title: βDKO_sorted_3

city: Indianapolis

first: Jason

last: Spaeth

state: IN

address: 1210 Waterway Blvd

department: Pediatrics

institute: Indiana University

data_processing:
The generated FASTQ files were processed and interpreted using the Genialis visual informatics platform (https://www.genialis.com). Sequence quality checks were performed on raw and trimmed reads with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc), and Trimmomatic was used to trim adapters and filter out poor quality reads. Trimmed reads were then mapped to the mm10 UCSC reference genome using the HISAT2 aligner. Gene expression levels were quantified with HTSeq-count, and differential gene expression analyses performed with DESeq2. Poorly expressed genes, which have expression count summed over all samples below 10, were filtered out from the differential expression analysis input matrix
Genome_build: mm10
Supplementary_files_format_and_content: Processed Data File is presented as Transcripts per Million (TPM) and contains triplicates for Control and bDKO RNA-Sequencing datasets

source_name: Flow-Sorted islet β cells

growth_protocol: Isolated islets from Tamoxifen treated Control (MIP-CreERT;Brg1f/+;Brm+/-;R26LSL-tdTomato/+; ) or βDKO (MIP-CreERT; Brg1f/f; Brm-/-; R26LSLtdTomato/+) animals were dispersed into a single cell suspension (Accumax, Sigma A7089), stained with DAPI, and sorted by fluorescence activated cell sorting.

extract_protocol: RNA was isolated from FACS-purified β cells using the Maxwell 16 LEV simplyRNA Tissue Kit (Promega-TM351), then DNAse treated and analyzed on an Agilent 2100 Bioanalyzer. Only samples with an RNA Integrity Number above 8.0 were used for cDNA synthesis and library preparation

value: 7 Weeks

value: Mixed (C57BL/6J; 129SV)

value: Flow-Sorted islet beta cells

tag: genotype

value: BetaDKO


title: AGM1_GFPpAPCn

status: Public on Jun 01 2019

type: SRA

city: Edinburgh

first: Elaine

last: Dzierzak

address: 47 Little France Crescent

country: United Kingdom

institute: The University of Edinburgh

library_source: transcriptomic

data_processing:
Fastq files of 51bp single-end reads were quality controlled using FASTQC. Reads were then aligned to the GENCODE M14 mouse reference genome (mm10) using STAR aligner (version 2.3) for Linux Ubuntu, with default options, and ran over 8 threads per sample. For improved accuracy, the exon junction coordinates from the reference annotation were used. Resulting BAM files from different lanes were merged into one sample. Gene quantification on the merged samples was performed using featureCounts from the subRead package.
Genome_build: GENCODE Mouse Genome Release M14 (GRCm38.p5)
Supplementary_files_format_and_content: tab-delimited files per sample  include raw counts

molecule: total RNA

organism: Mus musculus

extract_protocol:
AGM were dissected from E10.5 MacGreen embryos, lysed with collagenase for 45 minutes at 37˚C and the cells were then FACS-sorted according to GFP and CD206-APC expression.
RNA was exctracted with the RNeasy micro kit (Qiagen) and RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: MacGreen (Csf1r-EGFP)

tag: developemental stage

tag: region

value: aorta-gonad- mesonephros (AGM)

tag: cell population


title: Mixture2.CBU1CANXX.SM2_103117p2_G2

city: Cambridge

first: Aviv

last: Regev

state: MA

address: 415 Main Street

department: Klarman Cell Observatory

country: USA

institute: Broad Institute

description:
Sex: Female for HEK293 and Male for NIH3T3
scRNA-seq
full-length
mixture_hg19_mm10_count_matrix.mtx, mixture_hg19_mm10_gene.tsv, mixture_hg19_mm10_cell.tsv

data_processing:
For scRNA-seq and snRNA-seq data, scumi v0.1.0 (https://bitbucket.org/jerry00/scumi-dev/src/master/) was used to produce cell by gene sparse matrices (UMI count matrices for 3'-end methods and read count matrices for Smart-seq2). More specifically, STAR v2.6.1a was used for alignment except for Smart-seq2 and CEL-Seq2 data where HISAT v2.0.5 was used. featureCounts from the Subread package, v1.6.2 was used to tag each alignment with a gene tag. For bulk RNA-Seq data, reads were mapped to the reference genomes using Bowtie v0.12.9, and further quantified by RSEM v1.3.0 to generate transcripts per million values.
Genome_build: scRNA-seq data: a merged hg19 and mm10 geome for human and mouse mixture datasets, hg38 (GRCh38) for human PBMCs, and mm10 for mouse cortex data; bulk RNA-Seq data, hg38 (GRCh38) for human data and mm10 for mouse data
Supplementary_files_format_and_content: scRNA-seq data: mtx, a gene by cell count matrix in the sparse matrix market format
Supplementary_files_format_and_content: scRNA-seq data: cell.tsv, cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: scRNA-seq data: gene.tsv, gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: Bulk RNA-Seq data: TPM_bulk.tsv, tab-delimited text files of transcripts per million measurements of genes in each sample
Supplementary_files_format_and_content: mixture_hg19_mm10_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: mixture_hg19_mm10_count_matrix.mtx :A gene by cell count sparse matrix in the matrix market format
Supplementary_files_format_and_content: mixture_hg19_mm10_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: pbmc_hg38_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: pbmc_hg38_count_matrix.mtx :A gene by cell count matrix in the matrix market format
Supplementary_files_format_and_content: pbmc_hg38_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: cortex_mm10_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: cortex_mm10_count_matrix.mtx :A gene by cell count sparse matrix in the matrix market format
Supplementary_files_format_and_content: cortex_mm10_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: HEK293_PBMC_TPM_bulk.tsv :A matrix of transcripts per million measurements
Supplementary_files_format_and_content: NIH3T3_cortex_TPM_bulk.tsv :A matrix of transcripts per million measurements

organism:
Homo sapiens
Mus musculus

source_name: Mixture of human HEK293 and murine NIH3T3 cell lines

extract_protocol:
Total RNA from bulk samples was extracted using Quick-RNA Mini Prep (Zymo Research) following the vendor protocol with a DNase treatment step
For library construction methods, see SAMPLES, description: Library Construction field. For details see the Methods section in the manuscript

tag: Sex

value: Pooled male and female

tag: library construction


title: Mixture2.CBU1CANXX.SM2_103117p2_G10


title: OL day3

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: Rat mRNA comparison

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

organism: Rattus norvegicus

source_name: Rat oligodendrocyte precursors

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Rat oligodendrocyte precursors are cultured in standard Raff medium and grown.

extract_protocol: RNA samples were extracted from cells using RNesy mini kit (Quiagen).

treatment_protocol: Rat oligodendrocyte precursors are cultured in Raff medium and allowed to be differentiated in standard grwoth factor changes.

tag: lymphocyte

value: Rat oligodendrocyte precursors

tag: cit induced switching

value: Differentiated condition (after differentiation)


title: βDKO_sorted_2

tag: age

tag: cell type


title: PBMC1.CC7W2ANXX.SM2_120717p3_G1

description:
scRNA-seq
full-length
pbmc_hg38_count_matrix.mtx, pbmc_hg38_gene.tsv, pbmc_hg38_cell.tsv

organism: Homo sapiens

source_name: Peripheral blood mononuclear cell

value: Male


title: Mixture2.CBU1CANXX.SM2_103117p2_F9


title: MHC-II0:CD8ab Tg CD4-CD8- mature thymocytes 2

city: Kyoto

first: Wooseok

last: Seo

address: Yoshida-Konoe-cho, Sakyo-ku

institute: Kyoto University Graduate School of Medicine

data_processing:
Reads were mapped by Tophat v2.1.1 onto mouse genome mm10 and counts were generated using HTSeq v.0.6.1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_counts.txt: Read count by genes. WT counts were obtained from GSE48138.

source_name: Mouse CD8+ mature thymocytes

extract_protocol: Sequencing libraries were prepared by NEBNext RNA Library Prep Kit for Illumina according to the manufacturer’s protocol (NEB, E7530). Single end 50bp reads were obtained by Illumina HiSeq 1500.

tag: strain/background

tag: genotype/variation

value: MHC-II0:CD8ab Tg

value: CD8+ mature thymocytes


title: βDKO_sorted_1


title: Mixture2.CBU1CANXX.SM2_103117p2_F8


title: PBMC1.CC7W2ANXX.SM2_120717p3_F6


title: H3K27ac_E12.5_Rep1

city: Berlin

first: Daniel

middle: Murad

last: Ibrahim

state: Berlin

address: Augustenburger Platz 1

department: Center for Regenerative Therapies

country: Germany

institute: Berlin Institute of Health

library_source: genomic

data_processing:
The data was processed as described in Andrey et al., 2017. Briefly, single-end reads from ChIP-seq experiments were mapped with bowtie (v2.2.6) to the reference genome mm9. Mapped reads were filtered for mapping quality MAPQ ≥10, and duplicates were removed using samtools (v1.8). Reads were extended (Rad21 and CTCF: 200bp; histone modifications: 300bp) and scaled by the total number of unique reads (total count of reads/106) to produce coverage tracks that could be visualized in UCSC. ChIP-seq data for WT forelimbs of H3K4me1, H3K4me3, H3K27ac, H3K27me3 and CTCF was taken from Andrey et al., 2017 (GEO accession number: GSE84795). ChIP-seq experiments for WT forelimbs of H3K9me3 were generated and performed as described above. Since H3K9me3 is often targeting repetitive regions, no mapping quality cutoff was applied.
The analysis of CTCF motif orientation in ChIP-seq peaks was performed using the FIMO algorithm with p<10^-4 of the MEME suite. The genomic sequence underlying a CTCF peak was used as input to determine the motif orientation. The CTCF motif matrix  used as input corresponds to the position weight matrix (PWM) of MA0139.1 from the JASPAR database.
Genome_build: mm9

molecule: genomic DNA

source_name: Embryonic limb bud

growth_protocol: Limb buds (stage E12.5) were micro-dissected from mouse embryos

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with the respective antibody.
We sheared chromatin using Bioruptor until reaching a fragment size of 200-500bp. 10-15μg of chromatin was then used for each replicate H3K27ac ChIP and 30μg for CTCF ChIP. Antibodies: H3K27ac (Diagenode, C15410174) and CTCF (Active motif: 613111) was then performed as in Ibrahim et al. 2013.
Libraries were prepared using the Nextera adaptors and sequenced

treatment_protocol: Dissected tissue from embryos was pooled and turned into a single-cell suspension by digestion with Trypsin-EDTA 0.05% (Gibco) for 10 min at 37°C shaking at 900 RPM.The cells were mixed with 10%FCS/PBS and homogenized using a 40 µm cell strainer (Falcon). After centrifugation, cells were fixed in 1% PFA/10%FCS/PBS for 10’ at room temperature. Cells were then lysed 3C-Lysis buffer and nuclei pelleted by centrifugation. Then, nuclei were resuspended in buffer 3 for sonication (Lee et al. 2006).

tag: tissue

value: Embryonic limb bud

value: WT

tag: embryonic stage

tag: background

value: G4 ESC


title: H3K27ac_E12.5_Rep2


title: CTCF_E12.5_Rep2


title: Mixture2.CBU1CANXX.SM2_103117p2_F6


title: Control_sorted_2

value: control


title: Control_sorted_3


title: CTCF_E12.5_Rep1


title: Mixture2.CBU1CANXX.SM2_103117p2_F7


title: PBMC1.CC7W2ANXX.SM2_120717p3_F4


title: PBMC1.CC7W2ANXX.SM2_120717p3_F5


title: OL day0

description: Rat mRNA comparison

value: Control condition (before differentiation)


title: ATAC_E12.5_Rep2

data_processing:
Paired-end reads were processed as described in the ENCODE (Encode Consortium, 2012) guidelines for mouse ATAC-seq samples. Firstly, ATAC-seq paired-end reads were trimmed to 30bp to allow fragments with closeby transposition events (<50bp) to map, i.e. increase read coverage at Nucleosome Free Regions. Secondly, trimmed reads were mapped with Bowtie2 (Langmead and Salzberg, 2012) and removed duplicated fragments with Picard RemoveDuplicates (https://broadinstitute.github.io/picard/). Lastly, bigWig files for display were generated with deepTools2 (Ramírez et al., 2016) for properly mapped read pairs (FLAG 0x2) with mapping quality ≥20.
Genome_build: mm9

extract_protocol:
50.000 cells were used for each reaction of tagmentation and protocol was performed as previously described (Buenrostro JD et al., 2015).
Libraries were prepared using the Nextera adaptors and sequenced

treatment_protocol: Limbs from E12.5 mouse embryos were homohenized with Collagenase solution to achieve single cell suspension.


