title: UPN-928-R1

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

data_processing:
Raw sequencing reads were demultiplexed, mapped to the human reference genome (build GRCh38) and gene-expression matrices were generated using CellRanger allowing for intron reads to be included in UMI counts (version 6.0.1). The resulting count matrices were further filtered in Seurat (https://satijalab.org/seurat/) to remove nuclei barcodes with less than  500 genes or 2500 UMIs, more than 1% of UMIs derived from mitochondrial genes, or more than 50,000 UMIs. This filtering resulted in 52,020 single nuclei across all samples. After normalization, these nuclei were clustered using the Seurat workflow based on dimensionality reduction by PCA using the 3,000 most variable genes. Coarse nuclei types were defined (immune, myeloid, and stroma cells) were assigned based on marker gene expression. Tumor nuclei were readily identified based on their discrete clustering patterns, and the presence of CNVs generated using inferCNV (v.1.3.6). We applied Harmony alignment (theta = 2) to correct for inter-sample variation due to experimental or sequencing batch effects[11].  After assessment of clustering using a variety of dimensions, we used 30 harmony dimensions to cluster the data and perform dimensionality reduction using Uniform Manifold Approximation and Projection (UMAP).
Assembly: GRCh38
Supplementary files format and content: UMI count matrix, cell barcodes, and gene names.
Supplementary files format and content: Cell metadata (cell sample id, clustering, and cell type)

source_name: Ependymoma tumor

extract_protocol:
Single nuclei were isolated from PFA frozen samples using CHAPS-based buffer protocol as previously described by Slyper et al.[10].  An additional wash step was included in the protocol to reduce cell-free RNA levels that can confound subsequent single-nuclei RNAseq analysis. Bright field microscopy was employed to determine yield, quality and membrane integrity of single-nuclei
Single-nuclei RNAseq was performed using the 10x Genomics Chromium platform at the UC Cancer Center Microarray and Genomics Core using a Chromium Controller and Chromium Single Cell V3.1 Chemistry Library Kits, Gel Bead & Multiplex Kit, and Chip Kit (10× Genomics). 4000 nuclei per sample were captured and barcoded to generate cDNA libraries that were sequenced using the Illumina NovaSeq6000 platform at approximately 50,000 reads per nuclei

value: Ependymoma tumor


title: UPN-928-P

status: Public on May 31 2023

type: SRA

country: USA

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Homo sapiens

tag: tissue


title: UPN-816-R1


title: UPN-897-R1


title: JB_65 [RNA-seq]

city: Halle (Saale)

first: Danny

last: Misiak

address: Kurt-Mothes-Str. 3a

department: Molecular Cell Biology

country: Germany

institute: Martin Luther University Halle-Wittenberg

description:
Neuroblastoma_tumor_totalRNA_TMM_FPKM.csv
DE_MNA_nMNA_protein_coding.csv
DE_17_unbalanced_protein_coding.csv

library_source: transcriptomic

data_processing:
Sequenced strand unspecific paired-end reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.18) with parameters -q 20 -O 7 -m 20 –trim-n
Trimmed reads were mapped against the human genome (hg38 UCSC) using HiSat2 (v 2.1.0) with parameters -q --dta -k 5
Secondary alignments were filtered out using samtools (v 1.10).
Mapped reads were summarized using featureCounts (v 2.0.0) with parameterst -p -s 0 -T 6 -M -t exon -g gene_id and Ensembl gene annotations (GRCh 38.96)
Differential gene expression was assessed using R/edgeR (v 4.0.3) using TMM normalization.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Comma-separated text files including FPKM, log2 fold change and false discovery rate values for each sample.

molecule: total RNA

source_name: primary neuroblastoma tumor

extract_protocol:
500 ng of total RNA were depleted of ribosomal RNA using the RiboMinus kit (Life Technologies) according to the instructions of the manufacturer. Depleted RNA was then fragmented by addition of 5 fragmentation buffer (200 mM Tris acetate, pH 8.2, 500 mM potassium acetate and 150 mM magnesium acetate) and heating at 94 °C for 3 min in a thermocycler followed by ethanol precipitation with ammonium acetate and GlycoBlue (Life Technologies) as carrier.
Fragmented RNA was then reverse transcribed using random hexamer and Superscript III (Life Technologies). The second strand was synthesized using the TargetAmp kit (Epicentre) according to the instructions of the manufacturer. The final steps of library preparation, e.g. blunt end repair, adapter ligation, adapter fill-in and amplification were done according to Meyer and Kircher (2010, PMID: 20516186). The barcoded libraries were purified and quantified using the Library Quantification Kit - Illumina/Universal (KAPA Biosystems) according to the instructions of the manufacturer. A pool of up to 10 libraries was used for cluster generation at a concentration of 10nM using an Illumina cBot. Sequencing of 2x100 bp was performed with an IlluminaHighScan-SQ sequencer at the sequencing core facility of the IZKF Leipzig (Faculty of Medicine, University Leipzig) using version 3 chemistry and flowcell according to the instructions of the manufacturer.

value: primary neuroblastoma tumor

tag: tumor stage

tag: mycn status

value: not amplified


title: JB_62 [RNA-seq]

description:
Neuroblastoma_tumor_totalRNA_TMM_FPKM.csv
DE_s123_s4_protein_coding.csv
DE_s1_s4_protein_coding.csv
DE_MNA_nMNA_protein_coding.csv
DE_17_unbalanced_protein_coding.csv
DE_17_unbalanced_MNA_protein_coding.csv

value: amplified


title: JB_58 [RNA-seq]


title: UPN-897-P


title: JB_61 [RNA-seq]


title: JB_64 [RNA-seq]

description:
Neuroblastoma_tumor_totalRNA_TMM_FPKM.csv
DE_MNA_nMNA_protein_coding.csv
DE_17_unbalanced_protein_coding.csv
DE_17_unbalanced_MNA_protein_coding.csv


title: JB_63 [RNA-seq]


title: JB_60 [RNA-seq]


title: JB_59 [RNA-seq]


title: JB_57 [RNA-seq]


title: UPN-816-P


title: UPN-723-R1


title: UPN-723-P


title: UPN-459-R1


title: UPN-691-R1


title: JB_53 [RNA-seq]

description:
Neuroblastoma_tumor_totalRNA_TMM_FPKM.csv
DE_s123_s4_protein_coding.csv
DE_s1_s4_protein_coding.csv
DE_MNA_nMNA_protein_coding.csv
DE_17_unbalanced_protein_coding.csv


title: JB_54 [RNA-seq]


title: UPN-691-P


title: JB_56 [RNA-seq]


title: JB_52 [RNA-seq]


title: JB_67 [RNA-seq]


title: JB_66 [RNA-seq]


title: JB_51 [RNA-seq]


title: UPN-459-P


title: UPN-1101-R1


title: JB_48 [RNA-seq]


title: JB_50 [RNA-seq]


title: JB_47 [RNA-seq]


title: JB_46 [RNA-seq]


title: UPN-1101-P


title: JB_43 [RNA-seq]

description:
Neuroblastoma_tumor_totalRNA_TMM_FPKM.csv
DE_s123_s4_protein_coding.csv
DE_MNA_nMNA_protein_coding.csv
DE_17_unbalanced_protein_coding.csv
DE_17_unbalanced_MNA_protein_coding.csv


title: UPN-928-X

data_processing:
High quality base calls at Q30>80% were obtained for 50 million 150bp paired-end reads and mapped to the human genome (CRCh38) by STAR 2.4.0.1.
Assembly: Hg38
Supplementary files format and content: Quantification of RNA expression, as fragments per kilobase per million (FPKM), was derived by Cufflinks. FPKM were processed to log2(FPKM+1) for further analyses, which is provided here

source_name: tumor - PFA ependymoma

extract_protocol:
RNA was isolated snap frozen PFA samples using an Allprep DNA/RNA mini kit (Qiagen) per manufacturers instructions
Libraries were prepared using the Tecan Universal Plus mRNA-Seq library preparation kit per manufacturers instructions

value: tumor - PFA ependymoma

tag: Sex

value: male

value: recurrence

tag: treatment


title: UPN-930-R1


title: JB_42 [RNA-seq]

description:
Neuroblastoma_tumor_totalRNA_TMM_FPKM.csv
DE_s123_s4_protein_coding.csv
DE_MNA_nMNA_protein_coding.csv
DE_17_unbalanced_protein_coding.csv


title: JB_41 [RNA-seq]


title: UPN-911-P

value: presentation


title: JB_44 [RNA-seq]


title: UPN-928-R1


title: UPN-897-R1


title: UPN-859-P


title: UPN-848-P

value: female


title: JB_40 [RNA-seq]


title: UPN-897-X


title: UPN-943-P


title: UPN-839-P


title: JB_36 [RNA-seq]


title: JB_39 [RNA-seq]


title: JB_35 [RNA-seq]


title: JB_34 [RNA-seq]


title: UPN-821-R2


title: UPN-965-P


title: JB_45 [RNA-seq]


title: JB_33 [RNA-seq]


title: UPN-821-R1


title: JB_32 [RNA-seq]


title: JB_31 [RNA-seq]


title: UPN-821-P


title: UPN-839-R1


title: JB_37 [RNA-seq]


title: JB_28 [RNA-seq]


title: JB_27 [RNA-seq]


title: JB_29 [RNA-seq]


title: UPN-816-R1


title: UPN-812-P


title: UPN-816-P


title: UPN-811-R2


title: UPN-80-P


title: UPN-781-P


title: UPN-811-R1


title: JB_24 [RNA-seq]


title: JB_26 [RNA-seq]


title: JB_25 [RNA-seq]


title: UPN-758-P


title: JB_22 [RNA-seq]


title: JB_23 [RNA-seq]


title: UPN-700-P


title: UPN-723-R1


title: JB_21 [RNA-seq]


title: UPN-691-R1


title: JB_20 [RNA-seq]


title: UPN-64-P


title: JB_19 [RNA-seq]


title: JB_30 [RNA-seq]


title: UPN-483-P


title: UPN-492-P


title: JB_18 [RNA-seq]


title: JB_17 [RNA-seq]


title: JB_16 [RNA-seq]


title: JB_15 [RNA-seq]


title: JB_14 [RNA-seq]


title: JB_11 [RNA-seq]


title: JB_12 [RNA-seq]


title: UPN-392-P


title: JB_13 [RNA-seq]


title: JB_10 [RNA-seq]


title: UPN-319-P


title: UPN-459-R1


title: UPN-393-R1


title: UPN-459-P


title: UPN-419-P


title: UPN-321-P


title: UPN-321-R1


title: UPN-318-P


title: JB_7 [RNA-seq]


title: UPN-246-P


title: JB_8 [RNA-seq]


title: JB_6 [RNA-seq]


title: UPN-195-P


title: JB_5 [RNA-seq]


title: JB_4 [RNA-seq]


title: HI 2

city: Pittsburgh

first: Partha

last: Dutta

state: PA

address: 200 Lothrop Street

department: Medicine

institute: University of Pittsburgh

data_processing:
The RNA-Seq analysis is done in several steps using CLC Genomics Workbench: First, all genes are extracted from the reference genome (using annotations of type gene). Other annotations on the gene sequences are preserved (e.g. CDS information about coding sequences etc). Next, all annotated transcripts (using annotations of type mRNA) are extracted. If there are several annotated splice variants, they are all extracted. Note that the mRNA annotation type is used for extracting the exon-exon boundaries.
Next, the reads are mapped against all the transcripts plus the entire gene
From this mapping, the reads are categorized and assigned to the genes, and expression values for each gene and each transcript are calculated. After that, putative exons are identified.
Genome_build: mm10
Supplementary_files_format_and_content: The excel file includes RPKM values for each Sample.

