title: Consortium_0dpi_037_RNA_Ln3

description: Library name: Consortium_0dpi_037_RNA_Ln3

value: Consortium


title: WT Liver NK cells, Control, Day3 2

status: Public on Jan 30 2026

type: SRA

city: Hiroshima

first: Tomoaki

last: Bekki

address: Kasumi1-2-3, Minamiku

country: Japan

institute: Hiroshima University

description:
Library name: Sample2
T0000-942

library_source: transcriptomic

data_processing:
Raw sequence reads were aligned to the [insert reference genome, e.g., GRCm39] reference genome using the Illumina DRAGEN Bio-IT Platform (version 4.3.6). Gene- and transcript-level expression abundances were quantified based on the genomic mapping coordinates and the [insert gene annotation, e.g., GENCODE vM33] gene definition file.
Assembly: mm10
Supplementary files format and content: TV0419_gene_expression.txt

molecule: total RNA

organism: Mus musculus

source_name: Liver NK cells

extract_protocol:
Total RNA was extracted from murine liver NK cells using the RNeasy Mini Kit (Qiagen, Venlo, Netherlands).
RNA libraries for RNA-seq were prepared using SMART-seq mRNA following manufacture's protocols.

treatment_protocol: Liver NK cells change was induced by metformin (200mg/kg) treatment for three days.

tag: cell type

value: immune cells

value: Liver NK cells

tag: genotype

value: WT

tag: treatment

value: PBS


title: Nasopharyngeal sample – TN_335_286

city: Santiago

first: mario

middle: Alberto

last: maulen

state: Región Metropolitana

address: Amunategui 425, depto 31

department: Facultad de Ingenieria

country: Chile

institute: Universidad San Sebastian

description:
Library name: TN_335_286
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.

library_source: genomic

data_processing:
Raw FASTQ files were demultiplexed using MetaScope v4.1.
Reads were processed with DADA2 (R v4.1.2) for quality filtering, dereplication, denoising, paired-end merging, and chimera removal.
Amplicon sequence variants (ASVs) were inferred using DADA2 default error-modeling parameters.
Taxonomic assignment of ASVs was performed with the SILVA v138 database.
ASV table, taxonomic annotations, and sample metadata were integrated into a phyloseq object (phyloseq R package) for downstream analysis.
Assembly: Not applicable (amplicon sequencing of bacterial 16S rRNA gene; no genome build used).
Supplementary files format and content: Processed data files consist of a tab-delimited ASV abundance matrix, a taxonomy annotation table, sample metadata, and a FASTA file containing ASV sequences. These files represent the fully processed outputs of the DADA2 pipeline and the final dataset used for microbial community and downstream statistical analyses. All files are provided in open, text-based formats.
Library strategy: 16S rRNA-seq

molecule: genomic DNA

organism: human metagenome

source_name: nasopharyngeal swab

extract_protocol:
Total nucleic acids were extracted from nasopharyngeal swab samples using the Mag-Bind® Viral DNA/RNA 96 Kit (Omega Bio-Tek) following the manufacturer’s protocol. Samples were stored at −80 °C prior to extraction.
The V3–V4 hypervariable region of the bacterial 16S rRNA gene was amplified using primers 515F (5′-GTGCCAGCMGCCGCGGTAA-3′) and 806R (5′-GGACTACHVGGGTWTCTAAT-3′). Amplicons were prepared for sequencing using Illumina MiSeq library construction workflows by the Environmental Sample Preparation and Sequencing Facility (Argonne National Laboratory). Sequencing was performed using Illumina MiSeq paired-end chemistry.

tag: tissue

value: nasopharyngeal swab


title: Nasopharyngeal sample – TN_333_284

description:
Library name: TN_333_284
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: WT Liver NK cells, Control, Day3 1

description:
Library name: Sample1
T0000-941


title: X2/0/1

type: RNA

city: Erfurt

first: Sindy

last: Chamas

address: Kuehnhaeuser Strasse 101

country: Germany

institute: Erfurt Research Centre for Horticultural Crops, University of Applied Sciences Erfurt

description: gene expression 0 hours post excision

hyb_protocol: Microarray design and hybridization was performed by the company Oaklabs GmBH. Based on the genome sequences of 1,265 genes of interest (605 from P. axillaris and 660 from P. 152 inflata), an Array-to-Go Custom microarray was designed. For this purpose, five to ten specific isothermal probes, each 45-60 bp in 154 length were designed for each gene of interest. An additional 1,000 probes from a previously used microarray (Yang et al. 2019, Annals of Botany 124: 1053–1066) were used for normalization.

scan_protocol: Scanning was performed by the company Oaklabs GmbH using etablished protocols.

data_processing:
Raw data were analysed and processed by the company Oaklabs GmbH using etablished protocols.The best-performing oligonucleotide probe(s) were selected for each gene based on the hybridization data and used for the subsequent data analysis.
Quantil normalization of the oligonucleotide probes for the genes of interest was performed by the company Oaklabs.

organism: Petunia axillaris

source_name: P. axillaris, replicate 2, 0 hpe, basal leaves

label_protocol: Quality control by use of Bioanalyzer & Nanodrop photometer and labeling of total RNA samples, that contained at least 5 µl total RNA at 50 ng/µl, with cy3 fluorescent dye was performed by the company OakLabs GmbH, Neuendorfstraße 16B, 16761 Hennigsdorf.

growth_protocol: For establishment of donor plants, seeds of P. axillaris N and P. inflata S6 were surface sterilized and thereafter germinated in Petri-dishes on ½ MS medium (Murashige and Skoog, 1962) at 24 °C and a 16 h photoperiod. After 12 days, seedlings were transplanted into peat-based substrate (Einheitserde Typ CL Pikier, Patzer, Sinntal-Jossa, Germany) in plastic trays and placed in the greenhouse. Plants were watered with tap water and repeatedly fertilized with Hakaphos soft spezial (16% N, 8% P2O5, 22% K2O, 3% MgO + micronutrients, COMPO EXPERT GmbH, Münster, Germany) aiming at the following concentrations of nutrients in the substrate: nitrate-N: 150 mgL-1, P: 100 mgL-1 and K: 100 mgL-1. Plants were shaded or received supplemental light from high-pressure sodium vapor lamps, when natural irradiance exceeded a PPFD (photosynthetic photon flux density) of 720 μmol m−2 s−1 (400–700nm) or fell below a PPFD of 144 μmol m−2 s−1 (400–700nm), respectively, while day length was restricted to 10 h with a black fabric. Heating/ventilation set points for temperatures were 18/20 °C (day) and 16/18°C (night). After four weeks, the small petunia plants were placed in pots (final volume 1.7 L) containing the peat substrate indicated above. After eight weeks, plants were pinched to remaining three leaves. Starting in week 12 after sowing, shoot tip cuttings that consisted of the terminal shoot with six leaves, of which two were fully developed, were excised at regular intervals and used for the experiments, always leaving two leaves/nodes at the stock plant.

extract_protocol: Total RNA was extracted from the sample of the petunia cuttings following the protocol of the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany). A maximum of 100 mg fresh mass was processed in regard to the lysis capacity of the RLT buffer and RNeasy spin columns. After following the manufacturer's protocol, 30 µl of total RNA was obtained. The total RNA concentration and quality were determined on a NanoDrop™ 2000/2000c spectral photometer (Thermo Fisher Scientific, Schwerte, Germany). Only high-quality RNA samples (OD260/280 = 1.8 - 2.2, OD260/230 ≥ 2) were used. The integrity of RNA used for the microarray was additionally checked by the Agilent 2100 bioanalyzer (Agilent Technologies Deutschland GmbH, Waldbronn, Germany).

treatment_protocol: Cuttings were planted in perlite Perligran A (Knauf Perlite GmbH, Dortmund, Germany) and cultivated in a growth chamber at following conditions: temperature: 22/20 °C (day/night), humidity outside the covered trays: 85/60% (day/night), PPFD 100 μmol m−2 s−1 at plant level during a 10 h photoperiod provided by white fluorescent tubes. At specified hours after excision (hpe) of the cuttings, their stem bases, the upper stem, longitudinal halves of the two basal leaves and the remaining upper leaves and the shoot apex including the smallest adjacent leaves were shock-frozen in liquid N and stored at –80 °C. Per each replicate (n=3), pooled material from 10 or 16 cuttings was ground manually in liquid nitrogen by using a mortar and pistil and aliquots of 100 mg fresh mass were used for extraction.

tag: hours post excision (hpe)

tag: condition

value: basal leaves


title: VSIG4 KO KC-4

city: Hefei

first: xia

last: zhou

address: huang shan Road 443

country: China

institute: university of science and technology of china

description: Library name: Sample-8

data_processing:
Htseq V0.6.1
Assembly: mm10
Supplementary files format and content: fpkm

source_name: liver

extract_protocol:
Liver tissues enriched for metastatic B16F10 melanomas were harvested from WT or Vsig4-/- mice, cut into small pieces and digested with 0.5 mg/mL collagenase IV (Sigma) and 5 U/mL DNase I (Sigma) for 20 mins at 37℃ under shaking. The cell suspension was filtered through a 70 µm cell strainer and centrifugated at 400g for 5 mins at 4℃, followed by lysis of red blood cell inn ACK buffer (Biolegend).DAPI-CD45+Tim-4+ Kupffer cells  were sorted by FACS and further processed for bulk RNA-seq.
RNA libraries for RNA-seq were prepared using VAHTS Universal V8 RNA-seq Library Prep kit  following manufacture's protocols.

value: liver

value: Kupffer cells

value: VSIG4 KO

value: liver bearing metastatic B16F10 melanomas


title: V_2

city: Cambridge

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

country: United Kingdom

institute: The Babraham Institute

description: Library name: V_2

data_processing:
Raw fastq files were trimmed with trim_galore v0.6.10 using default parameters
Reads were aligned to the GRCh38 genome using hisat2 v2.21 with options --no-softclip guided by gene annotations from Ensembl v87
Raw read counts were generated the seqmonk v1.48.1 RNA-Seq quantitation pipeline using gene annotations from Ensembl v108 counting in opposing strand specific mode.
Assembly: GRCh38
Supplementary files format and content: Tab delimited text file of raw read overlap counts per gene

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: HCT116 cells were sourced from ATCC. Cells were grown in McCoy’s 5A (Modified) media supplemented with 10% heat-inactivated FBS, and maintained in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
RNA was isolated and purified from snap-frozen cells using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. The purification included a DNase treatment using the RNase-free DNase Set. Purified RNA was submitted to the Genomics Facility at the Babraham Institute for library preparation and RNAseq. Overall RNA quality was assessed using the Agilent TapeStation (RIN scores > 9).
cDNA libraries were constructed using Watchmaker DNA Library Prep Kits.

