title: DSP.1001660039493.B.D08.dcc

description: Library name: DSP.1001660039493.B.D08.dcc

value: Hippocampus

tag: pmd

value: M


title: DSP.1001660039493.B.D11.dcc

status: Public on Aug 28 2025

type: SRA

city: London

first: Jack

last: Wood

state: County

address: Gower Street

department: Neuroscience, Physiology and Pharmacology

country: United Kingdom

institute: University College London

description: Library name: DSP.1001660039493.B.D11.dcc

library_source: transcriptomic

data_processing:
Demultiplex to FASTQ and convert to DCC with GeoMx NGS Pipeline/GUI.
Map oligo barcodes to human gene symbols using the GeoMx Human WTA PKC annotation.
AOI QC thresholds: ≥1,000 reads/AOI; ≥80% trimmed; ≥80% stitched; ≥75% aligned; ≥50% sequencing saturation. Failing AOIs were excluded.
Assembly: Gene identifiers derived from the GeoMx Human Whole Transcriptome (WTA) probe annotation (PKC file): Hs_R_NGS_WTA_v1.0.pkc
Supplementary files format and content: dcc/ - one .dcc file per AOI (barcode counts). dcc_stats/ - per-AOI .stats.txt files generated by GeoMx NGS.
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: Hippocampus

extract_protocol:
FFPE blocks were sectioned at 8 μm using a rotary microtome. Three of these tissue squares were mounted per SuperFrost Plus slide within the designated GeoMx scan area.
Slide preparation followed the standard GeoMx Slide Preparation protocol . Probe mic: GeoMx Whole Transcriptome Probe Mix. Library quality was verified on an Agilent TapeStation D1000. Sequencing was performed on an Illumina NextSeq 2000 (X-LEAP chemistry), paired-end.

tag: tissue

tag: cell type

value: Microglia

tag: treatment

value: A

tag: batch

tag: group

value: Non-AD

tag: age

tag: braak

tag: ph

tag: weight

tag: csf

tag: area

tag: slide

tag: apoe

tag: Sex

value: F


title: DSP.1001660039493.B.D09.dcc

description: Library name: DSP.1001660039493.B.D09.dcc

value: PP

value: AD


title: DSP.1001660039493.B.D06.dcc

description: Library name: DSP.1001660039493.B.D06.dcc


title: DSP.1001660039493.B.D05.dcc

description: Library name: DSP.1001660039493.B.D05.dcc


title: DSP.1001660039493.B.D07.dcc

description: Library name: DSP.1001660039493.B.D07.dcc


title: Z2KO_D0_ChIP_H3K4me3_rep1

city: Santander

first: Alvaro

last: Rada-Iglesias

state: Cantabria

address: Albert Einstein 22, PCTCAN

country: Spain

institute: Institute of Biomedicine and Biotechnology of Cantabria

description: Library name: Sample 21

library_source: genomic

data_processing:
ChIP-Seq data was generated for (i) transcription factors (TFs) (i.e. ZIC3) and (ii) different histone marks (H3K27me3, H3K27ac, H3K4me1, H3K4me2, H3K4me3) in WT and Zic2-/- cells. In addition, ChIP-seq data for ZIC2 was generated in Zic2FLAG-HA cells. For all ChIP-seq samples, reads quality control and removal of low quality regions and/or adapters was performed with fastqc, MultiQC and Trimmomatic. Regarding the ChIP-seq samples concerning TFs, reads were mapped to the mouse reference assembly (mm10) using Bowtie2. Subsequently, reads with a mapping quality below 10 and duplicated reads were discarded with Samtools. For each sample, a BigWig based on RPKM normalization was generated. Finally, for conditions in which multiple replicates were available (i.e. ZIC2 ChIPs), an average BigWig file was created using Wiggletools mean and bedGraphToBigWig tools, to be used as consensus/reference in the different visualizations/quantifications in which BigWig files were used. Regarding the ChIP-seq samples for histone marks, in order to handle the exogenous DNA (human) added to the samples during their preparation, and following published guidelines, reads were mapped to a mm10-hg19 concatenated genome using Bowtie2. Subsequently, reads with a mapping quality below 10 and duplicated reads were discarded with Samtools. Next, reads mapping to each of the genomes (mm10 and hg19) were identified using split_bam.py from Spiker (https://spiker. readthedocs.io/en/latest/index.html). The bam file with the reads mapping exclusively to mm10 was the only one considered for downstream analyses. ChIP BigWigs were generated applying a quantile normalization between samples of the same histone mark (e.g., H3K27ac) and differentiation time point (e.g., D3). Regarding the particularities to generate them, first, the mm10 genome was split in bins of 100 bps with bedtools makeWindows and the resulting coordinates were converted into saf (simplified annotation format) format, to be accepted as an annotation file in featureCounts. Next, for each sample, considering their bam file and the saf file, the number of reads in each of the 100 bp genome windows was counted with featureCounts. The resulting counts matrix was loaded in R where two main steps were applied. In the first one, read counts per bin were converted to RPKMs. Next, the resulting values were quantile normalized among samples using the function normalize.quantiles() from the preprocessCore package. Then, bedgraphs with the quantile normalized values per 100 bp window were generated and subsequently converted to BigWigs with the usage of UCSC bedGraphToBigWig tool. Finally, a reference BigWig file per condition was created averaging the information of the different replicates with Wiggletools mean and bedGraphToBigWig tools.
Assembly: mm10
Supplementary files format and content: BigWig

molecule: genomic DNA

organism: Mus musculus

source_name: Z2KO E14Tg2a mESC D0

growth_protocol: mESC maintenance and AntNPCs differentiation protocol. E14Tg2a (E14) mouse ESC were cultured on gelatin-coated plates using Knock-out DMEM (Life Technologies, 10829018) supplemented with 15% FBS (Life Technologies, 10082147), leukemia inhibitory factor (LIF), antifungal and antibiotics (Sigma-Aldrich, A5955), β-mercaptoethanol (ThermoFisher Scientific, 21985023), Glutamax (ThermoFisher Scientific, 35050038) and MEM NEAA (ThermoFisher Scientific, 11140035). Cells were cultured at 37°C with 5% CO2. For the AntNPC differentiation, mESCs were plated at 20.000 cells/cm2 on geltrex-coated plates (ThermoFisher, A1413302) and grown in N2B27 medium: Advanced Dulbecco’s Modified Eagle Medium F12 (Life Technologies, 21041025) and Neurobasal medium (Life Technologies,12348017) (1:1), supplemented with 1 × N2 (R&D Systems, AR009), 1 × B27 (Life Technologies, 12587010), 2mM l-glutamine (Life Technologies, 25030024) and 0.1 mM 2-mercaptoethanol (Life Technologies, 31350010)). During the six days of differentiation, the N2B27 medium was additionally supplemented with the following components: bFGF (ThermoFisher Scientific, PHG0368) 10 ng/ml from day 0 to day 2, Xav939 (Sigma-Aldrich, X3004-5MG) 5 µM from day 2 to day 6, BSA (ThermoFisher Scientific, 15260037) 1 mg/ml at day 0 and 40 µg/mL the remaining days.

extract_protocol:
For TF ChIPs (ZIC2, ZIC3), one confluent 10 cm plate (~40–50 × 106 cells) was used; for histone mark ChIPs, 1/5 of a 10 cm plate was used (~10 × 106 cells). Cells were cross-linked directly on the tissue culture plate in 1% formaldehyde (Sigma-Aldrich, 252549-100ML) for 10 min at room temperature, followed by quenching with 0.125M Glycine (Sigma-Aldrich, G8898-1KG) during 5–10 min. After two washes with 1X PBS supplemented with cOmpleteª Protease Inhibitor ULTRA Tablets (SigmaAldrich, 5892791001), cell pellets were snap-frozen and stored at –80°C prior to use. Chromatin was extracted by sequential re-suspension in three lysis buffers (Lysis Buffer 1: 50 mM Hepes (pH 7.5), 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.2% TX-100, dH20 ;Lysis Buffer 2: 10 mM Tris pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, dH20; Lysis Buffer 3: 10 mM Tris pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, dH20), followed by centrifugation (5 min, 1350 g, 4 °C) between steps. Chromatin was sonicated using an EpiShear Probe Sonicator (Active Motif, 53052) under the following conditions: • Histone marks: 30% amplitude, 20 sec on / 30 sec off, 10 min total. • Transcription factors: 35% amplitude, 20 sec on / 30 sec off, 4 min 40 sec total. These conditions aimed to obtain chromatin with sizes 200-500 bp for histone ChIPs and 500-1000 bp for TF ChIPs. After sonication, samples were cleared by centrifugation (10 min, 16000 g, 4 °C), and supernatants were aliquoted. Each aliquot was incubated overnight at 4 °C with 3–5 µg antibody (for histone marks) or 10 µg (for TFs). A 10% aliquot was reserved as input control. The next day, pre-blocked Dynabeads™ Protein G (Thermo Fisher Scientific, 10004D) were added (100 µl for TFs; 75 µl for histone marks) and incubated for 4 h at 4 °C. Beads were washed five times with RIPA buffer (50 mM Hepes pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate, dH2O) and once with TE buffer containing 50 mM NaCl (Sigma-Aldrich, S9888). Chromatin was eluted from the beads by heating at 65°C with occasional vortex. After this, crosslinking was reversed by overnight incubation at 65°C. DNA was purified using DNA Clean & Concentrator kit (Zymo Research, D4034) for inputs and ChIP DNA Clean & Concentrator kit (Zymo Research, D5205) for ChIP samples. Purified DNA concentration was measured with a Qubit 4 Fluorimeter (Thermo Fisher Scientific, Q33238) using the Qubit™ dsDNA HS Assay Kit (Thermo Scientific, Q32854) for ChIP DNA, and the Qubit™ dsDNA BR Assay Kit (Thermo Scientific, Q32853) for input samples.
Libraries were prepared for the ChIP and input samples from D0, D3, and D6 by Macrogen Inc. (Korea) using the Illumina TruSeq ChIP-seq protocol. Libraries were sequenced (paired-end 150 bp, 40M reads/sample) on a NovaSeq6000 platform.

treatment_protocol: Zic2 and Zic3 deletions using CRISPR-Cas9.Pairs of sgRNAs were designed to flank Zic2 coding region using Benchling’s genome engineering toolbox (https://www. benchling.com/). Guides were selected for high on target efficiency and minimal off target potential. Complementary oligonucleotides containing BbsI (NEB, R0539L) overhangs were synthesized and annealed (see Supplementary Data 4) by heating to 95°C for 5 min, followed by gradual cooling down to 25°C at -5 °C/min. Annealed oligos were ligated into BbsI-digested pX330A-hCas9-longchimeric-gRNA-G2P vector using T4 DNA ligase (NEB, M0202L) and transformed into chemically competent E. coli (TOP10) via heat shock. Colonies were plated on LB-ampicillin agar and screened by colony PCR to confirm the presence of the desired insert (see Colony PCR section). Plasmids were purified using the NZY Miniprep Kit (NZYTech, MB01001) and verified by Sanger sequencing using the pX330A_R reverse primer (see Supplementary Data 4). Verified clones were stored as glycerol stocks at -140°C. mESCs were plated on gelatin-coated 12- or 6-well plates and co-transfected with Lipofectamine 3000 transfection reagent (Thermo Fisher Scientific, L3000001) and one or two sgRNA-expressing pX330A vectors. For 12-well plates, 150.000 mESC were transfected with 1.5 µl of Lipofectamine 3000. Transfection efficiency was assessed via GFP fluorescence 24 h later. Cells with 70–90% transfection efficiency underwent puromycin (Sigma-Aldrich, P8833-25MG) selection (2 µg puromycin/ml during 48 h). Puromycin-resistant cells were serially diluted and plated in 96-well plates for clonal expansion. After 10–12 days, individual colonies were split into duplicate wells: one for gDNA extraction and PCR based genotyping and another for expansion and maintenance of each clone. Positive knock-out mESC clones were expanded and cryopreserved at -140 °C for future use.Genomic insertions by CRISPR-Cas9-mediated homology directed repair (HDR). To generate the DNA double strand break that would favour a genomic insertion through homology directed repair (HDR), a single gRNA was designed in order to cut as close as possible to the insertion site according to the instructions of the genome engineering toolbox from Benchling (https://www.benchling.com/). The steps followed for the design were the same as the ones described previously. In order to introduce the desired insertion, a ssDNA repair template was designed and synthesized as an Ultramer™ (for fragments up to 200 bp; IDT) or as a Megamer™ (for fragments up to 500 bp; IDT). The repair template contained the sequence of the epitope (i.e. Flag-HA, FKBPV36-HA) flanked with two homology arms, complementary to the sequences upstream and downstream of the gRNA-Cas9 cutting site. mESC were transfected as described above, including the ssDNA sequence as an additional component of the transfection reactions. Subsequent steps to derive mESC clonal lines with the desired genomic insertion were as the ones described for genomic deletions.

