title: CD133highCD71lowFSCmid-high

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

data_processing:
bcl2fastq v2.20 (loaded by cellranger mkfastq (3.0.1)) software used for basecalling.
reads were aligned to refdata-cellranger-mm10-1.2.0 genome assembly using cellranger v3.0.1
Counting data of reference gene expression levels were generated by cellranger v3.0.1 (automatic identification of chemistry properties)
Assembly: mm10
Supplementary files format and content: Tab separated values; MatrixMarket

source_name: Pancreas

growth_protocol: adult mice (C57BL/6J; 8-12 weeks old)

extract_protocol:
Pancreata from adult normal mice (n=5 mice per experiment) were dissociated by collagenase B, and FACS sorted to obtain the CD133(hi)CD71(low)FSC(mid-high) (abbreviated as FSC-MH) or the CD133(hi)CD71(low)FSC(low) (abbreviated as FSC-L) sub-populations. These two sub-populations were then captured on a 10xGenomics Chromium controller using a Chromium single cell 3' library & Gel Bead kit V3 kit.
Reverse transcription was performed in emulsion droplet with 10xGEM beads, full length cDNA was amplified and 3' expression library was constructed with Tn5 transposase based method (with 10xGenomics chromium single cell 3' Library Constraction Kit V2).

tag: tissue

value: Pancreas


title: 1_012

status: Public on Dec 04 2023

type: SRA

city: Columbus

first: Jose

middle: Javier

last: Otero

state: Ohio

address: 333 W 10th Ave, 4170 Graves Hall

department: Pathology

country: USA

institute: The Ohio State University

library_source: transcriptomic

data_processing:
FASTQ files were processed through the GeoMx NGS pipeline, uploaded to the GeoMx, and standard QC applied to flag individual collections with <1000 raw reads, <80% aligned reads, <50% sequencing saturation, nuclei count <100, or No Template control counts are >1000. Additionally, segments were filtered out if they contained fewer than 10% of probes above threshold LOQ (=2*neg probe geomean or 2, whichever is higher), and probes were filtered out if they were above the LOQ in 10% of the segments or more.
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached PKC file (Hs_R_NGS_WTA_COVID19_v1.0.pkc)
Supplementary files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary files format and content: Values represented in the processed data file are the geometric mean of the probes for a given target--in the case that multiple probes were used-- and excludes any targets flagged as outliers. Analyzed counts represent the upper quartile normalized collapsed counts across the study after removing QC flagged segments and features.
Library strategy: GeoMx Seq

molecule: total RNA

organism: Homo sapiens

source_name: Brain

extract_protocol:
hyb protocol: Slides were incubated with a cocktail of barcoded ISH probes overnight at 37C in a hybridization oven, and then at RT blocked for 30 minutes then incubated for 1 hour (also RT) with a cocktail of DNA stain (SYTO13) with fluorescent antibodies.
scan protocol: Slides were scanned at low resolution on the GeoMx to identify tissue regions, and then High-Resolution scans using the 20X objective were performed using the pre-built scanning conditions for the Fluorescent antibody kit from Nanostring.
Samples were pooled during library preparation. Individual FASTQ files were generated for each ROI, forward & reverse primers.

tag: slide id

value: Slide 1 (case 12-10)

tag: roi number

tag: segment type

value: Full ROI

tag: diagnosis

value: glioblastoma

tag: disease state

value: PD

tag: histology

value: Inflammatory

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: 2_6_CD4_PanCK_WTA | 020 | PanCK

city: Palo Alto

first: Audrey

last: Lee

state: CA

address: 240 Pasteur Dr. 1500 BMI

institute: Stanford University

description: GeoMx DSP

data_processing:
FASTQ files generated upon sequencing were converted to Digital Count Conversion (DCC) files using the NanoString Technologies publicly available pipeline (v2.0.21) (GeoMx® NGS Pipeline (illumina.com)). Through the pipeline, individual probe alignment was performed using identification of read tag sequences (RTS), and duplicate counts of probes generated during the library preparation polymerase chain reaction were removed through evaluation of the probe unique molecular identifier (UMI) sequences.
Supplementary files format and content: DCC files
Library strategy: GeoMx DSP

molecule: polyA RNA

organism: Mus musculus

source_name: FFPE lung tissue section

extract_protocol:
Murine lungs were harvested, formalin-fixed and paraffin-embedded. FFPE tissues were sectioned for GeoMx digital spatial profiling (DSP).
For library preparation, Illumina i5 and i7 dual indexing primers were added to the oligonucleotide tags during PCR to uniquely index each AOI. Next generation sequencing (NGS) library preparation was performed according the NanoString Technologies published protocol (GeoMx DSP NGS Readout User Manual (nanostring.com)).

value: Lungs

tag: cell type

value: CD4 and PanCK+ cells

tag: stained with

value: PanCK

tag: slide

tag: region of_interest_id

value: ROI 020

tag: strain

tag: treatment


title: 2_6_CD4_PanCK_WTA | 019 | PanCK

description: GeoMx DSP

tag: tissue

value: ROI 019


title: 2_6_CD4_PanCK_WTA | 030 | PanCK

description: GeoMx DSP

value: ROI 030


title: 2_6_CD4_PanCK_WTA | 023 | PanCK

description: GeoMx DSP

value: ROI 023


title: 2_6_CD4_PanCK_WTA | 024 | PanCK

description: GeoMx DSP

value: ROI 024


title: 2_6_CD4_PanCK_WTA | 018 | PanCK

description: GeoMx DSP

value: ROI 018


title: 1_016

description: Samples were pooled during library preparation. Individual FASTQ files were generated for each ROI, forward & reverse primers.

tag: slide id

tag: roi number

tag: segment type

tag: diagnosis

tag: disease state

tag: histology


title: Ly6GC negative cells, GEX

city: White/Caucasian

first: Tammy

last: Kielian

state: NE

address: 985900 Nebraska Medical Center

institute: UNMC

description:
polyA RNA
Monocytes_GEX

data_processing:
*library strategy: CITE-seq
CellRanger v4 count and aggr functions to aggregate reads across sequencing lanes into a single set of barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz for each sample.
Cell barcodes from CellRanger output were used to quantify ADTs using CITE-seq-Count.
Assembly: mm10
Supplementary files format and content: CellRanger output files for Ly6GC positive sample: Ly6GC_plus_barcodes.tsv.gz, Ly6GC_plus_features.tsv.gz, and Ly6GC_plus_matrix.mtx.gz.
Supplementary files format and content: CellRanger output files for Ly6GC negative sample: Monocytes_barcodes.tsv.gz, Monocytes_features.tsv.gz, and Monocytes_matrix.mtx.gz.

source_name: implant-associated tissue

extract_protocol:
Ly6G+Ly6C+ and Ly6C+G- cells (13,627 and 1,624, respectively) were processed using a 10X Genomics platform by the UNMC Genomics Core. Briefly, single cells were lysed, RNA was reverse-transcribed and barcoded using a Chromium Single-Cell 3’ Reagent Kit v3 (10X Genomics) according to the manufacturer’s protocol.
Illumina compatible cDNA libraries were created and quantified by quantitative PCR using the KAPA Library Quant Kit (Illumina) and were loaded at a concentration of 1.3 pM on an Illumina NovaSeq instrument. Samples were sequenced following the parameters suggested by 10X Genomics to an average read depth of 100,000 reads/cell.

value: implant-associated tissue

value: Ly6GC negative cells

tag: library type

value: mRNA


title: Ly6GC positive cells, GEX

description:
polyA RNA
LY6GC_Plus_GEX

value: Ly6GC positive cells


title: 2_6_CD4_PanCK_WTA | 021 | PanCK

description: GeoMx DSP

value: ROI 021


title: 1_011

value: Slide 1 (case 12-10)

value: Full ROI

value: glioblastoma

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: 1_010

value: PD

value: Inflammatory

tag: stitchedreads

tag: sequencingsaturation


title: CD133highCD71lowFSClow

tag: tissue

value: Pancreas

tag: strain


title: 2_6_CD4_PanCK_WTA | 017 | PanCK

description: GeoMx DSP

value: Lungs

tag: cell type

value: CD4 and PanCK+ cells

tag: stained with

value: PanCK

tag: slide

tag: region of_interest_id

value: ROI 017

tag: treatment


title: 1_009

tag: slide id

tag: roi number

tag: segment type

tag: diagnosis

tag: disease state

tag: histology


title: 2_6_CD4_PanCK_WTA | 016 | PanCK

description: GeoMx DSP

value: ROI 016


title: islet_particle_2

first: Avnesh

middle: S

last: Thakor

state: California

address: 3155 Porter Drive

department: Radiology

data_processing:
Sequenced reads were trimmed for adaptor sequence,
Then mapped to mouse genome Mus Musculus using HISTAT
HTSeq was used to generate the raw read counts
DESeq2 was used for differential gene expression analysis
Assembly: (GRCm39/mm39)
Supplementary files format and content: tab-delimited text file include FPKM values for all samples
Supplementary files format and content: tab-delimited text file include raw counts for all samples

source_name: pancreatic islets

extract_protocol:
total RNA was extracted from each replicate using the RNAeasy minikit (qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: pancreatic islets

value: primary

tag: genotype

value: wt

value: inflammatory cocktail with particle


title: 2_6_CD4_PanCK_WTA | 015 | PanCK

description: GeoMx DSP

value: ROI 015


title: 2_6_CD4_PanCK_WTA | 014 | PanCK

description: GeoMx DSP

value: ROI 014

value: BCG


title: islet_particle_3


title: 2_6_CD4_PanCK_WTA | 014 | CD4

description: GeoMx DSP


title: 1_008

value: Slide 1 (case 12-10)

value: Full ROI

value: Hypercellular

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: islet_particle_1

tag: tissue

tag: cell type

tag: strain


title: 2_6_CD4_PanCK_WTA | 013 | PanCK

description: GeoMx DSP

tag: stained with

tag: slide

tag: region of_interest_id

value: ROI 013

tag: treatment


title: islet_inflam_3

value: inflammatory cocktail


title: 1_007

tag: slide id

tag: roi number

tag: segment type

tag: diagnosis

value: glioblastoma

tag: disease state

value: PD

tag: stitchedreads

tag: sequencingsaturation


title: Ly6GC positive cells, CSP

description:
Antibody-derived oligonucleotide (ADT)
Ly6GC_plus_barcodes.tsv.gz
Ly6GC_plus_features.tsv.gz
Ly6GC_plus_matrix.mtx.gz
Ly6GC_Plus_CSP

library_source: other

molecule: protein

value: implant-associated tissue

value: Ly6GC positive cells

tag: library type

value: ADT

tag: adt

value: TotalSeq-B0114 F4/80, TotalSeq-B0117 I-A/I-E


title: 1_006

tag: histology

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: 2_6_CD4_PanCK_WTA | 012 | CD4

description: GeoMx DSP

tag: tissue

value: Lungs

tag: cell type

value: CD4 and PanCK+ cells

tag: stained with

tag: slide

tag: region of_interest_id

value: ROI 012

tag: strain

tag: treatment


title: islet_inflam_2

value: pancreatic islets

value: primary

tag: genotype

value: wt


title: 1_005

tag: slide id

value: Slide 1 (case 12-10)

tag: roi number

tag: segment type

tag: diagnosis

tag: disease state

tag: stitchedreads

tag: sequencingsaturation


title: islet_inflam_1


title: 2_6_CD4_PanCK_WTA | 011 | CD4

description: GeoMx DSP

value: ROI 011

value: BCG


title: 1_004

value: Full ROI

tag: histology

value: Hypercellular

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: 2_6_CD4_PanCK_WTA | 010 | CD4

description: GeoMx DSP

tag: tissue

tag: cell type

tag: stained with

tag: slide

tag: region of_interest_id

value: ROI 010

tag: strain


title: isle_control_3

tag: genotype

tag: treatment

value: no


title: Ly6GC negative cells, CSP

description:
Antibody-derived oligonucleotide (ADT)
Monocytes_barcodes.tsv.gz
Monocytes_features.tsv.gz
Monocytes_matrix.mtx.gz
Monocytes_CSP

value: implant-associated tissue

value: Ly6GC negative cells

tag: library type

tag: adt


title: 1_003

tag: slide id

tag: roi number

tag: segment type

tag: diagnosis

value: glioblastoma

tag: disease state

value: PD

tag: histology

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: 2_6_CD4_PanCK_WTA | 009 | PanCK

description: GeoMx DSP

tag: tissue

value: Lungs

tag: cell type

tag: stained with

value: PanCK

value: ROI 009


title: 1_002

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: isle_control_2

value: pancreatic islets

tag: strain

tag: genotype

tag: treatment


title: 2_6_CD4_PanCK_WTA | 008 | PanCK

description: GeoMx DSP

value: CD4 and PanCK+ cells

tag: slide

tag: region of_interest_id

value: ROI 008


title: 2_6_CD4_PanCK_WTA | 008 | CD4

description: GeoMx DSP


title: 2_6_CD4_PanCK_WTA | 007 | CD4

description: GeoMx DSP

value: ROI 007


title: 1_001

tag: slide id

value: Slide 1 (case 12-10)

