title: RNAseq_A375 shNIPBL_#2 6D rep2

data_processing:
RNA-seq reads were trimmed and filtered for quality using Trimmomatic (v0.38).
Processed reads were then aligned to hg19 using STAR (v2.7.1a).
For each GENCODE (v19) gene, reads were counted using featureCounts (v1.6.4).
Gene counts were used to perform differential analysis using DESeq2 (v1.22.2).
TPM normalized bigWig tracks were generated using deepTools (v3.1.10 bamCoverage with `--normalizeUsing BPM`) for each replicate. BedGraph files from each replicate, converted from bigWig using bigWigToBedGraph, were combined using bedtools (v2.27.1) unionbedg and scores were averaged for each condition. The averaged bedgraph files were converted to TPM averaged bigWig tracks using bedGraphToBigWig (v4). TPM counts was generated with stringtie (v2.1.1) using BAM files and GENCODE (v19) gtf.
Assembly: hg19
Supplementary files format and content: TPM normalized gene count
Supplementary files format and content: Differential gene expression analysis by DESeq2

extract_protocol:
Cells were lyzed directly on culture dish with TRIzol RNA isolation reagent (Thermo fisher scientific). Total RNA was extracted by thorough mixing with chloroform and isopropanol precipitation of upper aqueous phase.
500 ng of total RNA was used for poly-A selection of RNA and library construction using TruSeq stranded mRNA LT Kit (Illumina, RS-122-2102).
Samples were barcoded and run on a HiSeq 4000 in PE50 to generate 40-50 M reads.

tag: tissue

value: skin

value: melanoma


title: DrpoZ_1h_rep1

status: Public on May 01 2025

type: RNA

city: Freiburg

first: Wolfgang

middle: R.

last: Hess

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

country: Germany

institute: University of Freiburg

description: Gene expression after 1h at 3% CO2

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505C US90900275, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09 for Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. Median signal intensities were normexp background substracted (offset=50) and quantile normalized.

molecule: total RNA

organism: Synechocystis sp. PCC 6803

source_name: liquid culture

label_protocol: DNase-treated RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol. Further details of the labeling and hybridization protocol were published in:  Voß,B. and Hess,W.R. (2014) The identification of bacterial non-coding RNAs through complementary approaches. In Handbook of RNA Biochemistry. WILEY-VCH, Weinheim, Germany, Vol. 2, pp. 787–800.

growth_protocol: All strains were maintained in BG-11 medium supplemented with 20 mM Hepes pH 7.5, continuous illumination at photosynthetic photon flux density 40 µmol m-2 s-1, 32 °C. Liquid cultures were shaken at 90 rpm. For the experiments, liquid cultures were grown without antibiotics in ambient air or in high CO2 by supplementing growth chamber air with 3% CO2.

extract_protocol: Cells were collected by centrifugation at 7000 g for 5 min at 4°C and the pellet was frozen in liquid nitrogen. Total RNA was prepared using the hot-phenol method.

treatment_protocol: Cells were shifted to 3% CO2 at an OD750 of 0.8-1. Cell samples were collected immediately before and 3 h and 24 h after the shift.

tag: strain

value: strain GT-T

tag: genotype

value: drpoZ mutant

tag: condition

value: after 1h at 3% CO2


title: RNAseq_A375 shNIPBL_#2 6D rep1

type: SRA

city: New York

first: Elissa

middle: WP

last: Wong

state: NY

address: 1275 York Avenue

department: HOPP

country: USA

institute: Memorial Sloan Kettering Cancer Center

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

source_name: skin

growth_protocol: All cells lines were cultured in media supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin. All cells were cultured at 37 ºC in 5% CO2.

treatment_protocol: Cells that were transduced with lentivirus carrying puromycin-resistant shRNA plasmids were treated with 2 µg/ml puromycin.

tag: cell line

tag: cell type

tag: treatment


title: DrpoZ_0min_rep2

description: Gene expression under low CO2

value: under low CO2


title: NL_M35_3

city: Grand Forks

first: John

middle: Andrew

last: Watt

state: North Dakota

address: 504 Nth Hameline St

department: Biomedical Sciences

institute: University of North Dakota

data_processing:
Sequence reads were trimmed for adaptor sequences and low-quality using trimmomatic v0.39.
Reads were aligned to the rat assembly (rn7) using Hisat2 v2.2.1, and sorted/indexed by Samtools v1.13.
Annotation/Counts was performed by featureCounts (Subread v2.0.1).
Normalization and differential gene expression analysis was performed by DESeq2 v1.34.0
Assembly: rn7
Supplementary files format and content: Comma-separated values (csv) file, containing normalized counts for each sample

organism: Rattus norvegicus

source_name: Neurohypophysis (Neural Lobe)

extract_protocol:
Rats were anesthetized with isoflurane and euthanized via transcardial perfusion with PBS. Brains were removed from the skull to gain access to the pituitary gland. The neurohypophysis was removed and immediately flash frozen by liquid nitrogen.
Frozen tissue was ground under liquid nitrogen. RNA was collected via phenol-chloroform extraction and Rneasy Mini Kit (Qiagen). Approximately 1.5 ug  of total RNA was used for QC and library construction.
RNA libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB), and NEBNext Ultra II RNA-seq library kit for Illumina (NEB).

treatment_protocol: Rats were grown to the ages of 35 days old or 125 days old prior to tissue collection.

value: Neurohypophysis (Neural Lobe)

tag: Sex

value: Male

value: Sprague Dawley

value: Age - 35 days old (Control)


title: Exp-V1K_4A_Cell-HaCaT_Power-1_Frequency-27_Time-48_Treatment-exposed

type: genomic

city: Bremen

first: Jyoti

last: Jyoti

state: Bremen

address: Campus Ring 6

department: School of Science

institute: Constructor University

description:
S5
P1_HaCat_Beta_detP.txt-S5
P1_HaCat_Beta_detP.txt

hyb_protocol: The microarray hybridization was performed according to the Infinium HD Assay Methylation Protocol Guide (Illumina, Inc.). The bisulfite-converted DNA samples were hybridized at 48°C for 16 hrs on separate Illumina Infinium MethylationEPIC Arrays. DNA fragments anneal to locus-specific 50 mers which are covalently linked to different bead types. After hybridization and washing of the microarrays, the primers on the BeadChips were extended complementary to the binding DNA sample. This reaction incorporates labelled nucleotides. Incorporation of a G corresponds to the methylated state, A to the unmethylated state on the complementary strand. Allele-specific single base extension of the primer incorporates a biotin nucleotide or a dinitrophenyl labelled nucleotide (C and G nucleotides are biotin labelled; A and T nucleotides are dinitrophenyl labelled.). Hybridized DNA was then removed and the labelled extended primers were stained and dried.

scan_protocol: Fluorescent signal intensities of the labelled and stained nucleotides on the BeadChips were detected with a dual color channel approach and the Illumina iScan™ System.

data_processing:
The software tool GenomeStudio V2011.1 (Illumina, Inc.) including the Methylation Module Version 1.9.0 was used for quality control and visualization of the performance of microarray analysis as well as for methylation analysis. Raw microarray data were imported into GenomeStudio V2011.1 and analyzed without normalization.
Beta Values with depection P values

label: Cy3 and Cy5

molecule: genomic DNA

source_name: HaCaT

label_protocol: Illumina protocol

growth_protocol: Cells were cultured in DMEM, high glucose, supplemented with 10% FBS and 1% penicillin streptomycin in an incubator with 37°C, 5% CO2 and saturated humidity.

extract_protocol:
To keep the homogeneity of the transmitting power flux density or SAR as high as possible, the cells outside a defined area were excluded during harvesting. After exposure, the medium of the cell dishes was discarded and a template made with a 3D printer (at 27 GHz an ellipse with a radius of 24 mm/23 mm; at 40.5 GHz a capped circle with a radius of 24 mm and a distance of the capped area to the center of 19 mm) was applied to the outside of the bottom of the dish and the areas to be omitted were marked. The cells were removed according to the marking with a cell scraper and the cell monolayer was then rinsed twice with PBS.
Cells were harvested by washing the remaining cell monolayer once with PBS and transferring 350 ul lysis buffer to each of the dishes. The cell lysates were collected using a cell scraper and transferring them into reaction tubes. The lysates were frozen at -80C until further processing. DNA and RNA extraction was done using the DNA/RNA Allprep Mini Kit (Qiagen) or the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol:
For each exposure experiment 120,000 HDF or 200,000 HaCaT cells were seeded onto a 60 mm cell culture dish. Cells were used in passages 6-7 (HDF) and 35 (HaCaT). One day (48h experiments) or three days (2h experiments) after seeding, the dishes were transferred to the exposure incubators and cells were exposed or sham-exposed for 2h or 48h, with a frequency of 27 GHz or 40.5 GHz, and a power flux density of 1 mW/cm2 or 10 mW/cm2. In all experiments, the temperature was measured continuously using a fiber optic sensor. The internal temperature of the incubator in which the exposure takes place was reduced in the 10 mW/cm2 experiments manually, so that an average temperature of 37C could be maintained in the petri dishes and a lid heater was used to prevent condensation in the exposed petri dish and maintain blinding conditions.
Temperature controls: Cells were exposed or sham exposed at 40.5 GHz and 10 mW/cm2 for 48h without compensating for the temperature increase. The starting temperature of the medium was 37.0C in these experiments and increased to an average of 38.3C in the exposed samples. No lid heaters were used, so that the heating of the medium in the exposed samples led to medium condensation.
UV controls: Three replicates each of HaCaT and HDF cells were exposed or sham-exposed at a wavelength of 254 nm and an illuminance of 1 mW/cm2. The medium was removed and collected, rinsed twice with PBS and the cells were thinly coated with 600 ul PBS per dish. Exposure was performed without the dish lid for 20 sec, for sham exposure the dishes were stored in the dark at room temperature. The PBS was then aspirated, the cells were layered with the previously collected medium, and incubated for 2h at 37C and 5%CO2.

value: HaCaT

value: exposed

tag: column header in matrix processed file

tag: date

tag: trial

tag: incubator

value: A

tag: frequency [ghz]

tag: power [mw/cm2]

tag: exposuretime [hr]

tag: batch

tag: aliquot

tag: passage

value: b

value: a


title: Exp-V1K_4B_Cell-HaCaT_Power-1_Frequency-27_Time-48_Treatment-sham

description:
S6
P1_HaCat_Beta_detP.txt-S6
P1_HaCat_Beta_detP.txt

value: sham

value: B


title: NL_M125_1

tag: tissue

tag: strain

value: Age - 125 days old


title: RNAseq_A375 shNIPBL_#1 6D rep2

value: skin

value: melanoma

tag: genotype


title: IPRN1

city: Ji'nan

first: Kai

last: Cheng

address: Qingdao Road,6699

country: China

institute: Shandong First Medical University

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of <research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform. Using the Illuminapaired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-endreads. Reads obtained from the sequencing machines includes raw reads containing adapters or lowqualitybaseswhich will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9)
Assembly: ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/
Supplementary files format and content: Reads obtained from the sequencing machines includes raw reads containing adapters or lowqualitybaseswhich will affect the following assembly and analysis.

organism: Mus musculus

source_name: Embryo

extract_protocol:
After extracting total RNA from the samples, enrich eukaryotic mRNA using magnetic beads with Oligo(dT) (for prokaryotes, remove rRNA with a kit before proceeding to the next step).
Add fragmentation buffer to break the mRNA into short fragments. Using mRNA as a template, synthesize the first cDNA strand with random hexamers (six-nucleotide random primers). Add buffer, dNTPs, RNase H, and DNA polymerase I to synthesize the second cDNA strand. After purification with a QiaQuick PCR kit and elution with EB buffer, perform end repair and ligate sequencing adapters. Use agarose gel electrophoresis for fragment size selection, followed by PCR amplification. Finally, sequence the constructed library.