tag: cell line

value: Z2KO E14Tg2a mESC D0

tag: genotype

value: Culture in S+LIF; H3K4me3 antibody (Active Motif, 39159)


title: DSP.1001660039493.B.E06.dcc

description: Library name: DSP.1001660039493.B.E06.dcc

tag: pmd


title: DSP.1001660039493.B.D03.dcc

description: Library name: DSP.1001660039493.B.D03.dcc

tag: tissue


title: Z2KO_D0_ChIP_H3K4me1_rep1

description: Library name: Sample 17

value: Culture in S+LIF; H3K4me1 antibody (Active Motif, 39297)


title: WT_D0_ChIP_H3K27me3_rep1

description: Library name: Sample 14

source_name: E14Tg2a mESC D0

value: E14Tg2a mESC D0

value: WT

value: Culture in S+LIF; H3K27me3 antibody (Active Motif, 39155)


title: WT_D0_ChIP_H3K27ac_rep2

description: Library name: Sample 13

value: Culture in S+LIF; H3K27ac antibody (Active Motif, 39133)


title: Z2KO_D0_ChIP_H3K27me3_rep2

description: Library name: Sample 26


title: Z2KO_D0_ChIP_H3K4me2_rep1

description: Library name: Sample 19

value: Culture in S+LIF; H3K4me2 antibody (Active Motif, 39141)


title: DSP.1001660039493.B.D02.dcc

description: Library name: DSP.1001660039493.B.D02.dcc

tag: cell type

value: P


title: DSP.1001660039493.B.D01.dcc

description: Library name: DSP.1001660039493.B.D01.dcc

value: Hippocampus

tag: treatment


title: DSP.1001660039493.B.D04.dcc

description: Library name: DSP.1001660039493.B.D04.dcc

tag: batch

value: M


title: WT_D0_ChIP_H3K27ac_rep1

description: Library name: Sample 12


title: Z2KO_D0_ChIP_H3K4me1_rep2

description: Library name: Sample 18


title: WT_D0_ChIP_H3K4me3_rep2

description: Library name: Sample 11


title: DSP.1001660039493.B.C11.dcc

description: Library name: DSP.1001660039493.B.C11.dcc

value: Microglia

tag: group

value: CU-AP


title: WT_D0_ChIP_H3K4me3_rep1

description: Library name: Sample 10


title: DSP.1001660039493.B.C10.dcc

description: Library name: DSP.1001660039493.B.C10.dcc

value: A

tag: age


title: WT_D0_ChIP_H3K4me2_rep2

description: Library name: Sample 9


title: WT_D0_ChIP_H3K4me2_rep1

description: Library name: Sample 8


title: DSP.1001660039493.B.C09.dcc

description: Library name: DSP.1001660039493.B.C09.dcc

tag: braak


title: Z2KO_D0_Input_HistoneMarks_rep1

description: Library name: Sample 16

value: Culture in S+LIF; no antibody


title: DSP.1001660039493.B.C08.dcc

description: Library name: DSP.1001660039493.B.C08.dcc

tag: ph


title: DSP.1001660039493.B.C07.dcc

description: Library name: DSP.1001660039493.B.C07.dcc

value: PP

tag: weight


title: WT_D0_ChIP_H3K4me1_rep1

description: Library name: Sample 6


title: Z2KO_D0_ChIP_ZIC3_rep1

description: Library name: Sample 4

value: Culture in S+LIF; ZIC3 antibody (Abcam, ab222124)


title: DSP.1001660039493.B.C04.dcc

description: Library name: DSP.1001660039493.B.C04.dcc

value: AD

tag: csf

value: F


title: DSP.1001660039493.B.C06.dcc

description: Library name: DSP.1001660039493.B.C06.dcc

tag: area


title: WT_D0_ChIP_H3K27me3_rep2

description: Library name: Sample 15


title: Z2KO_D0_Input_ZIC3_rep1

description: Library name: Sample 3


title: WT_D0_ChIP_H3K4me1_rep2

description: Library name: Sample 7

value: Culture in S+LIF; H3K4me1 antibody (Active Motif, 39297)


title: DSP.1001660039493.B.C05.dcc

description: Library name: DSP.1001660039493.B.C05.dcc

tag: slide


title: Aorta, Tagln Cre +, Rep 3

city: Philadelphia

first: Ryan

middle: Patrick

last: Calhoun

state: PA

address: 3400 Civic Center Boulevard

country: USA

institute: University of Pennsylvania

description:
Library name: KO_T3
KO_T3

data_processing:
The raw fastq files were first analyzed with FastQC (version 0.11.9) for quality control checks. The paired-end reads were mapped to the GRCm39 Ensembl reference transcriptome for Mus musculus using kallisto (version 0.44.0).
The abdundance.tsv files generated by kallisto were read into R (version 4.3.0) at the gene level using the tximport package (version 1.28.0).
Raw counts were batch corrected using Combat_Seq from the package sva (version 3.35.2) and processed using edgeR (version 3.42.4) to obtain library scaled CPM TMM normalized data for visualizations.
Limma (version 3.56.2) was used for differential gene expression analysis on the raw un-batch corrected counts where condition and run were specified in the model matrix.
Genes with an adjusted p-value less than 0.05 were considered significant.
Assembly: GRCm39
Supplementary files format and content: Kallisto output abundance file for each samples tab-separated values
Supplementary files format and content: Raw counts read without any corrections done to the expression matrix as a tab-separated values
Supplementary files format and content: Raw counts batch corrected with a batch correction performed to the expression matrix
Supplementary files format and content: Batch corrected log2 counts per million expression with a trimmed-mean of M-values normalization

source_name: Cleaned Aorta

extract_protocol:
The aorta was isolated, freed of PVAT and adventitia, cut open and the endothelial layer was gently brushed off. RNA was then isolated using the PicoPure RNA isolation kit (ThermoFisher).
Next-generation sequencing (NGS) using Illumina NGS technology was generated by Genewiz using the NovaSeq 6000 analyzer and library construction was performed according to manufacturer’s specifcations by Genewiz

value: Cleaned Aorta

tag: strain

tag: floxed allele

value: Prdm16 fl/fl

value: male

tag: tamoxifen status

value: 12 weeks

tag: cre status

value: Tagln Cre

tag: samples grouped

tag: sequencing run


title: DSP.1001660039493.B.C12.dcc

description: Library name: DSP.1001660039493.B.C12.dcc

tag: tissue

tag: cell type

tag: pmd

tag: apoe

tag: Sex


title: WT_D0_Input_ZIC3_rep1

description: Library name: Sample 1

tag: cell line

value: E14Tg2a mESC D0

tag: genotype

value: WT

tag: treatment


title: DSP.1001660039493.B.B10.dcc

description: Library name: DSP.1001660039493.B.B10.dcc

value: Hippocampus

tag: batch

tag: group

tag: age

tag: braak

tag: ph

tag: weight

tag: csf


title: DSP.1001660039493.B.C03.dcc

description: Library name: DSP.1001660039493.B.C03.dcc

value: Microglia

tag: area

tag: slide


title: Aorta, Tagln Cre +, Rep 2

description:
Library name: KO_T2
KO_T2

tag: tissue

tag: strain

tag: floxed allele

tag: tamoxifen status

tag: cre status

tag: samples grouped

tag: sequencing run


title: DSP.1001660039493.B.B11.dcc

description: Library name: DSP.1001660039493.B.B11.dcc

tag: cell type

tag: treatment

value: P

tag: pmd

tag: apoe

tag: Sex


title: DSP.1001660039493.B.B12.dcc

description: Library name: DSP.1001660039493.B.B12.dcc

tag: batch

tag: group

tag: age

tag: braak

tag: ph


title: Aorta, Tagln Cre +, Rep 4

description:
Library name: KO_T4
KO_T4

tag: tissue


title: WT_D0_ChIP_ZIC3_rep1

description: Library name: Sample 2

tag: cell line

tag: genotype


title: DSP.1001660039493.B.C01.dcc

description: Library name: DSP.1001660039493.B.C01.dcc

tag: weight

tag: csf

tag: area

tag: slide


title: Aorta, Tagln Cre +, Rep 1

description:
Library name: KO_T1
KO_T1

tag: strain

tag: floxed allele

tag: tamoxifen status

tag: cre status

tag: samples grouped

tag: sequencing run


title: Aorta, Tagln Cre +, Rep 5

description:
Library name: KO_T5
KO_T5

tag: Sex


title: DSP.1001660039493.B.C02.dcc

description: Library name: DSP.1001660039493.B.C02.dcc

tag: cell type

tag: treatment

tag: batch

tag: group

tag: age

tag: pmd

tag: apoe


title: DSP.1001660039493.B.B09.dcc

description: Library name: DSP.1001660039493.B.B09.dcc

tag: tissue

value: A

value: CU-AP

tag: braak

tag: ph

tag: weight

tag: csf


title: DSP.1001660039493.B.B07.dcc

description: Library name: DSP.1001660039493.B.B07.dcc

value: PP

tag: area

tag: slide


title: Aorta, Tagln Cre -, Rep 5

description:
Library name: Ctrl_T5
Ctrl_T5

tag: strain

tag: floxed allele

tag: tamoxifen status

tag: cre status

value: No Cre

tag: samples grouped


title: DSP.1001660039493.B.B08.dcc

description: Library name: DSP.1001660039493.B.B08.dcc

tag: cell type

tag: treatment

tag: batch

tag: Sex


title: Aorta, Tagln Cre -, Rep 3

description:
Library name: Ctrl_T3
Ctrl_T3

tag: age

tag: sequencing run


title: DSP.1001660039493.B.B06.dcc

description: Library name: DSP.1001660039493.B.B06.dcc

tag: tissue

tag: group

tag: braak

tag: pmd

tag: apoe


title: Aorta, Tagln Cre -, Rep 4

description:
Library name: Ctrl_T4
Ctrl_T4


title: DSP.1001660039493.B.B05.dcc

description: Library name: DSP.1001660039493.B.B05.dcc

tag: ph

tag: weight

tag: csf

tag: area

tag: slide


title: Aorta, Tagln Cre -, Rep 2

description:
Library name: Ctrl_T2
Ctrl_T2

tag: strain

tag: floxed allele

tag: tamoxifen status

tag: cre status

tag: samples grouped


title: WT_D0_Input_HistoneMarks_rep1

description: Library name: Sample 5

tag: cell line

tag: genotype

tag: treatment

value: Culture in S+LIF; no antibody


title: Aorta, Tagln Cre -, Rep 1

description:
Library name: Ctrl_T1
Ctrl_T1

tag: tissue

tag: Sex

tag: age

tag: sequencing run


title: Aorta, Tamoxifen Treated, Myh11 CreER -, Rep 3

description:
Library name: Ctrl_M3
Ctrl_M3


title: DSP.1001660039493.B.B02.dcc

description: Library name: DSP.1001660039493.B.B02.dcc

tag: cell type

tag: batch

tag: group

value: AD

tag: braak

tag: pmd

tag: ph

tag: apoe

value: M


title: DSP.1001660039493.B.B03.dcc

description: Library name: DSP.1001660039493.B.B03.dcc

tag: weight

tag: csf

tag: area

tag: slide


title: DSP.1001660039493.B.B04.dcc

description: Library name: DSP.1001660039493.B.B04.dcc

value: F


title: Aorta, Tamoxifen Treated, Myh11 CreER -, Rep 2

description:
Library name: Ctrl_M2
Ctrl_M2

value: Cleaned Aorta

tag: strain

tag: floxed allele

value: Prdm16 fl/fl

tag: tamoxifen status

tag: cre status

tag: samples grouped


title: DSP.1001660039493.B.B01.dcc

description: Library name: DSP.1001660039493.B.B01.dcc

tag: tissue

tag: treatment

tag: age

tag: Sex


title: Aorta, Tamoxifen Treated, Myh11 CreER + , Rep 3

description:
Library name: KO_M3
KO_M3

value: male

value: 12 weeks

value: Myh11 CreERT2

tag: sequencing run


title: Aorta, Tamoxifen Treated, Myh11 CreER -, Rep 1

description:
Library name: Ctrl_M1
Ctrl_M1


title: DSP.1001660039493.B.A09.dcc

description: Library name: DSP.1001660039493.B.A09.dcc

tag: cell type

tag: batch

tag: group

tag: braak

tag: pmd


title: DSP.1001660039493.B.A10.dcc

description: Library name: DSP.1001660039493.B.A10.dcc

tag: ph

tag: weight

tag: csf

tag: area

tag: apoe


title: Aorta, Tamoxifen Treated, Myh11 CreER +, Rep 2

description:
Library name: KO_M2
KO_M2

tag: strain

tag: floxed allele

tag: tamoxifen status

tag: cre status


title: DSP.1001660039493.B.A07.dcc

description: Library name: DSP.1001660039493.B.A07.dcc

tag: tissue

tag: treatment

tag: age

tag: slide


title: Aorta, Tamoxifen Treated, Myh11 CreER +, Rep 1

description:
Library name: KO_M1
KO_M1

tag: Sex

tag: samples grouped

tag: sequencing run


title: DSP.1001660039493.B.A08.dcc

description: Library name: DSP.1001660039493.B.A08.dcc

tag: cell type

tag: batch

tag: group

tag: braak

tag: pmd


title: DSP.1001660039493.B.A06.dcc

description: Library name: DSP.1001660039493.B.A06.dcc

tag: ph

tag: weight

tag: csf

tag: area

tag: apoe


title: DSP.1001660039493.B.A05.dcc

description: Library name: DSP.1001660039493.B.A05.dcc

tag: tissue


title: Placebo rep 1

city: Seoul

first: Mi-Ock

last: Lee

address: 1 Gwanak-ro

department: College of Pharmacy

country: South Korea

institute: Seoul National University

description:
Library name: Sample 1
10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw BCL files were demultiplexed into FASTQ format using Cell Ranger v8.0.1 (10x Genomics), and reads were aligned to the mouse reference genome (mm10-2020-A) using the cellranger count pipeline, which also performed UMI quantification and cell barcode filtering.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: lung

extract_protocol:
Two mice at 13-weeks-old in each tamoxifen (5-weeks of 5 mg, 60-day release pellet) (Innovative Research of America, SE-361) or placebo pellet (SE-111) inoculated PyMT group were used. Lung tissues were perfused and subsequently inflated via a catheter in the trachea by an enzyme mix containing dispase (2.2 U/mL), collagenase (2 mg/mL), elastase (1 mg/mL), and DNase (5 U/mL). After tying off the trachea, the lung was removed and immediately minced to small pieces. The tissue was transferred into enzyme mix for enzymatic digestion for 30 min at 37°C. After enzyme activity was stopped by adding DMEM/F12 supplemented with 10% FBS, dissociated cells in suspension were passed through a 70 μm strainer and centrifuged at 500 × g for 5 min at 4 °C. The cells were counted using a hematocytometer and assessed for single-cell separation and viability.
Single-cell suspensions were processed using the 10x Genomics Chromium Single Cell 5' Gene Expression assay (R2-only chemistry), following the manufacturer's protocol. Barcoded cDNA libraries were generated and sequenced on an Illumina NovaSeq 6000 platform.

