title: HCCW34T

city: Shinjuku-ku

first: Yutaka

last: Kurebayashi

state: Tokyo

address: 35 Shinanomachi

institute: Keio University School of Medicine

data_processing:
Sequence reads were generated by Novaseq system (Illumina).
Sequenced reads were aligned to human transcript reference sequence [Homo_sapiens (human) GRCh38/hg38] using HISAT2.
Raw read count and TPM were calculated using featureCounts.
Genome_build: GRCh38
Supplementary_files_format_and_content: TPM_Matrix_HCC.txt: Tab-delimited text file includes Transcripts per million (TPM) values for each Sample.

source_name: Human tumor tissue

extract_protocol:
Total RNA was extracted from fresh frozen tumor tissues using AllPrep DNA/RNA/Protein Kit (Qiagen).
RNA library was prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA) and NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs).

value: Hepatocellular carcinoma

tag: treatment

value: treatment-naive


title: Dia c3 rep2a

status: Public on Sep 25 2021

type: SRA

city: Mainz

first: Nir

last: Yogev

address: Langenbeck Str.1

country: Germany

institute: University Medical Center of the Johannes Gutenberg University of Mainz

description:
Dia c3 R2a
yogev_normcounts_2.tsv

library_source: transcriptomic

data_processing:
Sequenced reads were mapped to the mouse genome reference sequence with STAR (version 2.4.0j)
The ENSEMBL Mus_musculus.GRCm38 was chosen as reference genome, alignments were processed with the featureCounts function of the Rsubread package. The corresponding gtf annotation for the reference (ENSEMBL v76) was used.
Exploratory data analysis was performed with the pcaExplorer package (Marini et al., 2016)
Differential expression analysis was performed with DESeq2 (version 1.20.0), setting the False Discovery Rate to 0.05
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw counts from DESeq2 for each sample

molecule: total RNA

organism: Mus musculus

source_name: Diaphragm C3 macrophages

extract_protocol:
Mice were anesthetized and peripheral blood was flushed by cardiac perfusion using saline solution. Dura mater was removed, digested, and dural macrophages were sorted using BD FACS Aria II flow cytometer. RNA was harvested from bulk sorted dural macrophages using Qiagen RNeasy Plus Micro Kit (Cat# 74034). 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using standard NEBNext® Ultra™ II RNA library prep kit protocols. All samples were sequenced with reads of 75 nucleotides, using a single-end library preparation (unstranded sequencing kit).

tag: strain

tag: tissue

value: Diaphragm

tag: age

value: 17 weeks

tag: genotype

value: wild type

tag: condition

value: steady state


title: Dia c3 rep2

description:
Dia c3 R2
yogev_normcounts_2.tsv


title: HCCW52T

country: Japan

organism: Homo sapiens


title: HCCW20T


title: HCCW27T


title: Dia c2 rep2

description:
Dia c2 R2
yogev_normcounts_2.tsv

source_name: Diaphragm C2 macrophages


title: HCCN51T


title: HCCW12T


title: Dia c1 rep2

description:
Dia c1 R2
yogev_normcounts_2.tsv

source_name: Diaphragm C1 macrophages


title: HCCN49T


title: Dia c1 rep1

description:
Dia c1 R1
yogev_normcounts_2.tsv


title: HCCW40T


title: HCCW36T


title: HCCN46T


title: HCCN47T


title: Dia c1 rep2a

description:
Dia c1 R2a
yogev_normcounts_2.tsv


title: HCCW26T


title: HCCW25T


title: Dura c3 rep2

description:
Dura c3 R2
yogev_normcounts_2.tsv

source_name: Dural C3 macrophages

value: Dura


title: HCCN45T


title: HCCN41T


title: HCCN43T


title: Donor3_M2IL4

city: Saarbruecken

first: Jessica

last: Hoppstaedter

address: Campus C2 3

department: Pharmacy

institute: Saarland University

data_processing:
RNA libraries were sequenced for 2 × 55 bp on an Illumina HiSeq2500 Sequencer using a V3 paired-end flow cell.
Raw reads were subjected to quality control (QC) through FastQC v 0.11.2. Library adaptor removal and trimming was done using CutAdapt v.1.4.1 and TrimGalore! v0.3.3, respectively.
Trimmed reads were mapped with STAR v2.4.0f1 to the human reference genome (hs37d5).
Gene expression was quantified using the Salmon software (Patro et al., 2017) using Ensembl gene annotation (v88).
Genome_build: hs37d5
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

source_name: MDMs

growth_protocol: Buffy coats were obtained from healthy adult blood donors (Blood Donation Center, Klinikum Saarbrücken, Germany). The use of human material for the isolation of primary cells was approved by the local ethics committee (permission no. 173/18).  Monocytes were isolated and polarized as previously described (Dahlem et al., Cancers (Basel), 2020; Dembek et al., Immunobiology, 2017). In brief, peripheral blood mononuclear cells (PBMCs) were isolated from buffy coats by density gradient centrifugation using Lymphocyte Separation Medium 1077 (PromoCell) and LeucoSEP tubes (Greiner Bio-One). Monocytes were purified by magnetic cell sorting using anti-CD14 microbeads (Miltenyi Biotec) and LS Columns (Miltenyi Biotec) according to the manufacturer’s instructions, except that only 10% of the recommended bead amount was used (Dembek et al., Immunobiology, 2017). Monocytes were seeded into a 12-well plate at a density of 500,000 cells/well and differentiated into macrophages in MDM medium, i.e., standard growth medium (RPMI 1640 with 10% FCS, 100 U/ml penicillin G, 100 mg/ml streptomycin, 2 mM glutamine) supplemented with macrophage-colony stimulating factor (M-CSF, Miltenyi Biotec) for 6 d. The medium was changed every other day.

extract_protocol:
Total RNA was extracted using the Direct-zo RNA MiniPrep Kit (Zymo Research) according to the manufacturer’s instructions. Prior to RNA isolation, cells were lysed with QIAzol Lysis Reagent (Qiagen). Residual genomic DNA was removed by treatment with Ambion DNase I (ThermoFisher Scientific).
For transcriptome analysis of TMDM subsets, high throughput sequencing of cDNA using next-generation sequencing (NGS) was performed.   Libraries were prepared from 250 ng MDM samples with an RNA integrity (RIN) > 9, according to Agilent2100 Bioanalyzer and Agilent RNA 6000 Pico Kit (Agilent Technologies). Poly(A) enrichment was performed on the input total RNA using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) according to the manufacturer’s instructions. The cDNA library preparation was conducted with the NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (New England Biolabs) as recommended by the supplier. In brief, first- and second-strand cDNA synthesis and chemical fragmentation were performed, followed by adapter ligation and PCR amplification of the final library (10 PCR cycles). PCR cleanup was performed using Agencourt AM-Pure® XP beads (Beckmann Coulter).

treatment_protocol: After differentiation, human monocyte-derived macrophages (MDMs) were polarized for another 24 h. To this end, MDM medium was supplemented with 20 ng/ml  IFNγ (Miltenyi Biotec) and 100 ng/ml LPS (Invivogen) for M1 polarization; either 20 ng/ml IL4 (Miltenyi Biotec) or IL10 (Miltenyi Biotec) for M2 polarization; or left without further supplementation for M0 macrophages. TAM-like macrophages were generated by cultivation in tumor cell-conditioned medium (TCM) supplemented with 20 ng/ml M-CSF. TCM was generated by seeding 1 x 106 A549 lung adenocarcinoma cells into a T75 culture flask. After 3 d, the supernatant was discarded, and fresh standard growth medium was added to the cells. After 48 h, the medium was sterile filtered (0.22 µm) and used immediately for macrophage polarization

value: 20 ng/ml M-CSF, 20 ng/ml IL4


title: Donor3_TAMlike

value: TCM, 20 ng/ml M-CSF


title: Dura c2 rep3

description:
Dura c2 R3
yogev_normcounts_2.tsv

source_name: Dural C2 macrophages


title: Donor3_M2IL10

value: 20 ng/ml M-CSF, 20 ng/ml IL10


title: Dura c2 rep1

description:
Dura c2 R1
yogev_normcounts_2.tsv


title: HCCN32T


title: HCCB42T


title: HCCB37T


title: Donor3_M1

value: 20 ng/ml M-CSF, 100 ng/ml LPS, 20 ng/ml IFN-y


title: Dura c1 rep3

description:
Dura c1 R3
yogev_normcounts_2.tsv

source_name: Dural C1 macrophages


title: HCCN39T


title: Dura c3 rep3

description:
Dura c3 R3
yogev_normcounts_2.tsv


title: Dura c3 rep1

description:
Dura c3 R1
yogev_normcounts_2.tsv


title: Dura c2 rep2

description:
Dura c2 R2
yogev_normcounts_2.tsv


title: Donor3_M0

value: 20 ng/ml M-CSF


title: HCCB48T


title: HCCB33T


title: HCCB36T


title: Donor2_TAMlike


title: HCCB29T


title: HCCB27T


title: Donor2_M2IL4


title: Dura c1 rep1

description:
Dura c1 R1
yogev_normcounts_2.tsv


title: HCCB23T


title: HCCN40T


title: HCCB18T


title: IL22 M rep3

description:
IL22 M R1
yogev_normcounts_1.tsv

source_name: Dural macrophages

value: 16-19 weeks

value: Rag1 ko

value: 6.5 weeks post IL22 ko T cell reconstitution


title: Donor2_M2IL10


title: Donor2_M0


title: Donor2_M1


title: sorted CD45+ VDJ batch3 (E2_TEL_fastqs)

city: San Francisco

first: Jeffrey

middle: A

last: Bluestone

state: California

address: 513 Parnassus Ave

country: USA

institute: UCSF

data_processing:
Library strategy: VDJ-seq
Cell Ranger Single-Cell Software Suite (version 3.1.0, 10x Genomics)
VCF genotype files and scRNAseq BAM files were used to run Demuxlet with default parameters. Demultiplexing results were largely concordant with freemuxlet (https://github.com/statgen/popscle/). Subsequently, the multiplexed single cell RNAseq and single cell TCRseq data were filtered according to a singlet whitelist extracted from the demuxlet.best output file.
Using Scanpy (Wolf et al., 2018), we performed BBKNN batch correction after poolong all the demuxletted samples, PCA on the gene expression matrix and we then build a nearest neighbor graph to calculate a UMAP and find clusters via the louvain algorithm
Supplementary_files_format_and_content: 20201228_adata.h5ad is the combination of all the h5 files (cell ranger output), demuxleted and annotated for TCRs, patients ID, timepoints

source_name: frozen PBMC

extract_protocol:
Chromium Single Cell V(D)J Enriched and 5' Gene Expression libraries generation and sequencing under the guidance of the official instruction manual
illumina Novaseq sequencing

treatment_protocol: Cells were thawed into X-vivo media, counted and sorted for CD45+/live dead

tag: cell type

value: PBMC

tag: sequencing kit

value: 10X genomics VDJ 5'

tag: number of samples that has been pooled

tag: patient id, time point


title: sorted CD45+ gene expression batch3 (E2_GEXL_fastqs)

data_processing:
Cell Ranger Single-Cell Software Suite (version 3.1.0, 10x Genomics)
VCF genotype files and scRNAseq BAM files were used to run Demuxlet with default parameters. Demultiplexing results were largely concordant with freemuxlet (https://github.com/statgen/popscle/). Subsequently, the multiplexed single cell RNAseq and single cell TCRseq data were filtered according to a singlet whitelist extracted from the demuxlet.best output file.
Using Scanpy (Wolf et al., 2018), we performed BBKNN batch correction after poolong all the demuxletted samples, PCA on the gene expression matrix and we then build a nearest neighbor graph to calculate a UMAP and find clusters via the louvain algorithm
Supplementary_files_format_and_content: 20201228_adata.h5ad is the combination of all the h5 files (cell ranger output), demuxleted and annotated for TCRs, patients ID, timepoints

value: 10X genomics gene expression 5'


title: Donor1_TAMlike


title: sorted CD45+ VDJ batch3 (E3_TEL_fastqs)


title: sorted CD45+ VDJ batch3 (E1_TEL_fastqs)


title: IL17A F rep2

description:
IL17A F R2
yogev_normcounts_1.tsv

value: 6.5 weeks post IL-17AF koT cell reconstitution


title: Dura c1 rep2

description:
Dura c1 R2
yogev_normcounts_2.tsv


title: sorted CD45+ gene expression batch3 (D3_GEXL_fastqs)


title: sorted CD45+ gene expression batch3 (E1_GEXL_fastqs)


title: Donor1_M2IL4


title: sorted CD45+ VDJ batch3 (D3_TEL_fastqs)


title: IL17A F rep1

description:
IL17A F R1
yogev_normcounts_1.tsv


title: sorted CD45+ VDJ batch3 (D2_TEL_fastqs)


title: sorted CD45+ gene expression batch3 (D2_GEXL_fastqs)


title: Donor1_M2IL10


title: sorted CD45+ VDJ batch3 (D1_TEL_fastqs)


title: Donor1_M1


title: sorted CD45+ gene expression batch3 (D1_GEXL_fastqs)


