title: B6_V265D_2mo_ColumbiaU_scRNA_2

city: New York

first: Nicholas

last: Tolman

state: NY

department: Ophthalmology

institute: Columbia University

description: Library name: Sample6

data_processing:
Demultiplexed data was processed using the CellRanger count pipeline
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Limbal strip

extract_protocol:
(Columbia University scRNA-seq samples): Tissues were digested enzymatically using Papain and Deoxyribonuclease I (Worthington Biochemical Corporation, Cat. no. LK003153) for 20 min at 37°C and stopped using Earl’s balanced salt solution (EBSS, Thermo Fisher Scientific, Cat no. 24010-043). Cells were triturated using an 18-gauge needle, centrifuged at 300g at 4 °C, washed with cold DMEM, and filtered using a 100 μm Flowmi Cell Strainer (H13680-0040, Bel-Art. Cells were resuspended in cold DMEM and placed on ice immediately. (Columbia University multiome sample): Limbal strip samples for multiome analysis were snap-frozen on dry ice immediately following dissection and stored at -80C until processing. To isolate nuclei, tissue was homogenized in 100 μL of chilled lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween20, and 0.01% digitonin – from [142] supplemented with 1% BSA). Afterwards, samples were incubated for 5 min on ice, gently agitated by pipetting, and incubated for an additional 10 minutes on ice. We then added 1 mL of chilled wash buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20, 1% BSA) to the cells and centrifuged at 500 rcf for 5 min at 4°C. Cells were resuspended in chilled Diluted Nuclei Buffer (PN-2000153, 10x Genomics) and filtered through a 40 μm Flowmi Cell Strainer (H13680-0040, Bel-Art). Cells were resuspended in cold DMEM and placed on ice immediately. (Duke University scRNA-seq sample): Single cell dissociation was performed using Collagenase IV (Worthington Biochemical Cat. no. LS004188), Dispase II (Sigma Cat. No. D4693) and DNAse I (Roche Cat no. 50225500) for 60 min and then trypsin/EDTA for 10 min at 37°C. Cells were triturated using a 1 ml pipette tip, centrifuged at 300g at 4°C, washed with cold DMEM containing 10% FBS, and filtered using a 70 μm cell strainer (Fisher). Cells were resuspended in cold DMEM containing 5% FBS and placed on ice immediately
Single-cell and single-nucleus RNA-seq was performed at the single-cell sequencing core in Columbia Genome Center (Columbia University) or Duke Molecular Genomics Core (MGC, Duke University). Single cells or nuclei were loaded into chromium microfluidic chips with v3 chemistry and barcoded with a 10x chromium controller (10x Genomics). RNA from the barcoded cells was reverse-transcribed, and sequencing libraries were constructed with a Chromium Single Cell v3 reagent kit (10x Genomics). Sequencing at both institutions was performed on NovaSeq 6000 (Illumina).

value: Limbal strip

value: Lmx1b V265D/+


title: Heart macrophages macrophages, control sample 12, LysMCretdT>Fthfl/fl bone marrow chimera

status: Public on Nov 10 2025

type: SRA

city: Oeiras

first: Rui

last: Martins

address: Rua da Quinta Grande 6

department: Inflammation

country: Portugal

institute: Gulbenkian Institute for Molecular Medicine

description: Library name: H12M

library_source: transcriptomic

data_processing:
Fastq reads were aligned against the mouse reference genome GRCm39 using the annotation GENCODE M27 (STAR; v.2.5.2a)
Read summarization was performed using FeatureCounts (v1.5.0-p1)m by assigning uniquely mapped reads to genomic features
Gene expression tables were imported into the R programming language and environment (v.4.1.0)
Analysis of differential gene expression was performed using the DESeq2 R package (Love et al., 2014) (v.1.31.7)
Gene expression was modeled per organ based on chimera genotype combination.
Genes not expressed or presenting an average expression inferior to 5 counts across the 18 samples were removed resulting in 22,529 (liver), 23,327 (WAT) and 29,821 (heart) genes for downstream differential gene expression analysis
Assembly: GRCm39
Supplementary files format and content: Single table containing the normalized counts per feature (geneid) and sample

molecule: polyA RNA

organism: Mus musculus

source_name: Heart macrophages from LysMCretdT>Fthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth - Sample 12

extract_protocol:
Viable, CD45+, CD11b+, dTomato+ (LysM+), Ly6G-, CD3-, CD19- cells (monocytes/macrophages) were sorted directly into QIAgen RLT+ buffer and used for SMART-seq2 cDNA library generation
Full-length cDNAs and sequencing libraries were generated following the SMART-Seq2 protocol, as previously described (Picelli et al, 2014). Quality control (Agilent Technologies) and "tagmentation" - PCR-mediated adaptor addition and amplification of the adapted libraries was performed following the Nextera library preparation protocol (llumina Tagment DNA Enzyme and Buffer, Illumina #20034211; KAPA HiFi HotStart ReadyMix, Roche #07958935001; Nextera XT Index Kit v2 Set A, Illumina #15052163; Nextera XT Index Kit v2 Set D, Illumina #15052166), essentially as previously described (Baym et al, 2015). Libraries were sequenced (NextSeq2000 sequencing; Illumina) using 100 SE P2 and sequence information was extracted in FastQ format, using Illumina DRAGEN FASTQ Generation v3.8.4, producing on average approximately 38x10^6 (liver), 32x10^6 (WAT) and 43x10^6 (heart) reads per sample.

treatment_protocol: Bone marrow chimeras (LysMCretdT>Fthfl/fl; LysMCretdT>R26CreFthfl/fl; LysMCretdT-Fthfl/fl>R26CreFthfl/fl) were given Tamoxifen (50mg/kg, in 100µl corn oil, 5% Ethanol) 3 times, every other day.

tag: tissue

tag: genotype

value: LysMCretdT>Fthfl/fl bone marrow chimera

tag: treatment

value: Tamoxifen 50mg/kg 3x, every other day


title: Liver macrophages, control sample 5, LysMCretdT>Fthfl/fl bone marrow chimera

description: Library name: L5M

source_name: Liver macrophages from LysMCretdT>Fthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth - Sample 5


title: Heart macrophages macrophages, deleted sample 8, LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera

description: Library name: H8M

source_name: Heart macrophages, from LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth, Sample 8


title: Yoda1_Vascular tissues_3weeks

city: Palo Alto

first: Yu

last: Liu

state: CA

address: 1215 Welch Road

department: CVI

country: USA

institute: Stanford University

description:
Library name: Yoda1_Vascular tissues_3weeks
paired-end

library_source: transcriptomic single cell

data_processing:
The read counts of each cell was calculated by using Cellranger
The analysis of single cell RNAseq data was performed by Seurat
Assembly: mm10
Supplementary files format and content: features.tsv, barcodes.tsv, matrix.mtx

molecule: total RNA

source_name: vascular tissue

extract_protocol:
Following arterial digestion, cells were resuspended in MACS sorting buffer containing 0.5% BSA at 1,000 cells/μL. Approximately 10,000 cells per sample were processed using the Chromium™ Single-Cell 3' Reagent Kit (10x Genomics) according to the manufacturer’s protocol.
Single cells were partitioned into microfluidic chambers on a 10x Genomics Chromium Controller and encapsulated in gel beads containing sequencing adapters, primers, molecular barcodes, unique molecular identifiers (UMIs), and oligo-dT primers. This generated single-cell barcoded droplets (GEMs). After GEM formation, mRNA was reverse transcribed to produce barcoded cDNA libraries.

value: vascular tissue

value: WT

tag: batch

value: paired-end


title: Heart macrophages macrophages, deleted sample 4, LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera

description: Library name: H4M

source_name: Heart macrophages, from LysMCretdT-Fthfl/fl>R26CreFthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth, Sample 4


title: T regulatory type 1 cells - activated (Donor 9632)

city: Philadelphia

first: Khanh

middle: Bao

last: Trang

state: PA

address: 3615 Civic Center Blvd

department: Human Genetics

institute: Children's Hospital of Philadelphia

data_processing:
Bases were called using Illumina bcl2fastq2 conversion v2.29
The pair-end fastq files were mapped to the genome assembly hg19 by STAR (v2.6.0c) independently for each replicate.
The GencodeV19 annotation was used for gene feature annotation and the raw read count for gene feature was calculated by htseq-count (v0.6.1) with parameter settings -f bam - r pos -s yes -t exon -m union.
The gene features localized on chrM or annotated as rRNAs, small coding RNA, or pseudo genes were removed from the final sample-by-gene read count matrix.
Assembly: hg19
Supplementary files format and content: HTSeq raw count

organism: Homo sapiens

source_name: Regulatory T cells

extract_protocol:
RNA was isolated from ∼ 1 million of each cell stage using Trizol Re-agent (Invitrogen), purified using the Directzol RNA Miniprep Kit (Zymo Research), and depleted of contaminating genomic DNA using DNAse I. Purified RNA was checked for quality on a Bioanlayzer 2100 using the Nano RNA Chip and samples with RIN>7 were used for RNA-seq library preparation. RNA samples were depleted of rRNA using QIAseq Fastselect RNA removal kit (Qiagen).
Samples were then processed for the preparation of libraries using the SMARTer Stranded Total RNA Sample Prep Kit (Takara Bio USA) according to the manufacturer’s instructions. Briefly, the purified first-strand cDNA is amplified into RNA-seq libraries using SeqAmp DNA Polymerase and the Forward and the Reverse PCR Primers from the Illumina Indexing Primer Set HT for Illumina. Quality and quantity of the libraries was assessed using the Agilent 2100 Bioanalyzer system and Qubit fluorometer (Life Technologies). Sequencing was performed on the NovaSeq 6000 platform at the CHOP Center for Spatial and Functional Genomics.

tag: cell line

value: Regulatory T cells

tag: cell type

value: T regulatory type 1 cells

tag: markers

value: LPS-activated

tag: biomaterial provider

value: Levings Lab - BC Children's Hospital


title: B6_V265D_2mo_ColumbiaU_scRNA_1

description: Library name: Sample5


title: TKI_Vascular tissues_3weeks

description:
Library name: TKI_Vascular tissues_3weeks
paired-end


title: Control_Vascular tissues_3weeks

description:
Library name: Control_Vascular tissues_3weeks
paired-end


title: B6_WT_2mo_ColumbiaU_multiome_ATAC_1

description: Library name: Sample4

library_source: genomic single cell

molecule: genomic DNA


title: T regulatory type 1 cells (Donor 3199)


title: T helper 2cells (Donor 0155)

source_name: T helpercells

value: T helpercells

value: T helper 2cells


title: untreated_17_01

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

country: Germany

institute: University Münster

data_processing:
Reads were quality checked with package FastQC (version Version 0.11.9) then quality trimmed using Trimgalore (version 0.6.7)
Trimmed reads were mapped to mouse genome using STAR aligner (version 2.7.9a) with default settings.
Mapped reads were counted using RsubRead (version 2.8.1)
Raw counts were normalized using DESeq2 (version 1.36.0)
Assembly: ENSMBL Mus_musculus.GRCm39, release 104
Supplementary files format and content: txt matrix with log2 normalized values per sample.
Supplementary files format and content: note that data analyzed in publication were generated from batch-corrected data including batch1 and batch 2 (two separate GEO entries)

source_name: lung

extract_protocol:
Lung lobes were prepared and transferred to an enzyme mix to dissociate cells. CD45-positive cells were bound to CD45 antibody-coupled beads and then discarded. CD45-negative cells were bound to CD31 antibody-coupled magnetic beads for positive cell sorting. After washing, RNA was isolated from cells. PolyA+RNA was purified  from 100 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).
Directional RNA Library Prep, single reads run 72 Nu with an average of 26.3 M reads per sample

treatment_protocol: Mice were anesthetized, the cecum mobilized after median laparotomy and the cecum ligated and punctured. The abdomen was closed and treatment substances injected invtravenously. Mice were awakened and sacrificed after 18h.