title: Mixture2.CBU1CANXX.SM2_103117p2_F5


title: PBMC1.CC7W2ANXX.SM2_120717p3_F3


title: Control_sorted_1

value: 7 Weeks


title: ATAC_E12.5_Rep1


title: PBMC1.CC7W2ANXX.SM2_120717p3_F2


title: P30-C57_rep3 [re-analysis]

city: Saclay

first: Jerome

middle: Eric

last: Roger

state: Please select

address: 151 Route de la Rotonde, Campus CEA Saclay - Bat 151

department: CERTO

country: France

institute: CNRS-Universite Paris Sud

description:
R42015-069pf_WT_Retina-23
This is duplicated sample record of GSM2477834 for the convenient retrieval

data_processing:
Paired-end sequencing of 40 bases length was performed on NextSeq 500 (Illumina)
Pass-filtered reads were mapped using HISAT2 2.1.0 and aligned to Ensembl mouse reference genome GRCm38.84.
Count table of the gene features was obtained using FeatureCounts
Normalization, differential expression analysis and FPKM (fragments per kilobase of exon per million fragments mapped) values were computed using EdgeR
Genome_build: Ensembl GRCm38.84
Supplementary_files_format_and_content: tab-delimited text files include counts from FeatureCounts and List of Differentially expressed genes with FPKM values for each Sample, fold change, p-value and adjusted p-value

source_name: wild type mouse retina at age postnatal day 30

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Nucleospin RNA Plus kit, which includes DNase treatment. 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 directional next-generation sequencing using a modified TruSeq RNA Sample Preparation Kit protocol as described. The protocol utilizes the labeling of the second strand of cDNA with uracil, which allows the degradation of this strand prior to sequencing.

tag: strain background

value: wild type

value: post natal day 30

value: Retina


title: Mixture2.CBU1CANXX.SM2_103117p2_F3


title: Mixture2.CBU1CANXX.SM2_103117p2_F2


title: P30-C57_rep2 [re-analysis]

description:
R42015-068pf_WT_Retina-4
This is duplicated sample record of GSM2477833 for the convenient retrieval


title: PBMC1.CC7W2ANXX.SM2_120717p3_E6


title: Mixture2.CBU1CANXX.SM2_103117p2_F1


title: P30-C57_rep1 [re-analysis]

description:
R42015-067pf_WT_Retina-1
This is duplicated sample record of GSM2477832 for the convenient retrieval


title: PBMC1.CC7W2ANXX.SM2_120717p3_E5


title: PBMC1.CC7W2ANXX.SM2_120717p3_E4


title: Mixture2.CBU1CANXX.SM2_103117p2_F12


title: Ost_mock_Day8_2

city: Baltimore

first: Vivek

last: Thumbigere Math

state: MD

address: 650 W Baltimore Street

department: Periodontics

institute: Universityof Maryland

data_processing:
Convert from BCL and demultiplex using Casava 1.8.4 or bcl2fastq 2.17.1
Map to mm10 using Tophat 2.1.0
Calculate RPKM using Partek GS 6.6
ANOVA comparisons on Log2 RPKM (with 0.1 offse) using Partek GS 6.6
PCA plots of RPKM values using Partek GS 6.6
Normalized BigWig files using deepTools bamCoverage
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files

source_name: cultured BMM

extract_protocol:
RNAeasy extraction of total RNA was performed according to the manufacturer's (Qiagen) instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMMs from Irf8-/- and Irf8+/+ mice were cultured in the presence of MCSF and RANKL for 8 days to generate terminally differentiated osteoclasts. For transduction studies, BMMs from Irf8-/- mice were transduced with hIRF8WT, hIRF8G388S, or hIRF8379-389, followed by treatment with MCSF and RANKL for 8 days to generate terminally differentiated osteoclasts.

value: Osteoclast

tag: genotype

value: mock

tag: time point


title: PBMC1.CC7W2ANXX.SM2_120717p3_E3


title: Ost_mock_Day8_1


title: Mixture2.CBU1CANXX.SM2_103117p2_F11

value: Pooled male and female


title: Ost_mock_Day4_3


title: PBMC1.CC7W2ANXX.SM2_120717p3_E2


title: Mixture2.CBU1CANXX.SM2_103117p2_F4


title: Mixture2.CBU1CANXX.SM2_103117p2_F10


title: PBMC1.CC7W2ANXX.SM2_120717p3_G2


title: Transient Embryonic Cartilage

city: Vienna

first: Florien

last: Jenner

address: Veterinärplatz 1

department: Equine Surgery

country: Austria

institute: University of Veterinary Medicine Vienna

description: gene expression joint development

hyb_protocol: samples were hybridized overnight (17 hours, 65°C) to an Agilent Whole Horse Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven.

scan_protocol: Fluorescence signals of the hybridized microarrays were detected using Agilent’s Microarray Scanner System.

data_processing: The Agilent Feature Extraction Software was used to read out and process the microarray image files using default parameters.

organism: Equus caballus

source_name: cartilage

label_protocol: RNA was amplified using SuperAmp (Agilent Technologies, Paolo Alto, CA, USA), a global PCR protocol using mRNA-derived cDNA, according to the manufacturer’s protocol. Yields of cDNA were measured with a NanoDrop ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies, Wilmington, USA). The integrity of the cDNA was checked via the Agilent 2100 Bioanalyzer platform. 250 ng of each of the cDNAs was labelled with Cyanine 3-CTP (Cy-3)

extract_protocol: The harvested cells were lysed for 30 minutes using RLT lysis buffer (RNeasy® Micro kit, Qiagen Sciences Inc, Hilden, Germany), then vortexed and frozen at −20°C. Total RNA was extracted from cell lysates using RNeasy Micro Kits according to manufacturer's protocols. RNA was stored at −80°C.

treatment_protocol: Cartilage samples and the E40 hindlimbs were placed in the cryostat chamber for temperature equilibration, embedded in frozen section medium (Neg-50,ThermoFisher, Walldorf) and sectioned along their sagittal axis using a cryostat (Hyrax C 50 Cryostat, Carl Zeiss Microscopy GmbH, Jena, Germany) at a −25°C chamber/chuck temperature. Sections (10μm) were mounted onto precooled RNAse-free polyethylene naphthalate (PEN)-coated slides (Zeiss MembraneSlide 1.0 PEN NF) and stained with cresyl violet according to a standard protocol from Zeiss Labs, Munich, Germany (step 1: fixation in 70% Ethanol for 2 min; step 2: 30 sec in 1% cresyl violet acetate solution; step 3: dip into 70% followed by 100% Ethanol; step 4: air-dry 1-2 min). The cartilage thickness was measured from the articular surface to the tidemark, confirming the reported cartilage thickness of the equine stifle of 1500 – 2000 μm [30] and divided into a superficial (superficial 10%; AACS), middle (adjacent 20-30%; AACM) and deep (50-90% depth; AACD) layer (figure 1) [3,14]. Cells were selected from the ACCS, ACCM, ACCD, II, OI and EC using laser capture microdissection (PALM MicroBeam system, Carl Zeiss Microscopy GmbH), catapulting the selected tissues of each sample group directly into separate 500 μl AdhesiveCap tubes (Carl Zeiss Microscopy GmbH), avoiding contact with any surface and thereby RNase contamination.

tag: developmental stage

value: fetus - gestational day 40

value: cartilage

tag: tissue subtype

value: Transient Embryonic Cartilage


title: PBMC1.CC7W2ANXX.SM2_120717p3_F1

value: Male


title: Outer Interzone

description: gene expression joint development

source_name: interzone

value: interzone

value: outer (OI)  interzone layers


title: Adult Articular Cartilage Deep Zone

description: gene expression articular cartilage zones

value: adult - 15 years

value: deep (AACD)  adult articular cartilage zone


title: Ost_mock_Day4_2


title: Intermediate Interzone

description: gene expression joint development

value: intermediate (II) interzone layers


title: Mixture2.CBU1CANXX.SM2_103117p2_E9


title: Adult Articular Cartilage Middle Zone

value: middle (AACM) adult articular cartilage zone


title: PBMC1.CC7W2ANXX.SM2_120717p3_E1


title: Ost_mock_Day4_1


title: Adult Articular Cartilage Superficial Zone

value: superficial (AACS) adult articular cartilage zone


title: SHR 49 2016

city: Denver

first: David

last: Bertolatus

state: CO

address: Campus Box 171, PO BOX 173364

department: Integrative Biology

institute: University of Coloroado Denver

hyb_protocol: Agilent Technologies One-Color Microarray-Based Gene Expression Analysis Protocol was used. There was 600 ng of Cy3-labeled cRNA used.

scan_protocol: Microarrays were kept in the dark until scanned at 5 um, channel G, Agilent HD (61x21.6mm) using the Agilent DNA Microarray Scanner with SureScan High ResolutionTechnology.

data_processing: Agilent Feature Extraction Software was used. Data are processed signal intensity values, Log 2 transformed, quantile normalized, and filtered to 1.28 as limit of detection

organism: Pimephales promelas

label_protocol: Agilent one color protocol for Cy3 following manufacturer's protocol

extract_protocol: Trizol protocol for total RNA following manufacturer's protocol

treatment_protocol: Adult male fathead minnows (Pimephales promelas) were exposed to water from sites througout the Shenandoah River watershed (VA, USA) in flow-through mobile laboratoires for 7 days.

