title: B1_bzcj2

city: Chengdu

first: Bo

last: Zeng

state: Sichuan

address: 211 Huimin road, Wenjiang district

institute: Sichuan Agricultural University

description: HE staining photos of muscle section and H5 gene expression data for Spatial transcriptomic sequencing study.

data_processing:
Sample demultiplexing, image alignment, barcode processing, and gene counting were performed by using Space Ranger (version 1.1) according to the 10× GENOMICS Spatial Gene Expression analysis pipelines (https://support.10xgenomics.com/spatial-gene-expression/software/overview/welcome).
Annotation information of MYH2 and MYH4 genes (from old Sscrofa11.1 release-90, representative gene of muscle fiber type IIA and IIB) were added in the GTF file, because of annotation information of MYH2 and MYH4 genes are lacking in ensembl release-102.
We used the "spaceranger counts" command for reads mapping and gene counting.
The H&E stained photos of tissue sections, slide serials and capture area information of each sequencing sample were provided in this counting step for automatic fiducial alignment and tissue detection.
The Loupe Browser software (10X) was used to quickly visualize the spatial results. We evaluated the biological reliability of all spots in each sample and unreliable spots were filter out by using the Manual Alignment function.
Assembly: ensembl-Sscrofa11.1-release102
Supplementary files format and content: H5 Matrix table with clean gene counts for every gene and every spots.

organism: Sus scrofa

source_name: longissimus dorsi muscle

extract_protocol:
RNA catpure: The tissue sections on Visium Spatial slide were permeabilized according to the protocol provided by 10x Genomics
Fragmented and barcoded porcine RNA were used as the carrier material. The spike-in constituted around 25% of the libraries. ST cDNA libraries were diluted to 4nM and sequenced on the Illumina NovaSeq 6000 platform using paired-end sequencing. Sequenced at a mean depth of 50 million paired-end reads depth which resulted in an average library saturation at above 90%.

treatment_protocol: The representative longissimus dorsi muscle (LDM) were collected from three pigs for ST experiments. Fresh porcine LDM tissue were cut into about 6.5mm*6.5mm*1cm size and snap-frozen in liquid nitrogen to avoid crystal formation. Then tissue samples were embedded in Optimal Cutting Temperature (OCT) and stored at -80℃. For ST analysis, the samples were sectioned on a cryostat at a thickness of 15μm and place the section within a capture area on the Visium Spatial slide.

tag: tissue

value: longissimus dorsi muscle

value: skeletal muscle

tag: breed

value: Berkshire

tag: treatment

value: Space Ranger counting


title: B2_bzcj3

status: Public on May 17 2022

type: SRA

country: China

library_source: transcriptomic

molecule: polyA RNA

tag: cell line

tag: cell type


title: TSA-PD4_ATAC_WT_Rep2

city: Seoul

first: Jin Yong

last: Kim

address: 101 Daehak-ro, Jongno-gu

department: Department of Dermatology

country: South Korea

institute: Seoul National University College of Medicine

library_source: genomic

data_processing:
Sequencing reads were aligned using Bowtie2 v1.1.1 with the parameters “-X2000 --very-sensitive” for paired-end reads. Duplicates were removed using Picard v2.7.1.
Peaks for each replicate were called using MACS2 v2.1.2 with the parameter “-f BEDPE -q 0.001 --nomodel --call-summits”.
ATAC peak files per each sample were merged to achieve a consensus peak file representing peaks that were called across all samples.
Deeptools v3.4.2 bamCoverage (ATAC-seq) or bamCompare (ChIP-seq) function was used to generate bigWigs of bam files for the consensus peak regions.
For quantitative analysis of ChIP-seq, H3K27ac signals of each timepoint were normalized to merged input signals with scale factors calculated by the total amount ratio of H3K27ac protein to H3 protein.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files

molecule: genomic DNA

organism: Mus musculus

source_name: FACS-sorted CD140a+CD26+ dermal fibroblasts after in vivo TSA treatment

extract_protocol:
Freshly FACS-sorted CD140a+CD26+ cells from mouse dermis were subjected to ATAC-seq and ChIP-seq library preparation.
For ATAC-seq, cells were incubated with cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630), then were immediately subjected to a transposition reaction for 30 min at 37°C with TN5 transposase (Illumina). Transposed DNA was purified using Qiagen MiniElute purification kit and PCR amplified with 10-15 cycles. Library construction was performed using Nextera primers (Illumina). The libraries were sequenced using Illumina HiSeq 2500 platform using a 50-bp paired-end setting. ATAC-seq experiments were independently repeated for two times.  For ChIP-seq, library preparation was performed using ChIPmentation method (Nat Methods 12, 963–965 (2015).). Briefly, cells were fixed with 1% paraformaldehyde in PBS for 10 min at 25C, then were collected at 500 g for 10 min at 4°C and washed twice with 1 μM phenylmethyl sulfonyl fluoride (PMSF) in PBS. The pellet was sonicated a Branson 102C sonicator on ice until the size of fragments was in the range of 200–700 bp. The lysate was centrifuged and the supernatant containing the sonicated chromatin was transferred to a new tube. The sonicated lysate was brought to in 200 μl RIPA buffer per immunoprecipitation. For each immunoprecipitation, 10 μl Dynabeads Protein A were washed twice and resuspended with 0.1% BSA in PBS. The antibody was added and bound to the beads by rotating for 2 h at 4 °C. Anti-H3K27ac antibody (1 μg per immunoprecipitation, Diagenode pAB-196-050) and a nonspecific IgG rabbit antibody (2.5 μg per immunoprecipitation, Millipore 12-370) were used. Blocked antibody-conjugated beads were then placed on a magnet, supernatant was removed, and the sonicated lysate was added to the beads followed by incubation by rotating for 3 h at 4°C. Beads were washed subsequently with RIPA, RIPA-HS and RIPA-LiCl buffers. Beads were washed with cold Tris-HCl pH 8.0 and then resuspended in 25 μl tagmentation reaction buffer (10 mM Tris pH 8.0, 5 mM MgCl2, 10% v/v dimethylformamide) containing 1 μl TN5 transposase enzyme (Illumina) and incubated for 5 min at 37 °C in a thermocycler. Beads were washed with RIPA and cold Tris-HCl pH 8.0 and then incubated with 70 μl elution buffer (10 mM Tris-HCl pH 8.0, 5 mM EDTA, 300 mM NaCl, 0.4% SDS) containing 2 μl of Proteinase K (NEB) for 1 h at 55 °C and for 6 h at 65 °C, and supernatant was transferred to a new tube. Transposed DNA was purified with Qiagen MiniElute purification kit, and PCR amplified using Kapa HiFi HotStart ReadyMix (Kapa Biosystems). Enriched libraries were purified using SPRI AMPure XP beads at a beads-to-sample ratio of 1:1, followed by a size selection using AMPure XP beads to recover libraries with a fragment length of 200–400 bp. Library construction was performed using TruSeq ChIP Library Preparation Kit (Illumina). The libraries were sequenced using Illumina HiSeq 2500 platform using a 100-bp paired-end setting.

tag: developmental stage

tag: agent

value: TSA


title: FKBP12-PCGF35_dTAG36h_Dox24h_H3K27me3_Rep2

city: Oxford

first: Joseph

middle: S

last: Bowness

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

data_processing:
Raw fastq read pairs were mapped to the “N-masked” the N-masked mm10 genome concatenated with the dm6 Drosophila genome by bowtie2 (v2.2.6) using parameters “--very-sensitive --no-discordant --no-mixed -X 2000”
Alignment files were filtered to remove unmapped read pairs and PCR duplicates (picard-tools MarkDuplicates). Bam files were then sorted and indexed using samtools commands.
Sequencing reads mapping to mm10 and dm6 genomes were counted for each sample using "samtools view" commands. Calibration factors were then calculated according to the derived formula for occupancy ratio (ORi) (Hu et al., 2015) and are provided in Supplemental File 2 of associated publication.
Alignments files were processed into bedGraph format by genomeCoverageBed (BEDtools), normalised to the total library size of the sample, and scaled by calibration factor.
BigWig files were generated using samtools bamCoverage and scaled by library size and calibration factor.
The custom script ExtractInfoFrombedGraph_AtBed.py (https://github.com/guifengwei) was used on calibrated bedGraph files to extract values for windows 250 kb of the 103.5Mb region of ChrX1 proximal to Xist that can be allelically-assigned. Line graphs displayed in report were generated in R by further transformation of these windowed files: first enrichment over a combined input file (IP/input for each allelic file), then differential allelic enrichment (Xi - Xa) for each window.
Genome_build: mm10; dm6
Supplementary_files_format_and_content: txt (tables of calibrated ChIP signal for 250KB windows); bigwig

source_name: iXist-ChrX-Dom(mESC)

growth_protocol: ES cells were grown in ES cell medium, which consisted of Dulbecco’s Modified Eagle Medium (DMEM, from Life Technologies) supplemented with 9% foetal calf serum (FCS, from Seralab), 2mM L-glutamine, 1x non-essential amino acids, 50 μM β-mercaptoethanol, 50g/mL penicillin/streptomycin (all from Invitrogen) and LIF- conditioned medium, made in house, at a concentration equivalent to 1000U/mL. Cells were grown at 37ºC in a humid atmosphere with 5% CO2. Cells were passaged and colleced with TrypLE (ThermoFisher) and frozen in FCS + 10% DMSO. Mitomycin C-inactivated mouse fibroblasts were used as feeders and removed prior to plating out for experiments by pre-plating.

extract_protocol:
Calibrated native ChIP-seq was performed largely as described in our previous studies (Nesterova et al., 2019; Rodermund et al., 2021) using buffers supplemented with 5 mM of the deubiquitinase inhibitor N-ethylmaleimide (Merck Life Science) for H2AK119ub1 ChIP. 4 x 107 mESCs and 1 x 107 Drosophila Sg4 Cells (20% cellular spike-in) were carefully counted using a Countess 3 Automated Cell Counter (ThermoFisher) and pooled. Cells were then lysed in RSB (10 mM Tris pH8, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40) for 5 min on ice with gentle inversion before nuclei collection by centrifugation (1500 g for 5 min at 4oC). Nuclei were resuspended in 1 mL of RSB + 0.25 M sucrose + 3 mM CaCl2, treated with 200U of MNase (Fermentas) for 5 min at 37oC, quenched with 4 µl of 1M EDTA, then centrifuged at 2000 g for 5 min. The supernatant was transferred to a fresh tube as fraction S1. The remaining chromatin pellet was incubated for 1 hour in 300 µl of nucleosome release buffer (10 mM Tris pH7.5, 10 mM NaCl, 0.2 mM EDTA), carefully passed five times through a 27G needle, and then centrifuged at 2000 g for 5 min. The supernatant from this S2 fraction was combined with S1 to make the final soluble chromatin extract. For each ChIP reaction, 100 µl of chromatin was diluted in Native ChIP incubation buffer (10 mM Tris pH 7.5, 70 mM NaCl, 2 mM MgCl2, 2 mM EDTA, 0.1% Triton) to 1 mL and incubated with Ab overnight at 4 °C. Samples were incubated for 1 hour with 40 µl protein A agarose beads pre-blocked in Native ChIP incubation buffer with 1 mg/mL BSA and 1 mg/mL yeast tRNA, then washed a total of four times with Native ChIP wash buffer (20 mM Tris pH 7.5, 2 mM EDTA, 125 mM NaCl, 0.1% Triton-X100) and once with TE pH 7.5. All washes were performed at 4oC. The DNA was eluted from beads by resuspension in elution buffer (1% SDS, 100 mM NaHCO3) and shaking at 1000rpm for 30 min at 25oC, and was purified using the ChIP DNA Clean and Concentrator kit (Zymo Research).
Libraries were prepared from 25-100ng ChIP DNA using NEBNext Ultra II DNA Library Prep Kit

treatment_protocol: Xist expression driven by TetO promoter was induced by adding doxycycline (1μg/mL) to the culture medium for 24h. For PCGF3/5 degradation, dTAG-13 was added at 100uM 12 hours prior to Xist (Dox) induction.