tag: roi number

tag: segment type

tag: diagnosis

tag: disease state

tag: histology

tag: trimmedreads


title: 2_6_CD4_PanCK_WTA | 013 | CD4

description: GeoMx DSP

tag: tissue

tag: cell type

tag: stained with

value: ROI 013

value: BCG


title: 2_6_CD4_PanCK_WTA | 011 | PanCK

description: GeoMx DSP

value: ROI 011


title: 2_6_CD4_PanCK_WTA | 006 | CD4

description: GeoMx DSP

value: ROI 006


title: 2_6_CD4_PanCK_WTA | 007 | PanCK

description: GeoMx DSP


title: 2_6_CD4_PanCK_WTA | 006 | PanCK

description: GeoMx DSP


title: 2_6_CD4_PanCK_WTA | 012 | PanCK

description: GeoMx DSP

value: ROI 012


title: snmC-seq2 of mus musculus: adult male ventral hippocampus WSB [WSB_vhipp_1_methyl]

city: Los Angeles

first: Patrick

last: Chen

address: 635 Charles E Young Dr S

department: Psychiatry

institute: UCLA

description:
WSB_vhipp_1_methyl
allc_allstrains_alltypes_updatedcelltypes.tar

library_source: genomic

data_processing:
snmC2-seq
Reads were mapped using Bismark V0.22.3, followed by cell filtering based on mCCC levels, global mCG levels, global mCH levels, total mapped reads, Bismark mapping rate, and percent genome covered
Methylation features were calculated as fractions of methylcytosine over total cytosine across gene bodies ± 2kb flanking regions and 100kb bins spanning the entire genome. Methylation features were further split into CG and CH methylation types. Principal component analysis was run using Scanpy followed by knn using only the top 16 principal components by amount of variance explained and k=15. Harmony was used to correct batch between strains and unbias clusters arising from strain differences. After Harmony was applied, iterative clustering was performed with a combination of leiden unsupervised clustering and UMAP dimensionality reduction, identifying clusters as cell types by marker gene hypomethylation
Assembly: mm10
Supplementary files format and content: tab-separated file including raw pseudobulk counts for each sample and cell type
Supplementary files format and content: tab-separated file including number of cells for each sample and cell type

molecule: genomic DNA

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2032
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2032

value: WSB

value: Brain

tag: age

value: adult

tag: Sex

value: male


title: snmC-seq2 of mus musculus: adult male ventral hippocampus WSB [WSB_vhipp_2_methyl]

description:
WSB_vhipp_2_methyl
allc_allstrains_alltypes_updatedcelltypes.tar

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2033
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2033

tag: strain


title: s005_IMR90ISS 1G

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were aligned using STAR v2.7.3a.(Dobin et al.)
Transcript abundance was estimated in STAR during alignment using the algorithm or htseq-count
Assembly: GRCh38 Ensemble release 86: Homo_sapiens.GRCh38.dna.primary_assembly.fa, Homo_sapiens.GRCh38.86.gtf
Supplementary files format and content: comma delimited text file containing ensembl ID, gene symbol, gene description and raw read counts for each sample (in columns) for each annotated transcript (in rows).

source_name: cardiomyocytes

extract_protocol:
RNA was isolated using RNeasy Mini Kit (Qiagen) as per the manufacturer's instructions. RNA concentration was measured using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific)
Two nanograms of total RNA was used as input for cDNA synthesis, using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using the NexteraXT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on an Agilent 4200 TapeStation, pooled at equimolar concentrations, and sequenced on an Illumina NovaSeq 6000 at 100SR.

value: cardiomyocytes

tag: cell line

value: ISS 1G


title: s006_IMR90ISS 1G

tag: treatment


title: 2_6_CD4_PanCK_WTA | 010 | PanCK

description: GeoMx DSP

value: Lungs

value: PanCK

tag: slide

value: ROI 010


title: 2_6_CD4_PanCK_WTA | 005 | PanCK

description: GeoMx DSP

value: CD4 and PanCK+ cells

tag: region of_interest_id

value: ROI 005


title: snmC-seq2 of mus musculus: adult male ventral hippocampus PWK [PWK_vhipp_2_methyl]

description:
PWK_vhipp_2_methyl
allc_allstrains_alltypes_updatedcelltypes.tar

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2031
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2031

value: PWK


title: s004_IMR90ISS 1G


title: 2_6_CD4_PanCK_WTA | 005 | CD4

description: GeoMx DSP


title: snmC-seq2 of mus musculus: adult male ventral hippocampus PWK [PWK_vhipp_1_methyl]

description:
PWK_vhipp_1_methyl
allc_allstrains_alltypes_updatedcelltypes.tar

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2030
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2030


title: 2_6_CD4_PanCK_WTA | 004 | PanCK

description: GeoMx DSP

value: ROI 004


title: 2_6_CD4_PanCK_WTA | 003 | PanCK

description: GeoMx DSP

value: ROI 003

value: BCG


title: 2_6_CD4_PanCK_WTA | 004 | CD4

description: GeoMx DSP


title: 2_6_CD4_PanCK_WTA | 009 | CD4

description: GeoMx DSP

value: ROI 009


title: s003_IMR90ISS µG

value: ISS uG


title: isle_control_1

value: pancreatic islets

value: primary

tag: genotype

value: wt

value: no


title: 2_6_CD4_PanCK_WTA | 003 | CD4

description: GeoMx DSP


title: s002_IMR90ISS µG

value: cardiomyocytes


title: snmC-seq2 of mus musculus: adult male ventral hippocampus CAST [CAST_vhipp_2_methyl]

description:
CAST_vhipp_2_methyl
allc_allstrains_alltypes_updatedcelltypes.tar

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2029
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2029

value: CAST

value: Brain

value: adult

value: male


title: 2_6_CD4_PanCK_WTA | 002 | PanCK

description: GeoMx DSP

value: Lungs

value: CD4 and PanCK+ cells

value: PanCK

value: ROI 002


title: snmC-seq2 of mus musculus: adult male ventral hippocampus CAST [CAST_vhipp_1_methyl]

description:
CAST_vhipp_1_methyl
allc_allstrains_alltypes_updatedcelltypes.tar

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2028
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2028


title: 2_6_CD4_PanCK_WTA | 001 | PanCK

description: GeoMx DSP

value: ROI 001


title: 2_6_CD4_PanCK_WTA | 002 | CD4

description: GeoMx DSP

value: BCG


title: s001_IMR90ISS µG


title: 2_6_CD4_PanCK_WTA | 001 | CD4

description: GeoMx DSP


title: 1_6_CD4_PanCK_WTA | 030 | PanCK

description: GeoMx DSP

value: ROI 030


title: 6287_Striatopallidal-medium-spiny-neuron_HSB3881_HD

city: New York

first: Kert

last: Matlik

state: NY

address: 1230 York Avenue

institute: Rockefeller University

description:
6287
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

data_processing:
Sequence and transcript coordinates for human hg38 UCSC genome and gene models were retrieved from the BSgenome.Hsapiens.UCSC.hg38 Bioconductor package (version 1.4.1) and TxDb.Haspiens.UCSC.hg38.knownGene (version 3.4.0) Bioconductor libraries respectively. FANSseq reads were aligned to the genome using Rsubread's subjunc method (version 1.30.6).
Aligned reads were exported as bigWigs normalized to reads per million using the rtracklayer package (version 1.40.6).
Aligned reads in genes were counted using the featurecounts function within the Rsubread package against gene exons.
Assembly: BSgenome.Hsapiens.UCSC.hg38
Supplementary files format and content: BigWig files, Counts files

molecule: nuclear RNA

source_name: Anterior caudate

extract_protocol:
RNA extraction was carried out with AllPrep DNA/RNA FFPE Kit (Qiagen, #80234).
RNA-seq libraries were prepared with Trio RNA-Seq™ library preparation kit (Tecan, #0506-A01) and pooled for sequencing on NovaSeq6000 (SP 2 x 150bp).

treatment_protocol: Nuclei were isolated from fresh-frozen post-mortem human caudate nucleus and putamen, labeled with cell type-specific probes and separated by FACS as described by Matlik et al. 2023.

value: Anterior caudate

value: Striatopallidal medium spiny neuron

value: 43CAG / 25CAG

tag: donor

value: Male

tag: pmi (hrs)

tag: disease

value: HD


title: snmC-seq2 of mus musculus: adult male ventral hippocampus BALBC [BALBC_vhipp_2_methyl]

description:
BALBC_vhipp_2_methyl
allc_allstrains_alltypes_updatedcelltypes.tar

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2027
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2027

value: BALBC


title: 6286_Striatonigral-medium-spiny-neuron_HSB3881_HD

description:
6286
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)

value: Striatonigral medium spiny neuron


title: snmC-seq2 of mus musculus: adult male ventral hippocampus BALBC [BALBC_vhipp_1_methyl]

description:
BALBC_vhipp_1_methyl
allc_allstrains_alltypes_updatedcelltypes.tar

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2026
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2026

value: Brain


title: 1_6_CD4_PanCK_WTA | 028 | PanCK

description: GeoMx DSP

value: ROI 028

value: unimmunized


title: 1_6_CD4_PanCK_WTA | 027 | PanCK

description: GeoMx DSP

value: Lungs

value: ROI 027


title: 1_6_CD4_PanCK_WTA | 026 | PanCK

description: GeoMx DSP

value: CD4 and PanCK+ cells

value: PanCK

value: ROI 026


title: 6283_Interneuron--Non-Fast-Spiking_UWA-6971_HD

description:
6283
RNA extracted from SST-positive striatal interneuron nuclei (SST+, TAC3-, ETV1-)

source_name: Anterior putamen

value: Anterior putamen

value: Interneuron, Non-Fast Spiking

value: 43CAG / 22CAG


title: 1_6_CD4_PanCK_WTA | 025 | PanCK

description: GeoMx DSP

value: ROI 025


title: snmC-seq2 of mus musculus: adult male ventral hippocampus FVB [FVB_vhipp_2_methyl]

description:
FVB_vhipp_2_methyl
allc_allstrains_alltypes_updatedcelltypes.tar

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2025
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2025

value: FVB

value: adult

value: male


title: 6281_Astrocyte_BEB18116_CTRL

description:
6281
RNA extracted from astrocyte nuclei (EAAT1+, IRF8-, NeuN-, OLIG2-)

source_name: Posterior caudate

value: Posterior caudate

value: Astrocyte

value: Male

value: CTRL


title: snmC-seq2 of mus musculus: adult male ventral hippocampus FVB [FVB_vhipp_1_methyl]

description:
FVB_vhipp_1_methyl
allc_allstrains_alltypes_updatedcelltypes.tar

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2024
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2024

value: Brain


title: snmC-seq2 of mus musculus: adult male ventral hippocampus AJ [AJ_vhipp_2_methyl]

description:
AJ_vhipp_2_methyl
allc_allstrains_alltypes_updatedcelltypes.tar

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2023
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2023

value: AJ


title: 1_6_CD4_PanCK_WTA | 024 | CD4

description: GeoMx DSP

value: Lungs

value: ROI 024

value: unimmunized


title: 6280_Microglia_BEB18116_CTRL

description:
6280
RNA extracted from microglial nuclei (IRF8+, EAAT1-, NeuN-, OLIG2-)

value: Microglia


title: 1_6_CD4_PanCK_WTA | 024 | PanCK

description: GeoMx DSP

value: CD4 and PanCK+ cells

value: PanCK


title: 1_6_CD4_PanCK_WTA | 023 | PanCK

description: GeoMx DSP

value: ROI 023


title: 1_6_CD4_PanCK_WTA | 025 | CD4

description: GeoMx DSP

value: ROI 025


title: 1_6_CD4_PanCK_WTA | 022 | PanCK

description: GeoMx DSP

value: ROI 022


title: snmC-seq2 of mus musculus: adult male ventral hippocampus AJ [AJ_vhipp_1_methyl]

description:
AJ_vhipp_1_methyl
allc_allstrains_alltypes_updatedcelltypes.tar

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2022
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2022

value: adult


title: 6279_Oligodendrocyte_BEB18116_CTRL

description:
6279
RNA extracted from oligodendrocyte nuclei (OLIG2+, EAAT1-, NeuN-, IRF8-)

value: Oligodendrocyte


title: 1_6_CD4_PanCK_WTA | 022 | CD4

description: GeoMx DSP

extract_protocol:
Murine lungs were harvested, formalin-fixed and paraffin-embedded. FFPE tissues were sectioned for GeoMx digital spatial profiling (DSP).
For library preparation, Illumina i5 and i7 dual indexing primers were added to the oligonucleotide tags during PCR to uniquely index each AOI. Next generation sequencing (NGS) library preparation was performed according the NanoString Technologies published protocol (GeoMx DSP NGS Readout User Manual (nanostring.com)).