tag: treatment

value: SHR

value: Liver

value: Adult

value: male


title: Ost_mock_Day0_2

value: Osteoclast

value: mock


title: PBMC1.CC7W2ANXX.SM2_120717p3_D6

tag: Sex


title: PBMC1.CC7W2ANXX.SM2_120717p3_D4

tag: library construction


title: Ost_mock_Day0_3


title: PBMC1.CC7W2ANXX.SM2_120717p3_D5


title: Mixture2.CBU1CANXX.SM2_103117p2_E7

value: Pooled male and female


title: NFSRA 35 2016

value: NFSRA


title: IC 7 2016

value: Initial Control


title: Ost_mock_Day0_1


title: PBMC1.CC7W2ANXX.SM2_120717p3_D3

value: Male


title: Ost_IRF8WT_Day8_3


title: Mixture2.CBU1CANXX.SM2_103117p2_E5


title: PBMC1.CC7W2ANXX.SM2_120717p3_D2


title: SFSR 25 2016

value: SFSR


title: Ost_IRF8WT_Day8_2


title: PBMC1.CC7W2ANXX.SM2_120717p3_D1


title: Mixture2.CBU1CANXX.SM2_103117p2_E3


title: Ost_IRF8WT_Day8_1


title: SHR 41 2016


title: Ost_IRF8WT_Day4_3


title: Ost_IRF8WT_Day4_1


title: Mixture2.CBU1CANXX.SM2_103117p2_E1


title: Mixture2.CBU1CANXX.SM2_103117p2_E12


title: PBMC1.CC7W2ANXX.SM2_120717p3_C5


title: Mixture2.CBU1CANXX.SM2_103117p2_E2


title: Mixture2.CBU1CANXX.SM2_103117p2_E6


title: NFSRB 65 2016

value: NFSRB


title: Mixture2.CBU1CANXX.SM2_103117p2_E4


title: PBMC1.CC7W2ANXX.SM2_120717p3_C3


title: NFSRB 66 2016


title: PBMC1.CC7W2ANXX.SM2_120717p3_C2


title: Ost_IRF8WT_Day0_2


title: IC 5 2016


title: Ost_IRF8WT_Day0_1


title: IC 3 2016


title: PBMC1.CC7W2ANXX.SM2_120717p3_C1


title: Mixture2.CBU1CANXX.SM2_103117p2_E10


title: Mixture2.CBU1CANXX.SM2_103117p2_E8


title: Mixture2.CBU1CANXX.SM2_103117p2_D9


title: PBMC1.CC7W2ANXX.SM2_120717p3_C4


title: PBMC1.CC7W2ANXX.SM2_120717p3_C6


title: PBMC1.CC7W2ANXX.SM2_120717p3_B6


title: Ost_IRF8KO_Day8_3


title: SHR 44 2016


title: Mixture2.CBU1CANXX.SM2_103117p2_D8


title: Mixture2.CBU1CANXX.SM2_103117p2_E11


title: PBMC1.CC7W2ANXX.SM2_120717p3_B5


title: Mixture2.CBU1CANXX.SM2_103117p2_D7


title: Ost_IRF8KO_Day8_1


title: PBMC1.CC7W2ANXX.SM2_120717p3_B4


title: NFSRA 36 2016


title: Mixture2.CBU1CANXX.SM2_103117p2_D6


title: SFSR 24 2016


title: Ost_IRF8KO_Day4_3


title: NFSRW 59 2016

value: NFSRW


title: NFSRW 54 2016


title: Mixture2.CBU1CANXX.SM2_103117p2_D4


title: Mixture2.CBU1CANXX.SM2_103117p2_D5


title: Ost_IRF8KO_Day4_2


title: NFSRW 57 2016


title: NFSRB 63 2016


title: PBMC1.CC7W2ANXX.SM2_120717p3_B2


title: PBMC1.CC7W2ANXX.SM2_120717p3_B3


title: Ost_IRF8KO_Day8_2


title: Ost_IRF8KO_Day4_1


title: Mixture2.CBU1CANXX.SM2_103117p2_D3


title: Ost_IRF8KO_Day0_3


title: PBMC1.CC7W2ANXX.SM2_120717p3_B1


title: IC 6 2016


title: SFSR 30 2016


title: SHR 42 2016


title: PBMC1.CC7W2ANXX.SM2_120717p3_A6


title: Mixture2.CBU1CANXX.SM2_103117p2_D2


title: PBMC1.CC7W2ANXX.SM2_120717p3_A5


title: Ost_IRF8KO_Day0_2


title: Mixture2.CBU1CANXX.SM2_103117p2_D1


title: NFSRW 58 2016


title: NFSRA 38 2016


title: Ost_IRF8KO_Day0_1


title: Mixture2.CBU1CANXX.SM2_103117p2_D12


title: PBMC1.CC7W2ANXX.SM2_120717p3_A4


title: Ost_hIRF8WT_Day8_2


title: Mixture2.CBU1CANXX.SM2_103117p2_D11


title: Ost_hIRF8WT_Day8_1


title: Mixture2.CBU1CANXX.SM2_103117p2_D10


title: PBMC1.CC7W2ANXX.SM2_120717p3_A2


title: PBMC1.CC7W2ANXX.SM2_120717p3_A1


title: Ost_hIRF8WT_Day0_3


title: Mixture2.CBU1CANXX.SM2_103117p2_C9


title: Ost_hIRF8WT_Day0_2


title: PBMC1.CC7W2ANXX.SM2_120717p2_H6


title: NFSRA 39 2016


title: NFSRB 67 2016


title: Ost_hIRF8WT_Day0_1


title: Mixture2.CBU1CANXX.SM2_103117p2_C8


title: PBMC1.CC7W2ANXX.SM2_120717p2_H5


title: SHR 50 2016


title: NFSRB 62 2016


title: Mixture2.CBU1CANXX.SM2_103117p2_C7


title: NFSRW 56 2016


title: Ost_hIRF8G388S_Day8_2


title: PBMC1.CC7W2ANXX.SM2_120717p3_A3


title: SHR 43 2016


title: PBMC1.CC7W2ANXX.SM2_120717p2_H4


title: SFSR 29 2016


title: Ost_hIRF8G388S_Day8_1


title: Mixture2.CBU1CANXX.SM2_103117p2_C6


title: PBMC1.CC7W2ANXX.SM2_120717p2_H3


title: Ost_hIRF8G388S_Day4_3


title: Mixture2.CBU1CANXX.SM2_103117p2_C5


title: Mixture2.CBU1CANXX.SM2_103117p2_C4


title: Ost_hIRF8G388S_Day4_2


title: PBMC1.CC7W2ANXX.SM2_120717p2_H1


title: Ost_hIRF8G388S_Day4_1


title: Mixture2.CBU1CANXX.SM2_103117p2_C3


title: IC 10 2016


title: NFSRB 68 2016


title: PBMC1.CC7W2ANXX.SM2_120717p2_G6


title: Mixture2.CBU1CANXX.SM2_103117p2_C2


title: PBMC1.CC7W2ANXX.SM2_120717p2_G5


title: Ost_hIRF8G388S_Day0_3


title: Ost_hIRF8G388S_Day0_2


title: Mixture2.CBU1CANXX.SM2_103117p2_C1


title: Mixture2.CBU1CANXX.SM2_103117p2_C12


title: SFSR 27 2016


title: PBMC1.CC7W2ANXX.SM2_120717p2_G4


title: Mixture2.CBU1CANXX.SM2_103117p2_C11


title: Ost_hIRF8G388S_Day0_1


title: PBMC1.CC7W2ANXX.SM2_120717p2_H2


title: SHR 45 2016


title: Ost_hIRF8379-389_Day8_3


title: Mixture2.CBU1CANXX.SM2_103117p2_C10


title: NFSRA 33 2016


title: SFSR 23 2016


title: IC 8 2016


title: Ost_hIRF8379-389_Day8_2


title: PBMC1.CC7W2ANXX.SM2_120717p2_G1


title: SFSR 26 2016


title: Ost_hIRF8379-389_Day8_1


title: PBMC1.CC7W2ANXX.SM2_120717p2_F6


title: Mixture2.CBU1CANXX.SM2_103117p2_B9


title: Mixture2.CBU1CANXX.SM2_103117p2_B8


title: PBMC1.CC7W2ANXX.SM2_120717p2_G3


title: Ost_hIRF8379-389_Day4_3


title: SHR 46 2016


title: PBMC1.CC7W2ANXX.SM2_120717p2_F5


title: PBMC1.CC7W2ANXX.SM2_120717p2_F4


title: Mixture2.CBU1CANXX.SM2_103117p2_B6


title: PBMC1.CC7W2ANXX.SM2_120717p2_G2


title: Ost_hIRF8379-389_Day4_1


title: PBMC1.CC7W2ANXX.SM2_120717p2_F2


title: PBMC1.CC7W2ANXX.SM2_120717p2_F3


title: Ost_hIRF8379-389_Day0_2


title: Mixture2.CBU1CANXX.SM2_103117p2_B4


title: IC 9 2016


title: Ost_hIRF8379-389_Day0_3


title: NFSRW 60 2016


title: PBMC1.CC7W2ANXX.SM2_120717p2_F1


title: IC 4 2016


title: NFSRB 61 2016


title: Ost_hIRF8379-389_Day4_2


title: Ost_hIRF8379-389_Day0_1


title: SFSR 28 2016


title: PBMC1.CC7W2ANXX.SM2_120717p2_E6


title: Mixture2.CBU1CANXX.SM2_103117p2_B2


title: Mixture2.CBU1CANXX.SM2_103117p2_B7


title: MNA_TDM_2

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

institute: Uniklinikum Erlangen

description:
GEO_NGS_killy_lang.txt
X195287_trimmed_

data_processing:
Base-calling Illumina HiSeq 2500 platform (100 bp single-end)
Sequenced reads were trimmed for adaptor sequence
quality trimming fastx toolkit v0.0.14, base position 99 and 100 were trimmed
trimmed reads were mapped  to the Mus musculus reference genome GRCm38.89 using STAR v2.5.3a --outSAMstrandField intronMotif --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM
transcript/ gene level quantification with Salmon (version 0.8.2)
data normalization using TMM, edgeR, Bioconductor R-package, statistical analysis for differentially expressed genes using limma Bioconductor R-package, limma-trend
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include log2 fold changes for each comparison and log2 CPM (counts per million reads) for each sample

source_name: bone marrow derived macrophages

growth_protocol: macrophage differentiation for 7 days in M-CSF containing cDMEM (DMEM Gibco™ supplemented with 10% FCS, 1% Penicillin (10000 U)/ Streptomycin (10mg/ml), 0,05% β-mercaptoethanol (50µM))

extract_protocol:
total RNA from BMDM was isolated usin the PeqGold RNA Micro Kit (Peqlab Biotechnology GmbH, Erlangen, Germany) for total RNA isolation, DNase digestion was performed on the provided columns, elution volume 21,5µl
Illumina TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: stimulatin with TDM 2µg/ml or Isopropanol (solvent control) for 24h

tag: strain

value: bone marrow

value: macrophage

value: Mincle-/-

tag: stimulation

value: TDM

tag: Stage

value: M-CSF day 7


title: PBMC1.CC7W2ANXX.SM2_120717p2_E5


title: Mixture2.CBU1CANXX.SM2_103117p2_B1


title: WT_TDM_2

description:
GEO_NGS_killy_lang.txt
X195286_trimmed_

tag: cell type

value: wildtype


title: Mixture2.CBU1CANXX.SM2_103117p2_B5


title: NFSRW 51 2016

value: Liver

tag: age

value: Adult


title: SFSR 79 2015

hyb_protocol: Agilent Technologies One-Color Microarray-Based Gene Expression Analysis Protocol was used May, 2010.

scan_protocol: Microarrays were kept in the dark until scanned at 5 um, channel G, Agilent HD (61x21.6mm) at 100% PMT (Agilent Microarray Scanner with SureScan Technology).  Agilent Feature Extraction Software (v10.7)  calculated parameters for Extended Dynamic Range.

data_processing: Normalized signal intensity provided here is quantile normalization with a minimum intensity cut off of 2.9

source_name: Liver, adult male

label_protocol: Agilent one color protocol for Cy3

extract_protocol: Trizol protocol for total RNA

treatment_protocol: Agilent one color protocol for Cy3

tag: site


title: SFSR 80 2015


title: PBMC1.CC7W2ANXX.SM2_120717p2_E4


title: Mixture2.CBU1CANXX.SM2_103117p2_B12


title: MNA_Isopropanol_2

description:
GEO_NGS_killy_lang.txt
X195285_trimmed_

tag: tissue

value: Isopropanol


title: WT_Isopropanol_2

description:
GEO_NGS_killy_lang.txt
X195284_trimmed_


title: Mixture2.CBU1CANXX.SM2_103117p2_B3


title: Mixture2.CBU1CANXX.SM2_103117p2_B11


title: Ost_IRF8WT_Day0_3

value: Osteoclast


title: MNA_TDM_1

description:
GEO_NGS_killy_lang.txt
X195283_trimmed_


title: PBMC1.CC7W2ANXX.SM2_120717p2_E1


title: Mixture2.CBU1CANXX.SM2_103117p2_A9

value: Pooled male and female


title: Mixture2.CBU1CANXX.SM2_103117p2_B10


title: PBMC1.CC7W2ANXX.SM2_120717p2_D6


title: PBMC1.CC7W2ANXX.SM2_120717p2_D5


title: Mixture2.CBU1CANXX.SM2_103117p2_A8


title: MNA_Isopropanol_1

description:
GEO_NGS_killy_lang.txt
X195281_trimmed_


title: Mixture2.CBU1CANXX.SM2_103117p2_A7


title: NFSRD 60 2015

value: NFSRD


title: PBMC1.CC7W2ANXX.SM2_120717p2_E2


title: PCFH 68 2015

value: PCFH


title: PBMC1.CC7W2ANXX.SM2_120717p2_D4

value: Male


title: Mixture2.CBU1CANXX.SM2_103117p2_A6


title: PCFH 70 2015


title: SFSR 77 2015

value: SFSR


title: SFSR 78 2015


title: NFSRD 59 2015


title: PCFH 67 2015


title: PBMC1.CC7W2ANXX.SM2_120717p2_D3


title: Mixture2.CBU1CANXX.SM2_103117p2_A5


title: RNA-seq WT 2 Ac2h

city: Beijing

first: Bofeng

last: Liu

address: Haidian District

department: School of Life Science

country: China

institute: Tsinghua University

data_processing:
Basecalls performed using CASAVA version 1.8
ATAC-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
RNA-Seq reads were aligned to the mm9 genome assembly using STAR version 2.4.0, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.2.1
ChIP-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
Genome_build: mm9
Supplementary_files_format_and_content: The wig files counted by the number of reads falling into 100bp bin in the genome. Tab-delimited text files include RPKM values for each sample

source_name: mouse embryonic stem cell

growth_protocol:
Trim33 WT ESCs in C57Bl/6J background ESCs were induced into differentiation on ultra-low plates with 15% serum medium withdraw LIF and cells were harvested at d2.5 before activin A (50 ng/ml, R&D Systems) treated for 2hs
mESCs were maintained on gelatin-coated plates with ESCs culture serum medium as descriped in Wang et al.2017

extract_protocol:
Total RNA purified from d2.5 EBs with Trim33 WT ESCs in C57Bl/6J background (as described (Xi et al., 2008) was quantified by Ribogreen and quality assessed by Agilent BioAnalyzer 2000
The RNA-seq library preparation and sequencing was performed as descripted before (Wang et al.,2017)
After scraped from plate, embryonic stem cells were washed with PBS and incubated in lysis buffer.

treatment_protocol:
differentiatino was induced on ultra-low plates with medium withdraw LIF and cells were harvested at d2.5 before activin A (50 ng/ml, R&D Systems) treated for 2hs
Embryoid body (EB) formation and differentiation were carried out as described by the supplier (ATCC). Prior to total RNA extraction cells were treated with activin A (50 ng/ml, R&D Systems) or SB431542 (10 mM, TOCRIS).

value: activin A (50 ng/ml, R&D Systems)

tag: genotype/variation

value: Trim33 WT

value: C57Bl/6J background ESCs(Xi et al., 2011)

value: d2.5 EBs


title: PBMC1.CC7W2ANXX.SM2_120717p2_D2


title: Mixture2.CBU1CANXX.SM2_103117p2_A4


title: RNA-seq WT 1 SB2h

growth_protocol:
Trim33 WT ESCs in C57Bl/6J background ESCs were induced into differentiation on ultra-low plates with 15% serum medium withdraw LIF and cells were harvested at d2.5 before SB431542 (10 mM, TOCRIS) treated for 1h
mESCs were maintained on gelatin-coated plates with ESCs culture serum medium as descriped in Wang et al.2017

treatment_protocol:
differentiatino was induced on ultra-low plates with medium withdraw LIF and cells were harvested at d2.5 before SB431542 (10 mM, TOCRIS) treated for 1h
Embryoid body (EB) formation and differentiation were carried out as described by the supplier (ATCC). Prior to total RNA extraction cells were treated with activin A (50 ng/ml, R&D Systems) or SB431542 (10 mM, TOCRIS).