value: lung

value: endothelial cells

value: untreated


title: untreated_18_02


title: B6_WT_2mo_ColumbiaU_multiome_RNA_1

description: Library name: Sample3

molecule: nuclear RNA


title: Liver macrophages, control sample 11, LysMCretdT>Fthfl/fl bone marrow chimera

description: Library name: L11M

source_name: Liver macrophages from LysMCretdT>Fthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth - Sample 11


title: Sham_23_09

value: Sham


title: Heart macrophages macrophages, control sample 5, LysMCretdT>Fthfl/fl bone marrow chimera

description: Library name: H5M

source_name: Heart macrophages from LysMCretdT>Fthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth - Sample 5


title: T helper 2cells (Donor 2000)


title: T helper 2cells (Donor 5002)


title: B6_WT_2mo_DukeU_scRNA_1

description: Library name: Sample7

value: Limbal strip


title: T regulatory type 1 cells - activated (Donor 3199)


title: B6_WT_2mo_ColumbiaU_scRNA_1

description: Library name: Sample1


title: T helper 2cells- activated (Donor 0155)


title: LPS-treated Optn knockout BV2: KO_LPS-3

city: Trieste

first: Maurizio

last: Romano

address: Via A. Valerio 28

department: Department of Life Sciences

country: Italy

institute: University of Trieste

description:
Library name: KO_LPS-3
LPS-treated Optn knockout BV2 from a biological triplicate: KO_LPS_12

data_processing:
Original raw data from Illumina were transformed to sequenced reads by CASAVA base recognition. Raw reads are filtered to remove reads with adapter contamination or reads with low quality. The filtering process consists in discard reads with adaptor contamination; discard reads when uncertain nucleotides constitute more than 10% of either read (N > 10%); discard reads when low quality nucleotides (base quality less than 5) constitute more than 50% of the read. Only clean reads were used in the downstream analyses. Paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full length transcripts representing multiple splice variants for each gene locus.
Gene-level counts were quantified using featureCounts v1.5.0-p3 to count the number of reads mapped to each gene.
The input data for differential gene expression analysis were read counts from gene expression level analysis using DEseq2 package v1.40.0.
The overall distribution of differentially expressed genes (DEGs) were evaluated using the following cut-off: adjusted p-value < 0.05 and an absolute log₂ fold change (|log₂FC|) ≥ 0.5.
Assembly: Mus musculus GRCm38.p6
Supplementary files format and content: The RNA-Seq datasets generated during this study were deposited in the NCBI Gene Expression Omnibus (GEO).
Supplementary files format and content: Gene-level counts were generated using featureCounts.

source_name: Brain

growth_protocol: BV2 microglial cell line was maintained in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, and antibiotic/antimycotic solution: 10,000 U/mL penicillin, 10 mg/mL streptomycin, 25 µg/mL amphotericin B). Optineurin knockout (KO) cells were previously generated using CRISPR/Cas9 with two guide RNAs targeting the Optn gene. KO cells were selected with 2 µg/mL puromycin, the lowest concentration that fully eliminated non-transfected wild-type cells. Puromycin was withdrawn shortly before seeding. Cells were plated in puromycin-free medium, and treatments were applied the following day[cite: 282, 283]. Each condition was prepared in biological triplicate from three independent experiments.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (QIAGEN, Cat. No. 74104) according to the manufacturer’s protocol. RNA concentration and purity were assessed on a BioDrop Duo spectrophotometer; all samples had 260/280 and 260/230 ratios of ~2 and were deemed suitable for sequencing
mRNA library preparation (poly-A enrichment) and RNA sequencing were performed by Novogene.

treatment_protocol: Both wild-type (CTRL) and KO cells were treated with or without 2 µg/mL lipopolysaccharide (LPS; Sigma-Aldrich, Cat. No. L4391) for 24 h.

value: Brain

value: microglia

value: optineurin knockout (KO)

value: LPS (2 µg/mL for 24 h)


title: Heart macrophages macrophages, control sample 11, LysMCretdT>Fthfl/fl bone marrow chimera

description: Library name: H11M

source_name: Heart macrophages from LysMCretdT>Fthfl/fl bone marrow chimera 19 days post tamoxifen induced deletion of Fth - Sample 11

value: LysMCretdT>Fthfl/fl bone marrow chimera

value: Tamoxifen 50mg/kg 3x, every other day


title: T regulatory type 1 cells - activated (Donor 1064)

value: Regulatory T cells


title: LPS-treated Optn knockout BV2: KO_LPS-2

description:
Library name: KO_LPS-2
LPS-treated Optn knockout BV2 from a biological triplicate: KO_LPS_11


title: T helper 2cells (Donor 1234)


title: untreated_19_04


title: Sham_25_16


title: T helper 2cells- activated (Donor 2000)


title: Sham_24_15


title: untreated_128_23


title: B6_WT_2mo_ColumbiaU_scRNA_2

description: Library name: Sample2

value: WT


title: T helper 1cells(Donor 0155)

value: T helper 1cells


title: Sham_125_19


title: T helper 2cells- activated (Donor 1234)

value: LPS-activated

value: Levings Lab - BC Children's Hospital


title: CLP_plus_Sita_21_08


title: CLP_plus_Sita_20_07


title: CLP_plus_Sita_22_14


title: T helper 1cells(Donor 2000)

value: T helpercells


title: CLP_27_17

value: lung

value: CLP


title: CLP_26_06

value: endothelial cells


title: T helper 1cells(Donor 1234)


title: Untreated Optn knockout BV2: KO-2

description:
Library name: KO-2
Untreated Optn knockout BV2 from a biological triplicate: KO_8


title: untreated_129_24

value: untreated


title: CLP_28_18


title: LPS-treated Optn knockout BV2: KO_LPS-1

description:
Library name: KO_LPS-1
LPS-treated Optn knockout BV2 from a biological triplicate: KO_LPS_10


title: untreated_127_3


title: Sham_126_20

value: Sham


title: Untreated Optn knockout BV2: KO-3

description:
Library name: KO-3
Untreated Optn knockout BV2 from a biological triplicate: KO_9

value: Brain


title: CLP_plus_Sita_123_22


title: CLP_plus_Sita_122_21


title: T helper 1cells- activated (Donor 0155)


title: T helper 1cells- activated (Donor 1234)


title: Sham_124_10


title: Untreated Optn knockout BV2: KO-1

description:
Library name: KO-1
Untreated Optn knockout BV2 from a biological triplicate: KO_7

value: microglia


title: LPS-treated wild-type BV2: LPS-3

description:
Library name: LPS-3
LPS-treated wild-type BV2 from a biological triplicate: LPS_6


title: CLP_plus_Sita_121_13


title: T helper 17cells (Donor 2000)

value: T helper 17cells


title: T helper 1cells- activated (Donor 2000)


title: T helper 17cells (Donor 1234)


title: CLP_118_5


title: LPS-treated wild-type BV2: LPS-2

description:
Library name: LPS-2
LPS-treated wild-type BV2 from a biological triplicate: LPS_5

value: LPS (2 µg/mL for 24 h)


title: CLP_119_11


title: CLP_120_12


title: T helper 17cells (Donor 0155)


title: LPS-treated wild-type BV2: LPS-1

description:
Library name: LPS-1
LPS-treated wild-type BV2 from a biological triplicate: LPS_4


title: Untreated wild-type BV2: CTRL-3

description:
Library name: CTRL-3
Untreated wild-type BV2 from a biological triplicate: CTRL_3


title: MARV 3 days post infection_1

city: Boston

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

description: Library name: MG-MA-28

data_processing:
Reads were mapped to GRCh38
Counts per gene were summarized using the featureCounts function from the subread package
edgeR package was used to import and filter the counts
Differential expression using MAST models
The limma package with its voom method, namely, linear modelling and empirical Bayes moderation was used to test differential expression (moderate t-test). P-values were adjusted for multiple testing using Benjamini-Hochberg correction (false discovery rate-adjusted p-value; FDR). Differentially expressed genes for each comparison were visualized using Glimma package, and FDR<0.05 was set as the threshold for determining significant differential gene expression. Enrichment analyses were carried out using Fgsea package.
Assembly: GRCh38
Supplementary files format and content: CSV file having raw read count for each sample in singular file

source_name: iPSC-derived HCO

growth_protocol: CDX2-eGFP iPSC knock-in reporter line to track the emergence of hindgut progen, sorted on day 15 for CDX2/GFP positivity and seeded in 3D matrigel. Distal HCOs were cultured in CKDCI media.

extract_protocol:
The cells were dissociated to a single cell suspension using 0.05% and subsequently sorted for live cells using Calcein blue and CDX2 GFP positivity.
Total RNA was extracted using the Zymo Research RNA extraction kit

treatment_protocol: iPSC-derived HCOs were infected with EBOV and MARV

value: iPSC-derived HCO

value: BU1 CDX2 GFP

value: iPSC-dervied proximal HIOs in 3D

value: MARV


title: MARV 1 day post infection_3

description: Library name: MG-MA-27


title: MARV 3 days post infection_3

description: Library name: MG-MA-30


title: MARV 3 days post infection_2

description: Library name: MG-MA-29


title: MARV 1 day post infection_1

description: Library name: MG-MA-25


title: MARV 1 day post infection_2

description: Library name: MG-MA-26


title: T helper 17cells- activated (Donor 2000)


title: Untreated wild-type BV2: CTRL-2

description:
Library name: CTRL-2
Untreated wild-type BV2 from a biological triplicate: CTRL_2

value: WT


title: T helper 17cells- activated (Donor 1234)

value: LPS-activated


title: Untreated wild-type BV2: CTRL-1

description:
Library name: CTRL-1
Untreated wild-type BV2 from a biological triplicate: CTRL_1


title: EBOV 3 days post infection_3

description: Library name: MG-MA-24

value: EBOV


title: EBOV 3 day post infection_1

description: Library name: MG-MA-22


title: T helper 17cells- activated (Donor 0155)

value: T helpercells

value: Levings Lab - BC Children's Hospital


title: EBOV 1 day post infection_ 3

description: Library name: MG-MA-21


title: WT 8

city: Turku

first: Matti

last: Poutanen

address: Kiinamyllynkatu 10

country: Finland

institute: University of Turku

description: Library name: RNA_S12421Nr15

data_processing:
For the analysis of the sequencing results, demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (version 2.20).
Adapters were trimmed using Skewer (version 0.2.2).
Trimmed raw reads were aligned to mm10 using STAR (version 2.7.3).
Assembly: mm10
Supplementary files format and content: Text file containing normalized genewise read counts, reads per kilobase million

source_name: ovary

extract_protocol:
The mice were euthanized at selected time point using CO2-asphyxiation followed by cervical dislocation. Ovaries were dissected, snap-frozen in liquid nitrogen and stored at -80C. After homogenization, total RNA was extracted with Trisure reagent according to manufacturer's instructions.
Library preparation was performed using the Illumina TruSeq Stranded mRNA kit

value: ovary

tag: age

value: 6 months

tag: estrous cycle_stage

value: estrus


title: Plasmacytoid dendritic cells(Donor ND538)

source_name: Plasmacytoid dendritic cells

value: Plasmacytoid dendritic cells

value: Wells Laboratory - Children’s Hospital of Philadelphia


title: WT 7

description: Library name: RNA_S12421Nr14


title: EBOV 1 day post infection_ 2

description: Library name: MG-MA-20


title: EBOV 1 days post infection_ 1

description: Library name: MG-MA-19


title: WT 6

description: Library name: RNA_S12421Nr13


title: Mock 3 days post infection_3

description: Library name: MG-MA-18

value: Mock


title: Plasmacytoid dendritic cells(Donor ND519)


title: Mock 3 days post infection_1

description: Library name: MG-MA-16


title: WT 5

description: Library name: RNA_S12421Nr12


title: Mock 1 day post infection_3

description: Library name: MG-MA-15


title: Mock 1 day post infection_1

description: Library name: MG-MA-13


title: WT 4

description: Library name: RNA_S12421Nr11


title: Mock 1 day post infection_2

description: Library name: MG-MA-14


title: EBOV 3 days post infection_2

description: Library name: MG-MA-23


title: WT 3

description: Library name: RNA_S12421Nr10


title: Mock 3 days post infection_1

description: Library name: S7

source_name: iPSC-derived HIO

growth_protocol: CDX2-eGFP iPSC knock-in reporter line to track the emergence of hindgut progen, sorted on day 15 for CDX2/GFP positivity and seeded in 3D matrigel. Proximal HIOs were cultured in IMCK media.

treatment_protocol: iPSC-derived HIOs were infected with EBOV and MARV

value: iPSC-derived HIO


title: Mock 3 days post infection_3

description: Library name: S9


title: Natural killer cells (Donor ND574)

source_name: Natural killer cells

value: Natural killer cells


title: Natural killer cells (Donor ND581)


title: CD1c+conventional dendritic cells(Donor ND538)

source_name: conventional dendritic cells

value: conventional dendritic cells

value: CD1c+conventional dendritic cells


title: WT 2

description: Library name: RNA_S12421Nr9


title: Natural killer cells (Donor ND578)


title: Mock 3 days post infection_2

description: Library name: S8

value: BU1 CDX2 GFP

value: iPSC-dervied proximal HIOs in 3D


title: WT 1

description: Library name: RNA_S12421Nr8

value: WT


title: EBOV 3 days post infection_2

description: Library name: S5


title: MARV 3 days post infection_3

description: Library name: S3

value: MARV


title: EBOV 3 days post infection_1

description: Library name: S4

value: EBOV


title: Plasmacytoid dendritic cells(Donor ND535)


title: HSD17B1-KI 7

description: Library name: RNA_S12421Nr7

value: HSD17B1 Ser143Ala


title: CD1c+conventional dendritic cells(Donor ND535)


title: Mock 3 days post infection_2

description: Library name: MG-MA-17

value: iPSC-derived HCO


title: MARV 3 days post infection_2

description: Library name: S2


title: CD1c+conventional dendritic cells(Donor ND519)


title: MARV 3 days post infection_1

description: Library name: S1


title: H1,1-10 KO,rep3,ectoderm

city: shanghai

first: shao

last: zhen

address: 320 Yueyang Road

country: China

institute: Shanghai Institute of Nutrition and Health

data_processing:
RNA-seq reads were aligned to hg19 reference genome using STAR with RefSeq annotated genes.
Gene expression levels were counted using featureCounts.
Differential expression analysis comapring each sample with vehicle-treated WT hESCs was performed by DESeq2.
Assembly: hg19
Supplementary files format and content: DESeq2 output for normalization data
Supplementary files format and content: DESeq2 output for differential analysis results

extract_protocol:
Total RNA was extracted with TRIzol™ (ThermoFisher), 500 ng RNA was used for sequencing library construction.
polyA RNA was enriched with NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), then corresponding RNA libararies were prepared with NEBNext® Ultra II RNA Library Prep Kit for Illumina® (New England Biolabs).