value: lung

tag: strain

value: FVB/NJ

value: whole lung cells

value: 13 weeks old

value: female

tag: treatment

value: Negative (vehicle) control


title: DSP.1001660039493.B.A03.dcc

description: Library name: DSP.1001660039493.B.A03.dcc

value: Hippocampus

value: Microglia

value: A

value: CU-AP

tag: age

tag: slide


title: Tamoxifen rep 2

description:
Library name: Sample 4
10x Genomics

tag: Sex

value: Tamoxifen


title: DSP.1001660039492.A.H11.dcc

description: Library name: DSP.1001660039492.A.H11.dcc

value: AD

value: F


title: Th17p_WT3_S15

city: CAMBRIDGE

first: Jacques

last: Deguine

state: Massachusetts

address: 415 Main Street, 415M-7175 - Xavier lab

department: Immunology Program

institute: Broad Institute

description: Library name: Th17p_WT3_S15

data_processing:
Sequencing data was processed with the “atacseq” pipeline v1.2.1 using default parameters (https://nf-co.re/atacseq/1.2.1) from the nf-core workflows (Ewels et al.). The pipeline is briefly summarized below.
First step: Demultiplexing, QC and adapter removal (TrimGalore)
Second step: Alignment (bwa) and merging/filtering (picard, SAMtools, BAMtools)
Third step: Peak calling (MACS2) and differential accessibilty (DESeq2)
Assembly: GRCm38
Supplementary files format and content: Pile-up deposited as aggregated bigWig file for each condition (genotype x treatment)

source_name: T cell

extract_protocol:
Cells were lysed with 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin, and nuclei were transposed with 100 nM Tn5 for 30 minutes at 37°C in a thermomixer.
Reactions were cleaned up with Zymo DNA Clean and Concentrator 5 columns and pre-amplified for 5 cycles following the Omni-ATAC protocol (Corces et al.). 5 μL of the pre-amp reaction was used to determine final cycle numbers by qRT-PCR (with a target cycle number N reaching 1/3 linear amplification minus ~1 cycle), and the rest of the product was amplified for N cycles.

treatment_protocol: Naïve CD4+ T cells were isolated by using EasySep Mouse Naïve CD4+ T Cell isolation Kit and 1 million/mL of cells was cultured in 2 μg/mL anti-CD3/anti-CD28-coated 96-well plates under different cytokine conditions for 3 days: Th0: no added cytokines, Th17n: 25ng/mL IL-6 and 2ng/mL TGF-b1, Th17p: 25ng/mL IL-6 and 20ng/mL IL-1b and 20ng/mL IL-23. Cells were harvested on day 3, dead cell removal was performed with the EasySep Dead Cell Removal (Annexin V) Kit , and 6,000 cells were frozen in 180 μL Bambanker.

value: T cell

tag: genotype

tag: animal


title: Placebo rep 2

description:
Library name: Sample 2
10x Genomics

tag: cell type


title: DSP.1001660039493.B.A04.dcc

description: Library name: DSP.1001660039493.B.A04.dcc

tag: batch

tag: group

value: M


title: Th17p_WT3_S33

description: Library name: Th17p_WT3_S33


title: DSP.1001660039493.B.A02.dcc

description: Library name: DSP.1001660039493.B.A02.dcc

tag: braak

tag: pmd


title: Th17p_WT2_S32

description: Library name: Th17p_WT2_S32


title: DSP.1001660039492.A.H10.dcc

description: Library name: DSP.1001660039492.A.H10.dcc

value: Non-AD

tag: ph

tag: weight


title: Th17p_WT1_S31

description: Library name: Th17p_WT1_S31


title: Th17p_WT2_S14

description: Library name: Th17p_WT2_S14


title: Th17p_WT1_S13

description: Library name: Th17p_WT1_S13


title: DSP.1001660039492.A.H07.dcc

description: Library name: DSP.1001660039492.A.H07.dcc

tag: csf

tag: area


title: DSP.1001660039492.A.H08.dcc

description: Library name: DSP.1001660039492.A.H08.dcc

tag: tissue

tag: apoe


title: DSP.1001660039492.A.H06.dcc

description: Library name: DSP.1001660039492.A.H06.dcc

tag: treatment


title: Th17p_KO3_S36

description: Library name: Th17p_KO3_S36


title: DSP.1001660039492.A.H05.dcc

description: Library name: DSP.1001660039492.A.H05.dcc

tag: age


title: Tamoxifen rep 1

description:
Library name: Sample 3
10x Genomics

tag: strain


title: Th17p_KO2_S17

description: Library name: Th17p_KO2_S17


title: DSP.1001660039492.A.H04.dcc

description: Library name: DSP.1001660039492.A.H04.dcc

tag: slide

tag: Sex


title: DSP.1001660039492.A.H03.dcc

description: Library name: DSP.1001660039492.A.H03.dcc


title: Th17p_KO1_S34

description: Library name: Th17p_KO1_S34

tag: genotype

tag: animal


title: DSP.1001660039492.A.G12.dcc

description: Library name: DSP.1001660039492.A.G12.dcc

tag: cell type

tag: batch


title: DSP.1001660039492.A.G11.dcc

description: Library name: DSP.1001660039492.A.G11.dcc

value: PP

tag: group

tag: braak


title: Th17n_WT3_S9

description: Library name: Th17n_WT3_S9


title: DSP.1001660039492.A.G09.dcc

description: Library name: DSP.1001660039492.A.G09.dcc

tag: pmd

tag: ph


title: Th17n_WT3_S27

description: Library name: Th17n_WT3_S27


title: DSP.1001660039492.A.G08.dcc

description: Library name: DSP.1001660039492.A.G08.dcc

value: P

tag: weight

tag: csf


title: Th17n_WT2_S8

description: Library name: Th17n_WT2_S8


title: DSP.1001660039492.A.G06.dcc

description: Library name: DSP.1001660039492.A.G06.dcc

tag: tissue

tag: area


title: Th17n_WT2_S26

description: Library name: Th17n_WT2_S26

tag: treatment


title: Th17n_KO3_S12

description: Library name: Th17n_KO3_S12


title: Th17n_KO3_S30

description: Library name: Th17n_KO3_S30


title: DSP.1001660039492.A.G04.dcc

description: Library name: DSP.1001660039492.A.G04.dcc

tag: age

tag: apoe


title: DSP.1001660039492.A.G03.dcc

description: Library name: DSP.1001660039492.A.G03.dcc

tag: slide


title: DSP.1001660039492.A.G02.dcc

description: Library name: DSP.1001660039492.A.G02.dcc

tag: Sex


title: Th17n_WT1_S25

description: Library name: Th17n_WT1_S25

tag: genotype


title: Th17n_KO2_S29

description: Library name: Th17n_KO2_S29

tag: animal


title: DSP.1001660039492.A.G01.dcc

description: Library name: DSP.1001660039492.A.G01.dcc

tag: cell type


title: Th17p_KO2_S35

description: Library name: Th17p_KO2_S35


title: Th17p_KO3_S18

description: Library name: Th17p_KO3_S18


title: Th17p_KO1_S16

description: Library name: Th17p_KO1_S16


title: Th17n_KO2_S11

description: Library name: Th17n_KO2_S11


title: Th17n_KO1_S10

description: Library name: Th17n_KO1_S10


title: Th0_WT3_S3

description: Library name: Th0_WT3_S3


title: DSP.1001660039492.A.F12.dcc

description: Library name: DSP.1001660039492.A.F12.dcc

tag: batch


title: DSP.1001660039492.A.G10.dcc

description: Library name: DSP.1001660039492.A.G10.dcc

tag: group


title: DSP.1001660039492.A.F10.dcc

description: Library name: DSP.1001660039492.A.F10.dcc

tag: braak


title: DSP.1001660039492.A.F11.dcc

description: Library name: DSP.1001660039492.A.F11.dcc

tag: pmd


title: Th17n_KO1_S28

description: Library name: Th17n_KO1_S28


title: DSP.1001660039492.A.F08.dcc

description: Library name: DSP.1001660039492.A.F08.dcc

tag: ph


title: DSP.1001660039492.A.G07.dcc

description: Library name: DSP.1001660039492.A.G07.dcc

tag: weight


title: Th17n_WT1_S7

description: Library name: Th17n_WT1_S7


title: DSP.1001660039492.A.F07.dcc

description: Library name: DSP.1001660039492.A.F07.dcc

tag: csf


title: Th0_WT3_S21

description: Library name: Th0_WT3_S21


title: Th0_WT1_S1

description: Library name: Th0_WT1_S1


title: DSP.1001660039492.A.F06.dcc

description: Library name: DSP.1001660039492.A.F06.dcc

tag: tissue


title: DSP.1001660039492.A.G05.dcc

description: Library name: DSP.1001660039492.A.G05.dcc

tag: area


title: Th0_WT2_S2

description: Library name: Th0_WT2_S2

tag: treatment


title: DSP.1001660039492.A.F04.dcc

description: Library name: DSP.1001660039492.A.F04.dcc

tag: age


title: DSP.1001660039492.A.F05.dcc

description: Library name: DSP.1001660039492.A.F05.dcc

tag: apoe


title: DSP.1001660039492.A.F03.dcc

description: Library name: DSP.1001660039492.A.F03.dcc

tag: slide


title: DSP.1001660039492.A.F02.dcc

description: Library name: DSP.1001660039492.A.F02.dcc

tag: Sex


title: Th0_WT1_S19

description: Library name: Th0_WT1_S19

tag: genotype


title: Th0_KO2_S5

description: Library name: Th0_KO2_S5

tag: animal


title: DSP.1001660039492.A.F01.dcc

description: Library name: DSP.1001660039492.A.F01.dcc

tag: cell type


title: Th0_KO2_S23

description: Library name: Th0_KO2_S23


title: Th0_KO3_S6

description: Library name: Th0_KO3_S6


title: DSP.1001660039492.A.E12.dcc

description: Library name: DSP.1001660039492.A.E12.dcc

tag: batch


title: Th0_KO1_S4

description: Library name: Th0_KO1_S4


title: Th0_KO1_S22

description: Library name: Th0_KO1_S22


title: DSP.1001660039492.A.E11.dcc

description: Library name: DSP.1001660039492.A.E11.dcc

tag: group


title: Tir1.rep9

city: Princeton

first: Yuri

last: Pritykin

state: NJ

address: 245 Carl Icahn Lab

department: QCB

institute: Princeton

description: Library name: mouse09_IGO_17450_9_1

data_processing:
RNA-seq was aligned to mm39 with bowtie2 and read counts were calculated using FeatureCounts. Differential gene expression was calculated using DESeq2
Assembly: mm39
Supplementary files format and content: Counts matrices, .tsv

source_name: Spleen & Lymph nodes

extract_protocol:
RNA extraction was  performed according to the manufacturer’s instructions. Briefly, phase separation in cells lysed in 1mL TRIzol Reagent was induced with 200 µL chloroform. RNA was extracted from 350 µL of the aqueous phase using the miRNeasy Micro Kit (Qiagen catalog # 217084) on the QIAcube Connect (Qiagen) according to the manufacturer’s protocol. Samples were eluted in 15-18 µL RNase-free water.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 1-2 ng total RNA with RNA integrity numbers ranging from 5.5 to 9.3 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification. 4.5-8 ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Roche 07962363001) using 8 cycles of PCR.