value: Embryo

tag: cell line

value: Fibroblast

value: WT

value: IPRN


title: RNAseq_A375 shNIPBL_#1 6D rep1

tag: cell type


title: Exp-V1K_3B_Cell-HaCaT_Power-1_Frequency-27_Time-48_Treatment-exposed

description:
S4
P1_HaCat_Beta_detP.txt-S4
P1_HaCat_Beta_detP.txt

tag: treatment


title: DMSO3

value: DMSO vehicle


title: RNAseq_A375 shLuc 6D rep2

value: shLuc


title: DrpoZ_0min_rep1

description: Gene expression under low CO2

value: strain GT-T

value: drpoZ mutant

tag: condition

value: under low CO2


title: Exp-V1K_3A_Cell-HaCaT_Power-1_Frequency-27_Time-48_Treatment-sham

description:
S3
P1_HaCat_Beta_detP.txt-S3
P1_HaCat_Beta_detP.txt

value: HaCaT

tag: column header in matrix processed file

value: A


title: R2_1h_rep1

description: Gene expression after 1h at 3% CO2

value: after 1h at 3% CO2


title: DMSO2


title: R2_1h_rep2

description: Gene expression after 1h at 3% CO2


title: DMSO1


title: DrpoZ_24h_rep1

description: Gene expression after 24h at 3% CO2

value: after 24h at 3% CO2


title: R2_24h_rep2

description: Gene expression after 24h at 3% CO2


title: R2_24h_rep1

description: Gene expression after 24h at 3% CO2


title: RNAseq_A375 shLuc 6D rep1


title: Exp-V1K_2B_Cell-HaCaT_Power-1_Frequency-27_Time-48_Treatment-exposed

description:
S2
P1_HaCat_Beta_detP.txt-S2
P1_HaCat_Beta_detP.txt

value: exposed

tag: date

value: B

value: b

value: a


title: RNAseq_COLO800 shNIPBL_#2 6D rep2

value: skin

value: melanoma


title: C3, replicate2, scRNA-seq

city: ｂｅｉｊｉｎｇ

first: Zheng

last: Li

address: 22 Zhongguancun South Avenue

institute: Peking University School and Hospital of Stomatology

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software v6.1.2 (https:/support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cel-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BsA. Cells were added to each channel with a targeted cell recovery estimate of 10000 cells.After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). cDNA was then amplified by PCR with appropriate cycles which depend on the recovery cells. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, index adaptor ligated and library amplification.
RNA libraries were prepared with Chromium Next GEM Single Cell 3ʹ Kit v3.1 according to the manufacturer's protocols.

value: polycationic hydrogel


title: C4, replicate3, scRNA-seq


title: Exp-V1K_2A_Cell-HaCaT_Power-1_Frequency-27_Time-48_Treatment-sham

description:
S1
P1_HaCat_Beta_detP.txt-S1
P1_HaCat_Beta_detP.txt

value: sham

tag: trial


title: RNAseq_COLO800 shNIPBL_#2 6D rep1


title: C2, replicate1, scRNA-seq


title: NPC-IDH1-dox-10 days-iN-2 days (duplicated)

city: Palo Alto

first: Lingjun

last: Meng

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

description: oncogene mutation overexpression for 10 days, iN differentiation for 2 days

hyb_protocol: Bisulfite converted DNA was amplified, Fragmented and hybridized to human Infinium MethylationEPIC BeadChip (Illumina) using stanford Illumina protocol

scan_protocol: Arrays were imaged using BeadArray (HiScan) and standard recommended Illumina scanner setting

data_processing:
RnBeads package in R environment (v4.1.1)
Average Beta

source_name: human induced neuronal (iN) cells

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated from the indicated cell populations through standard methods (QIAGEN) according to the manufacturer’s instructions.

value: human induced neuronal (iN) cells


title: R2_0min_rep1

description: Gene expression under low CO2


title: NPC-KRAS-dox-10 days-iN-2 days (duplicated)

value: KRAS


title: C1, replicate1, scRNA-seq


title: RNAseq_COLO800 shNIPBL_#1 6D rep2


title: NPC-TP53-dox-10 days-iN-2 days (duplicated)


title: RNAseq_COLO800 shNIPBL_#1 6D rep1


title: B4, replicate3, scRNA-seq

value: zwitterionic hydrogel


title: R1_24h_rep2

description: Gene expression after 24h at 3% CO2

value: strain GT-T


title: RNAseq_COLO800 shLuc 6D rep2

value: shLuc


title: R1_1h_rep2

description: Gene expression after 1h at 3% CO2


title: RNAseq_COLO800 shLuc 6D rep1


title: NPC-wt-10 days-iN-2 days (duplicated)

value: wt


title: R1_1h_rep1

description: Gene expression after 1h at 3% CO2


title: NPC-IDH1-dox-10 days-iN-2 days


title: B3, replicate2, scRNA-seq


title: R2_0min_rep2

description: Gene expression under low CO2

value: under low CO2


title: B2, replicate1, scRNA-seq


title: NPC-KRAS-dox-10 days-iN-2 days


title: RNAseq_501mel shNIPBL_#2 6D rep2


title: B1, replicate1, scRNA-seq


title: A4, replicate2, scRNA-seq

value: polyanionic hydrogel


title: RNAseq_501mel shNIPBL_#2 6D rep1


title: RNAseq_501mel shNIPBL_#1 6D rep2


title: RNAseq_501mel shNIPBL_#1 6D rep1


title: A3, replicate1, scRNA-seq


title: WT_24h_rep2

description: Gene expression after 24h at 3% CO2

value: wild type

value: after 24h at 3% CO2


title: NPC-wt-10 days-iN-2 days


title: NPC-IDH1-dox-10 days (duplicated)

description: oncogene mutation overexpression for 10 days

source_name: human neural progenitor cells (NPCs)

value: human neural progenitor cells (NPCs)


title: R1_24h_rep1

description: Gene expression after 24h at 3% CO2


title: R1_0min_rep1

description: Gene expression under low CO2


title: RNAseq_501mel shLuc 6D rep2


title: NPC-KRAS-dox-10 days (duplicated)


title: WT_24h_rep1

description: Gene expression after 24h at 3% CO2


title: A2, replicate2, scRNA-seq


title: NPC-TP53-dox-10 days (duplicated)


title: WT_1h_rep2

description: Gene expression after 1h at 3% CO2

value: after 1h at 3% CO2


title: RNAseq_501mel shLuc 6D rep1


title: RNAseq_COLO800

value: no treatment


title: NPC-wt-10 days (duplicated)


title: NPC-TP53-dox-10 days-iN-2 days


title: HO_3

city: Taipei

first: Bon-chu

last: Chung

address: No. 128, Sec. 2 Academia Rd., Nangang Dist.

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

description: WT_HO.txt (column U)

data_processing:
Sequenced data was analyzed by NextSeq Control Software 2.2.0
The de-multiplexing, adaptor removal and FASTQ file transformation were performed by bcl2fastq Conversion Software 2.17 (Illumina Inc.)
The FASTQ files were imported into CLC Genomics Workbench v.11.0.1 (QIAGEN) to remove low quality reads including reads with lengths less than 30 nucleotides or with Phred quality score lower than 20
The trimmed reads were mapped to zebrafish genome GRCz11 and TPM were calculated by CLC Genomics Workbench v.11.0.1 (QIAGEN)
Genome_build: GRCz11
Supplementary_files_format_and_content: txt files contain expression data for all cells

organism: Danio rerio

source_name: gonad

extract_protocol:
Trunks of foxl2l:egfp;foxl2l-/- or foxl2l:egfp;foxl2l+/+ containing gonad were dissociated by 0.2% collagenase and 0.25% trypsin at 21 dpf. Around 300 EGFP+ germ cells of each genotype were sorted by fluorescence activated cell sorter. cDNA was synthesized by SMART-Seq HT kit seq (Takara Bio).
cDNA library was constructed by Nextera XT DNA Library Prep Kit (Illumina Inc.) following the manufacturer's protocols.

value: TL

value: germ cell

tag: age

value: 21 days post fertilization


title: R1_0min_rep2

description: Gene expression under low CO2


title: WT_1h_rep1

description: Gene expression after 1h at 3% CO2


title: HO_2

description: WT_HO.txt (column Q)


title: Adipocyte, KO, D8, rep2

city: Wuhan

first: Haochen

last: Jiang

address: No.9. BoXue Road, economic development District

institute: Jianghan university

description: Xap5 Adipocyte_counts

data_processing:
The quality of raw data was evaluated using FastQC (v0.11.2)
Sequencing reads were trimmed for adaptor/low-quality sequence using cutadapt (version 1.11)
Clean data were aligned to reference genome via software Hisat2 (v2.1.0)
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes counts for WAT of Xap5 WT and cKO mice at p42
Supplementary files format and content: tab-delimited text file includes counts for in-vitro cultured adipocyte of Xap5 WT and cKO mice after 8 days adipogenic induction

source_name: Adipocyte

growth_protocol: The pre-adipocyte were isolated from sWAT of P0-P3 wild type or cko mice and maintained in DMEM containing 10% FBS and antibiotics in humidified atmosphere with 5%CO2 at 37℃.Adipogenesis was subsequently induced using DMEM/F12 with 10% FBS and a differentiation cocktail (1 mg/mL insulin, 1 mM dexamethasone, 0.5 mM IBMX). After two days of differentiation, the media was replaced with DMEM/F12 containing 10% FBS and 1 mg/mL insulin. The maintenance media was refreshed every 2-3 days, with a total differentiation time of 4-8 days.

extract_protocol:
Total RNA was extracted from the samples using the TRIzol reagent (Invitrogen).
RNA libraries for sequencing were prepared using the MGIEasy mRNA Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: WAT from WT and Xap5 Adiponectin-cKO mice were harvested; Pre-adipocyte from WT and Xap5 Adiponectin-cKO WAT were extracted and cultured for adipogenic induction.

value: Adipocyte

value: XAP5 KO


title: WT_0min_rep1

description: Gene expression under low CO2


title: Adipocyte, KO, D8, rep1

description: Xap5 Adipocyte_counts


title: NPC-KRAS-dox-10 days

value: KRAS


title: RNAseq_SKMEL-1128

value: skin

value: melanoma


title: NPC-IDH1-dox-10 days


title: WT_3

description: WT_HO.txt (column AG)


title: Adipocyte, WT, D8, rep3

description: Xap5 Adipocyte_counts

value: WT


title: RNAseq_SKMEL-23


title: NPC-TP53-dox-10 days


title: A1, replicate1, scRNA-seq


title: Adipocyte, KO, D8, rep3

description: Xap5 Adipocyte_counts


title: Adipocyte, WT, D8, rep2

description: Xap5 Adipocyte_counts


title: WT_2

description: WT_HO.txt (column AC)


title: NB_siACSS2-3

city: Mineola

first: Qing

middle: Robert

last: Miao

address: 101 Mineola Blvd

department: Foundations of Medicine

institute: NYU Long Island School of Medicine

data_processing:
First, the raw data in fastq format was processed using fastp software, resulting in the extraction of clean reads. This was achieved by removing adapter-containing reads, reads with ploy-N, and low-quality reads. All further analyses were conducted on this high-quality, clean data. The reference genome and gene model annotation files were directly downloaded from a genome website. The reference genome index was constructed using Hisat2 v2.0.5, and the paired-end clean reads were aligned to the reference genome using the same version of Hisat2. Hisat2 was chosen for mapping due to its ability to create a splice junction database from the gene model annotation file, providing superior mapping results compared to other non-splice mapping tools.
Finally, featureCounts v1.5.0-p3 was employed to quantify the number of reads mapped to each gene.
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (4.3.1).
Assembly: hg19
Supplementary files format and content: Rawcounts_NB_NS_NB_siAC2.csv

growth_protocol: BE(2)-C cells  were cultured in DMEM medium with penicillin, streptomycin and 10% (v/v) calf serum (Invitrogen)

extract_protocol:
RNA was harvaested using Rneasy mini plus-ki (Qiagen).1.5 ug of total RNA was used for construction of sequencing libraries
RNA libraries fro RNA-seq were prepared using SMARTER mRNA-seq library Prep Kit following manufacturer's protocols.