value: Human embryonic stem cell

value: ZNF263 homozygous KO


title: 8648-TD-4 AR

city: Ann Arbor

first: Antonio

middle: Marcondes

last: Lerario

state: MI

address: 109 Zina Pitcher Place, 1528 BSRB

department: MEND

institute: University of Michigan

description:
Library name: TD-4
NextSeq P1 100 cycle

library_source: genomic

data_processing:
We used bowtie2 (Langmead and Salzberg, 2012) to align the reads to the mm10 version of the muose genome.
For peak calling, we used genrich (Gaspar, 2018).
BigWig files were generated with bam_to_bigwig function from R/Bioconductor package GenomicAlignments
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

source_name: adrenal gland

extract_protocol:
280 000 nuclei were used per Cut&Tag reaction using the kit CUT&Tag-IT (Active motifi, #53170) and AMPure XP reagent (Beckman Coulter, A63880)
Cut&Tag libraries were prepared using the kit CUT&Tag-IT (Active motifi, #53170) following manufacturer's instructions. Libraries were amplified using 13 cycles on a thermal cycler. Libraries were cleaned up by performing SPRI Bead clean-up from the kit and AMPure XP reagent (Beckman Coulter, A63880)

value: adrenal gland

tag: Sex

value: male

value: 6-9 week-old


title: HSD17B1-KI 6

description: Library name: RNA_S12421Nr6

value: ovary

value: 6 months

value: estrus


title: 37C_120min_Rep2

city: singapore

first: YUE

last: WAN

address: 1, #20-10 Fusionopolis Way, Connexis, North Tower, 138632

country: Singapore

institute: Genome Institute of Singapore,A*STAR

description: Library name: RYY812

data_processing:
Raw reads were trimmed for adapter sequences and filtered for low-quality reads using the software Cutadapt
The trimmed reads were mapped to the C. albicans transcriptome using Bowtie2 with default parameters
The raw counts of each transcript were quantified using featureCounts
FPKM values for each gene were calculated across different timepoints post structure probing (0mins, 20mins, 40mins, 60mins, 120mins)
The FPKM values across 5 timepoints and at 30°C and 37°C respectively, were analysed using StepMiner  to determine significantly stable and decaying transcripts.
Assembly: candida bruno_et_al_2010_tx_loci.fasta
Supplementary files format and content: *.featurecount

organism: Candida albicans SC5314

growth_protocol: C. albicans (SC5314) was inoculated in 10ml YPD medium for 16-18 hours at 30ºC, with constant shaking at 250rpm. We then transferred 2ml of the overnight culture to a fresh tube (1:50) of 100ml YPD medium with shaking for 3-5hours at 250rpm until the culture reaches an OD600 of 0.5-0.6. For hyphae induction, we added 10% FBS to the 30°C C. albicans culture, transferred it to 37°C with shaking at 250rpm for 1hour. We then collected the cell pellet after centrifugation at 4000 RPM for 5min. The cell pellet was stored at -80°C until needed.

extract_protocol:
To extract RNA from C. albicans, we first thawed the frozen pellet at room temperature and then placed it on ice. The pellets were re-suspended in 2.8ml yeast lysis buffer (100ml lysis buffer: 0.7ml 1M Tris-HCl, pH 7.0, 0.3ml 1M Tris-HCl, pH 8.0, 2ml of 0.5M EDTA, 5ml of 10%SDS). We transferred 700μl of this mixture into a 1.5ml Eppendorf tube, added 700μl of acid phenol, and vortexed rigorously. We then incubated the tubes at 65°C in a thermomixer for one hour, with constant shaking at 1000 rpm. After the incubation, we centrifuged the sample at maximum speed for 10 minutes at 4°C. We then transferred the aqueous phase into a new tube, added the same volume of fresh acid phenol, vortexed it, and spun it at maximum speed for 10 minutes at 4°C. We performed acid phenol extraction at least 2-3 times until the aqueous phase looked clear. To precipitate the RNA from the aqueous phase, we transferred the aqueous phase into a 2 ml tube and added 1/10 volume of 3M sodium acetate and 3x ice-cold 100% ethanol. We precipitated the RNA at -20°C for 1 hour before spinning it at maximum speed for 20-30 mins at 4°C. The pelleted RNA was then washed in 800μl of ice-cold 70% ethanol, centrifuged to remove the ethanol, and then air dried for 2 min before being dissolved in 50μl of nuclease-free water.
The RNA half-life was measured as previously described. Briefly, C. albicans (sc5314) was inoculated into 10ml of liquid YPD media and grown overnight shaking at 30°C and 250rpm. Aliquot the overnight cultured Candida albicans cells to fresh medium (1:100), and continue culture at 30°C, 250rpm for around 3 hours until OD600=0.6. The aliquot Candida albicans culture was then centrifuged and resuspended in 30°C or 37°C prewarmed YPD medium. The Thiolutin (Merck, CAS RN 87-11-6) was then added to each aliquot to a final concentration of 10μg/ml. The culture aliquots were then cultured for 20min, 40min, 60min, and 120min at 30°C or 37°C, respectively. The cells were collected, and the RNA was extracted as described above, and the RNA library was then prepared using Illumina Nextra library prep kit. The library is sequenced on a NEXTSEQ-HIGH to generate 1X76 base reads.

treatment_protocol: c. albicans were treated with Thiolutin for RNA half-life experiments

tag: strain


title: 37C_60min_Rep2

description: Library name: RYY811


title: H1,1-10 KO,rep1,ectoderm


title: HSD17B1-KI 5

description: Library name: RNA_S12421Nr5


title: H1,1-10 KO,rep2,ectoderm


title: 37C_120min_Rep1

description: Library name: RYY802


title: 8648-TD-2 H3K27ac

description:
Library name: TD-2
NextSeq P1 100 cycle


title: H1,WT,rep3,ectoderm


title: EBOV 3 days post infection_3

description: Library name: S6

value: iPSC-derived HIO


title: 37C_20min_Rep1

description: Library name: RYY799


title: HSD17B1-KI 4

description: Library name: RNA_S12421Nr4


title: 37C_0min_Rep1

description: Library name: RYY798


title: 37C_0min_Rep2

description: Library name: RYY808


title: HSD17B1-KI 3

description: Library name: RNA_S12421Nr3


title: male_WT2

city: Rochester

first: Cameron

last: Baker

address: 601 Elmwood Ave

institute: University of Rochester

description: Library name: male_WT2

data_processing:
Data Formatting - bcltofastq-2.19.1
Data Cleaning - fastp 0.23.1, --in1 ../${SAMPLE}_R1.fastq.gz --out1 clt_${SAMPLE}_R1.fastq.gz --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j ${SAMPLE}_fastp.json
Genome Alignment - STAR_2.7.9a, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification - subread-2.0.1, featurecounts, -s 2 -t exon -g gene_name
Assembly: GRCm39 + Gencode M31
Supplementary files format and content: Raw gene counts as determined by featureCounts

source_name: Bone

growth_protocol: MSCs were cultured in MEM α without ascorbic acid (Gibco) supplemented with 15% FBS and 100 IU/mL Penicillin/Streptomycin (Gibco).

extract_protocol:
Rneasy Plus Micro Kit (Qiagen, Valencia, CA)
1ng of total RNA was used as input in the SMART-Seq mRNA LP (Takara Bio USA, San Jose, CA) library prep workflow per manufacturer’s recommendations. Briefly, full-length cDNA was synthesized via oligo-dT priming and template-switching at the 5’ end. cDNA libraries were then amplified by long-distance PCR. The quantity and quality of the amplified cDNA was determined using the Qubit Fluorometer (Life Technologies, Carlsbad, CA) and the Agilent Bioanalyzer 2100 (Santa Clara, CA). Subsequently, 1ng of amplified cDNA was used for library construction through enzymatic fragmentation and ligation of stem-loop adapters, which provide binding sites for final library amplification. Lastly, Illumina-compatible libraries were amplified using unique dual-indexed primers. Amplified libraries were assessed for quantity and quality using the Qubit Fluorometer and the Agilent Fragment Analyzer and prepared to sequence on the Illumina NovaSeq X Plus (Illumina, San Diego, CA) 10B flowcell with paired-end reads of 150nt.

value: Bone

value: MSC


title: 37C_40min_Rep2

description: Library name: RYY810


title: HSD17B1-KI 1

description: Library name: RNA_S12421Nr1


title: 30C_120min_Rep1

description: Library name: RYY797


title: 37C_60min_Rep1

description: Library name: RYY801


title: 37C_20min_Rep2

description: Library name: RYY809


title: 30C_60min_Rep2

description: Library name: RYY806


title: H1,WT,rep2,ectoderm


title: H1,WT,rep1,ectoderm


title: 37C_40min_Rep1

description: Library name: RYY800


title: HSD17B1-KI 2

description: Library name: RNA_S12421Nr2


title: 30C_60min_Rep1

description: Library name: RYY796


title: 30C_120min_Rep2

description: Library name: RYY807


title: female_KO1

description: Library name: female_KO1

value: TauT KO

value: female


title: H1,1-10 KO,rep2,mesoderm


title: H1,WT,rep3,mesoderm

value: WT


title: male_WT1

description: Library name: male_WT1


title: 30C_20min_Rep2

description: Library name: RYY804


title: H1,1-10 KO,rep3,mesoderm


title: H1,WT,rep2,mesoderm


title: 30C_40min_Rep2

description: Library name: RYY805


title: male_KO3

description: Library name: male_KO3


title: female_WT2

description: Library name: female_WT2


title: 30C_20min_Rep1

description: Library name: RYY794


title: 50mM_NAIN3_Ligand_rep2

description: Library name: RBB804

library_source: other

data_processing:
Raw reads of riboswitch and riboSNitch obtained from SHAPE experiments were trimmed the adapter and poor-quality reads using the software cutadapt
The trimmed reads were processed by ‘Shapemapper-2.15’ of Weeks et al to calculate the SHAPE values for each position with the minimum effective sequencing depth1000.
Assembly: riboswitch/ribosnitch used synthetic 14 riboswitch/ribosnitch reference
Supplementary files format and content: *.bam

molecule: other

organism: synthetic construct

source_name: synthetic, IVT

extract_protocol:
The 8-strip tube was placed in a thermocycler to ran the primer annealing program (72°C 3min, 4°C 10min, 4°C hold). 6ul of RT reaction mix were then added into each tube and mixed it gently. The composition of the RT reaction mix is 1X First-strand buffer [(50mM Tris PH 8.0, 75mM KCl), 1 uM TSO (5-AAG CAG TGG TAT CAA CGC AGA GTA CAT rGrGrG-3), 1U/ul SUPERase In RNase Inhibitor, 5mM DTT, 6mM MnCl2, 10U/ul SSII]. We then ran the RT program using the following conditions: 25°C 5min, 42°C 4hours, 70°C 10min, 4°C hold. After RT, we added the following PCR reaction mix [working concentration of 0.1uM ISPCR primer (5-AAG CAG TGG TAT CAA CGC AGA GT-3), 1X HIFI KAPA master mix) to each tube, and ran the following PCR program: [98°C 3min, (98°C 20sec, 67°C 15sec, 72°C 3min), 72°C 5min]. we use 12-15 cycles for NAI-N3-treated samples, and 9-12 cycles for DMSO-treated samples.
The PCR products were then purified using Ampure XP beads twice, before being used for library preparation using the Illumina Nextra XT kit. Briefly, we diluted each sample into 0.6-0.8ng/ul and transferred 1ul of each sample into a 96-well PCR tube. We then added 2ul of the Tagmentation DNA buffer and 1ul of amplicon tagmentation mix to the sample in the 96-well PCR tube and incubated the reaction at 55°C for 5min. We immediately added 1ul NT buffer to the mixture, mixed it up and down, and incubated the mixture at RT for 5min to stop the tagmentation reaction. We then added 1ul of i5 and 1ul of i7 barcoded primers before adding 3ul of NPM to each tube. We then ran the PCR program [72°C 3min, 95°C 30sec, (95°C 10 Sec, 55°C 30 Sec, 72°C 30 Sec), 72°C 5min, hold at 10°C]. The prepared libraries were sequenced using Illumina novaseq X.