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
We used pico pure RNA extraction kit (Applied Biosystems) to extract RNA from sorted cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: mouse strain

value: hindlimb ischemia


title: HI 3


title: HI 1


title: UPN-319-R1


title: JB_9 [RNA-seq]


title: UPN-1513-P


title: JB_3 [RNA-seq]


title: Sham 3

value: sham


title: UPN-1400-R1


title: Sham 2


title: Sham 1


title: JB_2 [RNA-seq]


title: JB_1 [RNA-seq]


title: UPN-1320-R1


title: UPN-1295-P


title: UPN-1269-P


title: Shoot_32TGRooZ_1

city: Pozuelo de Alracon

first: Juan

middle: Carlos

last: del Pozo

state: Madrid

address: Campus de Montegancedo, UPM

department: Biotechnology

country: Spain

institute: Centro de Biotecnología y Genómica de Plantas

data_processing:
After sequencing, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads using SOAPnuke software developed by BGI
SOAPnuke software filter parameters: " -n 0.001 -l 20 -q 0.4 --adaMR 0.25 --ada_trim --minReadLen 150
if the length of the sequencing read is less than 150 bp, discard the entire read
Obtain Clean reads: the output read quality value system is set to Phred+33.
Alaigned with STAR aligner (v2.5.3a)
Reads are mapped to a reference sequences  (TAIR 42.gff3) using HISAT2 with 8 mismatches allowed.
differential gene expression was conducted with DESeq2
Assembly: Atabidopsis thaliana Araport 11
Supplementary files format and content: tab-delimited text files including normalized counts.

organism: Arabidopsis thaliana

source_name: shoot 10 day old

growth_protocol: Arabidopsis wild type seedlings were grown   for 4 days in MS1/2  at 22ºC  and then they were transferred to 22ºC, 32ºC or  32ºc in the shoot with a decreasing temperature gradient in the root for  6 extra days

extract_protocol:
Total  RNA was isolated from Arabidopsis plants after temperature treatment  using the Trizol reagent and RNeasy columns (Qiagen). Quantity and quality measurements were taken using a NanoDrop spectrophotometer and bioanalizer.
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA. 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

tag: tag

value: wild type

value: grown at 32 C with the root  in a T^a gradient_replica_1


title: Shoot_32SR_2

treatment_protocol: Arabidopsis wild type seedlings were grown   for 4 days in MS1/2  at 22ºC  and then they were transferred to 22ºC, 32ºC or  32ºc in the shoot with a decreasing temperature gradient in the root for  6 extra days

value: grown at 32 C homogeneously_replica_2


title: Shoot_32SR_3

value: grown at 32 C homogeneously_replica_3


title: Shoot_32SR_1

value: grown at 32 C homogeneously_replica_1


title: Shoot_32TGRooZ_3

value: grown at 32 C with the root  in a T^a gradient_replica_3


title: Shoot_22SR_1

value: grown at 22 C homogeneously_replica_1


title: Shoot_32TGRooZ_2

value: grown at 32 C with the root  in a T^a gradient_replica_2


title: UPN-1536-P


title: UPN-1239-P


title: Root_32TGRooZ_3

source_name: root 10 day old


title: Root_32TGRooZ_2


title: UPN-110-P


title: Root_32TGRooZ_1


title: UPN-1101-R1


title: UPN-1347-P


title: Root_32SR_3


title: UPN-1101-P


title: Root_22SR_2

value: grown at 22 C homogeneously_replica_2


title: Shoot_22SR_2


title: UPN-1091-P


title: Root_22SR_1


title: UPN-1010-P


title: UPN-1048-P


title: UPN-02001-P


title: Root_32SR_2


title: Root_32SR_1


title: A549 cells, shTIGD1,Rep 1

type: RNA

city: Xi'an

first: Yiqun

last: Wei

address: No. 157, Xiwu Road, Xi'an, Shaanxi, 710004, China

country: China

institute: the Second Affiliated Hospital of Xi'an Jiaotong University

description: Gene expression changes in A549 cells transfected with TIGD1 shRNA

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00‐0331‐220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00‐0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix,Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA,US) with default settings.

data_processing: CEL files were processed using Affymetrix GCOS software and normalized with RMA method. RMA files were imported into GeneSpring 7.3 software (Agilent Technologies) and further analyzed.

label: biotin

source_name: lung cancer

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Cells were grown in Dulbecco's Modified Eagle's medium (DMEM) with 10% FBS, 5% penicillin/streptomycin.

extract_protocol: Total RNA was extracted using TRIZOL Reagent following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany)

treatment_protocol: ShRNA targeting TIGD1 (shTIGD1) and negative control shRNA (shNC) were obtained from Genechem Company Limited (Shanghai, China). The sequences were as follows: shTIGD1, 5'-CTGCTAACACAACATCCAT-3'; shNC, 5'-TTCTCCGAACGTGTCACGT-3'. The shTIGD1 and shNC lentiviruses were transfected into A549 cells as per the manufacturer’s instructions.

tag: cell line

tag: transfection

value: TIGD1 shRNA


title: A549 cells, shControl,Rep 3

description: Gene expression changes in A549 cells transfected with control shRNA

value: Control shRNA


title: A549 cells, shControl,Rep 1


title: A549 cells, shTIGD1,Rep 3


title: A549 cells, shControl,Rep 2


title: RNA0000908

city: Brussels

first: clement

last: triaille

address: avenue hippocrate

country: Belgium

institute: UCLouvain

data_processing:
Data were processed using a standard RNAseq analysis pipeline including FastQC-0.11.8 for quality control of raw data, and Trimmomatic-0.38 to remove low quality reads and trim adapters from sequences.
Hisat2-2.1.0 was used to align reads to the genome (GRCh38)
Gene expression levels were evaluated using featureCounts from subread-2.0.0  and Homo_sapiens.GRCh38.94.gtf.
Assembly: (GRCh38)
Supplementary files format and content: tab-delimited text files include raw count for each Sample (ENSEMBL_ID)

source_name: bulk synovial tissue

extract_protocol:
Total RNA was extracted from synovial biopsies using the NucleoSpin RNA II extraction kit (Macherey-Nagel) including DNAse treatment. RNA quality control was performed on a 2100 Bioanalyzer (Agilent). RNASeq was performed on 350 ng of RNA, for  samples that yielded a RNA Integrity Number (RIN) of 5 or more
Sequencing was performed by Macrogen Europe using a standardized protocol. cDNA libraries were constructed with the TruSeq Stranded mRNA LT Sample Prep Kit and sequenced on an Illumina sequencer.

treatment_protocol: Synovial tissue biopsies were obtained in a clinically involved joint of early, untreated RA patients. Three to five synovial fragments were obtained from each joint by needle arthroscopy  or US guided small joint biopsy and stored at -80°C after overnight incubation in RNA-Later solution (Invitrogen)

tag: disease state

value: rheumatoid arthritis

value: bulk synovial tissue

tag: rin

value: M

value: bio

tag: acpa

tag: rf

value: K

tag: crp_bl (mg/dl)

value: ND


title: A549 cells, shTIGD1,Rep 2


title: RNA0000906

value: F


title: RNA0000904

value: mtx

value: N


title: RNA0000903

value: W


title: pt66_DS-BCP-ALL

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

description: Gene expression data from bone marrow sample of Down Syndrome patient at disgosis of BCP-ALL

hyb_protocol: 15 ug were fragmented; following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing:
The data were normalized using R software [www.r-ptoject.org] with BioConductor package [www.bioconductor.org] using RMA
RMA and Combat sva package for batch remove between different protocol.

source_name: Bone Marrow

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol starting  from 100ng of Total RNA using the Affymetrix 3' IVT Plus Kit or 1ug using Affymetrix One cycle Protocol

extract_protocol: RNA was extracted using Trizol

treatment_protocol: No treatment

value: BCP-ALL at diagnosis

value: Bone Marrow


title: pt70_DS-BCP-ALL


title: pt65_DS-BCP-ALL


title: pt56_DS-BCP-ALL


title: pt62_DS-BCP-ALL


title: pt60_DS-BCP-ALL


title: pt59_DS-BCP-ALL


title: pt69_DS-BCP-ALL


title: RNA0000905


title: pt68_DS-BCP-ALL


title: pt61_DS-BCP-ALL


title: pt63_DS-BCP-ALL


title: pt64_DS-BCP-ALL


title: pt52_DS-BCP-ALL


title: RNA0000901

value: Y

value: MCP


title: RNA0000894


title: RNA0000893


title: RNA0000895


title: pt50_DS-BCP-ALL


title: RNA0000892


title: pt58_DS-BCP-ALL


title: RNA0000890


title: RNA0000889


title: RNA0000891


title: RNA0000888


title: pt48_DS-BCP-ALL


title: pt43_DS-BCP-ALL


title: pt44_DS-BCP-ALL


title: pt45_DS-BCP-ALL


title: pt51_DS-BCP-ALL


title: RNA0000887


title: pt67_DS-BCP-ALL


title: pt42_DS-BCP-ALL


title: pt41_DS-BCP-ALL


title: pt40_DS-BCP-ALL


title: pt39_DS-BCP-ALL


title: RNA0000886


title: RNA0000885


title: pt37_DS-BCP-ALL


title: pt35_DS-BCP-ALL


title: pt38_DS-BCP-ALL


title: pt36_DS-BCP-ALL


title: RNA0000884


title: RNA0000883


title: pt34_DS-BCP-ALL


title: RNA0000882


title: pt33_DS-BCP-ALL


title: pt30_DS-BCP-ALL


title: pt31_DS-BCP-ALL


title: pt32_DS-BCP-ALL


title: RNA0000879

value: PCBO


title: pt29_DS-BCP-ALL


title: pt46_DS-BCP-ALL


title: RNA0000877


title: RNA0000857


title: pt28_DS-BCP-ALL


title: pt26_DS-BCP-ALL


title: RNA0000827


title: pt24_DS-BCP-ALL


title: pt27_DS-BCP-ALL


title: RNA0000824


title: pt19_DS-BCP-ALL


title: pt16_DS-BCP-ALL


title: pt22_DS-BCP-ALL


title: pt21_DS-BCP-ALL


title: pt20_DS-BCP-ALL


title: pt14_DS-BCP-ALL


title: pt15_DS-BCP-ALL


title: pt23_DS-BCP-ALL


title: pt12_DS-BCP-ALL


title: pt11_DS-BCP-ALL


title: RNA0000822


title: pt13_DS-BCP-ALL


title: pt18_DS-BCP-ALL


title: pt10_DS-BCP-ALL


title: RNA0000823


title: RNA0000816


title: cardiomyocytes (TC25-F4-07)

city: Mulhouse

first: Anne

last: ARIES

address: 87 Av d'Alkirch

country: France

institute: IRHT

description: Gene expression in cardiomyocytes

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >15.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25× Agilent Fragmentation Buffer and 10x Agilent Gene Expression Blocking Agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE v2 8x60K Microarray (G4858A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by very slow removing.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.5 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 039494_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.
The data were filtered and normalized using Agilent Genespring GX software

source_name: human cardiomyocytes

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Low Input Quick Amp WT Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human umbilical cord blood (Hu-UCB) samples were obtained from healthy, consenting donors undergoing normal deliveries.  The cells were incubated in Iscove’s modified medium (IMDM) supplemented with 12.5% fetal bovine serum, 2.5% horse serum, 2 mM L-glutamine,, 7 μM 1-thioglycerol , 1% penicillin/streptomycin, BMP2, bFGF, VEGF, IGF1), and BMP4

extract_protocol: Total RNA was extracted from UCB-CD34+- and UCB-CD34+-treated cells and, at different stages of differentiation, cardiac progenitors (CMPCs) and cardiomyocytes (4 pools of quadruplets).