treatment_protocol: BE(2)-C cell were infected with lentivirus carrying non-silencing shRNAi (NS) or shRNAi targeting ACSS2 (shACSS2), stable NS or shNgBR cell lines were established by puromycin selection

value: neuroblastoma cells

value: ACSS2 deficiency


title: WT_0min_rep2

description: Gene expression under low CO2

value: strain GT-T

value: under low CO2


title: NPC-SOX17-dox-2 days [LM24]

description:
oncogene mutation overexpression for 2 days
LM24


title: RNAseq_A375


title: NB_siACSS2-1


title: NPC-wt-10 days

value: wt


title: HO_1

description: WT_HO.txt (column M)


title: WT_1

description: WT_HO.txt (column Y)


title: WAT, cKO, D42, rep2

description: Xap5 WAT_counts

source_name: WAT

value: WAT


title: NB_NS-3

value: Wildtype


title: NPC-NRAS-dox-2 days [LM22]

description:
oncogene mutation overexpression for 2 days
LM22

value: NRAS

value: human neural progenitor cells (NPCs)


title: NPC-HRAS-dox-2 days [LM23]

description:
oncogene mutation overexpression for 2 days
LM23

value: HRAS


title: WAT, cKO, D42, rep3

description: Xap5 WAT_counts


title: WAT, cKO, D42, rep1

description: Xap5 WAT_counts


title: NB_NS-2


title: NPC-IDH1-dox-2 days [LM21]

description:
oncogene mutation overexpression for 2 days
LM21


title: WAT, WT, D42, rep3

description: Xap5 WAT_counts


title: NPC-KRAS-dox-2 days [LM20]

description:
oncogene mutation overexpression for 2 days
LM20


title: NB_NS-1


title: K_1709_KO_IFE_Tail

city: Fukuoka

first: Aiko

last: Sada

address: 3-1-1 Maidashi, Higashi-ku, Fukuoka City, Fukuoka 812-8582, Japan

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

description: Library name: KO_4

data_processing:
Read count extraction and normalization were performed using CLC genomic benchwork
mm10
Assembly: mouse
Supplementary files format and content: raw counts for each sample
Supplementary files format and content: txt files includes FPKM values for each sample

source_name: Tail epidermis

growth_protocol: The subcutaneous and fat tissues were removed from the tail skin and incubated overnight at 4 C in 0.25% trypsin/EDTA and the next day at 37 C for 30 minutes. Single-cell suspensions were prepared by gentle scraping of the epidermis and subsequent filtering with 70 μm and 40 μm filters. Cells were stained with the following antibodies for 30 minutes on ice: CD34-biotin (1:50, eBioscience, 13-0341), Streptavidin-APC (1:100, BD Biosciences, 554067), α6-integrin-BUV395 (1:100, BD Biosciences, custom order), and Sca-1-BV421 (1:100, BD Biosciences, 562729). Dead cells were excluded by 7-AAD (BD Biosciences) staining. Cells were isolated using the FACS Aria flow cytometer (BD Biosciences). Data were analyzed using FlowJo software (BD Biosciences).

extract_protocol:
FACS-isolated cells from Fbln5 WT and KO mice were directly sorted into Trizol (Ambion, 10296028) and submitted to Tsukuba i-Laboratory LLP, the University of Tsukuba. RNA integrity was analyzed with Agilent 2100 bioanalyzer. The RNA-seq library was prepared with SMARTer® Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara), and sequencing was performed in the Next Generation Sequencing platform using NextSeq500 (Illumina).
The data were analyzed with CLC Genomics 20 software (Qiagen). After normalization, genes that showed ≥2-fold changes were selected.

treatment_protocol: no treatmnet

value: Tail epidermis

value: Epidermis

value: KO

value: no treatment


title: WAT, WT, D42, rep2

description: Xap5 WAT_counts


title: NB_siACSS2-2


title: K_1883_KO_IFE_Tail

description: Library name: KO_3


title: Fetal Lung epithelium 3

first: Abdulvasey

last: Mohammed

state: CA

address: 240 Pasteur Dr

department: Pediatrics

institute: Stanford

data_processing:
Sequencing data were trimmed using Trim Galore v 0.6.6 with a Quality Phred score cutoff of 20.
Expression levels of transcripts were quantified using selective alignment in Salmon v1.8.0, with human genome GRCh38.p14 used to construct the reference transcriptome.
Transcript counts were summed for gene count quantification.
Assembly: GRCh38.p14
Supplementary files format and content: Count matrix of number of reads mapping to genes across all samples.

source_name: Lung epithelium

extract_protocol:
Human fetal thymus and lung samples (pcw 16 -18) were mechanically dissected into <2 mm^3 pieces using surgical scissors. Human fetal bronchus samples (pcw 16 -18) were opened longitudinally and mechanically scraped with scalpel to harvest the inner epithelial layer of bronchus and esophagus, respectively. All tissue samples were enzymatically digested with DNAse (10 mg/ml) and Liberase (2.5 mg/ml, Sigma Aldrich) per 10 g tissue using a tissue dissociator (gentleMACS, C tube, program m_spleen_02 (Miltenyi), 1-3 runs depending on tissue). For fetal thymic tissue (16-18 pcw) only, thymocytes were isolated from cell suspension using Human CD45 MicroBeads (Miltenyi) while other immune cells were depleted using LD depletion columns (Miltenyi),108 cells/column, according to the manufacturer’s instructions. Single cell suspensions of all tissues, (CD45-depleted thymus, bronchus and lung) were enriched for epithelial cells using Human CD326 (EPCAM) Microbeads and LS positive selection columns (Miltenyi) according to the manufacturer’s instructions. Quality control for thymocyte depletion and epithelial cell enrichment for thymic single cell suspensions was performed by flow cytomery on Beckman FACSAria II with CD45-APC, CD3-FITC, CD205-PE, EPCAM-APC, and Live Dead-Near InfraRed-APC-Cy7 prior to MACS purification. Due to epitope blockage from magnetic bead antibodies, additional markers, i.e. CD7-AF647 (thymocytes) and CD105-PerCP/Cy5.5 (thymic mesenchymal cells) were used to assess post enrichment purity. Total RNA was extracted from thymocytes and EPCAM positive selected epithelial cells using the Qiagen RNeasy kit.
Takara SMART-Seq v4 Ultra low Input RNA kit
500pg-5ng of total RNA input were used followed by pooling of 2-12 samples into Hiseq4000 and NovaSeq6000 lanes at a 2 x 100 bp read length.

value: Lung epithelium


title: Adipocyte, WT, D8, rep1

description: Xap5 Adipocyte_counts

value: Adipocyte


title: WAT, WT, D42, rep1

description: Xap5 WAT_counts

value: WT


title: Fetal Bronchial epithelium 3

source_name: Bronchial epithelium

value: Bronchial epithelium


title: Drp1LiKO_Pal_200 μM

first: Lixiang

last: Wang

state: Fukuoka

address: 3-1-1, Maidashi, Higashi-ku

department: Department of Medicine and Bioregulatory Science

institute: Graduate School of Medical Sciences, Kyushu University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: primary hepatocytes, knockout, 200 μM palmitate-treated

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Miice were anesthetized with pentobarbital sodium (50 mg/kg body weight), and liver tissues were perfused with pre-warmed Hank’s balanced salt solution (HBSS) supplemented with 0.5 mM EGTA and 10 mM HEPES for 5 minutes, followed with digestion buffer [low glucose Dulbecco’s modified Eagle’s medium (1000mg/L) supplemented with 0.8 mg/ml collagenase type 1 (Worthington Biochemical Corporation, Lakewood, NJ, USA)]. Single cell suspensions were filtered through a 70-μm cell strainer (BD Falcon, Bedford, MA, USA) and centrifuged at 50 g for 1 min, the cell supernatants were collected separately for the preparation of non-parenchymal cells as described below. The hepatocytes in the pellet were washed twice and suspended in high glucose Dulbecco’s modified Eagle’s medium (4500mg/L) supplemented with 1μM insulin, 2mM L-glutamine, 10 IU/mL penicillin, 10 IU/mL streptomycin and 10% fetal bovine serum and seeded at 300,000 cells/well on 6-well plastic plates coated with collagen type I (Cellmatrix type I-P, Nitta Gelatin, Osaka, Japan). After 4 hours incubation in a 5% CO2 incubator at 37 °C, the culture medium was changed to discard floating unattached cells. We conducted  microarray analysis with primary hepatocyte harvested 24 hours after seeding.

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

value: primary hepatocytes


title: NPC-TP53-dox-2 days [LM18]

description:
oncogene mutation overexpression for 2 days
LM18


title: Drp1flox_Pal_200 μM

source_name: primary hepatocytes, wild-type, 200 μM palmitate-treated


title: Control primary hepatocytes.

description: same raw data as GSM4749314

source_name: primary hepatocytes, wild-type


title: Fetal Thymic epithelium 2

source_name: Thymic epithelium

value: Thymic epithelium


title: mouse liver fed with ethanol diet, AAV-H19_28

city: Indianapolis

first: Zhihong

last: Yang

institute: Indiana University

data_processing:
For the bioinformatics analysis, HISAT was used to map reads to the genome after removing adaptor contamination, low quality bases and undetermined bases. The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. StringTie was used to perform expression level for mRNAs by calculating FPKM (Fragments per kilobase of exon per million fragments).
Assembly: The mapped reads of each sample were assembled using StringTie.
Supplementary files format and content: excel file includes raw counts for each sample
Supplementary files format and content: Excel file includes FPKM values for each sample

source_name: Liver

extract_protocol:
Direct-Zol RNA kits
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol.

value: Liver


title: Drp1LiKO primary hepatocytes.