title: snmC-seq2 of mus musculus: adult male ventral hippocampus BL6 [B6_vhipp_2_methyl]

description:
B6_vhipp_2_methyl
allc_allstrains_alltypes_updatedcelltypes.tar

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2021
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2021

value: male


title: 6191_Interneuron--Other_UWA-6971_HD

description:
6191
RNA extracted from TAC3-positive striatal interneuron nuclei (TAC3+, ETV1+, PPP1R1B-)

value: Anterior putamen

value: Interneuron, Other

value: 43CAG / 22CAG

value: HD


title: 1_6_CD4_PanCK_WTA | 029 | PanCK

description: GeoMx DSP

value: ROI 029


title: 1_6_CD4_PanCK_WTA | 021 | PanCK

description: GeoMx DSP

value: Lungs

value: ROI 021


title: 1_6_CD4_PanCK_WTA | 021 | CD4

description: GeoMx DSP

value: unimmunized


title: 1_6_CD4_PanCK_WTA | 020 | PanCK

description: GeoMx DSP

value: ROI 020


title: snmC-seq2 of mus musculus: adult male ventral hippocampus BL6 [B6_vhipp_1_methyl]

description:
B6_vhipp_1_methyl
allc_allstrains_alltypes_updatedcelltypes.tar

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2020
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2020

value: Brain


title: 1_6_CD4_PanCK_WTA | 020 | CD4

description: GeoMx DSP

value: CD4 and PanCK+ cells


title: 1_6_CD4_PanCK_WTA | 019 | PanCK

description: GeoMx DSP

value: PanCK

value: ROI 019

value: BCG


title: snmC-seq2 of mus musculus: adult male ventral hippocampus DBA [DBA_vhipp_2_methyl]

description:
DBA_vhipp_2_methyl
allc_allstrains_alltypes_updatedcelltypes.tar

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2019
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2019

value: DBA

value: adult


title: 1_6_CD4_PanCK_WTA | 019 | CD4

description: GeoMx DSP


title: 6190_Striatopallidal-medium-spiny-neuron_UWA-6971_HD

description:
6190
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

value: Striatopallidal medium spiny neuron

value: Male


title: 6189_Striatonigral-medium-spiny-neuron_UWA-6971_HD

description:
6189
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)

value: Anterior putamen

value: Striatonigral medium spiny neuron


title: snmC-seq2 of mus musculus: adult male ventral hippocampus DBA [DBA_vhipp_1_methyl]

description:
DBA_vhipp_1_methyl
allc_allstrains_alltypes_updatedcelltypes.tar

extract_protocol:
Bisulfite conversion were carried out on isolated/sorted nuclei as described in Luo et al 2018
Libraries were prepared from bisulfite-converted samples as described in Luo et al 2018

value: male


title: 1_6_CD4_PanCK_WTA | 018 | PanCK

description: GeoMx DSP

value: ROI 018


title: 1_6_CD4_PanCK_WTA | 018 | CD4

description: GeoMx DSP

value: Lungs


title: snATAC-seq of mus musculus: adult male ventral hippocampus BL6 [B6_vhipp_2_ATAC]

description:
B6_vhipp_2_ATAC
hpc.L2.counts.ATAC.tsv
hpc.L2.metadata.ATAC.tsv

data_processing:
snATAC-seq
Reads were mapped, assigned cell barcodes, and the UMIs were collapsed using Cell Ranger ATAC V2.0.0 to generate a fragments file
We first used Model-based Analysis for ChIP-Seq (MACS) to call sample specifc de-novo peaks from its fragments file, then merged this between samples to generate a unified peaks set while filtering for peak length. Cells were filtered out based on useable read-pairs, number of fragments overlapping peaks, ratio of fragments overlapping peaks, nucleosome signal, and TSS enrichment score
We built a gene-by-cell transcriptional activity matrix that counts per cell, at the gene body and 2000bp upstream to capture the promoter region, the total number of ATAC-seq counts. We transferred the single-nucleus RNA annotation onto the single-nucleus ATAC cells by linking the RNAs expression profiles with ATAC transcriptional activity profiles through canonical correlation analysis (CCA) described in Seurat.
Assembly: mm10
Supplementary files format and content: tab-separated file including raw pseudobulk counts for each sample and cell type
Supplementary files format and content: tab-separated file including number of cells for each sample and cell type

extract_protocol:
DNA was prepared from isolated/sorted nuclei using 10X Genomics protocol (CG000209)
Libraries were prepared using 10X Genomics protocol (CG000209)


title: 1_6_CD4_PanCK_WTA | 017 | PanCK

description: GeoMx DSP

value: ROI 017


title: 6187_Microglia_BEB18117_CTRL

description:
6187
RNA extracted from microglial nuclei (IRF8+, EAAT1-, NeuN-, OLIG2-)

value: Anterior caudate

value: Microglia

value: CTRL


title: 1_6_CD4_PanCK_WTA | 017 | CD4

description: GeoMx DSP

value: CD4 and PanCK+ cells


title: 6188_Astrocyte_BEB18117_CTRL

description:
6188
RNA extracted from astrocyte nuclei (EAAT1+, IRF8-, NeuN-, OLIG2-)

value: Astrocyte


title: 1_6_CD4_PanCK_WTA | 016 | PanCK

description: GeoMx DSP

value: PanCK

value: ROI 016


title: snATAC-seq of mus musculus: adult male ventral hippocampus BL6 [B6_vhipp_1_ATAC]

description:
B6_vhipp_1_ATAC
hpc.L2.counts.ATAC.tsv
hpc.L2.metadata.ATAC.tsv

value: Brain


title: 1_6_CD4_PanCK_WTA | 016 | CD4

description: GeoMx DSP

value: BCG


title: 6186_Oligodendrocyte_BEB18117_CTRL

description:
6186
RNA extracted from oligodendrocyte nuclei (OLIG2+, EAAT1-, NeuN-, IRF8-)

value: Oligodendrocyte


title: 1_6_CD4_PanCK_WTA | 015 | PanCK

description: GeoMx DSP

value: ROI 015


title: 6184_Interneuron--Fast-Spiking_HCTSU_CTRL

description:
6184
RNA extracted from striatal fast-spiking interneuron nuclei (ETV1+, TAC3-, PPP1R1B-)

value: Anterior putamen

value: Interneuron, Fast Spiking

value: HCTSU

value: Female


title: snATAC-seq of mus musculus: adult male ventral hippocampus DBA [DBA_vhipp_2_ATAC]

description:
DBA_vhipp_2_ATAC
hpc.L2.counts.ATAC.tsv
hpc.L2.metadata.ATAC.tsv

value: DBA

value: adult

value: male


title: snATAC-seq of mus musculus: adult male ventral hippocampus DBA [DBA_vhipp_1_ATAC]

description:
DBA_vhipp_1_ATAC
hpc.L2.counts.ATAC.tsv
hpc.L2.metadata.ATAC.tsv


title: 1_6_CD4_PanCK_WTA | 014 | PanCK

description: GeoMx DSP

value: Lungs

value: ROI 014


title: 1_6_CD4_PanCK_WTA | 013 | PanCK

description: GeoMx DSP

value: CD4 and PanCK+ cells

value: ROI 013


title: 6183_Interneuron--Other_HCTSU_CTRL

description:
6183
RNA extracted from TAC3-positive striatal interneuron nuclei (TAC3+, ETV1+, PPP1R1B-)

value: Interneuron, Other

value: CTRL


title: 1_6_CD4_PanCK_WTA | 012 | PanCK

description: GeoMx DSP

value: PanCK

value: ROI 012


title: snRNA-seq of mus musculus: adult male ventral hippocampus BL6 [B6_vhipp_2_RNA]

description:
B6_vhipp_2_RNA
hpc.L2.counts.RNA.tsv
hpc.L2.metadata.RNA.tsv

data_processing:
snRNA-seq
Reads were mapped, assigned cell barcodes, and the UMIs were collapsed using Cell Ranger V6.0.2 to generate a count matrix
Cells were filtered based on total UMI count, unique genes expressed, and mitochondrial fraction
Gene counts were normalized using SCTransform, cells were integrated using recirpocal principal components analysis in Seurat 4.0.5, and cell types were called by performing PCA on all integrated genes and running a de-novo Louvain clustering algorithm in the top 15 principal components space with resolution set to 0.1
Assembly: mm10
Supplementary files format and content: tab-separated file including raw pseudobulk counts for each sample and cell type
Supplementary files format and content: tab-separated file including number of cells for each sample and cell type

extract_protocol:
RNA was prepared from isolated/sorted nuclei using 10X Genomics protocol (CG000286)
Libraries were prepared using the 10X Genomics protocol (CG000286)

value: Brain


title: 1_6_CD4_PanCK_WTA | 012 | CD4

description: GeoMx DSP

value: BCG


title: 1_6_CD4_PanCK_WTA | 011 | PanCK

description: GeoMx DSP

value: ROI 011


title: snRNA-seq of mus musculus: adult male ventral hippocampus BL6 [B6_vhipp_1_RNA]

description:
B6_vhipp_1_RNA
hpc.L2.counts.RNA.tsv
hpc.L2.metadata.RNA.tsv


title: 1_6_CD4_PanCK_WTA | 011 | CD4

description: GeoMx DSP


title: 6142_Oligodendrocyte_BEB19051_CTRL

description:
6142
RNA extracted from oligodendrocyte nuclei (OLIG2+, EAAT1-, NeuN-, IRF8-)

source_name: Posterior putamen

value: Posterior putamen

value: Oligodendrocyte

value: Male


title: snRNA-seq of mus musculus: adult male ventral hippocampus DBA [DBA_vhipp_2_RNA]

description:
DBA_vhipp_2_RNA
hpc.L2.counts.RNA.tsv
hpc.L2.metadata.RNA.tsv

value: DBA


title: 6141_Astrocyte_HCT-17-HFG_CTRL

description:
6141
RNA extracted from astrocyte nuclei (EAAT1+, IRF8-, NeuN-, OLIG2-)

value: Anterior putamen

value: Astrocyte


title: 1_6_CD4_PanCK_WTA | 010 | CD4

description: GeoMx DSP

value: Lungs

value: ROI 010


title: 1_6_CD4_PanCK_WTA | 010 | PanCK

description: GeoMx DSP

value: CD4 and PanCK+ cells


title: 1_6_CD4_PanCK_WTA | 009 | PanCK

description: GeoMx DSP

value: ROI 009


title: snRNA-seq of mus musculus: adult male ventral hippocampus DBA [DBA_vhipp_1_RNA]

description:
DBA_vhipp_1_RNA
hpc.L2.counts.RNA.tsv
hpc.L2.metadata.RNA.tsv

value: adult

value: male


title: 1_6_CD4_PanCK_WTA | 008 | PanCK

description: GeoMx DSP

value: PanCK

value: ROI 008


title: 1_6_CD4_PanCK_WTA | 008 | CD4

description: GeoMx DSP


title: 1_6_CD4_PanCK_WTA | 009 | CD4

description: GeoMx DSP


title: 6139_Oligodendrocyte_HCT-17-HFG_CTRL

description:
6139
RNA extracted from oligodendrocyte nuclei (OLIG2+, EAAT1-, NeuN-, IRF8-)

value: CTRL


title: 1_6_CD4_PanCK_WTA | 007 | PanCK

description: GeoMx DSP

value: ROI 007

value: BCG


title: 6121_Interneuron--Non-Fast-Spiking_HSB3358_HD

description:
6121
RNA extracted from SST-positive striatal interneuron nuclei (SST+, TAC3-, ETV1-)

value: Anterior caudate

value: Interneuron, Non-Fast Spiking

value: 43CAG / 21CAG

value: Female

value: HD


title: 6120_Interneuron--Fast-Spiking_HSB3358_HD

description:
6120
RNA extracted from striatal fast-spiking interneuron nuclei (ETV1+, TAC3-, PPP1R1B-)

value: Interneuron, Fast Spiking


title: 1_6_CD4_PanCK_WTA | 006 | PanCK

description: GeoMx DSP

value: Lungs

value: ROI 006


title: 1_6_CD4_PanCK_WTA | 006 | CD4

description: GeoMx DSP

value: CD4 and PanCK+ cells


title: CD4+ T lymphocytes, F1

city: Blacksburg

first: Zhuang

last: Wang

state: VA

address: 1739 Autumn Splendor Way

institute: VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY

data_processing:
FastQC and Cutadapt for raw sequence quality control and processing
Bismark for alignment
Differential methylation sites and regions analysis performed with Bioconductor packages in R
Assembly: GRCm39
Supplementary files format and content: MRLvsMRL-lpr_DMR_anno.xlsx (meanMethy1 is the average value of the control group (MRL-28, MRL-29, MRL-30) and meanMethy2 is the average value of the experiment group (lpr-8, lpr-24, lpr-25))  (Compared to "sheet1", the locations of each DMR at different genomic features are annotated in "sheet1(2)".)
Supplementary files format and content: MRLvsMRL-lpr_DMS_anno.xlsx (the results are used to generate figures for manuscript)
Supplementary files format and content: EGR2_annotated_DMR.xlsx
Supplementary files format and content: EGR2_annotated_DMS.xlsx