title: PBMC1.CC7W2ANXX.SM2_120717p2_D1


title: Mixture2.CBU1CANXX.SM2_103117p2_A3


title: WT_Isopropanol_1

description:
GEO_NGS_killy_lang.txt
X195280_trimmed_

value: bone marrow

value: macrophage


title: RNA-seq WT 1 Ac2h


title: PCFH 66 2015


title: RNA-seq WT 2 SB2h


title: Mixture2.CBU1CANXX.SM2_103117p2_A2


title: RNA-seq KO 4 SB2h

growth_protocol:
Trim33 null ESCs in C57Bl/6J background ESCs were induced into differentiation on ultra-low plates with 15% serum medium withdraw LIF and cells were harvested at d2.5 before SB431542 (10 mM, TOCRIS) treated for 1h
mESCs were maintained on gelatin-coated plates with ESCs culture serum medium as descriped in Wang et al.2017

extract_protocol:
Total RNA purified from d2.5 EBs with Trim33 null ESCs in C57Bl/6J background (as described (Xi et al., 2008) was quantified by Ribogreen and quality assessed by Agilent BioAnalyzer 2000
The RNA-seq library preparation and sequencing was performed as descripted before (Wang et al.,2017)
After scraped from plate, embryonic stem cells were washed with PBS and incubated in lysis buffer.

value: Trim33 null


title: SFSR 76 2015


title: PBMC1.CC7W2ANXX.SM2_120717p2_C5


title: Mixture2.CBU1CANXX.SM2_103117p2_A1


title: Mixture2.CBU1CANXX.SM2_103117p2_A12


title: RNA-seq KO 1 SB2h


title: PBMC1.CC7W2ANXX.SM2_120717p2_C4


title: NFSRD 58 2015


title: NFSRD 57 2015


title: Mixture2.CBU1CANXX.SM2_103117p2_A11


title: RNA-seq KO 1 Ac2h

growth_protocol:
Trim33 null ESCs in C57Bl/6J background ESCs were induced into differentiation on ultra-low plates with 15% serum medium withdraw LIF and cells were harvested at d2.5 before activin A (50 ng/ml, R&D Systems) treated for 2hs
mESCs were maintained on gelatin-coated plates with ESCs culture serum medium as descriped in Wang et al.2017


title: RNA-seq KO 4 Ac2h


title: PBMC1.CC7W2ANXX.SM2_120717p2_C2


title: PBMC1.CC7W2ANXX.SM2_120717p2_C1


title: PBMC1.CC7W2ANXX.SM2_120717p2_C6


title: Mixture2.CBU1CANXX.SM2_103117p2_A10


title: Mixture2.CBU1CANXX.SM2_103117p1_H9


title: RNA-seq ES LKO Ac II

growth_protocol:
E14 WT ESCs were cultured on galetin coated plate with LIF-supplemented 15% serum medium
mESCs were maintained on gelatin-coated plates with ESCs culture serum medium as descriped in Wang et al.2017

extract_protocol:
Total RNA purified from mouse ES cells (as described (Xi et al., 2008) was quantified by Ribogreen and quality assessed by Agilent  BioAnalyzer 2000
The RNA-seq library preparation and sequencing was performed as descripted before (Wang et al.,2017)
After scraped from plate, embryonic stem cells were washed with PBS and incubated in lysis buffer.

treatment_protocol:
E14 WT ESCs were cultured on galetin coated plate with LIF-supplemented medium and treated with activin A (50 ng/ml, R&D Systems) for 2hs
Embryoid body (EB) formation and differentiation were carried out as described by the supplier (ATCC). Prior to total RNA extraction cells were treated with activin A (50 ng/ml, R&D Systems) or SB431542 (10 mM, TOCRIS).

value: wild type

value: embryonic stem cell


title: PCFH 64 2015


title: NFSRD 51 2015


title: PBMC1.CC7W2ANXX.SM2_120717p2_B6


title: SFSR 74 2015


title: RNA-seq ES LKO Ac I


title: Mixture2.CBU1CANXX.SM2_103117p1_H8


title: SFSR 73 2015


title: NFSRD 56 2015


title: WT_TDM_1

description:
GEO_NGS_killy_lang.txt
X195282_trimmed_

value: wildtype

value: TDM

value: M-CSF day 7


title: PBMC1.CC7W2ANXX.SM2_120717p2_B5


title: PBMC1.CC7W2ANXX.SM2_120717p2_C3


title: PCFH 63 2015


title: Mixture2.CBU1CANXX.SM2_103117p1_H7

value: Pooled male and female


title: Mixture2.CBU1CANXX.SM2_103117p1_H6


title: Mouse WT P60 Hipp 1

city: Paris

first: Lam Son

last: Nguyen

state: IDF

address: 24 Bld du Montparnasse

department: Institute Imagine

institute: INSERM U1163

description: Mouse P60 Processed File.txt

data_processing:
Sequence reads were aligned to the mouse mm9 reference genome using the Burrows-Wheeler Alignment version 0.6.2.13.
Gene expression was analyzed by three different tools: limma, Deseq and EdgeR. Differentially expressed genes were determined by threshold P<0.05 and fold change >1.2 for mouse brains.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample as analyzed by EdgeR for reference.

source_name: WT

growth_protocol: GIBCO® human neural stem cells (H9 hESC-Derived) was purchased commercially (N7800100, ThermoFisher Scientific). Cells were cultured in flasks or plates previously coated for at least 1H with GelTrex™ LDEV-Free, hESC-qualified, reduced growth factor basement membrane matrix (A1413302, ThermoFisher Scientific). Cells were maintained in Complete StemPro® NSC SFM medium (growth media) consisting of KnockOut™ D-MEM/F-12 (12660012, ThermoFisher Scientific) supplemented with 2% StemPro® Neural Supplement (A1050901, ThermoFisher Scientific), 20 ng/mL EGF (PHG0315, ThermoFisher Scientific), 20 ng/mL bFGF (GF003, ThermoFisher Scientific), 2 mM GlutaMax™-I (35050038, ThermoFisher Scientific) and 10 μg/mL Penicillin-Streptomycin (15140122, ThermoFisher Scientific). For passaging, cells were washed once with DPBS (14190169, ThermoFisher Scientific) and detached from the surface by StemPro™ Accutase (A1110501, ThermoFisher Scientific), centrifuged at 1500 RPM for 5 minutes, and replated in fresh growth media. To initiate spontaneous differentiation, H9 cells were plated at a density of 20-25000 cells/cm2 in growth media for 24H, after which media was replaced with differentiating media (growth media without growth factors). Differentiating media was changed every 2-3 days during the course of the differentiation process.

extract_protocol:
Total RNA was extracted using TRizol reagent (15596026, ThermoFisher Scientific) and RNeasy Mini Kit (74104, QIAGEN) with DNase I treatment step (79254, QIAGEN) following the manufacturer’s protocol. The integrity of RNA was determined by RNA ScreenTape (5067-5576, Agilent Technologies) on the Agilent 4200 TapeStation (Agilent Technologies).
RNAseq libraries were prepared starting from 600 ng of total RNA using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) as recommended by the manufacturer. Half of the oriented cDNA produced from the poly-A+ fraction were PCR amplified (11 cycles). The RNAseq libraries were sequenced on an Illumina HiSeq2500 (Paired-End sequencing 130x130 bases, High Throughput Mode). A minimum of 10 million of paired-end reads was produced per library sample.

tag: region

value: Hippocampus


title: Mouse WT P60 Hipp 2

description: Mouse P60 Processed File.txt


title: Mouse WT P60 Hipp 3

description: Mouse P60 Processed File.txt


title: PBMC1.CC7W2ANXX.SM2_120717p2_B4


title: PCFH 62 2015

value: PCFH


title: PBMC1.CC7W2ANXX.SM2_120717p2_B3

value: Male


title: Mouse KO P60 Hipp 2

description: Mouse P60 Processed File.txt

source_name: miR-146a KO


title: NFSRD 55 2015

value: NFSRD


title: Mixture2.CBU1CANXX.SM2_103117p1_H5


title: PBMC1.CC7W2ANXX.SM2_120717p2_B2


title: SFSR 71 2015

value: SFSR


title: PBMC1.CC7W2ANXX.SM2_120717p2_B1


title: Mixture2.CBU1CANXX.SM2_103117p1_H4


title: PBMC1.CC7W2ANXX.SM2_120717p2_A6


title: Mixture2.CBU1CANXX.SM2_103117p1_H2


title: Mouse WT P60 Cort 3

description: Mouse P60 Processed File.txt

value: Frontal cortex


title: Mouse KO P60 Hipp 1

description: Mouse P60 Processed File.txt


title: PBMC1.CC7W2ANXX.SM2_120717p2_A5


title: Mouse WT P60 Cort 2

description: Mouse P60 Processed File.txt


title: Mixture2.CBU1CANXX.SM2_103117p1_H1


title: PBMC1.CC7W2ANXX.SM2_120717p2_A4


title: Mixture2.CBU1CANXX.SM2_103117p1_H12


title: Mouse WT P60 Cort 1

description: Mouse P60 Processed File.txt


title: PBMC1.CC7W2ANXX.SM2_120717p2_A3


title: Mouse KO P60 Cort 4

description: Mouse P60 Processed File.txt


title: PCFH 79 2014

hyb_protocol: Agilent Technologies One-Color Microarray-Based Gene Expression Analysis Protocol was used.

data_processing: Normalized signal intensity provided here is Loess Normalization with a minimum intensity cut off of 2.7


title: NRWU 60 2014

value: NRWU


title: PCFH 80 2014


title: NRWD 70 2014

value: NRWD


title: NRWU 52 2014


title: Mouse KO P60 Cort 3

description: Mouse P60 Processed File.txt


title: PBMC1.CC7W2ANXX.SM2_120717p2_A2


title: Mixture2.CBU1CANXX.SM2_103117p1_H3


title: Mixture2.CBU1CANXX.SM2_103117p1_H10


title: PBMC1.CC7W2ANXX.SM2_120717p2_A1


title: PCFH 78 2014


title: PBMC1.CC7W2ANXX.SM2_120717p4_C3


title: SFSR 49 2014


title: Mouse KO P60 Cort 2

description: Mouse P60 Processed File.txt


title: Mouse KO P60 Cort 1

description: Mouse P60 Processed File.txt


title: PBMC1.HKH3FBCX2.inDrops

description:
scRNA-seq
3'-end
pbmc_hg38_count_matrix.mtx, pbmc_hg38_gene.tsv, pbmc_hg38_cell.tsv

value: inDrops


title: NRWD 68 2014


title: Mixture2.CBU1CANXX.SM2_103117p1_G8


title: Mouse WT P60 Amy 3

description: Mouse P60 Processed File.txt

value: Amygdala


title: Mixture2.CBU1CANXX.SM2_103117p1_H11


title: PBMC1.HKGWKBCX2.July2018-SeqWell_V1R2

value: Seq-Well


title: Mixture2.CBU1CANXX.SM2_103117p1_G7


title: PBMC1.HKGWKBCX2.July2018-SeqWell_V1R1


title: Mixture2.CBU1CANXX.SM2_103117p1_G6


title: Mixture2.CBU1CANXX.SM2_103117p1_G5


title: PBMC1.HKGWFBCX2.inDrops


title: Mouse WT P60 Amy 2

description: Mouse P60 Processed File.txt


title: Mouse KO P60 Amy 4

description: Mouse P60 Processed File.txt


title: NRWD 67 2014


title: Mouse WT P60 Amy 1

description: Mouse P60 Processed File.txt


title: NRWU 58 2014


title: NRWU 57 2014


title: Mixture2.CBU1CANXX.SM2_103117p1_G9


title: PBMC1.HJTJGBCX2.inDrops


title: SFSR 47 2014


title: Mixture2.CBU1CANXX.SM2_103117p1_G4


title: PBMC1.H5VV5BCX2.inDrops.1


title: Mouse KO P60 Amy 3

description: Mouse P60 Processed File.txt


title: PBMC1.CD370ANXX.011719V3_10X_D

value: 10x Chromium (v3)


title: PBMC1.CD370ANXX.011719V3_10X_C


title: PBMC1.CD370ANXX.011719V3_10X_B


title: PBMC1.CC7W2ANXX.SM2_120717p4_C4


title: Mixture2.CBU1CANXX.SM2_103117p1_G12


title: Mouse WT P30 Hipp 4

description: Mouse P30 Processed File.txt


title: Mixture2.CBU1CANXX.SM2_103117p1_G1


title: PBMC1.CD370ANXX.011719V3_10X_A


title: Mixture2.CBU1CANXX.SM2_103117p1_G2


title: PBMC1.CD370ANXX.011719V2_10X_D

value: 10x Chromium (v2)