value: Spleen & Lymph nodes

value: Treg

value: Foxp3-AID ROSA26-TIR1(F74G)

value: 5-ph-IAA 14 Days


title: DSP.1001660039492.A.E09.dcc

description: Library name: DSP.1001660039492.A.E09.dcc

tag: braak


title: DSP.1001660039492.A.F09.dcc

description: Library name: DSP.1001660039492.A.F09.dcc

tag: pmd


title: Th0_WT2_S20

description: Library name: Th0_WT2_S20


title: Tir1.rep10

description: Library name: mouse10_IGO_17450_10_1


title: DSP.1001660039492.A.E10.dcc

description: Library name: DSP.1001660039492.A.E10.dcc

tag: ph


title: DSP.1001660039492.A.E08.dcc

description: Library name: DSP.1001660039492.A.E08.dcc

tag: weight


title: Tir1.rep8

description: Library name: mouse08_IGO_17450_8_1


title: DSP.1001660039492.A.E07.dcc

description: Library name: DSP.1001660039492.A.E07.dcc

tag: csf


title: Tir1.rep7

description: Library name: mouse07_IGO_17450_7_1

tag: tissue


title: Th0_KO3_S24

description: Library name: Th0_KO3_S24


title: DSP.1001660039492.A.E06.dcc

description: Library name: DSP.1001660039492.A.E06.dcc

tag: area


title: DSP.1001660039492.A.E05.dcc

description: Library name: DSP.1001660039492.A.E05.dcc

tag: treatment


title: Tir1.rep5

description: Library name: mouse05_IGO_17450_5_1


title: DSP.1001660039492.A.E04.dcc

description: Library name: DSP.1001660039492.A.E04.dcc

tag: age


title: WT.rep3

description: Library name: mouse03_IGO_17450_3_1

value: Foxp3-AID ROSA26-WT


title: DSP.1001660039492.A.E03.dcc

description: Library name: DSP.1001660039492.A.E03.dcc

value: Hippocampus

tag: apoe


title: WT.rep2

description: Library name: mouse02_IGO_17450_2_1


title: DSP.1001660039492.A.E02.dcc

description: Library name: DSP.1001660039492.A.E02.dcc

value: Microglia

tag: slide


title: DSP.1001660039492.A.E01.dcc

description: Library name: DSP.1001660039492.A.E01.dcc

tag: Sex


title: WT.rep1

description: Library name: mouse01_IGO_17450_1_1

tag: genotype


title: DSP.1001660039492.A.D12.dcc

description: Library name: DSP.1001660039492.A.D12.dcc


title: DSP.1001660039492.A.D10.dcc

description: Library name: DSP.1001660039492.A.D10.dcc

value: A


title: BV2_hyp_cc_rep3_H3K27ac

city: Warsaw

first: Monika

last: Dzwigonska

address: 3 Pasteur Street

country: Poland

institute: Nencki Institute of Experimental Biology, PAS

description: Library name: BV2_hyp_cc_rep3_H3K27ac

data_processing:
The quality of raw fastq data was assessed using FASTQC software. Adapter sequences and low-quality bases at the 5′ and 3′ ends were removed using Trimmomatic. Paired-end reads were then aligned to mm10 reference genome using Bowtie2 with parameters --very-sensitive --no-mixed --no-discordant -I 10 -X 800 74. Duplicate reads were marked and removed using Picard (MarkDuplicates command). Only properly paired and uniquely mapped reads were kept for downstream analysis. BAM files were converted to bigWig format using the bamCoverage command with CPM normalization.
Assembly: mm10
Supplementary files format and content: Bigwig files were generated from BAM files using deeptools (bamCoverage) with CPM normalization.
Library strategy: CUT&Run

growth_protocol: Glioma cells (GL261) were seeded in DMEM supplemented with 10% FBS and antibiotics. After 24 h, the medium was changed to a microglia culture medium DMEM with GlutaMAX™ supplemented with 2% FBS and antibiotics and the microglia BV2 cells were co-seeded onto GL261 cells at a 1:2 ratio relative to GL261 cells. Following 24h, the cells were cultured under normoxic or hypoxic conditions for another 16 hours and used in further assays. The control BV2 was grown as monoculture.

extract_protocol:
CUT&RUN was performed on BV2 cells exposed to hypoxic or normoxic condition, as described previously, using EpiCypher CUTANA ChIC/CUT&RUN Kit (Version 4, EpiCypher, 14-1048), according to the manufacturer’s protocol with minor modifications. Briefly, cells were subjected to mild crosslinking with 1% formaldehyde for 3 min, followed by FACS. Then, 5x105 cells per reaction were washed with PBS, and nuclei were isolated using nuclear extraction buffer (20 mM HEPES pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% glycerol, 1 mM MnCl2, 1X cOmplete Mini-Tablet and 0.5 mM spermidine). Activated ConA beads were added directly to the to the nuclear suspensions, followed by overnight incubation at 4°C with H3K27ac (Cell Signaling, 8173S). Chromatin digestion was performed using protein pAG-MNase, and the released DNA fragments were recovered after reverse crosslinking overnight at 55°C in the presence of SDS and proteinase K.
Sequencing libraries were prepared with the QIAseq® Ultralow Input Library Kit (Qiagen), according to the manufacturer's instructions.

treatment_protocol: Cells were incubated at <0.1% in a M35 Hypoxystation (Don Whitley) hypoxic chamber in the presence of 5% CO2 at 37°C for 16h.

tag: cell line

value: Murine microglial

tag: condition

value: Co-culture

value: hypoxia <0.1% O2


title: DSP.1001660039492.A.D09.dcc

description: Library name: DSP.1001660039492.A.D09.dcc

tag: cell type

tag: batch

value: AD

value: F


title: DSP.1001660039492.A.D11.dcc

description: Library name: DSP.1001660039492.A.D11.dcc

tag: group

tag: braak


title: BV2_norm_cc_rep3_H3K27ac

description: Library name: BV2_norm_cc_rep3_H3K27ac

value: normoxia 21% O2


title: DSP.1001660039492.A.D08.dcc

description: Library name: DSP.1001660039492.A.D08.dcc

tag: pmd

tag: ph


title: BV2_norm_cc_rep2_H3K27ac

description: Library name: BV2_norm_cc_rep2_H3K27ac


title: Tir1.rep6

description: Library name: mouse06_IGO_17450_6_1


title: Transfer-Organ-scRNA-seq

description: Library name: Transfer-Organ-scRNA-seq

data_processing:
scRNA-seq was aligned using CellRanger and demultiplexed using hashtag oligos. Cells and genes were filtered according to mean counts, and leiden clustering was performed at a resolution of 0.25. Then, data were pseudobulked and differential expression was performed using DESeq2.
Assembly: mm39
Supplementary files format and content: adata: processed data for each organ and transfer condition

source_name: SLO, Liver, Lung, LILP

extract_protocol:
Cells from individual Foxp3DTR mice were pooled and cells from individual Tcrbd KO mice were pooled. Each pool was fixed in Fixation Buffer B (10X genomics) at 4C for 20 hours. After quenching and washing of cells per manufacturer instructions (10X genomics, Demonstrated Protocol CG000782 Rev A), cells were resuspended in 500 μL Quenching Buffer B. Reporter positive live/dead stain negative Tregs (TCRβ+CD8α-CD4+ZsGreen+mCherry+ or mCherry-) were isolated from fixed single cell suspensions using FACS and sorted into PBS with 1% nuclease-free BSA Fraction V (Millipore Sigma, 126609) and 0.2 U/μL RNase-inhibitor (Millipore Sigma, PN-3335399001). mCherry+ and mCherry- cells were sorted into separate tubes for each condition. All sorted mCherry+ cells were pooled and all sorted mCherry- cells were pooled. Probe hybridization was performed per manufacturer instructions.
Single cell preparation was performed using GEM-X Flex (10X genomics). Probe hybridization was performed per manufacturer instructions. Cells from ROSA26TIR1(F74G) and ROSA26WT genotypes were hybridized with separately barcoded probes. The remaining steps were performed per manufacturer instructions (10X genomics, User Guide CG000788 Rev A). In brief, cells were hybridized for 18 hours and washed. Cells from this experiment and the Foxp3DTR vs Tcrbd KO experiment, which were hybridized with unique barcoded probes, were pooled and encapsulated in one lane targeting 80,000 cells. Indexing PCR steps were performed using 9 amplification cycles for both the gene expression and cell surface protein libraries. Final sequencing libraries were sequenced on an Element Biosciences AVITI24 system (index 1: 10 cycles, index 2: 10 cycles, read 1: 28 cycles, read 2: 90 cycles).

value: SLO, Liver, Lung, LILP

value: Foxp3-AID ROSA26-WT & Foxp3-AID ROSA26-TIR1(F74G)

value: 5-ph-IAA 7 days


title: DSP.1001660039492.A.D06.dcc

description: Library name: DSP.1001660039492.A.D06.dcc

value: PP

tag: weight

tag: csf


title: BV2_norm_cc_rep1_H3K27ac

description: Library name: BV2_norm_cc_rep1_H3K27ac


title: BV2_hyp_cc_rep1_H3K27ac

description: Library name: BV2_hyp_cc_rep1_H3K27ac


title: DSP.1001660039492.A.D07.dcc

description: Library name: DSP.1001660039492.A.D07.dcc

tag: tissue

value: P

tag: area


title: BV2_hyp_ctrl_rep3_H3K27ac

description: Library name: BV2_hyp_ctrl_rep3_H3K27ac

value: Monoculture

tag: treatment


title: BV2_hyp_ctrl_rep2_H3K27ac

description: Library name: BV2_hyp_ctrl_rep2_H3K27ac


title: DSP.1001660039492.A.D03.dcc

description: Library name: DSP.1001660039492.A.D03.dcc

tag: age

tag: apoe


title: WT.rep4

description: Library name: mouse04_IGO_17450_4_1

value: Spleen & Lymph nodes

value: Treg

value: 5-ph-IAA 14 Days


title: DSP.1001660039492.A.D04.dcc

description: Library name: DSP.1001660039492.A.D04.dcc

value: Hippocampus

value: Microglia

tag: slide

tag: Sex


title: BV2_norm_ctrl_rep3_H3K27ac

description: Library name: BV2_norm_ctrl_rep3_H3K27ac

tag: cell line

value: Murine microglial


title: BV2_hyp_ctrl_rep1_H3K27ac

description: Library name: BV2_hyp_ctrl_rep1_H3K27ac

tag: condition


title: DSP.1001660039492.A.D01.dcc

description: Library name: DSP.1001660039492.A.D01.dcc

tag: cell type

value: A

value: CU-AP


title: BV2_norm_ctrl_rep2_H3K27ac

description: Library name: BV2_norm_ctrl_rep2_H3K27ac


title: BV2_norm_ctrl_rep1_H3K27ac

description: Library name: BV2_norm_ctrl_rep1_H3K27ac


title: DSP.1001660039492.A.C12.dcc

description: Library name: DSP.1001660039492.A.C12.dcc

tag: batch


title: DSP.1001660039492.A.C11.dcc

description: Library name: DSP.1001660039492.A.C11.dcc

tag: group


title: BV2_hyp_cc_rep2_H3K27ac

description: Library name: BV2_hyp_cc_rep2_H3K27ac

value: Co-culture

value: hypoxia <0.1% O2


title: BV2_hyp_pano_rep2_RNAseq

description:
Library name: BV2_H_Pano_n2
BV2_H_Pano_n2

data_processing:
Low-quality reads and adapters were trimmed using Trimmomatic (version 0.36) The resulting RNA sequencing reads were mapped to mm10 reference genome sequence using STAR aligner (version 2.6). Only uniquely maped reads were kept for the downstream analysis with samtools view -q 255. Quantification of mapped reads and summarisation by gene was performed using HTSeq-count (version 0.9.1), with reverse stranded mode (-s reverse).
Assembly: mm10
Supplementary files format and content: Bigwig files were generated from BAM files using deeptools (bamCoverage) and were normalized to genome coverage (RPKM).
Supplementary files format and content: raw counts

growth_protocol: For direct co-culture experiment GL261 cells were seeded in DMEM supplemented with 10% FBS and antibiotics (100 U/mL penicillin, 100 µg/mL streptomycin). After 24 h, the medium was changed to a BV2 culture medium (DMEM with GlutaMAX? supplemented with 2% FBS and antibiotics) or BMDM culture medium (DMEM with GlutaMAX? supplemented with 10% FBS and antibiotics). Following 24h, either BV2 cells or BMDM cell were co-seeded onto GL261 cell at a ratio of 1:2 (BV2:GL261) or 1:1 (BMDM:GL261), cultured under normoxic or hypoxic conditions for another 16 hours and used in further assays. The control BV2, BMDMs or GL261 were grown as monoculture. For the HDAC inhibitor (HDACi) treatment experiments, BV2 or BMDM were seeded in DMEM with GlutaMAX supplemented with 2% or 10% FBS, respectively. Following 24h cells were cultured under normoxic or hypoxic conditions and treated with Panobinostat or DMSO.

extract_protocol:
Cells cultured under hypoxic or normoxic conditions, either as monocultures or co-cultures, were fixed on ice using a 3% glyoxal fixation solution, as previously described (Channathodiyil et al., PLoS One, 2021). Total RNA was isolated using the RNeasy Plus Kit (Qiagen), following the manufacturer’s instructions. RNA quality was assessed using the Agilent 2100 Bioanalyzer with the RNA 6000 Pico Kit (Agilent Technologies).
PolyA enriched RNA libraries were prepared with the KAPA Stranded mRNA Sample Preparation Kit (Kapa Biosystems). The RNAseq libraries were sequenced at 2x151 bp paired-end on NovaSeq 6000 at the Laboratory of Sequencing (Nencki Institute).

treatment_protocol: Cells were incubated at <0.1% in a M35 Hypoxystation (Don Whitley) hypoxic chamber in the presence of 5% CO2 at 37°C for 16h. Panobinostat (10 nM) or an equivalent volume of DMSO was added during incubation.