source_name: CD4+ T lymphocytes

extract_protocol:
DNeasy Blood and Tissue Kit (Qiagen)
ZYMO EZ DNA Methylation-Gold Kit
Qubit 2.0 DNA HS Assay and Tapestation High Sensitivity D1000 Assay

value: CD4+ T lymphocytes

value: EGR2 fl/fl B6/lpr


title: CD4+ T lymphocytes, E2

value: EGR2 KO B6/lpr


title: 1_6_CD4_PanCK_WTA | 007 | CD4

description: GeoMx DSP


title: 6119_Interneuron--Other_HSB3358_HD

description:
6119
RNA extracted from TAC3-positive striatal interneuron nuclei (TAC3+, ETV1+, PPP1R1B-)

value: Interneuron, Other


title: 1_6_CD4_PanCK_WTA | 005 | CD4

description: GeoMx DSP

value: ROI 005


title: 6118_Cholinergic-interneuron_BEB18117_CTRL

description:
6118
RNA extracted from striatal cholinergic interneuron nuclei (TRPC3+, COL6A6+, PPP1R1B-)

value: Posterior putamen

value: Cholinergic interneuron

value: Male

value: CTRL


title: CD4+ T lymphocytes, E1


title: 6140_Microglia_HCT-17-HFG_CTRL

description:
6140
RNA extracted from microglial nuclei (IRF8+, EAAT1-, NeuN-, OLIG2-)

value: Anterior putamen

value: Microglia


title: 1_6_CD4_PanCK_WTA | 003 | PanCK

description: GeoMx DSP

value: PanCK

value: ROI 003

value: BCG


title: 1_6_CD4_PanCK_WTA | 004 | PanCK

description: GeoMx DSP

value: Lungs

value: ROI 004


title: 1_6_CD4_PanCK_WTA | 004 | CD4

description: GeoMx DSP

value: CD4 and PanCK+ cells


title: 5848_Interneuron--Non-Fast-Spiking_HCT-17-HFG_CTRL

description:
5848
RNA extracted from SST-positive striatal interneuron nuclei (SST+, TAC3-, ETV1-)

value: Posterior caudate

value: Interneuron, Non-Fast Spiking


title: CD4+ T lymphocytes, F2

value: CD4+ T lymphocytes

value: EGR2 fl/fl B6/lpr


title: 4C_ifKO,rep2

city: San Juan de Alicante

first: Sergio

last: Niñerola

state: Alicante

address: Avenida Santiago Ramon y Cajal, s/n

department: Molecular Neurobiology and Neuropathology

country: Spain

institute: CSIC-Instituto de Neurociencias de Alicante

data_processing:
For RNA, adapters were trimmed using cutadapt v1.18 selecting reads longer than 25 bp.  HISAT2 (Kim et al., 2015) (v2.1.0) was used for reads alignment to the mouse genome (GRCm38.89, mm10) and reads with mapq > 30 and that mapped to nuclear chromosomes were quantified using HTSeq v0.11.1 (Anders et al., 2015). Data processing was performed with custom R scripts (v3.5.1, 2018), Samtools v1.9 (Li et al., 2009), Bedtools v2.27.1 (Quinlan and Hall, 2010), and DeepTools v3.5.0 (Ramírez et al., 2016). Whole genome alignments were normalized to 10× RPM (read per 10 million sequenced reads).
For ChIPs, Adapters were trimmed using TrimGalore v 0.6.4_dev (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), and the reads obtained were mapped to the mouse genome (mm10) with Bowtie2 (v2.3.4.3) (Langmead and Salzberg, 2012). Only those reads with a mapq > 30 were selected. Data was processed using Samtools v1.10 (Li et al., 2009), Deeptools v 3.5.0 (Ramírez et al., 2016), and Bedtools v2.25.0 (Quinlan and Hall, 2010). For BigWigs, ChIP-seq reads were normalized by reads per genomic content with Deeptools (Ramírez et al., 2016).
ChIA-PET, was processed by the ChIA-PIPE pipeline (Lee et al., 2020) using mm10 as a reference genome and default parameters. The resulting *hic file for 2D contact maps and *bigwig file for protein binding coverage were used for visualizing on Juicebox (Durand et al., 2016) Within ChIA-PIPE, peaks were called via MACS2 without input control and only those with the maximum coverage greater than 50 (which is twice the median of all peaks) were kept by pybedgraph (Zhang et al., 2020), resulting in 34,885 confident peaks. Using these peaks, the loops reported in *bedpe format with 7th column denoting PET counts are further filtered to have PET count greater than or equal to 3 and to have both left and right anchors to overlap with at least one peak.
For 4C-seq analysis all samples were trimmed to 75 bp. The wig and peaks were calculated using pipe4C and peakC as mentioned in (Krijger et al., 2020).
Assembly: mm10
Supplementary files format and content: For RNA tab-delimited text file contains raw counts data for each sample, BigWig files
Supplementary files format and content: BigWig files for ChIP-seq data
Supplementary files format and content: BigWig, Bedgraph and hic files for ChIAPet data
Library strategy: 4C-seq

source_name: Hippocampus

extract_protocol:
For RNA, total RNA was extracted from hippocampal tissue with TRI reagent (Sigma-Aldrich) as recommended by the manufacturer.  Subsequently, genomic DNA was eliminated by a treatment with DNAse I (Qiagen) for 30 min at 25ºC. Followed by precipitation with phenol-chloroform-isoamyl alcohol (Sigma-Aldrich).
ChIPs were performed as previously described in detail (Galvão-Ferreira et al., 2017) with minor modifications. Briefly, 3 μg of antibody were incubated with Dynabeads coated to Protein G (Invitrogen) in RIPA-150 buffer (50 mM Tris-HCl, 150 mM NaCl, 1 mM, EDTA, 0.1% SDS, 1% Triton X-100, and 0.1% sodium deoxycholate; pH 8) for 6-18 h at 4°C in agitation. Nuclei from hippocampal cells were extracted in a dounce homogenizer as explained for the FANS method. Samples were fixed with 1% formaldehyde (Sigma-Aldrich) for 10 min at room temperature followed by 0.1 M glycine for 5 min to stop the fixation. Nuclei were centrifuged at 1,5 G, and the pellet was resuspended in 100 μL of SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris; pH 8) prior to its sonication in a Bioruptor Pico (Diagenode) for 12 cycles of 15 s on/30 s off. After 6 min of centrifugation at 13000 rpm, the supernatant containing isolated chromatin was collected. Samples were diluted in 900 μL of ChIP Dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, 167 mM NaCl; pH 8) and incubated overnight at 4°C with the antibody-Dynabeads mix. Beads were thoroughly rinsed at 4ºC as follows: two washes in RIPA-150 buffer, three washes in RIPA-500 buffer (50mM Tris-HCl, 500 mM NaCl, 1 mM, EDTA, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate; pH 8), two washes in RIPA LiCl buffer (50 mM Tris-HCl, 1 mM EDTA, 1% NP-40, 0.7%, sodium deosycholate, 500 mM LiCl2), and two final washes in TE buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA; pH 8.0), five minutes each. Samples were resuspended in 200 μl Elution buffer (10 mM Tris-HCl, 5 mM EDTA, 300 mM NaCl, 0.5% SDS; pH 8) and treated with 1 μl of 10 mg/mL RNase A (Fermentas) overnight at 65°C in agitation for crosslink reversion. Samples were treated with 3 μl of 20 mg/mL Proteinase K (Thermo Scientific) for 2 hours at 55°C in agitation. Last, DNA precipitation was performed by phenol-chloroform-isoamyl alcohol (Sigma-Aldrich). For Kdm1a ChIP, some modification were applied as in (Lipinski et al., 2020). In brief, samples required a stronger fixation treatment in 1% PFA for 30 min at 37ºC. To fragment these highly fixed samples, 43 cycles of sonication (30 s On, 30 s Off) were applied in a Bioruptor Pico (Diagenode). SDS lysis buffer was modified to RIPA buffer (0.1% SDS, 1% IGEPAL, and 0.5% sodium deoxycholate).
Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET) using a CTCF-specific antibody (Abclonal Cat # ab70303) was performed as described in the in situ ChIA-PET protocol (Wang et al., 2021) on approximately 10 million nuclei of hippocampal excitatory neurons sorted by FANS as described above.
4C-seq, was performed as previously described (Krijger et al., 2020) with minimal changes. Approximately 5 million hippocampal nuclei were fixed at 1 % with PFA. The restriction enzyme cutting order was Dpn II as the primary enzyme and Csp6I as the secondary enzyme. Ligated chromatin was phenol-chloroform extracted and ethanol precipitated. Reactions were then further purified with Ampure XP beads with a 0.8x ratio of bead solution to library following the manufactures instructions. Samples were then quantified with Qubit and 4C-seq libraries were sequenced using an Illumina high-throughput sequencing equip.
For RNA three mice were used per genotype (Kdm1a-ifKO and their control littermates) and Poly-A libraries were generated. For RNA and ChIPseq,  libraries were generated for each independent sample and single-end sequenced in a HiSeq 2500 apparatus from Illumina. For ChIAPet, librearies were generated and paired end and 150 pb were sequenced and emrged from Miseq, Nextseq 500/550 and Hiseq 3000/4000 aparatus.
PolyA RNAseq, ChIP-seq, 4C-seq and ChIAPet

value: Hippocampus

value: ifKO

value: Tamoxifen


title: 5847_Interneuron--Fast-Spiking_HCT-17-HFG_CTRL

description:
5847
RNA extracted from striatal fast-spiking interneuron nuclei (ETV1+, TAC3-, PPP1R1B-)

value: Interneuron, Fast Spiking

value: Male


title: 1_6_CD4_PanCK_WTA | 002 | PanCK

description: GeoMx DSP

value: ROI 002


title: 4C_ifKO,rep4


title: 1_6_CD4_PanCK_WTA | 002 | CD4

description: GeoMx DSP


title: 1_6_CD4_PanCK_WTA | 003 | CD4

description: GeoMx DSP


title: 4C_WT,rep5

value: WT


title: 5846_Interneuron--Other_HCT-17-HFG_CTRL

description:
5846
RNA extracted from TAC3-positive striatal interneuron nuclei (TAC3+, ETV1+, PPP1R1B-)

value: Interneuron, Other

value: CTRL


title: 4C_WT,rep4


title: 1_6_CD4_PanCK_WTA | 001 | PanCK

description: GeoMx DSP

value: PanCK

value: ROI 001

value: BCG


title: 1_6_CD4_PanCK_WTA | 001 | CD4

description: GeoMx DSP

value: Lungs

value: CD4 and PanCK+ cells


title: ChIP-Seq of Fusarium graminearum PH-1:H3K27me3-H3K4me3 in the PH-1 infection_ip_2

city: Hefei

first: zhao

middle: xiao

last: zhen

address: Anhui Agricultural University, 130 Changjiangxilu, Shushan District, Hefei, Anhui Province, China

country: China

institute: Anhui Agricultural University

data_processing: For ChIP-seq analysis, 50 bp single-end reads of ChIP-seq were obtained, and quality was controlled using SOAPnuke(v2.1.7). The parameters were as follows: remove reads containing adapters or more than 1% of unknown nucleotides (N); delete the read if there are more than 40% bases having a quality value lower than 20.  Clean reads were mapped to the Fg reference genome by Bowtie2 (version 2.4.5) with default parameters.  The visualization of the average read coverage over 2 kb upstream and downstream of the TSS was performed by Deeptools.  BigWig files generated by Deeptools were used for visualization in Integrative Genome Viewer (version 2.8.9).  Assembly: reference genome of F. graminearum strain PH-1 GCA_900044135.1  Supplementary files format and content: BPM  were calculated to normalized reads using bamCompare tool in Deeptools (version 2.4.1) with input DNA as a contorl.