title: Mouse WT P30 Hipp 3

description: Mouse P30 Processed File.txt


title: PBMC1.CC7W2ANXX.SM2_120717p2_E3


title: PCFH 77 2014


title: Mouse WT P30 Hipp 2

description: Mouse P30 Processed File.txt


title: Mouse KO P60 Amy 1

description: Mouse P60 Processed File.txt


title: Mixture2.CBU1CANXX.SM2_103117p1_G10


title: Mixture2.CBU1CANXX.SM2_103117p1_G11


title: SFSR 48 2014


title: Mixture2.CBU1CANXX.SM2_103117p1_G3


title: Mouse WT P30 Hipp 1

description: Mouse P30 Processed File.txt


title: Mouse KO P60 Amy 2

description: Mouse P60 Processed File.txt


title: PBMC1.CD370ANXX.011719V2_10X_C


title: Mixture2.CBU1CANXX.SM2_103117p1_F9


title: Mouse KO P30 Hipp 4

description: Mouse P30 Processed File.txt


title: PCFH 74 2014


title: PBMC1.CD370ANXX.011719V2_10X_B


title: Mixture2.CBU1CANXX.SM2_103117p1_F8


title: Mouse KO P30 Hipp 3

description: Mouse P30 Processed File.txt


title: Mixture2.CBU1CANXX.SM2_103117p1_F7


title: PBMC1.CD370ANXX.011719V2_10X_A


title: Mixture2.CBU1CANXX.SM2_103117p1_F6


title: Mouse KO P30 Hipp 2

description: Mouse P30 Processed File.txt


title: NRWU 55 2014


title: Mouse KO P30 Hipp 1

description: Mouse P30 Processed File.txt


title: PBMC1.CCLBDANXX.68.10X_D


title: Mouse WT P30 Cort 4

description: Mouse P30 Processed File.txt


title: PBMC1.CCLBDANXX.68.10X_C


title: Mixture2.CBU1CANXX.SM2_103117p1_F4


title: NRWD 65 2014


title: SFSR 46 2014


title: NRWD 64 2014


title: PCFH 75 2014


title: PBMC1.CCLBDANXX.68.10X_B


title: NRWD 63 2014


title: SFSR 45 2014


title: SFSR 43 2014


title: NRWU 54 2014


title: Mouse WT P30 Cort 2

description: Mouse P30 Processed File.txt


title: SFSR 44 2014


title: Mouse WT P30 Cort 3

description: Mouse P30 Processed File.txt


title: Mixture2.CBU1CANXX.SM2_103117p1_F3


title: PBMC1.CCLBDANXX.68.10X_A


title: Mixture2.CBU1CANXX.SM2_103117p1_F12


title: PBMC1.CC7W2ANXX.120717-DropSeq

value: Drop-seq


title: PBMC1.CCLBDANXX.July2018-SeqWell_V1R1


title: Mouse WT P30 Cort 1

description: Mouse P30 Processed File.txt


title: Mixture2.CBU1CANXX.SM2_103117p1_F2


title: PBMC1.CCLBDANXX.120717-DropSeq


title: Mixture2.CBU1CANXX.SM2_103117p1_F5


title: PCFH 73 2014


title: PCFH 76 2014


title: Mixture2.CBU1CANXX.SM2_103117p1_F1


title: PBMC1.CC7W2ANXX.120717CELseq4


title: Mixture2.CBU1CANXX.SM2_103117p1_F11


title: NRWU 51 2014


title: Mouse KO P30 Cort 3

description: Mouse P30 Processed File.txt


title: Mouse KO P30 Cort 4

description: Mouse P30 Processed File.txt


title: Mixture2.CBU1CANXX.SM2_103117p1_F10


title: NRWD 61 2014


title: NRWD 62 2014


title: Mouse WT P30 Amy 4

description: Mouse P30 Processed File.txt


title: PBMC1.CC7W2ANXX.120717CELseq1


title: PBMC1.CC7W2ANXX.120717CELseq3


title: Mouse KO P30 Cort 2

description: Mouse P30 Processed File.txt


title: Mouse WT P30 Amy 3

description: Mouse P30 Processed File.txt


title: PBMC1.CC7W2ANXX.120717CELseq2


title: SFSR 42 2014


title: Mixture2.CBU1CANXX.SM2_103117p1_E8


title: Mixture2.CBU1CANXX.SM2_103117p1_E9


title: Mixture2.CBU1CANXX.SM2_103117p1_E7


title: PBMC1.CC7W2ANXX.10X_D


title: PBMC1.CC7W2ANXX.10X_C


title: NR1

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description:
Arsenic resistant cell lines(APL)
NB4-EV-AsR1

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60 °C and hybridized on to a Agilent's human GXP_8X60k Array (AMADID: 039494) using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65°C for 16 hours.

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the percentile shift normalization method .

source_name: In house generated from NB4

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Cells were grown in 10% RPMI medium.

extract_protocol: RNA extraction was performed by using Qiagen Rneasy mini kit with Dnase Treatment.

tag: cell line

value: Leukemic cell lines

tag: arsenic sensitivity

value: resistant


title: Mouse WT P30 Amy 2

description: Mouse P30 Processed File.txt


title: PBMC1.CC7W2ANXX.10X_B


title: Mouse WT P30 Amy 1

description: Mouse P30 Processed File.txt


title: Mixture2.CBU1CANXX.SM2_103117p1_E6

value: Pooled male and female


title: Mouse KO P30 Cort 1

description: Mouse P30 Processed File.txt


title: NR3


title: Mouse KO P30 Amy 4

description: Mouse P30 Processed File.txt


title: Mixture2.CBU1CANXX.SM2_103117p1_E5


title: PBMC1.CC7W2ANXX.10X_A


title: Mixture2.CBU1CANXX.SM2_103117p1_E4


title: Mixture2.CBU1CANXX.SM2_103117p1_E3


title: RELA ChIP-seq - Control

city: Singapore

first: Lisa

last: Borghini

state: Singapore

address: 60 Biopolis Street, Genome, #02-01

department: Infectious Diseases

country: Singapore

institute: GIS

data_processing:
mapping of the reads to hg19 with BWA
Filtering with samtools 1.2 (samtools view -bh -F 1804 -q 20)
Peak calling with Dfilter 1.5  For RELA ChIP-seq, 2 calls were carried out against different controls: (a) against no treatment control RELA ChIP-seq and (b) against input DNA, using the following command: run_dfilter15.sh -f=bam -ks=20 -bs=50 -lpval=2 -nonzero -refine -wig. The first 100,000 most confident peaks were extracted from each call. Irreproducibility Discovery Rate (IDR) analysis was performed between calls (a) and (b). This strategy allows discovery of reproducible peaks against the 2 controls and a stringent threshold of IDR<=0.005 was applied to identify final RELA peaks in FaDu cells.  For H3K27ac ChIP-seq, a simple peak calling was performed with Dfilter 1.5 in each condition (Control no treatment and LPS treatment) against input DNA using the following command: run_dfilter15.sh -d=ChIP.bam -c=Input.bam -o=peaks -f=bam -ks=60 -bs=100 -lpval=6  A bedGraph file generated with Homer is also provided for each of the ChIP sample.
Black listed regions were removed found in wgEncodeDacMapabilityConsensusExcludable.bed (http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeMapability/) were removed from the final list of peaks using bedtools intersect command. Any peaks falling in chromosome Y was also filtered out as the cell line studied is derived from a female.
Genome_build: hg19
Supplementary_files_format_and_content: For all ChIP-seq samples, bedGraph files are provided (generated with Homer makeTagDirectory command followed by makeUCSCfile command).  A list of peaks (bed files) generated as described in data processing are also provided for Control and LPS treated H3K27ac ChIP-seq as well as LPS-induced RELA ChIP-seq.

source_name: FaDu cultured cells

growth_protocol: FaDu cells were purchased from ATCC and cultured in RPMI medium (Gibco) supplemented with 10% fetal bovine serum performance (Gibco), 100U/ml penicillin, 100ug/ml streptomycin (Gibco) and 1mM sodium pyruvate (Gibco).

extract_protocol:
After treatment, cells were crosslinked with 0.75% formaldehyde for 8 minutes and cross-linking was quenched with 180mM Glycine for 10 minutes at room temperature. Cells were then lysed with cell lysis buffer (0.25% Triton X-100, 10mM EDTA, 0.1M NaCl in 10mM Tris-HCl pH8) for 20 minutes at 4°C. Nuclei were collected by centrifugation at 4,000rpm for 10 minutes at 4°C and lysed in nuclei lysis buffer (1% NP-40, 0.5% NaDOC, 0.1% SDS in PBS) for 20 minutes at 4°C.  Chromatin shearing was performed using a sonicator (Bioruptor, Diagenode) on high setting for 40 cycles of 30 seconds ON/45 seconds OFF, leading to a fragment range of 100-250bp.
ChIP-seq libraries were built following the library-on-beads protocol from Wallerman et al. (Wallerman et al. 2015). Chromatin was incubated with antibodies bound to protein G magnetic beads (Dyanabeads protein G, Thermo Fisher scientific) prepared by mixing the antibody with the beads in PBS+0.5%BSA for 4 to 6 hours at room temperature. Four ug of anti-RELA antibody (NFKB p65 (c20): sc-372) or 5 ug of anti-H3K27ac (Active motif, reference 39138) were mixed with 40 uL or 50 uL of beads respectively.  Immunoprecipitation was performed by rotation at 4°C overnight. After immunoprecipitation, samples were washed twice with nuclei lysis buffer, twice with nuclei lysis buffer complemented with 350mM NaCl, twice with LiCl/NP-40 buffer (0.25M LiCl, 1mM EDTA, 0.5% NP-40, 0.5% NaDOC in 10mM Tris-HCl pH8) and once with PBS. Libraries on beads were then built using NEBnext DNA library prep kit (New England Biolabs) according to the manufacturer’s instructions. Due to the nature of the samples, minor adjustments were done: two washes with PBS were performed in between each step of the preparation and elution of the DNA from the beads was done after adaptor ligation. ChIP samples were eluted in Elution buffer (10mM EDTA, 1% SDS in 50mM Tris-HCl pH7.5) for 4 hours at 65°C and purified with Agencourt AMPure XP beads (Beckman Coulter). PCR reaction was performed using Phusion High-Fidelity PCR Master Mix (Thermo scientific) and custom primers for multiplexing. The following program was applied: 3 minutes at 98°C; 17x(30 seconds at 98°C, 30 seconds at 65°C, 30 seconds at 72°C); 5 minutes at 72°C. Samples were loaded on a DNA1000 bioanalyzer chip (Agilent) to check the size of the libraries as well as the concentration. As a control, 2-5% of input DNA was reverse cross-linked at 65°C for minimum 6 hours and libraries were prepared using the same library preparation kit.  Samples were sequenced on an Illumina HiSeq Rapid 2x76bp for the RELA ChIP-seq and on an Illumina NextSeq High 1x76bp for the H3K27ac ChIP-seq.

treatment_protocol: FaDu cells were treated with LPS at 1μg/mL for 60 minutes. For each experiment, a “no treatment” control consisting of a change of culture medium was processed along with the LPS treated sample.

value: FaDu

tag: chip antibody

value: RELA


title: Mixture2.CBU1CANXX.SM2_103117p1_E2

extract_protocol:
Total RNA from bulk samples was extracted using Quick-RNA Mini Prep (Zymo Research) following the vendor protocol with a DNase treatment step
For library construction methods, see SAMPLES, description: Library Construction field. For details see the Methods section in the manuscript


title: U1

description:
Arsenic resistant cell lines(APL)
UF1

source_name: Hospital Saint Louis Paris


title: U2

description:
Arsenic resistant cell lines(APL)
UF1


title: NR2


title: Mouse KO P30 Amy 2

description: Mouse P30 Processed File.txt

tag: developmental stage


title: Mouse KO P30 Amy 1

description: Mouse P30 Processed File.txt


title: Mixture2.CBU1CANXX.SM2_103117p1_E1

source_name: Mixture of human HEK293 and murine NIH3T3 cell lines


title: Mixture2.CBU1CANXX.SM2_103117p1_E12


title: Mouse WT E14 Cort 3

description: Mouse E14 Processed File.txt

value: Whole cortex


title: Mouse WT E14 Cort 4

description: Mouse E14 Processed File.txt


title: PLA98_PBMC_2

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

description: Sample collection protocol: Cryopreserved mononuclear cells were thawed and rested for 1 hour at 37℃. Fc receptors on all cells were blocked using human IgG, followed by staining with panels outlined in Table 1 and separation on BD Aria Fusion sorter. A dump channel consisting of viability dye and antibodies to CD14, CD16, and CD19 was used to exclude unwanted cell types

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 platform.
Reads were trimmed using Trim Galore v0.4.4 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence.  They were mapped to the mouse GRCm38 genome assembly using HISAT2 2.1.0 (no soft clipping). BAM files were imported to Seqmonk v1.43.0. (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: GRCm38
Supplementary_files_format_and_content: A log2RPM count quantitation was carried in SeqMonk (v1.45.0) using the RNA-Seq pipeline. The file is tab delimited and contains the following columns: (1) Gene (2) Chromosome; (3) Start; (4) End; (5) Strand (6-..) log2 RPM for each sample

source_name: peripheral blood mononuclear cells

extract_protocol:
mRNA was isolated from sorted T helper cell populations (CD4+CD45RA- cells and markers CXCR5 and PD1 as described in the sample information using the SMART-SeqV4 Ultra-low input RNA kit (Takara-Clontech) and sorting 40-1000 cells directly into lysis buffer.
cDNA libraries were subsequently generated using the Nextera XT DNA kit (Illumina).