title: sorted CD45+ VDJ batch3 (C3_TEL_fastqs)


title: Th17 M rep7

description:
Th17 M R7
yogev_normcounts_1.tsv

value: 6.5 weeks post IL6Ra ko/IL21R ko T cell reconstitution


title: Th17 M rep6

description:
Th17 M R6
yogev_normcounts_1.tsv


title: sorted CD45+ gene expression batch3 (C3_GEXL_fastqs)


title: IL22 F rep2

description:
IL22 F R2
yogev_normcounts_1.tsv


title: sorted CD45+ gene expression batch3 (E3_GEXL_fastqs)


title: sorted CD45+ VDJ batch3 (C2_TEL_fastqs)


title: IL22 F rep1

description:
IL22 F R1
yogev_normcounts_1.tsv


title: Donor1_M0


title: Donor3_AM_Rep3

source_name: healthy lung tissue

growth_protocol: Tumor associated macrophgaes (TAMs) and alveolar macrophages (AMs) were isolated from human lung tumor tissue or the autogenic non-tumor lung tissue obtained from patients undergoing lung resection. TAMs were isolated after the tumor tissue had beed enzymatically digested using the human tumor dissociation (Miltenyi Biotec) and the  gentleMACS Octo Dissociator according to the manufacturer’s instructions. Cells were washed, resuspended in RPMI 1640 medium without supplements, and incubated for 0.5 h in a T175 flask. Adherent cells were thoroughly washed with PBS to remove non-adherent cells, and further cultivated in AM/TAM medium (RPMI 1640, 5% FCS, 100 U/ml penicillin G, 100 µg/ml streptomycin, 2 mM glutamine). TAMs were detached with accutase and seeded at a density of 0.5 × 106 cells per well into a 12-well plate. For AM isolation visible bronchi were removed, the lung tissue was chopped and washed with 100–200 ml PBS. Washing buffer was collected, and AMs were obtained by centrifugation. The remaining erythrocytes were lysed by quickly resuspending the pellet in autoclaved water, immediately followed by washing with PBS. The cell pellet was mock-digested and seeded as described for TAMs.

extract_protocol:
Total RNA from TAMs/AMs was extracted using the Direct-zo RNA MiniPrep Kit (Zymo Research) according to the manufacturer’s instructions. Prior to RNA isolation, cells were lysed with QIAzol Lysis Reagent (Qiagen). Residual genomic DNA was removed by treatment with Ambion DNase I (ThermoFisher Scientific).
For transcriptome analysis of TAMs/AMs, high throughput sequencing of cDNA using next-generation sequencing (NGS) was performed.   Libraries were prepared from 500 ng TAM/AM samples with an RNA integrity (RIN) > 9, according to Agilent2100 Bioanalyzer and Agilent RNA 6000 Pico Kit (Agilent Technologies). Poly(A) enrichment was performed on the input total RNA using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) according to the manufacturer’s instructions. The cDNA library preparation was conducted with the NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (New England Biolabs) as recommended by the supplier. In brief, first- and second-strand cDNA synthesis and chemical fragmentation were performed, followed by adapter ligation and PCR amplification of the final library (10 PCR cycles). PCR cleanup was performed using Agencourt AM-Pure® XP beads (Beckmann Coulter).

value: alveolar macrophages


title: sorted CD45+ gene expression batch3 (C2_GEXL_fastqs)


title: Th17 M rep4

description:
Th17 M R4
yogev_normcounts_1.tsv


title: Th17 M rep5

description:
Th17 M R5
yogev_normcounts_1.tsv


title: Th17 F rep3

description:
Th17 F R3
yogev_normcounts_1.tsv


title: sorted CD45+ VDJ batch3 (C1_TEL_fastqs)


title: sorted CD45+ gene expression batch3 (C1_GEXL_fastqs)


title: sorted CD45+ gene expression batch3 (B3_GEXL_fastqs)


title: sorted CD45+ VDJ batch3 (B3_TEL_fastqs)


title: Th17 F rep1

description:
Th17 F R1
yogev_normcounts_1.tsv


title: sorted CD45+ VDJ batch3 (B2_TEL_fastqs)


title: IFNg F rep2

description:
IFNg F R2
yogev_normcounts_1.tsv

value: 6.5 weeks post IFNg koT cell reconstitution


title: Th17 F rep2

description:
Th17 F R2
yogev_normcounts_1.tsv


title: Donor3_AM_Rep2


title: Donor3_TAM_Rep2

source_name: lung tumor tissue

value: tumor-associated macrophages


title: Donor3_TAM_Rep3


title: sorted CD45+ gene expression batch3 (B1_GEXL_fastqs)


title: sorted CD45+ VDJ batch3 (A2_TEL_fastqs)


title: sorted CD45+ gene expression batch3 (B2_GEXL_fastqs)


title: sorted CD45+ gene expression batch3 (A3_GEXL_fastqs)


title: sorted CD45+ VDJ batch3 (B1_TEL_fastqs)


title: Donor3_TAM_Rep1


title: sorted CD45+ VDJ batch3 (A3_TEL_fastqs)


title: HCCW44T

value: Hepatocellular carcinoma

value: treatment-naive


title: sorted CD45+ gene expression batch3 (A2_GEXL_fastqs)


title: IFNg F rep1

description:
IFNg F R1
yogev_normcounts_1.tsv

value: Dura


title: Donor2_AM_Rep3


title: Th1 F rep2

description:
Th1 F R2
yogev_normcounts_1.tsv

value: 6.5 weeks post Tbet ko T cell reconstitution


title: Donor3_AM_Rep1


title: Donor2_AM_Rep2


title: sorted CD45+ VDJ batch2 (sample_V_3_TEL_fastqs)


title: Th1 F rep1

description:
Th1 F R1
yogev_normcounts_1.tsv


title: sorted CD45+ VDJ batch2 (sample_V_2_TEL_fastqs)


title: sorted CD45+ gene expression batch2 (sample_V_3_5primeGEX_fastqs)


title: sorted CD45+ VDJ batch3 (A1_TEL_fastqs)


title: Donor2_AM_Rep1


title: sorted CD45+ gene expression batch3 (A1_GEXL_fastqs)


title: Tall M rep5

description:
Tall M R2
yogev_normcounts_1.tsv

value: 6.5 weeks post total B6 T cell reconstitution


title: sorted CD45+ gene expression batch2 (sample_V_2_5primeGEX_fastqs)


title: sorted CD45+ VDJ batch2 (sample_V_1_TEL_fastqs)


title: sorted CD45+ gene expression batch2 (sample_V_1_5primeGEX_fastqs)


title: Tall F rep4

description:
Tall F R4
yogev_normcounts_1.tsv


title: Donor1_AM_Rep3


title: Donor2_TAM_Rep2


title: Tall F rep1

description:
Tall F R1
yogev_normcounts_1.tsv


title: Donor2_TAM_Rep3


title: sorted CD45+ gene expression batch2 (sample_IV_1_5primeGEX_fastqs)


title: sorted CD45+ VDJ batch2 (sample_IV_1_TEL_fastqs)


title: sorted CD45+ VDJ batch2 (sample_IV_2_TEL_fastqs)


title: sorted CD45+ gene expression batch2 (sample_IV_2_5primeGEX_fastqs)


title: sorted CD45+ VDJ batch2 (sample_IV_3_TEL_fastqs)


title: Tall F rep2

description:
Tall F R2
yogev_normcounts_1.tsv


title: sorted CD45+ gene expression batch2 (sample_III_3_5primeGEX_fastqs)


title: sorted CD45+ gene expression batch2 (sample_IV_3_5primeGEX_fastqs)


title: Donor2_TAM_Rep1


title: Rag M rep5

description:
Rag M R1
yogev_normcounts_1.tsv

value: steady state


title: Rag F rep1

description:
Rag F R1
yogev_normcounts_1.tsv

value: 16-19 weeks


title: 3691_shEYA2-2

city: San Diego

first: Jeremy

last: Rich

state: CA

address: 9500 Gilman Drive #0695

institute: University of California, San Diego

description:
counts.xlsx
shEYA2.776 = shEYA2-2 = TRCN0000051947

data_processing:
The Fastq files of the RNA-seq data were processed to read quality control by running ‘FastQC’ (Galaxy version 0.72) in Galaxy (usegalaxy.org) and then to remove the adapters by running ‘Trim Galore!’ (Galaxy version 0.4.3.1). The trimmed reads were mapped to human genome 38 by ‘HISAT2’ (Galaxy version 2.1.0+galaxy 4) and the mapped reads were then counted with ‘featureCounts’ (Galaxy version 1.6.3+galaxy 2). The counts were processed to differentially expressed gene analysis with R package ‘DESeq2’ (Version 1.14.1). Volcano plots were generated using GraphPad Prism. Downregulated genes upon EYA2 knockdown were processed to GO analysis (http://geneontology.org/). Pre-ranked genes by fold change were processed to GSEA (Gene Set Enrichment Analysis; Broad institute).
Genome_build: hg19
Supplementary_files_format_and_content: counts

source_name: Patient Derived Glioma Stem Cell

growth_protocol:
Cells from a primary patient derived GBM tumor model were injected intracranially into a immunocompromised NSG mouse and allowed to grow into a tumor. Cells were dissociated and passaged in vitro.
Xenografted tumors were dissociated using a papain dissociation system according to the manufacturer’s instructions. Cells were then cultured in Neurobasal medium supplemented with 2% B27, 1% L-glutamine, 1% sodium pyruvate, 1% penicillin/streptomycin, 10 ng/ml basic fibroblast growth factor (bFGF), and 10 ng/ml epidermal growth factor (EGF) for at least 6 hours to recover expression of surface antigens. Because cell surface markers are not uniformly informative for marking GSCs, we utilized a combination of functional criteria to validate GSCs. Both GSCs and DGCs were derived immediately following dissociation or following transient xenograft passage in immunocompromised NSG mice using prospective sorting followed by assays to confirm stem cell marker expression, sphere formation, and secondary tumor initiation. Cells were labeled with CD133/2(293C)-Allophycocyanin (APC) antibody kit (Miltenyi Biotec, 130098826), and the CD133+ cells were sorted and analyzed by flow cytometry. The sorted CD133+ cells were cultured in NBM-B27 medium containing 20 ng/ml of both epidermal growth factor (EGF) (R&D system, 236-EG-01M) and recombinant human FGF basic (FGF) (R&D system, 4114-TC-01M) for a short period before treatment and analyzed. GSC phenotypes were validated by expression of stem cell markers (SOX2 and OLIG2) and functional assays of self-renewal. Corresponding differentiated glioma cells were obtained by culturing the GSCs in DMEM medium supplemented with 10% FBS for at least 2 weeks.

extract_protocol: Total RNA from GSCs transduced with shCONT or shEYA2 were collected with miRNeasy mini kit (Qiagen) and processed to library construction with TruSeq RNA library Prep Kit (illumine).

treatment_protocol: Lentiviral clones expressing two or three non-overlapping shRNAs directed against human EYA2 (TRCN0000051947 and TRCN0000051946), human GNAi1 (TRCN0000036472, TRCN0000036473 and TRCN0000036470), human GNAi2 (TRCN0000029518, TRCN0000029517 and TRCN0000029514) or a non-targeting control shRNA were obtained from Sigma-Aldrich. 293FT cells were used to generate lentiviral particles through co-transfection of the packaging vectors pCMV-dR8.2 dvpr and pCI-VSVG using a standard calcium phosphate transfection method in DMEM plus 10% FBS. 12 hours later after transfection, medium was changed to neurobasal complete medium. Neurobasal complete medium containing lentiviral particles was collected by filtering with 0.45uM filter for immediate use or stock in -80°C.