organism: Fusarium graminearum PH-1

source_name: Mycelium

extract_protocol: fresh mycelia of each sample were cross-linked with 1% formaldehyde for 10 min. Fixation was stopped with 125 mM glycine for 5 min. Subsequently, fixed culture samples were grounded in liquid nitrogen, and re-suspended in 10 ml of nuclear extraction buffer I (0.4 M sucrose, 10 mM Tris-HCl, pH 8.0, 10 mM MgCl2, 5mM β-mercaptoethanol, 0.1 mM PMSF, 1× protease inhibitor). DNA was sheared into 200~500 bp fragments with 30 s on and 6 min off by using a Covaris E220 DNA Sonicator (Covaris, Woburn, MA). After centrifugation, the pellets were suspended in 4 ml of nuclear extraction buffer II (1.7 M sucrose, 10 mM Tris-HCl, pH 8.0, 10 mM MgCl2, 1% Triton X-100, 5 mM β-mercaptoethanol and 1×protease inhibitor). Re-suspended samples were then centrifuged at 13,000 g for 15 min at 4 °C. The resulting pellets were re-suspended in 300 μL of nuclear lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS and 1× protease inhibitor). Samples were then sonicated by two pulses of 30 s sonication and 1 min rest. After centrifugation at 4000 g for 5 min at 4°C, the supernatant was transformed into a clear tube, and was diluted with 10×ChIP dilution buffer (1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.0 and 167 mM NaCl). Immunoprecipitation was conducted using the monoclonal anti-GFP (ab290, Abcam, Cambridge, UK) antibody, anti-H3K18ac (39755, Active Motif Inc., Carlsbad, USA) antibody, or anti-H2BK11ac (ab240613, Abcam, Cambridge, UK) together with the protein A agarose beads (sc-2003, Santa Cruz, CA, USA). The beads were subsequently washed by low salt wash buffer, high salt wash buffer, LiCl wash buffer, and TE buffer. After washing, eluting, reversing the crosslinking, and removing all proteins, the resulting pellets were re-suspended in 50 μL of distilled water.  End repair and adapter ligation:Fill the ends of IP/Input DNA followed by 5' phosphorylation. A 3' sticky-end with an overhanging A is formed, which could ligate with an overhanging T at the 3' end of the bubble adapter; PCR amplification: PCR amplify the ligated products with specific primers; Single-strand separation and circularization: Separate PCR products into single-strands by thermal denaturation. Then circularize the single-stranded DNA through a bridge primer to obtain single-stranded circular DNA library; Sequencing: Amplified products DNA Nanoballs (DNBs) are used for sequencing

value: Mycelium

tag: infection

value: YES

value: ChIP experiments using 48 hour post-inoculation of  mycelium


title: 4C_ifKO,rep3

value: Hippocampus


title: ChIP-Seq of Fusarium graminearum PH-1:H3K27me3-H3K4me3 in the PH-1 infection_ip_1


title: ChIP-Seq of Fusarium graminearum PH-1:H3K27me3-H3K4me3_ip_1

value: NO

value: ChIP experiments using Day 2 of fresh mycelium


title: 1_6_CD4_PanCK_WTA | 005 | PanCK

description: GeoMx DSP

value: ROI 005


title: ChIP-Seq of Fusarium graminearum PH-1:H3K27me3-H3K4me3_ip_2


title: 4C_WT,rep2

value: Male

value: Tamoxifen


title: 5842_Cholinergic-interneuron_HCT-17-HFG_CTRL

description:
5842
RNA extracted from striatal cholinergic interneuron nuclei (TRPC3+, COL6A6+, PPP1R1B-)

extract_protocol:
RNA extraction was carried out with AllPrep DNA/RNA FFPE Kit (Qiagen, #80234).
RNA-seq libraries were prepared with Trio RNA-Seq™ library preparation kit (Tecan, #0506-A01) and pooled for sequencing on NovaSeq6000 (SP 2 x 150bp).

value: Posterior putamen

value: Cholinergic interneuron


title: 5841_Cholinergic-interneuron_BEB19051_CTRL

description:
5841
RNA extracted from striatal cholinergic interneuron nuclei (TRPC3+, COL6A6+, PPP1R1B-)

value: CTRL


title: 5840_Cholinergic-interneuron_BEB20057_CTRL

description:
5840
RNA extracted from striatal cholinergic interneuron nuclei (TRPC3+, COL6A6+, PPP1R1B-)


title: ChIP-Seq of Fusarium graminearum PH-1:H3K4me3-H3K27me3 in the PH-1 infection_ip rep2

data_processing:
For ChIP-seq analysis, 50 bp single-end reads of ChIP-seq were obtained, and quality was controlled using SOAPnuke(v2.1.7). The parameters were as follows: remove reads containing adapters or more than 1% of unknown nucleotides (N); delete the read if there are more than 40% bases having a quality value lower than 20.
Clean reads were mapped to the Fg reference genome by Bowtie2 (version 2.4.5) with default parameters.
The visualization of the average read coverage over 2 kb upstream and downstream of the TSS was performed by Deeptools.
BigWig files generated by Deeptools were used for visualization in Integrative Genome Viewer (version 2.8.9).
Assembly: reference genome of F. graminearum strain PH-1 GCA_900044135.1
Supplementary files format and content: BPM  were calculated to normalized reads using bamCompare tool in Deeptools (version 2.4.1) with input DNA as a contorl.

extract_protocol:
fresh mycelia of each sample were cross-linked with 1% formaldehyde for 10 min. Fixation was stopped with 125 mM glycine for 5 min. Subsequently, fixed culture samples were grounded in liquid nitrogen, and re-suspended in 10 ml of nuclear extraction buffer I (0.4 M sucrose, 10 mM Tris-HCl, pH 8.0, 10 mM MgCl2, 5mM β-mercaptoethanol, 0.1 mM PMSF, 1× protease inhibitor). DNA was sheared into 200~500 bp fragments with 30 s on and 6 min off by using a Covaris E220 DNA Sonicator (Covaris, Woburn, MA). After centrifugation, the pellets were suspended in 4 ml of nuclear extraction buffer II (1.7 M sucrose, 10 mM Tris-HCl, pH 8.0, 10 mM MgCl2, 1% Triton X-100, 5 mM β-mercaptoethanol and 1×protease inhibitor). Re-suspended samples were then centrifuged at 13,000 g for 15 min at 4 °C. The resulting pellets were re-suspended in 300 μL of nuclear lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS and 1× protease inhibitor). Samples were then sonicated by two pulses of 30 s sonication and 1 min rest. After centrifugation at 4000 g for 5 min at 4°C, the supernatant was transformed into a clear tube, and was diluted with 10×ChIP dilution buffer (1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.0 and 167 mM NaCl). Immunoprecipitation was conducted using the monoclonal anti-GFP (ab290, Abcam, Cambridge, UK) antibody, anti-H3K18ac (39755, Active Motif Inc., Carlsbad, USA) antibody, or anti-H2BK11ac (ab240613, Abcam, Cambridge, UK) together with the protein A agarose beads (sc-2003, Santa Cruz, CA, USA). The beads were subsequently washed by low salt wash buffer, high salt wash buffer, LiCl wash buffer, and TE buffer. After washing, eluting, reversing the crosslinking, and removing all proteins, the resulting pellets were re-suspended in 50 μL of distilled water.
End repair and adapter ligation:Fill the ends of IP/Input DNA followed by 5' phosphorylation. A 3' sticky-end with an  overhanging A is formed, which could ligate with an overhanging T at the 3' end of the bubble adapter;  PCR amplification: PCR amplify the ligated products with specific primers;  Single-strand separation and circularization: Separate PCR products into single-strands by thermal denaturation.  Then circularize the single-stranded DNA through a bridge primer to obtain single-stranded circular DNA library;  Sequencing: Amplified products DNA Nanoballs (DNBs) are used for sequencing

tag: chip antibody

value: anti-H3K4me3 (abcam, ab8580) and anti-H3K27me3 (Thermofisher, 39155)


title: 4C_WT,rep1

value: WT


title: ChIP-Seq of Fusarium graminearum PH-1:l PH-1 infection-sequential ChIP_input rep2


title: 5624_Interneuron--Fast-Spiking_UWA-7026_HD

description:
5624
RNA extracted from striatal fast-spiking interneuron nuclei (ETV1+, TAC3-, PPP1R1B-)

value: Anterior putamen

value: Interneuron, Fast Spiking

value: 43CAG / 17CAG

value: HD


title: I73T-FPRKO W2 - 2

city: Philadelphia

first: Michael

middle: Francis

last: Beers

state: PA

address: 3450 Hamilton Walk

department: Pulmonary

institute: University of Pennsylvania

library_source: transcriptomic single cell

data_processing:
none provided
Assembly: mm10
Supplementary files format and content: tab seperated values and matrix files

source_name: Lung

extract_protocol:
Single cell suspension prepared by physical and enzymatic dissociation followed by MACS sorting by LS columns with CD45+ cell removal using CD45 micobeads followed by followed by “spike-back” of immune cells (~20% of final suspensions)
Single cell libraries were generated using Chromium Single Cell 3' v2 Reagent Kit (10x Genomics) according to the manufacturer's protocol. The libraries were sequenced on an Illumina NovaSeq 6000.

value: Lung

value: SPC Mutant FPR KO - 2 Weeks after Induction


title: ChIP-Seq of Fusarium graminearum PH-1:H3K27me3 in the PH-1 infection_ip rep2

value: Mycelium

value: anti-H3K27me3 (Thermofisher, 39155)


title: 5618_Cholinergic-interneuron_BEB18116_CTRL

description:
5618
RNA extracted from striatal cholinergic interneuron nuclei (TRPC3+, COL6A6+, PPP1R1B-)


title: ChIP-Seq of Fusarium graminearum PH-1:H3K27me3 in the PH-1 infection_ip rep1

value: anti-H3K27me3 (Thermofisher,39155)


title: ChIP-Seq of Fusarium graminearum PH-1:H3K4me3 in the PH-1 infection_ip rep2

value: anti-H3K4me3 (abcam, ab8580)


title: ChIP-Seq of Fusarium graminearum PH-1:H3K4me3 in the PH-1 infection_ip rep1


title: I73T W2 - 2

value: SPC Mutant Wildtype FPR - 2 Weeks after induction


title: I73T-FPRKO W2 - 1


title: 5843_Cholinergic-interneuron_BEB19025_CTRL

description:
5843
RNA extracted from striatal cholinergic interneuron nuclei (TRPC3+, COL6A6+, PPP1R1B-)

value: Male


title: ChIP-Seq of Fusarium graminearum PH-1:PH-1 infection_Input rep2


title: I73T W2 - 1


title: ChIP-Seq of Fusarium graminearum PH-1:PH-1 infection_Input rep1


title: 5459_Interneuron--Other_BEB18135_CTRL

description:
5459
RNA extracted from TAC3-positive striatal interneuron nuclei (TAC3+, ETV1+, PPP1R1B-)

value: Anterior caudate

value: Interneuron, Other


title: ChIP-Seq of Fusarium graminearum PH-1:H3K4me3-H3K27me3_ip rep2


title: I73T-FPRKO W0

value: SPC Mutant FPR KO (before induction of the model)


title: 5458_Interneuron--Fast-Spiking_BEB18135_CTRL

description:
5458
RNA extracted from striatal fast-spiking interneuron nuclei (ETV1+, TAC3-, PPP1R1B-)

value: CTRL


title: ChIP-Seq of Fusarium graminearum PH-1:H3K4me3-H3K27me3_ip rep1

value: anti-H3K4me3 (abcam, ab8580) and anti-H3K27me3 (Thermofisher, 39155)


title: I73T W0

value: SPC Mutant FPR WT (before induction of the model)


title: ChIP-Seq of Fusarium graminearum PH-1:H3K4me3-H3K27me3 in the PH-1 infection_ip rep1


title: ChIP-Seq of Fusarium graminearum PH-1:H3K27me3_IP rep1


title: ChIP-Seq of Fusarium graminearum PH-1:H3K27me3_IP rep2


title: ChIP-Seq of Fusarium graminearum PH-1: PH-1 infection-sequential ChIP_input rep1


title: 4880_Interneuron--Non-Fast-Spiking_BEB18116_CTRL

description:
4880
RNA extracted from SST-positive striatal interneuron nuclei (SST+, TAC3-, ETV1-)

value: Anterior putamen

value: Interneuron, Non-Fast Spiking


title: I73T-FPRKO W4 - 2

value: SPC Mutant FPR KO - 4 Weeks after Induction


title: 4879_Interneuron--Fast-Spiking_BEB18116_CTRL

description:
4879
RNA extracted from striatal fast-spiking interneuron nuclei (ETV1+, TAC3-, PPP1R1B-)

value: Interneuron, Fast Spiking


title: I73T-FPRKO W4 - 1

value: Lung


title: ChIP-Seq of Fusarium graminearum PH-1:H3K4me3_IP rep1

value: Mycelium


title: ChIP-Seq of Fusarium graminearum PH-1:PH-1_Input rep2


title: ChIP-Seq of Fusarium graminearum PH-1:PH-1_Input rep1


title: 4878_Interneuron--Other_BEB18116_CTRL

description:
4878
RNA extracted from TAC3-positive striatal interneuron nuclei (TAC3+, ETV1+, PPP1R1B-)


title: RNA-Seq of Fusarium graminearum PH-1:PH-1 at 48hpi rep3

data_processing:
For RNA-seq analysis, all of the raw reads were filtered by Fastp (version 0.18.0) software to remove adapters and low quality reads (quality score≤20).
Clean reads were aligned to the Fg reference genome using Hisat2 (v1.3.3).
Expression levels for each sample were quantified to TPM
Assembly: reference genome of F. graminearum strain PH-1 GCA_900044135.1
Supplementary files format and content: Genes displaying log2 [fold change] ≥ 1.5 and an adjusted (false discovery rate) p value < 0.05 were classified as differentially expressed genes (DEGs) by using DESeq2 package.