tag: strain

value: Dom/129S x Cast

value: mESC

tag: Sex

value: Female

tag: cell engineering

value: Endogenous Xist promoter replaced with TetOn Promoter (Dom/129S allele); Degron FKBP12-PCGF3/5

tag: chip antibody

value: anti-H3K27me3 (Diagenode C15410069, rabbit pAb)

tag: spike-in

value: 20% cellular spike-in with Drosophila Sg4 cells for calibrated ChIP-seq


title: T2_bzcj2

value: Tibetan


title: 131/4-5B1

first: YOON-SEOB

last: KIM

state: Korea (the Republic of)

address: Banpodaero 222

institute: The Catholic University of Korea

data_processing:
Libraries were sequenced on HiSeq 2500 instruments
Using CellRanger 3.0.0 pipeline (10X Genomics), fastq data was aligned to a mouseh genome reference (mm10) and the unique molecular identifier (UMI) counts was quantified .
The raw gene expression matrix from the CellRanger pipeline was filtered using the Seurat R package (version 3.0) and selected according to the following criteria: cells with > 3000 genes, and < 7,000 genes, and < 0.2% of mitochondrial gene expression in UMI counts.
After filtering step, the raw gene expression matrix was normalized to the total UMI counts per cell and transformed to the natural log scale.
Further clustering and analysis were done under Seurat pipeline
Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Tab-deliminated text file containing the raw gene expression (UMI_raw_counts.txt) and the normalized gene expression (Natural_log_UMI_matrix.txt) for QC filtered cells, and cell annotation file.

organism: Homo sapiens

extract_protocol:
The cells were washed in PBS (0.04% BSA) and resuspended at a concentration of ~1000 cells/μl.
The cells were used for generating scRNA-seq libraries using Chromium Single-cell 3' Reagent Kits v2 (10x Genomics, Pleasanton, CA) according to the manufacturer’s protocol.

tag: phenotype

value: high potential of brain metastasis


title: FKBP12-PCGF35_NoDox0h_H3K27me3_Rep1


title: FKBP12-PCGF35_dTAG36h_Dox24h_H3K27me3_Rep1


title: PD2_ATAC_WT_Rep2

source_name: FACS-sorted CD140a+CD26+ dermal fibroblasts


title: 24 hours hfq 1xg control rep 2-1

city: Tempe

first: Jennifer

last: Barrila

state: AZ

address: 1001 S McAllister Ave

department: Biodesign Center for Fundamental and Applied Microbiomics

country: USA

institute: Arizona State University

description:
3-D co-culture model infected for 24 hours with the S. Typhimurium hfq mutant grown in the RWV in the control orientation
fpkm_TPM_sal_human.txt
hfq_1xg_24_4_R1.fastq.gz.merged.fastq.gz

data_processing:
bcl2fastq v2.17.1.14 used for basecalling
STAR v2.5.1b used for alignment
Stringtie-1.3.4c was used to report FPKM values (Fragments Per Kilobase of transcript per Million mapped reads), read counts and TPM (Transcripts Per Million).
Differential expression (DE) analysis was performed with EdgeR package from Bioconductor v3.2 in R 3.2.3.
Genome_build: Human: GRCh38.p7 primary assembly; Bacteria: S. Typhimurium LT2 genome
Supplementary_files_format_and_content: tab-delimited text files include FPKM and TPM values

molecule: total RNA

organism:
Homo sapiens
Salmonella enterica subsp. enterica serovar Typhimurium

growth_protocol: For RNA-Seq analysis of the bacteria just prior to infection, bacteria were cultured in Lennox Broth (LB) for 24 hr at 37 C and 25 rotations per minute (r.p.m.) in RWV bioreactors positioned in the LFS and control orientations. For infection studies, the 3-D co-culture model (HT-29 and U937 cells) was grown in the RWV bioreactor for 13-14 days in GTSF-2 medium at 10% CO2.

extract_protocol:
For RNA-Seq analysis of bacteria alone just prior to infection, wild type and hfq mutant S. Typhimurium were cultured to stationary phase in RWV bioreactors, fixed in RNAlater at a 2:1 ratio (fixative: sample) and stored at -80 C until processing. Bacteria were pelleted and resuspended in 200 µL RNase-free TE buffer (ThermoFisher Scientific) containing 2 mg/mL lysozyme (Sigma-Aldrich). Samples were incubated for 10 min at room temperature with intermittent vortexing to facilitate lysis. Qiazol was added to each sample (700 µL) and incubated at room temperature for 5 min with intermittent vortexing. Samples were transferred into prepared MaXtract tubes, 0.2 µL chloroform added, and shaken for 15 sec to mix. Following a 3 min incubation at room temperature, samples were centrifuged at 12,000 x g for 15 min at 4 C. The aqueous phase was then transferred to an RNase-free microfuge tube and 1.5 volumes of 100% molecular biology grade ethanol (Sigma-Aldrich) was added to each sample and inverted to mix. Samples were applied to a miRNeasy column (Qiagen) and purified with on-column DNase I treatment. Eluted samples were quantified using a Nanodrop spectrophotometer and RNA integrity confirmed using an Agilent Bioanalyzer.     For RNA-seq analysis of the host following infection, At the specified time points, infected and time-matched uninfected 3-D co-cultures were fixed in 1 mL Qiazol (Qiagen), vortexed and stored at -80 C until processing. To extract total RNA, samples were thawed, incubated for 5 min at room temperature with intermittent vortexing, and added to a prepared High Density MaXtract tube (Qiagen). To each sample, 0.2 mL chloroform (Sigma-Aldrich) was added and tubes were shaken for 15 seconds. Following a 3 min. incubation at room temperature, samples were centrifuged at 12,000 x g for 15 min. at 4 C. The aqueous phase was then transferred to an RNase-free microfuge tube and 1.5 volumes of 200-proof molecular biology grade ethanol (Sigma-Aldrich) was added and tubes were inverted to mix. Samples were applied to miRNeasy columns (Qiagen) and purified according to manufacturer’s instructions with a 20 min. on-column DNase I treatment. Eluted samples were quantified using a Nanodrop spectrophotometer and DNase-treated a second time using the TURBO DNA-free kit (ThermoFisher). RNA integrity was confirmed on an Agilent Bioanalyzer and all samples had an RNA Integrity Number (RIN) > 9.
cDNA was prepared from total RNA using the Ovation RNA-Seq System V2 via single primer isothermal amplification (NuGEN, 7102-A01) and automated on the Apollo 324 liquid handler (Wafergen). cDNA was quantified on the Nanodrop (Thermo Fisher Scientific) and then sheared to approximately 300 bp fragments using the Covaris M220 ultrasonicator. Libraries were generated using the Kapa Biosystem library preparation kit (KK8201). Fragments were end-repaired and A-tailed as described in the Kapa protocol. Individual indexes and adapters (Bioo, 520999) were ligated onto each separate sample. Adapter-ligated molecules were cleaned using AMPure beads (Agencourt Bioscience/Beckman Coulter, A63883) and amplified with Kapa HIFI enzyme (KK2502). Each library was then analyzed for fragment size on an Agilent Tapestation and quantified by qPCR (KAPA Library Quantification Kit, KK4835) on Quantstudio 5 (ThermoFisher Scientific) before multiplex pooling and sequencing on a 1x75 flow cell on the NextSeq platform (Illumina) at the Arizona State University Genomics Core facility.

treatment_protocol: For infection studies, 3-D models were counted and evenly seeded into multiwell plates at 1x10^6 cells/well. Cells were infected at a multiplicity of infection (m.o.i.) of ~15-30 for 30 minutes, 3 hours or 24 hours with either WT or hfq mutant S. Typhimurium grown in the RWV. To eliminate extracellular bacteria, gentamicin was added to the samples at concentrations of 50 µg/mL and 10 µg/mL at the 30 minute and 3 hour time points, respectively.

value: In vitro 3-D co-culture model comprised of human colonic epithelial cells and macrophages

tag: bacterial genotype

tag: bacterial growth orientation

value: control

tag: time post-infection

value: 24 hours


title: FKBP12-PCGF35_Dox24h_H3K27me3_Rep2


title: 24 hours hfq 1xg control rep 2

description:
3-D co-culture model infected for 24 hours with the S. Typhimurium hfq mutant grown in the RWV in the control orientation
fpkm_TPM_sal_human.txt
hfq_1xg_24_3_R1.fastq.gz.merged.fastq.gz


title: Naïve CD4 Tcell, ATACseq, Neonate, rep3

city: Iowa City

middle: Rachelle

last: Bermick

state: IA

address: 431 Newton Road, 505 EMRB

department: Pediatrics

institute: University of Iowa

data_processing:
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.39, discarding reads left with < 35 bp
ChIP-seq reads were aligned to the GRCh37 genome using default parameters in Bowtie2 version 2.3.4.2.
Peaks were called uing MACS2 V2.1.1.20160309 with the significance cut-off q-value <=0.05
bedgraph and narrowPeak files were generated using MACS v2 with default settings.
Assembly: GRCh37
Supplementary files format and content: bedgraph, narrowPeak

source_name: Naive CD4 T cells

extract_protocol: According to previously published ATAC-seq protocol (Buenrostro J, Wu B, Chang H, Greenleaf W. ATAC-seq: A method for assaying chromatin accessibility genome-wide. Curr Protoc Mol Biol, 2015, 109: 21.29.1-21.29.9). 50,000 cells were used as starting material.

value: Naive CD4 T cells

value: Term neonate


title: FKBP12-PCGF35_Dox24h_H3K27me3_Rep1


title: 24 hours hfq 1xg control rep 1-1

description:
3-D co-culture model infected for 24 hours with the S. Typhimurium hfq mutant grown in the RWV in the control orientation
fpkm_TPM_sal_human.txt
hfq_1xg_24_2_R1.fastq.gz.merged.fastq.gz


title: Naïve CD4 Tcell, ATACseq, Neonate, rep1


title: Naïve CD4 Tcell, ATACseq, Neonate, rep2

value: Male


title: FKBP12-PCGF35_NoDox0h_input_Rep2


title: 24 hours hfq 1xg control rep 1

description:
3-D co-culture model infected for 24 hours with the S. Typhimurium hfq mutant grown in the RWV in the control orientation
fpkm_TPM_sal_human.txt
hfq_1xg_24_1_R1.fastq.gz.merged.fastq.gz


title: Naïve CD4 Tcell, ATACseq, Adult, rep3

value: Adult


title: 24 hours hfq LFS rep 2-1

description:
3-D co-culture model infected for 24 hours with the S. Typhimurium hfq mutant grown in the RWV in the LFS orientation
fpkm_TPM_sal_human.txt
hfq_LS_24_4_R1.fastq.gz.merged.fastq.gz

value: LFS


title: FKBP12-PCGF35_NoDox0h_input_Rep1


title: Naïve CD4 Tcell, ATACseq, Adult, rep2


title: FKBP12-PCGF35_dTAG36h_Dox24h_input_Rep2


title: 24 hours hfq LFS rep 2

description:
3-D co-culture model infected for 24 hours with the S. Typhimurium hfq mutant grown in the RWV in the LFS orientation
fpkm_TPM_sal_human.txt
hfq_LS_24_3_S3_R1.fastq.gz


title: FKBP12-PCGF35_dTAG36h_Dox24h_input_Rep1


title: 24 hours hfq LFS rep 1-1

description:
3-D co-culture model infected for 24 hours with the S. Typhimurium hfq mutant grown in the RWV in the LFS orientation
fpkm_TPM_sal_human.txt
hfq_LS_24_2_R1.fastq.gz.merged.fastq.gz


title: Naïve CD4 Tcell, ATACseq, Adult, rep1


title: P4Sa

type: RNA

city: Mexico City

first: Jorge

middle: Yassen

last: Blancas

state: CDMX

address: Periferico Sur 4809

department: Research

country: Mexico

institute: INMEGEN

description: Blood platelets from PDAC patient before surgery

hyb_protocol: Samples were processed using the FlashTag Biotin HSR RNA Labeling Kit for Affymetrix GeneChip miRNA 4.0 according to the manufacturer's instructions

data_processing: All samples underwent microarray analysis on Affymetrix GeneChip miRNA 4.0 arrays. Data was normalised using Expression Console software (Affymetrix) prior to generating a list of differentially expressed genes

label: biotin

source_name: PDAC patient

growth_protocol: Blood was drawn in sodium citrate 3.4% tubes and processed within 30  minutes of draw. Pancreatic drainage was collected from Penrose drainaje recollection bag into 50ml Falcon Tubes. Samples of pancreatic drainage was processed within 30 minues of collection.

extract_protocol: Total RNA was extracted by Trizol RNA isolation (invitrogen) according to manufacturer's instrictions

treatment_protocol: All samples were initially spun at 100g for 15 minutes to separate the plasma from the Buffy Coat and Red Blood Cells. Plasma rich platelet were separately and  isolated from whole blood fractionated through micropipette. The plasma was re-centrifuged at 1500g for 10 minutes to obtain the platelet pellet. This pellet was used for total RNA isolation. The same protocol was used for the pancreatic drainage, discarting the first centifugation pellet.

