells grown as epithelium in Air-liquid interface (ALI)

value: wild-type

tag: disease state

value: normal


title: CF ALI Polyps cells - CF donor PCF2

description:
Polyps cells obtained from nasal brushings of CF donor and differenciated about 40 days on 1 cm2 transwell inserts
NCF-CF-ALI-Polyps-miRNA.xlsx
CF2-Po-PCF2

value: CF homozygous


title: 0124-V03

value: Test


title: 26-3A-AD [5hmC]


title: NCF ALI Polyps cells - healthy donor PNCF3

description:
Polyps cells obtained from nasal brushings of healthy donor and differenciated about 40 days on 1 cm2 transwell inserts
NCF-CF-ALI-Polyps-miRNA.xlsx
NCF3-Po-PNCF3


title: NCF ALI Polyps cells - healthy donor PNCF2

description:
Polyps cells obtained from nasal brushings of healthy donor and differenciated about 40 days on 1 cm2 transwell inserts
NCF-CF-ALI-Polyps-miRNA.xlsx
NCF2-Po-PNCF2


title: NCF ALI Polyps cells - healthy donor PNCF1

description:
Polyps cells obtained from nasal brushings of healthy donor and differenciated about 40 days on 1 cm2 transwell inserts
NCF-CF-ALI-Polyps-miRNA.xlsx
NCF1-Po-PNCF1


title: CF ALI Polyps cells - CF donor PCF1

description:
Polyps cells obtained from nasal brushings of CF donor and differenciated about 40 days on 1 cm2 transwell inserts
NCF-CF-ALI-Polyps-miRNA.xlsx
CF1-Po-PCF1


title: 0123-V05


title: CF ALI Nasal cells - CF donor P25

description:
Nasal cells obtained from nasal brushings and differenciated about 30 days on 1 cm2 transwell inserts
NCF-CF-ALI-Nasal-miRNA.xlsx
CF3-Na-P25

source_name: ALI Nasal cells

value: Nasal cells grown as epithelium in Air-liquid interface (ALI)


title: 0122-V05


title: CF ALI Nasal cells - CF donor P18

description:
Nasal cells obtained from nasal brushings and differenciated about 30 days on 1 cm2 transwell inserts
NCF-CF-ALI-Nasal-miRNA.xlsx
CF2-Na-P18


title: CF ALI Nasal cells - CF donor P15

description:
Nasal cells obtained from nasal brushings and differenciated about 30 days on 1 cm2 transwell inserts
NCF-CF-ALI-Nasal-miRNA.xlsx
CF1-Na-P15


title: 25-5T-AD [5hmC]


title: 24-3T-AD [5hmC]


title: NCF ALI Nasal cells - healthy donor T25

description:
Nasal cells obtained from nasal brushings and differenciated about 30 days on 1 cm2 transwell inserts
NCF-CF-ALI-Nasal-miRNA.xlsx
NCF3-Na-T25


title: 23-2A-AD [5hmC]


title: NCF ALI Nasal cells - healthy donor T24

description:
Nasal cells obtained from nasal brushings and differenciated about 30 days on 1 cm2 transwell inserts
NCF-CF-ALI-Nasal-miRNA.xlsx
NCF2-Na-T24


title: 0122-V03


title: 29-6T-AD [5hmC]


title: CF ALI Polyps cells - CF donor PCF4

description:
Polyps cells obtained from nasal brushings of CF donor and differenciated about 40 days on 1 cm2 transwell inserts
NCF-CF-ALI-Polyps-miRNA.xlsx
CF4-Po-PCF4


title: CF ALI Polyps cells - CF donor PCF3

description:
Polyps cells obtained from nasal brushings of CF donor and differenciated about 40 days on 1 cm2 transwell inserts
NCF-CF-ALI-Polyps-miRNA.xlsx
CF3-Po-PCF3


title: 0121-V05

description:
Human infant whole blood RNA-sequencing data
ribosomal and globin RNA depleted

value: Fever


title: NCF ALI Nasal cells - healthy donor T16

description:
Nasal cells obtained from nasal brushings and differenciated about 30 days on 1 cm2 transwell inserts
NCF-CF-ALI-Nasal-miRNA.xlsx
NCF1-Na-T16


title: 2-12A-Young [5hmC]

value: young


title: CF ALI Bronchial cells - CF donor 48502

description:
Bronchial cells obtained from surgery and differenciated about 40 days on 0.33cm2 transwell inserts (obtained from Epithelix®)
NCF-CF-ALI-Bronchial-miRNA.xlsx
CF5-Br-hAECB48502

source_name: ALI bronchial cells

value: Bronchial cells grown as epithelium in Air-liquid interface (ALI)


title: 21-1A-AD [5hmC]


title: 0119-V05

value: Whole blood


title: CF ALI Bronchial cells - CF donor 43703

description:
Bronchial cells obtained from surgery and differenciated about 40 days on 0.33cm2 transwell inserts (obtained from Epithelix®)
NCF-CF-ALI-Bronchial-miRNA.xlsx
CF1-Br-hAECB43703