tag: replicate

value: peripheral blood mononuclear cells

tag: markers

value: CXCR5+ve; PD1-ve


title: PLA98_PBMC_3

value: CXCR5+ve; PD1int


title: Hela_12h_ASO_sample2

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

country: Italy

institute: European Brain Research Institute

description: Standard commercial immotalized cell line originally derived from cervical tumor

hyb_protocol: One-color mixes of labelled cRNA pairs were hybridized to Agilent 8X60K whole human genome oligonucleotide microarrays (Grid ID 039494) , at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit. The hybridized microarrays were disassembled at room temperature in Agilent Gene Expression Wash Buffer 1. After the disassembly, the microarrays were washed in Gene Expression Buffer 1 for one minute at room temperature, followed by washing with Gene Expression Wash Buffer 2 for one minute at 37°C. The microarrays were then treated with acetonitrile for one minute at room temperature.

scan_protocol: Post-hybridization image acquisition was accomplished using the Agilent Scanner G2564C. Data extraction from the 20 bits TIFF images was accomplished by Agilent Feature Extraction ver 10.7 software using the standard Agilent one-color gene expression extraction protocol (GE1_107_Sep09).

data_processing: The “gProcessedSignal” data column of the Feature Extraction *.txt output file was used, containing the median signals corrected by spatial and multiplicative detrend. Data quality filtering was performed using Microsoft Excel, discarding features with the Feature Extraction flag gIsWellAboveBG=0 in any sample, wich is a statistical method approximately equivalent to discarding features with a Signal/Noise ratio smaller than 2.0-3.0, where Signal = (median of the spot - median spot background level) and Noise is the Standard Deviation of the median spot background. Data were normalized to the 75th percentile in Log2 scale. Data were were further filtered by excluding mRNA probes with a coefficient of variation |Dev.st/Mean |>5%  in Log2 expression values between biological replicates, across all samples, to obtain a final selection 17703 transcripts. Differentially expressed genes were selected by a combination of fold change and moderated T-test thresholds by the R-Bioconductor  tool Limma (p-value<0.05; |Log2 fold-change ratio| >0.56 equivalent to 1.5 fold in linear scale).

label_protocol: For each sample 200ng of Poly A+RNA were labelled, using Cyanine 3-CTP (Agilent) in separate labelling reactions, with the Agilent Low Imput Linear Amplification Kit and purified with Qiagen’s RNeasy mini spin columns.

growth_protocol: HeLa tumor cell lines were grown in DMEM containing 10% FCS and Gentamicin in a 5% CO2 humidified atmosphere at 37 Celsius degrees.

extract_protocol: Total RNA was extracted at 2 or 8h after medium adding. Total RNA was isolated from HeLa cells using Absolutely RNA Miniprep kit (Agilent Technologies) for microarray analysis and qRT-PCR. Total RNA was extracted  using Trizol (Invitrogen) and DNAse treated by Qiagen columns. Quality and integrity of each sample was checked using the Agilent BioAnalyzer 2100 (Agilent RNA 6000 nano kit): samples with a RNA Integrity Number (RIN) index lower than 8.0 were discarded. All the experimental steps involving the labelling, hybridization and washing of the samples were done following the one-color Agilent protocol.

treatment_protocol: For transfection procedure Thermo Fisher Scientific Protocol for Oligofectamine reagent was used. We transfected cell with antisense oligonucleotides (ASO) specifically inducing CSB mRNA degradation . Moreover, we used three different experimental controls: mock treated cells (CTRL), transfection reagents alone (OLF) and cells treated with sense oligonucleotides (SO), the reverse of ASO. Briefly the day before transfection 1x10^5 cells were plated in 6-well dishes using medium without antibiotics. Immediately before transfection the medium was replaced with Optimem and oligonucleotides (200 nM final concentration) were delivered using Oligofectamine transfection reagent. The cells were transfected with ASO or SO or simply exposed to the transfectant reagent (OLF). Four hours after transfection Optimem was replaced with fresh complete medium.

value: cervical cancer

value: Hela

tag: treatment

value: infected with antisense oligonucleotides (ASO) against CSB mRNA

tag: sample type

value: CSB induced degradation

tag: gender

value: female

tag: time post transfection


title: Mouse KO P30 Amy 3

description: Mouse P30 Processed File.txt

value: Amygdala


title: PLA98_PBMC_1

value: CXCR5-ve; PD1-ve


title: Mouse WT E14 Cort 2

description: Mouse E14 Processed File.txt


title: Hela_12h_ASO_sample1


title: Hela_12h_OLF_sample2

value: infected with reagents alone (OLF)

value: control


title: Mouse WT E14 Cort 1

description: Mouse E14 Processed File.txt


title: Mixture2.CBU1CANXX.SM2_103117p1_E10

data_processing:
For scRNA-seq and snRNA-seq data, scumi v0.1.0 (https://bitbucket.org/jerry00/scumi-dev/src/master/) was used to produce cell by gene sparse matrices (UMI count matrices for 3'-end methods and read count matrices for Smart-seq2). More specifically, STAR v2.6.1a was used for alignment except for Smart-seq2 and CEL-Seq2 data where HISAT v2.0.5 was used. featureCounts from the Subread package, v1.6.2 was used to tag each alignment with a gene tag. For bulk RNA-Seq data, reads were mapped to the reference genomes using Bowtie v0.12.9, and further quantified by RSEM v1.3.0 to generate transcripts per million values.
Genome_build: scRNA-seq data: a merged hg19 and mm10 geome for human and mouse mixture datasets, hg38 (GRCh38) for human PBMCs, and mm10 for mouse cortex data; bulk RNA-Seq data, hg38 (GRCh38) for human data and mm10 for mouse data
Supplementary_files_format_and_content: scRNA-seq data: mtx, a gene by cell count matrix in the sparse matrix market format
Supplementary_files_format_and_content: scRNA-seq data: cell.tsv, cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: scRNA-seq data: gene.tsv, gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: Bulk RNA-Seq data: TPM_bulk.tsv, tab-delimited text files of transcripts per million measurements of genes in each sample
Supplementary_files_format_and_content: mixture_hg19_mm10_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: mixture_hg19_mm10_count_matrix.mtx :A gene by cell count sparse matrix in the matrix market format
Supplementary_files_format_and_content: mixture_hg19_mm10_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: pbmc_hg38_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: pbmc_hg38_count_matrix.mtx :A gene by cell count matrix in the matrix market format
Supplementary_files_format_and_content: pbmc_hg38_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: cortex_mm10_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: cortex_mm10_count_matrix.mtx :A gene by cell count sparse matrix in the matrix market format
Supplementary_files_format_and_content: cortex_mm10_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: HEK293_PBMC_TPM_bulk.tsv :A matrix of transcripts per million measurements
Supplementary_files_format_and_content: NIH3T3_cortex_TPM_bulk.tsv :A matrix of transcripts per million measurements

tag: Sex

tag: library construction


title: PLA98_LN_3

source_name: lymph node

value: lymph node


title: U3

description:
Arsenic resistant cell lines(APL)
UF1

tag: cell type

value: Leukemic cell lines

value: resistant


title: Mixture2.CBU1CANXX.SM2_103117p1_E11

value: Pooled male and female


title: Mixture2.CBU1CANXX.SM2_103117p1_D9


title: Hela_12h_OLF_sample1


title: Mouse KO E14 Cort 4

description: Mouse E14 Processed File.txt

value: Whole cortex


title: Mouse KO E14 Cort 5

description: Mouse E14 Processed File.txt


title: N1

description:
Arsenic sensitive cell lines(APL)
NB4 naive

source_name: RAPH, Australia

value: sensitive


title: Hela_12h_SO_sample1

value: infected with sense oligonucleotides (SO)


title: PLA98_LN_2

value: CXCR5+ve; PD1-ve


title: Mouse KO E14 Cort 3

description: Mouse E14 Processed File.txt


title: Mixture2.CBU1CANXX.SM2_103117p1_D7


title: Hela_12h_CTRL_sample1

value: cervical cancer

value: mock treated cells (CTRL)


title: Hela_12h_CTRL_sample2

value: Hela


title: PLA98_LN_1


title: Mouse KO E14 Cort 2

description: Mouse E14 Processed File.txt


title: PLA81_PBMC_4

value: peripheral blood mononuclear cells

value: CXCR5+ve; PD1+++


title: PLA98_LN_4


title: Mixture2.CBU1CANXX.SM2_103117p1_D5


title: PLA81_PBMC_3

value: CXCR5+ve; PD1int


title: Mouse KO E14 Cort 1

description: Mouse E14 Processed File.txt


title: Mixture2.CBU1CANXX.SM2_103117p1_D8


title: RELA ChIP-seq - LPS

value: FaDu

value: LPS

value: RELA


title: Mixture2.CBU1CANXX.SM2_103117p1_D4


title: ChIPseq_input_kd

city: New York

first: Patrizia

last: Casaccia

state: NY

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

data_processing:
RNA-seq: Reads were mapped to mm9 build of the mouse genome from University of California Santa Cruz (UCSC) genome database using TopHat version 2.0.12 with the aligner Bowtie [41] with their default parameters and by supplying the gene model annotations from Ensemble (version NCBIM37.65).
RNA-seq: Differential expression analysis was performed by Cuffdiff 2.2.1 with threshold of FDR less than 0.05 and fold change more than 1.5.
ChIPseq: The ChIP-seq data was first checked for quality using the various metrics generated by FastQC (v0.11.2).
ChIPseq: Raw sequencing reads were then aligned to the mouse mm10 genome using default settings of Bowtie (v2.2.0).
ChIPseq: Peak-calling was performed using MACS (v2.1.1) with default settings.
Genome_build: mm9 and mm10
Supplementary_files_format_and_content: A single text file with tabulated RPKM values for all RNAseq samples and genes
Supplementary_files_format_and_content: One bigWig file per ChIPseq sample

source_name: Oli-neu cells

growth_protocol: OPCs were cultured in plates coated with Poly-D-lysine and proliferation medium supplemented with bFGF and PDGFA.

extract_protocol:
mRNAs were extracted with Tryzol and the RNeasy kit from Qiagen; chromatin from the cells were extracted and digested with Mnase for the ChIP experiments.
Library construction for the RNA-seq was performed with the TruSeq Total RNA Stranded kit from Illumina; library construction for the ChIP-seq was performed with a constomized protocol at the laboratory of Emily Bernstein.

treatment_protocol: OPCs were infected by lenti-EGFP-CRISPR (control) and lenti-PRMT5-CRISPR (PRMT5-KD) respectively, and harvested after 6 days of infection

value: oligodendrocyte progenitor cells

tag: immortalized with

value: neu

tag: derived from

value: NMRI mice p15

value: without PRMT5 expression

value: input


title: PLA81_LN_4

tag: tissue

value: lymph node


title: Mixture2.CBU1CANXX.SM2_103117p1_D3

value: Pooled male and female


title: PLA81_PBMC_2

value: CXCR5+ve; PD1-ve


title: Mixture2.CBU1CANXX.SM2_103117p1_D2


title: Hela_6h_ASO_sample1

value: cervical cancer

value: infected with antisense oligonucleotides (ASO) against CSB mRNA

value: CSB induced degradation

value: female


title: Hela_6h_OLF_sample2

value: Hela

value: infected with reagents alone (OLF)

value: control


title: Mixture2.CBU1CANXX.SM2_103117p1_D6


title: Hela_6h_ASO_sample2


title: ChIPseq_h4k5ac_kd

tag: genotype/variation

value: H4K5ac, Active Motif 39699, LOT# 34509001


title: Hela_6h_OLF_sample1

tag: cell line


title: PLA81_LN_3

value: CXCR5+ve; PD1int


title: PLA81_LN_2


title: Mixture2.CBU1CANXX.SM2_103117p1_D1


title: Hela_6h_SO_sample2

value: infected with sense oligonucleotides (SO)


title: Mixture2.CBU1CANXX.SM2_103117p1_D12


title: Hela_12h_SO_sample2


title: ChIPseq_h4k5ac_ctrl

value: oligodendrocyte progenitor cells

value: neu


title: ChIPseq_h3k9ac_kd

value: NMRI mice p15

value: without PRMT5 expression


title: PLA81_LN_1

value: lymph node

value: CXCR5-ve; PD1-ve


title: DAM-zGFP

city: Heidelberg

first: Javier

last: Vázquez-Marín

state: Baden-Württemberg

address: Im Neuenheimer Feld 230, 5th floor

department: Centre for Organismal Studies (COS)

institute: Heidelberg University

data_processing:
Library strategy: DamID-seq
Raw sequencing data was pre-processed using the Cutadapt tool to discard short reads (-m 34 parameter) and the ones corresponding to the adaptors used for deep sequencing.
Reads from zebrafish and medaka proteins were mapped against the GRCz10/danRer10 and the NIG/UT MEDAKA1/oryLat2 genome versions of each breed, respectively, using Bowtie2.
Duplicated reads were removed using Samtools rmdup.
The set of specific DAM-YAP1, DAM-TAZ and DAM-YAP1B peaks as well as their respective control peaks was obtained using the R package iDEAR (available at https://bitbucket.org/juanlmateo/idear).
Each DamID peak was assigned to its closest TSS using bedtools closest. The position of the transcription start site (TSS) of each gene was obtained from ENSEMBL database (Version 89) using the online tool Biomart (www.ensembl.org/biomart).
Motif enrichment analysis was carried out using DREME and AME. GO enrichment analysis was performed using PANTHER.
Genome_build: oryLat2 (medaka) and danRer10 (zebrafish)
Supplementary_files_format_and_content: tab-limited bed files for each DAM-TF sample indicating the number, coordinates and iDEAR score for each specific peak and for each control peak.