treatment_protocol: cells were treated on days 1 and 2 with  valproic acid (VPA) and 5-azacytidine (5’AZA), respectively. From day 3, the medium was renewed 3 times per week with previous medium containing  ascorbic acid and  TGF-β1 until day 14.

value: cardiomyocytes

tag: cell type


title: pt7_DS-BCP-ALL


title: RNA0000815

value: PIP


title: LK1_Gut_ZF

city: Rotterdam

first: Naomi

last: Kakiailatu

address: Naomi

department: Clinical Genetics

country: Netherlands

institute: Erasmus MC

description: 10x Genomics

data_processing:
Cellranger count (v 4.0.0) was employed for barcode processing, gene counting and aggregation of the samples
Downstream analysis was performed in Seurat (v 4.1.1)
Assembly: GRCz10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: Whole gut

growth_protocol: Zebrafish were kept on a 14/10h light/dark cycle. Embryos and larvae were kept in an incubator at 28.5°C in HEPES-buffered E3 medium.

extract_protocol:
In total 244 intestines of 5 days post-fertilization (dpf) larvae were isolated, cells were dissociated using 2.17mg/mL papain and the live cells were sorted using FACS. Cells were then loaded onto the 10X platform for single-cell RNA sequencing.
Libraries were made according to the manufacter’s instructions (Single Cell 3' v3 chemistry, 10x Genomics)

treatment_protocol:
N/A
N/A

value: Enteric nervous system cells

value: Whole gut

tag: line

value: wt tg(phox2bb:GFP)

tag: age

value: 5 days post fertilization


title: pt17_DS-BCP-ALL

tag: tissue


title: pt6_DS-BCP-ALL


title: cardiomyocytes (TC10-10)

description: Gene expression in cardiomyocytes


title: RNA0000435

value: rheumatoid arthritis

value: bulk synovial tissue

value: K


title: RNA0000191

value: F

value: bio

value: MTP


title: RNA0000173

value: M

value: ND


title: cardiomyocytes (6215)

description: Gene expression in cardiomyocytes


title: 0000861_B_RNA

value: mtx

value: N


title: pt9_DS-BCP-ALL

value: BCP-ALL at diagnosis

value: Bone Marrow


title: 0000858_B_RNA

value: Y


title: pt8_DS-BCP-ALL


title: pt3_DS-BCP-ALL


title: pt4_DS-BCP-ALL


title: pt2_DS-BCP-ALL


title: 0000786_B_RNA

value: MCP


title: cardiomyocytes (ASD-061)

description: Gene expression in cardiomyocytes

value: cardiomyocytes


title: CMPC  (TC10-03)

description: Gene expression in CMPC

source_name: human cardiac biopsies

value: cardiac biopsies

value: CMPC


title: 0000652_B_RNA

value: rheumatoid arthritis


title: pt1_DS-BCP-ALL


title: 0000647_B_RNA

value: bulk synovial tissue

value: W


title: 0000646_B_RNA

value: F

value: PIP


title: LBF_Ast_CD51P_CD71P_CD63P_3

city: Chicago

first: Chian-Yu

last: Peng

state: IL

address: Department of Neurology, 10-233 Ward Building, 303 E Chicago Ave.

institute: Northwestern University, Feinberg School of Medicine

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.36
Trimmed sequence reads were mapped to GrCM38/ STAR 2.7.2a
Read count extraction and normalization were performed using featureCounts v1.5.3 in Subread package
with gene annotation included in GENCODE release 31
Normalized gene expression were obtained through TMM normalization with library size correction
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: H7 ESC

extract_protocol:
RNA was harvested using RNAqueous Micro total RNA isolation kit (Thermo Fisher AM1931). 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: H7 ESC

value: ESC derived astrocyte progenitor

tag: genotype

value: WT

value: astrocytic lineage differentiation

tag: time

value: Day 160


title: LBF_Ast_CD51P_CD71P_CD63N_2


title: LBF_Ast_CD51P_CD71N_CD63N_3


title: CMPC  (ASD-060-2)

description: Gene expression in CMPC


title: LBF_Ast_CD51P_CD71P_CD63P_2


title: 0000639_B_RNA

tag: Sex

value: mtx


title: CMPC  (TC25-F4-01)

description: Gene expression in CMPC


title: CMPC  (ASD-060)

description: Gene expression in CMPC


title: pt5_DS-BCP-ALL

tag: treatment

value: BCP-ALL at diagnosis

value: Bone Marrow


title: Diff d14 (CM254-05)

description: Gene expression after differentiation d14

source_name: human umbilical cord blood

value: umbilical cord blood

value: CD34+ stem cells

tag: Stage

value: differentiation d14


title: Diff d14 (CM255-04)


title: LBF_Ast_CD51P_CD71P_CD63N_3


title: LBF_Ast_CD51P_CD71N_CD63P_2


title: Diff d14 (CM248-05)


title: Diff d14 (CM245-06)


title: Diff d3 (CM248-03)

description: Gene expression after differentiation d3

value: differentiation d3


title: Diff d3 (CM254-03)


title: MDSLCDA, Vehicle, 72h

city: Kurume

first: Taichi

last: Matsumoto

state: Fukuoka

address: 422, Tsubuku-honmachi

department: Basic Medical Science Unit

country: Japan

institute: St. Mary's Research Center

description: Gene expression in MDS-L/CDA cells treated with 0 μM AZA fo 72h

hyb_protocol: Please contact Cell Innovator (http://www.cell-innovator.com/)

source_name: MDS-L/CDA, 0.1% DMSO, 72h

growth_protocol: Both MDS-L and MDS-L/CDA cells were cultured in RPMI1640 medium supplemented with 10% FBS, 20 ng/mL IL-3, and 50 μM 2-mercaptoethanol

extract_protocol: Total RNA was isolated with ISOGEN Thermo Fisher Scientific K.K.). RNA quality was checked using Agilent 220 TapeStation (Agilent Technologies Japan, Ltd., Tokyo, Japan), and all RNA showed > 9.8 RNA Integrity Number.

treatment_protocol: Both MDS-L and MDS-L/CDA cells were treated with either vehicle (0.1% DMSO) or 1 μM AZA for 72 h.

value: MDS-L/CDA

value: 1 μM AZA


title: MDSLCDA, 1 mM AZA, 72h

description: Gene expression in MDS-L/CDA cells treated with 1 μM AZA fo 72h

scan_protocol: Please contact Cell Innovator (http://www.cell-innovator.com/)

source_name: MDS-L/CDA, 1 μM AZA, 72h


title: MDSL, 1 mM AZA, 72h

description: Gene expression in MDS-L cells treated with 1 μM AZA fo 72h

data_processing: Please contact Cell Innovator (http://www.cell-innovator.com/)

source_name: MDS-L, 1 μM AZA, 72h

value: MDS-L

value: 0.1% DMSO


title: Diff d3 (CM255-03)


title: LBF_Ast_CD51P_CD71N_CD63P_3


title: MDSL, Vehicle, 72h

description: Gene expression in MDS-L cells treated with 0 μM AZA fo 72h

source_name: MDS-L, 0.1% DMSO, 72h

label_protocol: Please contact Cell Innovator (http://www.cell-innovator.com/)


title: LBF_Ast_CD51P_CD71P_CD63N_1


title: 0000637_B_RNA

value: rheumatoid arthritis

value: bulk synovial tissue

value: F

value: N

value: W


title: 0000605_B_RNA

value: M


title: LBF_Ast_CD51P_CD71N_CD63N_1

value: H7 ESC

value: ESC derived astrocyte progenitor

value: WT

value: astrocytic lineage differentiation

value: Day 160


title: LBF_Ast_CD51P_CD71N_CD63N_2


title: LBF_Ast_CD51P_CD71N_CD63P_1


title: LBF_Ast_CD51P_CD71P_CD63P_1


title: 0000602_B_RNA

value: mtx

value: MCP


title: Diff d3 (CM245-03)

value: umbilical cord blood

value: CD34+ stem cells

value: differentiation d3


title: CD34+ stem cells_4 (CM255-01)

description: Gene expression in CD34+ stem cells from blood cord


title: 0000599_B_RNA

value: bio

value: K

value: ND


title: L3.6_ARID1Ako_rep1

city: Goettingen

first: Zhe

last: Zhang

state: Niedersachsen

address: Robert-Koch-Strasse 40

department: Department of Gastroenterology & GI oncology

institute: University Medical Center, Goettingen

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FASTQ trimmer (Galaxy version 1.1.5)
Single-end 50bp reads were aligned to human genome GRCh37/hg19 by TopHat (Version 2.1.1)
Transcripts normalization and differential expression analysis were performed by Cuffnorm (Version 2.2.1.2) and Cuffdiff (version 2.2.1.5) with FDR cutoff 0.05
Assembly: hg19
Supplementary files format and content: Matrix table with normalized gene counts corresponding with gene names

growth_protocol: L3.6pl cells were maintained in Minimum Essential Media (MEM) supplemented with 10% fetal calf serum (FCS) in humidified atmosphere with 5% CO2 at 37  ̊C

extract_protocol:
Total RNA was harvested by TRIzol method from triplicate samples and quality was assessed by RNA electrophoresis.
Libraries were prepared from 500 ng RNA utilizing Truseq RNA Library Prep Kit v2 following manufacturer’s instructions. mRNA was captured by RNA purification beads and eluted. The first strand and second strand cDNA were synthesized and the overhangs of the fragments were repaired into blunt ends. The 3’ end was added with a single adenine to prevent mutual ligation during the following adapter conjugation. Finally, the DNA fragments with both flow-cell-hybridization adapters were amplified and the library was quantified by Agilent Bioanalyzer 2100. Size selection was optional if the main population of the library exceeds the appropriate size for sequencing or small fragments such as primer-dimers exist.

value: pancreatica cancer cell line


title: L3.6_ARID1Ako_rep3


title: L3.6_parental_rep2


title: L3.6_ARID1Ako_rep2


title: L3.6_parental_rep3


title: MZsap130b 3

first: Michael

last: Tsang

address: 3501 Fifth Ave. BST3-5062

department: Cell Biology

data_processing:
fastq files were analyzed using CLC genomics workbench 20.0
sequence reads were mapped onto Danio rerio GRC.z11
EDGE test was performed using CLC genomics workbench
Assembly: Danio rerio GRC.z11
Supplementary files format and content: .xlsx files. Data shows expression counts, TPM and RKPM.

source_name: whole embryo

growth_protocol: Zebrafish emrbyos were obtained from natural mating

extract_protocol:
Zebrafish embryos at 36hpf were sorted based on genotype and heart ventricle size for one study. The other study isolated heart tissue from embryos at 48hpf.
RNA was harvested using Trizol reagent and Quiagen RNeasy micro kit (Cat# 74004).