treatment_protocol: Resistant HCT116 cell lines were established over a period of 3 months by continuous exposure to increasing concentrations of HRO761 or VVD-13321 (Supplementary Figure 5), starting from the IC50 dose in media. 0.1% DMSO was maintained throughout. If viabilities were low, media would be drug-free until the cells recovered. For a control, HCT116 cell line chronically treated with 0.1% DMSO was also maintained.

tag: cell line

value: VVD 600 nM

tag: batch


title: V_1

description: Library name: V_1


title: Nasopharyngeal sample – TN_331_282

description:
Library name: TN_331_282
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_354_305

description:
Library name: TN_354_305
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: VSIG4 KO KC-3

description: Library name: Sample-7


title: X1/0/3

description: gene expression 0 hours post excision

source_name: P. axillaris, replicate 1, 0 hpe, shoot apex

value: shoot apex


title: Nasopharyngeal sample – TN_350_301

description:
Library name: TN_350_301
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Consortium_0dpi_037_RNA_Ln1

city: Ames

first: Torey

last: Looft

state: Iowa

address: 1920 Dayton Avenue

department: Food Safety and Enteric Pathogens Research Unit

country: USA

institute: USDA-ARS

description: Library name: Consortium_0dpi_037_RNA_Ln1

data_processing:
Sequence files for individual lanes per sample were trimmed for quality and adaptor sequences using Trimmomatic (v 0.39)
Quality checked sequences from the 4 lanes per sample were concatenated into a single file per sample
Sequences were aligned to the reference genome using STAR aligner (v 2.7.10)
Open reading frames were counted from aligned reads per sample using  “featurecounts” from the R (v 4.3.2) Bioconductor (v  3.18) package Rsubread (v 2.16.1)
Assembly: ENSEMBL Gallus gallus reference genome Galgal_GRCg6a_111
Supplementary files format and content: .txt file contains raw counts for each sample

organism: Gallus gallus

extract_protocol:
RNA was extracted from RNAlater stablized cecal tissue using the Qiagen Rneasy Mini kit with optional on-column DNase digestion
Poly-A tail selection

value: cecal tissue

value: epithelial

tag: microbialgroup

tag: samplenumber

tag: age

value: 7 days

tag: salmonella status

tag: days post_salmonella


title: F1/0/4

description: gene expression 0 hours post excision

organism: Petunia integrifolia subsp. inflata

source_name: P. inflata, replicate 1, 0 hpe, upper shoot

value: upper shoot


title: Nasopharyngeal sample – TN_347_298

description:
Library name: TN_347_298
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_328_279

description:
Library name: TN_328_279
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: WT Liver NK cells, Metformin, Day3 3

description:
Library name: Sample6
T0000-946

value: Metformin


title: X1/0/1

description: gene expression 0 hours post excision

source_name: P. axillaris, replicate 1, 0 hpe, basal leaves


title: Nasopharyngeal sample – TN_327_278

description:
Library name: TN_327_278
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: P_2

description: Library name: P_2

value: No treatment


title: VSIG4 KO KC-1

description: Library name: Sample-5


title: Nasopharyngeal sample – TN_324_275

description:
Library name: TN_324_275
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: X2/0/2

description: gene expression 0 hours post excision

source_name: P. axillaris, replicate 2, 0 hpe, upper leaves

value: upper leaves


title: WT Liver NK cells, Metformin, Day3 1

description:
Library name: Sample4
T0000-944

value: immune cells

value: Liver NK cells

value: WT


title: Nasopharyngeal sample – TN_323_274

description:
Library name: TN_323_274
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.

value: nasopharyngeal swab


title: Nasopharyngeal sample – TN_325_276

description:
Library name: TN_325_276
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: E_3

description: Library name: E_3


title: Nasopharyngeal sample – TN_338_289

description:
Library name: TN_338_289
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: F2/0/5

description: gene expression 0 hours post excision

source_name: P. inflata, replicate 2, 0 hpe, stem base

value: stem base


title: Nasopharyngeal sample – TN_321_271

description:
Library name: TN_321_271
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: WT KC-3

description: Library name: Sample-3

value: liver

value: Kupffer cells


title: Nasopharyngeal sample – TN_334_285

description:
Library name: TN_334_285
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: WT KC-2

description: Library name: Sample-2

value: liver bearing metastatic B16F10 melanomas


title: V_3

description: Library name: V_3

value: VVD 600 nM


title: Nasopharyngeal sample – TN_318_268

description:
Library name: TN_318_268
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_332_283

description:
Library name: TN_332_283
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: WT KC-1

description: Library name: Sample-1


title: E_1

description: Library name: E_1


title: Nasopharyngeal sample – TN_329_280

description:
Library name: TN_329_280
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_330_281

description:
Library name: TN_330_281
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_286_230

description:
Library name: TN_286_230
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: VSIG4 KO KC-2

description: Library name: Sample-6

value: VSIG4 KO


title: XE 2-4, mouse embryonic stem cells, H3K27ac (ChIP), technical replicate3

city: Bar Harbor

first: Christopher

middle: Lee

last: Baker

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

description: Library name: chip128

data_processing:
Adaptors were trimmed from reads using trimmomatic (version 0.39). Samples were mapped using hisat2 (version 2.2.1). Duplicate reads were removed using PicardTools (version 2.0.1).  Peaks were called using MACS (version 1.4.2). A comprehensive set of open chromatin locations (i.e., peakome) was generated by combining all peaks identified across a strain and  and peaks overlapping by 1 bp merged using bedtools (version 2.9.2). For H3K9me3 ChIP, peak counts were gathered against previously identified chromatin accessibility peaks (Byers, et. al., EMBO Journal, 2021.). Read matrices were TMM-normalized and log2-transformed downstream differential analysis of histone modification using edgeR.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: bigwig files for each sample

growth_protocol: Cells were grown in DMEM high glucose base medium supplemented with 15% fetal bovine serum, 1X Pen/Strep, 2 mM GlutaMAX, 1 mM sodium pyruvate, 0.1 mM MEM NEAA, 0.1 mM 2-Mercaptoethanol, 103 IU LIF, 1 μM PD0325901, and 3 μM CHIR99021

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. 3 million cells were lysed, fragmented using Mnase, and immunoprecipitated.
Libraries were constructed using the KAPA HyperPrep Kit. Libaries were sequenced to a depth of ~ 40 million reads with 75 bp on an Illumina NextSeq.

tag: strain

value: mouse embryonic stem cells

tag: chip antibody

value: H3K27ac (Cell Signaling Technology, #8173S)


title: P_4

description: Library name: P_4


title: Nasopharyngeal sample – TN_284_228

description:
Library name: TN_284_228
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: DMSO_3umV_2

description: Library name: DMSO_3umV_2

value: DMSO treated with 3um VVD


title: Nasopharyngeal sample – TN_326_277

description:
Library name: TN_326_277
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: DMSO_3umV_1

description: Library name: DMSO_3umV_1


title: P_1

description: Library name: P_1


title: Nasopharyngeal sample – TN_283_227

description:
Library name: TN_283_227
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_272_212

description:
Library name: TN_272_212
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: WT KC-4

description: Library name: Sample-4


title: Nasopharyngeal sample – TN_322_272

description:
Library name: TN_322_272
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_273_213

description:
Library name: TN_273_213
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: E_2

description: Library name: E_2


title: Nasopharyngeal sample – TN_320_270

description:
Library name: TN_320_270
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: DMSO_13umE_1

description: Library name: DMSO_13umE_1

value: DMSO treated with 13um HR0761


title: Nasopharyngeal sample – TN_265_204

description:
Library name: TN_265_204
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: QJ 6-1, mouse embryonic stem cells, H3K27ac (ChIP), technical replicate1

description: Library name: chip118


title: D2 5-5, mouse embryonic stem cells, H3K27ac (ChIP), technical replicate3

description: Library name: chip125


title: Nasopharyngeal sample – TN_317_267

description:
Library name: TN_317_267
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_263_201

description:
Library name: TN_263_201
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_262_200

description:
Library name: TN_262_200
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_287_231

description:
Library name: TN_287_231
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: D2 5-5, mouse embryonic stem cells, H3K27ac (ChIP), technical replicate2

description: Library name: chip124


title: D2 5-5, mouse embryonic stem cells, H3K27ac (ChIP), technical replicate1

description: Library name: chip123


title: 3VR_3

description: Library name: 3VR_3

value: VVD 3 uM


title: DMSO_3umV_3

description: Library name: DMSO_3umV_3


title: Nasopharyngeal sample – TN_250_186

description:
Library name: TN_250_186
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: XE 2-4, mouse embryonic stem cells, H3K27ac (ChIP), technical replicate2

description: Library name: chip127


title: Nasopharyngeal sample – TN_249_185

description:
Library name: TN_249_185
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: D_2

description: Library name: D_2

value: DMSO 0.1%


title: 3VR_2

description: Library name: 3VR_2


title: Nasopharyngeal sample – TN_242_174

description:
Library name: TN_242_174
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: XE 2-4, mouse embryonic stem cells, H3K27ac (ChIP), technical replicate1

description: Library name: chip126


title: Nasopharyngeal sample – TN_270_210

description:
Library name: TN_270_210
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_240_172

description:
Library name: TN_240_172
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: QJ 6-1, mouse embryonic stem cells, H3K27ac (ChIP), technical replicate2

description: Library name: chip119


title: Nasopharyngeal sample – TN_269_209

description:
Library name: TN_269_209
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_285_229

description:
Library name: TN_285_229
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: 1umE_3

description: Library name: 1umE_3


title: QJ 6-1, mouse embryonic stem cells, H3K27ac (ChIP), technical replicate3

description: Library name: chip120


title: Nasopharyngeal sample – TN_237_169

description:
Library name: TN_237_169
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: DMSO_13umE_2

description: Library name: DMSO_13umE_2


title: Nasopharyngeal sample – TN_268_208

description:
Library name: TN_268_208
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_266_205

description:
Library name: TN_266_205
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_267_206

description:
Library name: TN_267_206
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: DMSO_13umE_3

description: Library name: DMSO_13umE_3


title: Nasopharyngeal sample – TN_264_202

description:
Library name: TN_264_202
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: D_4

description: Library name: D_4


title: XE 2-4, mouse embryonic stem cells, H3K9me3 (ChIP), technical replicate2

description: Library name: chip143

value: H3K9me3 (Active Motif, #39161)


title: Nasopharyngeal sample – TN_235_167

description:
Library name: TN_235_167
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: D_3

description: Library name: D_3


title: Nasopharyngeal sample – TN_234_166

description:
Library name: TN_234_166
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_253_189

description:
Library name: TN_253_189
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_251_187

description:
Library name: TN_251_187
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: 1umE_1

description: Library name: 1umE_1


title: Nasopharyngeal sample – TN_233_165

description:
Library name: TN_233_165
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: B6 5-1, mouse embryonic stem cells, H3K27ac (ChIP), technical replicate3

description: Library name: chip117


title: 3VR_1

description: Library name: 3VR_1


title: PSP3

city: Catanzaro

first: Barbara

last: Puccio

address: Viale Europa

department: Dept of Surgical and Medical Sciences

country: Italy

institute: Magna Graecia University of Catanzaro

description: Library name: Sample 3

data_processing:
The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.
After quality control, paired-end clean reads were aligned to the reference genome (Homo Sapiens(GRCh38/hg38)) using Hisat2 v2.0.5.
Assembly: GRCh38/hg38
Supplementary files format and content: xlsx file includes gene counts for each Sample
Supplementary files format and content: xlsx file includes fpkm values for each Sample

source_name: induced pluripotent stem cell derived dopaminergic neurons

extract_protocol:
Total RNA was extracted by using TRIzol Reagents (Invitrogen, 15596026), according to the manufacturer’s protocol.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis.