title: CF ALI Bronchial cells - CF donor 45303

description:
Bronchial cells obtained from surgery and differenciated about 40 days on 0.33cm2 transwell inserts (obtained from Epithelix®)
NCF-CF-ALI-Bronchial-miRNA.xlsx
CF4-Br-hAECB45303


title: 0119-V04

value: Pre-vaccination


title: CF ALI Bronchial cells - CF donor 44502

description:
Bronchial cells obtained from surgery and differenciated about 40 days on 0.33cm2 transwell inserts (obtained from Epithelix®)
NCF-CF-ALI-Bronchial-miRNA.xlsx
CF2-Br-hAECB44502


title: NCF ALI Bronchial cells - healthy donor hAECB458401

description:
Bronchial cells obtained from surgery and differenciated about 40 days on 0.33cm2 transwell inserts (obtained from Epithelix®)
NCF-CF-ALI-Bronchial-miRNA.xlsx
NCF4-Br-hAECB458401


title: CF ALI Bronchial cells - CF donor 45201

description:
Bronchial cells obtained from surgery and differenciated about 40 days on 0.33cm2 transwell inserts (obtained from Epithelix®)
NCF-CF-ALI-Bronchial-miRNA.xlsx
CF3-Br-hAECB45201


title: 0116-V05

value: Control


title: 19-11A-Old [5hmC]

value: Lateral temporal lobe from Frozen postmortem brain tissue

value: old


title: NCF ALI Bronchial cells - healthy donor hAECB1149500

description:
Bronchial cells obtained from surgery and differenciated about 40 days on 0.33cm2 transwell inserts (obtained from Epithelix®)
NCF-CF-ALI-Bronchial-miRNA.xlsx
NCF5-Br-hAECB1149500


title: 20-1T-AD [5hmC]


title: NCF ALI Bronchial cells - healthy donor hAECB405501

description:
Bronchial cells obtained from surgery and differenciated about 40 days on 0.33cm2 transwell inserts (obtained from Epithelix®)
NCF-CF-ALI-Bronchial-miRNA.xlsx
NCF1-Br-hAECB405501


title: 18-10A-Old [5hmC]


title: 0116-V04

value: Female


title: NCF ALI Bronchial cells - healthy donor hAECB453201

description:
Bronchial cells obtained from surgery and differenciated about 40 days on 0.33cm2 transwell inserts (obtained from Epithelix®)
NCF-CF-ALI-Bronchial-miRNA.xlsx
NCF3-Br-hAECB453201


title: 17-9A-Old [5hmC]


title: NCF ALI Bronchial cells - healthy donor hAECB440001

description:
Bronchial cells obtained from surgery and differenciated about 40 days on 0.33cm2 transwell inserts (obtained from Epithelix®)
NCF-CF-ALI-Bronchial-miRNA.xlsx
NCF2-Br-hAECB440001


title: 16-14T-Old [5hmC]


title: 0114-V05

value: Male


title: 0114-V03


title: 0112-V03


title: 0110-V05


title: 14-7A-Old [5hmC]


title: 15-13T-Old [5hmC]


title: 13-11T-Old [5hmC]


title: 11-10T-Old [5hmC]


title: 12-6A-Old [5hmC]


title: 0106-V05


title: 0107-V04


title: 0112-V05


title: 10-8A-Old [5hmC]


title: 0110-V03


title: BatchF_ISO_0052_d18

city: Los Angeles

first: Michael

last: Workman

address: 8700 Beverly Blvd., AHSP Suite 8405

institute: Cedars-Sinai Medical Center

description: processed data file: BatchF_10X_UMIcounts.csv

data_processing:
Raw sequencing reads were demultiplexed and processed to FASTQ using Illumina bcl2fastq.
Sample reads were aligned to the transcriptome and uniquely mapped reads were counted and assigned to cell specific barcodes. For ddSEQ libraries, reads were aligned and demultiplexed using Illumina Single-Cell RNA Seq BaseSpace Workflow (v1.0.0) with STAR Aligner (v2.5.2b) and hg19 reference genome. For 10X libraries, reads were aligned and demultiplexed using 10X Genomics Cell Ranger (v2.1.0) with STAR Aligner (v2.5.1) and GRCh38 reference genome.
Cell barcodes used to generate processed UMI counts for each sample are contained in CellBarcodes.csv
Genome_build: hg19 or GRCh38
Supplementary_files_format_and_content: processed UMI counts

source_name: iPSC-derived motor neurons

growth_protocol: Differentiation was performed essentially as described in Maury et al. Nat Biotechnol, 2015

extract_protocol:
Live cells were dissociated with 0.25% Trypsin-EDTA, filtered, and counted. Single cell capture was performed using the Illumina Bio-Rad ddSEQ System or 10X Genomics Chromium Controller. Sample specific information can be found in the 'Capture Platform' column in the Samples section.
cDNA libraries were prepared following the manufacturer's instructions using the Illumina Bio-Rad SureCell WTA 3′ Library Prep Kit or 10X Chromium Single Cell 3’ Library & Gel Bead Kit v2. Sample specific information can be found under the 'Library Construction Kit' column in the Samples section.