value: Glioblastoma


title: sorted CD45+ VDJ batch2 (sample_II_2_TEL_fastqs)


title: Tall F rep3

description:
Tall F R3
yogev_normcounts_1.tsv

value: Rag1 ko


title: sorted CD45+ VDJ batch2 (sample_III_3_TEL_fastqs)

value: PBMC


title: Rag M rep6

description:
Rag M R2
yogev_normcounts_1.tsv


title: Donor1_AM_Rep2


title: Donor1_TAM_Rep3


title: 3691_shEYA2-1

description:
counts.xlsx
shEYA2.175 = shEYA2-1 = TRCN0000051946


title: sorted CD45+ VDJ batch2 (sample_III_1_TEL_fastqs)

value: 10X genomics VDJ 5'


title: sorted CD45+ VDJ batch2 (sample_I_3_TEL_fastqs)


title: 3691_shNT

description: counts.xlsx

value: shNT


title: Donor1_AM_Rep1


title: PBL009_TCR

city: Little Rock

first: Yong-Chen

middle: William

last: Lu

address: 4301 W Markham St

department: Pathology

institute: University of Arkansas for Medical Sciences

data_processing:
Library strategy: TCR-seq
Fastq files were generated by Cell Ranger pipeline from 10X Genomics
Genome_build: hg19
Supplementary_files_format_and_content: with 10X Genomics, Cell Ranger can be performed to generate the data matrix

source_name: Peripheral blood lymphocytes (PBL)

extract_protocol:
PBL were thawed and cultured overnight. PBLs were then stimulated with HPV peptides. IFN-g-positive T cells were sorted and subjected to single-cell analysis.
Single-cell libraries were prepared for sequencing using standard single-cell VDJ protocol from 10X Genomics

value: Peripheral blood lymphocytes


title: sorted CD45+ VDJ batch2 (sample_I_2_TEL_fastqs)


title: Rag F rep4

description:
Rag F R4
yogev_normcounts_1.tsv


title: sorted CD45+ VDJ batch2 (sample_III_2_TEL_fastqs)


title: Rag F rep3

description:
Rag F R3
yogev_normcounts_1.tsv


title: PBL009_GEX

data_processing:
Fastq files were generated by Cell Ranger pipeline from 10X Genomics
Genome_build: hg19
Supplementary_files_format_and_content: with 10X Genomics, Cell Ranger can be performed to generate the data matrix


title: Rag F rep2

description:
Rag F R2
yogev_normcounts_1.tsv


title: sorted CD45+ VDJ batch2 (sample_II_1_TEL_fastqs)


title: sorted CD45+ gene expression batch2 (sample_III_2_5primeGEX_fastqs)

value: 10X genomics gene expression 5'


title: sorted CD45+ VDJ batch2 (sample_II_3_TEL_fastqs)


title: Donor1_TAM_Rep1


title: sorted CD45+ gene expression batch2 (sample_II_2_5primeGEX_fastqs)


title: sorted CD45+ gene expression batch2 (sample_II_1_5primeGEX_fastqs)


title: Donor1_TAM_Rep2


title: sorted CD45+ gene expression batch2 (sample_II_3_5primeGEX_fastqs)


title: sorted CD45+ gene expression batch2 (sample_I_1_5primeGEX_fastqs)


title: sorted CD45+ VDJ batch2 (sample_I_1_TEL_fastqs)


title: 3565_shEYA2-1


title: 3565_shNT

description: counts.xlsx


title: POH1 siRNA

city: Shanghai

first: Wandong

last: Yu

state: China

address: No. 801, Heqing Road, Minhang District, Shanghai

country: China

institute: The Fifth People’s Hospital of Shanghai, Fudan University

data_processing:
CASAVA used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 in the human genome using HISAT2
The gene transcript expression count was performed by Hiseq RNA-seq to generate a matrix of transcripts per kilobase of exon model per million mapped reads
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

source_name: PC3 cells

extract_protocol:
RNA was harvested using Trizol reagent. VAHTS mRNA-seq V2 Library Prep Kit for Illumina (Cat#NR602-01/02) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: prostate cancer cell line

tag: genotype/variation

value: POH1 siRNA


title: sorted CD45+ gene expression batch1  (11-13)


title: sorted CD45+ VDJ batch1  (10-15_TEL)


title: fetal lungs, Combo-blockade-3

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

data_processing:
Raw sequencing data was processed aligned to the Rhesus macaque reference Mmul_8.0.1 (Ensembl version 91) with Cell Ranger version 3.0.2 (10X Genomics) generating expression count matrix files.
Genome_build: Mmul_8.0.1
Supplementary_files_format_and_content: HDF5 Cell Ranger Filtered Count Matrix

organism: Macaca mulatta

source_name: Combo-blockade fetal lungs

extract_protocol:
The fetal lung was removed, and left lobe was processed into single cell suspensions as described previously 56. The large airways were removed and approximately ~500mg of airway free tissue was collected in a gentleMACS C-tube (Miltenyi Biotec, Auburn, CA) and 5mL digest buffer was added and placed on a gentleMACS octo dissociator for programmed runs. Following dissociation, the cell suspension was passed through a 100µm filter and washed with PBS. After washing, cells underwent red cell lysis (eBioscience, San Diego, CA) along with another pass through a 40um filter after neutralization.
~50,000 cells per lung were submitted for single cell sequencing at the Cincinnati Children’s Hospital Medical Center DNA Sequencing and Genotyping Core. Approximately ~16,000 cells were loaded into one channel of the Chromium system using the 3 prime v3 single cell reagent kit (10X Genomics, Pleasanton, CA). Following capture and lysis, cDNA was synthesized and amplified as per the manufacturer’s protocol (10X Genomics).
The amplified cDNA was used to construct Illumina sequencing libraries that were each sequenced using an Illumina HiSeq 4000 machine.

treatment_protocol: The Institutional Animal Care and Use Committee at the University of California, Davis approved all animal procedures. Normally cycling, adult female Rhesus macaques (Macaca mulatta) were time mated. At approximately 130 days of gestation (about 80% of term gestation), the pregnant dams received either 1 ml saline solution or 1mg of LPS (Sigma-Aldrich, St. Louis MO) in 1 ml saline solution by ultrasound guided IA injection. IA administration of LPS or saline was performed in mothers of similar weights and ages with fetus with similar fetal genders and gestational ages. Fetuses were surgically delivered 16, 48 or 120 hrs later by cesarean section. Delivered fetuses were euthanized with pentobarbital and tissues collected. There were no spontaneous deaths or preterm labor in the animals. Some pregnant dams were given, in addition to IA LPS, either the IL-1 receptor antagonist (IL-1RA, Kineret® Sobi, Stockholm, Sweden), or the anti-TNF Ab (Adalimubab HUMIRA® AbbVie Chicago, IL), or both.  These inhibitors were administered subcutaneously (100mg or 40mg for IL-1RA and anti-TNF respectively) 3hrs before IA LPS as well as IA (50mg or 40 mg for IL-1RA and anti-TNF respectively) 1hr before IA LPS.

tag: gestation age (days)

tag: weight at birth (g)

tag: fetal sex

value: Male

value: fetal lungs

value: Combo-blockade


title: sorted CD45+ gene expression batch1  (10-15)


title: sorted CD45+ gene expression batch2 (sample_I_2_5primeGEX_fastqs)


title: sorted CD45+ gene expression batch2 (sample_III_1_5primeGEX_fastqs)


title: sorted CD45+ gene expression batch2 (sample_I_3_5primeGEX_fastqs)


title: fetal lungs, Combo-blockade-2

value: Female


title: Control siRNA

value: Control siRNA


title: 3565_shEYA2-2


title: MPs_ KO_ rep1 [MeDIP-seq]

city: Berlin

first: Xiaoyan

last: Wei

address: Thielallee 63

institute: Free University of Berlin

library_source: genomic

data_processing:
Reads were aligned to the mouse reference genome mm9 using bwa v0.7.15 [v.s.].
QSEA Bioconductor package v.1.12.0 was used for analyzing.
CpG enrichment profiles were calibrated using blind calibration method.
Differentially methylated regions (DMRs) were called at 250 base windows at an FDR of 10%, and annotated with promoter (TSS +/- 500 bases), exonic, and gene body regions as well as model based CpG islands (CGI).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigWig files

molecule: genomic DNA

source_name: Muscle Progenitors

extract_protocol:
Genomic DNA from 1x10e6 FACS sorted p7 MPs from one animal was isolated with the All Prep DNA / RNA / Protein Mini Kit (Qiagen) and used as one sample. Replicate samples from each genotype were used.
The low input MeDIP protocol (PMID: 22402632) was used for library preparation. Libraries were amplified in a final PCR step using barcoded TruSeq primers (Index_prime; 12 cycles) and size selected on a 2 % agarose gel (230-320bp, peak at 282-294bp).

value: Nf1flox/floxMyf5Cre+ (KO)

value: Skeletal muscle progenitors

value: Postnatal day 7


title: sorted CD45+ VDJ batch1  (12-14_TEL)


title: MPs_ Het_ rep2 [MeDIP-seq]

value: Nf1flox/+ Myf5Cre+ (Control)


title: Ad-NC

type: RNA

city: Pingyi City

first: Yixiu

last: Chen

address: No.7 Jinhua Road, Pingyi Economic Development Zone, Shandong Province, 273300, P.R. China

institute: Neurosurgery, Pingyi people's Hospital

description:
HepG2 cells were transfected with Ad-NC for 48 h and RNA was collected for detection.
microRNA

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.10 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: HepG2 cells

label_protocol: The miRNAs were labeled using the Agilent miRNA labeling reagent. Total RNA (200 ng) was dephosphorylated and ligated with pCp-Cy3, the labeled RNA was purified and hybridized to miRNA arrays.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

tag: transfection

value: Ad-NC


title: sorted CD45+ VDJ batch1  (11-13_TEL)

value: PBMC


title: MPs_ KO_ rep2 [MeDIP-seq]


title: sorted CD45+ VDJ batch1  (020218_9_TEL)

value: 10X genomics VDJ 5'


title: ad-LINC01126

description:
HepG2 cells were transfected with ad-LINC01126 for 48 h and RNA was collected for detection.
microRNA


title: fetal lungs, Combo-blockade-1


title: Rumen papillae, S2502Nr42

city: Vienna

first: Cátia

last: Pacífico

state: Vienna

address: Veterinaerplatz 1

country: Austria

institute: University of Veterinary Medicine Vienna

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.20).
Adapters were trimmed with Skewer (version 0.2.2) (Jiang et al. 2014).
When performing paired-end sequencing, the first three nucleotides of the second sequencing read (Read 2) are derived from the Pico v2 SMART Adapter. Those three nucleotides have been trimmed.
Genome_build: bosTau9
Supplementary_files_format_and_content: tab-delimited text file include raw counts of all samples
Supplementary_files_format_and_content: tab-delimited text file include DESeq2-normalized counts of all samples

organism: Bos taurus

source_name: Rumen papillae

extract_protocol:
Total RNA was extracted using NucleoSpin miRNA kit (Macherey-Nagel, Germany).
Libraries were prepared from 10 ng total RNA using SMART Seq Stranded Total RNA-Seq Kit (Takara).

tag: breed

value: Holstein

value: Papillae

tag: diet

value: Grain

value: PHY


title: sorted CD45+ gene expression batch1  (020218_9)

value: 10X genomics gene expression 5'


title: Rumen papillae, S2502Nr41

tag: treatment


title: MPs_ Het_ rep1 [MeDIP-seq]

tag: strain


title: sorted CD45+ gene expression batch1  (12-14)


title: Rumen papillae, S2502Nr40

tag: tissue


title: fetal lungs, ILRA-blockade-3

source_name: IL-RA-blockade fetal lungs

value: IL-RA-blockade


title: Rumen papillae, S2502Nr39


title: sorted CD45+ VDJ batch1  (020218_8_TEL)


title: H4K16ac_KO_rep2 [ChIP-seq]

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bwa v0.7.15.
Fast and accurate short read alignment with Burrows-Wheeler Transform.
Peaks were called using MACS2 version 2.1.2 and annotated with overlapping and proximal genes in R with the ChIPpeakAnno library.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigWig files
Supplementary_files_format_and_content: *_peaks.txt: Peak text files

source_name: Muscle progenitor cells

extract_protocol:
Chipmentation protocol with the help of Tn5 enzyme (Illumina #FC-131-1024) was used for low cell number ChIP-seq analysis in here.
Samples were eluted using the MinElute kit (Qiagen #28004), followed by 16-18 cycles PCR amplification. AMPureXP beads (Beckman Coulter #A63881) were used for library product size selection.

treatment_protocol: Freshly FACS sorted p7 MPs from one animal were used for each sample and replicate samples were used for each genotype. Antibodies against acetyl-Histone H4 (Lys16), trimethyl-Histone H3 (Lys4) and trimethyl-Histone H3 (Lys27) were used.

tag: genotype

value: Skeletal muscle progenitor cells

tag: age

tag: chip antibody


title: sorted CD45+ gene expression batch1  (020218_8)

tag: cell type

tag: sequencing kit


title: Rumen papillae, S2502Nr38

value: control


title: H4K16ac_Het_rep2 [ChIP-seq]


title: fetal lungs, TNF-alpha-blockade-3

source_name: TNF-alpha-blockade fetal lungs

value: Male

value: fetal lungs

value: TNF-alpha-blockade


title: Rumen papillae, S2502Nr37


title: fetal lungs, ILRA-blockade-1


title: H4K16ac_KO_rep1 [ChIP-seq]

value: Nf1flox/floxMyf5Cre+ (KO)


title: H3K27me3_KO_rep2 [ChIP-seq]

value: Postnatal day 7


title: sorted CD45+ VDJ batch1  (020218_6_TEL)

tag: number of samples that has been pooled

tag: patient id, time point


title: sorted CD45+ VDJ batch1  (020218_7_TEL)


title: fetal lungs, TNF-alpha-blockade-2

value: Female


title: sorted CD45+ gene expression batch1  (020218_7)


title: Rumen papillae, S2502Nr35


title: sorted CD45+ gene expression batch1  (020218_6)


title: Rumen papillae, S2502Nr34


title: H3K27me3_Het_rep1 [ChIP-seq]

value: Nf1flox/+ Myf5Cre+ (Control)


title: fetal lungs, TNF-alpha-blockade-1


title: sorted CD45+ VDJ batch1  (020218_5_TEL)

value: PBMC


title: fetal lungs, LPS-2

source_name: LPS-treated fetal lungs

value: LPS


title: Rumen papillae, S2502Nr33

value: Holstein

value: Forage


title: H3K27me3_Het_rep2 [ChIP-seq]


title: fetal lungs, ILRA-blockade-2


title: fetal lungs, LPS-1


title: fetal lungs, Saline-2

source_name: Saline-treated fetal lungs

value: Saline


title: Rumen papillae, S2502Nr36

value: Papillae

value: Grain


title: Rumen papillae, S2502Nr31

value: PHY


title: H3K4me3_KO_rep2 [ChIP-seq]

value: Skeletal muscle progenitor cells


title: H3K27me3_KO_rep1 [ChIP-seq]


title: H3K4me3_KO_rep1 [ChIP-seq]


title: sorted CD45+ VDJ batch1  (020218_4_TEL)

value: 10X genomics VDJ 5'


title: H4K16ac_Het_rep1 [ChIP-seq]


title: sorted CD45+ gene expression batch1  (020218_4)

value: 10X genomics gene expression 5'


title: sorted CD45+ VDJ batch1  (V8_TEL)


title: Rumen papillae, S2502Nr32


title: sorted CD45+ gene expression batch1  (020218_5)


title: H3K4me3_Het_rep1 [ChIP-seq]


title: Rumen papillae, S2502Nr29

value: control


title: fetal lungs, Saline-1

value: Male

value: fetal lungs


title: sorted CD45+ VDJ batch1  (V0_TEL)


title: MPs_ KO_ rep1 [RNA-seq]

data_processing:
Mapping was performed using STAR 2.4.2a software with mouse genome (mm9).
Read counts were generated with R Studio function Summarize Overlaps and normalized to RPKM based on the number of uniquely mapped reads.
Differential expression analysis was performed with DESeq2 using default settings.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include RPKM values for each Sample.