value: Panobinostat

value: hypoxia <0.1% O2 + Panobinostat


title: DSP.1001660039492.A.C10.dcc

description: Library name: DSP.1001660039492.A.C10.dcc

tag: braak

value: F


title: DSP.1001660039492.A.C09.dcc

description: Library name: DSP.1001660039492.A.C09.dcc

tag: pmd


title: DSP.1001660039492.A.D05.dcc

description: Library name: DSP.1001660039492.A.D05.dcc

value: AD

tag: ph


title: DSP.1001660039492.A.C08.dcc

description: Library name: DSP.1001660039492.A.C08.dcc

tag: weight


title: BV2_hyp_dmso_rep1_RNAseq

description:
Library name: BV2_H_n1
BV2_H_n1

value: DMSO


title: BV2_hyp_dmso_rep2_RNAseq

description:
Library name: BV2_H_n2
BV2_H_n2


title: BV2_norm_dmso_rep1_RNAseq

description:
Library name: BV2_N_n1
BV2_N_n1

value: normoxia 21% O2


title: DSP.1001660039492.A.C06.dcc

description: Library name: DSP.1001660039492.A.C06.dcc

value: P

tag: csf


title: DSP.1001660039492.A.C07.dcc

description: Library name: DSP.1001660039492.A.C07.dcc

tag: tissue

value: PP


title: BV2_norm_dmso_rep2_RNAseq

description:
Library name: BV2_N_n2
BV2_N_n2


title: DSP.1001660039492.A.C04.dcc

description: Library name: DSP.1001660039492.A.C04.dcc

tag: area

value: M


title: BMDM_hyp_pano_rep2_RNAseq

description:
Library name: BMDM_H_Pano_n2
BMDM_H_Pano_n2

source_name: primary cells

value: primary cells

value: Bone marrow-derived macrophage

tag: genotype

value: WT

tag: treatment


title: DSP.1001660039492.A.C05.dcc

description: Library name: DSP.1001660039492.A.C05.dcc

value: Hippocampus

value: Microglia

tag: age

tag: apoe


title: DSP.1001660039492.A.C03.dcc

description: Library name: DSP.1001660039492.A.C03.dcc

value: A

tag: slide

tag: Sex


title: DSP.1001660039492.A.D02.dcc

description: Library name: DSP.1001660039492.A.D02.dcc

value: CU-AP


title: BMDM_hyp_pano_rep1_RNAseq

description:
Library name: BMDM_H_Pano_n1
BMDM_H_Pano_n1

tag: cell line

tag: condition


title: BMDM_hyp_dmso_rep2_RNAseq

description:
Library name: BMDM_H_n2
BMDM_H_n2

tag: cell type

value: hypoxia <0.1% O2


title: BMDM_hyp_dmso_rep1_RNAseq

description:
Library name: BMDM_H_n1
BMDM_H_n1


title: BMDM_norm_dmso_rep2_RNAseq

description:
Library name: BMDM_N_n2
BMDM_N_n2


title: DSP.1001660039492.A.C02.dcc

description: Library name: DSP.1001660039492.A.C02.dcc

tag: batch

tag: group


title: BMDM_norm_dmso_rep1_RNAseq

description:
Library name: BMDM_N_n1
BMDM_N_n1


title: DSP.1001660039492.A.C01.dcc

description: Library name: DSP.1001660039492.A.C01.dcc

tag: braak

tag: pmd


title: BMDM_hyp_cc_rep3_RNAseq

description:
Library name: BMDM_cc_H_n3
BMDM_cc_H_n3

value: Co-culture


title: BV2_hyp_pano_rep1_RNAseq

description:
Library name: BV2_H_Pano_n1
BV2_H_Pano_n1

value: Murine microglial

value: Panobinostat

value: hypoxia <0.1% O2 + Panobinostat


title: DSP.1001660039492.A.B09.dcc

description: Library name: DSP.1001660039492.A.B09.dcc

value: AD

tag: ph

tag: weight


title: DSP.1001660039492.A.B10.dcc

description: Library name: DSP.1001660039492.A.B10.dcc

tag: tissue

tag: csf


title: BMDM_hyp_cc_rep2_RNAseq

description:
Library name: BMDM_cc_H_n2
BMDM_cc_H_n2

tag: genotype


title: DSP.1001660039492.A.B08.dcc

description: Library name: DSP.1001660039492.A.B08.dcc

tag: treatment

value: Non-AD

tag: area

value: F


title: DSP.1001660039492.A.B07.dcc

description: Library name: DSP.1001660039492.A.B07.dcc

tag: age

tag: apoe


title: BMDM_norm_cc_rep3_RNAseq

description:
Library name: BMDM_cc_N_n3
BMDM_cc_N_n3

value: normoxia 21% O2


title: BMDM_norm_cc_rep2_RNAseq

description:
Library name: BMDM_cc_N_n2
BMDM_cc_N_n2


title: DSP.1001660039492.A.B06.dcc

description: Library name: DSP.1001660039492.A.B06.dcc

value: PP

tag: slide

tag: Sex

value: M


title: BMDM_norm_cc_rep1_RNAseq

description:
Library name: BMDM_cc_N_n1
BMDM_cc_N_n1

tag: cell line

value: primary cells

value: Bone marrow-derived macrophage

tag: condition


title: BMDM_hyp_ctrl_rep2_RNAseq

description:
Library name: BMDM_ctrl_H_n2
BMDM_ctrl_H_n2

tag: cell type

value: WT

value: Monoculture


title: DSP.1001660039492.A.B05.dcc

description: Library name: DSP.1001660039492.A.B05.dcc

value: Hippocampus

value: Microglia

value: P

tag: batch

tag: group


title: BMDM_hyp_ctrl_rep1_RNAseq

description:
Library name: BMDM_ctrl_H_n1
BMDM_ctrl_H_n1

value: hypoxia <0.1% O2


title: DSP.1001660039492.A.B04.dcc

description: Library name: DSP.1001660039492.A.B04.dcc

value: A

tag: braak

tag: pmd


title: DSP.1001660039492.A.B03.dcc

description: Library name: DSP.1001660039492.A.B03.dcc

tag: ph

tag: weight


title: DSP.1001660039492.A.B02.dcc

description: Library name: DSP.1001660039492.A.B02.dcc

tag: tissue

tag: csf


title: BMDM_norm_ctrl_rep1_RNAseq

description:
Library name: BMDM_ctrl_N_n1
BMDM_ctrl_N_n1

tag: genotype

tag: treatment


title: DSP.1001660039492.A.B01.dcc

description: Library name: DSP.1001660039492.A.B01.dcc

tag: age

tag: area


title: cere_Li4

city: Tokyo

first: YUJIN

last: OHSUGI

address: 1-5-45, Yushima, Bunkyo-ku

department: Oral Biology

country: Japan

institute: Institute of Science Tokyo

description: Library name: Sample19

data_processing:
Low-quality and adapter sequences from the paired-end reads were trimmed using Trimmomatic v0.39
The quality of the trimmed reads was assessed using FastQC v0.11.9.
Trimmed paired-end reads were aligned to the mouse reference genome (GRCm39) using HISAT2 v2.2.1.
StringTie v2.1.7 was used to assemble transcripts and estimate abundance based on GRCm39 gene annotations.
Differential expression analysis was conducted using the DESeq2 v1.32.0 package for R.
Assembly: GRCm39
Supplementary files format and content: bam file

source_name: cerebellum

growth_protocol: C57BL/6J male mice 16-weeks-old

extract_protocol:
Total RNA from gingiva and bone tissues was extracted using a combination of TRIzol and NucleoSpin RNA kit
RNA-seq libraries were prepared from total RNA using poly (A) enrichment of mRNA (mRNA-seq) to remove ribosomal RNA (rRNA)

treatment_protocol: Ligature-induced periodontitis mice were established by a 6-0 silk ligature was placed around the maxillary left 2nd molar in 9-week-old male mice under anesthesia. And 5-0 silk ligature was replaced after every 1 week for 5 weeks under anesthesia induced by intraperitoneal injection

value: cerebellum

value: wild type

value: Ligature-induced periodontitis


title: DSP.1001660039492.A.B12.dcc

description: Library name: DSP.1001660039492.A.B12.dcc

value: AD

tag: slide

tag: apoe


title: DSP.1001660039492.A.A11.dcc

description: Library name: DSP.1001660039492.A.A11.dcc

value: Non-AD

tag: Sex


title: cere_Li5

description: Library name: Sample20


title: DSP.1001660039492.A.A10.dcc

description: Library name: DSP.1001660039492.A.A10.dcc


title: DSP.1001660039492.A.B11.dcc

description: Library name: DSP.1001660039492.A.B11.dcc


title: cere_Li3

description: Library name: Sample18


title: BMDM_hyp_cc_rep1_RNAseq

description:
Library name: BMDM_cc_H_n1
BMDM_cc_H_n1

tag: cell line

tag: condition

value: Co-culture


title: DSP.1001660039492.A.A09.dcc

description: Library name: DSP.1001660039492.A.A09.dcc

tag: cell type

tag: batch


title: cere_Li2

description: Library name: Sample17


title: cere_Li1

description: Library name: Sample16


title: DSP.1001660039492.A.A07.dcc

description: Library name: DSP.1001660039492.A.A07.dcc

value: PP

tag: group

tag: braak


title: DSP.1001660039492.A.A06.dcc

description: Library name: DSP.1001660039492.A.A06.dcc

tag: pmd

tag: ph

value: M


title: cere_Co5

description: Library name: Sample15

tag: tissue

value: Control


title: cere_Co4

description: Library name: Sample14


title: DSP.1001660039492.A.A05.dcc

description: Library name: DSP.1001660039492.A.A05.dcc

tag: weight

tag: csf


title: cere_Co3

description: Library name: Sample13

tag: genotype

tag: treatment


title: cere_Co2

description: Library name: Sample12


title: DSP.1001660039492.A.A04.dcc

description: Library name: DSP.1001660039492.A.A04.dcc

tag: age

tag: area


title: BMDM_norm_ctrl_rep2_RNAseq

description:
Library name: BMDM_ctrl_N_n2
BMDM_ctrl_N_n2

value: primary cells

value: Bone marrow-derived macrophage

value: normoxia 21% O2


title: cere_Co1

description: Library name: Sample11


title: DSP.1001660039492.A.A03.dcc

description: Library name: DSP.1001660039492.A.A03.dcc

value: Hippocampus

tag: slide

tag: apoe


title: DSP.1001660039492.A.A02.dcc

description: Library name: DSP.1001660039492.A.A02.dcc

value: Microglia

tag: Sex


title: PC_Li5

description: Library name: Sample10

source_name: Frontal cortex

value: Frontal cortex


title: PC_Li4

description: Library name: Sample9


title: PC_Li3

description: Library name: Sample8


title: PC_Li2

description: Library name: Sample7


title: DSP.1001660012998.D.H10.dcc

description: Library name: DSP.1001660012998.D.H10.dcc


title: DSP.1001660012998.D.H08.dcc

description: Library name: DSP.1001660012998.D.H08.dcc

value: CU-AP


title: PC_Li1

description: Library name: Sample6


title: DSP.1001660012998.D.H09.dcc

description: Library name: DSP.1001660012998.D.H09.dcc

value: P


title: PC_Co5

description: Library name: Sample5


title: DSP.1001660012998.D.H06.dcc

description: Library name: DSP.1001660012998.D.H06.dcc

value: A


title: DSP.1001660012998.D.H07.dcc

description: Library name: DSP.1001660012998.D.H07.dcc


title: DSP.1001660012998.D.H05.dcc

description: Library name: DSP.1001660012998.D.H05.dcc


title: DSP.1001660039492.A.A08.dcc

description: Library name: DSP.1001660039492.A.A08.dcc


title: DSP.1001660012998.D.H04.dcc

description: Library name: DSP.1001660012998.D.H04.dcc


title: Isogenic SW48 mutant cell line (SW48 KRAS +/G12C) - low nutrient conditions - FOXO1 inhibitor

city: Uxbridge

first: Alessandro

last: Esposito

state: Select a State/County

address: Kingston Lane

department: Centre for Genome Engineering and Maintanance

institute: Brunel University of London

description: Library name: SW48-G12C-LN-iFOXO1

data_processing:
The initial data analysis was carried out by BGI. The original image data is transferred into sequence data via base calling, which is defined as raw data or raw reads and saved as FASTQ file.
Reads were mapped to the human reference genome hg19  with the STAR (version 2.6.0c) splice-aware aligner (Dobin, A. et al. 2019) using annotation from Gencode (releases 24).
Low-quality reads (mapping quality <20) as well as known adapter and artifact contaminations were filtered out using Cutadapt (version 1.10.0).
Read counting was performed using Bioconductor package Rsubread (v1.28.1) (Liyao Y, et al., 2019)
Differential expression analysis with DESeq2 (v1.18.1) (Love M.I., et al, 2014).
Assembly: hg19
Supplementary files format and content: Comma separated files listing transcript name, average expression, log2 fold change relative to KRAS wild-type cell line, Wald statistics, p-value, FDR-corrected p value, gene name and gene type

growth_protocol: SW48 isogenic cells (SW48+/+, SW48+/G12A, SW48+/G12C, SW48+/G12D, SW48+/G12V), derived from colorectal adenocarcinoma were purchased from Horizon Discovery. Cells were cultured in their recommended conditions, also referred in the text as full media conditions, RPMI 1640 with GlutaMAX, HEPES (Gibco, # 11554526) and 10% foetal bovine serum (FBS; Gibco, #A5256701).