tag: cell line

value: Isogenic Control

tag: days of differentiation

tag: capture platform

value: 10X Genomics Chromium Controller

tag: library construction kit

tag: batch

value: Batch F

tag: genome alignment


title: BatchF_CTR_0465_d18

tag: genotype

value: 10X Chromium Single Cell 3’ Library & Gel Bead Kit v2


title: BatchF_C9O_6ZLD_d18

value: ALS C9orf72


title: 0105-V03

value: Test


title: 0106-V03


title: 0105-V05


title: 0103-V05


title: 0103-V03


title: BatchE_SPO_2XWC_d18

description: processed data file: BatchE_10X_UMIcounts.csv

value: ALS sporadic

value: Batch E


title: 0124-V05


title: 22-2T-AD [5hmC]


title: 0123-V03


title: 0102-V05


title: BatchE_ISO_0029_d18


title: P131_strom_cs

type: genomic

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

institute: University of British Columbia

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iSCAN using standard recommended Illumina scanner setting

data_processing: Beta value normalized with BMIQ and filtered for quality probes. See original publication for complete details.

label: Cy3, Cy5

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted by standard salt method and purified using Qiagen DNeasy Kit according to standard instructions

tag: fetal sex

value: F

tag: trimester

value: First

value: placenta

tag: cell type

value: Stromal cs

tag: well


title: 0102-V03

tag: tissue

value: Whole blood

tag: vaccination status

value: Pre-vaccination

value: Control


title: PM378_strom_cs

value: M

value: Third


title: BatchF_C9O_0052_d18


title: PM376_endo_cs

value: Endothelial cs


title: PM374_vc

value: Villi


title: BatchE_CTR_0179_d18

value: 10X Genomics Chromium Controller


title: PM375_vc


title: 0101-V05

tag: study group

tag: Sex

value: Male

value: Fever


title: PM366_tro2

value: Trophoblasts enz


title: PM377_strom_cs


title: PM362_endo_cs


title: PM364_strom_cs


title: PM362_hofb_cs

value: Hofbauer cs


title: PM367_endo_cs


title: PM372_troph_cs

value: Trophoblasts cs


title: PM372_strom_cs


title: 0101-V04

value: Test

tag: post-vaccination log10 (menb sba titres)

tag: post-vaccination fever


title: BatchE_C9O_0029_d18

tag: cell line

value: ALS C9orf72

value: 10X Chromium Single Cell 3’ Library & Gel Bead Kit v2

value: Batch E


title: PM366_hofb_cs

value: F

value: placenta


title: PL292_strom_cs

value: First

value: Stromal cs


title: PM366_vc_R1

value: Third


title: PM359_endo_cs

value: M

value: Endothelial cs


title: BatchD_SPO_2XWC_d18

description: processed data file: BatchD_ddSEQ_UMIcounts.csv

value: ALS sporadic

tag: days of differentiation

value: Illumina Bio-Rad ddSEQ System

value: Illumina Bio-Rad SureCell WTA 3′ Library Prep Kit

value: Batch D


title: PL295_v

value: Villi


title: BatchD_ISO_0029_d18

value: Isogenic Control

tag: capture platform


title: PL294_endo_cs


title: 0099-V05

value: Whole blood

value: Test

value: Male


title: BatchD_CTR_0179_d18

value: Control

tag: library construction kit


title: PM374_troph_cs

value: Trophoblasts cs


title: 0100-V03

value: Pre-vaccination

value: Fever


title: PM368_hofb_cs

value: placenta

value: Hofbauer cs


title: BatchD_CTR_0025_d18

tag: batch


title: 0099-V04


title: 0098-V05


title: PM369_troph_cs

value: F

value: Third


title: BatchC_CTR_0025_d18

description: processed data file: BatchC_ddSEQ_UMIcounts.csv

value: Batch C

tag: genome alignment


title: PM373_strom_cs

value: M

value: Stromal cs


title: 0098-V04


title: 0097-V05

value: Female


title: BatchC_C9O_0052_d18

tag: genotype

value: ALS C9orf72

value: Illumina Bio-Rad ddSEQ System

value: Illumina Bio-Rad SureCell WTA 3′ Library Prep Kit


title: PM366_endo_cs

tag: fetal sex

value: Endothelial cs


title: BatchC_C9O_0029_d18


title: PL290_troph_cs

tag: trimester

value: First


title: PL290_endo_cs

tag: cell type


title: PM374_hofb_cs

tag: well


title: PM377_vc

tag: tissue

value: Villi


title: 0095-V05

value: Whole blood

tag: vaccination status

value: Test


title: P128_strom_cs


title: BatchB_SPO_8BRM_d18

description: processed data file: BatchB2_ddSEQ_UMIcounts.csv

value: ALS sporadic

value: Batch B


title: PM370_endo_cs

value: placenta


title: 0100-V05

description:
Human infant whole blood RNA-sequencing data
ribosomal and globin RNA depleted

tag: study group

value: Male

value: Fever


title: BatchD_C9O_0029_d18

value: Batch D


title: BatchB_SPO_2XWC_d18


title: 0097-V03

value: Pre-vaccination

value: Control

tag: Sex


title: PM367_hofb_cs

value: F

value: Third

value: Hofbauer cs


title: PM375_troph_cs

value: Trophoblasts cs


title: PM359_vc

value: M


title: 0095-V04

value: Female

tag: post-vaccination log10 (menb sba titres)