source_name: primary hepatocytes, knockout


title: NPC-wt-dox-2 days [LM17]

description:
oncogene mutation overexpression for 2 days
LM17

value: wt


title: K_1843_KO_IFE_Tail

description: Library name: KO_2


title: K_1842_KO_IFE_Tail

description: Library name: KO_1


title: mouse liver fed with ethanol diet, AAV-H19_27


title: NPC-SOX17-dox-2 days

description:
L16
oncogene mutation overexpression for 2 days


title: Fetal Lung epithelium 2


title: K_1708_WT_IFE_Tail

description: Library name: WT_04


title: mouse liver fed with ethanol diet, AAV-H19_26


title: NPC-HRAS-dox-2 days

description:
L15
oncogene mutation overexpression for 2 days


title: Fetal Bronchial epithelium 2


title: K_1882_WT_IFE_Tail

description: Library name: WT_03


title: Fetal Lung epithelium 1


title: NPC-NRAS-dox-2 days

description:
L14
oncogene mutation overexpression for 2 days


title: NPC-BRAF-dox-2 days [LM19]

description:
oncogene mutation overexpression for 2 days
LM19

value: BRAF


title: K_1881_WT_IFE_Tail

description: Library name: WT_02


title: mouse liver fed with ethanol diet, AAV-Null_24

value: AAV-Null


title: Fetal Bronchial epithelium 1


title: mouse liver fed with ethanol diet, AAV-Null_23


title: K_1841_WT_IFE_Tail

description: Library name: WT_01


title: NPC-KRAS-dox-2 days

description:
L12
oncogene mutation overexpression for 2 days

value: KRAS


title: mouse liver fed with ethanol diet, AAV-Null_22


title: Young, 24H, 2

city: Buffalo

first: Michael

last: Battaglia

address: 955 Main St

department: Microbiology and Immunology

institute: SUNY at Buffalo

description: Library name: Sample_6

data_processing:
Per-cycle basecall files were convered to per-read FASTQ files using bcl2fastq v2.20.0.422
Reads were analyzed for quality for FASTQC v0.11.1 and summarized using MultiQC v1.6
Reads were mapped to  GRCm38 – mm10 reference genome utilizing HISAT2 v2.1.0 and sorted intobinary alignment map files using samtools v 1.16.1
Aligned reads were quanitified using featureCounts v1.6.2
Raw counts matrix was processed to generate normalized counts
Assembly: GRCM38-mm10
Supplementary files format and content: tab-delineated file containing normalized counts for each sample

source_name: Lung

extract_protocol:
RNA was extracted using Rneasy  miniprep (Qiagen)
Extracted RNA was subjected to cDNA library preparation using TrueSeq RNA sample preparation kit (Illumina)

treatment_protocol: Lungs isolated from mice were made into a single cell suspension and subjected to a customized Mouse Neutrophil Enrichment kit made by StemCell

value: Lung

value: 2 Months

value: Neutrophil


title: NPC-BRAF-dox-2 days

description:
L11
oncogene mutation overexpression for 2 days

value: human neural progenitor cells (NPCs)


title: ChIPseq_501mel shNIPBL_#2 6D SMC1A

library_source: genomic

data_processing:
ChIP-seq reads were aligned to hg19 using BWA (v0.7.17-r1188). Unmapped and low MAPQ reads (< 30) were filtered out using SAMtools (v1.9) and PCR duplicates were removed using Picard tools (v2.18.16). Depth normalized bigWig tracks were generated using deepTools (v3.1.1) bamCoverage with `bamCoverage -b ${input_bam} -o ${output_bigwig} --normalizeUsing RPGC --ignoreForNormalization chrX chrM -bl hg19-blacklist.v2.bed`.
Assembly: hg19
Supplementary files format and content: bigWig

source_name: skin

extract_protocol:
20 x 106 cells were harvested and fixed in 1% formaldehyde for 10 min with gentle shaking. Glycine was added to final concentration of 125 mM and incubated for 5 min. Cells were washed once with PBS, resuspended in LB1 [50mM HEPES (pH 7.5), 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100 and 1× complete EDTA-free protease inhibitor] and incubated with rotation at 4 °C for 10min. Samples were pelleted, resuspended in LB2 [10mM Tris-HCl (pH 8.0), 200mM NaCl, 1mM EDTA, 0.5mM EGTA and 1× complete protease inhibitor] and incubated rotating at 4 °C for 10min. Nuclei were pelleted, resuspended in LB3 with 0.5% SDS [0.5% SDS, 20mM Tris-HCl (pH 8.0), 150mM NaCl, 2mM EDTA, 1% Triton X-100 and 1× complete protease inhibitor] and sonicated using Covaris E220 focused ultrasonicator (peak power = 150 W, duty factor = 2%, cycle per burst = 200) for 12 min. Soluble chromatin extracts were cleared by centrifugation and 1% was kept as input DNA. Sheared chromatin was diluted to contain 0.16% SDS for antibody binding and incubated overnight at 4 °C with 2 ug anti-H3K27Ac (Abcam, ab4729) and anti-SMC1A (Bethyl lab, A300-055A). 20 ul Pierce ChIP-grade magnetic beads were used for precipitation at 4 °C for 6 hr. Beads were washed 3x LiCl buffer [250 mM LiCl, 10 mM Tris-HCl (pH 8.0), 1% sodium deoxycholate, 1% NP-40 and 1 mM EDTA], 1x RIPA wash buffer [500 mM LiCl, 50 mM HEPES-KOH (pH 7.6), 0.7% sodium deoxycholate, 1% NP-40 and 1 mM EDTA] and 1x TE [10 mM Tris-HCl (pH 8.0) and 1 mM EDTA] + 50 mM NaCl. Chromatin was eluted in elution buffer [1% SDS, 50 mM Tris-HCl (pH 8.0) and 10 mM EDTA] and incubated at 65 °C for 30 min. Eluate was reverse cross-linked at 65 °C overnight, treated with RNaseA (Roche) at 37 °C for 1 hr and Proteinase K (Roche) at 55 °C for 2 hr before recovered using a miniElute PCR purification kit from Qiagen.
Library was prepared using KAPA HTP library kit (KAPA biosystems).
ChIP libraries were sequenced to obtain 30-40 M reads for each sample on HiSeq 2500 or 4000 with either SR50 or PE50.

value: skin

value: melanoma

value: shNIPBL_#2, 6D

tag: antibody

value: SMC1A antibody


title: Young, 24H, 1

description: Library name: Sample_5

value: WT


title: mouse liver fed with ethanol diet, AAV-Null_21


title: ChIPseq_501mel shLuc 6D SMC1A

value: shLuc, 6D


title: NPC-TP53-dox-2 days

description:
L10
oncogene mutation overexpression for 2 days


title: Young, 12H, 3

description: Library name: Sample_4


title: NPC-wt-dox-2 days

description:
L9
oncogene mutation overexpression for 2 days


title: Young, 12H, 2

description: Library name: Sample_3


title: ChIPseq_SKMEL-1128 H3K27ac

value: no treatment

value: H3K27ac antibody


title: Uchl1_KO

city: xian yang

first: donghui

state: shaanxi

address: No. 3rd, Taicheng Road, Yangling, Shaanxi

institute: Northwest A&F University

description: 10x Genomics

data_processing:
The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150bp) by Guangzhou Gene Denovo Biotechnology Co. at a minimum depth of 20,000 reads per cell.
Assembly: GRCm39 (GCA_000001635.9)
Supplementary files format and content: Using 10 × Genomics single-cell data analysis software CellRanger (v6.1.0, https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) The raw BCL files were converted to fastq.gz files as well for comparison and count quantification. Reads with low-quality barcodes and unique molecular identifiers (UMIs) were then filtered out.

molecule: nuclear RNA

source_name: testis

extract_protocol:
Testicular tissue samples from Uchl1_KO mice were collected, and the frozen testicular tissues were handed over to Guangzhou Gene Denovo Biotechnology Co. for nuclei isolation, library preparation and sequencing according to the guidelines of 10 × Genomics (10 × Genomics, USA). About 300 mg of tissues from three mice were combined and dissociated into a mononuclear suspension. Cell nuclei were passed through a 40 × 10-6 M cell filter for removal of cellular debris and larger clumps. Nuclei concentration was manually assessed using 0.4% Taipan blue restaining and a blood cell counter.
The nuclei concentration was adjusted to 700-1200 nuclei/μL, and the cell suspension was loaded onto a 10 × Genomics GemCode Single Cell Instrument and subjected to cell capture and library preparation according to the Chromium Next GEM Single Cell 3′ kit v3.1 instructions. Because a large amount of snRNA-seq data on WT mouse testes have been published, we searched the database to find the testicular snRNA-seq data of WT mice with the same age, strain, sequencing platform, and sequencing method as the Uchl1_KO mice in this study as a control for the present experiments. Sequencing data of WT mouse testes were obtained from public databases (E-MTAB-6946 < ArrayExpress < BioStudies < EMBL-EBI)

value: testis


title: ChIPseq_A375 H3K27ac


title: mMA9_Gata2 KO_treat_H3K27ac

city: Philadelphia

first: Kathrin

last: Bernt

state: PA

address: 3501 Civic Center Boulevard,

institute: Children's Hospital of philadelphia

data_processing:
BWA Alignment
MACS2 peak calling
samtools convert files
IGV 2.8.0
Assembly: mm10
Supplementary files format and content: bigwig file

source_name: Bone marrow

growth_protocol: Cells were grown in IMDM medium supplemented with 15% heat inactivated FBS, 1% Penicillin/Streptomycin, 1% L-Glutamine, murine IL-3, murine IL-6 (10ng/mL), and murine SCF (20ng/mL).

extract_protocol:
MA9 leukemia cells were collected from bone marrow of primary animals and transduced with Cre or MIT as control, then sorted for GFP and tdTomato. After 7-9 days in culture ChIP was performed. Briefly, samples were crosslinked, lysed, sonicated and immunoprecipated with the indicated antibody overnight. After a series of washes they were reverse crosslinked overnight and DNA extracted.
Library prep was performed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®, Illumina NovaSeq 6000, 2x300bp paired-end reads, multiplexed

value: Bone marrow

value: AML

value: MA9 leukemia

value: Gata2 -/- (Gata2 KO)


title: Young, 12H, 1

description: Library name: Sample_2

value: Lung


title: mouse liver fed with ethanol diet, AAV-H19_25

value: Liver


title: hESC-HRAS-Q61R

description:
oncogene mutation overexpression for 9 days
LM-7

source_name: human embryonic stem cells (hESCs)

value: human embryonic stem cells (hESCs)


title: Old, 24H, 3

description: Library name: Sample_14

value: 18 Months

value: Neutrophil


title: mMA9_Gata2 ff_treat_H3K27ac

value: Gata2 f/f


title: IL10-KO rep3

city: Chengdu

first: Lili

state: Sichuan

address: 2222 Xinchuan Road

institute: West China Hospital, Sichuan University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced of library size (FPKM) were calculated using a protocol from Trapnell, Cole, et al., 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include readcount values for each Sample.

source_name: Colon

extract_protocol:
Colons were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina®(NEB #E7530S/L) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Colon

value: post natal day 56


title: NPC-IDH1-dox-2 days

description:
L13
oncogene mutation overexpression for 2 days

source_name: human neural progenitor cells (NPCs)

value: human neural progenitor cells (NPCs)


title: CD8 T cells activated with Ova peptide (0.5 μM) in combination with TEPP46 replicate 3

city: Washington

first: Lu

last: Jin

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University

description: Library name: VV006_S19

data_processing:
WGBS raw data (fastq or fasq.gz files) quality was checked using FastQC (v0.11.9), and adapter trimming on raw data was performed using Trimmomatic (v0.39). Reads with low quality (quality score < 33, error rate > 10%) or length are too short (<35 bp) after trimming were removed before alignment
We used the reference genome downloaded from UCSC mm10, a bowtie2 (v2.4.2) genome indexing was produced for the next step. Paired end trimmed read alignment, deduplication and methylation extraction were performed using bismark (v0.24.0).
Statistical analysis of DMRs were conducted using DMRichR (v1.7.8) R package, DMRs were annotated using ChIPseeker (v1.36.0) R package.
Assembly: mm10
Supplementary files format and content: bedGraph.gz files include beta value

source_name: C57BL/6J OT1 mice

growth_protocol: Four-to-six-week-old C57BL/6J or Balb/c wild type mice (5-6 weeks old; females) were purchased from Jackson Laboratory. In-house-bred pMel-1 mice [B6.Cg-Thy1a/Cy Tg (TcraTcrb)8Rest/J], which carry a rearranged TCR transgene (Vβ13) specific for the mouse homolog (pmel-17) of human gp10082, with transgenic CD8 T cells having a melanoma-gp100 peptide-specific TCR were used as outlined in various experiments. Similarly, OT-1 transgenic mice (Jax-Strain #003831) with specific anti-Ova257-264 T cell receptor (TCR) in CD8+ T cells were bred in-house and used in various experiments as listed. Animals had free access to water and food. All experiments were performed as per ARRIVE guidelines, under protocols approved by the Institutional Animal Care and Use Committee (IACUC) at the University of Minnesota.