extract_protocol:
Total RNA from 5x10e5 FACS sorted p7 MPs was isolated using the RNeasy Micro Kit (Qiagen). RNA quantity and quality was tested on a Qubit®Fluorometer (Invitrogen) and a Bioanalyzer 2100 (Agilent).
Sequencing libraries was prepared following Roche’s “KAPA stranded mRNA Seq” library preparation protocol. 11 cycles of PCR were used for libraries amplification followed by sequencing with an Illumina HiSeq 4000 system.

value: Nf1flox/floxMyf5Cre+ (KO)

value: Juvenile satellite cells from hindlimb skeletal muscle

value: Postnatal day 7


title: sorted CD45+ VDJ batch1  (V6_TEL)

value: PBMC


title: Rumen papillae, S2502Nr27


title: Rumen papillae, S2502Nr28


title: Rumen papillae, S2502Nr26


title: sorted CD45+ gene expression batch1  (V6)


title: MPs_ KO_ rep2 [RNA-seq]


title: Rumen papillae, S2502Nr30


title: MPs_ Ctr_ rep2 [RNA-seq]

value: Nf1flox/+ Myf5Cre+ (Control)


title: Rumen papillae, S2502Nr25

value: Holstein


title: scLv-24hpf

status: Public on Sep 24 2021

city: Durham

first: David

middle: R

last: McClay

address: 124 Science Drive room 4115

department: Biology

institute: Duke University

data_processing:
10x Cell Ranger v3.0.1 software "mkfastq" function
10x Cell Ranger v3.0.1 software "count" function
10x Cell Ranger v3.0.1 software "aggr" function
Seurat v3.1 software standard workflow
Genome_build: Lytechinus variegatus genome assembly v 3.0
Supplementary_files_format_and_content: comma-separated value text files with UMI counts for each of the samples
Supplementary_files_format_and_content: Interactive 10x cloupe file with all samples aggregated, analyzed, and visualized
Supplementary_files_format_and_content: RDS file with all samples aggregated, analyzed, and visualized into 63 clusters using Seurat

molecule: polyA RNA

organism: Lytechinus variegatus

source_name: Single cells 24 hours post fertilization

growth_protocol: Sea urchin embryos stirred and cultured at 23˚C in artificial sea water

extract_protocol:
Hourly embryo dissociations using calcium-free artificial sea water, glycine, EDTA, methanol, and 3x SSC.
10x Genomics Single Cell 3' kit v3; Samples sequenced using two S1 flow cells with two lanes each (4 lanes total)

treatment_protocol: Fertilization of sea urchin embryos in 03.g PABA/100 mL artificial sea water.

tag: embryonic stage

value: Early Larvae stage

value: Wild Type - Collected at Beaufort, NC.


title: scLv-24hpf-rep2

source_name: Single cells 24 hours post fertilization - replicate 2


title: sorted CD45+ gene expression batch1  (V0)

source_name: frozen PBMC


title: H3K4me3_Het_rep2 [ChIP-seq]


title: scLv-20hpf

source_name: Single cells 20 hours post fertilization

value: Prism stage


title: MPs_ Ctr_ rep1 [RNA-seq]


title: scLv-18hpf

source_name: Single cells 18 hours post fertilization

value: Late Gastrula


title: scLv-12hpf

source_name: Single cells 12 hours post fertilization

value: Late-Mesenchyme Blastula stage


title: Sham surgery rat#2, biological rep2

city: South San Francisco

first: Lei

last: Ling

address: 333 Oyster Point Blvd

institute: NGM Biopharmaceuticals

description:
Gene expression data from rat ileum
Rat_Sham-2

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix rat gene 1.0 ST whole-transcript Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Data were normalized using robust multi-array average (RMA) method.

label: biotin

organism: Rattus norvegicus

source_name: Ileum from Zucker fa/fa rat with sham operation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (GeneChip WT cDNA synthesis and amplification kit and GeneChip WT terminal labeling kit from Affymetrix).

growth_protocol: Surgical procedures were performed on 20-week old Zucker fa/fa rats (Envigo). DJBs were carried out as previously described (Jiao et al., 2013; Rubino and Marescaux, 2004).

extract_protocol: Rat ileum were snap-frozen in liquid nitrogen upon euthanization of animals. Total RNA was extracted using RNeasy Mini kit (Qiagen) and treated with DNase I according to the manufacturer's instructions.

treatment_protocol: Tthe abdominal cavity was exposed through a ventral midline incision, at 0.75-1 cm of the starting point of duodenum, a suture was tightly tied the duodenum vertically, and a 0.4 cm horizontal incision was performed at this area, and bowel continuity was interrupted at the level of the distal jejunum (10 cm from the ligament of Treitz). The distal limb was directly connected to the horizontal duodenum incision (duodenal-jejunal anastomosis) and the proximal limb carrying the biliopancreatic juices was reconnected downward to the alimentary limb at a distance of the same length of bypassed entire duodenum and proximal jejunum from the duodenal-jejunal anastomosis. For sham operations, rats were undergo a similar surgical procedure as DJB, however all resections were re-anastomosed to maintain the physiologic circuit of food through the bowel. Rats were sacrificed 14 days after surgery and intestines were harvested for RNA preparation and transcriptome profiling.

value: ileum

value: Zucker fa/fa

value: 20-week old


title: sorted CD45+ gene expression batch1  (V8)

value: 10X genomics gene expression 5'


title: scLv-16hpf

source_name: Single cells 16 hours post fertilization

value: Mid-Late Gastrula


title: scLv-14hpf

source_name: Single cells 14 hours post fertilization

value: Early-Mid Gastrula


title: scLv-10hpf

source_name: Single cells 10 hours post fertilization

value: Early-Mid Mesenchyme Blastula stage


title: Duodenum-jejunum bypass surgery rat#1, biological rep1

description:
Gene expression data from rat ileum
Rat_DJB-1

source_name: Ileum from Zucker fa/fa rat with duodenum-jejunum bypass operation

value: Duodenum-jejunum bypass surgery


title: Sham surgery rat#1, biological rep1

description:
Gene expression data from rat ileum
Rat_Sham-1

value: control


title: Duodenum-jejunum bypass surgery rat#3, biological rep3

description:
Gene expression data from rat ileum
Rat_DJB-3


title: Duodenum-jejunum bypass surgery rat#2, biological rep2

description:
Gene expression data from rat ileum
Rat_DJB-2


title: scLv-15hpf

source_name: Single cells 15 hours post fertilization

value: Mid-Gastrula


title: Sham surgery rat#3, biological rep3

description:
Gene expression data from rat ileum
Rat_Sham-3


title: scLv-8hpf

source_name: Single cells 8 hours post fertilization

value: Hatched Blastula stage


title: scLv-11hpf

source_name: Single cells 11 hours post fertilization

value: Mid-Mesenchyme Blastula stage


title: scLv-7hpf

source_name: Single cells 7 hours post fertilization

value: Early Blastula stage


title: scLv-5hpf

source_name: Single cells 5 hours post fertilization

value: ~256-cell stage

value: Wild Type - Collected at Beaufort, NC.


title: scLv-13hpf

source_name: Single cells 13 hours post fertilization

value: Early Gastrula


title: scLv-4hpf

source_name: Single cells 4 hours post fertilization

value: 60-cell stage


title: scLv-3hpf

source_name: Single cells 3 hours post fertilization

value: 16-cell stage


title: sci-RNA-seq on F121-6-CASTx129 differentiated to embryoid body - 4DNEXYO7LG9X

city: Boston

last: DCIC

state: MA

address: 10 Shattuck St

institute: 4D Nucleome - Data Coordination and Integration Center

description:
lab: Christine Disteche, UW
award: 1U54DK107979-01
4DN accession: 4DNEXYO7LG9X
strandedness: forward
submitted_by: Giancarlo Bonora
experiment_type: sci-RNA-seq
library_prep_kit: home-made sci-RNA-seq protocol
contributing_labs: William Noble, UW
biosample_quantity: 10000000 cells
fragment_size_range: 300-1500
fragmentation_method: tagmentation
average_fragment_size: 350
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-seq/4DNEXYO7LG9X/

data_processing:
See the file "TREE.sci-RNA-seq.txt" for an overview of the folders and files described herein.

sci-RNA-seq libraries were processed using a pipeline by the Trapnell lab (Cao J et al. Comprehensive single-cell transcriptional profiling of a multicellular organism. Science. 2017;357:661–7), but with reads aligned to an N-masked C57BL6/J reference genome (mm10) where every SNP locus (129 or cast for the F123, F121, and ES_Tsix-stop cell lines; B6 or spret for the Patski cell line) was substituted with an N to reduce mapping bias. The pipeline produces CellDataSet (CDS) files that contain genes-by-cell count matrices of unique molecular identifiers (UMIs) per gene, which were used for all downstream analysis. The folder "non-allelic_sci_RNA-seq_count_matrices" contains a 3-column sparse versions of the resulting CDS count matrices. Since d0 male and female cells were generated separately in their own plates, they had to be processed separately, and a separate d0 CDS file was generated. There are therefore two subfolders ("d0" and "d3-11andNPCs") that contain the CDS count matrices ("UMI.count.matrix.gz") along with associated cell IDs ("cell.annotations") and gene IDs ("gene.annotations").

The CDS was further filtered to include only cells with at least 200UMIs and then to exclude cells with extreme cells counts (beyond 2 standard deviations from the mean of the logged counts). The resulting matrix of counts can be found in the file "non-allelic_sci_RNA-seq_counts_filetered/non-allelic_sci-RNA-seq_mouseDiff_Nmasked.UMImatrix.filtered.200UMIs.final.tsv.gz" (see manuscript Additional file 1: Table S4).

Mapped single-end reads were segregated to their allele of origin if the read contained at least one SNP particular to exactly one of the parental strains. Reads containing no SNPs or containing SNPs belonging to both parental strains were discarded. The sci-RNA-seq preprocessing pipeline described above was adapted to handle allelically segregated reads. The folder "allelic_sci-RNA-seq_count_matrices" contains the resulting 3-column versions of the CDSs ("UMI.count.matrix.gz") within subfolders for each of the two separate libraries ("d0" and "d3-11andNPCs").  Associated cell IDs ("cellIDs.unique.txt") are contained in the folder "allelic_sci-ATAC-seq_count_matrices."