treatment_protocol: embryos were kept at 28.5C temperature in standard egg water

value: whole embryo

value: sap130b pt35a/pt35a


title: 0000590_B_RNA

value: rheumatoid arthritis

value: bulk synovial tissue

value: M

value: N


title: pt25_DS-BCP-ALL

value: BCP-ALL at diagnosis

value: Bone Marrow


title: CD34+ stem cells_3 (CM254-01)


title: L3.6_parental_rep1

value: WT


title: 0000588_B_RNA

value: F

value: mtx


title: MZsap130b 2


title: 0000587_B_RNA


title: CD34+ SC_2 (CM248-01)

value: umbilical cord blood

value: CD34+ stem cells


title: RNA expression, Tendinopathy

city: Chongqing

first: JUNFENG

last: GUO

state: Chongqing

address: No. 30, Gaotan Yanzheng Street,

department: Department of Orthopedics/Sports Medicine Center

institute: Southwest Hospital, Third Military Medical University

data_processing:
To be updated.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files. For Expression.txt file, the column name corresponds to the cell ID and the row name corresponds to the gene name. For the ATAC.txt file, the column name corresponds to the cell ID, and the row name corresponds to the peak name.

molecule: nuclear RNA

source_name: Achilles tendon

extract_protocol:
Tendinopathy tissue was placed in a 2-ml microcentrifuge tube, NP40 lysis buffer was added, and the mixture was incubated on ice for 5 min. Then, the mixture was filtered through a 70-µm filter and transferred to a new 2-ml microcentrifuge tube. After gradient centrifugation, the supernatant was removed. PBS, bovine serum albumin (BSA), and an RNase inhibitor were added and incubated on ice for 5 min. Repeated centrifugation resulted in a pure single-nuclei suspension.
The obtained nuclear suspension was incubated in a transposase mixture that entered the nuclei and preferentially fragmented DNA in open chromatin regions. Oligonucleotides containing an Illumina P5 sequence, a 16-nt 10x barcode and a spacer sequence were then released. Barcoded, full-length preamplified cDNA was further amplified via PCR to generate sufficient mass for gene expression library construction.

value: Achilles tendon

tag: condition

value: Tendinopathy


title: Injured_stimulated_retina_d8

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

institute: Vrije Universiteit Brussel - VIB

description: 10x Genomics

data_processing:
Raw data bcl files were demultiplexed using Cellranger mkfastq
Demultiplexed data was processed using the Cellranger count pipeline
Assembly: mm10
Supplementary files format and content: h5 files including raw counts (output CellRanger Count) per sample and text metadata files with information per cell

source_name: CD45+ CD11b cells from retina of mice 8 days after optic nerve crush and inflammatory stimulation with Pam3Cys combined with cAMP

extract_protocol: All Methods listed in Andries et al. Immune stimulation recruits a subset of pro-regenerative macrophages to the retina that promotes axonal regrowth of injured neurons. Acta Neuropathologica Communications. 2023.

value: retina

tag: strain


title: Injured_stimulated_retina_d4

description: 10x Genomics

source_name: CD45+ CD11b cells from retina of mice 4 days after optic nerve crush and inflammatory stimulation with Pam3Cys combined with cAMP


title: MZsap130b 1


title: Injured_retina

description: 10x Genomics

source_name: CD45+ CD11b cells from retina of mice 4 days after optic nerve crush

value: mice 4 days after optic nerve crush


title: 0000585_B_RNA

value: K


title: WT 3

value: whole embryo

value: AB*


title: Naive_retina

description: 10x Genomics

source_name: CD45+ CD11b cells from retina of naive mice

value: naive mice


title: CD34+ SC_1 (CM245-01)


title: WT 2


title: WT 1


title: 0000583_B_RNA

source_name: bulk synovial tissue

value: rheumatoid arthritis

value: bulk synovial tissue

value: ND


title: 0000582_B_RNA

value: N


title: KO2

city: Diepenbeek

first: Melanie

last: Loix

state: Limburg

address: Agoralaan gebouw C

department: Biomedical Research Institute

institute: Hasselt University

data_processing:
Trimmed using Trimmomatic v0.36 for adaptor sequences.
Aligned usiing HISAT2 v2.1.0 (default parameters; -p 2 --dta-cufflinks --rna-strandness R; genome: Ensembl v93, corresponding to GCA_000001635.8). Counts obtained using HTSeq v0.11.0     parameters: --stranded=reverse; default parameters used: --order=name --minaqual=10 --type=exon --idattr=gene_id --mode=union)    GTF: Ensembl release 93  + QC performed using FastQC v0.11.15

source_name: bone marrow

extract_protocol:
Total RNA was extracted from wild-type and Ube3a-/- BMDMs using Direct-zol RNA miniprep kit (Zymo Research) and quantified fluorometrically with a Qubit 3 Fluormeter (Invitrogen).
A KAPA mRNA hyperPrep kit (KAPA Biosystems) was used for mRNA library construction.

value: bone marrow

value: macrophage

value: UBE3A KO


title: KO3


title: WT3

value: Wild-type


title: WT1


title: WT2


title: 0000581_B_RNA

value: F

value: mtx


title: Control OE, Run1, scRNA-seq

city: Leuven

first: Kristofer

middle: James

last: Davie

address: Herestraat 49

department: Center for Brain and Disease Research

institute: Vlaams Instituut voor Biotechnologie

description: 10x Genomics 3'

data_processing:
Raw 10x Genomics data were processed using the Cellranger count command (v3.1.0), mapping to the GRCm38 assembly (ensembl 97 annotation). Filtered gene expression matrices were loaded into Scanpy (v.1.8.1) and further filtered to remove cells expressing less than 500 genes or with greater than 15% of UMIs being assigned to mitochondrial genes, Scrublet was then used to remove cells likely to be doublets (doublet_score > 0.25), and finally, samples were then combined into two datasets, miR-132 OE and miR-132 KD.
Following QC and filtering, samples were normalized to a total of 10000 UMIs per cell and log normalized; highly variable genes were detected using default parameters and the data were scaled to unit variance with a mean of 0, values greater than 10 were clipped. A principal component analysis was performed on the highly variable gene matrix and Harmony was used for batch correction between runs, 50 and 40 components were used respectively for miR-132 OE and miR-132 KD for downstream dimensionality reduction and clustering analyses
Clustering was performed at various resolutions using the Leiden algorithm and clusters were annotated with cell types based on their marker gene expression. Infiltrating immune cells segregated as distinct clusters and were removed from the analysis based on the expression of markers for monocytes (Cd44, Fn1, Gda), macrophages (Atf3, Cfp, Serpinb8), dendritic cells (Flt3) and lymphocytes (Lck). Cells from cell types we did not intend to sort per RUN, were excluded from further analysis [RUN 1: all hippocampal cells; RUN 2: only neurons and astrocytes; RUN 3: all hippocampal cells; RUN 4: only neurons and astrocytes; RUN 5: only neurons and astrocytes (Table S3)]. After removal of these cells, the analysis was repeated starting with the detection of highly variable genes, 46 and 42 principal components were used respectively for miR-132 OE and miR-132 KD for filtered datasets.
Assembly: mm10
Supplementary files format and content: Comma-separated matrix files, tab-separated values files and matrix files

source_name: Hippocampus

extract_protocol:
Mice received an overdose of pentobarbital and were perfused with ice-cold artificial CSF (aCSF). The aCSF was composed of (in mM): 93 NMDG, 2.5 KCl, 1.2 NaH2PO4, 30 NaHCO3, 20 HEPES, 25 glucose, 5 sodium ascorbate, 2 thiourea, 3 sodium pyruvate, 10 MgSO4, 0.5 CaCl2, and was adjusted to pH 7.4 and equilibrated in 95% O2 5% CO2. After perfusion, right hippocampi were microdissected and placed in cold Hibernate A Low Fluorescence (BrainBits), supplemented with 5 μM Actinomycin D (Cat#A1410-5MG, Sigma-Aldrich). Hippocampi were dissociated enzymatically using the Adult Brain Dissociation Kit, mouse and rat (Cat#130-107-677, Miltenyi Biotec) for 15 min at 37°C, with 5 μM Actinomycin D added. Subsequently mechanical dissociation was performed, cells were passed through a 70 µm cell strainer and washed with 10 ml ice-cold D-PBS supplemented with 0.5% BSA. Next, cells were centrifuged for 10 min at 300 g at 4°C and myelin and debris removal was performed according to manufacturer’s instructions. Afterwards, cells were resuspended in D-PBS (0.5% BSA) and labeled with the eBioscience™ Fixable Viability Dye eFluor™ 780 (1:2000, Cat#65-0865-14, Thermo Fisher Scientific, irreversibly labels dead cells) and in run 2, 4, 5 also with Anti-mouse ACSA-2-APC (1:20, Cat#130-116-142, Miltenyi Biotec) and BV421 Rat Anti-CD11b (1:10, Cat#562605, BD). Cells were incubated for 30 min in the dark at 4°C, washed with 1 ml D-PBS (0.5% BSA) and spun down for 10 min at 300 g at 4°C. Subsequently, cells were suspended in 200 μl D-PBS (0.5% BSA) for FACsorting. Only alive cells were sorted, as dead cells were excluded based on their staining with the eFluor™ 780 dye. Neurons were sorted based on YFP expression. For astrocyte isolation, ACSA-2 positive microglia were excluded by selection based on both CD11b and ACSA-2 expression. According to the run, an Influx (BD) or MACSQuant Tyto (Miltenyi Biotec) were used for sorting and different cell types were isolated.
10000-20000 cells were sorted per sample and further processing was conducted following manufacturer’s instructions (CG000183 ChromiumSingleCell3 v3 for RUN 1, 2, 3 and CG000204 ChromiumNextGEMSingleCell3 v3.1 for RUN 4, 5). Briefly, cells were loaded onto the Chromium Single Cell Chip B (RUN 1, 2, 3) or Chromium Next GEM Chip G (RUN 4, 5) for GEM formation and after consecutive steps of reverse transcription, cDNA clean-up and amplification, DNA libraries were generated. Libraries were loaded in an equimolar pool for sequencing on the HiSeq4000 or NovaSeq6000 platform (Illumina) aiming for 50000 reads/cell.

treatment_protocol: Mice were anesthetized using isoflurane and fixed in a stereotactic frame. A cannula was implanted unilaterally in the right hemisphere at position of injection (AP-0.1 mm, ML-1.0 mm, and DV-3.0 mm) and mice were left to recover for approximately 1 week. For miR-132 knockdown (miR-132 KD), mice were injected with 3 μl (0.33 nmol/μl) of miR-132 antagomiR (locked nucleic acid (LNA)-, 3′-cholesterol-modified oligonucleotide) (Exiqon, QIAGEN) resuspended in artificial cerebrospinal fluid (aCSF) (Harvard Apparatus). Control mice received a scrambled LNA oligonucleotide in aCSF. For miR-132 overexpression (miR-132 OE), mice received 150 pmol of either a miR-132 mimic or a negative control oligonucleotide (Dharmacon, Horizon Discovery) in a 3 μl mix with lipofectamine 2000 (at a 1:1 volume ratio) (Cat#11668019, Thermo Fisher Scientific). One week (miR-132 KD) or 48 h (miR-132 OE) after injection, mice were sacrificed and the injected right hippocampus was microdissected.