value: Blood


title: 24 hours hfq LFS rep 1

description:
3-D co-culture model infected for 24 hours with the S. Typhimurium hfq mutant grown in the RWV in the LFS orientation
fpkm_TPM_sal_human.txt
hfq_LS_24_1_S14_R1.fastq.gz


title: FKBP12-PCGF35_Dox24h_input_Rep2

value: Dom/129S x Cast


title: P3Sa

scan_protocol: Samples were processed using the FlashTag Biotin HSR RNA Labeling Kit for Affymetrix GeneChip miRNA 4.0 according to the manufacturer's instructions


title: P4JP

description: Pancreatic drainage derived platelets from PDAC patient after surgery

label_protocol: Samples were processed using the FlashTag Biotin HSR RNA Labeling Kit for Affymetrix GeneChip miRNA 4.0 according to the manufacturer's instructions

value: Pancreatic drainage


title: P2JP


title: 24 hours WT 1xg control rep 2-1

description:
3-D co-culture model infected for 24 hours with WT S. Typhimurium grown in the RWV in the control orientation
3225_fpkm_TPM.txt
JB28-24h_1xg-2-1.fastq.gz

value: wild type


title: P2Sa


title: Naïve CD4 Tcell, H3K4me3, Neonate, rep4

data_processing:
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.39, discarding reads left with < 35 bp
ChIP-seq reads were aligned to the GRCh37 genome using default parameters in Bowtie2 version 2.3.4.2.
Peaks were called uing MACS2 V2.1.1.20160309 with the significance cut-off q-value <=0.05
bedgraph and narrowPeak files were generated using MACS v2 with default settings.
Assembly: GRCh37
Supplementary files format and content: bedgraph, narrowPeak (except for Input sample)

extract_protocol:
Cells were fixed with 2% paraformaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Pico (Diagenode) with 5 minutes of sonication with 30 seconds 'on' and 30 seconds 'off'.
ChIP-seq libraries were prepared using the Diagenode MicroPlex Library Preparation Kit v3 and Diagenode Unique Dual Index sequence Set 1 barcodes. 10^6 cells were used as starting material for input and ip samples. Libraries were amplified using 8 cycles on the thermocycler. Post amplification libraries were size selected at 150-1000bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Male and female

tag: number of_pooled_samples


title: Naïve CD4 Tcell, Input, Neonate, rep4


title: FKBP12-PCGF35_Dox24h_input_Rep1

value: mESC

value: Female

value: Endogenous Xist promoter replaced with TetOn Promoter (Dom/129S allele); Degron FKBP12-PCGF3/5


title: 24 hours WT 1xg control rep 1-1

description:
3-D co-culture model infected for 24 hours with WT S. Typhimurium grown in the RWV in the control orientation
3225_fpkm_TPM.txt
JB27-24h_1xg-1-1.fastq.gz

tag: tissue


title: Sema3G_stimulated_rep2

city: Chiba

first: Shigeru

last: Tanaka

address: 1-8-1 Inohana

department: Allergy and Clinical Immunology

country: Japan

institute: Chiba University

data_processing:
The reads obained were mapped on mm10 genome and UMI counts were measured using Strand NGS (Agilent).
Expression data were normalized and differentially expressed genes were identified using EdgeR (v 3.12).
Genome_build: mm10
Supplementary_files_format_and_content: DEG.txt contains the gene expression of each sample.

source_name: Bone marrow derived macrophages

growth_protocol: Bone marrow cells were cultured in the presence of 50ng/ml M-CSF for 5 days to obtain macrophages. Bone marrow derived macrophages  were futher cultured with 100ng/ml LPS to be activated.

extract_protocol:
Cells were lysed in Trizol reagent and total RNAs were purified according to the protocol.
QuantSeq 3'mRNA-seq Library prep kit for illumina

treatment_protocol: Activated macrophages were cultured with either PBS or 100ng/ml Semaphorin3G for 18 hours.

value: Semaphorin 3G

value: Bone marrow derived macrophages


title: Sema3G_stimulated_rep3


title: Naïve CD4 Tcell, Input, Neonate, rep3


title: Sema3G_stimulated_rep1


title: P3JP


title: 24 hours WT 1xg control rep 1

description:
3-D co-culture model infected for 24 hours with WT S. Typhimurium grown in the RWV in the control orientation
3225_fpkm_TPM.txt
JB25-24h_1xg-1.fastq.gz

value: In vitro 3-D co-culture model comprised of human colonic epithelial cells and macrophages

value: control


title: Naïve CD4 Tcell, H3K4me3, Neonate, rep2

value: Naive CD4 T cells


title: P1Sa


title: P1JP


title: no treatment_rep2

value: PBS


title: 24 hours WT 1xg control rep 2

description:
3-D co-culture model infected for 24 hours with WT S. Typhimurium grown in the RWV in the control orientation
3225_fpkm_TPM.txt
JB26-24h_1xg-2.fastq.gz

value: 24 hours


title: Naïve CD4 Tcell, Input, Neonate, rep2

value: Term neonate


title: Naïve CD4 Tcell, H3K4me3, Neonate, rep3


title: no treatment_rep1


title: Naïve CD4 Tcell, H3K4me3, Neonate, rep1


title: 24 hours WT LFS rep 1-1

description:
3-D co-culture model infected for 24 hours with WT S. Typhimurium grown in the RWV in the LFS orientation
3225_fpkm_TPM.txt
JB23-24h_LS-1-1.fastq.gz

value: LFS


title: Naïve CD4 Tcell, Input, Neonate, rep1


title: CON3

description: Blood Platelets from healthy control

source_name: Healthy Donor

value: Blood


title: 542_E12.5_FB_ATAC_rep2

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL

description: II1TDOM 542 E12.5 Forebrain ATAC replicate 2

data_processing:
All command lines are available at https://github.com/lldelisle/scriptsForBoltEtAl2022
Adapter sequences and bad quality bases were removed with Cutadapt[Martin et al. 2016] version 1.16 with options -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA -q 30 -m 15.
Reads were mapped with bowtie[Langmead et al. 2012] 2.4.1 with parameters -I 0 -X 1000 --fr --dovetail --very-sensitive on mm10 or on the II1TDOM-542 mutant genome.
Alignments with a mapping quality below 30, discordant pairs, and reads mapping to the mitochondria, were discarded with bamtools version 2.4.0 [https://github.com/pezmaster31/bamtools].
PCR duplicates were removed with Picard[http://broadinstitute.github.io/picard/index.html] version 2.18.2 before the BAM to BED conversion with bedtools[Quinlan et al. 2010] version 2.30.0.
Coverage and peak calling were computed by macs2 [Zhang et al. 2008] version 2.1.1.20160309 with options --format BED --gsize 1870000000 --call-summits --keep-dup all --bdg --nomodel --extsize 200 --shift -100.
Genome_build: mm10 or the II1TDOM-542 mutant genome
Supplementary_files_format_and_content: bigwig: coverage from macs2
Supplementary_files_format_and_content: narrowPeak: peaks from macs2

source_name: forebrain

growth_protocol: Crosses were made between heterozygous adults. Animals were checked for vaginal plugs on the next morning, establishing the timepoint 0.5 embryonic days. Embryos were collected 12 days later.

extract_protocol:
The forelimbs or forebrains of embryos were dissected and placed into PBS with 10% FCS and 8ul collagenase at 50mg/ml (Sigma C9697) at 37º for approximately 5min. Cells were counted and 50,000 cells were isolated for processing with the Nextera Tn5 enzyme (Illumina FC-131-1096) as previously described (Buenrostro NatMeth 2013).
Tn5 treated DNA was amplified with Nextera Library primers using NEBNext library amplification master mix (NEB M0541).

treatment_protocol: No treatment

value: forebrain

tag: genotype

value: II1TDOM 542 (mutant)


title: 24 hours WT LFS rep 2-1

description:
3-D co-culture model infected for 24 hours with WT S. Typhimurium grown in the RWV in the LFS orientation
3225_fpkm_TPM.txt
JB24-24h_LS-2-1.fastq.gz

value: wild type


title: 24 hours WT LFS rep 1

description:
3-D co-culture model infected for 24 hours with WT S. Typhimurium grown in the RWV in the LFS orientation
3225_fpkm_TPM.txt
JB21-24h_LS-1.fastq.gz


title: CON4

description: Blood Platelets from healthy control


title: CON2

description: Blood Platelets from healthy control


title: Naïve CD4 Tcell, H3K4me3, Adult, rep3

value: Adult

value: Male


title: NucRNAseq_FTY3

city: La Jolla

first: Yasuyuki

last: Kihara

state: CA

address: 10901 N Torrey Pines Rd

institute: Sanford Burnham Prebys Medical Discovery Institute

description:
FTY3
Processed data file: JC_NS65_EX.txt
Processed data file: JC_NS65_EXINTRON.txt

data_processing:
The Genome Analyzer Pipeline Software (currently Casava v1.8.2) is used to perform the early data analysis of a sequencing run, which does the image analysis, base calling, and demultiplexing. The program called cutadapt is used to trim the adapter and low basepair called scores.
For the exon/gene annotations and the mRNA annotation, Partek® software, version 6.6 Copyright © 2012 Partek Inc., St. Louis, MO, USA is used.
Normalization is performed by the TMM (trimmed mean of M) method where the sample whose 75%-ile (of library-scale-scaled counts) is closest to the mean of 75%-iles as the reference. This adjustment is applied to the library size (total sample counts) to account for the compositional bias. In edgeR the scaling factor is used as an "offset" in the negative binomial model and the original count data is entered into the model.
RNA-seq and data processing were performed at the Sequencing Core of The Scripps Research Institute.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include CPM (counts per million) values for each Sample.

molecule: nuclear RNA

source_name: DAPI+NeuN-GFP+ nuclei

growth_protocol: Mice were immunized with MOG35-55/CFA to induce EAE. After 5 days post onset, DAPI+NeuN-GFP+ nuclei were isolated with BD FACSAria II.

extract_protocol:
Populations of 15,000 DAPI+NeuN-GFP+ nuclei were directly sorted into an extraction buffer for RNA isolation of PicopureTM RNA isolation kit (Arcturus, ThermoFisher). Deoxyribonuclease I (DNase I) (Qiagen) was used to remove genomic DNA.
A sequencing library was produced using 0.75 ng of the amplified cDNA in the Nextera XT Library Preparation Kit (Illumina).

treatment_protocol: EAE-Mice were treated with or without 1mg/kg FTY720 for 5 days.

tag: strain/background

tag: genotype/variation

value: FTY720-treated WT

value: Astrocytes


title: NucRNAseq_FTY2

description:
FTY2
Processed data file: JC_NS65_EX.txt
Processed data file: JC_NS65_EXINTRON.txt

tag: cell type


title: 3 hours hfq 1xg control rep 2-1

description:
3-D co-culture model infected for 3 hours with the S. Typhimurium hfq mutant grown in the RWV in the control orientation
fpkm_TPM_sal_human.txt
hfq_1xg_3_4_R1.fastq.gz.merged.fastq.gz

value: 3 hours


title: Naïve CD4 Tcell, Input, Adult, rep3

tag: developmental stage


title: 24 hours WT LFS rep 2

description:
3-D co-culture model infected for 24 hours with WT S. Typhimurium grown in the RWV in the LFS orientation
3225_fpkm_TPM.txt
JB22-24h_LS-2.fastq.gz


title: GATA2

city: Maebashi

first: Akira

last: Shimizu

state: Gunma

address: 3-39-11 showamachi, Maebashi

department: Dermatology

institute: Gunma university

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a Agilent fragmentation buffer and was hybridized at 65°C for 17 hr using Gene Expression Hybridization Kit.

scan_protocol: Microarray slides were scanned at 3 μm resolution using an Agilent G2505C Microarray Scanner System.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Agilent one-color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol

extract_protocol: Freshly drawn peripheral blood from a patient of GATA2 deficiency and a dehealthy volunteer were subjected to RNA extraction. RNA extraction was performed using Rneasy (Quiagen).The protocol includes differential lysis of red and white blood cells, and an DNase digestion.