For female (F121 cells), the allelic data was further filtered (as was done for the non-allelic data) and the counts for each allele of each chromosome were concatenated together for allelic trajectory analysis and topic modeling. Only genes expressed from one allele in at least 10 cells and cells with at least 10 UMIs in chr1 and in chrX were included. The resulting count matrices are saved to the folder "allelic_sci-RNA-seq_catenated_count_matrices" with one file per chromosome (e.g. "allelic_sci-RNA-seq.UMImatrix.filtered.minExpr0.1.minCells5.F121.chr1.stringentlyFiltered.min_counts_per_chromosome10.tsv.gz").

source_name: biosource_summary: F121-6-CASTx129 differentiated to embryoid body

growth_protocol:
description: Protocol for culturing F123 CASTx129 hybrid mouse cells
download: https://data.4dnucleome.org/protocols/1d39b581-9200-4494-8b24-3dc77d595bbb/@@download/attachment/4DN_F123_SOP_170425.pdf
description: Differentiation of mouse stem cells to embryoid bodies and subsequent NPC differentiation
download: https://data.4dnucleome.org/protocols/21a7a355-e3cf-43fc-a383-c41aa0952f02/@@download/attachment/Mouse%20NPC%20differentiation%20protocol.pdf

extract_protocol:
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4836442/
description: Cao et al. Comprehensive Single-Cell Transcriptional Profiling of a Multicellular Organism. PMID: 28818938

value: 129/Sv X Cast

value: embryoid body

tag: description

value: Day 11 F121-6 cells from an embryoid body differentiaton time course experiment

tag: Sex

value: female

value: in vitro differentiated cells

value: Gilbert Lab

tag: url


title: sci-RNA-seq on F121-6-CASTx129 - 4DNEXNPCRAKI

description:
lab: Christine Disteche, UW
award: 1U54DK107979-01
4DN accession: 4DNEXNPCRAKI
strandedness: forward
submitted_by: Giancarlo Bonora
experiment_type: sci-RNA-seq
library_prep_kit: home-made sci-RNA-seq protocol
contributing_labs: William Noble, UW
biosample_quantity: 10000000 cells
fragment_size_range: 300-1500
fragmentation_method: tagmentation
average_fragment_size: 350
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-seq/4DNEXNPCRAKI/

source_name: biosource_summary: F121-6-CASTx129

growth_protocol:
description: Protocol for culturing F123 CASTx129 hybrid mouse cells
download: https://data.4dnucleome.org/protocols/1d39b581-9200-4494-8b24-3dc77d595bbb/@@download/attachment/4DN_F123_SOP_170425.pdf

value: stem cell

value: Day 0 F121-6 cells from an embryoid body differentiaton time course experiment

value: stem cells


title: sci-RNA-seq on F121-6-CASTx129 differentiated to neuronal stem cell - 4DNEXPGR1CVZ

description:
lab: Christine Disteche, UW
award: 1U54DK107979-01
4DN accession: 4DNEXPGR1CVZ
strandedness: forward
submitted_by: Giancarlo Bonora
experiment_type: sci-RNA-seq
library_prep_kit: home-made sci-RNA-seq protocol
contributing_labs: William Noble, UW
biosample_quantity: 10000000 cells
fragment_size_range: 300-1500
fragmentation_method: tagmentation
average_fragment_size: 350
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-seq/4DNEXPGR1CVZ/

source_name: biosource_summary: F121-6-CASTx129 differentiated to neuronal stem cell

value: neuronal stem cell

value: Neural precursor cells clonally derived from day 11 F121-6 cells from an embryoid body differentiaton time course experiment


title: scLv-9hpf

source_name: Single cells 9 hours post fertilization

value: Early Mesenchyme Blastula stage


title: sci-RNA-seq on F123-CASTx129 - 4DNEX7A9NPK2

description:
lab: Christine Disteche, UW
award: 1U54DK107979-01
4DN accession: 4DNEX7A9NPK2
strandedness: forward
submitted_by: Giancarlo Bonora
experiment_type: sci-RNA-seq
library_prep_kit: home-made sci-RNA-seq protocol
contributing_labs: William Noble, UW
biosample_quantity: 10000000 cells
fragment_size_range: 300-1500
fragmentation_method: tagmentation
average_fragment_size: 350
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-seq/4DNEX7A9NPK2/

source_name: biosource_summary: F123-CASTx129

value: Day 0 F123 cells from an embryoid body differentiaton time course experiment

value: male


title: sci-RNA-seq on F121-6-CASTx129 differentiated to embryoid body - 4DNEXT7D5EOI

description:
lab: Christine Disteche, UW
award: 1U54DK107979-01
4DN accession: 4DNEXT7D5EOI
strandedness: forward
submitted_by: Giancarlo Bonora
experiment_type: sci-RNA-seq
library_prep_kit: home-made sci-RNA-seq protocol
contributing_labs: William Noble, UW
biosample_quantity: 10000000 cells
fragment_size_range: 300-1500
fragmentation_method: tagmentation
average_fragment_size: 350
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-seq/4DNEXT7D5EOI/

value: Day 7 F121-6 cells from an embryoid body differentiaton time course experiment


title: sci-RNA-seq on F121-6-CASTx129 differentiated to embryoid body - 4DNEXA8OVCDB

description:
lab: Christine Disteche, UW
award: 1U54DK107979-01
4DN accession: 4DNEXA8OVCDB
strandedness: forward
submitted_by: Giancarlo Bonora
experiment_type: sci-RNA-seq
library_prep_kit: home-made sci-RNA-seq protocol
contributing_labs: William Noble, UW
biosample_quantity: 10000000 cells
fragment_size_range: 300-1500
fragmentation_method: tagmentation
average_fragment_size: 350
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-seq/4DNEXA8OVCDB/

value: Day 3 F121-6 cells from an embryoid body differentiaton time course experiment


title: sci-RNA-seq on F123-CASTx129 differentiated to embryoid body - 4DNEX2VTS1YZ

description:
lab: Christine Disteche, UW
award: 1U54DK107979-01
4DN accession: 4DNEX2VTS1YZ
strandedness: forward
submitted_by: Giancarlo Bonora
experiment_type: sci-RNA-seq
library_prep_kit: home-made sci-RNA-seq protocol
contributing_labs: William Noble, UW
biosample_quantity: 10000000 cells
fragment_size_range: 300-1500
fragmentation_method: tagmentation
average_fragment_size: 350
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-seq/4DNEX2VTS1YZ/

source_name: biosource_summary: F123-CASTx129 differentiated to embryoid body

value: Day 11 F123 cells from an embryoid body differentiaton time course experiment


title: sci-RNA-seq on F123-CASTx129 differentiated to embryoid body - 4DNEXXCVEEE2

description:
lab: Christine Disteche, UW
award: 1U54DK107979-01
4DN accession: 4DNEXXCVEEE2
strandedness: forward
submitted_by: Giancarlo Bonora
experiment_type: sci-RNA-seq
library_prep_kit: home-made sci-RNA-seq protocol
contributing_labs: William Noble, UW
biosample_quantity: 10000000 cells
fragment_size_range: 300-1500
fragmentation_method: tagmentation
average_fragment_size: 350
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-seq/4DNEXXCVEEE2/

value: 129/Sv X Cast

value: Day 7 F123 cells from an embryoid body differentiaton time course experiment


title: sci-RNA-seq on F123-CASTx129 differentiated to neuronal stem cell - 4DNEXAY3ALVE

description:
lab: Christine Disteche, UW
award: 1U54DK107979-01
4DN accession: 4DNEXAY3ALVE
strandedness: forward
submitted_by: Giancarlo Bonora
experiment_type: sci-RNA-seq
library_prep_kit: home-made sci-RNA-seq protocol
contributing_labs: William Noble, UW
biosample_quantity: 10000000 cells
fragment_size_range: 300-1500
fragmentation_method: tagmentation
average_fragment_size: 350
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-seq/4DNEXAY3ALVE/

source_name: biosource_summary: F123-CASTx129 differentiated to neuronal stem cell

value: Neural precursor cells derived from day 11 F123 cells from an embryoid body differentiaton time course experiment


title: sci-RNA-seq on F123-CASTx129 differentiated to embryoid body - 4DNEXCWGVH6G

description:
lab: Christine Disteche, UW
award: 1U54DK107979-01
4DN accession: 4DNEXCWGVH6G
strandedness: forward
submitted_by: Giancarlo Bonora
experiment_type: sci-RNA-seq
library_prep_kit: home-made sci-RNA-seq protocol
contributing_labs: William Noble, UW
biosample_quantity: 10000000 cells
fragment_size_range: 300-1500
fragmentation_method: tagmentation
average_fragment_size: 350
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-seq/4DNEXCWGVH6G/

value: embryoid body

value: Day 3 F123 cells from an embryoid body differentiaton time course experiment


title: sci-ATAC-seq on F121-6-CASTx129 - 4DNEX55NM5L3

description:
lab: Christine Disteche, UW
award: 1U54DK107979-01
4DN accession: 4DNEX55NM5L3
pcr_cycles: 20
transposase: Tn5 Transposase
submitted_by: Giancarlo Bonora
experiment_type: sci-ATAC-seq
contributing_labs: William Noble, UW
biosample_quantity: 5000000 cells
primer_removal_method: SPRI beads
enzyme_incubation_time: 30
incubation_temperature: 55
url: https://data.4dnucleome.org/experiments-atacseq/4DNEX55NM5L3/

data_processing:
See the file "TREE.sci-ATAC-seq.txt" for an overview of the folders and files described herein.

-ATAC-seq libraries were processed using a pipeline created by the Trapnell lab (https://github.com/cole-trapnell-lab/ATAC-Pipeline-Dev), but with reads aligned to an N-masked C57BL6/J reference genome (mm10) where every SNP locus (129 or cast for the F123, F121, and ES_Tsix-stop cell lines; B6 or spret for the Patski cell line) was substituted with an N to reduce mapping bias. The sci-ATAC-seq pipeline produces CellDataSet (CDS) files that contain count matrices of unique molecular identifiers (UMIs) per accessible region. These regions are defined as peaks of accessibility called using MACS2 on the aggregated sci-ATAC-seq data. Accessible sites with coverage in at least 10 cells were included. The CDS files were used for all downstream analysis. The folder "non-allelic_sci_ATAC-seq_count_matrices" contains a 3-column sparse version of the CDS count matrix ("sciATAC_mouseDiff.counts.txt.gz") and associated cell IDs ("cellIDs.unique.txt").

The CDS was further filtered to include only cells with at least 500UMIs and then to exclude cells with extreme cells counts (beyond 2 standard deviations from the mean of the logged counts). The resulting matrix of counts can be found in the file "non-allelic_sci_ATAC-seq_counts_filetered/non-allelic_sci-ATAC-seq_mouseDiff_Nmasked.countsMatrix.filtered.500UMIs.final.tsv.gz" (and see manuscript Additional file 1: Table S3)

MAligned paired-end reads were segregated to their allele of origin, if at least one read contained at least one SNP particular to exactly one of the parental strains. Reads containing no SNPs or containing SNPs belonging to both parental strains were discarded. The sci-ATAC-seq preprocessing pipeline described above was adapted to handle allelically segregated reads. The resulting 2-column version of the CDS ("sciATAC_mouseDiff.allelic.counts.biallelicPeaks.txt.gz") and associated cell IDs ("cellIDs.unique.txt") are contained in the folder "allelic_sci-ATAC-seq_count_matrices."

For female (F121 cells), the allelic data was further filtered (as was done for the non-allelic data) and the counts for each allele of each chromosome were concatenated together for allelic trajectory analysis and topic modeling. Accessible regions with coverage along one allele in at least 10 cells and cells with at least 10 UMIs in chr1 and in chrX were included. The resulting count matrices are saved to the folder "allelic_sci-ATAC-seq_catenated_count_matrices" with one file per chromosome (e.g. "allelic_sci-ATAC-seq.UMImatrix.filtered.minExpr0.1.minCells5.F121.chr1.min_counts_per_chromosome10.tsv.gz").

extract_protocol:
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4836442/
description: Cusanovich et al. Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. PMID: 25953818

value: female

value: Gilbert Lab


title: sci-ATAC-seq on F121-6-CASTx129 differentiated to embryoid body - 4DNEXOKNIX5B

description:
lab: Christine Disteche, UW
award: 1U54DK107979-01
4DN accession: 4DNEXOKNIX5B
pcr_cycles: 20
transposase: Tn5 Transposase
submitted_by: Giancarlo Bonora
experiment_type: sci-ATAC-seq
contributing_labs: William Noble, UW
biosample_quantity: 5000000 cells
primer_removal_method: SPRI beads
enzyme_incubation_time: 30
incubation_temperature: 55
url: https://data.4dnucleome.org/experiments-atacseq/4DNEXOKNIX5B/

value: in vitro differentiated cells


title: sci-ATAC-seq on F123-CASTx129 differentiated to embryoid body - 4DNEXXXQ7SNN

description:
lab: Christine Disteche, UW
award: 1U54DK107979-01
4DN accession: 4DNEXXXQ7SNN
pcr_cycles: 20
transposase: Tn5 Transposase
submitted_by: Giancarlo Bonora
experiment_type: sci-ATAC-seq
contributing_labs: William Noble, UW
biosample_quantity: 5000000 cells
primer_removal_method: SPRI beads
enzyme_incubation_time: 30
incubation_temperature: 55
url: https://data.4dnucleome.org/experiments-atacseq/4DNEXXXQ7SNN/


title: sci-ATAC-seq on F123-CASTx129 - 4DNEXMJVA3ZW

description:
lab: Christine Disteche, UW
award: 1U54DK107979-01
4DN accession: 4DNEXMJVA3ZW
pcr_cycles: 20
transposase: Tn5 Transposase
submitted_by: Giancarlo Bonora
experiment_type: sci-ATAC-seq
contributing_labs: William Noble, UW
biosample_quantity: 5000000 cells
primer_removal_method: SPRI beads
enzyme_incubation_time: 30
incubation_temperature: 55
url: https://data.4dnucleome.org/experiments-atacseq/4DNEXMJVA3ZW/

value: stem cell

value: stem cells


title: sci-ATAC-seq on F121-6-CASTx129 differentiated to neuronal stem cell - 4DNEXP788IVD