value: Hippocampus

value: All hippocampal cells

value: negative control oligonucleotide


title: miR-132 OE, Run1, scRNA-seq

description: 10x Genomics 3'

value: miR-132 mimic


title: KO1


title: WT1 heart

source_name: heart

value: heart


title: 0000580_B_RNA

value: M

value: Y

value: K


title: miR-132 KD, Run1, scRNA-seq

description: 10x Genomics 3'

value: miR-132 antagomiR


title: Control KD, Run1, scRNA-seq

description: 10x Genomics 3'

value: scrambled LNA


title: WTCPM-dex-4-rep2

city: Hsinchu

first: Jinn-Moon

last: Yang

address: 75 Po-Ai Street

country: Taiwan

institute: National Chiao Tung University

description:
intranasally instilled WTCPM and intraperitoneal injection dexamethason
FPKM.6-4_S9_L002

data_processing:
The quality of reads was examined using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The reads were aligned to the Mus musculus genome mm10 (https://genome-idx.s3.amazonaws.com/hisat/mm10_genome.tar.gz  ) using HISAT2 (v.2.2.1).
The reads from HISAT2 were converd to BAM using samtools (v.1.12).
The reads from HISAT2 were mapped and assembled into transcripts using StringTie (v.2.1.5).
The expression proles of whole transcripts were evaluated and calculated based on fragments per kilobase of transcript per million fragments mapped (FPKM) using the Ballgown package (v.2.22.0) in R (v. 4.0.4).
The expression of two replicated samples were averaged.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample using ballgown package

source_name: Exposure to WTCPM with dexamethasone treatment

growth_protocol: C57BL/6J mouse was chosen because it is the most widely used and long history recognized strain to construct the animal model for the study of pulmonary effects. We used the pathogen-free, 6-8-week-old male C57/BL6 inbred mice that were purchased from the Jackson Laboratory (Bar Harbor, ME). They were maintained under the relative humidity of 30%-40% with a 12-hr light/ dark cycle specific pathogen-free conditions animal room at NYUSOM. 1-2 weeks of acclimatization were required before any experiments. They were maintained under the relative humidity of 30%-40% with a 12-hr light/ dark cycle specific pathogen-free conditions animal room at NYUSOM. 1-2 weeks of acclimatization were required before any experiments. Excepting the experimental period, the mice were fed freely with ad libitum access to standard laboratory chow and filtered water. All animal care and experimental studies strictly adhered to ‘The Guidebook for the Care and the Use of Live Animals in Teaching and Research”, and protocols were reviewed and approved by the Institutional Animal Care and Use Committee (IACUC).

extract_protocol:
The lung samples from 16 mice  belonging to four groups including WTCPM, WTCPM+ros, WTCPM+dex, and control (n = 4), werethen processed for RNA extraction and high-throughput sequencing. TRIzol (Invitrogen) was adopted to extract the RNA based on the commercial protocol.
The RNA quality and purity for each sample were assessed by Nanodrop 1000 spectrometer (Thermo Fisher Scientific, Wilmington, DE). DNA contamination was eliminated by following the manufacturer's instructions for using a DNA-free kit (Invitrogen).  Next, an Illumina HiSeq 4000 system (NYU Genome Technology Center) was used to perform sequencing  of 1 × 50 paired-end reads with 186,512 transcripts.
Illumina HiSeq 4000 system (NYU Genome Technology Center)

treatment_protocol: The WTC dust samples were collected from separate locations on/around Main Pile at Ground Zero during September 12-13, 2001. Because of the successive collisions of the concrete floor slabs of the 110-story towers, the bulk (about 80–90%) of this unique primary-source WTC dust was released during this time. The doses for Rrosoxacin and dexamethasone  were 5mg/kg and 0.1mg/kg separately.

tag: animal id

value: mouse 6-4

value: Lung

value: WT

tag: wtcpm treatment

value: Yes

tag: drug treatment

value: dexamethasone


title: WTCPM-dex-4-rep1

description:
intranasally instilled WTCPM and intraperitoneal injection dexamethason
FPKM.6-4_S9_L001


title: MZsap130a1 heart

value: sap130a pt32a/pt32a


title: MZsap130aSV 3

value: whole embryo

tag: sorted group

value: Small ventricle


title: MZsap130aSV 2


title: 0000579_B_RNA

tag: disease state

value: rheumatoid arthritis

value: bulk synovial tissue

tag: rin

value: F

value: mtx

value: N

tag: acpa

tag: rf


title: 0000584_B_RNA

value: M

tag: crp_bl (mg/dl)


title: MZsap130aSV 1

tag: tissue


title: 0000570_B_RNA

value: K


title: WTCPM-dex-3-rep2

description:
intranasally instilled WTCPM and intraperitoneal injection dexamethason
FPKM.6-3_S19_L002

value: mouse 6-3

tag: genotype


title: WTCPM-dex-2-rep2

description:
intranasally instilled WTCPM and intraperitoneal injection dexamethason
FPKM.6-2_S18_L002

value: mouse 6-2


title: WTCPM-dex-3-rep1

description:
intranasally instilled WTCPM and intraperitoneal injection dexamethason
FPKM.6-3_S19_L001


title: 0000567_B_RNA

value: Y

value: MCP


title: WTCPM-dex-2-rep1

description:
intranasally instilled WTCPM and intraperitoneal injection dexamethason
FPKM.6-2_S18_L001

value: Lung

value: WT


title: MZsap130aNV 3

value: Normal ventricle


title: WTCPM-dex-1-rep2

description:
intranasally instilled WTCPM and intraperitoneal injection dexamethason
FPKM.6-1_S22_L002

value: mouse 6-1

value: Yes

value: dexamethasone


title: 0000564_B_RNA

value: rheumatoid arthritis

value: ND


title: 0000561_B_RNA

value: bulk synovial tissue

value: F


title: WTCPM-ros-4-rep1

description:
intranasally instilled WTCPM and intraperitoneal injection rosoxacin
FPKM.3-4_S1_L001

source_name: Exposure to WTCPM with rosoxacin treatment

value: mouse 3-4

value: rosoxacin


title: WTCPM-ros-3-rep2

description:
intranasally instilled WTCPM and intraperitoneal injection rosoxacin
FPKM.3-3_S4_L002

value: mouse 3-3


title: MZsap130aNV 1

value: whole embryo

value: sap130a pt32a/pt32a


title: WTCPM-ros-4-rep2

description:
intranasally instilled WTCPM and intraperitoneal injection rosoxacin
FPKM.3-4_S1_L002


title: MZsap130aNV 2


title: WTCPM-dex-1-rep1

description:
intranasally instilled WTCPM and intraperitoneal injection dexamethason
FPKM.6-1_S22_L001


title: 0000557_B_RNA

value: M

value: mtx

value: N

value: K


title: WT2

value: AB*

value: Normal ventricle


title: 0000556_B_RNA

value: Y


title: WT3


title: WTCPM-ros-1-rep2

description:
intranasally instilled WTCPM and intraperitoneal injection rosoxacin
FPKM.3-1_S2_L002

value: mouse 3-1

value: Lung

value: WT

value: Yes


title: WT1


title: WTCPM-ros-3-rep1

description:
intranasally instilled WTCPM and intraperitoneal injection rosoxacin
FPKM.3-3_S4_L001


title: WTCPM-ros-2-rep1

description:
intranasally instilled WTCPM and intraperitoneal injection rosoxacin
FPKM.3-2_S3_L001

value: mouse 3-2


title: WTCPM-ros-1-rep1

description:
intranasally instilled WTCPM and intraperitoneal injection rosoxacin
FPKM.3-1_S2_L001


title: 0000555_B_RNA

value: rheumatoid arthritis

value: bulk synovial tissue

value: F


title: WTCPM-4-rep2

description:
intranasally instilled WTCPM
FPKM.1-4_S10_L002

source_name: Exposure to WTCPM

value: mouse 1-4

value: No


title: WTCPM-3-rep2

description:
intranasally instilled WTCPM
FPKM.1-3_S17_L002

value: mouse 1-3


title: WTCPM-4-rep1

description:
intranasally instilled WTCPM
FPKM.1-4_S10_L001


title: 0000554_B_RNA

value: mtx


title: WTCPM-3-rep1

description:
intranasally instilled WTCPM
FPKM.1-3_S17_L001


title: SEDXX3_IV_50000000_Unstimulated [UNSTIM_13]

city: Cambridge

first: Bryan

middle: B

last: Bryson

state: MA

address: 77 Massachusetts Avenue

department: Department of Biological Engineering

institute: Massachusetts Institute of Technology

description:
integrated_object.rds
myeloid_object.rds
tnk_object.rds
cell_metadata.tsv
genes.tsv.gz
barcodes.tsv.gz
matrix.mtx.gz

data_processing:
DropSeqTools and STAR (v2.7.0c) was used to generate DGEs
Assembly: mmul_8.0.1
Supplementary files format and content: Total Seurat object containing IV BCG dose cells as well as BCG route cells from Darrah et al. Nature (2020).
Supplementary files format and content: T and NK cell object containing IV BCG dose and route cells (Darrah et al. 2020)
Supplementary files format and content: Myeloid cell object containing IV BCG dose and route cells (Darrah et al. 2020)
Supplementary files format and content: Cell metadata for IV BCG dose samples
Supplementary files format and content: Genes for IV BCG dose samples
Supplementary files format and content: Barcodes for IV BCG dose samples
Supplementary files format and content: Raw count matrix for IV BCG dose samples

organism: Macaca mulatta

source_name: Bronchoalveolar lavage

extract_protocol: High-throughput single-cell mRNA sequencing by Seq-Well was performed on single-cell suspensions obtain from NHP BAL. 15,000 viable cells per sample were applied directly to the surface of a Seq-Well device. Two arrays were run for each sample: one unstimulated and one stimulated overnight with 20 ug/mL of PPD in R10.

value: Bronchoalveolar lavage

tag: nhp id

tag: time post-vaccination

value: 15 weeks

tag: vaccination route

value: IV

tag: vaccination dose

value: Untreated


title: WTCPM-2-rep2

description:
intranasally instilled WTCPM
FPKM.1-2_S12_L002

value: mouse 1-2


title: 0000553_B_RNA

tag: Sex

value: N

value: K


title: SEDXX2_IV_50000000_Unstimulated [UNSTIM_12]

tag: treatment


title: 0000558_B_RNA


title: WTCPM-ros-2-rep2

description:
intranasally instilled WTCPM and intraperitoneal injection rosoxacin
FPKM.3-2_S3_L002

tag: animal id

value: Lung

value: WT

value: rosoxacin


title: WTCPM-1-rep2

description:
intranasally instilled WTCPM
FPKM.1-1_S5_L002

value: mouse 1-1

tag: wtcpm treatment

value: Yes


title: WTCPM-2-rep1

description:
intranasally instilled WTCPM
FPKM.1-2_S12_L001

tag: drug treatment


title: 0000550_B_RNA

value: rheumatoid arthritis

value: bulk synovial tissue

value: F

value: bio

value: ND


title: 18319_NA_Naïve_Unstimulated [UNSTIM_10]

value: Bronchoalveolar lavage

value: DGCT

value: Naïve


title: SEDXX1_IV_50000000_Unstimulated [UNSTIM_11]

value: 15 weeks

value: IV

value: Untreated


title: Control-4-rep1

description:
Healthy control
FPKM.4-4_S7_L001

source_name: Healthy control

value: mouse 4-4

value: No


title: WTCPM-1-rep1

description:
intranasally instilled WTCPM
FPKM.1-1_S5_L001

value: Lung

value: WT


title: 0000188_B_RNA

value: mtx

value: N

value: K


title: 0000187_B_RNA

value: rheumatoid arthritis

value: bulk synovial tissue


title: Control-3-rep2

description:
Healthy control
FPKM.4-3_S15_L002

value: mouse 4-3


title: Control-2-rep1

description:
Healthy control
FPKM.4-2_S21_L001

value: mouse 4-2


title: SEDXX4_IV_50000000_Unstimulated [UNSTIM_14]

value: Bronchoalveolar lavage


title: 0000185_B_RNA

value: F


title: Control-4-rep2

description:
Healthy control
FPKM.4-4_S7_L002


title: Control-1-rep2

description:
Healthy control
FPKM.4-1_S23_L002

value: mouse 4-1


title: 0000181_B_RNA

value: Y


title: Control-2-rep2

description:
Healthy control
FPKM.4-2_S21_L002


title: 18219_IV_300000_Unstimulated [UNSTIM_8]

value: DGJR

value: 14 weeks

value: IV


title: 18019_IV_100000_Unstimulated [UNSTIM_9]

value: DGGG

value: Untreated


title: Control-1-rep1

description:
Healthy control
FPKM.4-1_S23_L001

value: Lung

value: WT

value: No


title: 18519_IV_300000_Unstimulated [UNSTIM_7]

value: DGHR


title: Liver, DEN+CCL4-3

city: Hanhzhou

first: fujing

last: ge

address: No. 866 Yuhangtang Road

institute: Zhejiang University

data_processing:
A cDNA library constructed by technology from the pooled RNA from liver samples of mice was sequenced run with Illumina 4000 sequence platform.
We aligned reads of sample 1-6 to the UCSC (http://genome.ucsc.edu/) homo sapiens reference genome using HISAT package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: FPKMs

source_name: liver

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 1000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Poly(A) RNA is purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: For diethylnitrosamine (DEN) + chronic administration of carbon tetrachloride (CCl4) (DEN+CCl4)-induced HCC model, male C57BL/6J mice (2 weeks old) were randomized into two groups: DEN+CCl4 group and control group. The mice in the DEN+CCl4 group received a single intraperitoneal (i.p.) injection of 1 mg/kg of DEN. Around 6 weeks later, 0.2 mL/kg of CCl4 was administered i.p. two times per week for up to 14 weeks.