extract_protocol:
total RNA extraction using TRIZOL reagent following the manufacturer’s instructions.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT)  beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic  Kit (Epicentre, Madison, WI, USA). Then the enriched mRNA was fragmented into short  fragments using fragmentation buffer and reverse transcripted into cDNA with random  primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and  buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen,  Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing  adapters.

value: WT

tag: time

value: 120 hour post-inoculation


title: RNA-Seq of Fusarium graminearum PH-1:PH-1 at 48hpi rep1


title: RNA-Seq of Fusarium graminearum PH-1:PH-1 at 48hpi rep2


title: I73T W4 -2

tag: tissue

value: SPC Mutant Wildtype FPR - 4 Weeks after induction


title: I73T W4 -1


title: RNA-Seq of Fusarium graminearum PH-1:PH-1 at 24hpi rep3

tag: cell type

value: 24 hour post-inoculation


title: RNA-Seq of Fusarium graminearum PH-1:PH-1 at 0hpi rep3

value: F. graminearum mycelia used for inoculation were collected to represent the time point of 0 hpi


title: RNA-Seq of Fusarium graminearum PH-1:PH-1 at 24hpi rep2


title: 4877_Microglia_BEB19051_CTRL

description:
4877
RNA extracted from microglial nuclei (IRF8+, EAAT1-, NeuN-, OLIG2-)

value: Posterior putamen

value: Microglia

value: Male


title: 4872_Microglia_HCTSU_CTRL

description:
4872
RNA extracted from microglial nuclei (IRF8+, EAAT1-, NeuN-, OLIG2-)

value: Anterior caudate

value: HCTSU

value: Female

value: CTRL


title: WT

value: Wild type Mouse


title: RNA-Seq of Fusarium graminearum PH-1:PH-1 at 0hpi rep2


title: RNA-Seq of Fusarium graminearum PH-1:PH-1 at 0hpi rep1


title: SPC WT FPR KO

value: FPR KO Mouse, no SPC Mutation


title: PHZ_SP_LSK

city: Houston

first: Jong

middle: H

last: Kim

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

description: 10x Genomic

data_processing:
Aligned with CellRanger Count v3.1.0
Analysis Using Seurat V3
ScaleData,Normalization,RunPCA,RunUMAP on each sample for DoubletFinder
DoubletFinder to identify Doublets
SCTransformation for Sample Integration
Seurat Integration
Assembly: mm10
Supplementary files format and content: RNA_Count.txt.gz = Raw RNA Count Data.frame
Supplementary files format and content: SCT_Matix.txt.gz = SCTransformed Data.frame
Supplementary files format and content: Integrated_Matrix.txt.gz = DataMatrix Generated from Sample Integration Step
Supplementary files format and content: Meta_Data.txt.gz = Dataframe of Seurat Object MetaData

source_name: spleen

extract_protocol:
Bone marrow cells were isolated by crushing the long bones, pelvic bones, vertebrae, and sternum with mortar and pestle in HBSS without calcium and magnesium, supplemented with 2% heat-inactivated bovine serum. Splenocytes were dissociated by smashing the entire spleen between slides. Cells were triturated and filtered through a 40 μm cell strainer to obtain a single-cell suspension. For isolation of LSK cells, cells were incubated with fluorescent-conjugated antibodies and pre-enriched by selecting c-kit+ cells using paramagnetic microbeads and autoMACS (Miltenyi Biotec). Nonviable cells were excluded from sorts and analyses using the viability dye DAPI. FACS was performed with FACSAria II (BD Biosciences).
The library was prepared following the manufacturer's instructions (Chromium Next GEM Single Cell 3’ Kit v3.1, 10x Genomics). In brief, sorted LSK cells were resuspended in the master mix and loaded into the chip, along with partitioning oil and gel beads, to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained within each individual GEM was reverse-transcribed to cDNA, which included an Illumina Read 1 primer sequence, Unique Molecular Identifier, and the 10x Barcode. The pooled barcoded cDNA was then cleaned up using Silane DynaBeads, amplified by PCR, and appropriately sized fragments were selected with SPRIselect reagent for subsequent library construction. During library construction, the Illumina Read 2 primer sequence, paired-end constructs with P5 and P7 sequences, and a sample index were added.

treatment_protocol: Intraperitoneal injections were administered for two consecutive days, either with 60 mg/kg of PHZ in PBS or an equivalent volume of PBS. At day 4 post-treatment, bone marrow and splenic cells were collected for further analysis.

value: spleen

value: LSK cells

value: wild type

value: PHZ


title: ChIP-Seq of Fusarium graminearum PH-1:H3K4me3_IP rep2

value: Mycelium

value: anti-H3K4me3 (abcam, ab8580)


title: 4870_Astrocyte_BEB20057_CTRL

description:
4870
RNA extracted from astrocyte nuclei (EAAT1+, IRF8-, NeuN-, OLIG2-)

value: Astrocyte


title: RNA-Seq of Fusarium graminearum PH-1:PH-1 at 24hpi rep1

value: WT

value: 24 hour post-inoculation


title: Donor_53_Bag

city: Goettingen

first: Linh

last: Dang

address: Robert Koch 40

country: Germany

institute: UMG

data_processing:
Reads from fastq files are trimmed by TrimGaloreversion 0.6.6) with Cutadapt (version 4.4)
The adapter for trimming is AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
Reads shoter than 30bp after trimming are removed
Sequence alignment tool is STAR (version 2.7.3a) for single end reads with default parameters
Gene-level count: using featureCounts from subread (version 2.0.2) with strand specific (reverse strandedness)
Assembly: CHM13 (version 2.0)
Supplementary files format and content: featureCounts_count_table.txt: a raw count table matrix, where rows are gene symbols and columns are samples
Supplementary files format and content: ALDEx2_BagvsPlate.txt: differential express analysis following ALDEx2 pipeline

source_name: Peripheral Blood

growth_protocol: Human primary monocytes were isolated via a double-density gradient centrifugation protocol as described previously (Menck et al, 2014). As starting material, blood from leukoreduction system chambers of five healthy donors provided by the Department of Transfusion Medicine at the University Hospital Muenster was used.

extract_protocol:
Total RNA was isolated using the High Pure RNA isolation kit (Roche). Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies).
Poly(A) mRNA were purified  from 300 ng total RNA using Poly(A) mRNA Magnetic Isolation module Kit (NEB E7490L, New England Biolabs). The RNA Sequencing library was prepared with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Monocytes were differentiated to macrophages in the presence of M-CSF (25 ng/ml) and cultured either in regular cell culture plates or Teflon-coated bags (#003300, CellGenix). After 7 days of culture, macrophages were harvested from the bags and seeded overnight in cell culture plates. The next day, all cells were washed once in PBS and subjected to total RNA isolation.

value: Peripheral Blood

value: Macrophages

value: derived from monocytes cultured in Teflon-coated bags

value: healthy

value: Differentiation induced with M-CSF


title: Donor_41_Bag


title: 4871_Oligodendrocyte_HCTSU_CTRL

description:
4871
RNA extracted from oligodendrocyte nuclei (OLIG2+, EAAT1-, NeuN-, IRF8-)

value: Anterior caudate

value: Oligodendrocyte

value: HCTSU

value: Female

value: CTRL


title: 5622_Interneuron--Non-Fast-Spiking_BEB18135_CTRL

description:
5622
RNA extracted from SST-positive striatal interneuron nuclei (SST+, TAC3-, ETV1-)

value: Interneuron, Non-Fast Spiking

value: Male


title: Donor_40_Bag


title: PHZ_BM_LSK

description: 10x Genomic

source_name: bone marrow

value: bone marrow

value: LSK cells

value: wild type

value: PHZ


title: Donor_29_Bag


title: Control_SP_LSK

description: 10x Genomic

value: spleen

value: PBS


title: 4868_Oligodendrocyte_BEB20057_CTRL

description:
4868
RNA extracted from oligodendrocyte nuclei (OLIG2+, EAAT1-, NeuN-, IRF8-)


title: Donor_53_Plate

value: Peripheral Blood

value: Macrophages

value: derived from monocytes cultured in regular cell culture plates


title: Donor_51_Plate

value: healthy

value: Differentiation induced with M-CSF


title: 4866_Microglia_BEB19051_CTRL

description:
4866
RNA extracted from microglial nuclei (IRF8+, EAAT1-, NeuN-, OLIG2-)

value: Posterior caudate

value: Microglia


title: 4873_Astrocyte_HCTSU_CTRL

description:
4873
RNA extracted from astrocyte nuclei (EAAT1+, IRF8-, NeuN-, OLIG2-)

value: Anterior caudate

value: Astrocyte

value: HCTSU

value: Female


title: Input_ChIPseq_mMA10

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

data_processing:
Illumina RTA was used to create .bcl files, and bcl2fastq v2.20.0.422 software was used for base calling (for samples split between flowcells and later merged per run)
ChIP-seq reads were aligned to the GRCm38 genome assembly using BWA with the following configurations…
Aligned reads were then sorted by samtools (version 1.10) and duplicated reads were tagged and removed by Picard MarkDuplicates tool (version 2.21.1)
peaks were called using MACS2 (version 2.1.1) and --SPMR option was used to generate normalized pileup files for downstream analysis.
RNA-seq reads aligned to the GRCm38 genome assembly using STAR_2.6.0a, Aligned reads was normalized by edgeR bioconductor package and outputed as rpkm.txt file
Assembly: GRCm38
Supplementary files format and content: bigwig file were generating using MACS2 and bdgToBW, scores represent pileup signals
Supplementary files format and content: raw count table in txt format of every sample in RNAseq project

source_name: MLL-AF9 leukemia

growth_protocol: Cas9-expressing mouse MLL-AF9 leukema cells transduced with sgCtrl or sgSgf29 and seleted in 2 ug/ml puromycine for 3 days.

extract_protocol:
Total RNA was extracted using the RNeasy kit (QIAGEN) for RNAseq.
Eukaryotic mRNA directional library prep were used for RNAseq.

treatment_protocol: sgCtrl and sgSgf29 were cloned into ipUSEPR vector and transduced via lentiviral infection.

value: leukemia


title: SGF29_TST_ChIPseq_mMA9

tag: antibody


title: Donor_29_Plate


title: 4865_Oligodendrocyte_BEB19051_CTRL

description:
4865
RNA extracted from oligodendrocyte nuclei (OLIG2+, EAAT1-, NeuN-, IRF8-)

value: Oligodendrocyte

tag: age

value: Male

value: CTRL


title: Oaries_thymus_MAIT

city: Paris

first: Martin

last: MESTDAGH

address: 26 rue d'ulm

country: France

institute: Institut Curie

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Oar_rambouillet_v1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Ovis aries

source_name: Thymus

extract_protocol:
A freshly isolated thymus was maintained in CO2-independent medium (Gibco) at 4°c until processing. Sample processing started less than 6 hours after euthanasia.  The thymus was minced with a sterile scalpel in a petri dish containing 5 mL of CO2-independent medium. Tissue pieces were then washed with 40 mL of FACS buffer (PBS supplemented with 2% fetal calf serum (FCS) and 2.5 mM EDTA) to recover single cell suspensions of thymocytes.  To generate scRNAseq data from O. aries, 109 thymocytes were stained for 30 min at room temperature with a PE-labeled cattle MR1 tetramer loaded with 5-OP-RU, then washed and stained with 70 mL of anti-PE microbeads (Miltenyi).  Magnetic enrichment of tetramer-labeled thymocytes was then performed. Following magnetic enrichment, thymocytes were stained for 30 min at 4°C with the following primary antibodies: mouse anti-bovine CD3 (clone MM1A, Bio-rad MCA6080) and mouse anti-bovine gd TCR (clone GB21A, Monoclonal Antibody Center BOV2058).  After washing with FACS buffer, sheep cells were stained with secondary anti-mouse IgG1 AF700 (clone RMG1-1, Biolegend 406631) and anti-mouse IgG2b PE-Cy7 (clone RMG2b-1, Biolegend 406713). Cells were then washed with FACS buffer and stained with DAPI (Sigma). A population of gd thymocytes were found to bind to the cattle MR1 tetramer and were gated out and excluded from the FACS-sorted population. DAPI- Tetramer+ CD3+ gd- thymocytes were flow-sorted (Aria III, BD) into PBS supplemented with 0.35% BSA (Sigma). Sorted cells were centrifuged, counted and 5,000 – 10,000 cells were loaded onto the Chromium 3’ chip. Reverse transcription, library preparation and sequencing were performed according to manufacturer’s recommendations (10x Genomics).
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: MAIT

value: Thymus

tag: condition

value: Steady State


title: H3K9ac_ChIPseq_mMA9_sgSgf29#3

tag: transduction


title: Donor_51_Bag

value: Peripheral Blood

value: Macrophages

value: derived from monocytes cultured in Teflon-coated bags


title: 4864_Astrocyte_HCT-17-HFG_CTRL

description:
4864
RNA extracted from astrocyte nuclei (EAAT1+, IRF8-, NeuN-, OLIG2-)