tag: disease state

value: GATA2 deficiency

value: blood


title: Normal

source_name: Normal

value: Healthy


title: NucRNAseq_FTY1

description:
FTY1
Processed data file: JC_NS65_EX.txt
Processed data file: JC_NS65_EXINTRON.txt


title: 3 hours hfq 1xg control rep 2

description:
3-D co-culture model infected for 3 hours with the S. Typhimurium hfq mutant grown in the RWV in the control orientation
fpkm_TPM_sal_human.txt
hfq_1xg_3_3_S16_R1.fastq.gz

value: In vitro 3-D co-culture model comprised of human colonic epithelial cells and macrophages

tag: strain

value: control


title: Day7 MP Nontarget Knockdown isotype, CUT&RUN

first: John

last: Chang

address: 9500 Gilman Drive

department: School of Medicine

institute: UC San Diego

description: CUT&RUN Libraries

data_processing:
Reads were mapped either to the mouse or yeast genome with bowtie2 -p 8 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 (v1.2.2). Mapped reads were then converted into bed files. A scale factor for Spike-In normalization was calculated for each sample by dividing 1000 from the sequencing depth of mapped yeast reads. Bed files were normalized using bedtools genomcov (v2.29.2) with the respective scaling factor calculated as describe above. Peaks calls were determined using macs2 macs2 callpeak -broad --broad-cutoff 0.1 -B --nomodel --keep-dup all -f BED (v2.1.2).
none provided by the submitter
Assembly: mm10
Supplementary files format and content: Normalized bedgraph files

source_name: Spleen

extract_protocol:
One-hundred thousand TE and MP Malat1 Knockdown and Nontarget P14 CD8+ T cells were sorted 7 days after LCMV
CUT&RUN libraries generated using the Cell Signaling CUT&RUN Assay kit according to manufacturer protocol (Catalog Number: 86652). Equal numbers of 100,000 cells per sample condition were isolated for isotype controls. Binding with primary anti-H3K27me3 antibody (07-449, EMD Millipore) and IgG control antibody binding was conducted overnight at 4°C. Fifty picograms of Spike-In Yeast DNA was added per sample after pAG-MNase activation with Calcium Chloride. DNA was purified and sequencing libraries generated using SimpleChIP ChIP-seq DNA Library Prep Kit for Illumina with Dual indices according to manufacturer protocol (Catalog number: 56795). Final libraries were amplified for 10 cycles.

value: CD8 T cells

value: Spleen

tag: age

value: 6-8 weeks old


title: OCM pig pancreatic tumor, Biological replicate 2, pig ID: 1092

city: Omaha

first: Hamid

last: Band

state: Nebraska

address: 42nd and Emile

department: Eppley

institute: University of Nebraska Medical Center

description: Gene expression data from OCM pig pancreatic tumor.

hyb_protocol: 2.5ug of fragmented single stranded and biotin labeled cDNA (sscDNA) for each sample was used to prepare the hybridization cocktail. Hybridization Cocktail was used to hybridize the GeneChip Porcine Gene 1.0 ST array (Life Technologies 901977) in a GeneChip Hybridization Oven 645 at 45C with 60rpm rotation for 16 hours. Arrays were washed and stained using the GeneChip Fluidics Station 450 running the FS 450-0002 fluidics profile with a single stain step using the GeneChip Hybridization, Wash, Stain Kit. Array was filled with Array Holding Buffer (from Hyb. Wash, stain kit) prior to scan.

scan_protocol: Array scan was performed using the GeneChip Scanner 3000 with Autoloader and 7G upgrade with a single scan per array.

data_processing: The data were analyzed with Transcriptome Analysis Console with gene level RMA and default analysis settings.

source_name: Pancreatic tumor

label_protocol: Target labeling was completed with the GeneChip Whole Transcript (WT) Plus reagent kit (Life Technologies 902280) to perform the WT Plus Expression Sense Target Protocol. Input RNA of 100ng per sample was used to initiate the target labeling protocol.

extract_protocol: RNA was isolated by AllPrep DNA/RNA Kits according to the manufacturer's protocol.

value: Oncopig Cancer Model

value: Prancreatic tumor tissue


title: OCM pig pancreatic tumor, Biological replicate 1, pig ID: 1090


title: Naïve CD4 Tcell, H3K4me3, Adult, rep2

value: Naive CD4 T cells

tag: Sex

value: Female


title: 3 hours hfq 1xg control rep 1-1

description:
3-D co-culture model infected for 3 hours with the S. Typhimurium hfq mutant grown in the RWV in the control orientation
fpkm_TPM_sal_human.txt
hfq_1xg_3_2_R1.fastq.gz.merged.fastq.gz


title: NucRNAseq_KO3

description:
B1_3
KO3
Processed data file: JC_NS65_EX.txt
Processed data file: JC_NS65_EXINTRON.txt

value: S1P1-astrocyte specific KO


title: CON1

description: Blood Platelets from healthy control

value: Blood


title: Wild type pancreas, Biological replicate 2

description: Gene expression data from normal pancreas.

source_name: Normal pancreas

value: Normal pancreatic tissue


title: Day7 MP Malat1 Knockdown isotype, CUT&RUN

description: CUT&RUN Libraries


title: Naïve CD4 Tcell, Input, Adult, rep2

value: Adult

tag: chip antibody


title: 3 hours hfq 1xg control rep 1

description:
3-D co-culture model infected for 3 hours with the S. Typhimurium hfq mutant grown in the RWV in the control orientation
fpkm_TPM_sal_human.txt
hfq_1xg_3_1_R1.fastq.gz.merged.fastq.gz

value: 3 hours


title: Day7 TE Nontarget Knockdown isotype, CUT&RUN

description: CUT&RUN Libraries


title: NucRNAseq_WT4

description:
WT4
Processed data file: JC_NS65_EX.txt
Processed data file: JC_NS65_EXINTRON.txt

value: WT

value: Astrocytes


title: NucRNAseq_KO1

description:
B1_1
KO1
Processed data file: JC_NS65_EX.txt
Processed data file: JC_NS65_EXINTRON.txt


title: Naïve CD4 Tcell, Input, Adult, rep1


title: 3 hours hfq LFS rep 2-1

description:
3-D co-culture model infected for 3 hours with the S. Typhimurium hfq mutant grown in the RWV in the LFS orientation
fpkm_TPM_sal_human.txt
hfq_LS_3_4_S2_R1.fastq.gz

value: LFS


title: Naïve CD4 Tcell, H3K4me3, Adult, rep1


title: 3 hours hfq LFS rep 1-1

description:
3-D co-culture model infected for 3 hours with the S. Typhimurium hfq mutant grown in the RWV in the LFS orientation
fpkm_TPM_sal_human.txt
hfq_LS_3_2_S13_R1.fastq.gz

value: In vitro 3-D co-culture model comprised of human colonic epithelial cells and macrophages


title: NucRNAseq_WT3

description:
WT3
Processed data file: JC_NS65_EX.txt
Processed data file: JC_NS65_EXINTRON.txt


title: 3 hours hfq LFS rep 2

description:
3-D co-culture model infected for 3 hours with the S. Typhimurium hfq mutant grown in the RWV in the LFS orientation
fpkm_TPM_sal_human.txt
hfq_LS_3_3_R1.fastq.gz.merged.fastq.gz


title: Day7 MP Nontarget Knockdown, replicate 1, CUT&RUN

description: CUT&RUN Libraries


title: NucRNAseq_KO2

description:
B1_2
KO2
Processed data file: JC_NS65_EX.txt
Processed data file: JC_NS65_EXINTRON.txt


title: NucRNAseq_WT2

description:
WT2
Processed data file: JC_NS65_EX.txt
Processed data file: JC_NS65_EXINTRON.txt


title: 3 hours WT 1xg control rep 2-1

description:
3-D co-culture model infected for 3 hours with WT S. Typhimurium grown in the RWV in the control orientation
3225_fpkm_TPM.txt
JB16-3h_1xg-3-1.fastq.gz

value: wild type

value: control


title: Day7 MP Nontarget Knockdown, replicate 2, CUT&RUN

description: CUT&RUN Libraries

value: CD8 T cells

value: Spleen


title: RIP-seq keloid-input

city: guangzhou

first: rong

middle: ke

last: xiang

state: china

address: shipai

institute: xiangkerong

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed using the Trimmomatic software. Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.Meanwhile, Use the SortMeRNA software for ribosomal RNA reads removal.After discarded the rRNA reads, the remainly clean reads were mapped to the reference genome GRCh38.p12 using HISAT2 with default parameters. Unique reads with high mapping quality were retained
The m6A-enriched peaks in each m6A immunoprecipitation sample were identified by MeTDiff peak calling software with the corresponding input sample  serving as control. MeTDiff was run with options (‘FRAGMENT_LENGTH=200,PEAK_CUTOFF_PVALUE = 0.05, PEAK_CUTOFF_FDR = 0.05’) for peak detection. Called peaks were annotated by intersection with gene architecture using ChIPseeker
Differential analysis for m6A-Seq identifies differences in RNA methylome in a case-control study, The differential peak were detected by MeTDiff with parameter  (‘FRAGMENT_LENGTH = 200, PEAK_CUTOFF_PVALUE = 0.01,DIFF_PEAK_CUTOFF_FDR = 0.05, PEAK_CUTOFF_FDR = 0.05’), after which,differential peak were annotated by ChIPseeker
Assembly: GRCh38.p12
Supplementary files format and content: bigWig files of every sample
Supplementary files format and content: Peak text files (except for Input sample)

source_name: keloid

extract_protocol:
Total RNA was extracted using mirVana miRNA Isolation Kit (Ambion) according to the manufacturer’s protocol.
We utilized input and post m6A-IP positive fraction for library construction utilizing the Illumina TrueSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego,  CA, USA) according to the manufacturer’s instructions.

value: keloid

tag: rip antibody


title: Day7 MP Malat1 Knockdown, replicate 2, CUT&RUN

description: CUT&RUN Libraries

value: 6-8 weeks old


title: NucRNAseq_WT1

description:
WT1
Processed data file: JC_NS65_EX.txt
Processed data file: JC_NS65_EXINTRON.txt


title: 3 hours WT 1xg control rep 2

description:
3-D co-culture model infected for 3 hours with WT S. Typhimurium grown in the RWV in the control orientation
3225_fpkm_TPM.txt
JB15-3h_1xg-2.fastq.gz


title: RIP-seq Normal skin-input

source_name: normal skin

value: normal skin


title: RNAseq_B12suf, rep2

description:
B12suf_2
Cultured in serum-free media.
Processed data file: JC_NS190_AstrocyteB12.txt

data_processing:
Salmon was used for transcript quantification while Counts Per Million (CPM) values were calculated using tximport.
RNA-seq and data processing were performed at the Sequencing Core of The Scripps Research Institute.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: JC_NS190_AstrocyteB12.txt: Tab-delimited text file includes CPM (counts per million) values for each Sample.

source_name: P0, Cortex

growth_protocol: Astrocytes were cultured in serum-free normal media or serum-free B12-free media for 2 weeks.

extract_protocol:
RNA was extracted using RNeasy minikit (Qiagen) (with DNase I treatment) as per manufacturer’s instructions.
150 ng of RNA per sample was employed in the generation of libraries using NEB Next Ultra Pure RNA library kit for Illumina (NEB) as per manufacturer’s instructions.

tag: media

value: serum-free


title: 3 hours hfq LFS rep 1

description:
3-D co-culture model infected for 3 hours with the S. Typhimurium hfq mutant grown in the RWV in the LFS orientation
fpkm_TPM_sal_human.txt
hfq_LS_3_1_S1_R1.fastq.gz

tag: bacterial genotype


title: Wild type pancreas, Biological replicate 1


title: Day7 TE Nontarget Knockdown, replicate 2, CUT&RUN

description: CUT&RUN Libraries


title: Day7 MP Malat1 Knockdown, replicate 1, CUT&RUN

description: CUT&RUN Libraries


title: RIP-seq Normal skin

value: Anti-m6A (Synaptic Systems, Cat. No 202 003)


title: RNAseq_B12suf, rep1

description:
B12suf_1
Cultured in serum-free media.
Processed data file: JC_NS190_AstrocyteB12.txt


title: Day7 TE Malat1 Knockdown isotype, CUT&RUN

description: CUT&RUN Libraries


title: Day7 TE Nontarget Knockdown, replicate 1, CUT&RUN

description: CUT&RUN Libraries


title: 3 hours WT 1xg control rep 1-1

description:
3-D co-culture model infected for 3 hours with WT S. Typhimurium grown in the RWV in the control orientation
3225_fpkm_TPM.txt
3hr_1xg-2-1-34031033.fastq.gz

tag: bacterial growth orientation


title: RNAseq_B12def, rep2

description:
B12def_2
Cultured in serum-free B12-free media.
Processed data file: JC_NS190_AstrocyteB12.txt

value: serum-free and B12-free


title: RNAseq_B12def, rep1

description:
B12def_1
Cultured in serum-free B12-free media.
Processed data file: JC_NS190_AstrocyteB12.txt


title: 3 hours WT 1xg control rep 1

description:
3-D co-culture model infected for 3 hours with WT S. Typhimurium grown in the RWV in the control orientation
3225_fpkm_TPM.txt
3hr_1xg-1-34007154.fastq.gz

tag: time post-infection


title: Day7 TE Malat1 Knockdown, replicate 2, CUT&RUN

description: CUT&RUN Libraries


title: Sample7_CAR T_N/SCM

city: Milan

first: Monica

last: Casucci

address: Via Olgettina, 58

department: Division of immunology, transplantation and infectious diseases

country: Italy

institute: IRCCS San Raffaele Scientific Institute

description: co-culture with B-ALL cell line and CAR T cells

data_processing:
Low quality reads and Illumina adapters were trimmed using Trimmomatic (version 0.39).
The remaining reads were mapped to the reference human genome GRCh38, using STAR aligner (version 2.5.3a)
Uniquely mapped reads were assigned to the corresponding genes using the featureCounts (version1.6.4). Only reads mapped to exons were considered in the counting procedure. Genomic features were annotated according to Gencode basic annotations (Gencode release 31).
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: monocytes

extract_protocol:
PicoPure RNA Isolation Kit (Thermo Fisher Scientific)
QC check of all RNA samples was done by TapeStation HS RNA. All the samples were processed with SMART-Seq v4 Ultra Low Input RNA Kit to ensure that the final cDNA libraries contain the 5′ end of the mRNA and maintain a true representation of the original mRNA transcripts. NGS library preparation for Illumina Sequencing was performed with Nextera XT DNA Library preparation kit. Limited-cycle PCR was used to amplify the insert DNA and to add index adapter sequences on both ends of the DNA as well.  All of the samples were barcoded, pooled and sequenced on an Illumina Nova-Seq 6000 machine (Illumina, San Diego, CA) sequencing system in SR (single read) mode, obtaining an average of 30 millions of single-end reads 100 nt long per sample.