value: liver

tag: strain

value: male

value: DEN+CCl4-induced HCC model


title: Liver, DEN+CCL4-2

tag: disease state


title: 18419_IV_300000_Unstimulated [UNSTIM_6]

value: DGFT


title: Liver, DEN+CCL4-1


title: 0000177_B_RNA

value: rheumatoid arthritis

value: bulk synovial tissue

tag: rin

value: M

value: mtx

value: N

value: K


title: 18119_IV_300000_Unstimulated [UNSTIM_5]

value: Bronchoalveolar lavage

value: DGFV

value: 14 weeks

value: IV


title: Control-3-rep1

description:
Healthy control
FPKM.4-3_S15_L001

value: mouse 4-3

value: Lung

value: WT


title: Liver, Control-3

value: liver

value: Control

value: control


title: 0000145_B_RNA

value: F

value: Y

tag: acpa


title: 18719_IV_100000_Unstimulated [UNSTIM_4]

value: HCZ

value: Untreated


title: Liver, Control-2

value: male


title: 18619_IV_300000_Unstimulated [UNSTIM_3]

value: HAR


title: 17919_IV_100000_Unstimulated [UNSTIM_2]


title: 0000010_B_RNA

value: rheumatoid arthritis

value: bulk synovial tissue

value: mtx

tag: rf

value: W


title: 0000012_B_RNA

value: K

tag: crp_bl (mg/dl)


title: Mettl14-cKO, scRNAseq

city: Stanford

first: Yue

last: Sun

state: CA

address: 290 Jane Stanford Way

institute: Stanford University

description: 10x Genomics, Chromium Gene Expression 3ʹ kit v3.1

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: retina

extract_protocol:
Mouse retinas were dissected in HBSS and incubated with digestion solution (20 U/ml Papain, 87.5 mM HEPES, 0.8 x HBSS, 2.5 mM cysteine, 0.5 mM EDTA, pH 7) at 37 °C for 5 min. Retinas were then spun down at 1800 rpm for 2.5 min, washed with 10% FBS/HBSS, and followed by gentle trituration in 0.4% BSA/DMEM with P1000 tips. The cell suspensions were filtered with a 35-um strainer and kept on ice until use.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: cell type

value: dissociated cells

tag: tissue

value: retina

value: Mettl14 fl/fl;Chx10-Egfp/Cre

tag: age


title: control, scRNAseq

tag: genotype

value: Mettl14 fl/fl or fl/wt


title: 17819_IV_600000_Unstimulated [UNSTIM_1]

value: Bronchoalveolar lavage

tag: nhp id

tag: time post-vaccination

value: 14 weeks

tag: vaccination route

value: IV


title: MBD3- ES cell population Hi-C rep 4

first: Ernest

last: Laue

address: 80 Tennis Court Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Cambridge

library_source: genomic

data_processing:
Cut&Run:
Cut&Run data was trimmed using trim_galore and then aligned using Bowtie standard parameters to the Mus Musculus reference genome (mm10).
Cut&Run bigwig tracks were calculated using BedTools and bedGraphToBigWig with standard parameters.
The coverage was calculated with computeMatrix reference-point with options --binSize 10.
Peaks were called using MACS2 to be at FDR 1% and above 5-fold enrichment.
Hi-C
Population Hi-C was mapped to the genome using NucProcess (https://github.com/tjs23/nuc_processing) and analysed further using NucTools (https://github.com/tjs23/nuc_tools).
Genome_build: UCSC GRCm38/mm10
Supplementary_files_format_and_content: Bigwig files were generated for Cut&Run datasets.
Supplementary_files_format_and_content: Population Hi-C txt file (.txt) is a tab-separated text format containing all the chromosomal coordinates for Hi-C contacts and the number observed (chromosome_A start position_A end position_A chromosome_B start position_B end position_B number observed).

molecule: genomic DNA

source_name: MBD3- ES cell population Hi-C

growth_protocol: Mouse embryonic stem cells (ESCs) were grown on gelatin-coated plates in 2i/LIF conditions as described (Ying et al., 2008).

extract_protocol:
Cut&Run experiments were carried out according to Meers et al., (2019) using a Drosophila genomic DNA spike-in and “input” controls consisting of samples which were processed in parallel with the Cut&Run samples but with untethered MNase.
Population Hi-Cs were carried out as previously outlined (Stevens et al., Nature, 2017). 5-10 million Haploid mouse ES cells were fixed for 5 min with 2 % formaldehyde in PBS and then the reaction was quenched for another 5 min in 0.125 M glycine. Nuclei were then extracted by incubating cells on ice for 30 min (inverting every 10 min) in 10 mM Tris pH 8.0, 10 mM NaCl, 0.2 % NP-40 (IGEPAL CA-630) and protease inhibitor cocktail (Roche).
Cut&Run experiments were carried out according to Meers et al., (2019) using a Drosophila genomic DNA spike-in and “input” controls consisting of samples which were processed in parallel with the Cut&Run samples but with untethered MNase.
Hi-C libraries were prepared as previously outlined (Stevens et al., Nature, 2017). Briefly, sonicated DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. Biotinylated junctions were captured on streptavidin M-280 dynabeads and the blunt, phosphorylated ends were treated with Klenow fragment (exo minus) and dATP to yield a protruding 3- 'A' base for ligation of custom adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 10 cycles and library fragments of ~300-700 bp (insert plus adaptor and PCR primer sequences) were isolated using AMPure beads (Beckman). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2500 following the manufacturer's protocols.

tag: background

tag: cell line

value: Mouse embryonic stem cells

tag: culture conditions


title: SEDXX4_IV_50000000_Stimulated_BCG [STIM_SampleR18]

value: 15 weeks

tag: vaccination dose

tag: treatment

value: BCG-Stimulated


title: FAS-AS1 overexpressed vector,rep2

city: Changsha

first: Zhen

last: Guo

state: hunan

address: Changsha Medical University, LeiFeng Avenue NO.1501

institute: Changsha Medical University

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp 1 and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: HNE1 cells were incubated in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: HNE1 cells were transfected with FAS-AS1 overexpression vector or control vector for 24 h.

value: Nasopharyngeal carcinoma cell

value: WT


title: Liver, Control-1

value: liver

value: Control

tag: strain

tag: Sex

value: male

tag: disease state

value: control


title: FAS-AS1 overexpressed vector,rep3

value: transfected with FAS-AS1 overexpression vector


title: 0000180_B_RNA

first: clement

last: triaille

address: avenue hippocrate

institute: UCLouvain

data_processing:
Data were processed using a standard RNAseq analysis pipeline including FastQC-0.11.8 for quality control of raw data, and Trimmomatic-0.38 to remove low quality reads and trim adapters from sequences.
Hisat2-2.1.0 was used to align reads to the genome (GRCh38)
Gene expression levels were evaluated using featureCounts from subread-2.0.0  and Homo_sapiens.GRCh38.94.gtf.
Assembly: (GRCh38)
Supplementary files format and content: tab-delimited text files include raw count for each Sample (ENSEMBL_ID)

extract_protocol:
Total RNA was extracted from synovial biopsies using the NucleoSpin RNA II extraction kit (Macherey-Nagel) including DNAse treatment. RNA quality control was performed on a 2100 Bioanalyzer (Agilent). RNASeq was performed on 350 ng of RNA, for  samples that yielded a RNA Integrity Number (RIN) of 5 or more
Sequencing was performed by Macrogen Europe using a standardized protocol. cDNA libraries were constructed with the TruSeq Stranded mRNA LT Sample Prep Kit and sequenced on an Illumina sequencer.

value: rheumatoid arthritis

value: bulk synovial tissue

tag: rin

value: F

value: mtx

value: Y

tag: acpa

tag: rf

value: K


title: SEDXX3_IV_50000000_Stimulated_BCG [STIM_SampleQ17]

tag: tissue

value: Bronchoalveolar lavage

value: IV


title: MBD3- ES cell population Hi-C rep 3

tag: cell type

value: Mouse embryonic stem cells


title: Subject: S148-2055; Sample Day: Day 97 (V7) with respect to first vaccination; Replicate: 1

type: protein

city: Irvine

first: Arlo

middle: Zan

last: Randall

address: 1 Technology Drive, Suite E309

institute: Antigen Discovery Inc

description:
S148-2055.V7
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.

hyb_protocol: Plasma samples were diluted 1:100 in a 3 mg mL-1 E. coli lysate solution in protein arraying buffer (Maine Manufacturing, Sanford, ME, USA) and incubated at room temperature for 30 min. Chips were rehydrated in blocking buffer for 30 min. Blocking buffer was removed, and chips were probed with pre-incubated serum samples using sealed, fitted slide chambers to ensure no cross-contamination of sample between pads. Chips were incubated overnight at 4°C with agitation. Chips were washed five times with TBS-0.05% Tween 20, followed by incubation with biotin-conjugated goat anti-human IgG (Jackson ImmunoResearch, West Grove, PA, USA) diluted 1:200 in blocking buffer at room temperature. Chips were washed three times with TBS-0.05% Tween 20, followed by incubation with streptavidin-conjugated SureLight P-3 (Columbia Biosciences, Frederick, MD, USA) at room temperature protected from light. Chips were washed three times with TBS-0.05% Tween 20, three times with TBS, and once with water. Chips were air dried by centrifugation at 1,000 x g for 4 min and dried overnight in dessicator before scanning.

scan_protocol: Probed microarrays (slides) were scanned using a GenePix 4300A High-Resolution Microarray Scanner (Molecular Devices, Sunnyvale, CA, USA) an image file (.tif) was saved for each array using GenePix Pro 7 software. The scanned image files were quantified using the Mapix software (Innopsys) auto gridding feature. For this process two input files are required: (1) a .gal file that defines the array and sub-array layout and (2) the tiff image file for an array. Once the auto-gridding is complete the overlay of the mapped array, subarray, and individual spot locations are shown in the graphical user interface (GUI). If the automatic gridding fails to map to the correct positions the mapping can be manually adjusted using the GUI. Once the gridding is confirmed to be correct the array spots are quantified and saved to an output .gpr file. For each spot on the slide the gpr file contains the foreground intensity (median of pixels inside of circle defining spot) and local background intensity (median of pixels just outside of circle defining spot).