title: PM381_vc

value: Villi


title: 0094-V05

value: Whole blood

tag: post-vaccination fever


title: PM371_troph_cs


title: PM375_endo_cs

value: Endothelial cs


title: PL294_strom_cs

value: First

value: Stromal cs


title: PM359_strom_cs

value: placenta


title: BatchB_CTR_0179_d18

tag: cell line

value: Illumina Bio-Rad ddSEQ System

value: Illumina Bio-Rad SureCell WTA 3′ Library Prep Kit

value: Batch B


title: 0091-V05

value: Test

value: Fever


title: BatchB_CTR_0083_d18

description: processed data file: BatchB1_ddSEQ_UMIcounts.csv

value: Control

tag: days of differentiation


title: 0091-V03

value: Pre-vaccination


title: BatchA_CTR_0083_d18

description: processed data file: BatchA_ddSEQ_UMIcounts.csv

tag: capture platform

value: Batch A


title: BatchC_C9O_0028_d18

value: ALS C9orf72

tag: library construction kit

value: Batch C


title: 0089-V05

value: Female


title: PM373_troph_cs

value: M

value: Third

value: Trophoblasts cs


title: BatchA_CTR_0083_d12

tag: batch


title: 0089-V04

value: Whole blood


title: PM379_endo_cs

value: F

value: Endothelial cs


title: BatchA_CTR_0083_d06

value: Illumina Bio-Rad ddSEQ System

tag: genome alignment


title: PM381_hofb_cs

value: placenta

value: Hofbauer cs


title: 0088-V05

value: Test

value: Male


title: BatchA_CTR_0083_d00

source_name: iPSC

tag: genotype

value: Control

value: Illumina Bio-Rad SureCell WTA 3′ Library Prep Kit


title: PM365_hofb_cs

tag: fetal sex


title: 0088-V03

value: Pre-vaccination

value: Fever


title: PSA-stimulated CD4+ T cells MD78

city: Cleveland

first: Brian

last: Cobb

state: OH

address: 10900 Euclid Avenue, WRB 5132

institute: Case Western Reserve University School of Medicine

description:
PSA-stimulated CD4+ T cells
CD4+ T cells activated with PSA and antigen presenting cells for 7 days

data_processing:
data QC: Cutadapt/perl
Alignment: Tophat v1.4.1
Assembly: Cufflinks v2.2.1
Differential Expression: Cufflinks v2.2.1
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: MS Excel format containing RPKM values and statistical p values

source_name: spleen

growth_protocol: Cells were cultured in Gibco Advanced RPMI1640 media with 10% fetal bovine serum for the indicated number of days at 37C with 5% CO2

extract_protocol:
Qiagen RNeasy
RNA library is prepared according to Illumina's protocol1 and sequencing is conducted on Illumina HiSeq 2500. The 3' adaptor (TGGAATTCTCGGGTGCCAAGG) for sequencing is removed from the raw reads. After removing the 3' adaptor, reads with the length less than 10 nt are excluded. The remaining reads are aligned against genome using Tophat v1.4.12 and assembled using Cufflinks v2.2.13. The abundance is estimated in Fragments Per Kilobase of transcript per Million mapped reads (FPKM) as defined in Cufflinks. Differential expression analysis is conducted using the Cuffdiff module of Cufflinks and the q-value (False-Discover-Rate adjusted p-value) of 0.05 is used as the cutoff to define genes showing significant difference.

treatment_protocol: Cells were either untreated (no PSA, day zero, freshly isolated) or stimulated with splenic antigen presenting cells and 50 ug/ml PSA for 7 days

tag: strain

tag: marker

value: T cell


title: 0087-V05

source_name: Whole blood

value: Female


title: PM362_strom_cs

value: M

tag: trimester

tag: cell type

value: Stromal cs

tag: well


title: PM374_strom_cs

value: Third

tag: tissue


title: PSA-stimulated CD4+ T cells MD76


title: P128_troph_cs

value: First

value: Trophoblasts cs


title: PM372_vc

value: Villi


title: PM373_vc


title: PM372_hofb_cs


title: PSA-stimulated CD4+ T cells MD74


title: resting CD4+ T cells MWBC3

description:
resting CD4+ T cells
resting CD4+ T cells from adult mouse spleen


title: 0084-V05

value: Whole blood

tag: vaccination status

tag: study group

tag: Sex


title: PL296_strom_cs

value: placenta


title: PL293_v_R1


title: resting CD4+ T cells MWBC2


title: PL290_strom_cs

value: F


title: PL294_hofb_cs

value: Hofbauer cs


title: P128_endo_cs

value: Endothelial cs


title: 0086-V04

value: Test

value: Male

tag: post-vaccination log10 (menb sba titres)