extract_protocol:
Genomic DNA was isolated from CD8 T cells after activation in the presence or absence of TEPP46 and treated with bisulfite by the EZ DNA Methylation gold kit (Zymo Research)
The library was generated by the EpiGnome kit (Epicentre) and Illumina HiSeq system was used for sequencing of Bisulfite-modified DNA

treatment_protocol: Isolated CD8 T cells from OT1 mice (1.5 ×106 cells per ml) were activated with Ova peptide (0.5 μM) either alone or in combination with TEPP46

value: C57BL/6J OT1 mice

value: CD8 T cells


title: Fetal Thymic epithelium 1

value: Thymic epithelium


title: CD8 T cells activated with Ova peptide (0.5 μM) in combination with TEPP46 replicate 2

description: Library name: VV005_S18


title: Old, 24H, 2

description: Library name: Sample_13

value: WT


title: hESC-NRAS-Q61R

description:
oncogene mutation overexpression for 9 days
LM-6


title: IL10-KO rep2


title: hESC-BRAF-V600E

description:
oncogene mutation overexpression for 9 days
LM-5


title: CD8 T cells activated with Ova peptide (0.5 μM) in combination with TEPP46 replicate 1

description: Library name: VV004_S17


title: Old, 24H, 1

description: Library name: Sample_12


title: IL10-KO rep1


title: CD8 T cells activated with Ova peptide (0.5 μM) replicate 3

description: Library name: VV003_S16


title: Old, 12H, 3

description: Library name: Sample_11


title: hESC-KRAS-G12C

description:
oncogene mutation overexpression for 9 days
LM-8


title: CD8 T cells activated with Ova peptide (0.5 μM) replicate 2

description: Library name: VV002_S15


title: WT rep3

value: wild type


title: Old, 12H, 2

description: Library name: Sample_10


title: WT rep2


title: CD8 T cells activated with Ova peptide (0.5 μM) replicate 1

description: Library name: VV001_S14


title: WT rep1


title: hESC-TP53-R273C

description:
oncogene mutation overexpression for 9 days
LM-3


title: hESC-IDH1-R132H

description:
oncogene mutation overexpression for 9 days
LM-2


title: Old, 12H, 1

description: Library name: Sample_9


title: Day_21_male_KO-1

city: Laval

first: Simona

last: Stager

state: Quebec

address: 531 Boul. des Prairies

department: Centre Armand-Frappier

country: Canada

institute: INRS

description: Library name: 6_Day_21_male_KO1

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Adapter sequences and low-quality bases in the resulting FASTQ files were trimmed from raw sequences using Trimmomatic version 0.39 with the following arguments: SE ILLUMINACLIP:TruSeq-SE_adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
Genome alignment was conducted for trimmed reads using HISAT2 version 2.2.1 on the mm10 mouse reference genome assembly.
Expression levels were quantified using strand-aware counting of reads aligning to exonic features using featureCounts (Subread package version 2.0.6) with annotations from GRCm38-Version M10 (Ensembl 85).
Assembly: mm10
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier and strand-aware counts for each genes

source_name: Spleen

growth_protocol: Isolated CD8 T cells from WT and Irf5-/- p14 mice were adoptively transferred into CD45.1 mice one day before infection with LCMV Cl13. Transferred cells were then sorted after 21 days post infection

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing.

treatment_protocol: Cells were sorted.

value: Spleen

value: CD8 T splenocytes

value: LCMV cl13 infection


title: CD8 T cells activated with Ova peptide (0.5 μM) in combination with TEPP46 for 48 hours replicate 4

description: Library name: T60-48-20

data_processing:
RNAseq raw data (fastq or fasq.gz files) quality was checked using FastQC (v0.11.9), and adapter trimming on raw data was performed using Cutadapt (v3.5). Reads with low quality (quality score < 33, error rate > 10%) or short length (<25 bp) after trimming were removed before alignment.
We used the reference genome downloaded from ENSEMBL GRCm38 release 102, and the reference index was built using Star (v2.7.9a) software. Paired end trimmed read alignment and raw read count calculation were performed using RSEM software (v1.3.1).
DESeq2 package (v1.36.0) was used for group wise statistical analysis. We considered the genes with fdr <0.05 differentially expressed.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes normalized count for each sample

source_name: CD8 T cells

extract_protocol:
Total RNA was extracted from cells using RNA isolation kit (Cat# 74104; QIAGEN). 2μg of total RNA was used for RNA sequencing.
RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, 23 Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). NEBNext Ultra II RNA Library Prep Kit (Illumina) was utilized for making RNA libraries and samples were sequenced by a 2x150bp Paired End (PE) configuration.

treatment_protocol: Isolated CD8 T cells from OT1 mice (1.5 ×106 cells per ml) were activated with Ova peptide (0.5 μM) either alone or in combination with TEPP46 at final concentration of 40 and 60 μM or DASA58 (30 μM) in T cell medium supplemented with 30 international units (IU) of IL-2 for 24h and 48h


title: genomic DNA from a FFPE H3K27M-mutant diffuse glioma with a non-midline location

city: Bron

first: Marc

last: Barritault

address: 59 boulevard Pinel

country: France

institute: Hospices Civils de Lyon

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human EPIC DNA methylation Beadchip  using standard Illumina protocol

scan_protocol: Scanning was performed on a nextseq 550 plateform

data_processing: no data processing. Raw intensity files

label: Cy5 and Cy3

source_name: male","brain", "H3K27M glioma", "non-midline location

extract_protocol: genomic DNA was extracted and purified from FFPE sample using Maxwell® RSC RNA FFPE Kit promega

value: glioma

tag: Sex

value: male

value: brain


title: CD8 T cells activated with Ova peptide (0.5 μM) in combination with TEPP46 for 48 hours replicate 3

description: Library name: T60-48-19


title: hESC-empty-vector

description:
oncogene mutation overexpression for 9 days
LM-1

data_processing:
RnBeads package in R environment (v4.1.1)
Average Beta

extract_protocol: Genomic DNA was isolated from the indicated cell populations through standard methods (QIAGEN) according to the manufacturer’s instructions.

value: empty-vector

value: human embryonic stem cells (hESCs)


title: WAT,THBru3

city: Harbin

first: yang

last: shi

address: No.157 Baojian Rd, Harbin, HEILONGJIANG

institute: Harbin medical university

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: white adipose tissue

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: white adipose tissue

tag: diet

value: HFD

value: treated with THBru


title: CD8 T cells activated with Ova peptide (0.5 μM) in combination with TEPP46 for 48 hours replicate 2

description: Library name: T60-48-18


title: STIM1 Kozak library replicate 5 later timepoint

city: Cleveland

first: Kenneth

last: Matreyek

state: OH

address: 2103 Cornell Rd

department: Pathology

institute: Case Western Reserve University

description:
Library name: ML_STIM1_r5_cells2
Supp_table_2_mixed_library_infection.csv

data_processing:
For short-read sequencing generated by the Illumina NextSeq, the forward and reverse reads were paired using PEAR (Zhang et al. 2014). Kozak sequences were counted from the paired reads using Enrich2 (Rubin et al. 2017), and filtered to exclude reads possessing nucleotides with quality scores less than 20. For longer-read sequencing generated by the Illumina MiSeq, generated through submission to the Amplicon-EZ service offered by Genewiz / Azenta, the reads were paired as above, except the paired reads were subsequently processed with a custom Python script “Extract_Kozak.py”, which identified true Kozak library reads from template molecule reads, and for each Kozak read, extracted the Kozak sequence found in that read. All subsequent analyses of the sequencing outputs were performed in R version 4.3.1 (2023-06-16). An R markdown file with code to recreate the analysis (Kozak.Rmd), along with the relevant data files and the various python scripts for the initial processing of FASTQ files, can be found in the MatreyekLab Github repository under “MatreyekLab/Kozak”. A table of the fastq files generated and analyzed for this work is included as Supplementary Table 4. The Kozak sort-seq scores were calculated similarly to previous work (Matreyek et al, 2018, 2021), with some minor changes. For samples sequenced to sufficient read depth, a density-plot of sequence counts normally yields a bimodal distribution, with one peak stemming from a log-normal distribution of counts with a median of 10 or greater, largely reflecting sequences of physical molecules amplified and sequenced from the sample, and a separate peak with a count of 1, largely reflecting sequences derived from sequencing error. We harnessed this property to computationally remove erroneous sequence counts. For each bin, we identified the local minima between these two peaks, and removed sequence counts below this sample-specific threshold value, to yield a dataset of filtered counts. For each sequenced sample, the filtered count of each variant was divided by the sum of counts recorded in that sample to obtain variant-specific frequencies (Fv,bin). For replicates 1 and 2, which both included separately sequenced amplification “technical” replicates derived from the same sorted genomic DNA, the technical replicate frequencies were averaged to yield an average frequency for each variant, which was used as the Fv,bin value. These frequencies were used to calculate a weighted average for each variant for each replicate (Wv,rep), using the following formula.  Wv,rep =(Fv,bin1 0) + (Fv,bin2 (1/3)) + (Fv,bin3 (2/3)) + (Fv,bin4 1)Fv,bin1 + Fv,bin2 + Fv,bin3 + Fv,bin4   Thus, all weighted average values ranged from a value of 0 to 1. Pairwise comparisons of variant-specific weighted averages are shown in Supplementary Fig 2. Once the weighted average values were calculated for each variant for each replicate, they were log10 transformed, averaged, and the base-10 exponential calculated to yield the geometric mean weighted average value. Correspondingly, the standard deviation of the log10 transformed values were calculated and used to calculate the upper and lower 95% confidence intervals, which were later transformed as a base-10 exponential to accompany the geometric mean weighted averages.  To calibrate these weighted averages to MFI equivalent values, we generated cells recombined with ACE2-miRFP670 constructs encoding 16 different Kozak sequences, which were measured for miRFP670 fluorescence intensity using analytical flow cytometry. A linear model was first generated to establish the conversion factor enabling scaling of our weighted average scores to MFI-equivalent values. While accurate for values between 1% and 100% of the consensus Kozak, the linear model performed poorly for extremely high or low values, with the minimum and maximum scaled values being 0.0003 and 3.89; both of these values were outside of the range physically observed with this assay. We thus used logistic regression to approximate the linear model, but furthermore bound all scaled values between 0.004 and 1.34. These resulting values are referred to as the calibrated scores.  Enrichment values for infection experiments were initially filtered similarly to the sort-seq scores, wherein we identified the local minima between the two peaks observed in a density plot representation of sequence counts, and removed sequence counts below his sample-specific threshold value, to yield a dataset of filtered counts. The counts for each variant were divided by the total counts for that sequence sample, to yield sample-specific variant frequencies. For infection samples that included separately sequenced amplification “technical” replicates derived from the same sorted genomic DNA, the geometric means of the technical replicate frequencies were used. Each hygromycin-selected infected sample had a corresponding unselected sample. For each pair, we divided variant-specific frequencies following selection by those prior to selection, obtaining an enrichment ratio. The STIM1 survival scores were calculated similarly, with the exception that the ratio was the quotient of each Kozak variant frequency recombined into cells divided by the frequency of that variant in the sequenced plasmid library.
Assembly: Custom synthetic amplicon
Supplementary files format and content: csv file with calibrated sort-seq scores and infection scores
Supplementary files format and content: csv file with ACE2 variant-specific infection scores

organism: synthetic construct

source_name: HEK 293T

extract_protocol:
Genomic DNA was isolated from each sample using the JetFlex™ Genomic DNA purification kit (Thermo Fisher, A30700).
ACE2 amplicon generation and high throughput sequencing A section of DNA spanning the recombination junction, and including the Kozak sequence preceding the ACE2 open reading frame, was amplified from the genomic DNA extracts using PCR. For each 50 µL PCR reaction, the following components were used: 2 µg genomic DNA (quantified by nanodrop), 0.25 µM  forward primer containing i7 index barcode and 0.25 µM  reverse primer containing i5 index barcode, and 25 µL of Phusion plus high fidelity PCR mix (Thermo Fisher, F548L). A total of five PCR reactions were performed per condition, which each tube initially incubated at 95 °C for 3 minutes, followed by 25 cycles of 95 °C for 15 seconds, 60 °C for 15 seconds, 72 °C for 30 seconds, followed by a final 72 °C incubation for 1 minute. PCR products were mixed with 6x DNA loading dye (NEB, B7024S) and separated on 1.5% agarose TAE gel. Bands corresponding to the expected 293 bp amplicon size were excised and extracted using the Freeze and Squeeze kit according to the manufacturer’s instructions (Bio-Rad, 7326166). Eluted PCR products were purified using a Zymo clean and concentrator kit (Zymo Research, D4003). Amplicon concentrations were measured using Qubit dsDNA BR assay kit (Life technologies, Q32853). Amplicons from all the experimental conditions were pooled in equimolar ratios and sequenced on an Illumina NextSeq550 with a 75-cycle high output kit. Oligonucleotide sequences for PCR and custom Illumina primers for sequencing are listed in Supplementary Table 3.