extract_protocol:
SW48 isogenic cells were thawed and cultured for 3 passages before sample preparation. 5 replicates from 3 different batches of each cell line were used for the RNAseq experiment. Briefly, 1.5 million cells were seeded on a 6 cm dish in full media conditions. 48 hours later, cells were washed once with cold PBS and collected by scraping with 1 ml PBS into 1.5 ml Eppendorf tubes. Samples were centrifuged for 3 minutes at 1,000 rpm and 4 °C. Pellets were stored at -80 °C until shipment. RNA extraction, library preparation and sequencing (20 million reads per sample) was performed by BGI Genomics (BGI Hong Kong Company Limited).
Libraries were prepared by BGI. 1)mRNA enrichment and purification: rRNA depletion or Oligo dT Selection to enrich the mRNA 2)RNA fragment and reverse transcription 3)End repair, add A and adaptor ligation 4)RCR amplification 5)Single strand separation and cyclization 6)DNA nanoball synthesis 7)Sequencing on BGISEQ platform

treatment_protocol: 1) FULL MEDIA: Cells were cultured in their recommended conditions, also referred in the text as full media conditions, RPMI 1640 with GlutaMAX, HEPES (Gibco, # 11554526) and 10% foetal bovine serum (FBS; Gibco, #A5256701). 2) LOW NUTRIENT CONDITIONS: RPMI 1% FCS, 2 mM Glucose 3) FOXO1 inhibition: For treatment with FOXO1 inhibitor, SW48 isogenic cells were plated on 6-well dishes 8x105 cells/well in full media conditions. 24 hours after seeding, cells were treated with either DMSO (0.003% v/v) vehicle control or FOXO1 inhibitor (1 μM) in full media conditions. After 24 hours of treatment,  RNA was extracted.

tag: cell line

value: heterozygous KRAS G12D

value: low nutrient conditions - AS1842857


title: Isogenic SW48 mutant cell line (SW48 KRAS +/G12D) - low nutrient conditions - FOXO1 inhibitor

description: Library name: SW48-G12D-LN-iFOXO1

value: heterozygous KRAS G12V

value: low nutrient conditions - AS1842858


title: PC_Co3

description: Library name: Sample3

value: wild type


title: DSP.1001660012998.D.H03.dcc

description: Library name: DSP.1001660012998.D.H03.dcc

tag: cell type

value: AD


title: DSP.1001660012998.D.H02.dcc

description: Library name: DSP.1001660012998.D.H02.dcc

value: PP

tag: batch

value: M


title: Isogenic SW48 cell line (parental, wild-type for KRAS) - low nutrient conditions - FOXO1 inhibitor

description: Library name: SW48-Par-LN-iFOXO1

value: KRAS WT

value: low nutrient conditions - AS1842856


title: DSP.1001660012998.D.H01.dcc

description: Library name: DSP.1001660012998.D.H01.dcc

tag: group


title: DSP.1001660012998.D.G12.dcc

description: Library name: DSP.1001660012998.D.G12.dcc

tag: braak

value: F


title: PC_Co2

description: Library name: Sample2

value: Control


title: DSP.1001660012998.D.G11.dcc

description: Library name: DSP.1001660012998.D.G11.dcc

value: Hippocampus

value: Microglia

tag: pmd


title: DSP.1001660012998.D.H11.dcc

description: Library name: DSP.1001660012998.D.H11.dcc

tag: ph


title: Isogenic SW48 mutant cell line (SW48 KRAS +/G12D) - low nutrient conditions - DMSO control

description: Library name: SW48-G12D-LN-DMSO

value: low nutrient conditions - DMSO control


title: DSP.1001660012998.D.G10.dcc

description: Library name: DSP.1001660012998.D.G10.dcc

tag: tissue


title: PC_Co1

description: Library name: Sample1

value: Frontal cortex


title: DSP.1001660012998.D.G09.dcc

description: Library name: DSP.1001660012998.D.G09.dcc

tag: weight


title: DSP.1001660012998.D.G08.dcc

description: Library name: DSP.1001660012998.D.G08.dcc

value: P

tag: csf


title: Isogenic SW48 cell line (parental, wild-type for KRAS) - low nutrient conditions - DMSO control

description: Library name: SW48-Par-LN-DMSO

tag: genotype


title: Isogenic SW48 mutant cell line (SW48 KRAS +/G12V - low nutrient conditions

description: Library name: SW48-G12V-LN

tag: treatment

value: low nutrient conditions


title: C10PC

description: Library name: Sample1

data_processing:
Raw sequencing reads (FASTQ files) and histology images were processed using the pipeline implemented in Space Ranger-2.0.0 (10x Genomics Inc.). The results were processed using Loupe Browser 8.0.0 (10x Genomics Inc.).
Same size area corresponding to frontal cortex in the HE-stained slides were manually selected in Loupe Browser.
The barcodes of these spots were exported and loaded into R to create a Seurat object for downstream analysis.
Assembly: @@@@@
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: tif: image of tissue
Supplementary files format and content: ndpi: align morphology with transcriptomic spatial data
Library strategy: Spatial Transcriptomics

extract_protocol:
Brain tissues were fixed by immersing in 10% neutral formalin for 24 h. After washing PBS, the tissues were penetrated with paraffin for 20 h and then embedded in paraffin. For RNA extraction from the FFPE blocks of mice, 8 slices (10 µm) from a region were pooled per specimen (approx. 5 mm × 5 mm).
Libraries for Visium were prepared according to the Visium Spatial Gene Expression for FFPE User Guide (CG000407 Rev C, 10x Genomics Inc.).


title: DSP.1001660012998.D.G07.dcc

description: Library name: DSP.1001660012998.D.G07.dcc

tag: age


title: Isogenic SW48 mutant cell line (SW48 KRAS +/G12C) - low nutrient conditions - DMSO control

description: Library name: SW48-G12C-LN-DMSO

value: heterozygous KRAS G12D


title: L12PC

description: Library name: Sample2

value: Ligature-induced periodontitis


title: DSP.1001660012998.D.G03.dcc

description: Library name: DSP.1001660012998.D.G03.dcc

value: CU-AP

tag: area


title: DSP.1001660012998.D.G05.dcc

description: Library name: DSP.1001660012998.D.G05.dcc

tag: slide


title: DSP.1001660012998.D.G04.dcc

description: Library name: DSP.1001660012998.D.G04.dcc

tag: apoe


title: DSP.1001660012998.D.G06.dcc

description: Library name: DSP.1001660012998.D.G06.dcc

tag: Sex


title: Isogenic SW48 mutant cell line (SW48 KRAS +/G12C) - low nutrient conditions

description: Library name: SW48-G12C-LN

tag: cell line

value: heterozygous KRAS G12C


title: DSP.1001660012998.D.F11.dcc

description: Library name: DSP.1001660012998.D.F11.dcc

tag: cell type

value: A


title: DSP.1001660012998.D.G02.dcc

description: Library name: DSP.1001660012998.D.G02.dcc

tag: batch


title: PC_Co4

description: Library name: Sample4

value: wild type


title: Isogenic SW48 mutant cell line (SW48 KRAS +/G12D) - low nutrient conditions

description: Library name: SW48-G12D-LN


title: Isogenic SW48 mutant cell line (SW48 KRAS +/G12A) - low nutrient conditions

description: Library name: SW48-G12A-LN

value: heterozygous KRAS G12A


title: Omomyc_transduced_2

city: Zürich

first: Johannes

last: Nemeth

address: Rämistrasse 100

department: Department of Infectious Diseases and Hospital Epidemiology

country: Switzerland

institute: University Hospital Zurich

description:
Library name: omoMYC_IFNg_2
c-Myc inhibition experiments; samples were mislabeled, omoMYC_IFNg is actually omoMYC

data_processing:
Trimming + filtering using fastp v0.20.0
Transcript abundance estimation carried out with Kallisto v0.46.0
Assembly: GRCh38.p6
Supplementary files format and content: Tab-delimited transcript abundances

source_name: bone marrow

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen), in combination with QIAshredder homogenization columns and the RNase-Free DNase Set (Qiagen), according to the manufacturer’s instructions.
The quality of the isolated RNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies, California, USA) and a Fragment Analyzer (Agilent, Santa Clara, California, USA). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. The TruSeq Stranded mRNA (Illumina, Inc, California, USA) was used in the succeeding steps. Briefly, total RNA samples (100-1000 ng) were polyA enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples was fragmented, end-repaired and adenylated before ligation of TruSeq adapters containing unique dual indices (UDI) for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR.  The quality and quantity of the enriched libraries were validated using Qubit® (1.0) Fluorometer and the Fragment Analyzer (Agilent, Santa Clara, California, USA).  The product is a smear with an average fragment size of approximately 260 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. Sequencing was performed as single-end 100 bp reads on the Illumina NovaSeq 6000 platform.

value: bone marrow

value: primary cells

value: bone marrow-derived macrophages

tag: strain

value: transduced


title: Omomyc_transduced_3

description:
Library name: omoMYC_IFNg_3
c-Myc inhibition experiments; samples were mislabeled, omoMYC_IFNg is actually omoMYC


title: Omomyc_transduced_1

description:
Library name: omoMYC_IFNg_1
c-Myc inhibition experiments; samples were mislabeled, omoMYC_IFNg is actually omoMYC


title: WT_3

description:
Library name: control_3
c-Myc inhibition experiments

value: untransduced


title: DSP.1001660012998.D.F07.dcc

description: Library name: DSP.1001660012998.D.F07.dcc

value: Hippocampus

value: Microglia

tag: group

value: Non-AD

tag: braak

value: F


title: DSP.1001660012998.D.F08.dcc

description: Library name: DSP.1001660012998.D.F08.dcc

tag: pmd

tag: ph

value: M


title: Isogenic SW48 cell line (parental, wild-type for KRAS) - low nutrient conditions

description: Library name: SW48-Par-LN

value: KRAS WT

value: low nutrient conditions


title: DSP.1001660012998.D.F09.dcc

description: Library name: DSP.1001660012998.D.F09.dcc

tag: tissue

value: CU-AP

tag: weight


title: WT_2

description:
Library name: control_2
c-Myc inhibition experiments


title: Isogenic SW48 mutant cell line (SW48 KRAS +/G12V)

description: Library name: SW48-G12V

tag: genotype

value: heterozygous KRAS G12V

value: full media


title: DSP.1001660012998.D.F05.dcc

description: Library name: DSP.1001660012998.D.F05.dcc

tag: treatment

value: A

tag: csf


title: WT_1

description:
Library name: control_1
c-Myc inhibition experiments


title: DSP.1001660012998.D.F04.dcc

description: Library name: DSP.1001660012998.D.F04.dcc

value: PP

value: AD

tag: age

tag: area


title: DSP.1001660012998.D.F03.dcc

description: Library name: DSP.1001660012998.D.F03.dcc

value: P

tag: slide

tag: apoe


title: Isogenic SW48 mutant cell line (SW48 KRAS +/G12D)

description: Library name: SW48-G12D

tag: cell line

value: heterozygous KRAS G12D


title: DSP.1001660012998.D.F02.dcc

description: Library name: DSP.1001660012998.D.F02.dcc

tag: cell type

tag: Sex


title: Isogenic SW48 mutant cell line (SW48 KRAS +/G12C)

description: Library name: SW48-G12C

value: heterozygous KRAS G12C


title: cMyc_transduced_3

description:
Library name: cMYC_3
c-Myc inhibition experiments

value: bone marrow

value: primary cells

value: bone marrow-derived macrophages

tag: strain

value: transduced


title: Isogenic SW48 mutant cell line (SW48 KRAS +/G12A)

description: Library name: SW48-G12A

value: heterozygous KRAS G12A


title: DSP.1001660012998.D.F01.dcc

description: Library name: DSP.1001660012998.D.F01.dcc

value: Hippocampus

value: Microglia

tag: batch

tag: group

value: M


title: cMyc_transduced_2

description:
Library name: cMYC_2
c-Myc inhibition experiments


title: DSP.1001660012998.D.F10.dcc

description: Library name: DSP.1001660012998.D.F10.dcc

tag: braak

tag: pmd


title: Isogenic SW48 cell line (parental, wild-type for KRAS)

description: Library name: SW48-Par

value: KRAS WT


title: cMyc_transduced_1

description:
Library name: cMYC_1
c-Myc inhibition experiments

tag: tissue


title: 24h_no_IFNg_2

description:
Library name: ES_C4_24h-after-infection_2
IFN-γ timing experiments

value: MTB infected


title: DSP.1001660012998.D.E10.dcc

description: Library name: DSP.1001660012998.D.E10.dcc

tag: ph

tag: weight


title: DSP.1001660012998.D.E12.dcc

description: Library name: DSP.1001660012998.D.E12.dcc

tag: treatment


title: DSP.1001660012998.D.E09.dcc

description: Library name: DSP.1001660012998.D.E09.dcc

tag: csf


title: DSP.1001660012998.D.F06.dcc

description: Library name: DSP.1001660012998.D.F06.dcc

value: Non-AD

tag: age

value: F


title: 24h_no_IFNg_1

description:
Library name: ES_C4_24h-after-infection_1
IFN-γ timing experiments


title: DSP.1001660012998.D.E08.dcc

description: Library name: DSP.1001660012998.D.E08.dcc

tag: area


title: DSP.1001660012998.D.E07.dcc

description: Library name: DSP.1001660012998.D.E07.dcc

value: PP

value: CU-AP

tag: slide


title: DSP.1001660012998.D.E06.dcc

description: Library name: DSP.1001660012998.D.E06.dcc

value: P

tag: apoe


title: DSP.1001660012998.D.E05.dcc

description: Library name: DSP.1001660012998.D.E05.dcc


title: WT_Batch2_Nil_Rep1[RNA_Seq]

city: San Antonio

first: Hui

last: Yan

state: TX

address: 7703 Floyd Curl Dr.