tag: Sex


title: H3K9ac_ChIPseq_mMA9_sgSgf29#2


title: 4863_Microglia_HCT-17-HFG_CTRL

description:
4863
RNA extracted from microglial nuclei (IRF8+, EAAT1-, NeuN-, OLIG2-)


title: 4862_Oligodendrocyte_HCT-17-HFG_CTRL

description:
4862
RNA extracted from oligodendrocyte nuclei (OLIG2+, EAAT1-, NeuN-, IRF8-)


title: H3K9ac_ChIPseq_mMA9_sgSgf29#1


title: 4784_Astrocyte_BEB19051_CTRL

description:
4784
RNA extracted from astrocyte nuclei (EAAT1+, IRF8-, NeuN-, OLIG2-)

value: Anterior putamen


title: 4869_Microglia_BEB20057_CTRL

description:
4869
RNA extracted from microglial nuclei (IRF8+, EAAT1-, NeuN-, OLIG2-)


title: Control_BM_LSK

description: 10x Genomic

value: bone marrow

value: LSK cells

tag: strain

value: wild type

tag: treatment

value: PBS


title: WT_Citro_D14_gp38#3

city: Boston

first: Meng

last: Wu

state: MA

address: 77 Avenue Louis Pasteur

department: Immunology

institute: Harvard Medical School

data_processing:
Reads were aligned to the mouse genome (GENCODE GRCm38/mm10 primary assembly and gene annotations vM25; https://www.gencodegenes.org/mouse/release_M25.html) with STAR 2.7.3a ImmGen.org (https://github.com/alexdobin/STAR/releases).
The ribosomal RNA gene annotations were removed from GTF (General Transfer Format) file. The gene-level quantification was calculated by featureCounts (http://subread.sourceforge.net/; version 2.0.0).
Raw reads counts tables were normalized by median of ratios method with DESeq2 package from Bioconductor (https://bioconductor.org/packages/release/bioc/html/DESeq2.html) and then converted to GCT and CLS format.
Samples with less than 1 million uniquely mapped reads were automatically excluded from normalization to mitigate the effect of poor quality samples on normalized counts.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Stromal cell

extract_protocol:
A thousand live epithelial (EpCAM+), CD45+, and stromal cells (EpCAM-CD45-CD31-PDPN+) were doubly sorted from colons of WT SPF mice by BD FACS Aria II. Sorted cells were directly lysed with 5mL of TCL buffer (Qiagen, 1031576) containing 1% 2-mercaptoenthanol (Sigma-Aldrich, M6250), then flash frozen using dry-ice and stored at -80C.
Smart-Seq2 libraries for low-input RNA-seq were prepared by the Broad Technology Labs and were subsequently sequenced through the Broad Genomics Platform according to the Immgen protocol (https://www.immgen.org/img/Protocols/ImmGenULI_RNAseq_methods.pdf)
Pooled libraries are normalized to 2nM and denatured using 0.1 N NaOH prior to sequencing. Flowcell cluster amplification and sequencing were performed according to the manufacturer’s protocols using either the NextSeq. Libraries are sequenced with a read structure of 2x38 bp.

value: Stromal cell

value: WT


title: 4783_Microglia_BEB19051_CTRL

description:
4783
RNA extracted from microglial nuclei (IRF8+, EAAT1-, NeuN-, OLIG2-)

value: Microglia


title: H3K9ac_ChIPseq_mMA9_sgCtrl#2

value: leukemia


title: 4782_Oligodendrocyte_BEB19051_CTRL

description:
4782
RNA extracted from oligodendrocyte nuclei (OLIG2+, EAAT1-, NeuN-, IRF8-)

value: Oligodendrocyte

value: Male


title: Donor_41_Plate

value: derived from monocytes cultured in regular cell culture plates

value: healthy

value: Differentiation induced with M-CSF


title: H3K9ac_ChIPseq_mMA9_sgCtrl#1


title: WT_Citro_D14_gp38#2


title: 4781_Astrocyte_BEB20057_CTRL

description:
4781
RNA extracted from astrocyte nuclei (EAAT1+, IRF8-, NeuN-, OLIG2-)

value: Posterior caudate

value: Astrocyte

value: CTRL


title: NCI-H1975 cells, Scramble, input_mRNA, rep2

city: Shanghai

first: zhenchuan

last: liu

address: No. 389, Xincun Road

department: Department of Thoracic Surgery

institute: Shanghai Tongji Hospital Affiliated with Tongji University

data_processing:
Trimming: Raw reads were subjected to filtering and trimming using Trimmomatic-0.30 based on recommended parameters (Adapter sequences were first trimmed, followed by removing leading pr trailing low quality or N bases, scaning the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15 and finally droping reads shorted than minimum length)
Aligning and annotation: Cleaned reads were mapped to genome sequences using HISAT2 (version 2.1.0). The acquired sam files were compressed, sorted and indexed using samtools (version: 1.10). Reads mapped to different genomic features (5'UTR, exon, 3'UTR, CDS) were analyzed and quantified using htseq-count (version 0.11.2).The gene expression level was normalized by using TPM.
Downstream analysis: the edgeR package in R software (http://www.r project.org) was used to conducting differentially expressed genes (DEGs) from obtained count files. Genes with a fold change ≥2 and a false discovery rate (FDR) <0.05 in a comparison were considered as significant DEGs.
Assembly: GRCH38
Supplementary files format and content: Tab-delimited text files including the raw counts for each sample

extract_protocol:
For mRNA-seq, total RNA was isolated using TRIzol (Invitrogen) and quantified by spectrophotometry. For ribo-seq, samples were lysed and subjected to nuclease digestion using the TruSeq Ribo Profile Library Prep Kit (Illumina) according to the manufacturer's instructions. Lysates were then purified using MicroSpin S-400 HR spin columns (Thermo Fisher). rRNA was then depleted using a Ribo-Zero Plus rRNA Depletion Kit (Illumina).
For mRNA-seq, extracted mRNA was enriched with oligo(dT) beads, subjected to fragmentation, and reverse transcribed into cDNA with random primers. cDNA samples were then purified, subjected to end-repair and oligo(A) added and ligated to Illumina adaptors according to the manufacturer's instructions; For Ribo-seq, rRNA-depleted samples were subjected to purification by PAGE, fragmentation, end repair and 3’ adapter ligation, reverse transcription, and cDNA circularization following a protocol described by Illumina.

treatment_protocol: For ribo-seq, H1975 cells were harvested after treatment with 100 μg/ml cycloheximide.

tag: cell line

value: lung adenocarcinoma

value: Scramble


title: NCI-H1975 cells, Scramble, input_mRNA, rep1


title: NCI-H1975 cells, Scramble, input_mRNA, rep3


title: WT_Citro_D14_gp38#1

tag: genotype


title: WT_Citro_D14_CD45#3

source_name: CD45+ cell

value: CD45+ cell


title: RNAseq_mMA9_sgSgf29#3


title: Donor_40_Plate

value: Peripheral Blood

value: Macrophages


title: WT_Citro_D14_CD45#2


title: 4780_Microglia_BEB20057_CTRL

description:
4780
RNA extracted from microglial nuclei (IRF8+, EAAT1-, NeuN-, OLIG2-)

tag: donor


title: WT_Citro_D14_IEC#3

source_name: IEC

value: IEC


title: RNAseq_mMA9_sgSgf29#2


title: H3K9ac_ChIPseq_mMA9_sgCtrl#3


title: WT_Citro_D14_IEC#2

value: WT


title: 4779_Oligodendrocyte_BEB20057_CTRL

description:
4779
RNA extracted from oligodendrocyte nuclei (OLIG2+, EAAT1-, NeuN-, IRF8-)

tag: pmi (hrs)


title: RNAseq_mMA9_sgSgf29#1


title: WT_Citro_D7_gp38#3

value: Stromal cell


title: 4774_Interneuron--Non-Fast-Spiking_HSB3881_HD

description:
4774
RNA extracted from SST-positive striatal interneuron nuclei (SST+, TAC3-, ETV1-)

source_name: Caudate

value: Caudate

value: Interneuron, Non-Fast Spiking

value: 43CAG / 25CAG

tag: disease

value: HD


title: WT_Citro_D7_gp38#2


title: RNAseq_mMA9_sgCtrl#2

value: leukemia


title: WT_Citro_D7_CD45#3


title: WT_Citro_D7_CD45#2


title: 4759_Microglia_BEB20057_CTRL

description:
4759
RNA extracted from microglial nuclei (IRF8+, EAAT1-, NeuN-, OLIG2-)

value: Posterior putamen

value: Microglia

value: Male


title: RNAseq_mMA9_sgCtrl#1


title: WT_Citro_D7_CD45#1


title: 4773_Interneuron--Non-Fast-Spiking_HCTSU_CTRL

description:
4773
RNA extracted from SST-positive striatal interneuron nuclei (SST+, TAC3-, ETV1-)

value: Posterior caudate

value: HCTSU

value: Female

value: CTRL


title: WT_Citro_D7_IEC#3


title: WT_Citro_D7_IEC#2


title: 4758_Interneuron--Other_HCTSU_CTRL

description:
4758
RNA extracted from TAC3-positive striatal interneuron nuclei (TAC3+, ETV1+, PPP1R1B-)

value: Interneuron, Other


title: AM-AM-18_D3_TM

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

description:
AM-AM-18
gene_counts_v2.txt
gene_norm_v2.txt

data_processing:
We used cutadapt to trim Truseq adapters and low quality ends from the 3' end of raw reads; a minimum trimmed length of 40bp was required. Trimmed reads were mapped to the reference genome using STAR, and gene expression quantified using featureCounts. For comparisons between KO groups, batch effect correction was performed based on the Day and Animal ID.
Assembly: mm10
Supplementary files format and content: gene_counts.txt: tab-delimited text file of counts per gene for each sample
Supplementary files format and content: gene_norm.txt: tab-delimited text file of CPM normalized expression for each sample

extract_protocol:
Neutrophils were mobilized to lung of 8-10 weeks old male Catchup (heterozygous) or non-labelled C57BL/6-background mice by exposure to 1mg/ml of nebulized LPS (Sigma, Escherichia coli O55:B5) inside the fumigation chamber. 20 micro grams of anti-Ly6G-BV421 antibody (Biolegend, #127628) was i.v. injected 2 minutes before sacrifice. Lungs were perfused with 10 ml of PBS through right ventricle of heart and collected for PMN isolation, biochemical, and histopathological analyses. For PMN isolation, a single cell suspension was prepared by digestion of minced lung lobes with collagenase A (1 mg/ml; Millipore-Sigma # SCR103) at a 370C shaking water bath for 45 min. Digested lung samples were passed through 16-17G needle and filtered through 40 mm cell strainer (Thermo Fisher, #08-771-1). Red blood cells were removed by using RBC lysis buffer (Thermo Fisher, #00-4333-57). A single cell suspension prepared from Catchup (heterozygous) mice were directly subjected to flow sorting for separation of td-Tomato-positive or double td-Tomato and anti-Ly6G-BV421-positive PMN. PMN, labelled with td-Tomato (or anti-Ly6G-AF-594) and td-Tomato and anti-Ly6G-BV-421 (or anti-Ly6G-AF-594 and anti-Ly6G-BV-421), were sorted in a sterile environment by MoFlo Astrios and MoFlo Astrios EQ (Beckman Coulter) cell sorter equipped with 405, 488, 561 and 635 nm lasers, and collected in RPMI-1640 medium (Thermo Fisher #72400047). Both the sorters are Gates were initially established on forward and side scatter, based on granularity and relative size. Aggregates were gated out accordingly. Selective gates were drawn to sort the single positive and dual positive PMN. Software SUMMIT, 6.1 (Beckman Coulter) was used for sorting and analysis.
RNA quality and quantity was assessed using the Agilent bio-analyzer. All samples showed RNA integrity number > 8. Strand-specific RNA-SEQ libraries were prepared using a TruSEQ mRNA RNA-SEQ library protocol (Illumina provided). Library quality and quantity was assessed using the Agilent bio-analyzer and libraries were sequenced using an Illumina NovaSEQ6000 (Illumina provided reagents and protocols).
TruSEQ mRNA RNA-SEQ library protocol (Illumina provided)

value: Lung

value: Neutrophil

value: Transmigrated

value: day 3

tag: animal id


title: WT_Citro_D7_IEC#1

value: IEC

value: WT


title: WT_uninfected_gp38#2

value: Stromal cell

value: Uninfected


title: WT_Citro_D14_CD45#1

value: CD45+ cell


title: AM-AM-17_D3_No-TM

description:
AM-AM-17
gene_counts_v2.txt
gene_norm_v2.txt

value: Non-transmigrated


title: 4756_Interneuron--Other_HSB3881_HD

description:
4756
RNA extracted from TAC3-positive striatal interneuron nuclei (TAC3+, ETV1+, PPP1R1B-)