value: HEK 293T

value: G542Ac3 landing pad


title: Day_21_male_WT-1

description: Library name: 5_Day_21_male_WT1


title: Day_21_male_KO-4

description: Library name: 20_Day_21_male_KO4


title: WAT,THBru2


title: WAT,THBru1


title: CD8 T cells activated with Ova peptide (0.5 μM) in combination with TEPP46 for 48 hours replicate 1

description: Library name: T60-48-17

value: C57BL/6J OT1 mice

value: CD8 T cells


title: STIM1 Kozak library replicate 5 earlier timepoint

description:
Library name: ML_STIM1_r5_cells1
Supp_table_2_mixed_library_infection.csv


title: Day_21_male_WT-4

description: Library name: 19_Day_21_male_WT4

value: WT


title: hESC-SOX17-S403I

first: Lingjun

institute: Stanford University

description:
oncogene mutation overexpression for 9 days
LM-4


title: WAT,HFD3

value: without THBru


title: STIM1 Kozak library unexpressed replicate 5

description:
Library name: ML_STIM1_r5_none
Supp_table_2_mixed_library_infection.csv


title: CD8 T cells activated with Ova peptide (0.5 μM) in combination with TEPP46 for 24 hours replicate 4

description: Library name: T60-24-9


title: WAT,HFD2


title: STIM1 Kozak library replicate 4 later timepoint

description:
Library name: ML_STIM1_r4_cells2
Supp_table_2_mixed_library_infection.csv


title: Day_21_female_WT-3

description: Library name: 15_Day_21_female_WT3

value: Spleen


title: Day_21_female_KO-3

description: Library name: 16_Day_21_female_KO3

value: CD8 T splenocytes


title: CD8 T cells activated with Ova peptide (0.5 μM) in combination with TEPP46 for 24 hours replicate 3

description: Library name: T60-24-12


title: STIM1 Kozak library replicate 4 earlier timepoint

description:
Library name: ML_STIM1_r4_cells1
Supp_table_2_mixed_library_infection.csv


title: Day_21_female_KO-2

description: Library name: 12_Day_21_female_KO2

value: LCMV cl13 infection


title: CD8 T cells activated with Ova peptide (0.5 μM) in combination with TEPP46 for 24 hours replicate 2

description: Library name: T60-24-11


title: CD8 T cells activated with Ova peptide (0.5 μM) for 48 hours replicate 4

description: Library name: O-48-16


title: Retina, mouse, P18, hyperoxia, IC100, animal 11

city: Miami

first: Augusto

middle: F

last: Schmidt

state: FL

address: 1611 NW 12th ave

institute: University of Miami Miller School of Medicine

data_processing:
Alignment with mouse genome version mmGRCm39.104 genome build with Kallisto
Gene summarization and feature counts with tximport
Differental expression with DESeq2
Assembly: mmGRCm39.104
Supplementary files format and content: Read counts summarized at gene level using tximport

source_name: retina

growth_protocol: C57BL/6J mice at P7 were exposed to 75% O2 along with nursing mothers in a closed and regulated chamber for 5 days. The mothers were rotated between room air and oxygen every other day. Mice were returned to room air at P12.

extract_protocol:
Total RNA was extracted from tissue homogenates with QIAGEN Rneasy kit per manufacturer's intructions
Afer polyA selection, paired-end RNA-sequencing with 150bp was done with a depth of 30M reads.

treatment_protocol: Animals were treated with placebo (PBS) or IC100 10 µg/g intraperitoneally on P12, P14, and P16

value: retina

tag: exposure

value: Hyperoxia 75% P7-P12

value: C57BL/6J wildtype


title: Mixed library SARS-CoV-2 spike pseudotyped virus selected replicate 6

description:
Library name: ML_SARS2_r6_sel
Supp_table_2_mixed_library_infection.csv


title: CD8 T cells activated with Ova peptide (0.5 μM) in combination with TEPP46 for 24 hours replicate 1

description: Library name: T60-24-10


title: Retina, mouse, P18, hyperoxia, IC100, animal 10


title: CD8 T cells activated with Ova peptide (0.5 μM) for 48 hours replicate 3

description: Library name: O-48-15


title: Mixed library SARS-CoV-2 spike pseudotyped virus selected replicate 5

description:
Library name: ML_SARS2_r5_sel
Supp_table_2_mixed_library_infection.csv


title: CD8 T cells activated with Ova peptide (0.5 μM) for 48 hours replicate 2

description: Library name: O-48-14


title: Retina, mouse, P18, hyperoxia, IC100, animal 9


title: Mixed library SARS-CoV-2 spike pseudotyped virus selected replicate 4

description:
Library name: ML_SARS2_r4_sel
Supp_table_2_mixed_library_infection.csv


title: Beta-cells from Pseudo-beta 37 (n=3)

city: Paris

first: Alexis

last: Fouque

address: 123 boulevard de Port-Royal

institute: Inserm

description: Library name: 321718_Ech6-Pseudo-B37

data_processing:
Fastq files were then aligned using STAR algorithm (version 2.7.6a), on the Ensembl Mus musculus GRCm38 reference, release 101
Reads were then count using RSEM (v1.3.1) and the statistical analyses on the read counts were performed with R (version 3.6.3) and the DESeq2 package (DESeq2_1.26.0) to determine the proportion of differentially expressed genes between two conditions
We used the standard DESeq2 normalization method (DESeq2’s median of ratios with the DESeq function), with a pre-filter of reads and genes (reads uniquely mapped on the genome, or up to 10 different loci with a count adjustement, and genes with at least 10 reads in at least 3 different samples).
Following the package recommendations, we used the Wald test with the contrast function and the Benjamini-Hochberg FDR control procedure to identify the differentially expressed genes
R scripts and parameters are availables on the plateform, release v1.202112.
Assembly: Mus musculus GRCm38
Supplementary files format and content: tsv files includes normalized reads value for each sample

source_name: Pancreas

growth_protocol: Reaggregation on mouse pancreatic endocrine cells was performed in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics for 5 days in an incubator at 37°C and 5% CO2

extract_protocol:
RNA was harvested using the RNeasy Micro Kit (Qiagen) and 5 ng of total RNA was used for the construction of sequencing libraries
RNA libraries for RNAseq were prepared using Ovation solo RNA-seq kit following manufacturer’s protocols

treatment_protocol: Mouse pancreatic beta-cells were reaggregated for 5 days either with all the other endocrine cell types or alone

value: Pancreas

value: pancreatic endocrine-cells

value: beta-cells

value: Beta-cells cultured alone

tag: time

value: Day 5


title: Beta-cells from Pseudo-beta 36 (n=2)

description: Library name: 321702_Ech4-Pseudo-B36


title: Retina, mouse, P18, hyperoxia, placebo, animal 8

value: Placebo


title: Mixed library SARS-CoV-2 spike pseudotyped virus selected replicate 3

description:
Library name: ML_SARS2_r3_sel
Supp_table_2_mixed_library_infection.csv

value: HEK 293T

value: G542Ac3 landing pad


title: Day_21_female_WT-2

description: Library name: 11_Day_21_female_WT2


title: CD8 T cells activated with Ova peptide (0.5 μM) for 48 hours replicate 1

description: Library name: O-48-13

value: C57BL/6J OT1 mice

value: CD8 T cells


title: Beta-cells from Pseudo-islets 37 (n=3)

description: Library name: 321710_Ech5-Pseudo-Total37

value: WT

value: Beta-cells cultured with all endocrine cell types


title: Retina, mouse, P18, hyperoxia, placebo, animal 7


title: WAT,HFD1

value: white adipose tissue

value: HFD

value: without THBru


title: CD8 T cells activated with Ova peptide (0.5 μM) for 24 hours replicate 4

description: Library name: O-24-8


title: Retina, mouse, P18, hyperoxia, IC100, animal 12

value: retina

value: Hyperoxia 75% P7-P12


title: Retina, mouse, P18, hyperoxia, placebo, animal 6

value: C57BL/6J wildtype


title: Beta-cells from Pseudo-islets 35 (n=1)

description: Library name: 321678_Ech1-Pseudo-Total35

value: Pancreas

value: pancreatic endocrine-cells


title: Retina, mouse, P18, hyperoxia, placebo, animal 5


title: Mixed library SARS-CoV-2 spike pseudotyped virus selected replicate 1

description:
Library name: ML_SARS2_r1_sel
Supp_table_2_mixed_library_infection.csv


title: STIM1 Kozak library unexpressed replicate 4

description:
Library name: ML_STIM1_r4_none
Supp_table_2_mixed_library_infection.csv


title: CD8 T cells activated with Ova peptide (0.5 μM) for 24 hours replicate 2

description: Library name: O-24-6


title: CD8 T cells activated with Ova peptide (0.5 μM) for 24 hours replicate 3

description: Library name: O-24-7


title: LL_3_4

city: Groningen

first: Bart

middle: J L

last: Eggen

address: Antonius Deusinglaan 2

country: Netherlands

institute: University Medical Center Groningen

data_processing:
ATAC-sequencing paired-end reads (FASTQ) were pre-processed using the official ENCODE ATAC-seq pipeline v2.2.2 (https://github.com/ENCODE-DCC/atac-seq-pipeline) (Dunham et al., 2012), using Python (v3.7.6) and Java (OpenJDK 17). This pipeline executes a number of programs to process and align sequencing reads and to generate quality control statistics.
In brief, FASTQ-files were trimmed with cutadapt (v1.9.1) and aligned with Bowtie2 (v2.2.6) (Langmead et al., 2009) to the mouse GRCm38/mm10 reference genome.
SAMtools (v1.7) and SAMstats (v0.2.1) (Li et al., 2009), MarkDuplicates (Picard v1.126), and bedtools (v2.26)  (Quinlan, 2014) were used to filter and clean data post-alignment.
MACS2 (v2.1.1) (Zhang et al., 2008) was used for peak calling.
The ATAC-seq pipeline also runs Irreproducible Discovery Rate (IDR) to detect peaks with high reproducibility (Li et al., 2011) using phantompeakqualtools (v1.2.1) (Kharchenko et al., 2008) and deeptools (v3.3.0) (Ramírez et al., 2016). The optimal peak sets that came out of these pipelines were used for downstream analysis.
HOMER (v4.9.1) (Heinz et al., 2010) was used to make tag directories. Quantification of ATAC-seq signal at peaks merged for all samples was performed using the HOMER annotatePeaks function. ATAC-seq peaks were annotated using annotatePeak function from ChIPseeker package (v1.38) (Yu et al., 2015) in R using TxDb.Mmusculus.UCSC.mm10.knownGene reference genome.
Assembly: mouse genome (GRCm38/mm10)
Supplementary files format and content: comma separated values (csv) file with metadata table for samples
Supplementary files format and content: comma separated values (csv) file with gene raw count data for each sample