treatment_protocol: The SHAPE-MAP library preparation is followed by our previous work with a few edits. Briefly, take the 0.5ul 100ng/ul 50mM NAI-N3 treated RNA from ‘Structure folding for riboswitches and riboSNitches’, and transferred into a prepared 8-strip tube. Each tube contains 3.5ul of annealing buffer [0.2U/ul SUPERase In RNase Inhibitor, 1uM oligo dT (5–AAG CAG TGG TAT CAA CGC AGA GTA CT30VN-3), 1mM dNTP].

value: synthetic, IVT


title: H1,1-10 KO,rep3,MEKi

data_processing:
RNA-seq reads were aligned to hg19 reference genome using STAR with RefSeq annotated genes.
Gene expression levels were counted using featureCounts.
Differential expression analysis comapring each sample with vehicle-treated WT hESCs was performed by DESeq2.
Assembly: hg19
Supplementary files format and content: featureCounts output
Supplementary files format and content: raw count for each sample


title: H1,WT,rep1,mesoderm


title: 30C_0min_Rep1

description: Library name: RYY793


title: male_KO4

description: Library name: male_KO4


title: mTOR

city: Montréal

first: Vincent

last: Giguère

state: QC

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

country: Canada

institute: McGill University

description: Library name: mTOR

data_processing:
ChIP-seq reads were first trimmed for adapter sequences and low-quality score bases using Trimmomatic v0.36. The resulting reads were mapped to the human reference genome (hg38) using BWA-MEM v0.7.12 in paired-end mode at default parameters. Only reads that had a unique alignment (mapping quality > 20) were retained and PCR duplicates were removed using Picard tools v2.0.1.
Peaks (summit +/- 150 bp) were called using MACS2 software suite v2.1.1.20160309 at an FDR < 0.05 using sequenced libraries of respective input DNA as control. Peaks in mitochondrial chromosome and scaffold regions were removed.
Peak annotations and intersections were performed using HOMER v4.11.1.
Assembly: hg38
Supplementary files format and content: Bigwig files for ChIP and input samples as well as a ChIP peak annotated text file

growth_protocol: MDA-MB-231 cells were maintained in DMEM supplemented with 10% serum and 5% penicillin-streptomycin.

extract_protocol:
Cross-linked protein-DNA complexes were enriched with a mTOR-specific antibody, de-crosslinked, treated with RNase A and Proteinase K and purified using a QIAquick PCR purification kit (Qiagen, Cat#28106).
Libraries were prepared at Novogene Bioinformatics Technology Co. Ltd using the NEBNext Ultra II DNA Library Prep Kit and sequenced as paired-end 150bp reads on an Illumina HiSeq 4000 sequencer.

value: Human triple-negative breast cancer

tag: chip antibody

value: mTOR (Abcam, cat#32028)


title: H1,1-10 KO,rep2,MEKi

value: Human embryonic stem cell


title: input

description: Library name: input


title: Regulatory T cells

data_processing:
Bases were called using Illumina bcl2fastq2 conversion v2.29
ATAC-seq peaks were called using the ENCODE ATAC-seq pipeline.
Pair-end reads from three biological replicates for each cell type were aligned to hg38 genome using bowtie2, and duplicate reads were removed from the alignment.
Narrow peaks were called independently for each replicate using macs2 (-p 0.01 --nomodel --shift −75 --extsize 150 -B --SPMR --keep-dup all --call-summits) and ENCODE blacklist regions were removed from peaks in individual replicates.
Reproducible peaks, peaks called in at least half the number of replicates, were used to generate a consensus peakset.
Assembly: hg38
Supplementary files format and content: bigwig files and ENCODE idr optimal peakcalls

extract_protocol:
A total of 50,000 to 100,000 FACS sorted fixed cells were thawed at 37ºC, followed by centrifuged at 550 g for 5 min at 4 °C. The cell pellet was washed with cold PBS and resuspended in 50 μL cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40/IGEPAL CA-630) and immediately centrifuged at 550 g for 10 min at 4 °C. Nuclei were resuspended in the Nextera transposition reaction mix (25 μL 2x TD Buffer, 2.5 μL Nextera Tn5 transposase (Illumina Cat #FC-121-1030), and 22.5 μL nuclease free H2O) on ice, then incubated for 45 min at 37 °C. The tagmented DNA was then purified using the Qiagen MinElute kit eluted with 10.5 μL Elution Buffer (EB).
Ten microliters of purified tagmented DNA was PCR amplified using Nextera primers for 12 cycles to generate each library. PCR reaction was subsequently cleaned up using 1.5x AMPureXP beads (Agencourt), and concentrations were measured by Qubit. Libraries were paired-end sequenced on the Illumina HiSeq 4000 platform (100 bp read length).

value: Regulatory T cells

value: Levings Lab - BC Children's Hospital


title: 50mM_NAIN3_Noligand_rep2

description: Library name: RBB803


title: H1,1-10 KO,rep1,MEKi

value: ZNF263 homozygous KO


title: H1,1-10 KO,rep1,mesoderm


title: Regulatory T cells - activated

value: LPS-activated


title: male_KO2

description: Library name: male_KO2

value: male


title: female_WT3

description: Library name: female_WT3


title: T regulatory type 1 cells

value: T regulatory type 1 cells


title: male_WT4

description: Library name: male_WT4


title: male_WT3

description: Library name: male_WT3


title: H1,WT,rep2,MEKi


title: DMSO_Ligand_rep1

description: Library name: RBB790

value: DMSO


title: 50mM_NAIN3_Noligand_rep1

description: Library name: RBB793


title: T regulatory type 1 cells - activated


title: T helper 2cells

value: T helpercells

value: T helper 2cells


title: H1,WT,rep1,MEKi


title: 50mM_NAIN3_Ligand_rep1

description: Library name: RBB794


title: DMSO_Noligand_rep2

description: Library name: RBB799


title: H1,1-10 KO,rep2,vehicle


title: female_KO4

description: Library name: female_KO4

value: Bone

value: MSC


title: T helper 2cells- activated


title: 30C_0min_Rep2

description: Library name: RYY803


title: male_KO1

description: Library name: male_KO1

value: TauT KO


title: DMSO_Ligand_rep2

description: Library name: RBB800


title: 30C_40min_Rep1

description: Library name: RYY795


title: juvenile brain of the normal (N) pelagic planktivorous phenotype, survey August 2023_6_1

city: České Budějovice

first: Radka

last: Symonova

address: Branisovska 1645/31a

department: Department of Applied Informatics

country: Czech Republic

institute: Faculty of Science, University of South Bohemia

description: Library name: N6

data_processing:
performed by the sequencing company AZENTA according to their standard procedure
Assembly: pikeperch reference genome SLUC_FBN_1.2 (GCA_008315115.2, GCF_008315115.2) using STAR aligner v2.5.2.b
Supplementary files format and content: raw_counts.txt
Supplementary files format and content: TPM_values.csv

organism: Sander lucioperca

source_name: whole brain

extract_protocol:
RNA was extracted using RNA Blue reagent based on guanidium thiocyanate-phenol-chloroform method
RNA libraries for RNA-seq were prepared by the sequencing company AZENTA according to their standard protocol

value: whole brain


title: female_KO3

description: Library name: female_KO3

value: female


title: juvenile brain of the normal (N) pelagic planktivorous phenotype, survey August 2023_5_1

description: Library name: N5


title: H1,1-10 KO,rep1,vehicle


title: T helper 1cells- activated

value: T helper 1cells


title: female_WT1

description: Library name: female_WT1

value: WT


title: neonatal_pbs_96hr_post_aspiration

first: Sylvia

middle: N

last: Michki

department: Pulmonary & Sleep Medicine

description: Library name: NPBS_S2

data_processing:
Read alignment and cell calling using STAR-solo (velocyto output)
Ambient-RNA correction using scvi-tools scAR
h5ad file creation using anndata
Assembly: GRCm39
Supplementary files format and content: HDF5 format anndata objects (.h5ad) for combined experiment, containing cell barcodes, feature names, and counts matrices. The log1p(CPM) expression matrix is loaded in the `X` slot. The `layers` dictionary contains the log1p(CPM), spliced, unspliced, counts_raw, and counts_scAR keys, corresponding to the ln(1+CPM) expression, velocyto spliced/unspliced counts, the raw total (spliced + unspliced + ambiguous) counts, and the scAR ambient-RNA corrected total counts, respectively.

extract_protocol:
10X Chromium GEX v3 3’-biased scRNA-seq chemistry was used to extract mRNA from individual cells.
10X Genomics 3’-biased gene expression library construction (v3.1).

value: lung

tag: time

value: pbs


title: H1,WT,rep3,vehicle

value: Human embryonic stem cell


title: juvenile brain of the normal (N) pelagic planktivorous phenotype, survey August 2023_4_1

description: Library name: N4


title: female_KO2

description: Library name: female_KO2


title: neonatal_ecoli_96hr_post_aspiration

description: Library name: Neo96P-SharonMcgrath-Morrow-11102022_S2


title: T helper 17cells

value: T helper 17cells

value: Levings Lab - BC Children's Hospital


title: T helper 17cells- activated

value: LPS-activated


title: juvenile brain of the littoral piscivorous/cannibal (C) phenotype, survey August 2023_4_1

description: Library name: C4


title: Epstein-Barr Virus transformed lymphoblastoid cell line

source_name: EBV-transformed B cell line

value: EBV-transformed B cell line

value: B cells

value: Wells Laboratory - Children’s Hospital of Philadelphia


title: H1,WT,rep1,vehicle


title: juvenile brain of the littoral piscivorous/cannibal (C) phenotype, survey August 2023_2_1

description: Library name: C2


title: H1,1-10 KO,rep3,vehicle

value: ZNF263 homozygous KO


title: DMSO_Noligand_rep1

description: Library name: RBB789

value: synthetic, IVT

value: DMSO


title: T helper 1cells

source_name: T helpercells

value: T helpercells


title: lgG,CUTTag,H1KO

data_processing:
The ZIC2 CUT&TAG data was aligned using Bowtie2  with parameters "--very-sensitive --no-mixed -X 2000".
Reads pairs with both ends properly aligned and mapping quality greater than 30 were kept.
Duplications were detected and removed by the “MarkDuplicates” command of Picard (ref).
Peaks were called using MACS (ref) with parameters "--nomodel --shiftsize 100 --llocal 50000 -p 0.0001".
Assembly: hg19
Supplementary files format and content: narrowPeak for TF binding sites
Supplementary files format and content: bigwig signal
Library strategy: Cut&Tag

extract_protocol:
hESCs were resuspended in 0.3 mL NE1 buffer (20 mM HEPES-KOH pH7.9, 10 mM KCl, 0.5 mM spermidine, 0.1% Triton X-100, 20% glycerol, plus protease inhibitor), then cell nuclei were obtained by centrifugation at 600 g for 5 min at 4°C.
We adapted CUT&Tag direct protocol53 with some modifications. 0.5 μL primary antibody (anti-ZIC2, ABCAM, Cat#150404) and 0.5 μL normal IgG (Rabbit IgG, Millipore, Cat#12-370) was respectively diluted with 25 µL of Antibody Buffer (10 mM HEPES pH7.5, 150 mM NaCl, 0.5 mM spermidine, 2 mM EDTA, 0.1% BSA, plus protease inhibitor) and mixed with the above conjugated beads at 4°C overnight. After thoroughly aspirating the supernatant, 0.25 µL secondary antibody (Guinea Pig anti-Rabbit IgG, Antibodies-online, Cat#ABIN101961) in 25 µL Wash Buffer were added and incubated with the beads at room temperature for 1 hr. Extra antibodies were removed by washing the beads twice with 0.25 mL Wash Buffer. Then, custom-assembled pA–Tn5 transposases54 were loaded to the beads in 25 µL of 300-Wash Buffer (Wash Buffer with 300 mM NaCl) at room temperature for 1 hr. Following, unbound transposases were washed away with 300-Wash Buffer from the beads, and tagmentation was conducted in 50 µL of 300-Wash Buffer supplemented with 10 mM MgCl2 at 37 °C for 1 hr. After thoroughly aspirating the supernatant, the beads were washed once with TAPS buffer (10 mM TAPS pH8.5, 0.2 mM EDTA), then 5 µL SDS release buffer (10 mM TAPS pH8.5, 0.1% SDS) were added and incubated at 58 °C for 1 hr. Amplified tagmentated DNA were purified from the supernatant using 1.3X AMPure XP Beads, and subject to library sequencing.