data_processing: Foreground spot intensities were adjusted by local background by subtraction, and negative values were converted to 1. Next, all foreground values were transformed using the base 2 logarithm. The dataset was normalized to remove systematic effects by subtracting the median signal intensity of the IVTT controls for each sample. Since the IVTT control spots carry the chip, sample and batch-level systematic effects, but also antibody background reactivity to the IVTT system, this procedure normalizes the data and provides a relative measure of the specific antibody binding to the non-specific antibody binding to the IVTT controls (a.k.a. background). With the normalized data, a value of 0.0 means that the intensity is no different than the background, and a value of 1.0 indicates a doubling with respect to background. Normalization was applied separately to arrays 1 and 2.

molecule: protein

source_name: plasma

extract_protocol: not provided

tag: treatment group

value: 1/8 dose ETVAX®

tag: etec colony pcr result at v1 (d0)

value: Negative

tag: etec colony pcr result at v7 (d97)

tag: gender

value: Female


title: Subject: S142-2057; Sample Day: Day 97 (V7) with respect to first vaccination; Replicate: 1

description:
S142-2057.V7
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.

value: Positive

value: Male


title: SEDXX2_IV_50000000_Stimulated_BCG [STIM_SampleP16]

tag: nhp id

tag: time post-vaccination

value: 15 weeks

tag: vaccination route

value: BCG-Stimulated


title: 0000028_B_RNA

value: W

tag: crp_bl (mg/dl)


title: Subject: S145-2052; Sample Day: Day 0 (V1) with respect to first vaccination; Replicate: 1

description:
S145-2052.V1
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.

value: 1/4 dose ETVAX®


title: Subject: S147-2049; Sample Day: Day 97 (V7) with respect to first vaccination; Replicate: 1

description:
S147-2049.V7
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.


title: SEDXX1_IV_50000000_Stimulated_BCG [STIM_SampleO15]

tag: vaccination dose

tag: treatment


title: MBD3- ES cell population Hi-C rep 2

tag: background

tag: cell line

tag: culture conditions


title: MBD3- ES cell population Hi-C rep 1


title: SEDXX4_IV_50000000_Stimulated [STIM_14]

value: Tuberculin Protein Purified Derivative-Stimulated ("PPD-stimulated")


title: Subject: S145-2052; Sample Day: Day 97 (V7) with respect to first vaccination; Replicate: 1

description:
S145-2052.V7
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.


title: Subject: S142-2057; Sample Day: Day 0 (V1) with respect to first vaccination; Replicate: 1

description:
S142-2057.V1
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.


title: Subject: S148-2055; Sample Day: Day 0 (V1) with respect to first vaccination; Replicate: 1

description:
S148-2055.V1
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.


title: nc vector, rep1

value: Nasopharyngeal carcinoma cell

tag: genotype

value: WT

value: transfected with nc vector


title: nc vector, rep2


title: SEDXX3_IV_50000000_Stimulated [STIM_13]


title: MBD3+ 48hrTam INPUT Rep 3

data_processing:
library strategy: Cut&Run
Cut&Run:
Cut&Run data was trimmed using trim_galore and then aligned using Bowtie standard parameters to the Mus Musculus reference genome (mm10).
Cut&Run bigwig tracks were calculated using BedTools and bedGraphToBigWig with standard parameters.
The coverage was calculated with computeMatrix reference-point with options --binSize 10.
Peaks were called using MACS2 to be at FDR 1% and above 5-fold enrichment.
Hi-C
Population Hi-C was mapped to the genome using NucProcess (https://github.com/tjs23/nuc_processing) and analysed further using NucTools (https://github.com/tjs23/nuc_tools).
Genome_build: UCSC GRCm38/mm10
Supplementary_files_format_and_content: Bigwig files were generated for Cut&Run datasets.
Supplementary_files_format_and_content: Population Hi-C txt file (.txt) is a tab-separated text format containing all the chromosomal coordinates for Hi-C contacts and the number observed (chromosome_A start position_A end position_A chromosome_B start position_B end position_B number observed).

source_name: MBD3+ 48hrTam INPUT

tag: experiment conditions

value: Tamoxifen


title: MBD3+ 48hrTam INPUT Rep 2


title: Subject: S131-2046; Sample Day: Day 97 (V7)with respect to first vaccination; Replicate: 1

description:
S131-2046.V7
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.


title: Subject: S147-2049; Sample Day: Day 0 (V1) with respect to first vaccination; Replicate: 1

description:
S147-2049.V1
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.


title: FAS-AS1 overexpressed vector,rep1

value: transfected with FAS-AS1 overexpression vector


title: HASMCs BACH1 H3K9me2-2

city: Shanghai

first: Jieyu

state: Shanghai

address: 138 Yixueyuan Rd,

institute: fudan university

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie2
Bigwig files were generated by deepTools
Assembly: hg19
Supplementary files format and content: BW

source_name: human aortic smooth muscle cells

growth_protocol: HASMC cells were maintained with SMCM at 37 °C in a humidiﬁed incubator with 5% CO2, and were passaged when about 70-90% intensity.

extract_protocol:
Chromatin immunoprecipitation (ChIP) sequencing: Cells were cross-linked with 1% formaldehyde for 10 minutes, quenched with 0.125 M glycine for 10 minutes; then, the cell pellets were resuspended in low salt Lysis buffer (50 mM HEPES/KOH, PH 7.5, 150 mM NaCl, 1% Trixon-X 100, 0.05% SDS, 10 mM EDTA, and proteinase inhibitors), and sonicated with a Q800R2 DNA shearing sonicator (Qsonica LLC, newtown, CT) for 20 min in 30-s intervals to shear the chromatin into 200- to 400-bp lengths. Chromatin was immunoprecipitated with the indicated antibodies and Protein A/G PLUS-Agarose (Santa Cruz, Santa Cruz, CA, #sc-2003). For, H3K9me2-ChIP ChIP, cells were cross-linked, quenched, and washed as described above. Furthermore, the sonicated chromatin was incubated with anti-H3K9me2 overnight at 4°C Then beads were washed with low salt lysis buffer and low salt buffer (10 mM Tris–HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% NP40, 0.5% Na-Deoxycholate), and DNA was eluted in elution buffer (50 mM Tris–HCl pH 8.0, 10 mM EDTA, 1% SDS) with Proteinase K (Yeasen, Shanghai, China, # 10401ES60) and RNase A (Thermo Fisher, Waltham, MA, #EN0531) in 65◦C for 4 h.
ChIP DNA libraries and input DNA samples were prepared as directed by the protocol of VAHTS Universal DNA Library Prep Kit for Illumina (Vazyme Biotech, Nanjing, China, #ND617-01) and Cut&Tag DNA libraries. were prepared by using HyperactiveTM In-Situ ChIP Library Prep Kit for Illumina (Vazyme Biotech, Nanjing, China, #TD901-01).

treatment_protocol: HASMC cells were treated with Ad-GFP or Ad-BACH1

value: human aortic smooth muscle cells

tag: antibody


title: Subject: S131-2046; Sample Day: Day 0 (V1) with respect to first vaccination; Replicate: 1

description:
S131-2046.V1
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.


title: HASMCs BACH1 H3K9me2-1

tag: cell type


title: Subject: S129-2043; Sample Day: Day 0 (V1) with respect to first vaccination; Replicate: 1

description:
S129-2043.V1
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.

tag: treatment group

value: Placebo


title: Subject: S129-2043; Sample Day: Day 97 (V7) with respect to first vaccination; Replicate: 1

description:
S129-2043.V7
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.

tag: etec colony pcr result at v1 (d0)


title: nc vector, rep3


title: SEDXX1_IV_50000000_Stimulated [STIM_11]

description:
integrated_object.rds
myeloid_object.rds
tnk_object.rds
cell_metadata.tsv
genes.tsv.gz
barcodes.tsv.gz
matrix.mtx.gz

tag: tissue

value: Bronchoalveolar lavage

value: IV


title: MBD3+ 48hrTam INPUT Rep 1

value: Mouse embryonic stem cells


title: 18319_NA_Naïve_Stimulated [STIM_10]

value: DGCT

value: Naïve


title: HASMCs Con H3K9me2-2

value: Ad-GFP


title: MBD3- NoTam INPUT Rep 3

source_name: MBD3- NoTam INPUT


title: MBD3+ ES cell population Hi-C rep1

source_name: MBD3+ ES cell population Hi-C


title: HASMCs Con H3K9me2-1


title: 18019_IV_100000_Stimulated [STIM_9]

value: DGGG

value: 14 weeks


title: Subject: S125-2040; Sample Day: Day 97 (V7) with respect to first vaccination; Replicate: 1

description:
S125-2040.V7
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.

value: 1/4 dose ETVAX®

value: Negative

tag: etec colony pcr result at v7 (d97)

value: Positive

tag: gender

value: Female


title: MBD3- NoTam INPUT Rep 2


title: SEDXX2_IV_50000000_Stimulated [STIM_12]

tag: nhp id

tag: time post-vaccination

value: 15 weeks

value: Tuberculin Protein Purified Derivative-Stimulated ("PPD-stimulated")


title: A549 cells, si-SF3B4, biol rep3

city: Jinan City

first: Tao

last: Li

address: No. 107, Wenhua West Road, Lixia District

institute: Qilu Hospital of Shandong University

data_processing:
Seqtk
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Seqtk (parameter- Quality limit: 0.01)
Trimmed sequence reads were mapped to GRCh38 using spliced mapping of Hisat2 (version:2.0.4) with default parameters.
Read count extraction and normalization were performed using Stringtie (version:1.3.0) and TMM (trimmed mean of M values) method.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: A549 cells were cultured in RPMI 1640 medium (Gibco, USA) with 10% of fetal bovine serum, 100 U/mL penicillin, and 100µg/mL streptomycin in an incubator at 37 °C,  5% CO2, 95% humidity.

extract_protocol:
Total RNA was extracted using MagBeads Total RNA Extraction Kit（Cat#T02-096) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer. 1.5 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina following manufacturer's protocols.

treatment_protocol: A549 cells were transfected with either SF3B4 siRNA or scramble siRNA were used for RNA-seq.

value: Non-Small Cell Lung Cancer Cells

value: SF3B6 knockdown

value: SF3B4 siRNA


title: 18219_IV_300000_Stimulated [STIM_8]

value: Bronchoalveolar lavage

value: DGJR

tag: vaccination route


title: MBD3- NoTam INPUT Rep 1

value: Mouse embryonic stem cells


title: Subject: S125-2040; Sample Day: Day 0 (V1) with respect to first vaccination; Replicate: 1

description:
S125-2040.V1
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.


title: A549 cells, si-SF3B4, biol rep2

value: SF3B5 knockdown


title: 18519_IV_300000_Stimulated [STIM_7]

value: DGHR

value: IV

tag: vaccination dose


title: MBD3+ 48hrTam SMC3 Rep 3

source_name: MBD3+ 48hrTam SMC3

value: Tamoxifen

tag: chip antibody

value: Smc3 (Abcam, ab9263)


title: 18419_IV_300000_Stimulated [STIM_6]

value: DGFT

value: 14 weeks

tag: treatment


title: A549 cells, si-SF3B4, biol rep1

tag: cell line

value: SF3B4 knockdown


title: MBD3+ 48hrTam SMC3 Rep 2

tag: background

tag: culture conditions


title: A549 cells, si-NC, biol rep2

tag: genotype

value: WT

value: NC siRNA


title: 18719_IV_100000_Stimulated [STIM_4]

value: HCZ

value: Tuberculin Protein Purified Derivative-Stimulated ("PPD-stimulated")


title: 18119_IV_300000_Stimulated [STIM_5]

value: DGFV


title: A549 cells, si-NC, biol rep1

value: Non-Small Cell Lung Cancer Cells


title: MBD3+ 48hrTam SMC3 Rep 1

tag: experiment conditions


title: MBD3- NoTam SMC3 Rep 3

source_name: MBD3- NoTam SMC3

tag: cell type


title: Subject: S107-2037; Sample Day: Day 0 (V1) with respect to first vaccination; Replicate: 1

description:
S107-2037.V1
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.