source_name: brain

growth_protocol: Microglia were isolated as previously described (Galatro et al., 2017b). After transcardiac perfusion with PBS, brains were removed from the skull and kept in cold medium A (HBSS (Gibco, 14170-088) with 0.6% glucose (Sigma, G8769) and 7.5 mM HEPES (Lonza, BE17-737E)). The olfactory bulbs were removed prior to mechanical dissociation of the tissue. All subsequent steps were performed on ice, and centrifugation was at 4°C. Brains were dissociated using a glass Potter–Elvehjem tissue homogenizer until a single cell suspension was obtained and filtered through a 70 µm cell strainer (Corning, 21008-950), to obtain a total cell suspension of 15 mL in medium A. Cells were pelleted by centrifugation at 300 RCF for 10 minutes. Myelin was removed by 24% Percoll (Fisher Scientific, 17-0891-01) in medium A (1x final concentration) and PBS density gradient centrifugation for 20 minutes at 950 RCF with brakes off. The microglia enriched cell pellet was resuspended in medium A and incubated with CD11b-PE (1:166 dilution, clone M1/70, eBiosciences, 12-0112-82), CD45-FITC (1:200 dilution, clone 30-F11, eBiosciences, 11-0451-82), and Ly6c-APC (1:133 dilution, clone HK1.4, Biolegend, 128016) antibodies for 30 min on ice. The cells were then washed once in medium A without phenol red and passed through a 35-μm nylon mesh, collected in fluorescence-activated cell sorting (FACS) round bottom tubes (Corning, 352235). Immediately before sorting, 1 µL of DAPI (200 µg/mL stock solution) per 100 µL cell suspension was added to the samples (final concentration 0.2 µg/mL). Microglia were sorted by gating single DAPInegCD11bhighCD45intLy6cneg events (Sup Fig 3 A) using the Beckman Coulter MoFlo Astrios or MoFlo XDP FACS sorters. Sorted microglia were collected in siliconized polypropylene microcentrifuge tubes (Sigma, T3406-250EA) containing medium A for further RNA extraction (RNA-seq) or assay for transposase-accessible chromatin (ATAC).

extract_protocol:
ATAC-sequencing libraries were generated using Nextera® DNA Sample Preparation Kit (Illumina, FC-121-1030) following methods previously described (Buenrostro et al., 2015, 2013). A total number of 80,000 microglia were pooled from two animals (40,000 cells from each) and collected in siliconized microcentrifuge tubes (Sigma, T3406-250EA) containing 300 µL medium A. For each group, at least two pools of two mice each were processed. Cells were pelleted by centrifugation (10 min, 4°C, 500×g), resuspended in 50 μL of cold lysis buffer (10 mM Tris–HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged as before. Next, nuclei were resuspended in 50 μL transposition reaction mix (1 × TD reaction buffer, 2.5 μL TN5 transposase) (Illumina, 20034197) and incubated at 37 °C for 30 min. Immediately following transposition, the DNA was purified using a minElute PCR purification kit (Qiagen, 28004) following the manufacturer’s instructions.
The transposed DNA fragments were further amplified and barcoded (Buenrostro et al., 2015, 2013) and purified with a ChIP DNA Clean and Concentrator kit (Zymo, D5205). The fragments were run on 2% E-Gel™ EX agarose gels (Thermo Fisher Scientific, G521802), and 150–550 bp fragments were excised, followed by purification with Zymoclean™ Gel DNA Recovery Kit (Zymo, D4007). Library concentration was determined with Qubit dsDNA HS kit (Thermo Fisher Scientific, Q33230) and confirmed with Agilent 4200 TapeStation System, after which the 13 samples were pooled and sequenced using NextSeq 500/550 Kit v2.5 (92 cycles) using paired-end reads on a NextSeq500 (Illumina).

treatment_protocol: C57BL/6J (Envigo) mice were used in the model for recurrent lipopolysaccharides (LPS)-induced peripheral inflammation and a cycle of enforced microglia repopulation (Fig 1 A, Fig 2 A). Animals were housed in standard macrolon cages with open tops, with ad libitum access to water and food, in a 12h dark/light cycle (lights on 8:00 am). All animal procedures were approved by the national authority for scientific procedures on animals (Centrale Commissie Dierproeven, CCD) and performed per ethical regulations (CCD license number AVD105002015360). Animals were group-housed throughout the experiment, with an acclimatization period of two weeks before the start of the experiment. 10-week-old male mice were challenged with 1 mg/kg intraperitoneal (i.p.) LPS from Escherichia coli O111:B4 (Sigma-Aldrich, L4391) and were housed in warming cabinets  (26 C) for the following two to three days until body weight returned to baseline. For unchallenged (PP, PBP) and naïve (PL, PBL) mice, sham injections consisted of the same volume/body mass of Dulbecco’s phosphate-buffered saline (DPBS) (Gibco, 14190-144). A week after the first challenge, microglia depletion was induced by colony-stimulating factor 1 receptor (CSF1R) inhibition for five days. Microglia depletion was established with daily administration via oral gavage of the CSF1R inhibitor (CSF1Ri) 4-((2-(((1R,2R)-2-hydroxycyclohexyl)amino)benzo[d]thiazol-6-yl)oxy)-N-methylpicolinamide (BLZ945 or Sotuletinib) (kindly provided by Novartis) at a dosage of 169 mg/kg per day (total cumulative dose of 845 mg/kg over the five days). Control (non-depleted) animals were treated with the same volume/body mass of vehicle containing 20% (w/v) 2-hydroxypropyl-beta-cyclodextrin (HPβCD). For the pilot experiment (Fig 1), mice were sacrificed on day 5 of BLZ945 treatment or 10 days after BLZ945 withdrawal (5 d + 10 d). For the main experiment (Fig 2 A), five weeks after the initial challenge, mice were similarly re-challenged with 1 mg/kg LPS (i.p.) and housed in warming cabinets for three hours before transcardiac perfusion under deep anesthesia (4% isoflurane with 7.5% O2) with cold saline (DPBS) and brain tissue collection. 80000 microglia cells (40000 cells from each two mice of the same group) were isolated via FACS and followed by chromatin transposition and library preparation for ATAC-seq.

value: brain

tag: age (weeks)

value: male

value: microglia

tag: challenge

value: vehicle

tag: facs sorter

value: XDP


title: Mixed library SARS-CoV spike pseudotyped virus selected replicate 6

description:
Library name: ML_SARS1_r6_sel
Supp_table_2_mixed_library_infection.csv

value: HEK 293T

value: G542Ac3 landing pad


title: CD8 T cells activated with Ova peptide (0.5 μM) for 24 hours replicate 1

description: Library name: O-24-5

tag: strain

value: C57BL/6J OT1 mice

value: CD8 T cells


title: Mixed library SARS-CoV spike pseudotyped virus selected replicate 5

description:
Library name: ML_SARS1_r5_sel
Supp_table_2_mixed_library_infection.csv

tag: cell line


title: Beta-cells from Pseudo-beta 35 (n=1)

description: Library name: 321686_Ech2-Pseudo-B35

tag: tissue

tag: cell type

value: beta-cells

tag: genotype

value: WT

value: Beta-cells cultured alone

value: Day 5


title: LL_1_2

tag: treatment


title: Retina, mouse, P18, room air, PBS, animal 3

value: retina

value: Room air

value: Placebo


title: CD8 T cells supplemented with 30 international units (IU) of IL-2 for 24 hours replicate 4

description: Library name: IL2-24-4


title: CD8 T cells supplemented with 30 international units (IU) of IL-2 for 24 hours replicate 3

description: Library name: IL2-24-3


title: LBL_3_4


title: Retina, mouse, P18, room air, PBS, animal 2

value: C57BL/6J wildtype


title: Mixed library SARS-CoV spike pseudotyped virus selected replicate 4

description:
Library name: ML_SARS1_r4_sel
Supp_table_2_mixed_library_infection.csv


title: LBL_1_2

value: brain


title: Retina, mouse, P18, room air, PBS, animal 1


title: Mixed library SARS-CoV spike pseudotyped virus selected replicate 3

description:
Library name: ML_SARS1_r3_sel
Supp_table_2_mixed_library_infection.csv


title: Mixed library SARS-CoV-2 spike pseudotyped virus selected replicate 2

description:
Library name: ML_SARS2_r2_sel
Supp_table_2_mixed_library_infection.csv


title: PL_3_4

value: male

value: Astrios


title: Beta-cells from Pseudo-islets 36 (n=2)

description: Library name: 321694_Ech3-Pseudo-Total36

value: Pancreas

value: pancreatic endocrine-cells

value: Beta-cells cultured with all endocrine cell types


title: CD8 T cells supplemented with 30 international units (IU) of IL-2 for 24 hours replicate 2

description: Library name: IL2-24-2


title: KCSox4KO - day 14 Caerulein

city: Copenhagen

first: Luis

last: Arnes

address: Ole Maaløes Vej 5

country: Denmark

institute: Biotech Research & Innovation Centre

description: 10X Genomics

library_source: other

data_processing:
Raw base call (BCL) files generated by Illumina sequencers were demultiplexed into FASTQ files using 10X Genomics’ Single-Cell Gene Expression Software Cell Ranger version 7.2.0 (“mkfastq” pipeline, default parameters). The nf-core sc-rnaseq pipeline, version 2.4.1 was selected to perform a best-practice analysis pipeline for processing 10x Genomics single-cell RNA-seq data. 10x Genomics provided the reference genome sequenced: Mouse reference (mm10) - 2020-A
Assembly: mm10
Supplementary files format and content: Tab-separeted values files and matrixes files
Supplementary files format and content: Tab-separeted values files and matrixes files (barcode, gene, count)

molecule: other

extract_protocol:
LSL-KrasG12D (MGI:2429948), Ptf1aCreER (MGI:3771322), R26RYFP (MGI:2449038), and Sox4flox (MGI:3773012) mouse strains were used for breeding. Mice were maintained on a genetically mixed background. Tamoxifen (T5648; Sigma-Aldrich) was administered through intraperitoneal injections every other day for 5 days (e.g., Monday, Wednesday, Friday) at a dose of 3mg per injection. Tamoxifen was dissolved in corn oil (C8267; Sigma-Aldrich) at a stock concentration of 30mg/ml (100l/injection). A standard wash-out of 2 weeks was performed. To induce tissue injury in the pancreas, the cholecystokinin analogue caerulein (C9026; Sigma-Aldrich) was administered through intraperitoneal injections every hour for 7 hours (8 injections/day) on 2 consecutive days at a concentration of 125g/kg body weight. Control mice were injected with equivalent volume of PBS following the same protocol. Pancreas tissue was finely chopped with scissors in digestion buffer (1mg/ml Collagenase (C9407-1G, Sigma-Aldrich), 1mg/ml DNase I (Sigma-Aldrich, 11284932001), 0,1mg/ml soybean trypsin inhibitor (STI, Fisher Scientific, 17-075-029) dissolved in Hank´s balanced salt solution (HBSS)). Digestion was performed in gentleMACS C Tubes using mTDK1 program on a gentleMACS™ Dissociator (Miltenyi Biotec). Reaction was stopped with STOP buffer (1mg/ml DNase I (Sigma-Aldrich, 11284932001), 0,1mg/ml STI and 5% Fetal bovine serum (FBS) dissolved in HBSS). Digested tissue was centrifuged 5 minutes at 2000 rpm and resuspended in 3 ml RBC lysis buffer (Thermo Scientific, 00-4333-57). After 2 minutes incubation cells were washed with STOP buffer twice and filtered through a 40 µm cell strainer. Cells were further processed for single cell sequencing.
Library was performed according to the manufacture's instruction (Single cell v3.1 Chemistry Dual Index, Dual Index Kit TT Set A, 96 rxns PN-100021510X genomics)