tag: post-vaccination fever


title: PM378_hofb_cs


title: PM378_troph_cs


title: 0083-V05


title: resting CD4+ T cells MWBC1


title: 0086-V05


title: PM369_strom_cs


title: PL294_v


title: PM379_strom_cs


title: PM369_vc


title: PM373_endo_cs


title: PM373_tro2

value: Trophoblasts enz


title: AML cells, Input

city: Tokyo

first: Takuro

last: Nakamura

address: 3-8-31 Ariake, Koto-ku

department: The Cancer Institute

country: Japan

institute: Japanese Foundation for Cancer Research

data_processing:
Base calls were performed using Bowtie 1.1.1.
ChIP-seq reads were aligned to the mm9 genome assembly using samtools 1.2.
Peak call was performed using MACS1.4.
For every 300 bp window, the mapped tag count for ChIP, Cc and that for Input, Ci were used for calculation. Ec and Ei indicates the estimate count for 300 bp window for ChIP and Input. Signal ratio of ‘target TF’ was calculated as, Cc/Ec + 1 ÷ Max(1, Ci/Ei + 1).
Genome_build: mm9
Supplementary_files_format_and_content: tdf

source_name: Hoxa9 single expressing AML cells

growth_protocol: AML cells are maintained in IMDM supplemented with 10% FBS and 10 ng/ml IL3

extract_protocol:
Lysates were clarified from sonicated nuclei and immunoprecipitated with each antibodies
Libraries were prepared according to Illumina's instructions accompanying the ThruPLEX DNA-seq 6S (12) Kit (R400523). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Trib1 cDNA was introduced by retrovirus-mediated gene transfer

tag: cell line

value: AML cell line

tag: chip antibody


title: PM369_hofb_cs


title: 0084-V03

value: Pre-vaccination

value: Control


title: AML cells, Hi-CEBPa

data_processing:
Base calls were performed using Bowtie 1.1.1.
ChIP-seq reads were aligned to the mm9 genome assembly using samtools 1.2.
Peak call was performed using MACS1.4.
Genome_build: mm9
Supplementary_files_format_and_content: For every 300 bp window, the mapped tag count for ChIP, Cc and that for Input, Ci were used for calculation. Ec and Ei indicates the estimate count for 300 bp window for ChIP and Input. Signal ratio of ‘target TF’ was calculated as, Cc/Ec + 1 ÷ Max(1, Ci/Ei + 1).

source_name: Hoxa9/Trib1 AML

value: Hoxa9- and Trib1-expressing murine AML cells

value: C/EBPa (Santa Cruz, sc-61, lot H3106)


title: AML cells, Null-H3K27ac

value: Histone H3K27ac (Active Motif, 39133, lot 28518012)


title: 0081-V04


title: 0081-V05


title: PM370_strom_cs

value: Third

value: Stromal cs


title: PM367_vc

value: Villi


title: AML cells, Null-CEBPa


title: PM376_troph_cs

value: Trophoblasts cs


title: AML cells, Null-FLAG


title: PM364_endo_cs

value: M

value: placenta


title: 0083-V04

value: Whole blood

value: Female

value: Fever


title: 0079-V05

value: Male


title: PM373_hofb_cs

value: Hofbauer cs


title: 0079-V04


title: AML cells, Hi-H3K27ac

source_name: Hoxa9- and Trib1-expressing murine AML cells

value: AML cell line

value: Hoxa9 and Trib1


title: PM381_strom_cs


title: PM370_vc

value: F


title: 0078-V04

value: Pre-vaccination

value: Control


title: AML cells, Hi-FLAG


title: 0075-V05

value: Test


title: 0075-V04


title: PM368_endo_cs

value: Third

value: Endothelial cs


title: 0074-V05


title: PM379_troph_cs


title: PM375_tro2

value: Trophoblasts enz


title: Wild Type 4 Gy irradiated, replicate 3

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

description: Gene expression data from aged Wild type mouse, 4 Gy irradiated

hyb_protocol: Labeled fragments were hybridized to Affymetrix Mouse Gene ST 2.0 arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization oven 645.

scan_protocol: After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software.

data_processing: CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.

label: Biotin

source_name: Wild Type 4 Gy irradiated

label_protocol: We used the Affymetrix WT Pico kit for cDNA synthesis, amplification, and second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin, as described by the manufacturer.

growth_protocol: Nipa WT and Nipa KO mice older than 20 months were at least ten-generation C57BL/6-backcrossed, mouse housing was in accordance with national and institutional guidelines for animal care and experiments.

extract_protocol: Extraction of total RNA was performed by RNeasy Micro Kit (Quiagen) according to the manufacturer's instructions.

treatment_protocol: BMCs out of femurs were flushed in DMEM (+10% FCS) followed by lysis of erythrocytes for 5 minutes at room temperature and staining for Lineage markers (B220, CD3, CD4, CD8a, CD11b, GR1, TER119), cKIT and SCA1. LSK (Lineage-, SCA1+, cKIT+) cells were sorted by Beckman Coulter MoFlo XDP and cultured in BM media (DMEM, 30% fetal calf serum, 10ng/ml mIL-3, 10ng/ml mIL-6, 50ng/ml mSCF) in a 96-well plate for 30 minutes at 37°C with 5% CO2. Either not treated or 4 Gray irradiated LSK cells were harvested after 3 hours of culture and cell pelletts were stored at -80°C.