treatment_protocol: co-culture with leukemic ALL cell line and CAR T cells

tag: donor id

value: donor 4

value: monocytes

tag: treatment

value: CAR T_N/SCM


title: RIP-seq keloid

tag: tissue


title: 3 hours WT LFS rep 2-1

description:
3-D co-culture model infected for 3 hours with WT S. Typhimurium grown in the RWV in the LFS orientation
3225_fpkm_TPM.txt
JB14-3h_LS-3-1.fastq.gz

value: 3 hours


title: Day7 TE Malat1 Knockdown, replicate 1, CUT&RUN

description: CUT&RUN Libraries


title: 320_nCATS

description: II1TDOM 320 E12.5 yolksac gDNA

data_processing:
Library strategy: nCATS
All command lines are available at https://github.com/lldelisle/scriptsForBoltEtAl2022
Bases were called from the fast5 files using Guppy basecaller (Oxford Nanopore Technologies) for CPU version 5.0.16+b9fcd7b.
Reads were mapped on mm10 with minimap2[Li et al. 2018] version 2.15 with parameter -ax map-ont.
Only primary aligments were kept with samtools view version 1.10  [Li et al. 2009 and Li et al. 2011].
bam was converted to bed with bedtools [Quinlan et al. 2010] 2.27.1
Genome_build: mm10
Supplementary_files_format_and_content: bed file where each line is an alignment

source_name: yolksac

extract_protocol:
Yolksacs were placed into Tail Digestion Buffer with Proteinase K at 55ºC overnight with no shaking. The following day the samples were incubated at 95ºC for 10 minutes to inactivate Proteinase K. The DNA was precipitated with ethanol and sodium acetate, washed two times with 70% ethanol and the pellet was dissolved in 200ul 10mM Tris pH7.5.
The gDNA was then processed through the nCATS protocol followed by the Oxford Nanopore minION library construction kit (SQK-LSK109).

value: yolksac

tag: genotype

value: II1TDOM 320 gDNA


title: RNA-seq Normal skin

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data (raw reads) were processed using Trimmomatic
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count. DEGs were identified using the DESeq(2012) R package functions estimateSizeFactors and nbinomTest. Pvalue < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression.
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: tab-delimited text files include read counts for each Sample

extract_protocol:
Total RNA was extracted using mirVana miRNA Isolation Kit (Ambion) according to the manufacturer’s protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform (HiSeqTM 2500 or Illumina HiSeq X Ten) and 125bp/150bp paired-end reads were generated.


title: 3 hours WT LFS rep 2

description:
3-D co-culture model infected for 3 hours with WT S. Typhimurium grown in the RWV in the LFS orientation
3225_fpkm_TPM.txt
JB13-3h_LS-2.fastq.gz

value: In vitro 3-D co-culture model comprised of human colonic epithelial cells and macrophages

value: LFS


title: Sample6_CAR T_N/SCM

value: donor 5


title: Sample5_CAR T_N/SCM

value: donor 1


title: TG_700_13

city: Turku

first: Michael

last: Gabriel

address: Kiinamyllynkatu 10

country: Finland

institute: University of Turku

data_processing:
Illumina Casava1.8 software used for basecalling.
Aligment performed using HISAT2 (2.0.5)
Transcript abundance was quantified using FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced).
Sequencing depth was at least 20 million reads per sample and reads were mapped to mouse genome (Mus_musculus_Ensemble_94) using HISAT2 (2.0.5).
Differential expression analysis between two conditions/groups was performed using the DESeq2 R package (2_1.6.3).
KEGG and GO analysis was performed using clusterProfiler (3.8.1)
Assembly: Mus_musculus_Ensemble_94
Supplementary files format and content: HSD17B1_TGvsWT_deg_FPKMcut1.xlsx contains files with FPKM for every gene and every sample.

source_name: Uterus

extract_protocol:
Uteri were weighed, snap-frozen in liquid N2 and stored at − 80 ℃,  RNA was isolated using Trizol reagent (Thermo Fisher Scientific), further purified with RNeasy columns (Qiagen), and treated with DNase (RNase-free DNase Set, Qiagen; or DNase I, Invitrogen, Thermo Fisher Scientific). The RNA concentrations were measured using Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and quality of RNA was verified using Bioanalyzer 2100 (Agilent).
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene

value: uterus

value: 4 months

value: transgenic


title: 3 hours WT LFS rep 1-1

description:
3-D co-culture model infected for 3 hours with WT S. Typhimurium grown in the RWV in the LFS orientation
3225_fpkm_TPM.txt
3hr_LS-1-1-34024050.fastq.gz

value: wild type


title: Sample4_CAR T_Bulk

value: CAR T_Bulk


title: 3 hours WT LFS rep 1

description:
3-D co-culture model infected for 3 hours with WT S. Typhimurium grown in the RWV in the LFS orientation
3225_fpkm_TPM.txt
3hr_LS-1-34013133.fastq.gz


title: PqsE+RhlR biol rep 2

city: Rome

first: Morgana

last: Letizia

address: Viale Guglielmo Marconi, 446

institute: Roma Tre University

description: Sample 11 - Group D

data_processing:
sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Pseudomonas_aeruginosa_PAO1 reference genome available on ENSEMBL using the Bowtie2 aligner v.2.2.6. BAM files were generated as a result of this step.
Unique gene hit counts were calculated using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within gene regions were counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed
The Wald test was used to generate p- values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Assembly: PAO1 GCA_000006765
Supplementary files format and content: tab-delimited text files include hit counts values for each Sample

organism: Pseudomonas aeruginosa

growth_protocol: P. aeruginosa cultures were grown overnight in LB at 37°C with shaking (200 rpm). Following overnight growth, bacteria were diluted to an OD600 of 0.01 into 15 mL of LB supplemented with 50 mM MOPS, 0.1% (w/v) L-arabinose, 10 µM C4-HSL, and/or 500 µM IPTG. The resulting cultures were incubated at 37°C with shaking. RNA was extracted from 1 mL of each culture at an OD600 of 1.8 (late exponential phase of growth).

extract_protocol:
mRNA was preserved immediately upon cell harvest using Qiagen RNAprotect. Cells were lysed using sonication and RNA was harvested using RNeasy Mini Kit (Qiagen) including the on-column DNase I digestion step. In addition, eluted RNA was treated for 1 h at 37°C with TURBO DNase (0.2 U per μg of RNA; Ambion) and with SUPERase-In (0.4 U per μg of RNA; Ambion). DNase I was removed with the RNeasy Column Purification Kit (Qiagen). 3 µg of total RNA was used for the construction of sequencing libraries.
rRNA depletion was performed using NEBNext rRNA Depletion Kit (Bacteria). RNA sequencing library preparation was performed using NEBNext Ultra II RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA).

treatment_protocol: rhlR gene expression was induced by L-arabinose, pqsE expression was induced by IPTG

value: mutant strain carrying in-frame deletions of pqsA, pqsH, pqsL, rhlI, rhlR, lasI, rsaL, lasR, phnA, phnB and pqsR, a chromosomally integrated construct for IPTG-inducible expression of pqsE, and the pHERD-rhlR plasmid for L-arabinose-inducible expression of rhlR [deltaQS-Eind(pHERD-rhlR)]

value: ∆QS-Eind(pHERD-rhlR) grown in LB supplemented with 0.1% (w/v) L-arabinose, 500 µM IPTG and 10 μM C4-HSL


title: RNA-seq keloid

value: keloid


title: WT_701_30

value: WT


title: PqsE+RhlR biol rep 3

description: Sample 12 - Group D


title: 30 min WT 1xg control rep 2-1

description:
3-D co-culture model infected for 30 minutes with WT S. Typhimurium grown in the RWV in the control orientation
3225_fpkm_TPM.txt
JB8-30min_1xg-2-1.fastq.gz

data_processing:
bcl2fastq v2.17.1.14 used for basecalling
STAR v2.5.1b used for alignment
Stringtie-1.3.4c was used to report FPKM values (Fragments Per Kilobase of transcript per Million mapped reads), read counts and TPM (Transcripts Per Million).
Differential expression (DE) analysis was performed with EdgeR package from Bioconductor v3.2 in R 3.2.3.
Genome_build: Human: GRCh38.p7 primary assembly; Bacteria: S. Typhimurium LT2 genome
Supplementary_files_format_and_content: tab-delimited text files include FPKM and TPM values

extract_protocol:
For RNA-Seq analysis of bacteria alone just prior to infection, wild type and hfq mutant S. Typhimurium were cultured to stationary phase in RWV bioreactors, fixed in RNAlater at a 2:1 ratio (fixative: sample) and stored at -80 C until processing. Bacteria were pelleted and resuspended in 200 µL RNase-free TE buffer (ThermoFisher Scientific) containing 2 mg/mL lysozyme (Sigma-Aldrich). Samples were incubated for 10 min at room temperature with intermittent vortexing to facilitate lysis. Qiazol was added to each sample (700 µL) and incubated at room temperature for 5 min with intermittent vortexing. Samples were transferred into prepared MaXtract tubes, 0.2 µL chloroform added, and shaken for 15 sec to mix. Following a 3 min incubation at room temperature, samples were centrifuged at 12,000 x g for 15 min at 4 C. The aqueous phase was then transferred to an RNase-free microfuge tube and 1.5 volumes of 100% molecular biology grade ethanol (Sigma-Aldrich) was added to each sample and inverted to mix. Samples were applied to a miRNeasy column (Qiagen) and purified with on-column DNase I treatment. Eluted samples were quantified using a Nanodrop spectrophotometer and RNA integrity confirmed using an Agilent Bioanalyzer.     For RNA-seq analysis of the host following infection, At the specified time points, infected and time-matched uninfected 3-D co-cultures were fixed in 1 mL Qiazol (Qiagen), vortexed and stored at -80 C until processing. To extract total RNA, samples were thawed, incubated for 5 min at room temperature with intermittent vortexing, and added to a prepared High Density MaXtract tube (Qiagen). To each sample, 0.2 mL chloroform (Sigma-Aldrich) was added and tubes were shaken for 15 seconds. Following a 3 min. incubation at room temperature, samples were centrifuged at 12,000 x g for 15 min. at 4 C. The aqueous phase was then transferred to an RNase-free microfuge tube and 1.5 volumes of 200-proof molecular biology grade ethanol (Sigma-Aldrich) was added and tubes were inverted to mix. Samples were applied to miRNeasy columns (Qiagen) and purified according to manufacturer’s instructions with a 20 min. on-column DNase I treatment. Eluted samples were quantified using a Nanodrop spectrophotometer and DNase-treated a second time using the TURBO DNA-free kit (ThermoFisher). RNA integrity was confirmed on an Agilent Bioanalyzer and all samples had an RNA Integrity Number (RIN) > 9.
cDNA was prepared from total RNA using the Ovation RNA-Seq System V2 via single primer isothermal amplification (NuGEN, 7102-A01) and automated on the Apollo 324 liquid handler (Wafergen). cDNA was quantified on the Nanodrop (Thermo Fisher Scientific) and then sheared to approximately 300 bp fragments using the Covaris M220 ultrasonicator. Libraries were generated using the Kapa Biosystem library preparation kit (KK8201). Fragments were end-repaired and A-tailed as described in the Kapa protocol. Individual indexes and adapters (Bioo, 520999) were ligated onto each separate sample. Adapter-ligated molecules were cleaned using AMPure beads (Agencourt Bioscience/Beckman Coulter, A63883) and amplified with Kapa HIFI enzyme (KK2502). Each library was then analyzed for fragment size on an Agilent Tapestation and quantified by qPCR (KAPA Library Quantification Kit, KK4835) on Quantstudio 5 (ThermoFisher Scientific) before multiplex pooling and sequencing on a 1x75 flow cell on the NextSeq platform (Illumina) at the Arizona State University Genomics Core facility.