title: PSP2

description: Library name: Sample 2

value: induced pluripotent stem cell derived dopaminergic neurons


title: Nasopharyngeal sample – TN_230_162

description:
Library name: TN_230_162
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: XE 2-4, mouse embryonic stem cells, H3K9me3 (ChIP), technical replicate3

description: Library name: chip144


title: Nasopharyngeal sample – TN_229_161

description:
Library name: TN_229_161
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_241_173

description:
Library name: TN_241_173
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_246_181

description:
Library name: TN_246_181
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_227_159

description:
Library name: TN_227_159
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: D2 5-5, mouse embryonic stem cells, H3K9me3 (ChIP), technical replicate2

description: Library name: chip141


title: Nasopharyngeal sample – TN_223_154

description:
Library name: TN_223_154
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_238_170

description:
Library name: TN_238_170
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_222_153

description:
Library name: TN_222_153
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: D2 5-5, mouse embryonic stem cells, H3K9me3 (ChIP), technical replicate1

description: Library name: chip140


title: B6 5-1, mouse embryonic stem cells, H3K27ac (ChIP), technical replicate2

description: Library name: chip116


title: Nasopharyngeal sample – TN_221_152

description:
Library name: TN_221_152
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: B6 5-1, mouse embryonic stem cells, H3K27ac (ChIP), technical replicate1

description: Library name: chip115


title: Nasopharyngeal sample – TN_236_168

description:
Library name: TN_236_168
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: 1umE_2

description: Library name: 1umE_2


title: Inp-NT_rep2

city: Chicago

first: Mahdi

last: Assari

state: Illinois

address: 1380 E HYDE PARK BLVD APT 806

department: Chemistry

institute: The University of Chicago

description: Library name: Sample 20

data_processing:
Raw sequencing reads were demultiplexed using Je to identify barcode sequences, after which they were aligned to a curated reference genome of human tRNAs.
Aligned reads were analyzed to quantify RNA abundance using a custom Python script. To detect RNA modifications, the reads were first sorted in BAM format with the sort function from Samtools (Li et al., 2009). Next, the count function in IGVtools was applied with parameters -z 5 -w 1 -e 250 --bases to generate WIG files. These WIG files were then processed using a custom Python pipeline to assess nucleotide-level mutations and read coverage.
Assembly: hg38_tRNA from GRCh38
Supplementary files format and content: tsv files with gene name and abundance per sample
Supplementary files format and content: .sam.tsv files with mutation, deletion, coverage for each gene position per sample

source_name: Epithelial cell line

growth_protocol: Knockout cells and wild-type HEK293T cells were cultured under standard culture conditions as recommended by ATCC with the same DMEM medium (Cytiva, SH30022.01) supplemented with 10% FBS (Genesee Sciences, 25-514H) and 1% Pen/Strep (ThermoFisher, 15070063).

extract_protocol:
Cells were harvested at 80–90% confluency, and total RNA was isolated using TRIzol reagent (Thermo Fisher Scientific, 15596026) according to the manufacturer’s instructions. RNA samples were subsequently purified with the RNA Clean & Concentrator-5 Kit (Zymo Research, R1013). One microgram of total RNA was used for sequencing library preparation. RNA integrity and concentration were evaluated using an Agilent Bioanalyzer.
MSR-seq (PMID 35513407)

treatment_protocol: MSR-seq with Bisulfite and Picoborane Treatments A total of 1 µg of purified RNA was processed according to the MSR-seq protocol [28]. To incorporate the bisulfite treatment [24], the RNA samples on beads—following the standard MSR-seq ligation and binding steps—were subjected to two washes with 500 µL high-salt buffer followed by one wash with 500 µL low-salt buffer using a magnetic rack in 1.5 mL Eppendorf tubes. After removing the wash buffer, 20% of the bead-bound RNA was resuspended in 100 µL of low-salt buffer and kept on ice, while the remaining 80% was treated with freshly prepared bisulfite reagent (2.4 M Na₂SO₃ and 0.36 M NaHSO₃) at 70 °C for 3 h. The post-reaction beads were washed again (two high-salt and one low-salt wash, 500 µL each), then incubated with 100 µL RNA Desulphonation Buffer (Zymo Research, R5001-3-40) at room temperature for 60 minutes. A final wash step (two high-salt and one low-salt) was performed before proceeding with the remaining steps of the MSR-seq protocol to generate cDNA libraries. For picoborane treatment [39], the protocol followed the same workflow as above, except the bisulfite reagent was replaced with a freshly prepared picoborane mix (40 µL water, 5 µL 3 M sodium acetate pH 5.2, and 5 µL 5 M picoborane). Samples were incubated at 70 °C for 3 hours. Desulphonation was not performed following picoborane treatment. The treated RNA was subsequently processed according to the standard MSR-seq protocol for library construction. Polysome tRNA profiling HEK293T cells were cultured in 15 cm plates to approximately 60% confluency and treated with 100 µg/ml cycloheximide (CHX) for 7 minutes at 37 °C. Following treatment, cells were washed twice with ice-cold 1× PBS containing 100 µg/ml CHX. They were then collected in 5 ml of ice-cold 1× PBS with 100 µg/ml CHX and pelleted by centrifugation at 1,000 × g for 5 minutes. Pellets were resuspended in 3–4 volumes of lysis buffer (20 mM HEPES, pH 7.6, 100 mM KCl, 5 mM MgCl₂, 2, 1% Triton X-100, 100 µg/ml CHX, freshly added 1× protease inhibitor [11873580001, Roche], and 40 U/µL RNase inhibitor [AM2696, ThermoFisher]) and incubated on ice for 20 minutes with intermittent mixing. Lysates were clarified by centrifugation at 16,000 × g for 15 minutes at 4 °C, and the supernatant was collected. To remove DNA, 4 µL of Turbo DNase (AM2238, ThermoFisher) was added to the supernatant and incubated at room temperature for 15 minutes. Sucrose gradients (5–50%) were prepared using a Biocomp Gradient Station in gradient buffer (20 mM HEPES, pH 7.6, 100 mM KCl, 5 mM MgCl₂, 2, 100 µg/ml CHX, freshly added 1× protease inhibitor, and 40 U/µL RNase inhibitor). Approximately 600 µL of buffer was removed from the top of each gradient, and an equal volume (typically 600 µL) of  lysate was carefully layered onto the gradient. Gradients were centrifuged at 28,000 RPM for 3 hours at 4 °C in a Beckman SW28.1 rotor. After centrifugation, gradients were fractionated using the Biocomp system to collect 30 fractions. Fractions were flash-frozen and stored at –80 °C for subsequent RNA extraction and library preparation.

value: Epithelial cell line

value: human embryonic kidney 293 cells


title: Nasopharyngeal sample – TN_219_150

description:
Library name: TN_219_150
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.

value: nasopharyngeal swab


title: Nasopharyngeal sample – TN_217_146

description:
Library name: TN_217_146
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_215_144

description:
Library name: TN_215_144
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: QJ 6-1, mouse embryonic stem cells, H3K9me3 (ChIP), technical replicate2

description: Library name: chip135


title: XE 2-4, mouse embryonic stem cells, H3K9me3 (ChIP), technical replicate1

description: Library name: chip142


title: Polysome-BStreated_rep1

description: Library name: Sample 17

value: WT

value: bisulfite treated


title: XE 2-4 mouse embryonic stem cells, H3K27ac (Dovetail HiChIP), technical replicate2

description: Library name: XE24rep2

data_processing:
HiChIP reads were processed using Dovetail’s HiChIP Loop Calling (readthedocs Revision 8f2e0b16). Reads were aligned to mm10 using bwa (v0.7.18). pairtools (version 1.1.2) was used to record and sort valid ligation events, remove PCR duplicates, and generate .pairs and bam files. Samtools (version 1.19.2) was used to create and index the final bam file. Libraries were verified to have no-dup read pairs > 50%, about 20% or greater of the total mapped non-dup pairs to be in cis and > 1 kb in length, and total reads in 1 kb around center of ChIP peaks > 2%. Filtered pairs were converted to Hi-C Pro valid pairs format. Loops were called using FitHiChIP (version 11.0) with the following parameters in the bias correction/coverage bias configuration file: Interaction type = peak to peak Bin size = 2500 Lower distance threshold = 10000 Upper distance threshold = 2000000 Bias types = coverages bias regression Merge filtering was employed (option 1) q-value = 0.01 Chromosome sizes correspond to mm10. Peak-to-peak interactions were imported into RStudio (version 4.1). diffloop (version 1.22.0) was used to adjust p-values using an FDR cutoff of 0.01. Interactions were filtered for at least four read counts in at least two samples. PET counts were normalized, and edgeR (version 3.34.1) was used to identify differential interactions (FDR < 0.2).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Library strategy: HiChIP

extract_protocol:
Cells extracted and crosslinked according to the Dovetail HiChIP Mnase Kit User Guide (version 2.0) for 10 million cells.
The Dovetail HiChIP MNase Kit User Guide (version 2.0) was used to process samples of 10 million cells. H3K27ac (Cell Signaling Technology, 8173) was used for immunoprecipitation. Libraries were paired end sequenced with a read length of 150 bp to a sequencing depth of 300 million reads per sample on an Illumina NovaSeq X Plus.