department: MIMG

institute: UTHSCSA

data_processing:
RNA samples were scored by FastQC
RNA samples were trimed by trim_galore
RNA samples were mapped by HISAT2
RNA samples were sored by samtools, removed duplicates
Reads count were extracted and normalized
Assembly: mm10
Supplementary files format and content: Normalized reads count in csv format.  Processed_data_RNA_Seq_WT_B_cells_Different_Stimuli.csv

source_name: B cell

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen)
RNA was processed using an Illumina TruSeq RNA sample prep kit v2 (Illumina)

value: B cell

tag: genotype

value: WT


title: 24h_full_IFNg_3

description:
Library name: ES_C3_24h-after-infection_3
IFN-γ timing experiments

value: bone marrow

tag: cell line

tag: cell type


title: DSP.1001660012998.D.E03.dcc

description: Library name: DSP.1001660012998.D.E03.dcc

value: A

tag: Sex


title: WT_Batch2_Nil_Rep2[RNA_Seq]


title: DSP.1001660012998.D.E02.dcc

description: Library name: DSP.1001660012998.D.E02.dcc

tag: batch


title: WT_Batch2_LPS_Rep2[RNA_Seq]

value: LPS


title: WT_Batch2_LPS_Rep1[RNA_Seq]


title: 24h_full_IFNg_2

description:
Library name: ES_C3_24h-after-infection_2
IFN-γ timing experiments

value: primary cells

value: bone marrow-derived macrophages

tag: strain


title: WT_Batch2_LC21_Rep2[RNA_Seq]


title: DSP.1001660012998.D.E01.dcc

description: Library name: DSP.1001660012998.D.E01.dcc

value: Hippocampus

tag: group

value: AD

tag: braak


title: 24h_full_IFNg_1

description:
Library name: ES_C3_24h-after-infection_1
IFN-γ timing experiments

tag: tissue


title: 24h_IFNg_after_infection_3

description:
Library name: ES_C2_24h-after-infection_3
IFN-γ timing experiments


title: WT_Batch2_LC21_Rep1[RNA_Seq]


title: DSP.1001660012998.D.D11.dcc

description: Library name: DSP.1001660012998.D.D11.dcc

value: Microglia

tag: pmd

tag: ph


title: DSP.1001660012998.D.E11.dcc

description: Library name: DSP.1001660012998.D.E11.dcc

tag: treatment

tag: weight

value: M


title: DSP.1001660012998.D.D09.dcc

description: Library name: DSP.1001660012998.D.D09.dcc

tag: age

tag: csf


title: DSP.1001660012998.D.D08.dcc

description: Library name: DSP.1001660012998.D.D08.dcc

tag: area

tag: slide


title: WT_Batch2_LC_Rep2[RNA_Seq]

tag: genotype


title: DSP.1001660012998.D.E04.dcc

description: Library name: DSP.1001660012998.D.E04.dcc

tag: apoe


title: DSP.1001660012998.D.D07.dcc

description: Library name: DSP.1001660012998.D.D07.dcc

tag: cell type


title: 24h_IFNg_after_infection_1

description:
Library name: ES_C2_24h-after-infection_1
IFN-γ timing experiments

tag: cell line

value: MTB infected


title: DSP.1001660012998.D.D10.dcc

description: Library name: DSP.1001660012998.D.D10.dcc

tag: batch

tag: Sex


title: DSP.1001660012998.D.D06.dcc

description: Library name: DSP.1001660012998.D.D06.dcc

tag: group


title: DSP.1001660012998.D.D05.dcc

description: Library name: DSP.1001660012998.D.D05.dcc

tag: braak


title: WT_Batch2_LC_Rep1[RNA_Seq]


title: WT_Batch2_CD154_Rep2[RNA_Seq]


title: DSP.1001660012998.D.D03.dcc

description: Library name: DSP.1001660012998.D.D03.dcc

tag: tissue


title: DSP.1001660012998.D.D04.dcc

description: Library name: DSP.1001660012998.D.D04.dcc

tag: pmd


title: 24h_IFNg_before_infection_3

description:
Library name: ES_C1_24h-after-infection_3
IFN-γ timing experiments

tag: strain


title: DSP.1001660012998.D.D02.dcc

description: Library name: DSP.1001660012998.D.D02.dcc

tag: treatment

tag: ph


title: WT_Batch2_CD154_Rep1[RNA_Seq]


title: DSP.1001660012998.D.D12.dcc

description: Library name: DSP.1001660012998.D.D12.dcc

tag: age

tag: weight


title: DSP.1001660012998.D.D01.dcc

description: Library name: DSP.1001660012998.D.D01.dcc

tag: csf

tag: area


title: 24h_IFNg_before_infection_2

description:
Library name: ES_C1_24h-after-infection_2
IFN-γ timing experiments


title: 24h_IFNg_before_infection_1

description:
Library name: ES_C1_24h-after-infection_1
IFN-γ timing experiments


title: 6h_no_IFNg_3

description:
Library name: ES_C4_6h-after-infection_3
IFN-γ timing experiments


title: DSP.1001660012998.D.C11.dcc

description: Library name: DSP.1001660012998.D.C11.dcc

tag: slide


title: DSP.1001660012998.D.C12.dcc

description: Library name: DSP.1001660012998.D.C12.dcc

tag: apoe


title: WT_Batch1_Nil_Rep2[RNA_Seq]

tag: cell type

tag: genotype


title: DSP.1001660012998.D.C10.dcc

description: Library name: DSP.1001660012998.D.C10.dcc

tag: batch


title: 24h_IFNg_after_infection_2

description:
Library name: ES_C2_24h-after-infection_2
IFN-γ timing experiments

tag: cell line


title: DSP.1001660012998.D.C09.dcc

description: Library name: DSP.1001660012998.D.C09.dcc

tag: group

tag: Sex


title: DSP.1001660012998.D.C08.dcc

description: Library name: DSP.1001660012998.D.C08.dcc

tag: tissue

tag: braak


title: WT_Batch1_Nil_Rep1[RNA_Seq]


title: DSP.1001660012998.D.C07.dcc

description: Library name: DSP.1001660012998.D.C07.dcc

value: Non-AD

tag: pmd


title: 6h_no_IFNg_2

description:
Library name: ES_C4_6h-after-infection_2
IFN-γ timing experiments

tag: strain

tag: treatment


title: DSP.1001660012998.D.C06.dcc

description: Library name: DSP.1001660012998.D.C06.dcc

tag: age

tag: ph


title: WT_Batch1_LPS_Rep2[RNA_Seq]


title: WT_Batch1_LPS_Rep1[RNA_Seq]


title: DSP.1001660012998.D.C05.dcc

description: Library name: DSP.1001660012998.D.C05.dcc

tag: weight

tag: csf


title: 6h_no_IFNg_1

description:
Library name: ES_C4_6h-after-infection_1
IFN-γ timing experiments


title: DSP.1001660012998.D.C03.dcc

description: Library name: DSP.1001660012998.D.C03.dcc

tag: area

tag: slide


title: 6h_full_IFNg_2

description:
Library name: ES_C3_6h-after-infection_2
IFN-γ timing experiments

tag: cell type


title: WT_Batch1_LC21_Rep2[RNA_Seq]

tag: genotype


title: DSP.1001660012998.D.C02.dcc

description: Library name: DSP.1001660012998.D.C02.dcc

tag: batch

tag: apoe


title: 6h_IFNg_after_infection_3

description:
Library name: ES_C2_6h-after-infection_3
IFN-γ timing experiments

tag: cell line


title: DSP.1001660012998.D.C01.dcc

description: Library name: DSP.1001660012998.D.C01.dcc

tag: group

tag: Sex


title: 6h_full_IFNg_3

description:
Library name: ES_C3_6h-after-infection_3
IFN-γ timing experiments

tag: tissue


title: DSP.1001660012998.D.C04.dcc

description: Library name: DSP.1001660012998.D.C04.dcc

tag: braak

tag: pmd


title: WT_Batch1_LC21_Rep1[RNA_Seq]

tag: treatment


title: WT_Batch1_LC_Rep2[RNA_Seq]


title: 6h_full_IFNg_1

description:
Library name: ES_C3_6h-after-infection_1
IFN-γ timing experiments

tag: strain


title: WT_Batch1_LC_Rep1[RNA_Seq]


title: 6h_IFNg_after_infection_2

description:
Library name: ES_C2_6h-after-infection_2
IFN-γ timing experiments


title: WT_Batch1_CD154_Rep2[RNA_Seq]


title: DSP.1001660012998.D.B11.dcc

description: Library name: DSP.1001660012998.D.B11.dcc

tag: age

tag: ph


title: 6h_IFNg_after_infection_1

description:
Library name: ES_C2_6h-after-infection_1
IFN-γ timing experiments


title: CD154_Rep2[RNA_Seq]

data_processing:
RNA samples were scored by FastQC
RNA samples were trimed by trim_galore
RNA samples were mapped by HISAT2
RNA samples were sored by samtools, removed duplicates
Reads counts were extracted and normalized
Assembly: mm10
Supplementary files format and content: Normalized reads count in csv format.  Processed_data_RNA_Seq_WT_B_cells_CD154_IL27_IL21_IFNgamma.csv


title: 6h_IFNg_before_infection_3

description:
Library name: ES_C1_6h-after-infection_3
IFN-γ timing experiments


title: CD154_Rep1[RNA_Seq]


title: PeripheralBlood_BreastCancer_A2365

type: RNA

city: Tomsk

first: Alexei

middle: A

last: Sleptcov

address: Ushaika 10

department: Research Institute of Medical Genetics

country: Russia

institute: Tomsk National Research Medical Center

hyb_protocol: conducted in accordance with the manufacturer’s protocol (version 6.9.1)

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D) using one color scan settings for 1×60K array slides (Scan Area 61×21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Signal processing was performed using the Feature Extraction software, version 10.7.3.1 (Agilent Technologies, USA). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Peripheral blood

extract_protocol:
sample collection: Blood was collected in tubes containing EDTA and  transported to the laboratory. RNA stabilization was performed using RNAlater/RNA Stabilization Reagent (Qiagen, Germany)
Mononuclear cells were isolated using a Ficoll density gradient (density 1.077 g/cm³, PanEco, Russia). Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific, USA, Cat. No. 15596026) in accordance with the manufacturer’s protocol
quality assessing: RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA), with the RNA Integrity Number (RIN) as the key parameter
cDNA synthesis: A cDNA Master Mix was prepared, containing, per sample: 2 µL of 5× First Strand Buffer, 1 µL of 0.1 M DTT, 0.5 µL of 10 mM dNTP Mix, and 1.2 µL of AffinityScript RNase Block Mix (containing a mixture of enzymes, added last). A volume of 4.7 µL of cDNA Master Mix was added to each tube to achieve a final volume of 10 µL, gently mixed using a vortex centrifuge, and incubated in a thermal cycler for 2 hours at 40°C, followed by 15 minutes at 70°C
cRNA synthesis: A Transcription Master Mix was prepared containing, per sample: 0.75 µL of nuclease-free water, 3.2 µL of 5× Transcription Buffer, 0.6 µL of 0.1 M DTT, 1 µL of NTP Mix, 0.21 µL of T7 RNA Polymerase Blend (containing a mixture of enzymes, added last), and 0.24 µL of Cyanine 3-CTP. A volume of 6 µL of the Transcription Master Mix was added to each tube to achieve a final volume of 16 µL. Samples were incubated in a thermal cycler for 2 hours at 40°C.

value: whole blood

tag: gender

value: female

tag: sample group

value: Breast cancer group


title: PeripheralBlood_BreastCancer_A2352

label_protocol: conducted in accordance with the manufacturer’s protocol (version 6.9.1)


title: DSP.1001660012998.D.B09.dcc

description: Library name: DSP.1001660012998.D.B09.dcc

value: P

tag: weight

tag: csf

tag: area

tag: slide


title: DSP.1001660012998.D.B08.dcc

description: Library name: DSP.1001660012998.D.B08.dcc

tag: cell type

value: PP

tag: batch

tag: apoe


title: DSP.1001660012998.D.B06.dcc

description: Library name: DSP.1001660012998.D.B06.dcc

tag: group

tag: Sex


title: DSP.1001660012998.D.B12.dcc

description: Library name: DSP.1001660012998.D.B12.dcc

tag: tissue

tag: braak


title: 6h_IFNg_before_infection_2

description:
Library name: ES_C1_6h-after-infection_2
IFN-γ timing experiments

tag: cell line

tag: treatment


title: PeripheralBlood_Control_7

value: Control group


title: 6h_IFNg_before_infection_1

description:
Library name: ES_C1_6h-after-infection_1
IFN-γ timing experiments

value: bone marrow

tag: strain


title: CD154_IL-27_Rep1[RNA_Seq]

value: B cell

tag: genotype

value: WT


title: DSP.1001660012998.D.B07.dcc

description: Library name: DSP.1001660012998.D.B07.dcc

tag: age

tag: pmd

tag: ph


title: PeripheralBlood_BreastCancer_A2333

tag: gender

tag: sample group


title: PeripheralBlood_Control_4


title: CD154_IL-21_Rep1[RNA_Seq]


title: not_treated_3

description:
Library name: ES_not-treated_before-infection_3
IFN-γ timing experiments

value: primary cells

value: uninfected


title: PeripheralBlood_Control_1


title: PeripheralBlood_BreastCancer_A2340


title: CD154_IL-27_Rep2[RNA_Seq]


title: CD154_IFNgamma_Rep2[RNA_Seq]

value: IFNgamma


title: DSP.1001660012998.D.B03.dcc

description: Library name: DSP.1001660012998.D.B03.dcc

value: Hippocampus

value: CU-AP

tag: weight

tag: csf

tag: area

tag: slide


title: CD154_IL-21_Rep2[RNA_Seq]

tag: cell type


title: Tumor-AID-scRNA-seq_GEX

description: Library name: Tumor-AID-scRNA-seq_GEX

data_processing:
scRNA-seq was aligned using CellRanger and demultiplexed using hashtag oligos. Cells and genes were filtered according to mean counts, and leiden clustering was performed at a resolution of 0.25. Then, data were pseudobulked and differential expression was performed using DESeq2.
Assembly: mm39
Supplementary files format and content: adata

source_name: Tumor, Lymph nodes

extract_protocol:
Treg cells were multiplexed together from SLO or tumor. For more details, refer to Methods.
RNA sequencing was performed using 10X genomics. For tumor: cells were hybridized for 18 hours, washed, and encapsulated in one lane targeting 60,000 cells. Indexing PCR steps were performed using 9 amplification cycles for both the gene expression and cell surface protein libraries. Final sequencing libraries were sequenced on an Illumina NovaSeq X Plus System (index 1: 10 cycles, index 2: 10 cycles, read 1: 28 cycles, read 2: 88 cycles). For SLO: Approximately 30,000 cells were targeted. Final libraries were sequenced on Illumina NovaSeq 6000 - S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles). Viable cells were identified on the basis of library size and complexity, whereas cells with >20% of transcripts derived from mitochondria were excluded from further analysis.