tag: age

value: older than 20 months

value: Wild type

tag: treatment

value: 4 Gy irradiated


title: PM370_troph_cs

value: placenta

value: Trophoblasts cs


title: Wild Type 4 Gy irradiated, replicate 2

tag: genotype


title: Wild Type 4 Gy irradiated, replicate 1


title: 0074-V03

value: Whole blood

value: Female

value: Fever


title: 0073-V03

value: Male


title: PL295_hofb_cs

tag: fetal sex

value: First

value: Hofbauer cs


title: PL293_troph_cs

value: M


title: PM381_troph_cs


title: Wild Type untreated, replicate 3

description: Gene expression data from aged Wild type mouse

source_name: Wild Type untreated

value: untreated


title: 0072-V05

value: Test


title: 0072-V04

value: Pre-vaccination


title: 0071-V05

value: Control


title: Wild Type untreated, replicate 2


title: 0071-V03


title: NIPA KO 4 Gy irradiated, replicate 3

description: Gene expression data from aged NIPA KO mouse, 4 Gy irradiated

source_name: NIPA KO 4 Gy irradiated

value: NIPA KO


title: 0068-V05


title: Wild Type untreated, replicate 1

value: older than 20 months


title: NIPA KO 4 Gy irradiated, replicate 2


title: NIPA KO 4 Gy irradiated, replicate 1


title: 0068-V04


title: 0067-V05


title: NIPA KO untreated, replicate 3

description: Gene expression data from aged NIPA KO mouse

source_name: NIPA KO untreated


title: 0067-V04


title: NIPA KO untreated, replicate 2


title: PL289_strom_cs

value: Stromal cs


title: P131_endo_cs

value: F

value: Endothelial cs


title: PM379_hofb_cs

value: Third

value: placenta


title: PM365_strom_cs


title: PM381_endo_cs


title: Drought idr1-1 rep2

city: Nanjing

first: gui

middle: Hong

last: La

address: XuanWu

country: China

institute: Nanjing Agricultural University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to tigr7 whole genome using hisat2 version 2.1.0
Reads counts were calculated using featureCounts version 1.6.3
Genome_build: tigr7
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Oryza sativa

source_name: leaf cell

extract_protocol:
5-week-old idr1-1 mutant and IAPAR9 plants were grown in concrete tanks for nonstressed or drought-stressed treatment and collected when soil moisture content was decreased to 10%. Total RNA was extracted from seedling using RNAiso Plus.(Takara, D9108B) for mRNA-seq.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: five-leaf-stage

tag: stress

value: Drought

value: leaf


title: Drought idr1-1 rep3


title: PM364_troph_cs

tag: trimester

value: Trophoblasts cs


title: Drought idr1-1 rep1


title: PM377_hofb_cs

tag: cell type

value: Hofbauer cs


title: PM366_troph_cs

tag: well


title: 0065-V05

tag: tissue

value: Whole blood

value: Male

value: Fever


title: 0063-V05

tag: vaccination status

value: Female


title: PM375_strom_cs


title: PL289_v

value: M

value: First

value: Villi


title: 0066-V04

value: Pre-vaccination

tag: study group

value: Test


title: PM379_vc

value: F


title: Drought wt rep2

value: wild type


title: 0063-V04

value: Control

tag: Sex


title: PM376_hofb_cs

value: Third

value: placenta


title: Drought wt rep1

value: five-leaf-stage

value: Drought

value: leaf


title: PM359_troph_cs

value: Trophoblasts cs


title: 0065-V03

value: Whole blood

value: Male

tag: post-vaccination log10 (menb sba titres)


title: 0062-V05

value: Female

tag: post-vaccination fever

value: Fever


title: Control idr1-1 rep3


title: 0062-V03


title: PM375_hofb_cs

value: Hofbauer cs


title: Control idr1-1 rep2


title: PL289_endo_cs

value: M

value: First

value: Endothelial cs


title: Drought wt rep3


title: 0061-V05


title: Control idr1-1 rep1


title: Control wt rep3


title: 0061-V03

value: Pre-vaccination


title: Control wt rep2

value: wild type


title: 0060-V04

value: Test


title: 0058-V05

value: Control


title: PM372_tro2

value: Third

value: placenta

value: Trophoblasts enz


title: Control wt rep1

value: five-leaf-stage

value: leaf


title: PM371_strom_cs

value: F

value: Stromal cs


title: 0058-V03

value: Whole blood

value: Male


title: 9311 96h-3 RNA-seq

city: Nanning

first: Jijing

last: Luo

state: Guangxi

address: 100 Daxue Rd.(East)

institute: Guangxi University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated. In short, the number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: MSU RGAP release 7.0
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Recovery treated seedlings

growth_protocol: The seedlings were grew under normal condition in growth chamber for 30 days

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

treatment_protocol: 30-day old seedlings were treated at day/night 10/8ºC for 3 days then recovered under normal condition for 24 h.