title: XE 2-4 mouse embryonic stem cells, H3K27ac (Dovetail HiChIP), technical replicate1

description: Library name: XE24rep1


title: Nasopharyngeal sample – TN_232_164

description:
Library name: TN_232_164
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_231_163

description:
Library name: TN_231_163
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_225_156

description:
Library name: TN_225_156
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: PSP1

description: Library name: Sample 1


title: QJ 6-1, mouse embryonic stem cells, H3K9me3 (ChIP), technical replicate1

description: Library name: chip134


title: Polysome-NT_rep2

description: Library name: Sample 16


title: Nasopharyngeal sample – TN_208_136

description:
Library name: TN_208_136
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Inp-BStreated_rep2

description: Library name: Sample 22


title: Nasopharyngeal sample – TN_205_132

description:
Library name: TN_205_132
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_224_155

description:
Library name: TN_224_155
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_220_151

description:
Library name: TN_220_151
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: B6 5-1, mouse embryonic stem cells, H3K9me3 (ChIP), technical replicate3

description: Library name: chip133


title: Inp-NT_rep1

description: Library name: Sample 19


title: Nasopharyngeal sample – TN_204_131

description:
Library name: TN_204_131
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_218_148

description:
Library name: TN_218_148
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: B6 5-1, mouse embryonic stem cells, H3K9me3 (ChIP), technical replicate2

description: Library name: chip132


title: Nasopharyngeal sample – TN_199_126

description:
Library name: TN_199_126
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: B6 5-1, mouse embryonic stem cells, H3K9me3 (ChIP), technical replicate1

description: Library name: chip131


title: Inp-BStreated_rep1

description: Library name: Sample 21


title: Nasopharyngeal sample – TN_213_142

description:
Library name: TN_213_142
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Polysome-BStreated_rep2

description: Library name: Sample 18


title: Nasopharyngeal sample – TN_212_141

description:
Library name: TN_212_141
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_211_140

description:
Library name: TN_211_140
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: B6 5-1 mouse embryonic stem cells, H3K27ac (Dovetail HiChIP), technical replicate2

description: Library name: B651rep2


title: Nasopharyngeal sample – TN_214_143

description:
Library name: TN_214_143
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_210_139

description:
Library name: TN_210_139
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_196_122

description:
Library name: TN_196_122
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: TRUB1KO-BStreated_rep2

description: Library name: Sample 11

value: TRUB1 knockout


title: QJ 6-1 mouse embryonic stem cells, H3K27ac (Dovetail HiChIP), technical replicate2

description: Library name: QJ61rep2


title: B6 5-1 mouse embryonic stem cells, H3K27ac (Dovetail HiChIP), technical replicate1

description: Library name: B651rep1


title: Nasopharyngeal sample – TN_195_121

description:
Library name: TN_195_121
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: D2 5-5 mouse embryonic stem cells, H3K27ac (Dovetail HiChIP), technical replicate2

description: Library name: D255rep2


title: Polysome-NT_rep1

description: Library name: Sample 15


title: QJ 6-1 mouse embryonic stem cells, H3K27ac (Dovetail HiChIP), technical replicate1

description: Library name: QJ61rep1


title: PUS7KO-BStreated_rep3

description: Library name: Sample 14

value: PUS7 knockout


title: Nasopharyngeal sample – TN_209_137

description:
Library name: TN_209_137
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_203_130

description:
Library name: TN_203_130
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: PUS7KO-BStreated_rep2

description: Library name: Sample 13


title: Nasopharyngeal sample – TN_202_129

description:
Library name: TN_202_129
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: D2 5-5 mouse embryonic stem cells, H3K27ac (Dovetail HiChIP), technical replicate1

description: Library name: D255rep1


title: TRUB1KO-BStreated_rep1

description: Library name: Sample 10


title: PUS7KO-BStreated_rep1

description: Library name: Sample 12


title: Nasopharyngeal sample – TN_198_125

description:
Library name: TN_198_125
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_194_120

description:
Library name: TN_194_120
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: XE 2-4, mouse embryonic stem cells, technical replicate3

description: Library name: ATAC309

data_processing:
Illumina adaptors were trimmed from reads using Trimmomatic (version 0.39) and then aligned to mouse reference genome (mm10) using bwa (version 0.7.5). Duplicate reads were removed using Picard Tools (version 2.0.1), and peaks were called for each sample using MACS (version 1.4.2). A  comprehensive set of open chromatin locations (i.e., peakome) was  generateed across all samples using bedtools (version 2.9.2). Read matrices were TMM-normalized and log2-transformed downstream differential analysis using edgeR (version 3.34.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Samples (100,000 cells)  were processed using the FAST-ATAC protocol (Corces et al., 2016).
DNA quality and quantity was determined using High Sensitivity D5000 ScreenTape (Agilent Technologies). Libraries were sequenced to a read depth of about 40 million reads per sample on an Illumina NovaSeq X Plus with a 150 bp read length.


title: Nasopharyngeal sample – TN_197_123

description:
Library name: TN_197_123
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_192_118

description:
Library name: TN_192_118
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: XE 2-4, mouse embryonic stem cells, technical replicate2

description: Library name: ATAC308


title: Nasopharyngeal sample – TN_189_115

description:
Library name: TN_189_115
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: PUS1KO-BStreated_rep3

description: Library name: Sample 9

value: PUS1 knockout


title: Nasopharyngeal sample – TN_188_114

description:
Library name: TN_188_114
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: PUS1KO-BStreated_rep2

description: Library name: Sample 8


title: XE 2-4, mouse embryonic stem cells, technical replicate1

description: Library name: ATAC307


title: Nasopharyngeal sample – TN_191_117

description:
Library name: TN_191_117
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_185_111

description:
Library name: TN_185_111
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_183_109

description:
Library name: TN_183_109
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: QJ 6-1, mouse embryonic stem cells, technical replicate2

description: Library name: ATAC306


title: QJ 6-1, mouse embryonic stem cells, technical replicate1

description: Library name: ATAC305


title: WT-PBtreated_rep2

description: Library name: Sample 6

value: picoborane treated


title: WT-PBtreated_rep1

description: Library name: Sample 5


title: WT-BStreated_rep2

description: Library name: Sample 4


title: Nasopharyngeal sample – TN_181_106

description:
Library name: TN_181_106
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_180_105

description:
Library name: TN_180_105
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_182_108

description:
Library name: TN_182_108
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: PUS1KO-BStreated_rep1

description: Library name: Sample 7


title: Nasopharyngeal sample – TN_187_113

description:
Library name: TN_187_113
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: D2 5-5, mouse embryonic stem cells, technical replicate3

description: Library name: ATAC300

value: mouse embryonic stem cells


title: D2 5-5, mouse embryonic stem cells, technical replicate2

description: Library name: ATAC299


title: Nasopharyngeal sample – TN_179_104

description:
Library name: TN_179_104
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_178_103

description:
Library name: TN_178_103
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_184_110

description:
Library name: TN_184_110
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: WT-BStreated_rep1

description: Library name: Sample 3


title: Nasopharyngeal sample – TN_177_102

description:
Library name: TN_177_102
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_172_096

description:
Library name: TN_172_096
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_175_100

description:
Library name: TN_175_100
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: D2 5-5, mouse embryonic stem cells, technical replicate1

description: Library name: ATAC298


title: WT-NT_rep2

description: Library name: Sample 2


title: PD3

description:
Library name: Sample 6
Column name in gene_count.txtx AND gene_fpkm.txtx:  PD3

data_processing:
The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.
After quality control, paired-end clean reads were aligned to the reference genome (Homo Sapiens(GRCh38/hg38)) using Hisat2 v2.0.5.
Assembly: GRCh38/hg38
Supplementary files format and content: txt file includes gene counts for each Sample
Supplementary files format and content: txt file includes fpkm values for each Sample


title: B6 5-1, mouse embryonic stem cells, technical replicate3

description: Library name: ATAC303


title: B6 5-1, mouse embryonic stem cells, technical replicate2

description: Library name: ATAC302


title: Nasopharyngeal sample – TN_176_101

description:
Library name: TN_176_101
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: WT-NT_rep1

description: Library name: Sample 1


title: Nasopharyngeal sample – TN_174_099

description:
Library name: TN_174_099
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_168_092

description:
Library name: TN_168_092
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_173_098

description:
Library name: TN_173_098
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_166_090

description:
Library name: TN_166_090
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: HC3

description:
Library name: Sample 3
Column name in gene_count.txtx AND gene_fpkm.txtx:  HC3


title: Nasopharyngeal sample – TN_170_094

description:
Library name: TN_170_094
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_169_093

description:
Library name: TN_169_093
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Has2 Exon 2 knock out + TGFB Replicate_4

city: Louisville

first: Richa

last: Singhal

state: KY

address: 580 S Preston Street, Baxter II Building, Office 321B

department: Medicine

institute: University of Louisville

description: Library name: R77_Cre_Tgfb

data_processing:
Raw sequences were checked for quality values using fastQC v0.10.1.  Quality trimming was not deemed necessary.
The sequences were directly aligned to the Mus musculus reference genome assembly (mm39) using Star version 2.6.
Read counts for gene regions were obtained with HTSeq v.0.10.0 using Ensembl annotations (GRCm39).
Assembly: mm39/GRCm39
Supplementary files format and content: tab-delimited file includes raw counts for each sample

source_name: Heart

growth_protocol: Fibroblasts were grown in DMEM/F-12 with GlutaMAX. Fetal Bovin Serum, Insulin-Transferrin-Selenium, Penicillin-Streptomycin, and basic fibroblast growth factor was added to the base media. Fibroblasts were plated at a ratio of 1 heart per 75 cm2 (10 mL/flask) and allowed to sediment for 2 h. Cardiac fibroblast media was changed following 2 h, 24 h, and subsequently every 2 d until reaching 70–80% confluency.

extract_protocol:
Tissue was disrupted and total RNA isolated using Trizol extraction followed by DNAse treatment
NEBNext Ultra II RNA Library Prep Kit for Illumina was used for library prep

treatment_protocol: Cardiac fibroblasts from Has2fl/fl mice were treated at P2. Cells (7 x 105) were plated in 60 mm dishes and allowed to adhere to the bottom of the dish overnight. Cells were then serum starved for 24 h. To treat, fibroblasts were given Cre adenovirus (Vector Biolabs 1045N), a Has2 overexpression adenovirus (Vector Biolabs), or GFP adenovirus as the control. After 5 hours, cells were given fresh media with 20 ng/mL of bFGF and TGFb, respectively. After 48 hours of stimulation, the cells were collected and total RNA was isolated from it.

value: Heart

tag: Sex

value: Male

value: Fibroblast

value: Wild Type C57BL/6J

value: Has2 Exon 2 knock out + TGFB

tag: group


title: PD2

description:
Library name: Sample 5
Column name in gene_count.txtx AND gene_fpkm.txtx:  PD2

tag: cell type


title: Nasopharyngeal sample – TN_164_088

description:
Library name: TN_164_088
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: B6 5-1, mouse embryonic stem cells, technical replicate1

description: Library name: ATAC301

tag: genotype


title: Control + TGFB Replicate_4

description: Library name: R77_Gfp_Tgfb

tag: treatment

value: Control + TGFB


title: Control Replicate_4

description: Library name: R77_Gfp_M

tag: tissue

value: Control

value: GFP


title: HC2

description:
Library name: Sample 2
Column name in gene_count.txtx AND gene_fpkm.txtx:  HC2

value: induced pluripotent stem cell derived dopaminergic neurons


title: Nasopharyngeal sample – TN_167_091

description:
Library name: TN_167_091
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.