value: ZNF263 homogeneous KO


title: neonatal_ecoli_48hr_post_aspiration

description: Library name: NEC_S3

source_name: lung

value: ecoli


title: Plasmacytoid dendritic cells

value: Plasmacytoid dendritic cells


title: neonatal_air_48hr_post_aspiration

description: Library name: Nair_S1

value: WT


title: juvenile brain of the littoral piscivorous/cannibal (C) phenotype, survey August 2023_1_1

description: Library name: C1

value: whole brain


title: Natural killer cells

value: Natural killer cells


title: lgG,CUTTag,H1WT

value: Human embryonic stem cell


title: juvenile_pbs_96hr_post_aspiration

description: Library name: Juv96P-SharonMcgrath-Morrow-11222022_S4

value: lung

value: pbs


title: juvenile brain (B) of the normal (N) pelagic planktivorous phenotype, survey August 2022_4_1

description: Library name: N4B


title: RNA004_DMSO_WT

description: Library name: RNA004_DMSO_WT

data_processing:
Preprocessing of raw signals.
Reads were base-called with Guppy version 4.2.2+effbaf8. Both passed- and failed-quality reads from nanopore direct RNA sequencing were mapped to the reference using the software Minimap2 with the following parameters:  -ax map-ont -F2064.
For reads that were not successfully mapped by Minimap2, their original fast5 files were used for mapping with subseqDTW.
Alignment  using subseqDTW to align event signal levels with expected signal levels.
After aligning of read signals to reference signals, events corresponding to the same reference  5-mer were collapsed.
Assembly: riboswitch/ribosnitch used synthetic 14 riboswitch/ribosnitch reference
Supplementary files format and content: *_final_alignment.txt.gz files. They contain the alignment results from DTW.

growth_protocol: IVT RNA only

extract_protocol: We used 600ng of in vitro transcribed (IVT) RNA for library preparation following the manufacturer’s protocol for the direct RNA library preparation kit SQK-RNA004 from Oxford Nanopore Technologies. The libraries were loaded onto FLO-PRO004RA PromethION RNA flow cells and sequenced on a PromethION 2 Solo device.The library preparation steps were the same as those for SQK-RNA002 except the following: 1) 1μl of SUPERase·In™ RNase Inhibitor (Invitrogen, AM2694) is added during the RT Adapter ligation reaction, 2) 6μl of RNA Ligation (RLA) instead of 6μl of RNA Adapter (RMX) is added in the second adapter ligation reaction, 3) the adapter-ligated RNA is eluted in 33μl of RNA Elution Buffer (REB), and 4) we prepared the sample for loading by adding 100μl of Sequencing Buffer (SB) and 68μl of Library Solution (LIS) to 32μl of the library sample.

treatment_protocol: The IVT RNAs  are treated with structure probine compound to table RNA structure


title: Zic2rep2,CUTTag,H1KO


title: CD1c+conventional dendritic cells

value: conventional dendritic cells

value: CD1c+conventional dendritic cells


title: juvenile_ecoli_96hr_post_aspiration

description: Library name: Juv96E-SharonMcgrath-Morrow-11222022_S3


title: juvenile brain (B) of the normal (N) pelagic planktivorous phenotype, survey August 2022_3_2

description: Library name: N3B


title: H1,WT,rep2,vehicle


title: juvenile brain (B) of the normal (N) pelagic planktivorous phenotype, survey August 2022_2_1

description: Library name: N2B


title: juvenile_pbs_48hr_post_aspiration

description: Library name: JPBS_S5


title: neonatal_pbs_48hr_post_aspiration

description: Library name: Neo96E-SharonMcgrath-Morrow-11102022_S1


title: juvenile brain (B) of the littoral (L) piscivorous phenotype, survey August 2022_3_1

description: Library name: L3B


title: juvenile_ecoli_48hr_post_aspiration

description: Library name: JEC_S6


title: juvenile brain (B) of the littoral (L) piscivorous phenotype, survey August 2022_2_1

description: Library name: L2B


title: RNA004_50mMNAIN3_MT

description: Library name: RNA004_50mMNAIN3_MT


title: H1, 1-10 KO, scRNA

data_processing:
Extracting cell barcode and UMI were made using the umi_tools extract function of UMI-tools software v1.1.2 (https://umi-tools.readthedocs.io/en/latest/index.html)
Mapping reads using the STAR software v2.7.10a .(https://github.com/alexdobin/STAR/tree/2.7.10a)
assigning reads to genes was made using featureCounts software v2.0.1 (https://sourceforge.net/projects/subread/)
counting unique reads per genes per cell  wasmade using umi_tools count function of UMI-tools software v1.1.2 (https://umi-tools.readthedocs.io/en/latest/index.html)
Assembly: hg38
Supplementary files format and content: sparse matrix

extract_protocol:
Routinely cultured hESCs were digested into single cells with TrypLE (Thermo Fisher) according to the manufacturer’s protocol. Then cells were re-suspended in 1 x DPBS (Thermo Fisher) and stained with a Viability Dye. High viability samples were subject to scRNA-seq library preparation.
Libraries were prepared using a method established in our lab which is adapted from Microwell-seq. Briefly, hESCs and barcoded beads were first distributed into wells of a microwell plate, with each well containing a single cell and a single bead. Then, polyA RNA from the cell lysate were captured and retrotranscripted into cDNA. The pooled cDNA were pre-amplified by PCR, then fragmented and tagmented with Tn5 Transposase. Finally, Illumina p5 and p7 sequences and sample indexes were introduced by another round of PCR. Fragment size of 300-600 bp were selected for sequencing.


title: 12RNAs_30As_50mMKethoxal_WTpool

description: Library name: 230518_12RNAs_30As_50mMKethoxal_WTpool

data_processing:
Preprocessing of raw signals.
Reads were base-called with Guppy version 4.2.2+effbaf8. Both passed- and failed-quality reads from nanopore direct RNA sequencing were mapped to the reference using the software Minimap2 with the following parameters:  -ax map-ont -F2064.
For reads that were not successfully mapped by Minimap2, their original fast5 files were used for mapping with subseqDTW.  For the C. albicans transcriptome, a GPU-accelerated cuDTW was used to do the mapping for unmapped reads from minimap2.
Alignment  using subseqDTW to align event signal levels with expected signal levels.
After aligning of read signals to reference signals, events corresponding to the same reference  5-mer were collapsed.
Assembly: riboswitch/ribosnitch used synthetic 14 riboswitch/ribosnitch reference, candida used candida bruno_et_al_2010_tx_loci.fasta
Supplementary files format and content: *_final_alignment.txt.gz files. They contain the alignment results from DTW.

growth_protocol: C. albicans (SC5314) was inoculated in 10ml YPD medium for 16-18 hours at 30ºC, with constant shaking at 250rpm. We then transferred 2ml of the overnight culture to a fresh tube (1:50) of 100ml YPD medium with shaking for 3-5hours at 250rpm until the culture reaches an OD600 of 0.5-0.6. For hyphae induction, we added 10% FBS to the 30°C C. albicans culture, transferred it to 37°C with shaking at 250rpm for 1hour. For in vivo structure probing, we added NAI-N3 to a final concentration of 100mM with shaking of the culture for 10min. We then collected the cell pellet after centrifugation at 4000 RPM for 5min. The cell pellet was stored at -80°C until needed.

extract_protocol:
To extract RNA from C. albicans, we first thawed the frozen pellet at room temperature and then placed it on ice. The pellets were re-suspended in 2.8ml yeast lysis buffer (100ml lysis buffer: 0.7ml 1M Tris-HCl, pH 7.0, 0.3ml 1M Tris-HCl, pH 8.0, 2ml of 0.5M EDTA, 5ml of 10%SDS). We transferred 700μl of this mixture into a 1.5ml Eppendorf tube, added 700μl of acid phenol, and vortexed rigorously. We then incubated the tubes at 65°C in a thermomixer for one hour, with constant shaking at 1000 rpm. After the incubation, we centrifuged the sample at maximum speed for 10 minutes at 4°C. We then transferred the aqueous phase into a new tube, added the same volume of fresh acid phenol, vortexed it, and spun it at maximum speed for 10 minutes at 4°C. We performed acid phenol extraction at least 2-3 times until the aqueous phase looked clear. To precipitate the RNA from the aqueous phase, we transferred the aqueous phase into a 2 ml tube and added 1/10 volume of 3M sodium acetate and 3x ice-cold 100% ethanol. We precipitated the RNA at -20°C for 1 hour before spinning it at maximum speed for 20-30 mins at 4°C. The pelleted RNA was then washed in 800μl of ice-cold 70% ethanol, centrifuged to remove the ethanol, and then air dried for 2 min before being dissolved in 50μl of nuclease-free water.
We used 600ng of in vitro transcribed (IVT) RNA for library preparation following the manufacturer’s protocol for the direct RNA library preparation kit SQK-RNA004 from Oxford Nanopore Technologies. The libraries were loaded onto FLO-PRO004RA PromethION RNA flow cells and sequenced on a PromethION 2 Solo device.The library preparation steps were the same as those for SQK-RNA002 except the following: 1) 1μl of SUPERase·In™ RNase Inhibitor (Invitrogen, AM2694) is added during the RT Adapter ligation reaction, 2) 6μl of RNA Ligation (RLA) instead of 6μl of RNA Adapter (RMX) is added in the second adapter ligation reaction, 3) the adapter-ligated RNA is eluted in 33μl of RNA Elution Buffer (REB), and 4) we prepared the sample for loading by adding 100μl of Sequencing Buffer (SB) and 68μl of Library Solution (LIS) to 32μl of the library sample.

treatment_protocol: The cells and IVT RNAs  are treated with structure probine compound to table RNA structure

value: Kethoxal


title: Zic2rep1,CUTTag,H1KO


title: Adrenal gland, Male, AS-Cre; ARKO, 25 weeks old, Sample 6

description:
Library name: 132370
column name in counts_rna.tsv:132370_GAATCCGT-CAACTCCA_S37

data_processing:
Reads were aligned to the mouse transcriptome (Gencode r.M28) using kallisto (Bray et al. 2016)
Transcript-level abundance estimates were summarized to gene-level expression values using the lengthScaledTPM method in tximport (Soneson et. al., 2015).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file that includes raw counts. Samples are identified by the column header.

extract_protocol:
Adrenal glands were removed, cleaned from surrounding fat and snapped-frozen in liquid nitrogen. RNAs were extracted using the Qiagen RNeasy Mini Kit #74104.
RNA libraries for RNAseq were prepared using NEB PolyA and NEB Ultra 2 directional RNA kits (Males 6 week old) and NEB PolyA and IDT xGen Broad-range RNA library prep (Female 6 week old).

value: adrenal gland

value: male

value: 25 weeks old

value: AS-Cre; ARflox/flox


title: H1, WT, scRNA


title: UNC0379-treated, HSV-1 2h (MOI5), anti-RNAPII replicate2

city: Bethesda

first: Jesse

middle: H

last: Arbuckle

state: MD

address: 33 North Dr, Bldg 33, Rm 3W10A

department: Laboratory of Viral Diseases

institute: National Institutes of Health, NIAID

description: Library name: RNAP_UNC_ChIP2

data_processing:
Reads were processed using our chrom-seek (1.2.0) pipeline (https://github.com/OpenOmics/chrom-seek).
Reads were trimmed with Cutadapt version 4.4 (39) and then aligned to a custom reference genome composed of the human hg38 genome plus the HSV-1 reference chromosome NC_001806.2 using BWA version 0.7.17 (40). All reads aligning to the Encode hg38 blacklist regions (41) were identified and removed with Picard SamToFastq (https://broadinstitute.github.io/picard/). Reads with a mapQ score less than 6 were removed with SAMtools version 1.17 (42) and PCR duplicates were removed with Picard MarkDuplicates.
Data was converted into bigwigs for viewing and normalized by reads per genomic content (RPGC) of the combined reference genome using deepTools version 3.5.1
Assembly: hg38 plus NC_001806.2
Supplementary files format and content: Bigwig

source_name: HFF

growth_protocol: HFF cells were pretreated with vehicle or 4 µM UNC0379 and infected with HSV-1 (MOI 5) for 2 h.

extract_protocol:
Isolated nuclei were lysed, and samples were sonicated using a Covaris M220 Focused-Ultrasonicator (8 min, 10% duty cycle, 75 W incident power, 200 burst per cycle) to obtain DNA fragments of 200-500 base pairs (bp). Chromatin samples (350-450 µg) were precleared with Protein G Dynabeads (ThermoFisher) for 1 h at 4°C followed by incubation with 3-5 µg antibodies for 14 h at 4°C. Chromatin samples were incubated with 1:1000 dilution of anti-RNAPII-NTD (Cell Signaling 14958)
Libraries were sequenced on a NovaSeq X Plus 1.5B to yield 3.10 - 3.60 x 108 paired-end reads per sample.