value: Tumor, Lymph nodes

value: Treg

value: Foxp3-AID ROSA26-WT & Foxp3-AID ROSA26-TIR1(F74G)

value: 5-ph-IAA 14 days


title: DSP.1001660012998.D.B02.dcc

description: Library name: DSP.1001660012998.D.B02.dcc

data_processing:
Demultiplex to FASTQ and convert to DCC with GeoMx NGS Pipeline/GUI.
Map oligo barcodes to human gene symbols using the GeoMx Human WTA PKC annotation.
AOI QC thresholds: ≥1,000 reads/AOI; ≥80% trimmed; ≥80% stitched; ≥75% aligned; ≥50% sequencing saturation. Failing AOIs were excluded.
Assembly: Gene identifiers derived from the GeoMx Human Whole Transcriptome (WTA) probe annotation (PKC file): Hs_R_NGS_WTA_v1.0.pkc
Supplementary files format and content: dcc/ - one .dcc file per AOI (barcode counts). dcc_stats/ - per-AOI .stats.txt files generated by GeoMx NGS.
Library strategy: Spatial Transcriptomics

value: Microglia

tag: batch

tag: group

tag: apoe

tag: Sex

value: M


title: zebrafish larvae, dexamethasone treatment combined with GCRV-II infection, Day 6, rep2

city: Wuhan

first: siyao

last: Zheng

address: No.7, Donghu South Road, Wuchang

country: China

institute: Institute of Hydrobiology, Chinese Academy of Sciences

description:
DG-WT-2
bony fishes

data_processing:
The libraries were sequenced on an Illumina NovaSeq platform to generate 150 bp paired-end reads, according to the manufacturer’s instructions.
The raw reads were further processed with a bioinformatic pipelinetool, BMKCloud (www.biocloud.net) online platform.
Assembly: Danio_rerio.GCF_000002035.6_GRCz11
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

organism: Danio rerio

source_name: larvae

extract_protocol:
The animal total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: AB

tag: tissue

value: larvae

tag: treatment

value: dexamethasone combined with GCRV-II infection

tag: time point

value: Day 6


title: D7_HTO_sc

description: Library name: 4328_WH-1961_Day7_HTO_IGO_12437

value: Spleen & Lymph nodes

tag: genotype

value: 5-ph-IAA 7 Days


title: not_treated_1

description:
Library name: ES_not-treated_before-infection_1
IFN-γ timing experiments

value: bone marrow

tag: cell line

value: primary cells

value: bone marrow-derived macrophages

tag: strain


title: not_treated_2

description:
Library name: ES_not-treated_before-infection_2
IFN-γ timing experiments

value: uninfected


title: DSP.1001660012998.D.B01.dcc

description: Library name: DSP.1001660012998.D.B01.dcc

extract_protocol:
FFPE blocks were sectioned at 8 μm using a rotary microtome. Three of these tissue squares were mounted per SuperFrost Plus slide within the designated GeoMx scan area.
Slide preparation followed the standard GeoMx Slide Preparation protocol . Probe mic: GeoMx Whole Transcriptome Probe Mix. Library quality was verified on an Agilent TapeStation D1000. Sequencing was performed on an Illumina NextSeq 2000 (X-LEAP chemistry), paired-end.

value: Hippocampus

value: P

value: CU-AP

tag: age

tag: braak

tag: pmd

tag: ph


title: DSP.1001660012998.D.B10.dcc

description: Library name: DSP.1001660012998.D.B10.dcc

value: PP

value: AD

tag: weight

tag: csf

tag: area


title: zebrafish larvae, dexamethasone treatment combined with GCRV-II infection, Day 6, rep1

description:
DG-WT-1
bony fishes

value: WT


title: Tumor-AID-scRNA-seq_CITE

description: Library name: Tumor-AID-scRNA-seq_CITE

value: Tumor, Lymph nodes

tag: cell type

value: Treg

value: Foxp3-AID ROSA26-WT & Foxp3-AID ROSA26-TIR1(F74G)

value: 5-ph-IAA 14 days


title: zebrafish larvae, GCRV-II infection, Day 6, rep3

description:
G-WT-3
bony fishes

value: AB

value: larvae

value: GCRV-II infection

value: Day 6


title: zebrafish larvae, dexamethasone treatment combined with GCRV-II infection, Day 6, rep3

description:
DG-WT-3
bony fishes

value: dexamethasone combined with GCRV-II infection


title: PeripheralBlood_Control_3

value: whole blood

tag: gender

value: female

tag: sample group

value: Control group


title: CD154_IFNgamma_Rep1[RNA_Seq]

value: B cell

value: IFNgamma


title: D3_HTO_sc

description: Library name: 4327_WH-1961_Day3_HTO_IGO_12437

value: Spleen & Lymph nodes

value: 5-ph-IAA 3 Days


title: zebrafish larvae, GCRV-II infection, Day 6, rep2

description:
G-WT-2
bony fishes

value: WT


title: IgD_Pos_GFP_Neg_Rep2[RNA_Seq]

data_processing:
RNA samples were scored by FastQC
RNA samples were trimed by trim_galore
RNA samples were mapped by HISAT2
RNA samples were sored by samtools, removed duplicates
Reads count were extracted and normalized
Assembly: mm10
Supplementary files format and content: Normalized reads count in csv format.Processed_data_RNA_Seq_invivo_Il27_GFP_B_cells.csv

value: Il27p28 GFP reporter

value: vaccinia virus (Western Reserve strain) infection


title: DSP.1001660012998.D.A12.dcc

description: Library name: DSP.1001660012998.D.A12.dcc

value: Hippocampus

value: Microglia

value: A

tag: batch

tag: group

value: CU-AP

tag: slide

tag: apoe

tag: Sex

value: M


title: zebrafish larvae, GCRV-II infection, Day 6, rep1

description:
G-WT-1
bony fishes

value: AB

tag: genotype

tag: tissue

value: larvae

tag: treatment

value: GCRV-II infection

tag: time point

value: Day 6


title: IgD_Pos_GFP_Neg_Rep1[RNA_Seq]


title: zebrafish larvae, dexamethasone treatment, Day 6, rep3

description:
D-WT-3
bony fishes

tag: strain

value: dexamethasone


title: D7_sc

description: Library name: 4328_WH-1961_Day7_IGO_12437

value: Treg

value: Foxp3-AID ROSA26-WT & Foxp3-AID ROSA26-TIR1(F74G)

value: 5-ph-IAA 7 Days


title: D0_sc

description: Library name: 4326_WH-1961_Day0_IGO_12437

value: Spleen & Lymph nodes


title: IgD_Neg_GFP_Pos_Rep2[RNA_Seq]

value: B cell


title: D0_HTO_sc

description: Library name: 4326_WH-1961_Day0_HTO_IGO_12437


title: zebrafish larvae, dexamethasone treatment, Day 6, rep2

description:
D-WT-2
bony fishes

value: WT


title: zebrafish larvae, dexamethasone treatment, Day 6, rep1

description:
D-WT-1
bony fishes


title: zebrafish larvae, control, Day 6, rep3

description:
WT-3
bony fishes

value: control


title: DSP.1001660012998.D.A10.dcc

description: Library name: DSP.1001660012998.D.A10.dcc

value: Hippocampus

value: AD

tag: age

tag: braak

tag: pmd

tag: ph

value: F


title: DSP.1001660012998.D.A06.dcc

description: Library name: DSP.1001660012998.D.A06.dcc

tag: cell type

value: Microglia

value: P

tag: weight

tag: csf

tag: area


title: DSP.1001660012998.D.B05.dcc

description: Library name: DSP.1001660012998.D.B05.dcc

tag: batch

tag: group

value: M


title: IgD_Neg_GFP_Neg_Rep2[RNA_Seq]

value: Il27p28 GFP reporter

value: vaccinia virus (Western Reserve strain) infection


title: DSP.1001660012998.D.A08.dcc

description: Library name: DSP.1001660012998.D.A08.dcc

value: A

tag: slide

tag: apoe


title: DSP.1001660012998.D.A11.dcc

description: Library name: DSP.1001660012998.D.A11.dcc

value: CU-AP

tag: Sex


title: IgD_Neg_GFP_Neg_Rep1[RNA_Seq]

tag: genotype


title: zebrafish larvae, control, Day 6, rep2

description:
WT-2
bony fishes

value: AB

tag: tissue

value: larvae

tag: treatment

value: Day 6


title: DSP.1001660012998.D.A09.dcc

description: Library name: DSP.1001660012998.D.A09.dcc


title: D7 TIR1 rep2

description: Library name: d7_degradation_AC382_IGO_15393_16_S117

data_processing:
ATAC-seq was aligned using bowtie2 to mm10. Peaks were called using MACS2  with a p-value cutoff of .05, --nomodel, --shift=-100, and --extsize of 200. IDR was run on replicates with an IDR threshold of .2. Reproducible peaks were merged into a single peak atlas, and peak summits overlapping these peaks (n=248805) were used for quantification. Reads were quantified with FeatureCounts and differential peaks were called with DESeq2.
Assembly: mm10
Supplementary files format and content: Counts matrices, .tsv

extract_protocol:
50,000 cells were washed in ice cold PBS and lysed in 50 µL of ATAC-seq lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40). Following lysis, nuclei were peletted and incubated in 1x transposition buffer (Nextera TD buffer) containing 2.5 μL Nextera Tn5 transposase for 30 min at 37 degrees.
Transposed DNA fragments were isolated using QIAGEN MinElute Reaction Cleanup kit and amplified using barcoded primers with Illumina adaptor sequences. The number of cycles used for library amplification was determined using a quantitative PCR side-reaction. Amplified libraries were purified and size selected using Ampure XP beads using consecutive purifications with bead-to-sample ratios of 0.5 and 1.8. After PicoGreen quantification and quality control by Agilent BioAnalyzer, libraries were sequenced on a on a NovaSeq 6000 in a PE100 run using the NovaSeq 6000 S4 Reagent Kit (200 cycles).

value: Spleen & Lymph nodes

value: Treg

value: Foxp3-AID ROSA26-TIR1(F74G)

value: 5-ph-IAA 7 Days


title: BATF3_WT_LA21_Rep3[RNA_Seq]

data_processing:
RNA samples were scored by FastQC
RNA samples were trimed by trim_galore
RNA samples were mapped by HISAT2
RNA samples were sored by samtools, removed duplicates
Reads counts were extracted and normalized
Assembly: mm10
Supplementary files format and content: Normalized reads count in csv format. Processed_data_BATF3_KO_RNA_Seq.csv

value: B cell

value: WT


title: zebrafish larvae, control, Day 6, rep1

description:
WT-1
bony fishes

tag: strain

value: control

tag: time point


title: D7 TIR1 rep3

description: Library name: d7_degradation_E512_IGO_15393_17_S118


title: BATF3_WT_LA21_Rep2[RNA_Seq]


title: IgD_Neg_GFP_Pos_Rep1[RNA_Seq]


title: BATF3_WT_LA21_Rep1[RNA_Seq]


title: D3_sc

description: Library name: 4327_WH-1961_Day3_IGO_12437

value: Foxp3-AID ROSA26-WT & Foxp3-AID ROSA26-TIR1(F74G)

value: 5-ph-IAA 3 Days


title: DSP.1001660012998.D.A05.dcc

description: Library name: DSP.1001660012998.D.A05.dcc

value: Hippocampus

value: Microglia

value: PP

value: AD

tag: age

tag: braak

value: F


title: BATF3_KO_LA21_Rep3[RNA_Seq]

value: Batf3 knockout


title: BATF3_KO_LA21_Rep2[RNA_Seq]


title: DSP.1001660012998.D.A03.dcc

description: Library name: DSP.1001660012998.D.A03.dcc

tag: pmd

tag: ph


title: D7 WT rep2

description: Library name: d7_degradation_AC370_IGO_15393_12_S114

source_name: Spleen & lymph nodes

value: Spleen & lymph nodes

tag: cell type

value: Foxp3-AID ROSA26-WT


title: DSP.1001660012998.D.A02.dcc

description: Library name: DSP.1001660012998.D.A02.dcc

source_name: Hippocampus

value: P

tag: weight

tag: csf


title: D7 TIR1 rep1

description: Library name: d7_degradation_AC307_IGO_15393_14_S116

value: Treg