value: control

value: 30 minutes


title: WT_698_10


title: Sample3_CAR T_Bulk

value: donor 3

value: monocytes


title: PqsE+RhlR biol rep 1

description: Sample 10 - Group D


title: Sample2_CAR T_Bulk

value: donor 2


title: 30 min WT 1xg control rep 2

description:
3-D co-culture model infected for 30 minutes with WT S. Typhimurium grown in the RWV in the control orientation
3225_fpkm_TPM.txt
JB6-30min_1xg-2.fastq.gz

value: In vitro 3-D co-culture model comprised of human colonic epithelial cells and macrophages


title: Sample1_CAR T_Bulk


title: RhlR biol rep 3

description: Sample 9 - Group C

value: ∆QS-Eind(pHERD-rhlR)  grown in LB supplemented with 0.1% (w/v) L-arabinose and 10 μM C4-HSL


title: WT_687_3


title: TG_681_1


title: GSC#Ge176

city: Genoa

first: Paolo

last: Malatesta

address: Largo Rosanna Benzi 10

institute: IRCCS Ospedale Policlinico San Martino

description:
Log2CPM-ExpressionData.csv
1740R-48-24

data_processing:
Basecalls and demultiplexing was performed using Illumina builtin software
fastq files were alligned with genome reference assembly GRCh38p13 with STAR 2.7.5c
RSEM 1.3.1 was used to generate read counts
edgeR was used for normalization
Supplementary_files_format_and_content: CSV file includes log2 counts per million values for each sample, generated by edgeR. Note: NAN were generated for those features that were not found in the given sample.

source_name: Glioblastoma stem cells

growth_protocol: Cells were maintained as a monolayer on Matrigel in medium containing Dulbecco's modified Eagle's medium/F-12 and Neurobasal (1:1), B27 supplement, 2 mm l-glutamine, recombinant human bFGF (10 ng/ml), and recombinant human EGF (20 ng/ml).

extract_protocol:
RNA was extracted from 10e6 cells with Qiagen RNeasy mini kit following manufacturer's recommendations. RNA Quality was checked with Agilent TapeStation and ranged between RIN 8.6 to 9.9.
Library preparation was carried out with Truseq stranded mRNA (Illumina) and sequenced on Illumina platform with a 150 cycles paired end flowcells.

value: M

tag: age at diagnosis

tag: glioma grade

value: IV

value: Glioblastoma stem cells


title: GSC#Ge037

description:
Log2CPM-ExpressionData.csv
1740R-48-22

value: F

tag: cell type


title: TG_678_88

value: uterus

value: 4 months

value: transgenic


title: 542_nCATS

description: II1TDOM 542 E12.5 yolksac gDNA

value: yolksac

value: II1TDOM 542 gDNA


title: WT_674_11

value: WT

value: wild type


title: TG_696_1


title: PqsE biol rep 2

description: Sample 5 - Group B

value: mutant strain carrying in-frame deletions of pqsA, pqsH, pqsL, rhlI, rhlR, lasI, rsaL, lasR, phnA, phnB and pqsR, and a chromosomally integrated construct for IPTG-inducible expression of pqsE [deltaQS-Eind(pHERD30T)]

value: ∆QS-Eind(pHERD30T) grown in LB supplemented with 0.1% (w/v) L-arabinose, 500 µM IPTG and 10 μM C4-HSL


title: RhlR biol rep 2

description: Sample 8 - Group C

value: mutant strain carrying in-frame deletions of pqsA, pqsH, pqsL, rhlI, rhlR, lasI, rsaL, lasR, phnA, phnB and pqsR, a chromosomally integrated construct for IPTG-inducible expression of pqsE, and the pHERD-rhlR plasmid for L-arabinose-inducible expression of rhlR [deltaQS-Eind(pHERD-rhlR)]


title: 30 min WT LFS rep 2-1

description:
3-D co-culture model infected for 30 minutes with WT S. Typhimurium grown in the RWV in the LFS orientation
3225_fpkm_TPM.txt
JB4-30min_LS-2-1.fastq.gz

value: LFS

value: 30 minutes


title: GSC#Ge025

description:
Log2CPM-ExpressionData.csv
1740R-48-21


title: baseline biol rep 3

description: Sample 3 - Group A

value: ∆QS-Eind(pHERD30T) grown in LB supplemented with 0.1% (w/v) L-arabinose and 10 μM C4-HSL


title: TG_673_10


title: PqsE biol rep 3

description: Sample 6 - Group B


title: 30 min WT LFS rep 2

description:
3-D co-culture model infected for 30 minutes with WT S. Typhimurium grown in the RWV in the LFS orientation
3225_fpkm_TPM.txt
JB2-30min_LS-2.fastq.gz

value: In vitro 3-D co-culture model comprised of human colonic epithelial cells and macrophages


title: GSC#Ge039

description:
Log2CPM-ExpressionData.csv
1740R-48-23

value: M

value: IV


title: WT_697_3


title: 30 min. WT LFS rep 1

description:
3-D co-culture model infected for 30 minutes with WT S. Typhimurium grown in the RWV in the LFS orientation
3225_fpkm_TPM.txt
JB1-30min_LS-1.fastq.gz


title: 30 min WT 1xg control rep 1-1

description:
3-D co-culture model infected for 30 minutes with WT S. Typhimurium grown in the RWV in the control orientation
3225_fpkm_TPM.txt
JB7-30min_1xg-1-1.fastq.gz

value: control


title: GSC#Ge177

description:
Log2CPM-ExpressionData.csv
1740R-48-20

value: F

value: Glioblastoma stem cells


title: PqsE biol rep 1

description: Sample 4 - Group B


title: 30 min WT 1xg control rep 1

description:
3-D co-culture model infected for 30 minutes with WT S. Typhimurium grown in the RWV in the control orientation
3225_fpkm_TPM.txt
JB5-30min_1xg-1.fastq.gz


title: RhlR biol rep 1

description: Sample 7 - Group C

value: ∆QS-Eind(pHERD-rhlR)  grown in LB supplemented with 0.1% (w/v) L-arabinose and 10 μM C4-HSL


title: 30 min. WT LFS rep 1-1

description:
3-D co-culture model infected for 30 minutes with WT S. Typhimurium grown in the RWV in the LFS orientation
3225_fpkm_TPM.txt
JB3-30min_LS-1-1.fastq.gz


title: Liver_dRRE_CT22_rep2

city: Minato City

first: Satoshi

last: Kawakami

address: 4-6-1 Shirokanedai

department: The Institute of Medical Science

institute: The University of Tokyo

data_processing:
Illumina RTA3.4.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and quality-controlled using trimmomatic v0.39, then mapped to mm10 whole genome using HISAT2 v2.1.0 with parameters -p 8 -q -x mm10
Fragments Per Kilobase of exon per Million mapped reads (FPKM) were calculated using StringTie v1.3.5 - Ballgown v2.18.0 pipeline. Transcripts annotation file was obtained from Ensembl95.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: Liver

extract_protocol:
Mouse livers from the mutant and WT male mice harvested at six time points throughout the day (CT2, 6, 10, 14, 18, and 22; n=2) were placed in Lysing Matrix D tubes (MP Biomedicals) with TRIzol reagent (Invitrogen), and homogenized by using Fast-Prep 24 instrument (MP Biomedicals). Total RNAs were prepared with the RNeasy Mini Kit (Qiagen), followed by ethanol precipitation. Poly(A)-tailed RNA was isolated from the total RNA by using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490) and NEBNext Ultra II Directional RNA Library Prep Kit (NEB, #E7760).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: delta-RRE

tag: time


title: GSC#Ge023

description:
Log2CPM-ExpressionData.csv
1740R-48-17


title: osteoclast-Ctsk-Cre;Ano1fl/fl mouse-rep3

city: Beijing

first: Weijia

last: Sun

address: No. 26 Beiqing Road, Haidian District

institute: China Astronaut Research and Training Center

description: osteoclasts derived from mice  were induced by RANKL for 5 days

hyb_protocol: 0.6  μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was   fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x   Agilent fragmentation buffer and 2x Agilent blocking agent following the   manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of   2x Agilent hybridization buffer was added to the fragmentation mixture and   hybridized to Agilent  microarray for 17 hours at 65°C in a   rotating Agilent hybridization oven. After hybridization, microarrays were washed 1   minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C   GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray   Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area   61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set   to 100%).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyzearray images to get raw data. Genespring (version 14.8, Agilent Technologies) were employedto finish the basic analysis with the raw data. To begin with, the raw data was normalizedwith the quantile algorithm. The probes that at least 1 conditions out of 2 conditions haveflags in “Detected” were chosen for further data analysis. Differentially expressed geneswere then identified through fold change as well as P value calculated with t-test. Thethreshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05.Afterwards, GO analysis and KEGG analysis were applied to determine the roles of thesedifferentially expressed mRNAs. Finally, Hierarchical Clustering was performed to displaythe distinguishable genes' expression pattern among samples.

source_name: osteoclast-Ctsk-Cre;Ano1fl/fl mouse

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color   Low RNA Input Linear Amplification PLUS kit (Agilent) according to the   manufacturer's instructions, followed by RNAeasy column purification (QIAGEN,   Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop   ND-1000 Spectrophotometer.

growth_protocol: Trizol

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n   AM1556 ) following the manufacturer's instructions.

treatment_protocol: osteoclasts derived from Ano1fl/fl mice or Ctsk-Cre;Ano1fl/fl mice were induced by RANKL for 5 days

value: bone marrow cells


title: GSC#Ge024

description:
Log2CPM-ExpressionData.csv
1740R-48-19


title: baseline biol rep 2

description: Sample 2 - Group A

tag: strain


title: Liver_dRRE_CT22_rep1


title: GSC#Ge014

description:
Log2CPM-ExpressionData.csv
1740R-48-18


title: 24 hours Uninfected rep 1-1 (hfq control)

description:
Time-matched uninfected 3-D co-culture model at 24 hours (uninfected control for hfq infection experiment)
fpkm_TPM_sal_human.txt
UNINFECT_24_2_S8_R1.fastq.gz

value: HT-29 (ATCC HTB-38) and U937 (ATCC CRL-1593.2)


title: 24 hours Uninfected rep1 (hfq control)

description:
Time-matched uninfected 3-D co-culture model at 24 hours (uninfected control for hfq infection experiment)
fpkm_TPM_sal_human.txt
UNINFECT_24_1_R1.fastq.gz.merged.fastq.gz


title: Liver_dRRE_CT18_rep2


title: Liver_dRRE_CT18_rep1


title: 24 hours Uninfected rep 2-1 (hfq control)

description:
Time-matched uninfected 3-D co-culture model at 24 hours (uninfected control for hfq infection experiment)
fpkm_TPM_sal_human.txt
UNINFECT_24_4_R1.fastq.gz.merged.fastq.gz


title: Liver_dRRE_CT14_rep2


title: Liver_dRRE_CT6_rep2


title: 24 hours Uninfected rep 2 (WT control)

description:
Time-matched uninfected 3-D co-culture model at 24 hours (uninfected control for wild type infection experiment)
3225_fpkm_TPM.txt
JB30-24h_UN-2.fastq.gz


title: GSC#Ge015

description:
Log2CPM-ExpressionData.csv
1740R-48-16


title: GSC#Ge010

description:
Log2CPM-ExpressionData.csv
1740R-48-15


title: Liver_dRRE_CT10_rep2


title: osteoclast-Ano1fl/fl mouse--rep3

source_name: osteoclast-Ano1fl/fl mouse


title: osteoclast-Ano1fl/fl mouse--rep1


title: GSC#Ge007

description:
Log2CPM-ExpressionData.csv
1740R-48-14


title: Liver_dRRE_CT14_rep1


title: GSC#Ge006

description:
Log2CPM-ExpressionData.csv
1740R-48-13


title: Liver_dRRE_CT10_rep1


title: GSC#Ge005

description:
Log2CPM-ExpressionData.csv
1740R-48-12


title: 24 hours Uninfected rep 2 (hfq control)

description:
Time-matched uninfected 3-D co-culture model at 24 hours (uninfected control for hfq infection experiment)
fpkm_TPM_sal_human.txt
UNINFECT_24_3_R1.fastq.gz.merged.fastq.gz


title: osteoclast-Ctsk-Cre;Ano1fl/fl mouse-rep2


title: spleen_control_rep3

city: Lanzhou

first: Dongmei

last: Chen

address: No. 35 Dingxi east road, chengguan district, Lanzhou, Gansu province

institute: Gansu University of Chinese Medicine

description: Gene expression in control group

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

label_protocol: cDNA labeled with a fluorescent dye (Cy5-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: we established the aging mice model, and used the traditional Chinese medicine Codonopsis pilosula to intervene. Then total RNA was extracted from spleen tissues in the control group, the model group and high dose Codonopsis pilosula intervention group (n=3 mice).