value: nasopharyngeal swab


title: Nasopharyngeal sample – TN_165_089

description:
Library name: TN_165_089
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Has2  Exon 2 knockout Replicate_4

description: Library name: R77_Cre

value: Has2  Exon 2 knockout

value: Cre


title: PD1

description:
Library name: Sample 4
Column name in gene_count.txtx AND gene_fpkm.txtx:  PD1


title: Nasopharyngeal sample – TN_150_073

description:
Library name: TN_150_073
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Sample 16 - Non-Progressive Sarcoidosis

city: Denver

first: Camille

last: Moore

state: CO

address: 1400 Jackson St.

institute: National Jewish Health

description:
Library name: Sample 16
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were made using the Cell Ranger software v3.1.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest).
Filtering, normalization, integration, clustering, and identification of cluster markers was performed using R v4.2.3(https://www.r-project.org/) and Seurat v5.1.0(https://satijalab.org/seurat/).
After clusters were identified as either macrophage or nonmacrophage cell types, the cells were separately into two datasets. Then potential doublets were identified for macrophages and cells with high hybrid doublet scores removed using scds v1.2.0 (https://bioconductor.org/packages/scds/). Cell counts were reclustering individually for macrophages and nonmacrophage using the programs defined above.
Assembly: Human hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bronchoalveolar lavage

extract_protocol:
Bronchoscopy with BAL was performed as previously described.(9, 10). Briefly, four to eight 60 ml aliquots of sterile normal saline at room temperature were instilled into the airway with a syringe then aspirated using low suction. For each collection from an individual patient, the aspirated BAL specimens were pooled, kept on ice, and processed within one hour of collection. The BAL cells were obtained by centrifugation and cryopreserved.
Cryopreserved cells were thawed and captured on 10X Chromium in the Genomics Core at National Jewish Health using 10x Genomics Single Cell 3′ v3 chemistry, followed by sequencing on Illumina NovaSeq.

value: Bronchoalveolar lavage

value: Female

tag: diagnosis

value: SarcNP


title: Control + TGFB Replicate_3

description: Library name: P413_Gfp_Tgfb


title: HC1

description:
Library name: Sample 1
Column name in gene_count.txtx AND gene_fpkm.txtx:  HC1


title: Nasopharyngeal sample – TN_157_080

description:
Library name: TN_157_080
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_160_083

description:
Library name: TN_160_083
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_154_077

description:
Library name: TN_154_077
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_145_068

description:
Library name: TN_145_068
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_152_075

description:
Library name: TN_152_075
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Sample 13 - Progressive Sarcoidosis

description:
Library name: Sample 13
10x Genomics

value: SarcP


title: Nasopharyngeal sample – TN_163_087

description:
Library name: TN_163_087
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Has2 Exon 2 knock out + TGFB Replicate_3

description: Library name: P413_Cre_Tgfb


title: Nasopharyngeal sample – TN_153_076

description:
Library name: TN_153_076
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_147_070

description:
Library name: TN_147_070
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Sample 12 - Non-Progressive Sarcoidosis

description:
Library name: Sample 12
10x Genomics


title: Nasopharyngeal sample – TN_151_074

description:
Library name: TN_151_074
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_149_072

description:
Library name: TN_149_072
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Control + TGFB Replicate_2

description: Library name: P410_Gfp_Tgfb


title: Nasopharyngeal sample – TN_138_059

description:
Library name: TN_138_059
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Has2  Exon 2 knockout Replicate_3

description: Library name: P413_Cre


title: Sample 10 - Control

description:
Library name: Sample 10
10x Genomics


title: Nasopharyngeal sample – TN_148_071

description:
Library name: TN_148_071
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Sample 15 - Non-Progressive Sarcoidosis

description:
Library name: Sample 15
10x Genomics


title: Sample 14 - Control

description:
Library name: Sample 14
10x Genomics


title: Control Replicate_3

description: Library name: P413_Gfp_F


title: Nasopharyngeal sample – TN_144_067

description:
Library name: TN_144_067
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Has2 Exon 2 knock out + TGFB Replicate_1

description: Library name: P406_Cre_Tgfb


title: Nasopharyngeal sample – TN_130_048

description:
Library name: TN_130_048
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Has2 Exon 2 knock out + TGFB Replicate_2

description: Library name: P410_Cre_Tgfb


title: Nasopharyngeal sample – TN_140_062

description:
Library name: TN_140_062
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_136_055

description:
Library name: TN_136_055
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_128_046

description:
Library name: TN_128_046
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Sample 11 - Non-Progressive Sarcoidosis

description:
Library name: Sample 11
10x Genomics


title: Control + TGFB Replicate_1

description: Library name: P406_Gfp_Tgfb


title: Has2  Exon 2 knockout Replicate_2

description: Library name: P410_Cre


title: Nasopharyngeal sample – TN_134_053

description:
Library name: TN_134_053
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_135_054

description:
Library name: TN_135_054
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_133_052

description:
Library name: TN_133_052
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_131_050

description:
Library name: TN_131_050
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Sample 9 - Progressive Sarcoidosis

description:
Library name: Sample 9
10x Genomics


title: Sample 8 - Control

description:
Library name: Sample 8
10x Genomics


title: Nasopharyngeal sample – TN_127_045

description:
Library name: TN_127_045
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Has2  Exon 2 knockout Replicate_1

description: Library name: P406_Cre


title: Control Replicate_2

description: Library name: P410_Gfp_F


title: Nasopharyngeal sample – TN_126_044

description:
Library name: TN_126_044
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_114_028

description:
Library name: TN_114_028
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_115_029

description:
Library name: TN_115_029
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_117_032

description:
Library name: TN_117_032
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Sample 5 - Non-Progressive Sarcoidosis

description:
Library name: Sample 5
10x Genomics


title: Nasopharyngeal sample – TN_124_041

description:
Library name: TN_124_041
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_116_031

description:
Library name: TN_116_031
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: OVCAR3_carboplatin_5

city: Yokohama

first: Naoki

last: Kimura

state: Kanagawa

address: 216 Totsukacho, Totsuka-ku, Chugai Life Science Park Yokohama

institute: Chugai Pharmaceutical Co.,ltd

description: 100ng RNA, 8 μL of Reporter CodeSet, and 2 μL Capture ProbeSet

hyb_protocol: Hybridisation processed under 'High Sensitivity' settings.

scan_protocol: High Sensitivity' FOV 555 in nCounter Digital Analyzer

data_processing: Data normalization was performed in nSolver 4.0 (NanoString)

label: Nanostrings

source_name: ovarian cancer

label_protocol: nCounter® PanCancer Immune Profiling Panel (NanoString Technologies, XT-CSO-HIP 1-12), see manufacturer's website. https://nanostring.com/

growth_protocol: NIH:OVCAR-3 (1 × 107 cells/mouse) cancer cells were implanted subcutaneously into the right flanks of humanized mice (huNOG) with Matrigel Basement Membrane Matrix (Corning). When the tumor size reached 150-200 mm³, animals were randomized into appropriate groups for the following studies.

extract_protocol: Tumors stored in RNAlater solution (Thermo Fisher Scientific) were homogenized using TissueLyserIII (QIAGEN). Total RNA from homogenized tissues was extracted using the RNAeasy mini kit (QIAGEN) according to the manufacturer’s instructions.

treatment_protocol: Mice were intraperitoneally administered saline (vehicle) or carboplatin (30 mg/kg) on days 0 and 7. Tumors were harvested 10 days after the second carboplatin administration and used for RNA purification

tag: cell culture condition

value: carboplatin


title: Sample 7 - Control

description:
Library name: Sample 7
10x Genomics


title: Sample 4 - Progressive Sarcoidosis

description:
Library name: Sample 4
10x Genomics


title: Nasopharyngeal sample – TN_113_027

description:
Library name: TN_113_027
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Sample 3 - Progressive Sarcoidosis

description:
Library name: Sample 3
10x Genomics


title: Nasopharyngeal sample – TN_112_025

description:
Library name: TN_112_025
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_111_024

description:
Library name: TN_111_024
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Sample 2 - Non-Progressive Sarcoidosis

description:
Library name: Sample 2
10x Genomics


title: OVCAR3_carboplatin_4


title: OVCAR3_carboplatin_3


title: Nasopharyngeal sample – TN_108_021

description:
Library name: TN_108_021
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_110_023

description:
Library name: TN_110_023
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Control Replicate_1

description: Library name: P406_Gfp_M

value: Heart


title: Sample 6 - Progressive Sarcoidosis

description:
Library name: Sample 6
10x Genomics

value: Male


title: Sample 1 - Progressive Sarcoidosis

description:
Library name: Sample 1
10x Genomics


title: Nasopharyngeal sample – TN_107_020

description:
Library name: TN_107_020
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_103_016

description:
Library name: TN_103_016
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: OVCAR3_vehicle_4

value: vehicle


title: Nasopharyngeal sample – TN_100_011

description:
Library name: TN_100_011
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: PLH62_IFN

city: Paris

first: Beatrice

last: Jacquelin

address: 28, rue du Dr Roux

country: France

institute: Institut Pasteur

hyb_protocol: Seventy microliters of hybridization buffer was added to the reporter code set to make a master mixture. 2,1µl of proteinase K were added. Eight microliters of this master mixture was then incubated in separate tubes with 5µl of the lysate's sample and 2 ul of the capture code set. This hybridization mixture was incubated at 65°C for 18 hours. The hybridization mixture bind to Cartridge with a NanoString Prepstation.

scan_protocol: The cartridgenCounter™ Analysis System allows then to collect image and count barcodes.

data_processing: Raw counts were normalized to geometric mean counts of the synthetic positive controls included on the codeset. nCAAM and the geNorm algorithm was used to normalize each dataset by taking the five most stable housekeeping genes across samples and using it on all datasets.  Data were analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step. Normalization, fold changes and p-values were calculated using criteria provided by Nanostring. ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library.

label: Nanostring label

source_name: Peripheral Blood Mononuclear Cells

label_protocol: The system uses molecular “barcodes” and single molecule imaging to detect and count hundreds of unique transcripts in a single reaction.

growth_protocol: CD14+ monocytes were isolated from PBMC using positive selection by MACS cell separation (ref. 130-097-052, Miltenyi). Enriched CD14+ cell purity was assessed using flow-cytometry defined as the percentage of CD14+ positive live single cells.