value: Caudate

value: 43CAG / 25CAG

value: HD


title: WT_uninfected_gp38#1


title: WT_Citro_D14_IEC#1


title: AM-AM-16_D3_TM

description:
AM-AM-16
gene_counts_v2.txt
gene_norm_v2.txt


title: WT_uninfected_CD45#1


title: RNAseq_mMA9_sgCtrl#3

value: leukemia


title: 4755_Interneuron--Fast-Spiking_HSB3881_HD

description:
4755
RNA extracted from striatal fast-spiking interneuron nuclei (ETV1+, TAC3-, PPP1R1B-)

value: Interneuron, Fast Spiking

value: Male


title: AM-AM-15_D3_No-TM

description:
AM-AM-15
gene_counts_v2.txt
gene_norm_v2.txt


title: 4711_Oligodendrocyte_BEB18135_CTRL

description:
4711
RNA extracted from oligodendrocyte nuclei (OLIG2+, EAAT1-, NeuN-, IRF8-)

value: Posterior putamen

value: Oligodendrocyte

value: CTRL


title: WT_Citro_D7_gp38#1


title: WT_uninfected_IEC#1


title: AM-AM-14_D3_TM

description:
AM-AM-14
gene_counts_v2.txt
gene_norm_v2.txt

value: Lung

value: Neutrophil

value: Transmigrated


title: 4757_Interneuron--Fast-Spiking_HCTSU_CTRL

description:
4757
RNA extracted from striatal fast-spiking interneuron nuclei (ETV1+, TAC3-, PPP1R1B-)

value: Posterior caudate

value: HCTSU

value: Female


title: 4710_Striatopallidal-medium-spiny-neuron_HSB2116_HD

description:
4710
RNA extracted from DRD2-expressing striatal projection neuron nuclei (PPP1R1B+, DRD2+, DRD1-)

value: Striatopallidal medium spiny neuron

value: 44CAG / 17CAG


title: AM-AM-13_D3_No-TM

description:
AM-AM-13
gene_counts_v2.txt
gene_norm_v2.txt

value: Non-transmigrated

value: day 3


title: Single-cell RNAseq (10X V3) of nasal epithelial and immune cells from alternaria-treated (2 doses) WT mice. Channel 2

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

institute: Harvard T. H. Chan School of Public Health

data_processing:
10X Chromium V3 Chemistry Single-cell RNA Seq
log transformation and TPM normalization (Seurat R package)
PCA (Seurat R package)
UMAP and clustering (Seurat R)
Assembly: mm10
Supplementary files format and content: Log2(Transcripts per million (TPM) + 1) expression values (derived from kallisto bustools  for each gene (rows) in each single-cell (columns)

source_name: Mouse nasal epithelial and immune cells sorted using FACS

growth_protocol: To isolate respiratory epithelium from olfactory mucosa, the tissue overlying the proximal part of the nasal septal and lateral wall, together with vomeronasal organ, was separated from olfactory epithelium, covering the distal portions of nasal cavity. The isolated olfactory and respiratory mucosa were processed as described previously (40). The separated tissue including cartilages and bone fragments was first incubated in a PBS solution with dispase (16 U/ml) and deoxyribonuclease I (DNase I; 20 μg/ml) for 30 min at room temperature on a shaker at 120 rpm. The digestion was terminated by adding cold DMEM supplemented with 5% fetal bovine serum (FBS).

extract_protocol:
Then, the nasal mucosa was separated from the bones mechanically and incubated in Tyrode's Solution with bicarbonate, HEPES, 0.25% BSA, without Ca2+ and added 31 U/ml of papain, 0.25 mg/ml L-cysteine and 20 μg/ml DNase I for 40 min at 37 °C on a rotating shaker at 220 rpm. The papain enzymatic activity was terminated with Tyrode's Solution with HEPES and Ca2+ and with 0.01 mg/ml leupeptin and the digested mucosa was triturated thoroughly and prepared for flow cytometric staining. All samples were pre-incubated with TruStain FcX™ (Biolegend) at 1µg per 106 cells in 100 µl volume for 10 minutes prior to immunostaining (Fig. S1A). 6,000-10,000 cells per sample were collected into PBS and 0.04% (w/v) bovine serum albumin (BSA) and submitted for scRNA-seq. Single-cell suspensions for low input (bulk) RNA-sequencing at 1,000 cells per sample were sorted into TCL buffer (Qiagen) supplemented with 1% 2-mercaptoethanol. We analyzed a total of 10 mice, treated with PBS (n=4), with one Alternaria challenge (n=4), and with two challenges (n=2).
Sorted samples, containing 6,000-10,000 cells each, were submitted for droplet-based single-cell RNA-sequencing (10X Genomics) to the Single Cell Genomic Core at Brigham and Women’s Hospital. Cells were washed and resuspended in PBS and 0.04% (w/v) bovine serum albumin (BSA) per the manufacturer’s guidelines. Purified samples were run through 10X controller and individually bar-coded libraries were generated and pooled. Pooled library samples were sequenced on a NovaSeq S1 (Illumina) in partnership with Dana Farber Cancer Institute (DFCI) Molecular Biology Core Facilities.
10X Chromium V3 Chemistry Single-cell RNA Seq

treatment_protocol: For assessment of the inflammatory and epithelial response to Alternaria by scRNAseq, the olfactory and respiratory epithelium were processed separately and CD45+ and EpCAM+ cells were sorted to represent 50% of cells in each location. The experiment was performed twice with the collected cells from olfactory mucosa of one mouse and respiratory mucosa from a different mouse of the opposite sex combined together to contribute equal proportions of a single sample.

value: WT

value: Alternaria 2 doses

tag: time point


title: Single-cell RNAseq (10X V3) of nasal epithelial and immune cells from alternaria-treated (1 dose) WT mice. Channel 3

value: Alternaria 1 dose


title: Single-cell RNAseq (10X V3) of nasal epithelial and immune cells from alternaria-treated (2 doses) WT mice. Channel 1


title: 4709_Striatonigral-medium-spiny-neuron_HSB2116_HD

description:
4709
RNA extracted from DRD1-expressing striatal projection neuron nuclei (PPP1R1B+, DRD1+, DRD2-)

data_processing:
Sequence and transcript coordinates for human hg38 UCSC genome and gene models were retrieved from the BSgenome.Hsapiens.UCSC.hg38 Bioconductor package (version 1.4.1) and TxDb.Haspiens.UCSC.hg38.knownGene (version 3.4.0) Bioconductor libraries respectively. FANSseq reads were aligned to the genome using Rsubread's subjunc method (version 1.30.6).
Aligned reads were exported as bigWigs normalized to reads per million using the rtracklayer package (version 1.40.6).
Aligned reads in genes were counted using the featurecounts function within the Rsubread package against gene exons.
Assembly: BSgenome.Hsapiens.UCSC.hg38
Supplementary files format and content: BigWig files, Counts files

value: Caudate

value: Striatonigral medium spiny neuron

value: HD


title: 4708_Interneuron--Non-Fast-Spiking_HSB3167_HD

description:
4708
RNA extracted from SST-positive striatal interneuron nuclei (SST+, TAC3-, ETV1-)

value: Interneuron, Non-Fast Spiking

value: 45CAG / 17CAG

value: Male


title: Single-cell RNAseq (10X V3) of nasal epithelial and immune cells from alternaria-treated (1 dose) WT mice. Channel 1


title: Single-cell RNAseq (10X V3) of nasal epithelial and immune cells from alternaria-treated (1 dose) WT mice. Channel 2


title: Single-cell RNAseq (10X V3) of nasal epithelial and immune cells from naïve WT mice. Channel 4

value: Naive


title: Single-cell RNAseq (10X V3) of nasal epithelial and immune cells from naïve WT mice. Channel 3


title: 4707_Interneuron--Fast-Spiking_HSB3167_HD

description:
4707
RNA extracted from striatal fast-spiking interneuron nuclei (ETV1+, TAC3-, PPP1R1B-)

value: Interneuron, Fast Spiking


title: AM-AM-09_D2_No-TM

description:
AM-AM-09
gene_counts_v2.txt
gene_norm_v2.txt

value: Lung

value: Neutrophil

tag: time

value: day 2


title: WT_uninfected_CD45#2

value: CD45+ cell

value: Uninfected


title: Single-cell RNAseq (10X V3) of nasal epithelial and immune cells from naïve WT mice. Channel 2


title: WT_uninfected_IEC#2

value: IEC


title: AM-AM-08_D2_TM

description:
AM-AM-08
gene_counts_v2.txt
gene_norm_v2.txt

tag: tissue

value: Transmigrated


title: 4706_Interneuron--Other_HSB3167_HD

description:
4706
RNA extracted from TAC3-positive striatal interneuron nuclei (TAC3+, ETV1+, PPP1R1B-)

tag: cell type

value: Interneuron, Other


title: Single-cell RNAseq (10X V3) of nasal epithelial and immune cells from naïve WT mice. Channel 1

value: WT


title: Single-cell RNAseq (10X V3) of nasal epithelial cells from Chat-eGFP mice. Mouse 4

source_name: Mouse nasal epithelial cells sorted using FACS

value: Chat-eGFP


title: AM-AM-07_D2_No-TM

description:
AM-AM-07
gene_counts_v2.txt
gene_norm_v2.txt

value: Non-transmigrated


title: Single-cell RNAseq (10X V3) of nasal epithelial cells from Chat-eGFP mice. Mouse 3


title: Single-cell RNAseq (10X V3) of nasal epithelial cells from Chat-eGFP mice. Mouse 2


title: 4705_Interneuron--Non-Fast-Spiking_HSB2116_HD

description:
4705
RNA extracted from SST-positive striatal interneuron nuclei (SST+, TAC3-, ETV1-)

value: Caudate

value: 44CAG / 17CAG

value: Female

value: HD


title: AM-AM-06_D1_TM

description:
AM-AM-06
gene_counts_v2.txt
gene_norm_v2.txt

value: day 1


title: AM-AM-10_D2_TM

description:
AM-AM-10
gene_counts_v2.txt
gene_norm_v2.txt


title: Bulk RNAseq of nasal OSN cells (WT). Treatment: Aspergillus and sample id: 221220_G8

value: Aspergillus


title: Single-cell RNAseq (10X V3) of nasal epithelial cells from Chat-eGFP mice. Mouse 1

value: Naive


title: AM-AM-05_D1_No-TM

description:
AM-AM-05
gene_counts_v2.txt
gene_norm_v2.txt

value: Lung

value: Neutrophil


title: 4704_Interneuron--Fast-Spiking_HSB2116_HD

description:
4704
RNA extracted from striatal fast-spiking interneuron nuclei (ETV1+, TAC3-, PPP1R1B-)

value: Interneuron, Fast Spiking


title: Bulk RNAseq of nasal OSN cells (WT). Treatment: Aspergillus and sample id: 221220_G7


title: Bulk RNAseq of nasal OSN cells (WT). Treatment: Aspergillus and sample id: 221220_G6


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Aspergillus and sample id: 221220_G3


title: Bulk RNAseq of nasal OSN cells (WT). Treatment: Naive and sample id: 221220_G5


title: 4581_Interneuron--Non-Fast-Spiking_BEB19025_CTRL

description:
4581
RNA extracted from SST-positive striatal interneuron nuclei (SST+, TAC3-, ETV1-)

source_name: Posterior caudate

value: Posterior caudate

value: Interneuron, Non-Fast Spiking

value: Male

value: CTRL


title: AM-AM-03_D1_No-TM

description:
AM-AM-03
gene_counts_v2.txt
gene_norm_v2.txt


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Aspergillus and sample id: 221220_G2

value: WT


title: 4580_Interneuron--Fast-Spiking_BEB19025_CTRL

description:
4580
RNA extracted from striatal fast-spiking interneuron nuclei (ETV1+, TAC3-, PPP1R1B-)


title: 4579_Interneuron--Other_BEB19025_CTRL

description:
4579
RNA extracted from TAC3-positive striatal interneuron nuclei (TAC3+, ETV1+, PPP1R1B-)

value: Interneuron, Other


title: Bulk RNAseq of nasal OSN cells (WT). Treatment: Naive and sample id: 221220_F9


title: AM-AM-02_D0_Ctrl fl No-TM

description:
AM-AM-02
gene_counts_v2.txt
gene_norm_v2.txt

value: Non-transmigrated

value: day 0


title: Bulk RNAseq of nasal HBC cells (WT). Treatment: Naive and sample id: 221220_F5


title: AM-AM-01_D0_Ctrl fl TM

description:
AM-AM-01
gene_counts_v2.txt
gene_norm_v2.txt

value: Transmigrated


title: 4578_Interneuron--Non-Fast-Spiking_BEB19051_CTRL

description:
4578
RNA extracted from SST-positive striatal interneuron nuclei (SST+, TAC3-, ETV1-)