value: spleen

tag: gender

value: female


title: osteoclast-Ano1fl/fl mouse--rep2


title: baseline biol rep 1

description: Sample 1 - Group A

value: mutant strain carrying in-frame deletions of pqsA, pqsH, pqsL, rhlI, rhlR, lasI, rsaL, lasR, phnA, phnB and pqsR, and a chromosomally integrated construct for IPTG-inducible expression of pqsE [deltaQS-Eind(pHERD30T)]


title: GSC#Ge003

description:
Log2CPM-ExpressionData.csv
1740R-48-11

tag: Sex


title: spleen_control_rep2

description: Gene expression in control group


title: osteoclast-Ctsk-Cre;Ano1fl/fl mouse-rep1


title: 3 hours Uninfected rep 2-1 (hfq control)

last: Barrila

address: 1001 S McAllister Ave

institute: Arizona State University

description:
Time-matched uninfected 3-D co-culture model at 3 hours (uninfected control for hfq infection experiment)
fpkm_TPM_sal_human.txt
UNINFECT_3_4_R1.fastq.gz.merged.fastq.gz


title: spleen_D-galactose,sodium nitrite_42d_rep3

description: Gene expression in aging mice

source_name: spleen_D-galactose,sodium nitrite_42d


title: 24 hours Uninfected rep 1-1 (WT control)

description:
Time-matched uninfected 3-D co-culture model at 24 hours (uninfected control for wild type infection experiment)
3225_fpkm_TPM.txt
JB31-24h_UN-1-1.fastq.gz


title: GSC#Ge002

description:
Log2CPM-ExpressionData.csv
1740R-48-10


title: Liver_dRRE_CT2_rep2


title: 24 hours Uninfected rep 1 (WT control)

description:
Time-matched uninfected 3-D co-culture model at 24 hours (uninfected control for wild type infection experiment)
3225_fpkm_TPM.txt
JB29-24h_UN-1.fastq.gz


title: PRDM1_3

city: Tokyo

first: Yuki

last: Kagoya

address: 35 Shinanomachi, Shinjuku

institute: Keio University

data_processing:
Illumina NovaSeq 6000 was used for base calling.
Sequenced reads were trimmed for adaptor sequence, and read lengths less than 20 nucleotides and a PHRED Quality Score of less than 15 were removed using the fastp software.
The trimmed reads were mapped to the GRCh38 human reference genome using HISAT2 (version 2.1.0).
Read counts for each gene were calculated using HTSeq (version 0.11.2).
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw read counts for each sample and gene were included in a tab-delimited text file.

source_name: chimeric antigen receptor-engineered T cells

growth_protocol: Human T cells were stimulated by K562 cells that express anti-CD3 mAb (clone OKT3)-derived scFV linked with the transmembrane and cytoplasmic domain of CD8a as well as CD80 (K562-OKT3/CD80) (day 0) and transduced with a CD19-targeting CAR gene (FMC63-28z) on day 2. The CAR-T cells were cultured in vitro with RPMI media supplemented with 10% FBS and 100 IU/ml human IL-2.

extract_protocol:
The stimulated CAR-T cells were collected three days after the third stimulation, and CD8+ CAR-T cell population was isolated by flow cytometry. The CAR-transduced T cells were detected by the expression of truncated NGFR. Total RNA was isolated from the purified CAR-T cells using the Nucleospin RNA Kit (Macherey-Nagel) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using the TruSeq Standard mRNA Library Prep kit according to standard Illumina protocols

treatment_protocol: CAR-T cells were electroporated with an RNP complex composed of Cas9 protein and single guide RNAs targeting the indicated genes and restimulated by the CD19+ luekmia cell line NALM-6 every three days.

value: CD8+ T cells

tag: donor

tag: genes targetd by crispr/cas9


title: 3 hours Uninfected rep 2 (hfq control)

city: Tempe

first: Jennifer

description:
Time-matched uninfected 3-D co-culture model at 3 hours (uninfected control for hfq infection experiment)
fpkm_TPM_sal_human.txt
UNINFECT_3_3_R1.fastq.gz.merged.fastq.gz


title: Liver_WT_CT22_rep1

value: WT


title: Liver_dRRE_CT2_rep1


title: 3 hours Uninfected rep 1-1 (hfq control)

description:
Time-matched uninfected 3-D co-culture model at 3 hours (uninfected control for hfq infection experiment)
fpkm_TPM_sal_human.txt
UNINFECT_3_2_R1.fastq.gz.merged.fastq.gz


title: PRDM1_2


title: spleen_control_rep1

description: Gene expression in control group

value: male


title: No Target_3

value: No target


title: BRD4_3


title: Liver_WT_CT22_rep2


title: Liver_WT_CT18_rep2


title: Liver_WT_CT18_rep1


title: 3 hours Uninfected rep 1 (hfq control)

description:
Time-matched uninfected 3-D co-culture model at 3 hours (uninfected control for hfq infection experiment)
fpkm_TPM_sal_human.txt
UNINFECT_3_1_S18_R1.fastq.gz

value: In vitro 3-D co-culture model comprised of human colonic epithelial cells and macrophages


title: BRD4_2


title: 3 hours Uninfected rep 2-1 (WT control)

description:
Time-matched uninfected 3-D co-culture model at 3 hours (uninfected control for wild type infection experiment)
3225_fpkm_TPM.txt
JB20-3h_UN-2-1.fastq.gz


title: Liver_WT_CT14_rep2


title: 3 hours Uninfected rep 2 (WT control)

description:
Time-matched uninfected 3-D co-culture model at 3 hours (uninfected control for wild type infection experiment)
3225_fpkm_TPM.txt
JB18-3h_UN-2.fastq.gz


title: PRDM1_1


title: Liver_WT_CT14_rep1


title: 3 hours Uninfected rep 1-1 (WT control)

description:
Time-matched uninfected 3-D co-culture model at 3 hours (uninfected control for wild type infection experiment)
3225_fpkm_TPM.txt
JB19-3h_UN-1-1.fastq.gz


title: 3 hours Uninfected rep 1 (WT control)

description:
Time-matched uninfected 3-D co-culture model at 3 hours (uninfected control for wild type infection experiment)
3225_fpkm_TPM.txt
JB17-3h_UN-1.fastq.gz


title: No Target_1


title: BRD4_1


title: No Target_2


title: 30 min Uninfected rep 2-1

description:
Time-matched uninfected 3-D co-culture model at 30 minutes (uninfected control for wild type infection experiment)
3225_fpkm_TPM.txt
JB12-30min_UN-2-1.fastq.gz


title: Liver_WT_CT10_rep1


title: Liver_WT_CT10_rep2


title: Liver_WT_CT6_rep2


title: D2987_day16_CART_PRDM1KO

data_processing:
Illumina NovaSeq 6000 was used for base calling.
Sequencing adapters and low-quality bases were trimmed using Trimmomatic 0.38.
Cleaned reads were aligned to the reference genome hg38 using bowtie2. Reads with low mapping quality (< 30) or those mapped to mitochondria were filtered using samtools 1.9. PCR or optical duplicates were marked using Picard 2.18.26 and removed.
Peak calling was performed using MACS2 with the following parameters: -q 0.05 -f BAMPE --nomodel --nolambda -g hs.
Genome_build: hg38
Supplementary_files_format_and_content: Peak .xls files

extract_protocol:
The stimulated CAR-T cells were collected three days after the third stimulation, and CD8+ CAR-T cell population was isolated by flow cytometry. The CAR-transduced T cells were detected by the expression of truncated NGFR. The purified T cells were resuspended with complete culture medium and incubated for 30 minutes at 37 degrees after supplemented with DNAse solution. The cells were washed with PBS once and cryopreserved in growth media with 10% DMSO. Sequencing analysis was performed with NovaSeq 6000 (Illumina).
Library preparation was performed using standard Illumina protocols.

treatment_protocol: CAR-T cells were electroporated with an RNP complex composed of Cas9 protein and single guide RNAs targeting PRDM1 and restimulated by the CD19+ luekmia cell line NALM-6 every three days.


title: 30 min Uninfected rep 2

description:
Time-matched uninfected 3-D co-culture model at 30 minutes (uninfected control for wild type infection experiment)
3225_fpkm_TPM.txt
JB10-30min_UN-2.fastq.gz


title: D2987_day16_CART


title: Liver_WT_CT6_rep1


title: spleen_D-galactose,sodium nitrite_42d_rep1

description: Gene expression in aging mice


title: D1_day16_CART_PRDM1KO


title: Mpcoi1-C20_vs_Mpcoi1-Mock_repl4

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

hyb_protocol: 825 ng of Cy3 and Cy5 probes were mixed and hybridized for 17 hours at 65ºC in GEx Hybridization Buffer HI-RPM in a hybridization oven. Arrays were washed according to the manufacturer’s instructions and dried by centrifugation

scan_protocol: Images were scanned at 2um resolution in an Agilent DNA Microarrays Scanner (G2565BA, Agilent Technologies) and  were with Feature Extraction 9.0 software (Agilent Technologies).

data_processing: Raw intensities were background-subtracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were  normalized by LOWESS algorithm followed by quantile normalization

organism: Marchantia polymorpha

label_protocol: 200 ng of total RNA were reverse transcribed used T7 primer and the cDNA converted to aRNA using T7 RNA polymerase, incorporating cyanine 3- or cyanine 5-labeled CTP, according to 'Two color Microarray-Based Gene Expression Analysis Protocol' (Agilent)

growth_protocol: Marchantia polymorpha accession Takaragaike-1 (Tak-1; male) and mutant Mpcoi1 were used in this work. Plants were subcultivated on 0.5 Gamborg’s B5 medium containing 1% agar for 3 weeks. Apical fragments of the plants, excluding gemma cups, were ground in liquid nitrogen prior RNA extraction. Every independent biological replicate contained 18 plants.

extract_protocol: Total RNA from Marchantia was extracted with Favorgen Plant RNA Extraction and DNase on-column digestion (Qiagen) was performed to remove genomic DNA contamination.

treatment_protocol: Plants were treated with C20 and frozen 2 hours after treatment

tag: genotype/variation

value: Mock


title: spleen_D-galactose,sodium nitrite_42d_rep2

description: Gene expression in aging mice


title: Liver_WT_CT2_rep2


title: Mpcoi1-C20_vs_Mpcoi1-Mock_repl3


title: spleen_Codonopsis pilosula(15 g•kg-1)_30d_rep3

description: Gene expression after intervention of Codonopsis pilosula


title: Liver_WT_CT2_rep1


title: D1_day16_CART


title: 30 min Uninfected rep 1

description:
Time-matched uninfected 3-D co-culture model at 30 minutes (uninfected control for wild type infection experiment)
3225_fpkm_TPM.txt
JB9-30min_UN-1.fastq.gz

tag: bacterial genotype


title: spleen_Codonopsis pilosula(15 g•kg-1)_30d_rep2


title: adult Nycticorax nycticorax 4

status: Public on May 16 2022

city: Xiamen

first: Haoran

last: Luo

state: Fujian

address: Xiang'annan Road, Xiang'an District

institute: Xiamen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Trimmomatic was used to remove adaptors and low-quality reads.Then reads mapped to reference genome using HISAT2
Transcripts were assembled by StringTie and counted Fragments Per Kilobase Million (FPKM) and Transcripts Per Kilobase Million (TPM，the sum of Transcripts Per Kilobase Million is 10 million).
Genome_build: JAKFQP000000000
Genome_build: GCA_000687185.1
Supplementary_files_format_and_content: Gtf from StringTie
Supplementary_files_format_and_content: tables with TPM and FPKM for every gene and every sample

organism: Nycticorax nycticorax

source_name: Nycticorax nycticorax Olfactory epithelium

extract_protocol:
Invitrogen TRIzol
NEBNext Ultra RNA Library Prep Kit for Illumina to construct 150bp paired-end RNA sequencing libraries.