extract_protocol: Gene expression profiling with NanoString nCounter analysis system (NanoString Technologies) was performed with whole cell lysates in RLT buffer (Qiagen). The protocol was adapted from NanoString instructions to prepare RNA from fresh frozen samples and used 50,000 cells in a total volume of 1.5µL of RLT buffer.

treatment_protocol: Unstimulated CD14+ monocytes are ex vivo monocytes without any culture nor stimulation. When stimulated CD14+ monocytes were cultured with 500 UI / mL of IFN-α2a (PBL Interferon Source, Tebu-Bio, ref 09311100-1) for 4 hours

value: CD14+ monocytes

tag: donor

value: People living with HIV (PLH)

value: male

tag: stimulation

value: cultured in the presence of 500 UI / mL IFN-α2a for 4 hours


title: PLH61_IFN

value: female


title: Nasopharyngeal sample – TN_105_018

description:
Library name: TN_105_018
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: OVCAR3_vehicle_3


title: Nasopharyngeal sample – TN_101_012

description:
Library name: TN_101_012
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_099_010

description:
Library name: TN_099_010
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: OVCAR3_carboplatin_2


title: Nasopharyngeal sample – TN_106_019

description:
Library name: TN_106_019
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Nasopharyngeal sample – TN_098_009

description:
Library name: TN_098_009
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: OVCAR3_carboplatin_1


title: Nasopharyngeal sample – TN_097_007

description:
Library name: TN_097_007
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: OVCAR3_vehicle_1


title: PLH63_IFN


title: Placenta, 4 days post SARS-CoV-2 Infection, Mouse Litter/Replicate 2

city: New Haven

first: Matthew

last: Yuen

state: Connecticut

address: 100 College

department: Neuroscience

institute: Yale School of Medicine

description:
Library name: I_5_217_360_S6
4 placentas from a single iltter pooled together 4 days post infection of dam

data_processing:
Quality control on FASTQ reads was performed using FastQC (version 0.11.9) and a threshold set for 95% of bases meeting Q30 within a given read to ensure high sequencing quality. Paired-end reads were trimmed using Fastp (version 0.23.2) with default arguments. Pseudoalignment to mm39 mouse genome (reference provided by the Yale Center for Genome Analysis) and quantification was performed using Salmon (version 1.4.0) with selective alignment enabled.
Assembly: mm39
Supplementary files format and content: *_quant.sf (Salmon quantification file) A tab-separated text file produced by Salmon that contains transcript-level quantification results. Each row corresponds to one transcript (or gene, if Salmon was run in gene mode). Typical columns include: Name (transcript ID), Length (transcript length in bp), EffectiveLength (bias-corrected length used for quantification), TPM (Transcripts Per Million, normalized expression value), and NumReads (estimated number of reads/fragments assigned to the transcript). This file is the main output used for downstream differential expression and expression profiling analyses.

source_name: Placenta

extract_protocol:
For bulk RNA-sequencing of the brain and placenta, pregnant dams were euthanized via cervical dislocation. Embryos were harvested from the dams and stored in ice-cold HBSS over ice as the placentas and embryonic brains were dissected in ice-cold HBSS. The placentas and dorsal cortex of offspring were dissected, placed in RNAProtect overnight, and  transferred to -20°C for later archival storage. To extract the RNA from placenta and dorsal cortices, tissue were homogenized using Lysis Matrix D ceramic beads. After centrifugation of the homogenate, the supernatant was extracted and total RNA was purified via the Qiagen RNeasy Mini kit. RNA samples were submitted to Yale’s Center for Genome Analysis for cDNA library preparation (Kapa mRNA HyperPrep) and sequenced (NovaSeq6000) at 100 million reads per sample.
RNA Seq Library Prep: mRNA is purified from a normalized input between 50-1000ng of total RNA with oligo-dT beads and sheared by incubation at 94C in the presence of Mg (Kapa mRNA Hyper Prep). Following first-strand synthesis with random primers, second strand synthesis and A-tailing are performed with dUTP for generating strand-specific sequencing libraries. Adapter ligation with 3’ dTMP overhangs are ligated to library insert fragments. Library amplification amplifies fragments carrying the appropriate adapter sequences at both ends. Strands marked with dUTP are not amplified. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent TapeStation. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: Mock Infection (50 uL of 1x PBS) or SARS-CoV-2 Infection (50μl of SARS-CoV-2 [3 × 107 PFU/ml]) of pregnant dams at embryonic day 11.

value: Placenta

value: Neurons + Glia

value: Wildtype

tag: batch


title: PLH59_IFN


title: PLH44_IFN


title: Placenta, 4 days post SARS-CoV-2 Infection, Mouse Litter/Replicate 3

description:
Library name: I_6_205_372_S7
4 placentas from a single iltter pooled together 4 days post infection of dam

value: SARS-CoV-2 Infection (50μl of SARS-CoV-2 [3 × 107 PFU/ml])


title: OVCAR3_vehicle_2

description: 100ng RNA, 8 μL of Reporter CodeSet, and 2 μL Capture ProbeSet


title: Nasopharyngeal sample – TN_094_004

description:
Library name: TN_094_004
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.

value: nasopharyngeal swab


title: Nasopharyngeal sample – TN_102_013

description:
Library name: TN_102_013
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: PLH60_IFN


title: PLH63

value: unstimulated


title: Nasopharyngeal sample – TN_091_001

description:
Library name: TN_091_001
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Placenta, 4 days post SARS-CoV-2 Infection, Mouse Litter/Replicate 1

description:
Library name: I_4_229_348_S5
4 placentas from a single iltter pooled together 4 days post infection of dam


title: Placenta, 4 days post SARS-CoV-2 Infection, Mouse Litter/Replicate 4

description:
Library name: I_7_193_384_S8
4 placentas from a single iltter pooled together 4 days post infection of dam


title: Progression - OVCAR3_carboplatin_5

description: 100ng RNA, 8 μL of Reporter CodeSet, and 5 μL Capture ProbeSet

label_protocol: nCounter® PanCancer Progression Panel  (NanoString Technologies, XT-CSO-PROG1-12), see manufacturer's website. https://nanostring.com/


title: Nasopharyngeal sample – TN_096_006

description:
Library name: TN_096_006
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Progression - OVCAR3_carboplatin_3

description: 100ng RNA, 8 μL of Reporter CodeSet, and 3 μL Capture ProbeSet


title: Nasopharyngeal sample – TN_093_003

description:
Library name: TN_093_003
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: PLH61


title: PLH59


title: Nasopharyngeal sample – TN_092_002

description:
Library name: TN_092_002
acterial 16S rRNA V3–V4 amplicon sequencing of nasopharyngeal sample.


title: Placenta, 4 days post Mock infection, Mouse Litter/Replicate 2

description:
Library name: C_5_265_312_S2
4 placentas from a single iltter pooled together 4 days post infection of dam

value: Mock Infection (50 uL of 1x PBS)


title: Placenta, 4 days post Mock infection, Mouse Litter/Replicate 1

description:
Library name: C_4_277_300_S1
4 placentas from a single iltter pooled together 4 days post infection of dam


title: Cerebral cortex, P30, SARS-CoV-2 Infection, Mouse Litter 4, Replicate 2

description:
Library name: Sample_P30_L7_2_159_034
Cerebral cortex of a single offspring, Postnatal Day 30

source_name: Cerebral cortex

value: Cerebral cortex


title: PLH49


title: OVCAR3_cisplatin_3

growth_protocol: NIH:OVCAR-3 was grown in RPMI 1640 supplemented with 20% FBS, 4.5 g/L glucose, 10 mM HEPES, 1 mM sodium pyruvate, and 10 µg/ml insulin.

extract_protocol: Cultured cell lines was extracted using the RNAeasy mini kit (QIAGEN, 74106) according to the manufacturer’s instructions

treatment_protocol: NIH:OVCAR-3 cells were were treated with 0.5 μg/ml of carboplatin, 0.1 μg/ml of cisplatin, 10 ng/ml of doxorubicin, and 1.2 ng/ml of paclitaxel. After culturing the cells for 5 days in the presence of chemotherapeutic agents, the medium was changed to fresh medium. The cells were then harvested 3 days later.

value: cisplatin


title: PLH48


title: PLH47


title: OVCAR3_cisplatin_2


title: Progression - OVCAR3_carboplatin_4

description: 100ng RNA, 8 μL of Reporter CodeSet, and 4 μL Capture ProbeSet

value: carboplatin


title: OVCAR3_carboplatin_2


title: OVCAR3_doxorubicin_2

value: doxorubicin


title: PLH62


title: Progression - OVCAR3_carboplatin_1


title: Placenta, 4 days post Mock infection, Mouse Litter/Replicate 4

description:
Library name: C_7_241_336_S4
4 placentas from a single iltter pooled together 4 days post infection of dam


title: OVCAR3_non-treated_2

value: non-treatment


title: Progression - OVCAR3_vehicle_4

value: vehicle


title: OVCAR3_non-treated_1


title: OVCAR3_high cell density_3

treatment_protocol: NIH:OVCAR-3 cells were cultured under low density, medium density, and high density. After one week of culture, cells were harvested and used for gene expression

tag: cell line

value: High cell density


title: PLH60

value: CD14+ monocytes

value: People living with HIV (PLH)


title: Progression - OVCAR3_vehicle_3


title: Placenta, 4 days post Mock infection, Mouse Litter/Replicate 3

description:
Library name: C_6_253_324_S3
4 placentas from a single iltter pooled together 4 days post infection of dam


title: Progression - OVCAR3_carboplatin_2

description: 100ng RNA, 8 μL of Reporter CodeSet, and 2 μL Capture ProbeSet


title: PLH45

value: male


title: HD3_IFN

value: healthy donor (HD)

value: female

value: cultured in the presence of 500 UI / mL IFN-α2a for 4 hours


title: OVCAR3_low cell density_3

value: Low cell density


title: Progression - OVCAR3_vehicle_2


title: Progression - OVCAR3_vehicle_1


title: PLH50


title: OVCAR3_low cell density_1


title: head_RU486_rep3

city: Shanghai

first: Lihong

last: Sheng

address: 131 Dongan Road

department: Institutes of Brain Science

institute: Fudan University

data_processing:
The obtained reads were mapped and analyzed utilizing the OnestopRNAseq platform (https://mccb.umassmed.edu/OneStopRNAseq).
Assembly: BDGP6
Supplementary files format and content: COUNT.xlsx includes raw counts for each sample

organism: Drosophila melanogaster

source_name: head

extract_protocol:
The RNA extracted from male fly brains (10 per replicate) was processed using TRIeasy (Cat#10606ES60, Yeason). Each sample, containing 500 ng of total RNA.
RNA libraries were prepared using VAHTSTM Stranded mRNA-seq Library Prep Kit (Cat#NR602, Vazyme) following manufacturer's protocols.