value: whole plants

value: 30 days

value: Chilling sensitive


title: PM377_endo_cs

value: Endothelial cs


title: 9311 96h-2 RNA-seq


title: 0056-V05

data_processing:
Human RNA-sequencing alignment against Homo sapiens genome build GRCh38 (https://ccb.jhu.edu/software/hisat2/index.shtml), using HISAT2 version 2.0.5.
Gene counting was conducted using the HTSeq version 0.9.1, utilizing human gene annotation gtf (General Transfer Format) version GRCh38.88 (www.ensembl.org).
Computational depletion of ribosomal RNA using SortMeRNA (version 2.1).
The R (version 3.4.4) software environment for statistical computing was used. R packages: edgeR, used TMM  (version 3.20.9), limma used voom function (version 3.34.9)

value: Fever


title: 0056-V03

value: Pre-vaccination


title: PL295_endo_cs

value: First


title: 9311 96h-1 RNA-seq


title: PM377_troph_cs

value: Trophoblasts cs


title: PM378_endo_cs

value: M

value: Third


title: PL296_endo_cs

value: placenta


title: 0055-V05

value: Control


title: 9311 84h-3 RNA-seq


title: PM371_vc

value: Villi


title: PM362_vc


title: NIPA KO untreated, replicate 1

value: older than 20 months

value: NIPA KO

value: untreated


title: 0055-V04

value: Whole blood

value: Male


title: 9311 84h-1 RNA-seq

value: whole plants

value: 30 days


title: 0053-V05

value: Test


title: 9311 72h-3 RNA-seq

source_name: Chilling treated seedlings

value: Chilling sensitive


title: 9311 72h-2 RNA-seq


title: 0053-V03

value: Pre-vaccination


title: 0052-V03

value: Female

value: Fever


title: 9311 24h-3 RNA-seq


title: 0050-V05


title: 0050-V04


title: 9311 72h-1 RNA-seq


title: 9311 24h-2 RNA-seq


title: 9311 24h-1 RNA-seq


title: PL292_v

value: M

value: First


title: PM368_strom_cs

value: Third

value: placenta

value: Stromal cs


title: 0047-V05

value: Control


title: 9311 12h-3 RNA-seq


title: 9311 12h-2 RNA-seq


title: 9311 12h-1 RNA-seq


title: PM365_troph_cs

value: F

value: Trophoblasts cs


title: 0048-V05

value: Whole blood


title: 9311 0h-3 RNA-seq


title: 0046-V05

value: Male


title: 0048-V04


title: PM371_endo_cs

value: Endothelial cs


title: 9311 0h-2 RNA-seq

value: whole plants

value: 30 days


title: PM365_vc

value: Villi


title: 0047-V03

value: Pre-vaccination


title: 9311 0h-1 RNA-seq

value: Chilling sensitive


title: W9 96h-3 RNA-seq

value: Chilling tolerance


title: PM369_endo_cs


title: PM359_hofb_cs

value: M

value: Hofbauer cs


title: PM364_vc

value: Third


title: 0041-V05

value: Test


title: P131_troph_cs

value: First

value: placenta


title: 0045-V05

value: Control

value: Fever


title: PL295_troph_cs

value: F

value: Trophoblasts cs


title: PL296_v


title: 0041-V04

value: Whole blood

value: Male


title: W9 96h-1 RNA-seq

value: whole plants

value: 30 days


title: PM378_vc

value: Villi


title: PM366_strom_cs

value: Stromal cs


title: PM362_troph_cs


title: 0039-V05

value: Female


title: PL293_hofb_cs

value: M


title: W9 84h-3 RNA-seq

value: Chilling tolerance


title: 0045-V04

value: Pre-vaccination


title: W9 84h-2 RNA-seq


title: PM367_troph_cs

value: Third


title: 0038-V05


title: PL290_v

value: First


title: PM376_strom_cs

value: placenta


title: W9 84h-1 RNA-seq


title: Autoimmune_hepatitis_3 ML-7

city: Oslo

first: Trine

last: Folseraas

state: Oslo

address: Sognsvannsveien 7

department: Transplantation Medicine

country: Norway

institute: Oslo University Hospital Rikshospitalet

hyb_protocol: Standard Affymetrix GeneChip hybridization control protocol/kit

scan_protocol: Standard Affymetrix hybridization protocol

data_processing: Standard Affymetrix GeneChip protocol

label: biotin

source_name: Liver tissue

label_protocol: cRNA  were prepared with the  Affymetric GeneChip WT CDNA syntheis and amplification kit and  Terminal Labeling Kit

extract_protocol: Total RNA was extracted from frozen liver tissue samples  using the RNeasy Mini Kit or Micro Kit (Qiagen).

tag: condition

value: Autoimmune hepatitis


title: Primary_biliary_cirrhosis_3 ML-8

value: Primary biliary cirrhosis


title: PM374_endo_cs

value: Endothelial cs


title: PM374_tro2

value: Trophoblasts enz


title: 0039-V03

extract_protocol:
Total RNA was extracted using the Blood RNA Kit (PreAnalytiX, Switzerland), using the automated protocol (QIAcube instrument, QIAGEN, Germany).
The ribodepleted and globin depleted fraction was selected from the total RNA using Ribo-ZeroTM Gold rRNA removal Kit (Illumina, USA). RNA was converted to cDNA, second-strand cDNA synthesis incorporated dUTP. The cDNA was end-repaired, A-tailed and adapter-ligated and prior to amplification, samples underwent uridine digestion (to ensure strand-specific sequencing)
The prepared libraries were size selected, multiplexed and quality controlled before 100bp paired-end sequencing (HiSeq4000). Sequencing was conducted at the Wellcome Trust Centre for Human Genetics (Oxford, UK).