value: Olfactory epithelium

tag: developmental stage

value: adult


title: spleen_Codonopsis pilosula(15 g•kg-1)_30d_rep1


title: adult Nycticorax nycticorax 6


title: adult Nycticorax nycticorax 5


title: nestling Nycticorax nycticorax 2

value: nestling


title: nestling Nycticorax nycticorax 3


title: adult Little Egret 6

organism: Egretta garzetta

source_name: Egretta garzetta Olfactory epithelium


title: adult Little Egret 4


title: nestling Nycticorax nycticorax 1


title: 30 min Uninfected rep 1-1

description:
Time-matched uninfected 3-D co-culture model at 30 minutes (uninfected control for wild type infection experiment)
3225_fpkm_TPM.txt
JB11-30min_UN-1-1.fastq.gz

tag: bacterial growth orientation

tag: time post-infection


title: adult Little Egret 5


title: Tak-1-C20_vs_Tak-1-Mock_repl3

tag: treatment


title: Tak-1-C20_vs_Tak-1-Mock_repl4


title: nestling Little Egret 2

tag: tissue


title: nestling Little Egret 1


title: 24 hours Uninfected rep 2-1 (WT control)

description:
Time-matched uninfected 3-D co-culture model at 24 hours (uninfected control for wild type infection experiment)
3225_fpkm_TPM.txt
JB32-24h_UN2-1.fastq.gz


title: nestling Little Egret 3


title: Mpcoi1-C20_vs_Mpcoi1-Mock_repl1

value: mock


title: Mpcoi1-C20_vs_Mpcoi1-Mock_repl2


title: Tak-1-C20_vs_Tak-1-Mock_repl1


title: Experiment 2, mRNA/attenuated vaccinated animal 4, 5dpi, lung sample for bulk RNA-seq

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description:
5d_lung16
reads5d_counts.txt.gz

data_processing:
The Mesocricetus auratus genome MesAur 2.0 was downloaded from https://www.ncbi.nlm.nih.gov/genome/11998. The GFF file was converted to GTF, the generic gene names (LOCxxx) replaced with mouse-derived official gene symbols for several key genes, and 3'-UTRs extended as described previously (doi: 10.1101/2021.10.02.462569). Then, the SARS-CoV-2 genome annotation was merged.
For bulk RNA-sequencing, alignments were done using hisat2 (Kim et al, 2015)
For single-cell RNA-sequencing data, fastq files were processed using a the mergend MesAur2.0/SARS-CoV-2 genome with the GTF file provided here by applying CellRanger 6.0.2 with standard parameters
For single-cell RNA-sequencing data, fastq files were processed using a merged Roborvski hamster/SARS-CoV-2 genome by applying CellRanger 6.0.2 with standard parameters
Assembly: MesAur 2.0
Assembly: SARS-CoV-2 MN908947
Supplementary files format and content: GTF file
Supplementary files format and content: tab-separated values
Supplementary files format and content: h5 matrix

organism: Mesocricetus auratus

source_name: Lung

growth_protocol:
Hamsters were vaccinated intramuscularly with either an experimental adenovirus vector vaccine containing the whole SARS-CoV-2 spike (5 _ 108 infectious units (IFU) per animal) (PMID: 34835096), or BNT162b2 (5 ug per animal) or intranasally with 1x105 pfu of the live-attenuated SARS-CoV-2 vaccine candidate sCPD9 (PMID: 34320400, PMID: 34851677). For the prime-boost experiment, immunity was boosted by a second vaccination with the respective vaccines at the same dose 21 days after primary vaccination. In, one group, animals were primed with BNT162b2 and boosted with sCPD9, all other groups received a homologues boost.
Hamsters were weighted daily and monitored for signs of disease twice-daily. Hamsters were selected randomly for all scheduled take-out time points (day 2 and 5).
Euthanasia prior analysis occurred by cervical dislocation exsanguination under anesthesia as previously described (PMID 32698441, 33271063). Peripheral blood was collected in EDTA-coated syringes and lung lobes were collected for follow-up analyses, in which the left lobe was used for histopathology, the right caudal lobe for single-cell analysis, the right cranial lobe for virological assessments and the right medial as backup to repeat virological analyses as needed.

extract_protocol:
Bulk and single-cell RNA-sequencing libraries were constructed using commercial kits:
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina
For isolation of single cells, the caudal lobe of the right lung was removed and placed in storage medium (1× PBS, 0.5 % BSA) until further processing. Storage and isolation media contained 2 µg/mL ActinomycinD. Tissues and cells were always spun at 350 x g for 6 minutes at 4 °C. Mechanical dissociation of lung lobes was achieved by clapping motions with tweezers for 2 minutes in enzymatic digestion medium (3,4 mg/mL Collagenase Cls II (Merck), 1 mg/mL DNase I (PanReac AppliChem), in 2 mL Dispase medium per lung lobe (Corning), 50 Caseinolytic Units/mL followed by 30 minutes incubation at 37°C and 5 % CO2.
Further tissue dissociation was achieved by repeated pipetting of digested lung tissue with 5 mL pipettes and passing of cell suspension with plungers through 70 µm cell strainers. Cells were pelleted from suspension by centrifugation and resuspended in red blood cell lysis buffer (BioLegend). Lysis reaction was stopped and cells washed with excessive volumes of PBS/BSA. Cells were centrifuged, resuspended in low-BSA buffer (1× PBS, 0.04 % BSA) and counted via hemocytometer and trypan blue.
Then, 1,000,000 lung cells per sample were subjected to Cell Multiplexing Oligo (CMO) labeling according to the manufacturers’ instructions (3ʹ-CellPlex-Kit-Set-A, 10x Genomics). Labelled cells from 12 samples were pooled, filtered (40 µm) and counted. Pooled cells were adjusted to a final concentration of ~1,600 cells / μL and filtered with 40 µm FloMi filters (Merck) suitable for low volumes prior subjection to scRNA sequencing.
For Lung RNA Bulk sequencing the lobus medialis of the right lung lobe was removed carefully and homogenzied in Trizol reagent using a bead mill procedure (Speedmill, Analytic Jena), RNA was extracted according to the manufacturer’s instructions.

treatment_protocol: 21 days following primary vaccination or 14 days following booster vaccination, hamsters were infected intranasally as previously described (PMID 32698441, 33271063). Briefly, hamster received 1 x 105 pfu SARS-CoV-2 Variant Delta. [SARS-CoV-2, Human, 2021, Germany ex India, 20A/452R (B.1.617)] intranasally under anesthesia.

tag: first vaccination

value: mRNA

tag: second vaccination

value: attenuated

tag: sampling timepoint

tag: adapter sequence

value: GATCGGAAGAGCACACGT


title: Experiment 2, 2xmRNA vaccinated animal 5, 5dpi, lung sample for bulk RNA-seq

description:
5d_lung27
reads5d_counts.txt.gz


title: Experiment 2, 2xmRNA vaccinated animal 3, 5dpi, lung sample for bulk RNA-seq

description:
5d_lung23
reads5d_counts.txt.gz


title: Experiment 2, mRNA/attenuated vaccinated animal 1, 5dpi, lung sample for bulk RNA-seq

description:
5d_lung11
reads5d_counts.txt.gz


title: Experiment 2, mRNA/attenuated vaccinated animal 3, 5dpi, lung sample for bulk RNA-seq

description:
5d_lung13
reads5d_counts.txt.gz


title: Experiment 2, mRNA/attenuated vaccinated animal 2, 5dpi, lung sample for bulk RNA-seq

description:
5d_lung12
reads5d_counts.txt.gz


title: Experiment 2, 2xmRNA vaccinated animal 2, 5dpi, lung sample for bulk RNA-seq

description:
5d_lung22
reads5d_counts.txt.gz


title: Tak-1-C20_vs_Tak-1-Mock_repl2


title: Experiment 2, 2xAdenovirus vaccinated animal 5, 5dpi, lung sample for bulk RNA-seq

description:
5d_lung37
reads5d_counts.txt.gz

value: adenovirus


title: Experiment 2, 2xmRNA vaccinated animal 1, 5dpi, lung sample for bulk RNA-seq

description:
5d_lung21
reads5d_counts.txt.gz


title: Experiment 2, 2xAdenovirus vaccinated animal 1, 5dpi, lung sample for bulk RNA-seq

description:
5d_lung31
reads5d_counts.txt.gz


title: Experiment 2, 2xAdenovirus vaccinated animal 4, 5dpi, lung sample for bulk RNA-seq

description:
5d_lung36
reads5d_counts.txt.gz


title: Experiment 2, 2xAdenovirus vaccinated animal 3, 5dpi, lung sample for bulk RNA-seq

description:
5d_lung33
reads5d_counts.txt.gz


title: Experiment 2, 2xattenuated vaccinated animal 5, 5dpi, lung sample for bulk RNA-seq

description:
5d_lung07
reads5d_counts.txt.gz


title: Experiment 2, mRNA/attenuated vaccinated animal 5, 5dpi, lung sample for bulk RNA-seq

description:
5d_lung17
reads5d_counts.txt.gz


title: Liver_dRRE_CT6_rep1

value: liver

tag: genotype

value: delta-RRE

tag: time


title: Experiment 2, 2xattenuated vaccinated animal 3, 5dpi, lung sample for bulk RNA-seq

description:
5d_lung03
reads5d_counts.txt.gz


title: Experiment 2, Non-vaccinated animal 3, 5dpi, lung sample for bulk RNA-seq

description:
5d_lung44
reads5d_counts.txt.gz


title: Experiment 2, Non-vaccinated animal 5, 5dpi, lung sample for bulk RNA-seq

description:
5d_lung48
reads5d_counts.txt.gz


title: Experiment 2, 2xattenuated vaccinated animal 1, 5dpi, lung sample for bulk RNA-seq

description:
5d_lung01
reads5d_counts.txt.gz


title: Experiment 2, Non-vaccinated animal 2, 5dpi, lung sample for bulk RNA-seq

description:
5d_lung43
reads5d_counts.txt.gz


title: Experiment 2, Non-vaccinated animal 4, 5dpi, lung sample for bulk RNA-seq

description:
5d_lung47
reads5d_counts.txt.gz


title: Experiment 2, 2xattenuated vaccinated animal 4, 5dpi, lung sample for bulk RNA-seq

description:
5d_lung06
reads5d_counts.txt.gz


title: Experiment 2, Non-vaccinated animal 1, 5dpi, lung sample for bulk RNA-seq

description:
5d_lung42
reads5d_counts.txt.gz


title: Experiment 2, mRNA/attenuated vaccinated animal 5, 2dpi, lung sample for bulk RNA-seq

description:
2d_lung20
reads2d_counts.txt.gz


title: Experiment 2, 2xmRNA vaccinated animal 4, 5dpi, lung sample for bulk RNA-seq

description:
5d_lung26
reads5d_counts.txt.gz


title: Experiment 2, 2xAdenovirus vaccinated animal 2, 5dpi, lung sample for bulk RNA-seq

description:
5d_lung32
reads5d_counts.txt.gz


title: Experiment 2, mRNA/attenuated vaccinated animal 3, 2dpi, lung sample for bulk RNA-seq

description:
2d_lung18
reads2d_counts.txt.gz


title: Experiment 2, 2xattenuated vaccinated animal 2, 5dpi, lung sample for bulk RNA-seq

description:
5d_lung02
reads5d_counts.txt.gz


title: Experiment 2, mRNA/attenuated vaccinated animal 2, 2dpi, lung sample for bulk RNA-seq

description:
2d_lung15
reads2d_counts.txt.gz


title: Experiment 2, 2xmRNA vaccinated animal 3, 2dpi, lung sample for bulk RNA-seq

description:
2d_lung29
reads2d_counts.txt.gz


title: Experiment 2, mRNA/attenuated vaccinated animal 1, 2dpi, lung sample for bulk RNA-seq

description:
2d_lung14
reads2d_counts.txt.gz


title: Experiment 2, 2xmRNA vaccinated animal 4, 2dpi, lung sample for bulk RNA-seq

description:
2d_lung28
reads2d_counts.txt.gz


title: Experiment 2, 2xmRNA vaccinated animal 5, 2dpi, lung sample for bulk RNA-seq

description:
2d_lung30
reads2d_counts.txt.gz


title: Experiment 2, 2xmRNA vaccinated animal 2, 2dpi, lung sample for bulk RNA-seq

description:
2d_lung25
reads2d_counts.txt.gz


title: Experiment 2, 2xAdenovirus vaccinated animal 5, 2dpi, lung sample for bulk RNA-seq

description:
2d_lung40
reads2d_counts.txt.gz