value: head


title: Cerebral cortex, P30, Mock Infection, Mouse Litter 5, Replicate 1

description:
Library name: Sample_P30_L8_2_147_046
Cerebral cortex of a single offspring, Postnatal Day 30

value: Neurons + Glia

value: Wildtype


title: OVCAR3_doxorubicin_3


title: head_RU486_rep2


title: OVCAR3_cisplatin_1


title: OVCAR3_doxorubicin_1


title: head_EtOH_rep3

value: EtOH


title: Cerebral cortex, P30, SARS-CoV-2 Infection, Mouse Litter 4, Replicate 1

description:
Library name: Sample_P30_L7_1_171_022
Cerebral cortex of a single offspring, Postnatal Day 30

value: Cerebral cortex

value: SARS-CoV-2 Infection (50μl of SARS-CoV-2 [3 × 107 PFU/ml])


title: OVCAR3_carboplatin_3

value: carboplatin


title: OVCAR3_carboplatin_1


title: HEK293T-CRAMP1-HA-dTAG No treatment

first: SHASHANK

last: SRIVASTAVA

state: IL

address: 303 E Superior St, SQE Lab 7-400

institute: Northwestern University

description: Library name: Control

data_processing:
Cleaned and filtered reads were aligned to hg38 via STAR using the nf-core RNAseq pipeline.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes count values for each sample

growth_protocol: DMEM, 5% CO2, 37°C

extract_protocol:
Trizol
Totla RNA was ribodpeletd using NEBNext rRNA Depletion Kit V2 (NEB Cat. E7400).  After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Sequencing was conducted by the NUSeq Core facility.

treatment_protocol: 500nM dTAG13 for times indicated before total RNA isolation

value: Epithelial

value: Untreated


title: Cerebral cortex, P30, SARS-CoV-2 Infection, Mouse Litter 3, Replicate 2

description:
Library name: Sample_P30_L6_2_183_010
Cerebral cortex of a single offspring, Postnatal Day 30


title: HEK293T-CRAMP1-HA-dTAG 7day dTAG treatment rep 3

description: Library name: dTAG_7_Rep3

data_processing:
Cleaned and filtered reads were aligned to hg38 via STAR using the nf-core RNAseq pipeline.
Quantitative comparisons between conditions were carried out using the edgeR package.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

extract_protocol:
Trizol
Total RNA was ribodpeletd using NEBNext rRNA Depletion Kit V2 (NEB Cat. E7400).  After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Sequencing was conducted by the NUSeq Core facility.

treatment_protocol: 500nM dTAG13 or equal volume of DMSO for times indicated before total RNA isolation


title: OVCAR3_non-treated_3

value: non-treatment


title: Cerebral cortex, P30, SARS-CoV-2 Infection, Mouse Litter 3, Replicate 1

description:
Library name: Sample_P30_L6_1_100_093
Cerebral cortex of a single offspring, Postnatal Day 30


title: Cerebral cortex, P30, Mock Infection, Mouse Litter 3, Replicate 1

description:
Library name: Sample_P30_L2_1_184_009
Cerebral cortex of a single offspring, Postnatal Day 30

value: Mock Infection (50 uL of 1x PBS)


title: HEK293T-CRAMP1-HA-dTAG 24hr treatment

description: Library name: dTAg-24Hr


title: PLH44

value: CD14+ monocytes

value: People living with HIV (PLH)

value: unstimulated


title: Cerebral cortex, P30, Mock Infection, Mouse Litter 4, Replicate 2

description:
Library name: Sample_P30_L5_2_112_081
Cerebral cortex of a single offspring, Postnatal Day 30


title: OVCAR3_high cell density_2

value: High cell density


title: HEK293T-CRAMP1-HA-dTAG 7day dTAG treatment rep 2

description: Library name: dTAG_7_Rep2


title: HEK293T-CRAMP1-HA-dTAG 24hr dTAG treatment rep 2

description: Library name: dTAG_24_Rep2


title: OVCAR3_high cell density_1


title: HD5_IFN

value: healthy donor (HD)

value: male

value: cultured in the presence of 500 UI / mL IFN-α2a for 4 hours


title: Cerebral cortex, P30, Mock Infection, Mouse Litter 4, Replicate 1

description:
Library name: Sample_P30_L5_1_124_069
Cerebral cortex of a single offspring, Postnatal Day 30

value: Neurons + Glia


title: HEK293T-CRAMP1-HA-dTAG 7day DMSO treatment rep 3

description: Library name: DMSO_7_Rep3

value: DMSO


title: Cerebral cortex, P30, SARS-CoV-2 Infection, Mouse Litter 2, Replicate 2

description:
Library name: Sample_P30_L4_2_136_057
Cerebral cortex of a single offspring, Postnatal Day 30

value: Wildtype


title: HEK293T-CRAMP1-HA-dTAG 7day DMSO treatment rep 2

description: Library name: DMSO_7_Rep2


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 6, Replicate 8

description:
Library name: Sample_P5_L9_8_221_356
Cerebral cortex of a single offspring, Postnatal Day 5

value: Cerebral cortex


title: OVCAR3_low cell density_2

value: Low cell density


title: HD1_IFN

value: female


title: ICC CAF cells, shSLC2A1, Hypoxic condition, 3

city: HANGZHOU

first: Jianing

last: Fan

address: NO. 3 EAST QINGCHUN ROAD

institute: Sir Run Run Shaw Hospital

description:
Library name: Sample12
CAFSHSLCHYPO_3

data_processing:
FastQC (version 0.12.0) was used to read all the raw data and perform quality control
Use Trim_Galore (version v0.6.10) to remove low-quality reads and adapters
The index and gene annotation files were downloaded, and reads were aligned using HISAT2 (version 2.2.1)
featureCounts (version 2.0.6) was used to count the reads numbers mapped to each gene
Assembly: GRCh38
Supplementary files format and content: CSV file including Reads count for each sample

source_name: Biliary tract tumor tissue

growth_protocol: ICC CAF cells were maintained in DMEM supplemented with 10% fetalbovine serum (FBS) and antibiotics at 37°C with 5% CO2 condition

extract_protocol:
RNA was harvested using Fast Pure Cell / Tissue Total RNA Isolation Kit (Vazyme). The minimum total amount of RNA used for constructing the sequencing library was 3.24 μg
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: Biliary tract tumor tissue

value: ICC CAF

value: Fibroblast

value: SLC2A1 knockdown


title: HEK293T-CRAMP1-HA-dTAG 7day DMSO treatment rep 1

description: Library name: DMSO_7_Rep1

value: Epithelial


title: Cerebral cortex, P30, SARS-CoV-2 Infection, Mouse Litter 2, Replicate 1

description:
Library name: Sample_P30_L4_1_148_045
Cerebral cortex of a single offspring, Postnatal Day 30

value: SARS-CoV-2 Infection (50μl of SARS-CoV-2 [3 × 107 PFU/ml])


title: head_RU486_rep1

value: head


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 6, Replicate 7

description:
Library name: Sample_P5_L9_7_233_344
Cerebral cortex of a single offspring, Postnatal Day 5


title: HD5

value: CD14+ monocytes

value: unstimulated


title: Cerebral cortex, P30, SARS-CoV-2 Infection, Mouse Litter 1, Replicate 1

description:
Library name: Sample_P30_L3_2_160_033
Cerebral cortex of a single offspring, Postnatal Day 30


title: HD3

value: healthy donor (HD)


title: HEK293T-CRAMP1-HA-dTAG 24hr DMSO treatment rep 2

description: Library name: DMSO_24_Rep2


title: head_EtOH_rep1

value: EtOH


title: Cerebral cortex, P30, Mock Infection, Mouse Litter 3, Replicate 2

description:
Library name: Sample_P30_L2_2_172_021
Cerebral cortex of a single offspring, Postnatal Day 30

value: Neurons + Glia

value: Mock Infection (50 uL of 1x PBS)


title: HD2

value: not determined


title: HEK293T-CRAMP1-HA-dTAG 6hr treatment

description: Library name: dTAG-6Hr


title: NOZ cells_B (Input)

first: Chuanxin

last: Yang

address: 600 Yishan Road

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description: Library name: Sample_B, Input

data_processing:
After obtaining the raw sequencing data, the initial step involves filtering the raw data to acquire high-quality clean data. The clean data are then aligned to the reference genome of the relevant species. Subsequently, genome-wide peak calling is performed on the alignment results to investigate the genomic binding preferences of the protein, followed by motif analysis of the identified binding sites.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: NOZ

extract_protocol:
NOZ cells were cross-linked with formaldehyde, and chromatin was extracted and sheared into fragments of 200-1000 bp.
The DNA library construction procedure involves end repair and A-tailing of the immunoprecipitated DNA, followed by ligation of sequencing adapters; target-sized fragments are then purified using magnetic beads and amplified via PCR to generate the final sequencing library; the constructed library is quality-checked by agarose gel electrophoresis and quantified using Qubit 2.0 to confirm its concentration is suitable for sequencing; after passing quality control, different libraries are pooled based on their effective concentration and required data output, followed by sequencing on the Illumina HiSeq platform.

value: NOZ

value: human gallbladder cancer

value: input


title: HD1

value: female


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 6, Replicate 4

description:
Library name: Sample_P5_L9_4_269_308
Cerebral cortex of a single offspring, Postnatal Day 5

value: Cerebral cortex

value: Wildtype


title: RPE PKO V5-CRAMP1 IgG IP rep 1

description: Library name: 19124FL-07-01V1-29

data_processing:
Analysis was conducted using the nf-core chipseq pipeline. Cleaned and filtered reads were aligned to hg38 via BWA.
Peak calling was conducted using MACS2
Assembly: GRCh38
Supplementary files format and content: bigWig for each sample

growth_protocol: DMEM/F-12, 10% fetal bovine serum, 1% penicillin/streptomycin, 5% CO2, 37°C

extract_protocol:
50x10^6 cells/IP were fixed with 1% paraformaldehyde for 10 minutes. After quencing and cell lysis, chromatin was sonicated using an E220 focused-ultrasonicator (Covaris). Chromatin amount was normalized across samples and 1% of the sonicated chromatin was removed for input. DNA-protein crosslinked complexes were immunoprecipitated overnight at 4C and then bound to protein A Dynabeads (Invitrogen) for 4 hours at 4C. After washing in RIPA buffer, reverse crosslinking was performed using proteinase K at 65C overnight. DNA was purified using a PCR purification kit (Qiagen).
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Preparation Kit complemented with NEBNext Unique Dual Index Primers (New England Biolabs). Input libraries and IP libraries were amplified using 4 or 11 cycles on the thermocycler respectively. Post amplification, libraries were right-side size selected at 200-900bp in length using Agencourt AMPure XP beads (Beckman Coulter). Libraries were validated using the Agilent D1000 TapeStation kit and Qubit Flourometer. Libraries were sequenced on the Illumina NovaSeq X Plus (Admera Health) with 2x150bp paired-end reads and with 1% PhiX as a control with 50M reads per sample.