value: HFF

tag: antibody

value: anti-RNAPII


title: H9, 9-D KO, rep3

description:
H9_6KO_vs_3WT_DESeq2_results.csv
H9_ZNF263_KO_read_cnt_table.txt

data_processing:
RNA-seq reads were aligned to hg19 reference genome using STAR with RefSeq annotated genes.
Gene expression levels were counted using featureCounts.
Differential expression analysis between ZNF263 knockout and wild-type samples was performed by DESeq2.
Assembly: hg19
Supplementary files format and content: DESeq2 output for normalized data
Supplementary files format and content: DESeq2 output for differential analysis results

value: ZNF263 homozygous KO


title: 12RNAs_30As_100mM1AI_WTpool

description: Library name: 230518_12RNAs_30As_100mM1AI_WTpool

value: synthetic, IVT


title: Adrenal gland, Male, WT, 25 weeks old, Sample 3

description:
Library name: 132368
column name in counts_rna.tsv:132368_GTCGTTAC-AGCTAAGC_S35

value: AS-Cre; AR-wt/wt


title: 12RNAs_30As_50mM2A3_WTpool

description: Library name: 230502_12RNAs_30As_50mM2A3_WTpool


title: H9, 9-D KO, rep1


title: H9, 9-D KO, rep2


title: 12RNAs_30As_35mMNAIN3_WTpool

description: Library name: 230530_12RNAs_30As_35mMNAIN3_WTpool


title: Adrenal gland, Male, AS-Cre; ARKO, 25 weeks old, Sample 5

description:
Library name: 132369
column name in counts_rna.tsv:132369_GTAACCGA-AAGACACC_S36


title: RNA004_DMSO_MT

description: Library name: RNA004_DMSO_MT

value: DMSO


title: RNA004_50mMNAIN3_WT

description: Library name: RNA004_50mMNAIN3_WT


title: AddHIVonly_30As_50mMNAIN3_MTpool

description: Library name: 230327_AddHIVonly_30As_50mMNAIN3_MTpool


title: Zic2rep2,CUTTag,H1WT

value: WT


title: Vehicle-treated, HSV-1 2h (MOI5), anti-RNAPII replicate1

description: Library name: RNAP_VEH_ChIP1


title: Zic2rep1,CUTTag,H1WT

value: Human embryonic stem cell


title: UNC0379-treated, HSV-1 2h (MOI5), Input control replicate2

description: Library name: INPUT_UNC_2

value: none; input


title: Adrenal gland, Male, AS-Cre; ARKO, 25 weeks old, Sample 7

description:
Library name: 132371
column name in counts_rna.tsv:132371_CATGAGCA-GATCTTGC_S38


title: juvenile brain (B) of the littoral (L) piscivorous phenotype, survey August 2022_1_1

description: Library name: L1B

value: whole brain


title: Adrenal gland, Male, WT, 25 weeks old, Sample 1

description:
Library name: 132366
column name in counts_rna.tsv:132366_CAAGGTAC-CGTATCTC_S33


title: AddHIVonly_30As_50mMNAIN3_WTpool

description: Library name: 230323_AddHIVonly_30As_50mMNAIN3_WTpool


title: H9, 9-1 KO, rep3


title: H9, 9-1 KO, rep2


title: UNC0379-treated, HSV-1 2h (MOI5), anti-RNAPII replicate1

description: Library name: RNAP_UNC_ChIP1


title: UNC0379-treated, HSV-1 2h (MOI5), Input control replicate1

description: Library name: INPUT_UNC_1


title: Adrenal gland, Female, SF1-Cre; HhexKO, 6 weeks old, #587

description:
Library name: CLP-8
column name in counts_rna.tsv: 5580-CLP-8_TTGCAACG-AGAGGAAG_S88

value: Female

value: 6 weeks old

value: SF1-Cre; Hhexflox/flox


title: Vehicle-treated, HSV-1 2h (MOI5), anti-RNAPII replicate2

description: Library name: RNAP_VEH_ChIP2


title: 12RNAs_30As_50mMNAIN3_MTpool

description: Library name: 230316_12RNAs_30As_50mMNAIN3_MTpool


title: Vehicle-treated, HSV-1 2h (MOI5), Input control replicate2

description: Library name: INPUT_VEH_2


title: Adrenal gland, Female, SF1-Cre; HhexKO, 6 weeks old, #556

description:
Library name: CLP-7
column name in counts_rna.tsv:5580-CLP-7_CAATTGCC-ATGATACC_S87

value: adrenal gland


title: H9, 9-1 KO, rep1


title: 12RNAs_30As_50mMNAIN3_WTpool

description: Library name: 230314_12RNAs_30As_50mMNAIN3_WTpool


title: Adrenal gland, Male, WT, 25 weeks old, Sample 2

description:
Library name: 132367
column name in counts_rna.tsv:132367_AGACCTTG-TTACGTGC_S34

value: male


title: Vehicle-treated, HSV-1 2h (MOI5), Input control replicate1

description: Library name: INPUT_VEH_1


title: Adrenal gland, Female, SF1-Cre; HhexKO, 6 weeks old, #538

description:
Library name: CLP-6
column name in counts_rna.tsv:5580-CLP-6_GTGGTATC-CCGGCAAT_S86


title: H9, WT, rep3


title: 15RNAs_30As_DMSO_WTpool

description: Library name: 230308_15RNAs_30As_DMSO_WTpool


title: Adrenal gland, Female, SF1-Cre; HhexKO, 6 weeks old, #532

description:
Library name: CLP-5
column name in counts_rna.tsv:5580-CLP-5_TCCACGGT-TTGCTGAA_S85


title: Multiome_Yoda1_Heart_3months

description: Library name: Yoda1_Heart_3months

data_processing:
The read counts of each cell was calculated by using Cellranger
The analysis of single cell RNAseq data was performed by Signac
Assembly: mm10
Supplementary files format and content: 3months_Heart_Control_filtered_feature_bc_matrix.h5
Supplementary files format and content: 3months_Heart_TKI_filtered_feature_bc_matrix.h5
Supplementary files format and content: 3months_Heart_Yoda1_filtered_feature_bc_matrix.h5
Supplementary files format and content: 3months_Heart_Control_atac_fragments.tsv.gz
Supplementary files format and content: 3months_Heart_TKI_atac_fragments.tsv.gz
Supplementary files format and content: 3months_Heart_Yoda1_atac_fragments.tsv.gz

source_name: heart tissues

extract_protocol:
Snap-frozen mouse hearts were thawed and prepared for nuclei isolation. Tissues were washed in ice-cold wash buffer (10 mM Tris, pH 7.4; 10 mM NaCl; 3 mM MgCl₂; 1% BSA; 1 mM DTT; 0.1% Tween-20; 1 U/μl RNase inhibitor), centrifuged, and resuspended in 100 μl chilled lysis buffer (10 mM Tris, pH 7.4; 10 mM NaCl; 3 mM MgCl₂; 1% BSA; 1 mM DTT; 0.1% Tween-20; 0.01% digitonin; 0.1% Nonidet P40 substitute; 1 U/μl RNase inhibitor). Samples were lysed on ice for 5 min and resuspended in 1 ml chilled wash buffer. Following centrifugation at 500 rcf for 5 min, the nuclei pellet was resuspended in 50 μl 10x Genomics Nuclei Buffer containing 1 U/μl RNase inhibitor.
For the Gene Expression arm, polyadenylated nuclear RNA was reverse-transcribed within GEMs to produce barcoded cDNA (cell barcode and UMI), followed by cDNA amplification and 3′ gene-expression library construction (fragmentation, end-repair/A-tailing, adapter ligation, and sample index PCR). For the ATAC arm, transposition was performed with Tn5 to fragment accessible chromatin and attach partial adapters; after GEM recovery, barcoded ATAC fragments were amplified and indexed.

value: heart tissues

value: paired-end


title: Vehicle-treated, HSV-1 1.5h (MOI 5), ATAC-seq replicate3

description: Library name: VEH_1.5h_ATAC3

growth_protocol: HFF cells were pretreated with vehicle or 4 µM UNC0379 and infected with HSV-1 (MOI 5) for 1.5 h.

extract_protocol:
Extraction and library construction were accomplished folllowing the protocol from: Caravaca JM, Mehta M, Gowda S, Tran B. 2022. ATAC Sequencing Protocol For Cryopreserved Mammalian Cells. Bio Protoc 12:e4294.
Libraries were sequenced on a NovaSeq X Plus 1.5B to yield 2.16 - 2.56 x108 paired-end reads per sample.

value: HFF


title: H9, WT, rep1

description:
H9_6KO_vs_3WT_DESeq2_results.csv
H9_ZNF263_KO_read_cnt_table.txt

extract_protocol:
Total RNA was extracted with TRIzol™ (ThermoFisher), 500 ng RNA was used for sequencing library construction.
polyA RNA was enriched with NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), then corresponding RNA libararies were prepared with NEBNext® Ultra II RNA Library Prep Kit for Illumina® (New England Biolabs).


title: Vehicle-treated, HSV-1 1.5h (MOI 5), ATAC-seq replicate2

description: Library name: VEH_1.5h_ATAC2


title: Adrenal gland, Female, WT (SF1-Cre), 6 weeks old, #543

description:
Library name: CLP-4
column name in counts_rna.tsv:5580-CLP-4_TGTTCAGC-GAACCGTG_S84

value: SF1-Cre; Hhexwt/wt


title: Adrenal gland, Female, WT (SF1-Cre), 6 weeks old, #542

description:
Library name: CLP-3
column name in counts_rna.tsv:5580-CLP-3_CGGAGGTA-TACACGAA_S83


title: Vehicle-treated, HSV-1 1.5h (MOI 5), ATAC-seq replicate1

description: Library name: VEH_1.5h_ATAC1


title: H1, 1-10 KO, rep3

description:
H1_1-10_3KO_vs_3WT_DESeq2_results.csv
H1_ZNF263_KO_read_cnt_table.txt

value: ZNF263 homozygous KO


title: Multiome_Control_Heart_3months

description: Library name: Control_Heart_3months


title: H1, 1-10 KO, rep2


title: Adrenal gland, Female, WT, 6 weeks old, #585

description:
Library name: CLP-2
column name in counts_rna.tsv:5580-CLP-2_TCTTCGTG-GATACCTC_S82


title: UNC0379-treated, HSV-1 1.5h (MOI 5), ATAC-seq replicate3

description: Library name: UNC_1.5h_ATAC3


title: UNC0379-treated, HSV-1 1.5h (MOI 5), ATAC-seq replicate2

description: Library name: UNC_1.5h_ATAC2


title: Adrenal gland, Female, WT, 6 weeks old, #551

description:
Library name: CLP-1
column name in counts_rna.tsv:5580-CLP-1_GCGCGGTT-AAGCTATA_S81


title: H1, 1-10 KO, rep1


title: Adrenal gland, Male, SF1-Cre; HhexKO, 6 weeks old, #517

description:
Library name: TD-8
column name in counts_rna.tsv:1916-TD-8_CCGCTTAA-ACGATGAC_S159


title: Mlkl_FLIP_dko_2

city: South San Francisco

first: Rohit

last: Reja

address: 1 DNA Way

institute: Genentech

description: Library name: SAM24448584

data_processing:
Reads were aligned to the GRCm38/mm10 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. Supplementary files use Ensemble gene IDs, counts and RPKM statistics.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: MEFs

extract_protocol:
Total RNA was isolated from cells and purified using RNeasy mini kits and on-column DNAse digestion per manufacturer (Qiagen) protocol. 0.5ug used for library preparation with a TruSeq RNA Sample Preparation Kit v2 (Illumina). The libraries were multiplexed and then sequenced on a HiSeq4000 (Illumina) to generate 30 million single end 50 bp reads.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: MEFs

value: Casp8 D387A KI Cflar KO Mlkl KO

tag: replicate

value: biol rep 2

value: No treatment


title: Mlkl_FLIP_dko_3

description: Library name: SAM24448585

value: biol rep 3


title: H1, WT, rep3

value: Human embryonic stem cell

value: WT


title: H9, WT, rep2


title: Mlkl_FLIP_dko_1

description: Library name: SAM24448583

value: biol rep 1


title: UNC0379-treated, HSV-1 1.5h (MOI 5), ATAC-seq replicate1

description: Library name: UNC_1.5h_ATAC1


title: Adrenal gland, Male, SF1-Cre; HhexKO, 6 weeks old, #516

description:
Library name: TD-7
column name in counts_rna.tsv:1916-TD-7_GACGTCAT-TCAACTGG_S158

value: 6 weeks old


title: Mlkl_ko_3

description: Library name: SAM24448582

value: Mlkl KO


title: juvenile_air_48hr_post_aspiration

description: Library name: Jair_S4

value: lung


title: H1, WT, rep1


title: H1, WT, rep2


title: Adrenal gland, Male, SF1-Cre; HhexKO, 6 weeks old, #511

description:
Library name: TD-6
column name in counts_rna.tsv:1916-TD-6_GGAGGAAT-AACCGTTC_S157