organism: Danio rerio

source_name: Whole embryos

extract_protocol:
We followed the protocol reported for medaka (Gutiérrez-Triana et al., 2016). WT zebrafish and medaka embryos were injected with each DAM-TF mRNA and its gDNA fraction was isolated when they reached the 80% epiboly stage. 40 embryos were used for each indipendent DamID replicate. gDNA was fragmented using DpnII restriction enzymes, dephosphorilated with phosphatase alkaline and cleaved at its GATC methylated sites using DpnI. Adapters, produced by hybridazing two oligos, were ligated to both ends for each fragment to build up DNA libraries through a 25-cycle PCR amplification step using a phosphorothioate primer. Each PCR product was run on a 1% agarose gel to check for the presence of a smear in DpnI-treated samples. Each library was amplified then five times before deep sequencing (Illumina HiSeq 2500 sequencing). Remaining DNA templates were removed with T7 exonuclease before sequencing. Three replicates for each sample were used for the iDamID-seq analysis.
DNA libraries were prepared for sequencing using standard Illumina protocols.

value: Whole embryos

value: 80% epiboly

value: DAM-zGFP


title: Hela_6h_CTRL_sample1

value: cervical cancer

value: mock treated cells (CTRL)


title: Hela_6h_CTRL_sample2

value: Hela

value: female


title: ChIPseq_h3k9ac_ctrl

value: control


title: Mixture2.CBU1CANXX.SM2_103117p1_D11

first: Aviv

last: Regev

address: 415 Main Street

institute: Broad Institute

value: Pooled male and female


title: ChIPseq_input_ctrl

value: input


title: Input DNA for RELA

value: FaDu

value: input for RELA


title: PLA35_PBMC_4

value: peripheral blood mononuclear cells

value: CXCR5+ve; PD1+++


title: ChIPseq_h3k4me3_kd

value: oligodendrocyte progenitor cells

value: neu

value: NMRI mice p15

value: without PRMT5 expression


title: PLA35_PBMC_3

value: CXCR5+ve; PD1int


title: Mixture2.CBU1CANXX.SM2_103117p1_D10


title: Mixture2.CBU1CANXX.SM2_103117p1_C9


title: DAM-zYap1

value: Whole embryos

value: 80% epiboly


title: DAM-zTaz

value: DAM-zTaz


title: Hela_6h_SO_sample1

value: cervical cancer

value: Hela

value: infected with sense oligonucleotides (SO)


title: PLA35_PBMC_2

value: CXCR5+ve; PD1-ve


title: DV90_siREG4-2

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan 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 hg38 whole genome using Hisat2
mRNA and lncRNA annotated in NCBI were quantified using featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

molecule: polyA RNA

extract_protocol:
Cellular RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using mRNA-seq protocols

value: REG4 siRNA


title: DV90_siREG4-1


title: Mixture2.CBU1CANXX.SM2_103117p1_C8

city: Cambridge

value: Pooled male and female


title: Mixture2.CBU1CANXX.SM2_103117p1_C7


title: PLA35_PBMC_1

value: CXCR5-ve; PD1-ve


title: DV90_NC

value: control


title: cypro240 [NGS247_0027R_RFS54]

city: Egham

first: Gerhard

last: Leubner-Metzger

state: Surrey

address: Bourne Building 3-30

department: Biological Sciences

institute: Royal Holloway University of London

data_processing:
Sequenced on Illumina HiSeqs 2000 system at 9 samples per lane; 100 bp SE reads
FastQ files aligned to Oryza sativa cv japonica genome v7 nuclear and organelle genomes using GSNAP verion 2011_03_38.
Count data were generated at gene level using annoations for nuclear, chloroplast and mitochondrial genomes using custom Python script; each gene received a count of +1 if FastQ file aligned in gene region definge in annotation (GFF) file for genome; single read counted multiple times:  if aligned to up to 6 gene regions
Futher processing for publication was done in R libraries EDAseq and EdgeR
Genome_build: Oryza sativa cv japonica genome v7 nuclear and organelle genomes
Supplementary_files_format_and_content: Data matrix of raw count data

organism: Oryza sativa

source_name: rice suspension culture

growth_protocol: Cell suspension cultures 5 day old; n=3

extract_protocol:
Total RNA was extracted using RiboPureTM RNA Purification Kit (Ambion, Inc.)
Illumina Kit

treatment_protocol: doesed with 5mM stokcs of metcamifen or cyprosulfamide, prepared in dimethyl fulfoxide (DMSO) to give a final concentration of 5uM, or DMSO alone as control treatmnet.  Cells sampled at 30,90, and 240 minutes.

value: Cyprosulfamide

tag: time point (minutes)

tag: cultivar

value: Tsukinohikari


title: PLA35_LN_4

value: lymph node

value: CXCR5+ve; PD1+++


title: cypro240 [NGS247_0025R_RFS52]


title: cypro90 [NGS247_0024R_RFS51]


title: PLA35_LN_3


title: Mixture2.CBU1CANXX.SM2_103117p1_C6


title: PLA35_LN_2


title: Mixture2.CBU1CANXX.SM2_103117p1_C4


title: PLA35_LN_1


title: KO rep2

first: Qicheng

last: Ni

address: 197 Ruijin 2nd Road

institute: Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine

description:
gene_expression.txt
KO-GFP-3

data_processing:
Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads.
We used Hisat v2.0.4 to map the cleaned reads to the mouse mm10 reference genome.
After genome mapping, Stringtie v1.3.0  and TMM were used to caculate FPKM values.
Differentially expressed genes were identified using edgeR. The p-value significance threshold in multiple tests was set by the false discovery rate (FDR).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample .

source_name: Islets

extract_protocol:
Total RNA was extraced from isolated islets using RNeasy Micro Kit (Qigen, Germany)
Preparation Kit (Illumina, USA) following TruSeq® RNA Sample Preparation Guide. Briefly, the poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.

tag: stain

value: islets

tag: age

value: 8 weeks

tag: genotype

value: Beta RapKO


title: KO DNMT3A rep2

description:
gene_expression.txt
KO-DNMT3A-3

value: Beta RapKO with Dnmt3a expression


title: KO DNMT3A rep1

description:
gene_expression.txt
KO-DNMT3A-2


title: cypro90 [NGS247_0023R_RFS50]

tag: treatment

tag: replicate


title: cypro90 [NGS247_0022R_RFS49]


title: ChIPseq_h3k4me3_ctrl

value: oligodendrocyte progenitor cells

value: neu

value: NMRI mice p15

tag: chip antibody


title: PLA33_PBMC_4

value: peripheral blood mononuclear cells

tag: markers


title: KO rep1

description:
gene_expression.txt
KO-GFP-1


title: cypro240 [NGS247_0026R_RFS53]


title: Mixture2.CBU1CANXX.SM2_103117p1_C3

tag: Sex


title: cypro30 [NGS247_0021R_RFS48]


title: PLA33_PBMC_3

value: CXCR5+ve; PD1int


title: WT rep2

description:
gene_expression.txt
WT-GFP-6

value: WT


title: PLA33_PBMC_2

value: CXCR5+ve; PD1-ve


title: Mixture2.CBU1CANXX.SM2_103117p1_C1

value: Pooled male and female

tag: library construction


title: Mixture2.CBU1CANXX.SM2_103117p1_C2


title: WT rep1

description:
gene_expression.txt
WT-GFP-3


title: Mixture2.CBU1CANXX.SM2_103117p1_C12


title: cypro30 [NGS247_0019R_RFS46]


title: Mixture2.CBU1CANXX.SM2_103117p1_C5


title: crest240 [NGS247_0018R_RFS45]

value: Metcamifen


title: H3K27ac ChIP-seq EB AC

growth_protocol:
E14 WT ESCs were induced into differentiation on ultra-low plates with 15% serum medium withdraw LIF and cells were harvested at d2.5 before activin A (50 ng/ml, R&D Systems) treated for 2hs
mESCs were maintained on gelatin-coated plates with ESCs culture serum medium as descriped in Wang et al.2017

extract_protocol:
Cells were cross-linked with 1% formaldehyde at 37 °C for 10 min and quenched with 0.125 M glycine for 5 min at room temperature. Then cells were scraped and ChIP was performed and DNA were extracted using a ChIP assay kit (Millipore) as described.
For library construction and sequencing, ChIP-Seq DNA samples were quantified and quality assessed by Qubit 2.0 and Agilent 2100. DNA fragments range from 200-600bp were selected constructed for ChIP-Seq library with TruSeq ChIP Sample Prep Kit (Illumina) according to manufacturer’s instructions.
After scraped from plate, embryonic stem cells were washed with PBS and incubated in lysis buffer.

value: activin A (50 ng/ml, R&D Systems)

value: wild type

tag: strain

tag: cell type

value: d2.5 EBs

tag: antibody


title: PLA33_PBMC_1

tag: tissue

value: CXCR5-ve; PD1-ve


title: PLA33_LN_4

value: lymph node

value: CXCR5+ve; PD1+++


title: Mixture2.CBU1CANXX.SM2_103117p1_C10


title: crest240 [NGS247_0017R_RFS44]

value: Tsukinohikari


title: H3K18ac ChIP-seq EB SB

growth_protocol:
E14 WT ESCs were induced into differentiation on ultra-low plates with 15% serum medium withdraw LIF and cells were harvested at d2.5 before SB431542 (10 mM, TOCRIS) treated for 1h
mESCs were maintained on gelatin-coated plates with ESCs culture serum medium as descriped in Wang et al.2017

tag: genotype/variation


title: Mixture2.CBU1CANXX.SM2_103117p1_B9


title: PLA33_LN_3


title: crest240 [NGS247_0016R_RFS43]


title: PLA33_LN_2


title: cypro30 [NGS247_0020R_RFS47]

value: Cyprosulfamide


title: Mixture2.CBU1CANXX.SM2_103117p1_B8


title: crest90 [NGS247_0015R_RFS42]


title: Mixture2.CBU1CANXX.SM2_103117p1_B7


title: H3K18ac ChIP-seq ES

treatment_protocol:
E14 WT ESCs were cultured on galetin coated plate with LIF-supplemented medium
Embryoid body (EB) formation and differentiation were carried out as described by the supplier (ATCC). Prior to total RNA extraction cells were treated with activin A (50 ng/ml, R&D Systems) or SB431542 (10 mM, TOCRIS).

value: untreated

value: embryonic stem cell


title: PLA33_LN_1


title: H3K18ac ChIP-seq EB AC


title: Mixture2.CBU1CANXX.SM2_103117p1_B6


title: crest90 [NGS247_0014R_RFS41]


title: PLA22_PBMC_3


title: H3K27ac ChIP-seq EB SB


title: ATAC-seq EB KO re2

growth_protocol:
Trim33 null ESCs in C57Bl/6J background were cultured on ultra-low plates  withdraw LIF and medium were changed every two days, cells were harvested at d2.5
mESCs were maintained on gelatin-coated plates with ESCs culture serum medium as descriped in Wang et al.2017

extract_protocol:
After dissociation with Trypsin, embryonic stem cells were washed with PBS and incubated in lysis buffer.
ATAC-Seq libraries were prepared using ATAC-seq developed by Buenrostro et al. with slightly modification
After scraped from plate, embryonic stem cells were washed with PBS and incubated in lysis buffer.

treatment_protocol:
Trim33 null ESCs in C57Bl/6J background were cultured on ultra-low plates withdraw LIF and cells were harvested at d2.5
Embryoid body (EB) formation and differentiation were carried out as described by the supplier (ATCC). Prior to total RNA extraction cells were treated with activin A (50 ng/ml, R&D Systems) or SB431542 (10 mM, TOCRIS).

value: Trim33 null

value: C57Bl/6J background ESCs(Xi et al., 2011)


title: crest90 [NGS247_0013R_RFS40]


title: Mixture2.CBU1CANXX.SM2_103117p1_C11


title: ATAC-seq EB WT re2

growth_protocol:
Trim33 WT ESCs in C57Bl/6J background were cultured on ultra-low plates  withdraw LIF and medium were changed every two days, cells were harvested at d2.5
mESCs were maintained on gelatin-coated plates with ESCs culture serum medium as descriped in Wang et al.2017

treatment_protocol:
Trim33 WT ESCs in C57Bl/6J background were cultured on ultra-low plates  withdraw LIF and cells were harvested at d2.5
Embryoid body (EB) formation and differentiation were carried out as described by the supplier (ATCC). Prior to total RNA extraction cells were treated with activin A (50 ng/ml, R&D Systems) or SB431542 (10 mM, TOCRIS).