value: IgG Rabbit


title: ICC CAF cells, shSLC2A1, Control condition, 2

description:
Library name: Sample8
CAFSHSLCCTRL_2

value: Biliary tract tumor tissue

value: ICC CAF

value: Fibroblast

value: SLC2A1 knockdown


title: head_EtOH_rep2

value: head


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 6, Replicate 3

description:
Library name: Sample_P5_L9_3_281_296
Cerebral cortex of a single offspring, Postnatal Day 5

value: SARS-CoV-2 Infection (50μl of SARS-CoV-2 [3 × 107 PFU/ml])


title: Cerebral cortex, P30, Mock Infection, Mouse Litter 2, Replicate 2

description:
Library name: Sample_P30_L1_2_101_092
Cerebral cortex of a single offspring, Postnatal Day 30


title: ICC CAF cells, shSLC2A1, Control condition, 1

description:
Library name: Sample7
CAFSHSLCCTRL_1


title: ICC CAF cells, shControl, Hypoxic condition, 3

description:
Library name: Sample6
CAFSHNCHYPO_3

value: WT


title: NOZ cells_B, RUVBL2 (ChIP)

description: Library name: Sample_B, ChIP

value: RUVBL2 (ChIP)


title: HEK293T-CRAMP1-HA-dTAG 7day dTAG treatment rep 1

description: Library name: dTAG_7_Rep1

value: Epithelial


title: ICC CAF cells, shControl, Hypoxic condition, 2

description:
Library name: Sample5
CAFSHNCHYPO_2


title: Cerebral cortex, P30, Mock Infection, Mouse Litter 2, Replicate 1

description:
Library name: Sample_P30_L1_1_113_080
Cerebral cortex of a single offspring, Postnatal Day 30

value: Neurons + Glia

value: Mock Infection (50 uL of 1x PBS)


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 6, Replicate 1

description:
Library name: Sample_P5_L9_1_210_367
Cerebral cortex of a single offspring, Postnatal Day 5


title: SK2

description: Library name: SK2


title: NOZ cells_A (Input)

description: Library name: Sample_A, Input

value: NOZ

value: human gallbladder cancer


title: SK1

description: Library name: SK1


title: HEK293T-CRAMP1-HA-dTAG 24hr dTAG treatment rep 3

description: Library name: dTAG_24_Rep3


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 5, Replicate 6

description:
Library name: Sample_P5_L8_6_222_355
Cerebral cortex of a single offspring, Postnatal Day 5


title: Cerebral cortex, P30, Mock Infection, Mouse Litter 1, Replicate 1

description:
Library name: Sample_P30_L10_1_123_070
Cerebral cortex of a single offspring, Postnatal Day 30


title: HEK293T-CRAMP1-HA-dTAG 24hr dTAG treatment rep 1

description: Library name: dTAG_24_Rep1


title: NOZ cells_A, RUVBL2 (ChIP)

description: Library name: Sample_A, ChIP


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 5, Replicate 5

description:
Library name: Sample_P5_L8_5_234_343
Cerebral cortex of a single offspring, Postnatal Day 5


title: ICC CAF cells, shControl, Control condition, 3

description:
Library name: Sample3
CAFSHNCCTRL_3


title: HEK293T-CRAMP1-HA-dTAG 24hr DMSO treatment rep 3

description: Library name: DMSO_24_Rep3

value: DMSO


title: HEK293 , LMNA , Rep3 , ATAC

city: Urbana

last: Lizarazo

address: 505 S Goodwin Ave

department: Molecular and Integrative Physiology

institute: University of Illinois Urbana Champaign

description:
Library name: HEK293_LMNA_3_ATAC
HEK293_LA_3

data_processing:
The processing of ATAC-Seq data was carried out by following and adapting established protocols. Briefly cCounts were extracted over a comprehensive RNAcentral database annotation of noncoding RNAs. For each gene, a total of 150 nucleotides were added to both the upstream and downstream regions to improve mapability. Additionally, counts were extracted from the regions upstream and downstream of the gene of interest. These regions were 500 bp, 5000 bp, and 50000 bp in size with a buffer region of 300 bp allowed between the genes and the additional mapped regions. For smallRNA-Seq counts were extracted over the same comprehensive RNAcentral database annotation of noncoding RNAs. All count matrices were TPM normalized subsequently.
Assembly: GRCh38
Supplementary files format and content: count files for both small RNA seq and ATAC Seq

extract_protocol:
HEK293 (ATCC) were cultured in complete Dulbecco’s Modified Eagle’s Medium (DMEM) (Corning) supplemented with 10% fetal bovine serum ( Corning) and 1% Penicillin-Streptomycin. Cells were maintained in 10-cm dishes by seeding 1 x 10^6 cells with complete medium every 2-3 days. Cells were maintained in a humidified atmosphere at 37 C with 5% CO2.
For ATAC-Seq, 100,000 cells were collected following overexpression of eGFP, LMNA, LMNB1, or LMNB2. Libraries were prepared using the ATAC-Seq Kit (Active Motif) according to the manufacturer’s protocol. For small RNA-Seq, cells from the same overexpression conditions (eGFP, LMNA, LMNB1, or LMNB2) were recollected, and total RNA enriched for small RNAs was extracted using the mirVana PARIS Kit (Thermo Fisher Scientific) following the manufacturer’s instructions. All sequencing was performed at the University of Illinois, Roy J. Carver Biotechnology Center.

value: Wild Type

value: LaminA Overexpression


title: ICC CAF cells, shSLC2A1, Hypoxic condition, 2

description:
Library name: Sample11
CAFSHSLCHYPO_2


title: HEK293T-CRAMP1-HA-dTAG 24hr DMSO treatment rep 1

description: Library name: DMSO_24_Rep1


title: RPE PKO V5-CRAMP1 V5 IP rep 3

description: Library name: 19124FL-07-01V1-36


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 6, Replicate 6

description:
Library name: Sample_P5_L9_6_245_332
Cerebral cortex of a single offspring, Postnatal Day 5

value: Cerebral cortex

value: Wildtype


title: RPE PKO V5-CRAMP1 IgG IP rep 3

description: Library name: 19124FL-07-01V1-35

value: IgG Rabbit


title: ICC CAF cells, shSLC2A1, Hypoxic condition, 1

description:
Library name: Sample10
CAFSHSLCHYPO_1

value: Biliary tract tumor tissue

value: ICC CAF

value: Fibroblast


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 6, Replicate 5

description:
Library name: Sample_P5_L9_5_149_044
Cerebral cortex of a single offspring, Postnatal Day 5

value: SARS-CoV-2 Infection (50μl of SARS-CoV-2 [3 × 107 PFU/ml])


title: HEK293 , LMNA , Rep1 , ATAC

description:
Library name: HEK293_LMNA_1_ATAC
HEK293_LA_1


title: ICC CAF cells, shControl, Control condition, 2

description:
Library name: Sample2
CAFSHNCCTRL_2

value: WT


title: HEK293 , GFP , Rep3 , ATAC

description:
Library name: HEK293_GFP_3_ATAC
HEK293_GFP_3

value: eGFP Overexpression


title: ICC CAF cells, shSLC2A1, Control condition, 3

description:
Library name: Sample9
CAFSHSLCCTRL_3

value: SLC2A1 knockdown


title: HEK293 , LMNB1 , Rep2 , ATAC

description:
Library name: HEK293_LMNB1_2_ATAC
HEK293_LB1_2

value: LaminB1 Overexpression


title: RPE PKO V5-CRAMP1 Input rep 3

description: Library name: 19124FL-07-01V1-34

value: Epithelial


title: RPE PKO V5-CRAMP1 V5 IP rep 1

description: Library name: 19124FL-07-01V1-30


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 5, Replicate 4

description:
Library name: Sample_P5_L8_4_246_331
Cerebral cortex of a single offspring, Postnatal Day 5

value: Neurons + Glia


title: Cerebral cortex, P5, SARS-CoV-2 Infection, Mouse Litter 6, Replicate 2

description:
Library name: Sample_P5_L9_2_198_379
Cerebral cortex of a single offspring, Postnatal Day 5


title: HEK293 , LMNB2 , Rep3 , smallRNA

description:
Library name: HEK293_LMNB2_3_smallRNA
LMNB23_sRNA

value: LaminB2 Overexpression


title: RPE PKO V5-CRAMP1 Input rep 1

description: Library name: 19124FL-07-01V1-28


title: Hypoxia CD38bright CLL-1bright rep3

city: Brighton

first: Chris

last: Pepper

address: Falmer

institute: University of Sussex

description:
Library name: Hpp3
KG1a bright, hypoxia

data_processing:
Base calling was performed using Illumina Real-Time Analysis (RTA) software, version used: RTA 3.4.4 (standard for NovaSeq 6000)
Adapter trimming and quality filtering were performed using Trimmomatic v0.39, with the following parameters: ILLUMINACLIP:adapter.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Assembly: Reads were aligned to the GRCh38 (hg38) human genome assembly using STAR aligner (v2.4.2a)
Supplementary files format and content: FASTQ files paired-end 150 bp reads

source_name: KG1a cells

growth_protocol: KG1a cells and primary AML cells were grown in RPMI media with 20% FBS

extract_protocol:
Total RNA was extracted from KG1a cells using Active Motif’s standard RNA extraction workflow. Sequencing was carried out on an Illumina NovaSeq 6000 platform, generating paired-end 150 bp reads.
Library construction was undertaken by Active Motif
mRNA enrichment and RNA-seq library preparation were performed by Active Motif using their validated commercial protocols.

treatment_protocol: Normoxia and hypoxia (3% oxygen)

value: KG1a cells


title: Hypoxia CD38bright CLL-1bright rep2

description:
Library name: Hpp2
KG1a bright, hypoxia


title: HEK293 , LMNB2 , Rep2 , smallRNA

description:
Library name: HEK293_LMNB2_2_smallRNA
LMNB22_sRNA

value: Wild Type


title: HEK293 , LMNB1 , Rep2 , smallRNA

description:
Library name: HEK293_LMNB1_2_smallRNA
LMNB12_sRNA


title: Hypoxia CD38bright CLL-1bright rep1

description:
Library name: Hpp1
KG1a bright, hypoxia


title: HEK293 , LMNB2 , Rep3 , ATAC

description:
Library name: HEK293_LMNB2_3_ATAC
HEK293_LB2_3