description:
lab: Christine Disteche, UW
award: 1U54DK107979-01
4DN accession: 4DNEXP788IVD
pcr_cycles: 20
transposase: Tn5 Transposase
submitted_by: Giancarlo Bonora
experiment_type: sci-ATAC-seq
contributing_labs: William Noble, UW
biosample_quantity: 5000000 cells
primer_removal_method: SPRI beads
enzyme_incubation_time: 30
incubation_temperature: 55
url: https://data.4dnucleome.org/experiments-atacseq/4DNEXP788IVD/

value: neuronal stem cell

value: Neural precursor cells clonally derived from day 11 F121-6 cells from an embryoid body differentiaton time course experiment


title: sci-ATAC-seq on F121-6-CASTx129 differentiated to embryoid body - 4DNEXOLF62PK

description:
lab: Christine Disteche, UW
award: 1U54DK107979-01
4DN accession: 4DNEXOLF62PK
pcr_cycles: 20
transposase: Tn5 Transposase
submitted_by: Giancarlo Bonora
experiment_type: sci-ATAC-seq
contributing_labs: William Noble, UW
biosample_quantity: 5000000 cells
primer_removal_method: SPRI beads
enzyme_incubation_time: 30
incubation_temperature: 55
url: https://data.4dnucleome.org/experiments-atacseq/4DNEXOLF62PK/

value: Day 11 F121-6 cells from an embryoid body differentiaton time course experiment


title: sci-ATAC-seq on F121-6-CASTx129 differentiated to embryoid body - 4DNEXX4XDGPO

description:
lab: Christine Disteche, UW
award: 1U54DK107979-01
4DN accession: 4DNEXX4XDGPO
pcr_cycles: 20
transposase: Tn5 Transposase
submitted_by: Giancarlo Bonora
experiment_type: sci-ATAC-seq
contributing_labs: William Noble, UW
biosample_quantity: 5000000 cells
primer_removal_method: SPRI beads
enzyme_incubation_time: 30
incubation_temperature: 55
url: https://data.4dnucleome.org/experiments-atacseq/4DNEXX4XDGPO/


title: sci-ATAC-seq on F123-CASTx129 differentiated to embryoid body - 4DNEXUTXVJNS

description:
lab: Christine Disteche, UW
award: 1U54DK107979-01
4DN accession: 4DNEXUTXVJNS
pcr_cycles: 20
transposase: Tn5 Transposase
submitted_by: Giancarlo Bonora
experiment_type: sci-ATAC-seq
contributing_labs: William Noble, UW
biosample_quantity: 5000000 cells
primer_removal_method: SPRI beads
enzyme_incubation_time: 30
incubation_temperature: 55
url: https://data.4dnucleome.org/experiments-atacseq/4DNEXUTXVJNS/

value: male


title: sci-ATAC-seq on F123-CASTx129 differentiated to embryoid body - 4DNEXOSQFCTM

description:
lab: Christine Disteche, UW
award: 1U54DK107979-01
4DN accession: 4DNEXOSQFCTM
pcr_cycles: 20
transposase: Tn5 Transposase
submitted_by: Giancarlo Bonora
experiment_type: sci-ATAC-seq
contributing_labs: William Noble, UW
biosample_quantity: 5000000 cells
primer_removal_method: SPRI beads
enzyme_incubation_time: 30
incubation_temperature: 55
url: https://data.4dnucleome.org/experiments-atacseq/4DNEXOSQFCTM/


title: scLv-2hpf

source_name: Single cells 2 hours post fertilization

value: 4- cell stage

value: Wild Type - Collected at Beaufort, NC.


title: P65_ChIPseq_MC38_3hours_TNF

first: Simon

middle: J

last: Hogg

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie

data_processing:
Raw sequencing reads were demultiplexed using bcl2fastq (v2.17.1.14) and quality control performed with FASTQC (v0.11.5).
Adaptor sequences were removed and reads aligned to the human reference genome (mm10) using CutAdapt (v1.14) and Bowtie2 (v2.3.5)
Samtools (v1.4.1) was used for processing of SAM and BAM files, from which Model-based Analysis of ChIP-Seq (MACS2, v2.2.5) peak calling was performed.
BAM files were converted into BigWig files using the bamCoverage function (Deeptools, v3.0.0) using the following settings (--normalizeUsing CPM --smoothLength 150 --binSize 50 -e 200 scaleFactor 1).Using Deeptools (v3.0.0), average profile plots and heatmaps were generated by computing read average read density (from BigWig files) across defined genomic intervals using computeMatrix, which we subsequently plot using plotProfile and plotHeatmap, respectively. Genomic regions spanning mm10 blacklist intervals (ENCODE) were excluded using Deeptools.
Genome_build: MM10
Supplementary_files_format_and_content: bigWig

source_name: Colon adenocarcinoma

growth_protocol: MC38-Ova cells were treated  under standard culture conditions for 3 hours prior in the presence or absence of RG6146 and recombinant murine TNF, prior to aspiration of media and one wash in ice-cold PBS.

extract_protocol:
Sonication was performed using a Covaris ultrasonicator at maximum power for 16 minutes to achieve an average DNA fragment size of 300-500bp. Immunoprecipitation reactions were performed overnight at 4ºC by diluting sonicated chromatin 1:1 in ChIP dilution buffer (20 mM Tris-HCl, 150 mM NaCl2, 2 mM EDTA, 1% Triton-X, and phosphatase/protease inhibitors in water) and addition of a 1:1 ratio of protein A and G magnetic beads (Life Technologies) were used to bind crosslinked protein/DNA.
Libraries were generated using the NEBNext Ultra II DNA Library Prep Kit (NEB, E7645) and sequenced on an Illumina NextSeq 550 with 75 b.p. paired-end reads. Library QC and quantification was performed using D1000 high-sensitivity screen tape with 4200 TapeStation Instrument (Agilent Technologies) and size selected for between 200 bp and 500 bp using a Pippin Prep system (Sage Science).

treatment_protocol: Cells were crosslinked directly in tissue culture plates with 1% formaldehyde for 20 minutes at room temperature and subsequently quenched with 1.25M glycine. Cells were manually scraped from plates, collected, and washed three times with ice-cold nuclear extraction buffer, prior to lysis in ChIP lysis buffer (20 mM Tris-HCl, 150 mM NaCl2, 2 mM EDTA, 1% IGEPAL CA-630 (Sigma-Aldrich) and 0.3% SDS in water).

tag: cell line

tag: timepoint

value: 3 hours

tag: treatment+dose

value: TNF, 10ng/mL

tag: chipseq antibody


title: Sh2d6− Tuft cells

city: Beijing

first: Zhen

last: Xiong

address: 15 Datun Road, Beijing 100101, China

department: Institute of Biophysics

institute: Chinese Academy of Sciences

description: Gene expression data from intestinal epithilial cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Clariom D human Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 3×10^5 Sh2d6+ Tuft cells (EGFP+EpCAM+Siglec-F+), 3×10*5 Sh2d6− Tuft cells (EGFP−EpCAM+Siglec-F+) and non-Tuft epithelial cells (EpCAM+Siglec-F−) from Sh2d6EGFP mice were sorted using flow cytometer.

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

treatment_protocol: Mice were infected with 5×10^7 CFU Shigella by oral gavage

tag: strain

value: 3 months

value: small intestine

value: Sh2d6- Tuft cells

tag: infected with

value: Shigella


title: P65_ChIPseq_MC38_3hours_RG6146

value: RG6146, 2.5microM


title: non-Tuft epithelial cells

source_name: non-Tuft epithelial cells (EpCAM+Siglec-F−)

value: female

tag: tissue

value: non-Tuft epithelial cells


title: P65_ChIPseq_MC38_3hours_RG6146_TNF

value: RG6146, 2.5microM + TNF, 10ng/mL


title: H3K27ac_ChIPseq_MC38_3hours_DMSO

value: DMSO

value: H3K27ac (Abcam, ab4729)


title: H3K27ac_ChIPseq_MC38_3hours_RG6146


title: H3K27ac_ChIPseq_MC38_3hours_TNF


title: Sh2d6+ Tuft cells

source_name: Sh2d6+ Tuft cells (EGFP+EpCAM+Siglec-F+)

tag: age

value: Sh2d6+ Tuft cells


title: scLv-6hpf

source_name: Single cells 6 hours post fertilization

value: ~1024-cell stage

tag: genotype


title: BRD4_ChIPseq_MC38_3hours_RG6146_TNF


title: P65_ChIPseq_MC38_3hours_DMSO


title: RNAseq_MC38_3hours_TNF+RG6146_Replicate1

data_processing:
Raw sequencing reads were demultiplexed with bcl2fastq (v2.17.1.14) and subsequently trimmed at the 5’-end and 3’ ends (to remove poly-A-tail derived reads) using CutAdapt (v1.14).
Reads were then mapped to reference genomes (mm10) using HISAT2 (v2.1.0) software.
Counting of reads across annotated genomic features (exons) was conducted using featureCounts (subread package, v1.5.2).
Differential gene expression analysis was performed using the Voom/Limma workflow to determine statistical significance. All further RNA-seq data analysis and figures generation was performed using Rstudio (v3.6.1) software.
Genome_build: MM10
Supplementary_files_format_and_content: Gene expression counts

extract_protocol:
Sequencing libraries were generated from 500ng input RNA using the QuantSeq 3’RNA-seq Library Prep Kit for Illumina (Lexogen), as per manufacturer’s instructions.
Libraries were sequenced on an Illumina NextSeq 500 with single-end 75bp reads to a depth of 5M reads per sample.

treatment_protocol: RNA was extracted immediately following drug treatment by resuspension in TRIzol reagent (Thermo Fisher Scientific) and isolation using the Direct-Zol RNA Miniprep kit (Zymo Research), as per manufacturer’s instructions.

tag: time point


title: RNAseq_MC38_3hours_TNF_Replicate3


title: Input_ChIPseq_MC38_3hours_DMSO


title: BRD4_ChIPseq_MC38_3hours_DMSO


title: RNAseq_MC38_3hours_DMSO_Replicate2


title: ATACseq_MC38_3hours_DMSO


title: RNAseq_MC38_3hours_TNF_Replicate1


title: RNAseq_E0771_3hours_TNF+RG6146_Replicate3

source_name: Breast adenocarcinoma


title: RNAseq_E0771_3hours_TNF_Replicate2


title: RNAseq_E0771_3hours_TNF+RG6146_Replicate1


title: RNAseq_E0771_3hours_TNF+RG6146_Replicate2


title: H3K27ac_ChIPseq_MC38_3hours_RG6146_TNF


title: RNAseq_E0771_3hours_RG6146_Replicate2


title: RNAseq_MC38_3hours_TNF+RG6146_Replicate2


title: RNAseq_MC38_3hours_TNF+RG6146_Replicate3


title: ATACseq_MC38_3hours_RG6146


title: RNAseq_MC38_3hours_RG6146_Replicate1


title: BRD4_ChIPseq_MC38_3hours_TNF


title: RNAseq_E0771_3hours_DMSO_Replicate1


title: RNAseq_MC38_3hours_DMSO_Replicate3


title: ATACseq_MC38_3hours_RG6146_TNF


title: BRD4_ChIPseq_MC38_3hours_RG6146


title: RNAseq_MC38_3hours_TNF_Replicate2


title: RNAseq_MC38_3hours_DMSO_Replicate1


title: Fig7_D4_50nM_rep4

city: Cambridge

first: Joseph

last: Barry

address: 675 West Kendall St

institute: Alnylam Pharmaceuticals

description: siRNA treatment

data_processing:
Raw RNAseq reads were filtered with minimal mean quality scores of 28 and minimal remaining length of 36, using the ea-utils software fastq-mcf v1.05.
Filtered reads were aligned to the Mus musculus genome (GRCm39/mm39) using STAR (ultrafast universal RNAseq aligner) v2.7.9a.
Uniquely aligned reads were counted by featureCounts v2.0.2 with the minimum mapping quality score set to 10.
For each sample, reads were summed across technical sequencing repeats to increase per-gene coverage.
Differential gene expression analysis was performed by the R package DESeq2 v1.32.0 with the betaPrior parameter set to TRUE to shrink log2 fold-change estimates for noisy, low-count genes.
Genome_build: GRCm39

source_name: PMH - D4_50nM

extract_protocol:
RNA was isolated using an automated protocol on a BioTek-EL406 platform using DYNABEADs (Invitrogen, cat # 61012).
cDNA libraries were prepared with the TruSeq Stranded Total RNA Library Prep Kit (Illumina) and sequenced on a NextSeq500 sequencer (Illumina), all according to manufacturers’ instructions.

treatment_protocol: Primary Mouse Hepatocytes (Thermo Fisher Scientific/Gibco) were transfected by adding 5.0 µL of a mixture containing Lipofectamine RNAiMax (Invitrogen, cat # 13778-150) and Opti-MEM plus (mixture composed of 0.1 µL of Lipofectamine and 5.0 µL of Opti-MEM plus) to each well, along with 5 µL of the desired siRNA duplex into a 384-well plate and incubated at room temperature for 15 minutes.  Cells were incubated for 24 hours at 37 °C and then processed for RNA purification. Cells were incubated for 24 hours at 37 °C and then processed for RNA purification.