value: Trim33 WT


title: PLA22_PBMC_1

value: peripheral blood mononuclear cells


title: Mixture2.CBU1CANXX.SM2_103117p1_B5


title: ATAC-seq ES KO re2

growth_protocol:
Trim33 null ESCs in C57Bl/6J background were cultured on galetin coated plates with LIF-supplemented and  15% serum medium
mESCs were maintained on gelatin-coated plates with ESCs culture serum medium as descriped in Wang et al.2017

treatment_protocol:
Trim33 null ESCs in C57Bl/6J background were cultured on galetin coated plates with LIF-supplemented medium
Embryoid body (EB) formation and differentiation were carried out as described by the supplier (ATCC). Prior to total RNA extraction cells were treated with activin A (50 ng/ml, R&D Systems) or SB431542 (10 mM, TOCRIS).


title: Mixture2.CBU1CANXX.SM2_103117p1_B4


title: ATAC-seq ES WT re2

growth_protocol:
Trim33 WT ESCs in C57Bl/6J background were cultured on galetin coated plates with LIF-supplemented and  15% serum medium
mESCs were maintained on gelatin-coated plates with ESCs culture serum medium as descriped in Wang et al.2017

treatment_protocol:
Trim33 WT ESCs in C57Bl/6J background were cultured on galetin coated plates with LIF-supplemented medium
Embryoid body (EB) formation and differentiation were carried out as described by the supplier (ATCC). Prior to total RNA extraction cells were treated with activin A (50 ng/ml, R&D Systems) or SB431542 (10 mM, TOCRIS).


title: PLA22_LN_4


title: Mixture2.CBU1CANXX.SM2_103117p1_B3


title: ATAC-seq EB KO re1


title: Mixture2.CBU1CANXX.SM2_103117p1_B2


title: ctrl240 [NGS247_0009R_RFS36]

value: DMSO


title: PLA22_LN_3

value: CXCR5+ve; PD1int


title: Mixture2.CBU1CANXX.SM2_103117p1_B1

value: Pooled male and female


title: crest30 [NGS247_0010R_RFS37]

value: Metcamifen


title: ctrl240 [NGS247_0008R_RFS35]


title: PLA22_PBMC_2

value: CXCR5+ve; PD1-ve


title: PLA22_LN_1


title: ATAC-seq ES KO re1


title: PLA22_LN_2


title: crest30 [NGS247_0012R_RFS39]


title: ctrl240 [NGS247_0007R_RFS34]


title: Mixture2.CBU1CANXX.SM2_103117p1_B11


title: ctrl90 [NGS247_0006R_RFS33]


title: PLA18_PBMC_3


title: Mixture2.CBU1CANXX.SM2_103117p1_B10


title: crest30 [NGS247_0011R_RFS38]


title: PLA18_PBMC_2


title: ctrl90 [NGS247_0005R_RFS32]


title: ATAC-seq ES WT re1


title: ctrl90 [NGS247_0004R_RFS31]


title: Mixture2.CBU1CANXX.SM2_103117p1_A9


title: PLA18_LN_4


title: PLA18_PBMC_1


title: ctrl30 [NGS247_0003R_RFS30]


title: Mixture2.CBU1CANXX.SM2_103117p1_A8


title: PLA18_LN_3


title: ctrl30 [NGS247_0001R_RFS28]


title: Mixture2.CBU1CANXX.SM2_103117p1_A6


title: ctrl30 [NGS247_0002R_RFS29]


title: PLA18_LN_1


title: Mixture2.CBU1CANXX.SM2_103117p1_A5


title: PLA18_LN_2


title: R40-28

description: Sample collection protocol: Cryopreserved mononuclear cells were thawed and rested for 1 hour at 37℃. Cell types were pre-enriched using MagniSort® CD19 Positive Selection followed by CD4 memory T cell enrichment (eBioscience). Fc receptors on all cells were blocked using human IgG, followed by staining with panels outlined in Table 1 and separation on BD Aria Fusion sorter. A dump channel consisting of viability dye and antibodies to CD14, CD16, and either CD19 or CD3 was used to exclude unwanted cell types from cTfh cell  sorts

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 platform.
Reads were trimmed using Trim Galore v0.4.4 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence.  They were mapped to the mouse GRCm38 genome assembly using HISAT2 2.1.0 (no soft clipping). BAM files were imported to Seqmonk v1.43.0. (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: GRCm38
Supplementary_files_format_and_content: A log2RPM count quantitation was carried in SeqMonk (v1.45.0) using the RNA-Seq pipeline. The file is tab delimited and contains the following columns: (1) Feature (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) Ensembl-ID; (7-..) log2 RPM for each sample

source_name: Blood

extract_protocol:
mRNA was isolated from sorted circulating Tfh cells (CD4+CD45RA-CXCR5+PD1+ICOS+CD38+ cells) using the SMART-SeqV4 Ultra-low input RNA kit (Takara-Clontech) and sorting 200 cells directly into lysis buffer.
cDNA libraries were subsequently generated using the Nextera XT DNA kit (Illumina).

value: Blood

tag: adjuvant

value: GLA-SE


title: ATAC-seq EB WT re1

value: d2.5 EBs


title: sa37_16hpf

city: Kanazawa

first: Isao

last: Kobayashi

state: Ishikawa

address: Kakumamachi

institute: Kanazawa University

description:
Sample 4
KB4

data_processing:
Illumina RTA software was used for base-calling.
Sequenced CAGE tags were mapped to the full genome sequences for Danio rerio (danRer10) using the Burrows-Wheeler Aligner (BWA) and HiSAT2 software.
Tags per million (TPM) were calculated using the CAGEr package of Bioconductor in R ver. 3.3.3 with the minimum TPM value of 0.5.
Genome_build: danRer10
Supplementary_files_format_and_content: Tab-delimited text files include tags per million (TPM) values for each sample.

source_name: whole embryo

extract_protocol:
Total RNAs were extracted from staged embryos using RNeasy Mini Kit (QIAGEN).
2μg of total RNAs from embryos were used for synthesis of the cDNA using a Library Preparation kit (DNAFORM). 5'caps of RNAs are biotinylated after reverse transcription. RNA-cDNA hybirds were then captured by streptavidin-conjugated magnetic beads. The cDNAs were released from RNAs and ligated with the 5′ linker, which includes the three nucleotide barcodes, followed by 3′ linker ligation. Second-strand synthesis was performed using the nAnT-iCAGE second primer, creating the final double-stranded DNA product.
Cap analysis gene expression (CAGE) sequencing

value: whole embryo

value: 16 hours post-fertilization


title: Mixture2.CBU1CANXX.SM2_103117p1_A4


title: sa37_12hpf

description:
Sample 3
KB3

value: 12 hours post-fertilization


title: R40-07


title: Mixture2.CBU1CANXX.SM2_103117p1_A3


title: Mixture2.CBU1CANXX.SM2_103117p1_A7


title: WT_12hpf

description:
Sample 1
KB1

value: wild type


title: WT_16hpf

description:
Sample 2
KB2


title: Mixture2.CBU1CANXX.SM2_103117p1_A2


title: R39-28


title: Mixture2.CBU1CANXX.SM2_103117p1_A1


title: R39-07


title: MYCN_ATAC

city: Boston

first: Leonard

last: Zon

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

data_processing:
All zebrafish ATAC-Seq datasets were aligned to build version DanRer7 of the human genome using Bowtie2 (version 2.2.1) (Langmead et al., 2012) with the following parameters: --end-to-end, -N0, -L20. We used the MACS2 version 2.1.0 (Zhang et al., 2008) peak finding algorithm to identify regions of ATAC-Seq peaks, with the following parameter --nomodel --shift -100 --extsize 200. A q-value threshold of enrichment of 0.05 was used for all datasets.
Genome_build: dr7
Supplementary_files_format_and_content: bed file of called peaks

source_name: EGFP+ neuroblastoma cells were harvested from tumor-bearing MYCN transgenic zebrafish

growth_protocol: EGFP+ neuroblastoma cells were harvested from tumor-bearing MYCN and MYC transgenic zebrafish. Tumors were mechanically homogenized and EGFP+ cells were sorted into PBS containing 10% FBS

extract_protocol:
5X104 EGFP+ neuroblasts were flow sorted using a BD FACSaria II cell sorter into PBS containing 10% FBS. Cells were washed once with 50 uL of cold 1X PBS and spinned down at 500 x g for 5 min, 4° C. After discarding supernatant, cells were lysed using 50 uL cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-360) and spinned down immediately at 500 x g for 10 mins, 4 deg C. Then the cells were precipitated and kept on ice and subsequently resuspended in 25 uL 2X TD Buffer (Illumina Nextera kit), 2.5 uL Transposase enzyme (Illumina Nextera kit, 15028252) and 22.5 uL Nuclease-free water in a total of 50 uL reaction. Transposase reaction was continued for 1 hr at 37° C. Immediately following the reaction, DNA was purified using Qiagen MinElute PCR purification kit (28004) in a final volume of 10 uL.
Libraries were purified according to Illumina protocol using the transposed DNA, NEB PCR master mix, Sybr green, universal and library-specific Nextera index primers. First round of PCR cycles was performed with the following cycles: 72° C, 5 min; 98° C, 30 sec; [98°C, 10 sec; 63 °C, 30 sec; 72 °C, 1 min] X 5 cycles; hold at 4°C. Reactions were kept on ice and using a 5 uL reaction aliquot, appropriate number of additional cycles required for further amplification were determined in a side qPCR reaction with the following procedure: 98 °C , 30 sec; [98 °C, 10 sec; 63 °C, 30 sec; 72 °C, 1 min] X 20 cycles; hold at 4 °C. Upon determining the additional number of PCR cycles required further for each sample, library amplification was conducted using the following conditions: 98°C, 30 sec; [98°C,10 sec; 63°C, 30 sec; 72 °C, 1 min] X appropriate number of cycles; hold at 4°C. Libraries prepared went through quality control analysis using an Agilent Bioanalyzer. Samples with appropriate nucleosomal laddering profiles were selected for next generation sequencing using Illumina Hiseq 2500 platform

value: dbh:EGFP+ tumor cells

value: Neuroblasts


title: MYC_ATAC

source_name: EGFP+ neuroblastoma cells were harvested from tumor-bearing MYC transgenic zebrafish


title: R39-00


title: R40-00


title: Mixture2.CBU1CANXX.SM2_103117p1_A11

department: Klarman Cell Observatory


title: Mixture2.CBU1CANXX.SM2_103117p1_A12


title: Mixture2.CBU1CANXX.SM2_103117p1_A10


title: Mixture2.CBU1CANXX.SM2_103117p1_B12


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_H9

description:
Sex: Female for HEK293 and Male for NIH3T3
scRNA-seq
3'-end
mixture_hg19_mm10_count_matrix.mtx, mixture_hg19_mm10_gene.tsv, mixture_hg19_mm10_cell.tsv

value: sci-RNA-seq


title: MHCCLM6_RNA-seq

city: Guangzhou

first: Zhibiao

last: Mai

state: Guangdong

address: Huang-Pu Avenue West 601

department: Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering

institute: Jinan University

data_processing:
Illumina basecalling
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: GRCh38
Supplementary_files_format_and_content: excel files include log2(rpkm) for each sample.

source_name: hepatocellular carcinoma cell line

extract_protocol:
Total RNA of MHCC97H, MHCCLM3 and MHCCLM6 were extracted using standard Trizol protocol. MHCCLM6 was washed by pre-chilled phosphate buffered saline twice and addition of 2ml cell lysis buffer [1% Triton X-100 in ribosome buffer (RB buffer) [20 mM HEPES-KOH (pH 7.4), 15 mM MgCl2, 200mM KCl, 100 mg/ml cycloheximide and 2mM dithiothreitol]. After 30-min ice-bath, cell lysates were scraped and transferred to pre-chilled 1.5 ml tubes. Cell debris was removed by centrifuging at 16 200 g for 10 min at 4C. Supernatants were transferred on the surface of 20 ml of sucrose buffer (30% sucrose in RB buffer). RNCs were pelleted after ultra-centrifugation at 185000 g for 5h at 4C. Then RNC-RNA were isolated by using standard TRIzol protocol.
PolyA+ mRNA was extracted from the Total RNA and RNC-RNA using RNA purification beads (Illumina). Then the library construction was performed using Vazyme mRNA-seq v2 Library Kit with the insert size 200~300bp. mRNA and RNC-mRNA libraries were sequenced in an Illumina HiSeq X Ten sequencer under PE150 mode.

tag: cell line


title: R37-07


title: MHCCLM3_RNA-seq


title: MHCCLM6_RNC-seq


title: R37-28


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_H7


title: R37-00


title: MHCC97H_RNA-seq


title: R36-07


title: R36-28


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_H8


title: R36-00