value: adrenal gland

value: male

value: SF1-Cre; Hhexflox/flox


title: WT_Cre-BL5

city: Dallas

first: Hao

last: Zhu

state: TX

address: 5323 Harry Hines Blvd

institute: UTSW

description: Library name: S25

data_processing:
The QBRC_BulkRnaSeqDE pipeline (https://www.github.com/QBRC/QBRC_BulkRnaSeqDE) was used for RNA-seq analysis.
Assembly: mm10
Supplementary files format and content: pooled_counts_plus_ctrl.csv : file of counts generated by QBRC_BulkRnaSeqDE pipeline for use in pipeline's DE script

source_name: Liver

extract_protocol:
Fragments of frozen tumors were homogenized in TRIzol using a tissue homogenizer. RNA was extracted using the Invitrogen PureLink RNA Mini Kit according to the manufacturer's protocol.
Libraries were prepared with the Ovation RNA-Seq Systems 1-16 (Nugen) using 100 ng of DNAse-treated RNA, and indexed libraries were multiplexed in a single flow cell

value: Liver


title: Mlkl_ko_2

description: Library name: SAM24448581


title: WT_Cre-BL4

description: Library name: S24


title: Multiome_TKI_Heart_3months

description: Library name: TKI_Heart_3months

value: heart tissues

value: paired-end


title: H1,WT,rep3,MEKi


title: Mlkl_ko_1

description: Library name: SAM24448580

value: MEFs


title: H1, 1-10 KO, no rep

description:
H1_RNAseq_rep1_1-10_KO_vs_WT_DESeq2.csv
H1_ZNF263_KO_RNA-seq_individual_rep_read_cnt.txt

value: ZNF263 homozygous KO


title: Adrenal gland, Male, SF1-Cre; HhexKO, 6 weeks old, #510

description:
Library name: TD-5
column name in counts_rna.tsv:1916-TD-5_AGGATAGC-AACCTTGG_S156


title: H1, 1-5 KO, no rep

description:
H1_RNAseq_rep1_1-5_KO_vs_WT_DESeq2.csv
H1_ZNF263_KO_RNA-seq_individual_rep_read_cnt.txt

value: ZNF263 heterozygous KO


title: Adrenal gland, Male, WT (SF1-Cre), 6 weeks old, #514

description:
Library name: TD-4
column name in counts_rna.tsv:1916-TD-4_TCCTCATG-AGGTGTAC_S155

value: SF1-Cre; Hhexwt/wt


title: WT_Cre-BL3

description: Library name: S23


title: KI_MLKL_cFLIP_DKO_3

description: Library name: SAM24478010

source_name: E18.5 intestine

value: E18.5 intestine

value: Casp8 C362A KI Cflar KO Mlkl KO

value: biol rep 3

value: No treatment


title: H1, WT, no rep

value: Human embryonic stem cell

value: WT


title: WT_Cre-BL2

description: Library name: S22


title: H1, 1-10 KO, His, input

data_processing:
The ChIP-seq data of ZNF263 were aligned using Bowtie2 (ref) with parameters "--very-sensitive --no-mixed -X 2000".
Reads pairs with both ends properly aligned and mapping quality greater than 30 were kept.
Duplications were detected and removed by the “MarkDuplicates” command of Picard (ref).
Peaks were called using MACS (ref) with parameters "--nomodel --shiftsize 100".
Assembly: hg19
Supplementary files format and content: bigwig for signal
Supplementary files format and content: narrowPeak for TF/histone binding sites

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor UCD-300 ultrasonicator (Diagenode).
5 ng of DNA was used as starting material for input and ip samples, then ChIP-seq libraries were prepared using NEBNext® Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer's protocol. No size selection was applied during the construction process, and all the libraries were validated using Agilent High Sensitivity DNA kit.


title: Adrenal gland, Male, WT (SF1-Cre), 6 weeks old, #513

description:
Library name: TD-3
column name in counts_rna.tsv:1916-TD-3_ATCTGACC-AAGTCGAG_S154

value: 6 weeks old


title: KI_MLKL_cFLIP_DKO_2

description: Library name: SAM24478009

value: biol rep 2


title: WT_Cre-BL6

description: Library name: S26


title: WT_Cre-BL1

description: Library name: S21


title: Adrenal gland, Male, WT, 6 weeks old, #521

description:
Library name: TD-2
column name in counts_rna.tsv:1916-TD-2_CTTAGGAC-CAGTGAAG_S153

value: adrenal gland

value: male


title: KI_MLKL_cFLIP_DKO_1

description: Library name: SAM24478008

value: biol rep 1


title: KI_MLKL_CASP1_DKO_3

description: Library name: SAM24478001

value: Casp8 C362A KI Mlkl KO Casp1 KO


title: H1, 1-10 KO, H3K27ac ChIP


title: H1, 1-10 KO, H3K27me3 ChIP


title: GAB294-M1

description: Library name: S19

value: Liver

value: C57BL/6J and Swiss Webster mix


title: H1, 1-10 KO, H3K4me3 ChIP

value: ZNF263 homozygous KO


title: GAB294-S

description: Library name: S18


title: GAB294-M2

description: Library name: S20


title: a4_34F

city: New Haven

first: Stephen

middle: M

last: Strittmatter.

state: Connecticut

address: 295 Congress Ave, BCMM Rm433

department: Neurology

institute: Yale University

description:
Library name: RK24
10x Genomics

data_processing:
Reads where aligned to mm10 mouse genome referemce and masked for low quality sequences using the Cell Ranger Software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Scanpy (Wolf F. et al, 2018) was used to generate a merged anndata objects of all study samples for QC processing and gene filtering.
Data was log-normalized and underwent sample based clustering using highly variable genes identified by Scanpy's implementation of Seurat_v3.
Post clustering batch corrections was preformed using the scVI probabilistic model from the scVI-tools package
Doublets was removed from data set based on clusters exhibiting an enrichment of multiple cell specific marker genes indicating a multi-cell expression profile
Assembly: Leiden clustering, UMAP embedding, cell type cluster assigments, DEG testing, and read count extraction was performed using Scanpy's data processing pipelin.
Supplementary files format and content: mm10-2020-A
Supplementary files format and content: comma separated gene count matrix files.

source_name: Motor Cortex

growth_protocol: Mice where ageed for 10 or 20 months

extract_protocol:
Motor corter was disected from the left brain hemisphere and processed for nuclei isolation via sucrose density gradient centrifugation with 8000-1000 nuclei used for 10x Genomics barcode mRNA sequencing.
RNA libraries were prepared using the 10x Genomics Chromium Single Cell 3P' v3  Kit following the manufacturer's protocols.

treatment_protocol: Age-matched adult (12-13 weeks) female mice of ApoE2 or ApoE4 genotype were subjected to a thoracic dorsal-over hemisection (injured) or shame (control) surgery.

value: Motor Cortex

value: Control

value: Female


title: H1, WT, His, input


title: GAB242-L

description: Library name: S17


title: KI_MLKL_CASP1_DKO_2

description: Library name: SAM24478000

value: E18.5 intestine


title: KI_MLKL_CASP1_DKO_1

description: Library name: SAM24477999


title: a2_62C

description:
Library name: RK22
10x Genomics


title: KI_MLKL_KO_3

description: Library name: SAM24477998

value: Casp8 C362A KI Mlkl KO

value: biol rep 3


title: H1, WT, H3K27me3 ChIP

value: Human embryonic stem cell


title: GAB242-M

description: Library name: S16


title: a4_027

description:
Library name: RK20
10x Genomics


title: a4_C58

description:
Library name: RK23
10x Genomics


title: KI_MLKL_KO_2

description: Library name: SAM24477997

value: No treatment


title: GAB242-S

description: Library name: S15


title: H1, WT, H3K27ac ChIP

value: WT


title: GAB235-S

description: Library name: S14


title: a2_D6F

description:
Library name: RK16
10x Genomics


title: Adrenal gland, Male, WT, 6 weeks old, #512

description:
Library name: TD-1
column name in counts_rna.tsv:1916-TD-1_CATGAGCA-GCAAGATC_S152

value: 6 weeks old


title: KI_MLKL_KO_1

description: Library name: SAM24477996


title: H1, WT, H3K4me3 ChIP


title: MLKL_KO_3_T

description: Library name: SAM24477995

value: Mlkl KO


title: a4ki_443

description:
Library name: RK15
10x Genomics

value: Injured


title: GAB229-M

description: Library name: S13


title: H1, 1-10 KO, ZNF263 FLAG ChIP

value: ZNF263 homozygous KO with ectopic expression of ZNF263-FLAG


title: GAB18-M

description: Library name: S12


title: CB6-L

description: Library name: S11

value: Cyp1a2-CreERT2; Ctnnb1(ex3)fl/+


title: MLKL_KO_1_T

description: Library name: SAM24477993

value: biol rep 1


title: a2ki_539

description:
Library name: RK12
10x Genomics


title: CAB239-M

description: Library name: S10

value: Liver

value: C57BL/6J and Swiss Webster mix


title: H1, WT, ZNF263 ENDO ChIP, rep2


title: H1, WT, ZNF263 ENDO, input


title: 12562_Casp1_FADD_QKO_3

description: Library name: SAM24481648

value: Casp8 D387A KI Cflar KO Mlkl KO Casp1 KO Fadd KO


title: a4ki_671

description:
Library name: RK11
10x Genomics

value: Motor Cortex


title: CAB228-M

description: Library name: S9


title: 12562_Casp1_FADD_QKO_1

description: Library name: SAM24481646


title: 12562_Casp1_FADD_QKO_2

description: Library name: SAM24481647

value: biol rep 2


title: H1, WT, ZNF263 ENDO ChIP, rep1


title: CAB225-L

description: Library name: S8


title: a2_07C

description:
Library name: RK10
10x Genomics

value: Control

value: Female


title: a4_D07

description:
Library name: RK09
10x Genomics


title: H99YPD3

city: Shanghai

first: Donglei

last: Sun

address: 800 Dongchuan RD. Minhang District

department: School of Life Sciences and Biotechnology

institute: Shanghai Jiao Tong University

description: Library name: YPD 3

data_processing:
HISAT2 2.1.0-beta
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using hisat2 2.1.0 and paired-end clean reads were aligned to the reference genome using HISAT2.
Assembly: CNA3
Supplementary files format and content: HTSeq v0.6.1
Supplementary files format and content: HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.

organism: Cryptococcus neoformans H99

source_name: fungal cells

growth_protocol: Fungal cells were cultured at 37 C with 5% CO2 for 12 hours.

extract_protocol:
Total RNA was extracted from freshly collected fungal cells using TRIzol reagent (Invitrogen) following the manufacturer’s protocol. RNA quantity and integrity were assessed using an Agilent 2100 Bioanalyzer, and only samples with a RNA Integrity Number (RIN) >7.0 were used for library construction.
Poly(A)+ mRNA was enriched using oligo(dT) magnetic beads and then fragmented using a fragmentation buffer. cDNA was synthesized using random hexamer primers and reverse transcriptase. The resulting cDNA was purified, end-repaired, A-tailed, ligated with Illumina sequencing adapters, size-selected, and PCR-amplified to construct the final sequencing libraries. Libraries were sequenced on the Illumina NovaSeq 6000 platform to produce 150 bp paired-end reads according to the standard protocols by Majorbio Bio-Pharm Technology Co. Ltd., generating an average of ~50 million high-quality reads per sample.

treatment_protocol: 1 × 10^7 fungal cells were cultured in 10 mL of either complete mouse serum or Sabouraud dextrose broth.