value: Not applicable

value: All pancreatic cell types

value: Ptf1aCreER; lsl-KrasG12D; Sox4fl/fl; lsl-YFP

value: Caerulein


title: CD8 T cells supplemented with 30 international units (IU) of IL-2 for 24 hours replicate 1

description: Library name: IL2-24-1

value: C57BL/6J OT1 mice

value: CD8 T cells


title: Mixed library VSVG pseudotyped virus selected replicate 4

description:
Library name: ML_VSVG_r4_sel
Supp_table_2_mixed_library_infection.csv

value: HEK 293T

value: G542Ac3 landing pad


title: Retina, mouse, P18, room air, PBS, animal 4

value: retina

value: Room air


title: upec-ace2

city: ZhengZhou

first: Ming

address: jianshe Road

institute: ZhengZhou university

data_processing:
these libraries were sequenced on an Illumina sequencing platform, and 125-bp/150-bp paired-end reads were generated
Assembly: mm10

extract_protocol:
the cells were collected in RNAiso Plus reagent for RNA isolation
RNA samples were then converted into libraries of cDNA fragments using the TruSeq Stranded mRNA LTSample Prep Kit

value: testis

value: testicular macrophage


title: PBL_4_5

value: brain

value: male

value: microglia

value: XDP


title: KCSox4KO - day 2 Caerulein

description: 10X Genomics

value: Pancreas


title: CSox4KO - day 2 Caerulein

description: 10X Genomics

value: Not applicable

value: Ptf1aCreER; Sox4fl/fl; lsl-YFP


title: Mixed library SARS-CoV spike pseudotyped virus selected replicate 1

description:
Library name: ML_SARS1_r1_sel
Supp_table_2_mixed_library_infection.csv


title: upec-ace1


title: PBL_3_4


title: upec2


title: PBL_1_2


title: Mixed library VSVG pseudotyped virus selected replicate 2

description:
Library name: ML_VSVG_r2_sel
Supp_table_2_mixed_library_infection.csv


title: PL_1_2

value: vehicle

value: Astrios


title: CSox4WT - day 2 Caerulein

description: 10X Genomics

value: All pancreatic cell types

value: Ptf1aCreER; lsl-YFP

value: Caerulein


title: Mixed library VSVG pseudotyped virus selected replicate 3

description:
Library name: ML_VSVG_r3_sel
Supp_table_2_mixed_library_infection.csv

value: HEK 293T

value: G542Ac3 landing pad


title: Mixed library SARS-CoV spike pseudotyped virus selected replicate 2

description:
Library name: ML_SARS1_r2_sel
Supp_table_2_mixed_library_infection.csv


title: Mixed library VSVG pseudotyped virus selected replicate 1

description:
Library name: ML_VSVG_r1_sel
Supp_table_2_mixed_library_infection.csv


title: PP_3_4


title: upec1


title: ChIP-seq_RAW264.7_macroH2AS139A_LPS_SPT16_rep2

city: beijing

first: ji

last: dengyu

address: 10 Xitoutiao, Youanmen, Fengtai District

institute: Capital Medical Universit

data_processing:
ChIP-seq: the ChIP-seq data were mapped to the Mus musculus (mm10) and D. melanogaster genome assembly (dm6) using bowtie2 with the default parameters.
Assembly: mm10
Supplementary files format and content: WIG

growth_protocol: MDA-MB-231 cells were infected with lentivirus, and stable cell lines were generated by puromycin (1 μg/mL) selection

extract_protocol:
The cells were crosslinked in adherent conditions with 1% formaldehyde for 15 min at room temperature and quenched with glycine to a final concentration of 125 nM. Fixed cells were lysed in nuclei lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS, protease inhibitors) to extract nuclei and sheared by sonication to 200-500-bp-sized fragments. Sheared chromatin was incubated with rabbit anti-HA antibodies (Abcam, ab9110, 3 μg) and protein A/G-Dynabeads (Life Technology, 10 μl) for 12 hours at 4 ℃. The beads were washed with RIPA150 (50 mMTris-HCl, pH 8.0,150 mM NaCl, 1 mM EDTA, pH 8.0, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate), RIPA500 (50 mM Tris-HCl, pH 8.0, 0.5 M NaCl,1 mM EDTA, pH 8.0, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate), RIPA-LiCl (50 mM Tris-HCl, pH 8.0, 1 mM EDTA, 1% NP-40, 0.7% sodium deoxycholate, 0.5 M LiCl) and TE buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA), respectively. The beads were resuspended with NLB buffer (10 mM Tris-HCl, pH 8.0, 300 mM NaCl, 5 mM EDTA, 0.5% SDS). After de-crosslinked at 65 ℃ for 6 hours, DNA fragments were digested with RNase A and proteinase K. Purified DNA fragments were generated libraries followed by high throughput sequencing using Illumina Novaseq6000.
Purified DNA fragments were generated libraries followed by high throughput sequencing using Illumina Novaseq6000.

value: macrophage


title: ctrl2

value: testis


title: Mixed library unselected replicate 7

description:
Library name: ML_VSVG_neg2
Supp_table_2_mixed_library_infection.csv


title: PP_1_2


title: ChIP-seq_RAW264.7_macroH2AS139A_LPS_SPT16_rep1


title: ctrl1

value: testicular macrophage


title: Mixed library unselected replicate 6

description:
Library name: ML_VSVG_neg1
Supp_table_2_mixed_library_infection.csv


title: ChIP-seq_RAW264.7_macroH2A_LPS_SPT16_rep2


title: Wild-type mouse, neuron, stroke, biol rep 8

city: Los Angeles

first: Yutaro

last: Komuro

address: 635 Charles E Young Dr S

department: Neurology

institute: University of California Los Angeles

data_processing:
Quality of sequencing was assessed using FastQC, followed by read alignment with STAR aligner.
The mm10 reference genome was used.
Following alignment, counts were read using htseq-count.
Differential gene expression was performed using DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw counts for each sample

source_name: Brain

extract_protocol:
RNA was extracted using the Rneasy conventional RNA preparation kit from Qiagen.
RNA libraries were prepared using the NuGEN Ovation Ultralow system with KAPA HyperPrep.

value: Brain

value: neuron

value: WT

value: stroke


title: PBP_3_4

value: brain

value: male

value: microglia


title: Mixed library unselected replicate 5

description:
Library name: ML_r34_neg
Supp_table_2_mixed_library_infection.csv


title: ChIP-seq_RAW264.7_macroH2A_LPS_SPT16_rep1


title: PBP_1_2


title: CSox4WT - PBS

description: 10X Genomics

value: Pancreas

value: Not applicable

value: PBS


title: ChIP-seq_RAW264.7_macroH2AS139A.siFACT_LPS_HA_rep2

value: HA


title: Spheroid_BMI1_GFP_3

city: Portland

first: Guanming

last: Wu

state: OR

address: 3181 S.W. Sam Jackson Park Road

institute: OHSU

data_processing:
Reads were aligned using bwa-mem
Aligned reads were deduplicated using samtools rmdup
Bam files were generated for merged replicates
Peaks were called on merged replicates as well as individual replicates
All called peaks were merged to generate the all_peaks master peak set
Assembly: mm10
Supplementary files format and content: bed files containing called peaks

source_name: Murine intestinal epithelial cells

extract_protocol:
Nuclei were extracted using nuclei isolaiton buffer (NIB)
Tagmentation on isolated nuclei was performed using Illumina Nextera reagents

value: Murine intestinal epithelial cells


title: Wild-type mouse, neuron, stroke, biol rep 6


title: Mixed library unselected replicate 3

description:
Library name: ML_r3_neg
Supp_table_2_mixed_library_infection.csv

value: HEK 293T


title: Spheroid_BMI1_GFP_2


title: Wild-type mouse, neuron, stroke, biol rep 5


title: Lgr5_GFP_2


title: ChIP-seq_RAW264.7_macroH2AS139A.siFACT_LPS_HA_rep1


title: Mixed library unselected replicate 2

description:
Library name: ML_r2_neg
Supp_table_2_mixed_library_infection.csv

value: G542Ac3 landing pad


title: ChIP-seq_RAW264.7_macroH2A.siFACT_LPS_HA_rep2

value: macrophage


title: Wild-type mouse, neuron, stroke, biol rep 4


title: Mixed library unselected replicate 1

description:
Library name: ML_r1_neg
Supp_table_2_mixed_library_infection.csv


title: Wild-type mouse, neuron, stroke, biol rep 3


title: Lgr5_GFP_1


title: ChIP-seq_RAW264.7_macroH2A.siFACT_LPS_HA_rep1


title: ChIP-seq_RAW264.7_macroH2AS139A_LPS_HA_rep2


title: Enteroid_Igr5_GFP_3


title: Wild-type mouse, neuron, stroke, biol rep 2


title: SARS-CoV-2 spike pseudotyped virus selected replicate 7

description:
Library name: SARS2_r7
Supp_table_1_kozak_sortseq_and_infection.csv


title: Enteroid_Igr5_GFP_2


title: Wild-type mouse, neuron, stroke, biol rep 1


title: ChIP-seq_RAW264.7_macroH2AS139A_LPS_HA_rep1


title: Wild-type mouse, neuron, stroke, biol rep 7


title: Enteroid_Igr5_GFP_1


title: Mixed library unselected replicate 4

description:
Library name: ML_r4_neg
Supp_table_2_mixed_library_infection.csv


title: Sarm1 -/- mouse, neuron, stroke, biol rep 7

value: Sarm1 -/-


title: SARS-CoV-2 spike pseudotyped virus selected replicate 6

description:
Library name: SARS2_r6
Supp_table_1_kozak_sortseq_and_infection.csv


title: SARS-CoV-2 spike pseudotyped virus selected replicate 4

description:
Library name: SARS2_r4
Supp_table_1_kozak_sortseq_and_infection.csv


title: Sarm1 -/- mouse, neuron, stroke, biol rep 6


title: SARS-CoV-2 spike pseudotyped virus selected replicate 5

description:
Library name: SARS2_r5
Supp_table_1_kozak_sortseq_and_infection.csv


title: ChIP-seq_RAW264.7_macroH2A_LPS_HA_rep1


title: E17.5_EpCam_4


title: Sarm1 -/- mouse, neuron, stroke, biol rep 5


title: ChIP-seq_RAW264.7_macroH2AS139A_SPT16_rep2


title: ChIP-seq_RAW264.7_macroH2AS139A_SPT16_rep1


title: SARS-CoV-2 spike pseudotyped virus selected replicate 8

description:
Library name: SARS2_r8
Supp_table_1_kozak_sortseq_and_infection.csv


title: SARS-CoV-2 spike pseudotyped virus selected replicate 3

description:
Library name: SARS2_r3
Supp_table_1_kozak_sortseq_and_infection.csv


title: SARS-CoV-2 spike pseudotyped virus selected replicate 2

description:
Library name: SARS2_r2
Supp_table_1_kozak_sortseq_and_infection.csv


title: E17.5_EpCam_2


title: E17.5_EpCam_1


title: E17.5_EpCam_3