tag: treatment group

value: 1/8 dose ETVAX®

value: Negative

value: Positive

value: Female


title: 18619_IV_300000_Stimulated [STIM_3]

value: Bronchoalveolar lavage

value: HAR


title: Subject: S114-2034; Sample Day: Day 97 (V7) with respect to first vaccination; Replicate: 1

description:
S114-2034.V7
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.

value: 1/4 dose ETVAX®

tag: etec colony pcr result at v1 (d0)


title: Subject: S114-2034; Sample Day: Day 0 (V1) with respect to first vaccination; Replicate: 1

description:
S114-2034.V1
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.


title: Monocultured macrophages, rep_3

city: Beijing

first: Qi

last: Tang

address: Chengfu Road #292

institute: Peking University

data_processing:
Raw FASTQ data were filtered by TrimGalore v0.6.5 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Reads with a mapping quality score Q < 30 were removed.
Reference human genome (GRCh38.p13) and gene model annotation files were downloaded from Gencode. Paired-end clean reads were aligned to the reference genome using STAR v2.7.6a with default parameters
The mapped reads were then counted to different genes by featureCounts v1.6.3
The following analysis was performed with R v4.1.3 and Rstudio v1.4.1717. Reads of exon model per million mapped reads (RPM) and FPKM for individual genes were calculated using an in-house R code.
Differential gene expression was performed using DESeq2 v1.34.0. Genes with a p-value greater than 0.05 for the comparison between proximal or distal cells and monocultured cells were removed from subsequent analysis. PCA was performed with the FactoMineR package v2.4. K-means was conducted using the kmeans() function in base R. PCA of different samples and genes were performed by using the scaled log2RPM values and the scaled FPKM values as the input, respectively. GSEA was performed by the clusterProfiler v4.2.2.
Assembly: hCh38.p13
Supplementary files format and content: The output txt file after the FeatureCounts process.

source_name: THP1-derived macrophage

growth_protocol: For the coculture of HER2+ MDA cells and MΦ, THP-1 cells were passaged at the final concentration of 2 × 106 cells / mL and stimulated with 250 nM PMA. After 48 h of stimulation, the obtained MΦ were washed with PBS for 3 times. HER2+ MDA cells were dissociated and resuspended in RPMI1640 medium at the final concentration of 5 × 104 cells / mL. The resulting HER2+ MDA cells were added to the MΦ culture with a ratio of 1:40. After 24 h of coculture, the cells were subjected to QMID. Cell cocultures were incubated with 2 μg/mL ZHER-βGal in the culture medium at 37°C. After 30 min of incubation, the cells were washed with PBS for 3 times. Next, the cells were incubated with gFQM-biotin or gFMeQM-biotin at indicated concentrations for 10 min. The cells were washed once with PBS and dissociated with trypsin. The resulting cell suspension was stained with streptavidin-AF647 for 30 min in PBS. After 3 more washes with PBS, the cells were subjected to FACS.

extract_protocol:
Total RNA was extracted from FACS-isolated cells using TRIzolTM (Thermo) following the manufacturers’ instructions. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer (5X). First-strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure was ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with the AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers, and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library was sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: THP1-derived macrophage

value: macrophage

value: Monocultured


title: 17819_IV_600000_Stimulated [STIM_1]

tag: tissue

value: 14 weeks

value: IV


title: 17919_IV_100000_Stimulated [STIM_2]


title: Monocultured macrophages, rep_2

value: WT


title: A549 cells, si-NC, biol rep3

value: NC siRNA


title: Monocultured macrophages, rep_1


title: MBD3+ 48hrTam CTCF Rep 3

source_name: MBD3+ 48hrTam CTCF

value: Mouse embryonic stem cells

value: Tamoxifen

value: CTCF(Millipore, 07-729)


title: Distal macrophages, rep_3

value: Distal to HER2+MDA-MB-231 cell


title: MBD3- NoTam SMC3 Rep 1

value: Smc3 (Abcam, ab9263)


title: MBD3+ 48hrTam CTCF Rep 2


title: KSP-3

first: Hui

last: Wang

state: China

address: Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, China

department: School of Pharmacy

institute: Shanghai Jiao Tong University

data_processing:
Seqtk
Remove the linker sequence contained in the reads
Remove bases with a quality Q lower than 20 at the 3' end, that is, the base error rate is less than 0.01, where Q=-10logerror_ratio
Remove reads whose length is less than 25
Remove the ribosome RNA reads of the species to which they belong
Assembly: CHOK1GS_HDv1
Supplementary files format and content: xls files include count and FPKM values for each sample

organism: Cricetulus griseus

source_name: Ovary

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Cat# 74106, Qiagen) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, US).
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (Vazyme) following manufacturer's protocols.

value: Ovary

value: Chinese hamster ovary cells (CHO-S)

value: Monclonal cell line

value: human anti-PD-1 mAb (HC, LC) knock in

value: site-specific integration of human anti-PD-1 mAb (HC, LC) at C12orf35 site of CHO cells


title: Subject: S103-2031; Sample Day: Day 0 (V1) with respect to first vaccination; Replicate: 1

description:
S103-2031.V1
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.

value: 1/8 dose ETVAX®

value: Negative

tag: etec colony pcr result at v7 (d97)

value: Female


title: Subject: S107-2037; Sample Day: Day 97 (V7) with respect to first vaccination; Replicate: 1

description:
S107-2037.V7
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.

value: Positive

tag: gender


title: KSP-2


title: KSP-1


title: MBD3+ 48hrTam CTCF Rep 1


title: MBD3- NoTam CTCF Rep 3

source_name: MBD3- NoTam CTCF


title: Distal macrophages, rep_2

value: THP1-derived macrophage

value: macrophage


title: Subject: S095-2025; Sample Day: Day 97 (V7) with respect to first vaccination; Replicate: 1

description:
S095-2025.V7
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.


title: MBD3- NoTam SMC3 Rep 2


title: Subject: S095-2025; Sample Day: Day 0 (V1) with respect to first vaccination; Replicate: 1

description:
S095-2025.V1
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.


title: Subject: S104-2028; Sample Day: Day 97 (V7) with respect to first vaccination; Replicate: 1

description:
S104-2028.V7
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.

value: 1/4 dose ETVAX®


title: Distal macrophages, rep_1

value: WT


title: Subject: S104-2028; Sample Day: Day 0 (V1) with respect to first vaccination; Replicate: 1

description:
S104-2028.V1
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.


title: Subject: S103-2031; Sample Day: Day 97 (V7) with respect to first vaccination; Replicate: 1

description:
S103-2031.V7
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.


title: CD33-3

value: human CD33 knock in

value: site-specific integration of human CD33 at C12orf35 site of CHO cells


title: MBD3- NoTam CTCF Rep 2

value: Mouse embryonic stem cells

value: CTCF(Millipore, 07-729)


title: CD33-2

value: Ovary


title: MBD3- NoTam CTCF Rep 1


title: Proximal macrophages, rep_3

value: Proximal to HER2+MDA-MB-231 cell


title: Subject: S094-2022; Sample Day: Day 0 (V1) with respect to first vaccination; Replicate: 1

description:
S094-2022.V1
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.

value: Male


title: Proximal macrophages, rep_2


title: CD33-1

value: Chinese hamster ovary cells (CHO-S)

value: Monclonal cell line


title: Proximal macrophages, rep_1


title: CLL1-3

value: human CLL1 knock in

value: site-specific integration of human CLL1 at C12orf35 site of CHO cells


title: Subject: S087-2019; Sample Day: Day 0 (V1) with respect to first vaccination; Replicate: 1

description:
S087-2019.V1
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.

value: Placebo

value: Negative

value: Female


title: CLL1-2


title: H3K27ac_siArid1aplusEGF_rep2

first: Zhe

last: Zhang

address: Robert-Koch-Strasse 40

institute: University Medical Center, Goettingen

data_processing:
Single-end 50bp reads were aligned to mouse genome MGSCv37/mm9 by Bowtie2 (Version 2.3.4.2)
Low-quality reads (MAPQ < 5) and PCR duplicates were filtered out using Samtools
Peaks were called by MACS2 (Version 2.1.1.20160309.0) with the criteria as fold enrichment > 5 compared to background and FDR < 0.05
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated usign MACS2, scores represent enrichment of the peaks and all the peaks are with FDR<0.05
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage (Version 3.0.2)

source_name: Acinar cell line 266-6

growth_protocol: 266-6 murine pancreatic acinar cell line was established as described before (Korc et al., 1992). Cells were cultured in Dulbecco’s modified Eagle’s Medium containing 4.5 g/L D-Glucose, L- Glutamine supplemented with 10% fetal calf serum (FCS) at 37 ºC incubator with 5 % carbon dioxide supply.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27ac antibody. ChIP-seq samples were prepared in duplicates per condition.
Library for ChIP-seq was prepared using Microplex Library Preparation V2 following the manufacturer’s instruction. 0.5 ng double-stranded ChIP-DNA was utilized as start material, repaired into blunt ends and subsequently ligated with stem-loop adaptors. Libraries were amplified and size-selected by AMPure beads. Library quantification was performed using Agilent Bioanalyzer 2100. Finally, library was prepared as 2 nmol/L for sequencing.

treatment_protocol: Transient ARID1A knockdown was performed by siRNAs (25 nM) purchased from Dharmacon (ON-TARGETplus ARID1A siRNA J-017263-07-0005 and J-017263-08-0005) with non-targeting siRNA NT5 (Ambion, UGGUUUACAUGUCGACUAA) as control. Reverse transfection was conducted using Lipofectamine RNAiMAX transfection reagent (Invitrogen, Karlsruhe, Germany) according to the specified protocol and sustained for 48 hours. Prior to EGF stimulation (Sigma-Aldrich, 40ng/ml), cells were starved in serum-free medium overnight and then treated with EGF or the control vehicle 0.1% BSA for 8 hours.

value: Acinar cell

value: 40ng/ml EGF

value: H3K27ac (GeneTex, Cat# GTX128944)


title: CLL1-1


title: H3K27ac_siArid1a_rep2

value: 0.1 BSA


title: Subject: S087-2019; Sample Day: Day 97 (V7) with respect to first vaccination; Replicate: 1

description:
S087-2019.V7
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.

value: Positive


title: H3K27ac_siArid1a_rep1


title: Subject: S085-2016; Sample Day: Day 97 (V7) with respect to first vaccination; Replicate: 1

description:
S085-2016.V7
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.

value: 1/4 dose ETVAX®


title: Subject: S094-2022; Sample Day: Day 97 (V7) with respect to first vaccination; Replicate: 1

description:
S094-2022.V7
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.


title: H3K27ac_EGF_rep2


title: Subject: S085-2016; Sample Day: Day 0 (V1) with respect to first vaccination; Replicate: 1

description:
S085-2016.V1
anti-IgG antibody
plasma samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.