value: fungal cells

value: 12 hours

value: YPD


title: H1, 1-10 KO, ZNF263 FLAG, input

value: Human embryonic stem cell


title: CAB52-L

description: Library name: S7


title: a4_D03

description:
Library name: RK08
10x Genomics


title: CAB44-L

description: Library name: S6


title: 12146_Casp1_Ifnar_QKO_2

description: Library name: SAM24481644

value: E18.5 intestine

value: Casp8 D387A KI Cflar KO Mlkl KO Casp1 KO Ifnar1 KO

value: No treatment


title: H99YPD2

description: Library name: YPD 2


title: 12146_Casp1_Ifnar_QKO_3

description: Library name: SAM24481645

value: biol rep 3


title: MLKL_KO_2_T

description: Library name: SAM24477994

value: Mlkl KO


title: H99YPD1

description: Library name: YPD 1


title: a2ki_F60

description:
Library name: RK14
10x Genomics

value: Injured


title: 12146_Casp1_Ifnar_QKO_1

description: Library name: SAM24481643

value: biol rep 1


title: a2ki_92F

description:
Library name: RK13
10x Genomics


title: a4ki_255

description:
Library name: RK06
10x Genomics


title: H99serum3

description: Library name: Serum 3

value: serum


title: CAB28-L

description: Library name: S5

value: Liver

value: C57BL/6J and Swiss Webster mix


title: 11893_Casp1_TKO_3

description: Library name: SAM24481639

value: Casp8 D387A KI Cflar KO Mlkl KO Casp1 KO


title: CAB28-S

description: Library name: S4


title: H99serum2

description: Library name: Serum 2


title: H99serum1

description: Library name: Serum 1


title: a4ki_135

description:
Library name: RK05
10x Genomics

value: Motor Cortex


title: 11893_Casp1_TKO_1

description: Library name: SAM24481637


title: 11893_Casp1_TKO_2

description: Library name: SAM24481638

value: biol rep 2


title: 30Cto37C_100mMNAIN3_bioreplicate2_techreplicate5

description: Library name: 250317_Candida_37C_100mMNAIN3_Rep4_5

organism: Candida albicans

source_name: Candida albicans

value: Candida albicans


title: a4ki_365

description:
Library name: RK04
10x Genomics

value: Female


title: CAB26-L

description: Library name: S3


title: 11449_DKO_3

description: Library name: SAM24481634

value: Casp8 D387A KI Cflar KO Mlkl KO


title: CAB145-L

description: Library name: S1


title: 30Cto37C_100mMNAIN3_bioreplicate2_techreplicate4

description: Library name: 250317_Candida_37C_100mMNAIN3_Rep4_4


title: a2ki_B38

description:
Library name: RK02
10x Genomics


title: 11449_DKO_1

description: Library name: SAM24481632


title: a2ki_50C

description:
Library name: RK01
10x Genomics


title: 11449_DKO_2

description: Library name: SAM24481633


title: 30Cto37C_100mMNAIN3_bioreplicate2_techreplicate3

description: Library name: 250317_Candida_37C_100mMNAIN3_Rep4_3


title: a2_938

description:
Library name: RK07
10x Genomics

value: Control


title: 6654_Casp8_D387A_KI_3

description: Library name: SAM24481631

value: E18.5 intestine

value: Casp8 D387A KI


title: 30C_100mMNAIN3_bioreplicate1_techreplicate4

description: Library name: 250317_Candida_30C_100mMNAIN3_Rep1_4


title: 30C_100mMNAIN3_bioreplicate1_techreplicate3

description: Library name: 250317_Candida_30C_100mMNAIN3_Rep1_3


title: juvenile_fibroblasts_pbs_rep4

description: Library name: McGrath_06232021_PBSfibro_juv_P4_S28

data_processing:
Reads demultiplexed to fastq using BCL2FASTQ v2.17.1.14 with default parameters
Reads in fastq format were aligned to the NCBI RefSeq mouse reference genome (mm10) and quantified at the gene level using the nf-core/rnaseq v3.8.1 Nextflow pipeline.
Differential gene expression analysis was performed using PyDESeq2
Assembly: mm10
Supplementary files format and content: Raw counts tables for fibroblasts or AT2 cells in tab-separated value (TSV) format.

extract_protocol:
Cells were digested from whole mouse lungs and subjected to FACS to isolate either alveolar epithelial type II cells (AT2) or PDGFRa+ fibroblasts. Total RNA was immediately extracted from sorted cells.
Bulk RNA-seq libraries prepared using QIAGEN AllPrep DNA/RNA micro kit and the TAKARA SMARTer Stranded Total RNA-seq Kit v2.

value: lung

value: fibroblasts

value: pbs


title: REVERB WT Treg, c-maf

city: La Jolla

first: Jingting

last: Yu

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

data_processing:
Raw read quality was checked using FASTQC v0.11.8 and the adaptors were trimmed with Trim Galore v0.4.4.
Reads were mapped to mm10 mouse genome using STAR v2.5.3a. Mapping was carried out using default parameters (up to 10 mismatches per read, and up to 9 multi-mapping locations per read).
Peaks were identified using HOMER ‘findpeaks’, using input IgG condition as background reference and default parameters (four-fold enrichment over input control, four-fold enrichment over local tag count, FDR < 0.001, and style factor).
Assembly: mm10
Supplementary files format and content: bigWig file for every sample
Library strategy: cut&run

source_name: Treg cells

growth_protocol: RPMI, FBS(10%), hIL-2(50U/ml), TFGβ(5ng/ml), anti-CD3(2μg/ml), anti-CD28(2μg/ml)

extract_protocol:
Cells were fixed with 1X Permeabilization buffer from ebioscience Foxp3 fixation kit . After antibody incubation, chromatin was cut using pA-MNase and DNA was extracted using QIAGEN MinElute kit.
cut&run libraries were prepared using the NEBNext® UltraTM II DNA Library Prep Kit for Illumina® (E7645)  from NEB. 6 ng of DNA was used as starting material for input and samples. Libraries were amplified using 14 cycles on the thermocycler. Post amplification libraries were size selected at 150-350bp in length using Agencourt AMPure XP beads.

treatment_protocol: IL-6(5ng/ml), VitC(100μg/ml)

value: Treg cells

value: REVERB WT

value: c-maf


title: REVERB WT Treg, IgG control for c-maf

value: IgG control


title: REVERB KO Treg, IgG control for c-maf

value: REVERB KO


title: invitro_37C_100mMNAIN3_bioreplicate2_techreplicate2

description: Library name: 230905_Candida_invitro_37C_100mMNAIN3_R2_3


title: juvenile_fibroblasts_pbs_rep1

city: Philadelphia

address: 3615 Civic Center Blvd

institute: Children's Hospital of Philadelphia

description: Library name: McGrath_06232021_PBSfibro_juv_P1_S25


title: CAB170-S2

description: Library name: S2

value: Liver

value: C57BL/6J and Swiss Webster mix


title: 6654_Casp8_D387A_KI_1

description: Library name: SAM24481629

value: biol rep 1

value: No treatment


title: invitro_37C_100mMNAIN3_bioreplicate2_techreplicate1

description: Library name: 230905_Candida_invitro_37C_100mMNAIN3_R2_2

value: Candida albicans


title: juvenile_fibroblasts_ecoli_rep4

description: Library name: McGrath_06232021_ecolifibro_juv_E4_S32

value: ecoli


title: a2ki_564

description:
Library name: RK03
10x Genomics

value: Motor Cortex

value: Injured

value: Female


title: invitro_37C_100mMNAIN3_bioreplicate1_techreplicate2

description: Library name: 230817_Candida_in_vitro_37C_100mMNAIN3_2


title: 6654_Casp8_D387A_KI_2

description: Library name: SAM24481630

value: E18.5 intestine

value: Casp8 D387A KI

value: biol rep 2


title: juvenile_fibroblasts_ecoli_rep3

description: Library name: McGrath_06232021_ecolifibro_juv_E3_S31

value: lung

value: fibroblasts


title: 11449_Control_2

description: Library name: SAM24481627

value: Mlkl KO


title: 11449_Control_3

description: Library name: SAM24481628

value: biol rep 3


title: REVERB KO Treg, c-maf

value: Treg cells

value: REVERB KO

value: c-maf


title: juvenile_fibroblasts_pbs_rep3

description: Library name: McGrath_06232021_PBSfibro_juv_P3_S27

value: pbs


title: REVERB WT Treg, IgG control for DEC1

value: REVERB WT

value: IgG control


title: invitro_37C_100mMNAIN3_bioreplicate1_techreplicate1

description: Library name: 230817_Candida_in_vitro_37C_100mMNAIN3_1

value: Candida albicans


title: juvenile_fibroblasts_ecoli_rep2

description: Library name: McGrath_06232021_ecolifibro_juv_E2_S30

value: ecoli


title: 11449_Control_1

description: Library name: SAM24481626

value: biol rep 1

value: No treatment


title: REVERB WT Treg, DEC1


title: REVERB KO Treg, IgG control for DEC1


title: juvenile_fibroblasts_pbs_rep2

description: Library name: McGrath_06232021_PBSfibro_juv_P2_S26


title: invitro_30C_100mMNAIN3_bioreplicate2_techreplicate2

description: Library name: 230907_Candida_invitro_30C_100mMNAIN3_R2_2


title: juvenile_fibroblasts_ecoli_rep1

description: Library name: McGrath_06232021_ecolifibro_juv_E1_S29


title: juvenile_at2_pbs_rep4

description: Library name: McGrath_05282021_PBSat2_juvPBS4_S20


title: REVERB KO Treg, DEC1


title: invitro_30C_100mMNAIN3_bioreplicate2_techreplicate1

description: Library name: 230831_Candida_invitro_30C_100mMNAIN3_R2


title: Naive WT 3

city: Columbus

first: Ken

last: Oestreich

state: Ohio

address: 460 W 12th Ave, Biomedical Research Tower

department: Microbial Infection and Immunity

institute: The Ohio State University College of Medicine

description:
Library name: Sample 11
Naive-WT3

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Assembly: mm10
Supplementary files format and content: csv files include raw counts for each sample

source_name: Spleen

extract_protocol:
Total RNA was isolated from cell pellets using the Macherey-Nagel Nucleospin RNA isolation kit according to the manufacturer's instructions.
Libraries were generated and sequenced according to standard protocols from Azenta Life Sciences, to which the samples were sent for library preparation and analysis.

treatment_protocol: Untreated CD8+ TVM cells were sorted from the spleen of WT and Aiolos KO mice following total CD8+ T cell isolation. Anti- CD8a, anti-Cd44, anti-CD62L, and anti-CD49d antibodies were used to sort the TVM cells. Naïve CD8+ T cells were isolated from the spleen of WT mice using naïve CD8+ T cell isolation kit.

value: Spleen

value: Naive CD8+ T cells

value: WT

value: untreated cells


title: Naive WT 4

description:
Library name: Sample 12
Naive-WT4


title: invitro_30C_100mMNAIN3_bioreplicate1_techreplicate2

description: Library name: 230814_Candida_in_vitro_30C_100mMNAIN3_2


title: REVERB KO Treg, transduced with RORc, RORgt

value: transduced with RORc

value: RORgt


title: Naive WT 2

description:
Library name: Sample 10
Naive-WT2


title: invitro_30C_100mMNAIN3_bioreplicate1_techreplicate1

description: Library name: 230814_Candida_in_vitro_30C_100mMNAIN3_1


title: juvenile_at2_pbs_rep3

description: Library name: McGrath_05282021_PBSat2_juvPBS3_S19

value: lung


title: juvenile_at2_pbs_rep1

description: Library name: McGrath_05282021_PBSat2_juvPBS1_S17


title: 30Cto37C_100mMNAIN3_bioreplicate2_techreplicate2

description: Library name: 230109_30Cto37C_100mMNAIN3_Rep4_2


title: juvenile_at2_pbs_rep2

description: Library name: McGrath_05282021_PBSat2_juvPBS2_S18


title: Naive WT 1

description:
Library name: Sample 9
Naive-WT1


title: REVERB KO Treg, retroviral vector, RORgt

value: Treg cells

value: retroviral vector


title: Aiolos KO TVM 8

description:
Library name: Sample 8
TVM-AKO8

value: CD8+ TVM cells


title: REVERB KO Treg, transduced with RORc, IgG control


title: 30Cto37C_100mMNAIN3_bioreplicate2_techreplicate1

description: Library name: 230109_30Cto37C_100mMNAIN3_Rep4_1


title: juvenile_at2_ecoli_rep4

description: Library name: McGrath_05282021_ecoliAT2_juvEC4_S24


title: 30Cto37C_100mMNAIN3_bioreplicate1_techreplicate4

description: Library name: 221027_30Cto37C_100mMNAIN3_Rep2_4


title: Aiolos KO TVM 7

description:
Library name: Sample 7
TVM-AKO7


title: juvenile_at2_ecoli_rep3

description: Library name: McGrath_05282021_ecoliAT2_juvEC3_S23


title: Aiolos KO TVM 6

description:
Library name: Sample 6
TVM-AKO6


title: juvenile_at2_ecoli_rep2

description: Library name: McGrath_05282021_ecoliAT2_juvEC2_S22


title: REVERB WT Treg, transduced with RORc, RORgt


title: 30Cto37C_100mMNAIN3_bioreplicate1_techreplicate3

description: Library name: 221027_30Cto37C_100mMNAIN3_Rep2_3


title: 30Cto37C_100mMNAIN3_bioreplicate1_techreplicate2

description: Library name: 221010_30Cto37C_100mMNAIN3_Rep2_2


title: REVERB WT Treg, transduced with RORc, IgG control


title: REVERB WT Treg, retroviral vector, RORgt


title: juvenile_at2_ecoli_rep1

description: Library name: McGrath_05282021_ecoliAT2_juvEC1_S21


title: WT TVM 8

description:
Library name: Sample 4
TVM-WT8


title: neonatal_at2_pbs_rep4

description: Library name: McGrath_04152021_PBSat2_P4_S12

value: pbs


title: REVERB WT Treg, retroviral vector, IgG control


title: 30Cto37C_100mMNAIN3_bioreplicate1_techreplicate1

description: Library name: 221005_30Cto37C_100mMNAIN3_Rep2