value: Whole blood

value: Test

value: Fever


title: 0038-V03

value: Control


title: 0046-V03

value: Male


title: Autoimmune_hepatitis_2 ML-5


title: W9 72h-3 RNA-seq

value: whole plants

value: 30 days


title: 0037-V05


title: Alcohol_related_1 ML-6

value: Alcohol related


title: W9 72h-2 RNA-seq

value: Chilling tolerance


title: 0037-V04

value: Pre-vaccination


title: W9 72h-1 RNA-seq


title: PL295_strom_cs

value: F

value: Stromal cs


title: 0036-V05


title: Haemochromatosis_1 ML-3

value: Haemochromatosis


title: PM372_endo_cs

value: M

value: Third

value: placenta


title: Autoimmune_hepatitis_1 ML-4

value: Autoimmune hepatitis


title: W9 24h-2 RNA-seq


title: 0035-V05

value: Whole blood


title: PM368_troph_cs

value: Trophoblasts cs


title: W9 24h-3 RNA-seq


title: W9 24h-1 RNA-seq


title: 0036-V04

value: Test

value: Fever


title: FLAG-NRF3-3

city: San Diego

first: Lara

last: Ibrahim

state: California

address: 10550 N Torrey Pines Rd

data_processing:
Basescaling was performed by BGI
Single end, 50 bp-long reads from RNA Seq experiments were aligned to the GRCh37.p13 human genome reference assembly using SeqMan NGen 11.2.1 or 12.2.0 (DNAStar Inc.) using default parameters.
The assembly data were imported into ArrayStar 12.2 with Qseq (DNAStar Inc.) to quantify the gene expression levels. The sequence counts were normalized to reads per kilobase per million (RPKM) after filtering out non-mRNA sequence features.
Genome_build: GRCh37.p13 human genome reference assembly
Supplementary_files_format_and_content: XLSX file contains raw counts data for each sample

source_name: human embryonic kidney cells

growth_protocol: HEK293T cells were maintained in standard DMEM supplemented with 10%FBS and 1%PSQ at 37C and 5% CO2

extract_protocol:
Three independent experiments were performed. Cells were lysed and total RNA was collected (RNeasy mini kit, Qiagen)
Libraries were constructed using standard protocols at BGI

treatment_protocol: Cells were treated transfected with Fugene for 24 hr.

tag: cell line

value: transiently transfected with NRF3


title: FLAG-NRF3-2


title: Primary_biliary_cirrhosis_2 ML-2

value: Primary biliary cirrhosis


title: Primary_sclerosing_cholangitis_6_b PSC_6_b

value: Primary sclerosing cholangitis


title: PM370_hofb_cs

value: Hofbauer cs


title: W9 12h-3 RNA-seq

value: whole plants

tag: age

value: 30 days

value: Chilling tolerance


title: PM368_vc

value: Villi


title: 0034-V05

city: Oxford

last: O'Connor

address: Churchill Hospital

value: Female


title: FLAG-NRF2-3

tag: treatment

value: transiently transfected with NRF2


title: FLAG-NRF3-1


title: W9 12h-2 RNA-seq

tag: genotype


title: 0035-V03

value: Pre-vaccination

value: Control

value: Male


title: 0034-V04

value: Whole blood


title: PM367_strom_cs

tag: fetal sex

value: F

value: Third

value: placenta

value: Stromal cs


title: Primary_sclerosing_cholangitis_4_b PSC_4_b


title: W9 12h-1 RNA-seq


title: 0033-V05

value: Fever


title: FLAG-NRF2-1


title: W9 0h-3 RNA-seq


title: Primary_sclerosing_cholangitis_5_b PSC_5_b

value: Primary sclerosing cholangitis


title: 0033-V03


title: Primary_sclerosing_cholangitis_3_b PSC_3_b


title: PM376_vc


title: W9 0h-2 RNA-seq


title: FLAG-NRF1-3

value: transiently transfected with NRF1


title: 0032-V05

value: Test


title: W9 0h-1 RNA-seq

value: whole plants

value: 30 days


title: PL292_endo_cs

value: M

value: First

value: Endothelial cs


title: FLAG-NRF1-1


title: PM371_hofb_cs

value: Hofbauer cs


title: 0032-V04

value: Pre-vaccination


title: Primary_sclerosing_cholangitis_2_b PSC_2_b


title: Empty Vector-3

value: transiently transfected with empty vector


title: PL293_strom_cs


title: W9 96h-2 RNA-seq

value: Chilling tolerance


title: 0030-V05

value: Whole blood

value: Control

value: Male


title: Primary_sclerosing_cholangitis_1_b PSC_1_b


title: 0030-V03


title: 0029-V05

value: Female


title: Empty Vector-2


title: Empty Vector-1


title: Primary_sclerosing_cholangitis_5_a PSC_5_a


title: Primary_sclerosing_cholangitis_4_a PSC_4_a


title: 0029-V04

value: Fever


title: Primary_sclerosing_cholangitis_6_a PSC_6_a

value: Primary sclerosing cholangitis


title: Primary_sclerosing_cholangitis_3_a PSC_3_a