tag: cell type

value: primary mouse hepatocyte

tag: treatment


title: Fig7_D3_10nM_rep4

description: siRNA treatment

source_name: PMH - D3_10nM


title: Fig7_D5_1nM_rep4

description: siRNA treatment

source_name: PMH - D5_1nM


title: Fig7_D3_1nM_rep4

description: siRNA treatment

source_name: PMH - D3_1nM


title: RNAseq_E0771_3hours_TNF_Replicate3


title: Fig7_mock_rep8

description: mock transfection control

source_name: PMH - mock

value: mock


title: Fig7_mock_rep7

description: mock transfection control


title: RNAseq_E0771_3hours_RG6146_Replicate3


title: Fig7_mock_rep6

description: mock transfection control


title: RNAseq_E0771_3hours_DMSO_Replicate3


title: RNAseq_E0771_3hours_TNF_Replicate1


title: RNAseq_E0771_3hours_DMSO_Replicate2


title: RNAseq_MC38_3hours_RG6146_Replicate2


title: ATACseq_MC38_3hours_TNF


title: RNAseq_E0771_3hours_RG6146_Replicate1


title: RNAseq_MC38_3hours_RG6146_Replicate3


title: Fig7_D6_50nM_rep4

description: siRNA treatment

source_name: PMH - D6_50nM


title: Fig7_D2_50nM_rep4

description: siRNA treatment

source_name: PMH - D2_50nM


title: Fig7_D1_50nM_rep4

description: siRNA treatment

source_name: PMH - D1_50nM


title: Fig7_D6_1nM_rep4

description: siRNA treatment

source_name: PMH - D6_1nM


title: Fig7_D4_1nM_rep4

description: siRNA treatment

source_name: PMH - D4_1nM


title: Fig7_D5_0.1nM_rep4

description: siRNA treatment

source_name: PMH - D5_0.1nM


title: Fig7_D5_50nM_rep4

description: siRNA treatment

source_name: PMH - D5_50nM


title: Fig7_D2_1nM_rep4

description: siRNA treatment

source_name: PMH - D2_1nM


title: Fig7_D3_50nM_rep4

description: siRNA treatment

source_name: PMH - D3_50nM


title: Fig7_D4_0.1nM_rep4

description: siRNA treatment

source_name: PMH - D4_0.1nM


title: Fig7_D5_10nM_rep4

description: siRNA treatment

source_name: PMH - D5_10nM


title: Fig7_D6_0.1nM_rep4

description: siRNA treatment

source_name: PMH - D6_0.1nM


title: Fig7_D1_10nM_rep4

description: siRNA treatment

source_name: PMH - D1_10nM


title: Fig7_D6_10nM_rep4

description: siRNA treatment

source_name: PMH - D6_10nM


title: Fig7_D2_10nM_rep4

description: siRNA treatment

source_name: PMH - D2_10nM


title: Fig7_D1_0.1nM_rep4

description: siRNA treatment

source_name: PMH - D1_0.1nM


title: Fig7_D1_1nM_rep4

description: siRNA treatment

source_name: PMH - D1_1nM


title: Fig7_D3_0.1nM_rep4

description: siRNA treatment

source_name: PMH - D3_0.1nM


title: Fig7_mock_rep5

description: mock transfection control

source_name: PMH - mock


title: Fig7_D5_1nM_rep3

description: siRNA treatment

source_name: PMH - D5_1nM


title: Fig7_D5_10nM_rep3

description: siRNA treatment


title: Fig7_D4_10nM_rep3

description: siRNA treatment

source_name: PMH - D4_10nM


title: Fig7_D3_0.1nM_rep3

description: siRNA treatment


title: Fig7_mock_rep3

description: mock transfection control


title: Fig7_D3_10nM_rep3

description: siRNA treatment

source_name: PMH - D3_10nM


title: Fig7_D3_1nM_rep3

description: siRNA treatment

source_name: PMH - D3_1nM


title: Fig7_D5_0.1nM_rep3

description: siRNA treatment

source_name: PMH - D5_0.1nM


title: Fig7_D2_10nM_rep3

description: siRNA treatment


title: Fig7_D2_50nM_rep3

description: siRNA treatment

source_name: PMH - D2_50nM


title: Fig7_D4_0.1nM_rep3

description: siRNA treatment


title: Fig7_D6_1nM_rep3

description: siRNA treatment

source_name: PMH - D6_1nM


title: Fig7_D4_1nM_rep3

description: siRNA treatment

source_name: PMH - D4_1nM


title: Fig7_D2_0.1nM_rep4

description: siRNA treatment

source_name: PMH - D2_0.1nM


title: Fig7_D6_50nM_rep3

description: siRNA treatment

source_name: PMH - D6_50nM


title: Fig7_D1_0.1nM_rep3

description: siRNA treatment


title: Fig7_D2_1nM_rep3

description: siRNA treatment

source_name: PMH - D2_1nM


title: Fig7_D4_10nM_rep4

description: siRNA treatment


title: Fig7_D4_50nM_rep3

description: siRNA treatment

source_name: PMH - D4_50nM


title: Fig7_mock_rep4

description: mock transfection control


title: Fig7_D6_10nM_rep3

description: siRNA treatment

source_name: PMH - D6_10nM


title: Fig7_D1_1nM_rep3

description: siRNA treatment


title: Fig7_D6_0.1nM_rep3

description: siRNA treatment

source_name: PMH - D6_0.1nM


title: Fig7_D2_0.1nM_rep3

description: siRNA treatment


title: Fig7_D5_0.1nM_rep2

description: siRNA treatment


title: Fig7_D4_0.1nM_rep2

description: siRNA treatment

source_name: PMH - D4_0.1nM


title: Fig7_D3_0.1nM_rep2

description: siRNA treatment

source_name: PMH - D3_0.1nM


title: Fig7_D1_0.1nM_rep2

description: siRNA treatment

source_name: PMH - D1_0.1nM


title: Fig7_D6_1nM_rep2

description: siRNA treatment


title: Fig7_D5_1nM_rep2

description: siRNA treatment

source_name: PMH - D5_1nM


title: Fig7_D6_10nM_rep2

description: siRNA treatment


title: Fig7_D2_1nM_rep2

description: siRNA treatment


title: Fig7_D4_1nM_rep2

description: siRNA treatment


title: Fig7_D4_10nM_rep2

description: siRNA treatment

source_name: PMH - D4_10nM


title: Fig7_D6_50nM_rep2

description: siRNA treatment


title: Fig7_D2_50nM_rep2

description: siRNA treatment


title: Fig7_D4_50nM_rep2

description: siRNA treatment


title: Fig7_D3_1nM_rep2

description: siRNA treatment


title: Fig7_D5_50nM_rep3

description: siRNA treatment

source_name: PMH - D5_50nM


title: Fig7_D5_10nM_rep2

description: siRNA treatment

source_name: PMH - D5_10nM


title: Fig7_D1_50nM_rep3

description: siRNA treatment

source_name: PMH - D1_50nM


title: Fig7_D2_10nM_rep2

description: siRNA treatment

source_name: PMH - D2_10nM


title: Fig7_D3_50nM_rep3

description: siRNA treatment

source_name: PMH - D3_50nM


title: Fig7_D1_10nM_rep2

description: siRNA treatment

source_name: PMH - D1_10nM


title: Fig7_D1_10nM_rep3

description: siRNA treatment


title: Fig7_D3_10nM_rep2

description: siRNA treatment

source_name: PMH - D3_10nM


title: Fig7_D3_50nM_rep2

description: siRNA treatment


title: Fig7_D1_50nM_rep2

description: siRNA treatment


title: Fig7_D6_0.1nM_rep2

description: siRNA treatment


title: Fig7_mock_rep1

description: mock transfection control

source_name: PMH - mock


title: Fig7_D1_1nM_rep2

description: siRNA treatment

source_name: PMH - D1_1nM


title: Fig7_D5_50nM_rep2

description: siRNA treatment


title: D1KO [RNA-seq]

city: Atlanta

first: Bingzhong

last: Xue

state: Georgia

address: 50 Decatur St SE

institute: Georgia State University

data_processing:
raw reads are filtered into clean reads which will be aligned to the reference sequences.
The alignment data is utilized to calculate distribution of reads on reference genes and mapping ratio.
Genes and isoforms expression level are quantified by a software package: RSEM(RNASeq by Expectation Maximization). FPKM method is used in calculated expression level
Genome_build: mm9
Supplementary_files_format_and_content: FPKM file

source_name: Brown adipose tissue

extract_protocol:
Brown adipose tissues were removed, flash frozen in liquid nitrogen, and RNA was harvested using Tri-reagent.
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000 or other sequencer when necessary

value: 36 week

value: Chow diet feeding for 36 weeks

value: Brown adipose tissue


title: Chow  [RNA-seq]

value: UTXfl/Y

value: 28 week

value: Chow diet feeding for 28 weeks


title: Fig7_D6_0.1nM_rep1

description: siRNA treatment


title: HF [RNA-seq]

value: Chow diet feeding for 5 weeks and high fat diet feeding for 23 weeks


title: Fig7_mock_rep2

description: mock transfection control


title: D1WT [RNA-seq]


title: Fig7_D2_0.1nM_rep2

description: siRNA treatment

source_name: PMH - D2_0.1nM


title: Fig7_D6_10nM_rep1

description: siRNA treatment

source_name: PMH - D6_10nM


title: Fig7_D6_50nM_rep1

description: siRNA treatment

source_name: PMH - D6_50nM


title: 4F48h-1

city: Louisville

first: Tamer

middle: M

last: Mohamed

state: KY

address: 580 S. Preston St., Baxter II Bldg., Room 122

department: Cardiology

institute: University of Louisville

data_processing:
Illumina Casava1.7 software used for basecalling.
Perform alignments with HISAT2 to the reference genome
Genome_build: GRCm38 mm10
Supplementary_files_format_and_content: FPKM

source_name: Neonatal cardiomyocytes

growth_protocol: Neonatal Cardiomyocytes P7

extract_protocol:
RNA from p7 cardiomyocytes were isolated using the Qiagen, miRNeasy Micro Kit, #210874, following homogenization of the tissue in QIAzol (Qiagen).
Using the Ovation RNA-seq System v2 Kit (NuGEN).

treatment_protocol: Adenovirus were added for 24, 48, or 72 hours

tag: duration

value: Neonatal cardiomyocytes


title: 4F-72h-2


title: 4F-24h-3


title: 4F48h-2


title: 4F-72h-1


title: 4F48h-3


title: Fig7_D5_1nM_rep1

description: siRNA treatment


title: Fig7_D5_10nM_rep1

description: siRNA treatment


title: Fig7_D5_50nM_rep1

description: siRNA treatment


title: Fig7_D4_50nM_rep1

description: siRNA treatment

source_name: PMH - D4_50nM


title: Fig7_D6_1nM_rep1

description: siRNA treatment

source_name: PMH - D6_1nM


title: Fig7_D4_0.1nM_rep1

description: siRNA treatment

source_name: PMH - D4_0.1nM


title: 4F-24h-2


title: Fig7_D4_10nM_rep1

description: siRNA treatment

source_name: PMH - D4_10nM


title: 4F-24h-1


title: LacZ-72h-2

value: LacZ


title: LacZ-72h-3


title: LacZ-72h-1


title: LacZ-48h-3


title: Fig7_D3_0.1nM_rep1

description: siRNA treatment

source_name: PMH - D3_0.1nM


title: Fig7_D2_0.1nM_rep1

description: siRNA treatment


title: Fig7_D3_1nM_rep1

description: siRNA treatment

source_name: PMH - D3_1nM


title: Fig7_D3_50nM_rep1

description: siRNA treatment


title: Fig7_D3_10nM_rep1

description: siRNA treatment


title: Fig7_D5_0.1nM_rep1

description: siRNA treatment

source_name: PMH - D5_0.1nM


title: 4F-72h-3


title: LacZ-48h-1


title: Fig7_D4_1nM_rep1

description: siRNA treatment

source_name: PMH - D4_1nM


title: Fig7_D2_1nM_rep1

description: siRNA treatment

source_name: PMH - D2_1nM


title: LacZ-24h-3


title: Fig7_D2_10nM_rep1

description: siRNA treatment

source_name: PMH - D2_10nM


title: LacZ-24h-1


title: Fig7_D1_0.1nM_rep1

description: siRNA treatment

source_name: PMH - D1_0.1nM


title: LacZ-24h-2


title: Fig7_D1_10nM_rep1

description: siRNA treatment

source_name: PMH - D1_10nM


title: LacZ-48h-2


title: SCH-7729824 LPS 24h [S2518_Nr51]

city: Warsaw

first: Michal

last: Mikula

address: Roentgena 5

department: Experimental Oncology

country: Poland

institute: Maria Skłodowska-Curie National Research Institute of Oncology

data_processing:
Raw sequences were trimmed according to quality using Trimmomatic (version 0.39) using default parameters
Trimmed sequences were mapped to Mus musculus, version mm10, reference genome using bowtie2 (version 2.2.6).
Duplicate reads were marked using Picard (2.24) and reads with MAPQ<30 and in the Encode black list regions were excluded with samtools (version 1.7)
Peaks were called with MACS2 (2.1.1)
Differentially Accessible Regions (DARs) were determined by DiffBind 3.0.12.
Genome_build: mm10
Supplementary_files_format_and_content: xls (MACS2 output)

growth_protocol: 50000 RAW 264.7 cells were seeded in a presence of 10% Fetal Bovine Serum (FBS) on a 6-well plate a day before the treatment

extract_protocol:
Nucleai isolation was performed according to Buenrostro et al. (ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide, Curr Protoc Mol Biol.;109: 21.29.1–21.29.9.)
The ATAC-seq library condstruction was done according to Buenrostro et al. (ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide, Curr Protoc Mol Biol.;109: 21.29.1–21.29.9.). ATAC-seq libraries were sequenced on Illumina NovaSeq 6000 Platform with 75 bps paired-end reads in duplicates at CeGaT GmbH.

treatment_protocol: Cells were pretreated with 500 nM SCH772984 for 1h and then challenged with 10µg/ml LPS  for 1h, 4h and 24hrs in 500 nM SCH772984 presence. Cells were collected and immediately subjected to ATAC-Seq protocol.

value: Raw 264.7 cells

value: LPS 24h

tag: passage

tag: agent

tag: rin values


title: Fig7_D1_1nM_rep1

description: siRNA treatment

source_name: PMH - D1_1nM


title: Fig7_D2_50nM_rep1

description: siRNA treatment

source_name: PMH - D2_50nM


title: SCH-772984 [S2518_Nr45]


title: SCH-772984 LPS 4h [S2518_Nr49]

value: LPS 4h


title: DMSO LPS 4H [S2518_Nr48]

value: vehicle


title: Fig7_D1_50nM_rep1

description: siRNA treatment

source_name: PMH - D1_50nM


title: DMSO [S2518_Nr44]

value: Control


title: SSRP1 WT rep2

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

country: France

institute: INSERM-UGA

data_processing:
Raw fastq files were processed by 5 prime trimming, keeping 30 bp-length fragments, using `fastx_trimmer` (with options -l 30 -Q33). The trimmed fastq files were aligned on the UCSC mm10 genome using the Bowtie2 with options –end-to-end, –no-mixed, –no-discordant).
The aligned read counts were converted into a 10 bp bin matrix of the signal 2Kb upstream and downstream genes TSS, using computeMatrix (from the package deepTools2, Ramirez et al., 2016)
The bam signal were normalized and smoothed using bamCoverage with options: –binSize 4 –minMappingQuality 30 –normalizeUsing RPKM.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: BigWig

source_name: Mouse embryonic stem cell 46C

growth_protocol: Mouse embryonic stem cell 46C was a gift from Philippe Avner. The gap-repair recombineering technique was used in ES cells to generate 46CAtad2-Tag cell line as described previously (Morozumi et al., 2016, PMID: 26459632). 46C ESCs and the derivative cells were cultured in DMEM medium containing LIF (ESG1107, Millipore), non-essential amino acids, 1% Penicillin-Streptomycin, β-mercaptoethanol, and supplemented with 15% fetal bovine serum (Invitrogen), on 0.1% gelatin-coated tissue culture dishes. All cells were incubated at 37°C with 5% CO2. Non-targeting or ATAD2-targeting oligonucleotides were cloned into the lentiviral vector pLKO.1-puromycin (Addgene) for shRNA expression and packaging as described (Morozumi et al., 2016, PMID: 26459632). An Atad2 knockout 46CAtad2-Tag ES cell line was also generated through the lentivirus infection approach as described (Morozumi et al., 2016).

extract_protocol:
ChIP samples were eluted from beads with elution buffer containing 1% SDS at 65°C for 20 min and were purified by phenol-chloroform extraction and ethanol precipitation in parallel with input samples.
For sequencing, ChIP libraries were prepared using MicroPlex Library Preparation Kit v2 (Diagenode) according to manufacturer’s instructions. Each library was quantified on Qubit with Qubit® dsDNA HS Assay Kit (Life Technologies) and size distribution was examined on the Fragment Analyzer with High Sensitivity NGS Fragment Analysis kit (Agilent).
Libraries were then sequenced on a High-output flow cell (400M clusters) using the NextSeq® 500 High Output v2.5 150 cycles kit (Illumina), in paired-end 75/75nt mode, according to manufacturer’s instructions at the TGML Platform of Aix-Marseille Université.

treatment_protocol: ChIP assays for SSRP1 and HIRA were carried out as previously described (Shiota et al., 2018, PMID: 30257209; Barral et al., 2017, PMID: 28366643). Five X 107 46CAtad2-Tag WT, Atad2 KO cells were pelleted, washed twice with PBS (with 10 mM Sodium Butyrate) and lysed in 1.5 ml lysis buffer (15 mM Tris-HCl pH 7.4, 60 mM KCl, 15 mM NaCl, 0.34 M sucrose, 2 mM EDTA, 0.5 mM EGTA, 0.65 mM spermidine, 1 mM DTT, 0.05% Triton-X 100, 1% glycerol, 1X protease cocktail inhibitors, 1X Phosphatase Inhibitor cocktail 1, 10 mM sodium butyrate) and incubated for 5 min at 4 °C. Cell nuclei were pelleted by centrifugation at 200 g for 15 min at 4°C and resuspended in wash buffer (15 mM Tris-HCl pH 7.4, 60 mM KCl, 15 mM NaCl, 0.34 M sucrose, 0.65 mM spermidine, 1 mM DTT, 1X protease cocktail inhibitors, 1X Phosphatase Inhibitor cocktail 1, 10 mM sodium butyrate) and centrifuged again. Cell nuclei were resuspended in MNase buffer (10 mM Tris-HCl pH 7.5, 10 mM KCl, 2 mM CaCl2, 1 mM DTT, 1X protease cocktail inhibitors, 1 × Phosphatase Inhibitor cocktail 1, 10 mM sodium butyrate). Then the cell nuclei solution was digested by micrococcal nuclease S7 (5U MNase per 100μg nuclei, Sigma) at 37°C for 7 min to obtain mononucleosomes. Small aliquots of mononucleosome solutions were collected for input and used to check the efficiency of digestion before immunoprecipitation (IP). IPs were carried out as follows: 5 μg anti-Ssrp1 and anti-HIRA antibodies were coupled with 50 µl Dynabeads and protein G (Thermo Fisher), respectively according to the manufacturer’s instructions. Digested mononucleosome solutions were diluted with LSDB500 buffer (50 mM HEPES pH 7.0, 3mM MgCl2, 500 mM KCl, 20% glycerol, 1X protease cocktail inhibitors, 1X Phosphatase Inhibitor cocktail 1, 10 mM sodium butyrate) to achieve the final KCl concentration of 350 mM. For each reaction, 100 μg of chromatin was incubated with antibody-coupled beads at 4°C for 16 hours. Immunoprecipitated beads were then washed three times with LSDB350 buffer (50 mM HEPES pH 7.0, 3 mM MgCl2, 350 mM KCl, 20% glycerol, 1 × protease cocktail inhibitors, 1X Phosphatase Inhibitor cocktail 1, 10 mM sodium butyrate) and once with elution buffer (10 mM Tris-HCl pH 8.5, 1 mM EDTA, 10 mM sodium butyrate).

value: Mouse embryonic stem cell 46C

tag: atad2 genotype

value: WT

tag: chip antibody


title: SSRP1 KO rep2

tag: cell line

value: KO


title: HIRA  WT rep2

value: HIRA


title: DMSO LPS 24H [S2518_Nr50]


title: SCH-772984 LPS 1h [S2518_Nr47]

value: LPS 1h


title: HIRA  KO rep2


title: Input WT rep1

extract_protocol:
ChIP samples were eluted from beads with elution buffer containing 1% SDS at 65°C for 20 min and were purified by phenol-chloroform extraction and ethanol precipitation in parallel with input samples.
For sequencing, ChIP libraries were prepared using MicroPlex Library Preparation Kit v2 (Diagenode) according to manufacturer’s instructions. Each library was quantified on Qubit with Qubit® dsDNA HS Assay Kit (Life Technologies) and size distribution was examined on the Fragment Analyzer with High Sensitivity NGS Fragment Analysis kit (Agilent).
Libraries were then sequenced on a High-output flow cell (400M clusters) using the NextSeq 500 High Output v2.5 150 cycles kit (Illumina), in paired-end 75/75nt mode, according to manufacturer's instructions at the TGML Platform of Aix-Marseille Université.

treatment_protocol: ChIP assays for SSRP1 and HIRA were carried out as previously described (Shiota et al., 2018, PMID: 30257209; Barral et al., 2017, PMID: 28366643). Five X 107 46CAtad2-Tag WT, Atad2 KO cells were pelleted, washed twice with PBS (with 10 mM Sodium Butyrate) and lysed in 1.5 ml lysis buffer (15 mM Tris-HCl pH 7.4, 60 mM KCl, 15 mM NaCl, 0.34 M sucrose, 2 mM EDTA, 0.5 mM EGTA, 0.65 mM spermidine, 1 mM DTT, 0.05% Triton-X 100, 1% glycerol, 1X protease cocktail inhibitors, 1X Phosphatase Inhibitor cocktail 1, 10 mM sodium butyrate) and incubated for 5 min at 4 °C. Cell nuclei were pelleted by centrifugation at 200 g for 15 min at 4°C and resuspended in wash buffer (15 mM Tris-HCl pH 7.4, 60 mM KCl, 15 mM NaCl, 0.34 M sucrose, 0.65 mM spermidine, 1 mM DTT, 1X protease cocktail inhibitors, 1X Phosphatase Inhibitor cocktail 1, 10 mM sodium butyrate) and centrifuged again. Cell nuclei were resuspended in MNase buffer (10 mM Tris-HCl pH 7.5, 10 mM KCl, 2 mM CaCl2, 1 mM DTT, 1X protease cocktail inhibitors, 1 × Phosphatase Inhibitor cocktail 1, 10 mM sodium butyrate). Then the cell nuclei solution was digested by micrococcal nuclease S7 (5U MNase per 100μg nuclei, Sigma) at 37°C for 7 min to obtain mononucleosomes. Small aliquots of mononucleosome solutions were collected for input and used to check the efficiency of digestion before immunoprecipitation (IP).   IPs were carried out as follows: 5 μg anti-Ssrp1 and anti-HIRA antibodies were coupled with 50 µl Dynabeads and protein G (Thermo Fisher), respectively according to the manufacturer’s instructions. Digested mononucleosome solutions were diluted with LSDB500 buffer (50 mM HEPES pH 7.0, 3mM MgCl2, 500 mM KCl, 20% glycerol, 1X protease cocktail inhibitors, 1X Phosphatase Inhibitor cocktail 1, 10 mM sodium butyrate) to achieve the final KCl concentration of 350 mM. For each reaction, 100 μg of chromatin was incubated with antibody-coupled beads at 4°C for 16 hours. Immunoprecipitated beads were then washed three times with LSDB350 buffer (50 mM HEPES pH 7.0, 3 mM MgCl2, 350 mM KCl, 20% glycerol, 1 × protease cocktail inhibitors, 1X Phosphatase Inhibitor cocktail 1, 10 mM sodium butyrate) and once with elution buffer (10 mM Tris-HCl pH 8.5, 1 mM EDTA, 10 mM sodium butyrate).

value: none (Input)


title: Input KO rep1


title: DMSO LPS 1H [S2518_Nr46]


title: DMSO LPS 24H [S2518_Nr42]


title: SCH-7729824 LPS 24h [S2518_Nr43]


title: Input KO rep2


title: Adult_CM_DOX6Water6 rep2

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Trimmomatic version 0.33 was employed to trim reads after a quality drop below a mean of Q20 in a window of 5 nucleotides. Only reads above 30 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl mouse genome version mm10 (GRCm38) using STAR 2.4.0a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 1.4.5-p1 tool from the Subread package
Reads overlapping multiple genes or aligning to multiple regions were excluded. (GEO) Differentially expressed gene analysis was performed using DESeq2
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Matrix table with normalized counts combined with data from GSE79883

source_name: Adult cardiomyocytes

extract_protocol:
adult cardiomycytes were isolated using langendorff-free method.RNA quality and yield were measured using RNA integrity number (RIN) algorithm, using the Fragment Analyzer (Agilent) preparation. 2 μg of total RNA was used as input VAHTS Stranded mRNA-seq Library preparation.
250-600ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Clontech).

value: isolated adult mouse cardiomyocytes

value: Doxycycline 6 days, and no doxcycline 6 days

value: 12-16 weeks


title: Input WT rep2


title: SCH-772984 LPS 4h [S2518_Nr41]


title: DMSO LPS 4H [S2518_Nr40]


title: SCH-772984 LPS 1h [S2518_Nr39]


title: Adult_CM_DOX6Water6 rep1


title: Adult_CM_DOX12 rep2

value: Doxycycline 12 days


title: Adult_CM_DOX12 rep1


title: Adult_CM_DOX6 rep1

value: Doxycycline 6 days