title: NGN2 iNeurons, 24hrs DMSO, pS65Ub ChIPseq, rep 2

city: South San Francisco

first: Daniel

last: Le

address: 1 DNA Way

institute: Genentech

description: Library name: SAM24449819_V2_pS65Ub_bw

data_processing:
ChIP Seq: The ENCODE analysis pipeline (v2.2.1) was used, with Bowtie2 (v2.3.4.3) employed to align reads to the reference genome (hg38). Duplicated or low-quality reads were filtered out using Picard (Broad Institute - v2.20.7) and samtools (v1.9), with further filtering to remove regions where genome assembly introduces erroneous signal. The SPP data processing pipeline was used to call peaks, with the level of background signal assessed via reference to input sample. DiffBind (v3.12.0) was used to identify differential peaks as follows. RPKM-normalized ChIP Seq data was visualized using IGV (2.18.4) genome browser
CUT&RUN: Indexed libraries generated using NEBNext library prep kit 32 (NEB) and NEBNext Multiplex Oligos for Illumina (NEB) as per manufacturers instructions. Paired-end reads were aligned to the reference genome (hg38) using Bowtie2 (-p 24 -X2000 -t -x) and sorted with Samtools (view -bS -F 4 -q 30 -u - | sort -T). PCR duplicates were marked using Picard MarkDuplicates (MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000 REMOVE_DUPLICATES=true ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT). Genome-wide coverage was determined using Bedtools genomecov (-ibam -bg -scale -g), converted to a BigWig file with wigToBigWig -clip.
Assembly: hg38
Supplementary files format and content: bigwig files for each sample
Supplementary files format and content: bed files for each sample

source_name: iPSC-derived NGN2-type cortical neurons

extract_protocol:
ChIP-Seq samples were extracted as follows: 50mM DSG (disuccinimidyl glutarate, #C1104 - ProteoChem) for 30 mins followed by 10 mins of 1% formaldehyde was used to double crosslink HeLa or iPSC-derived NGN2 neurons (5x106), followed by the addition of glycine to quench formaldehyde. Nuclei were released using ChIP Nuclear Isolation Buffer (20 mM Tris pH 8.0, 1% Triton X-100, 0.1% SDS, 150 mM NaCl and 1mM EDTA), and chromatin sheared via sonication (Covaris sonicator: Fill level – 10, Duty Cycle – 15, PIP – 350, Cycles/Burst – 200, Time – 8-mins). Solutions containing sheared chromatin were mixed with relevant antibodies and rotated at 4°C overnight before protein A magnetic beads were then added to isolate antibody-bound chromatin. The beads were washed twice in each of the following buffers: ChIP Wash Buffer #1 (20 mM Tris pH 8.0, 1% Triton X-100, 0.1% SDS, 150 mM NaCl, 1 mM EDTA, and 0.1% NaDOC), ChIP Wash Buffer #2. (20 mM Tris pH 8.0, 1% Triton X-100, 0.1% SDS, 500 mM NaCl, 1 mM EDTA, and 0.1% NaDOC) and ChIP Wash Buffer #3 (0.25 M LiCl, 0.5% NP-40, 1mM EDTA, 20 mM Tris, pH 8.0, 0.5% NaDOC), followed by single wash in TE buffer (200 mM Tris pH 8.0 and 10 mM EDTA). The mixtures were then shaken for 20 mins in Elution Buffer (100mM NaHCO3, 1% SDS), before overnight incubation at 65°C to de-crosslink DNA. The DNA fragments were purified with MinElute PCR purification kit (Qiagen), then quantified by Qubit. CUT&RUN was performed using the CUTANA ChIC/CUT&RUN Kit (Epicypher) as per manufacturers instructions with the addition of DUB inhibitor PR-619 (100μM) to Wash and Antibody buffers.
ChIP-Seq libraries were generated using Ovation Ultralow Library System V2 (Tecan) using 2ng of each sample according to the manufacturer’s instructions, then sequenced using paired-end 50bp read configuration. CUT&RUN libraries were generated using NEBNext library prep kit 32 (NEB) and NEBNext Multiplex Oligos for Illumina (NEB) as per manufacturers instructions.

value: iPSC-derived NGN2-type cortical neurons

value: Neuronal

value: 24hrs DMSO


title: Normal Phosphate Exercised Sample 1

status: Public on Jul 01 2026

type: SRA

city: Columbus

first: Kedryn

last: Baskin

state: OH

address: 460 W 12th Ave

department: Physiology and Cell Biology

country: USA

institute: The Ohio State University

description:
Library name: XJD947_1_HP18_9_NPE
NPE_1

library_source: transcriptomic

data_processing:
Fastq files were trimmed using TrimGalore, and aligned using the STAR aligner. Count matrices were analyzed in pairwise comparisons using DESeq2.
Assembly: GRCm39
Supplementary files format and content: excel file containing CPM values and pairwise comparison output from DESeq2

molecule: total RNA

organism: Mus musculus

source_name: GP

extract_protocol:
RNA was extracted using the TRI-zol kit and manufacterer instructions. At minumum, 500ng of RNA, quality determined by RIN, was used to generate libraries for each sample.
Libraries were generated by Plasmidsaurus sequencing service. Poly-A mRNA capture, second strand synthesis and tagmentation, and Illumina library amplification.

tag: tissue

value: GP

tag: sample group

value: Normal Phosphate Exercised


title: Multiome, central amygdala, RT00270N, AUD, human, GEX

city: New Haven

first: Matthew

last: Girgenti

state: CT

address: 34 Park St

department: Psychiatry

institute: Yale University

description: Library name: RT00270N_GEX

library_source: transcriptomic single cell

data_processing:
Multiome files were demultiplexed using Cellranger-arc mkfastq
Assembly: hg38
Supplementary files format and content: CellRanger output files: filtered_feature_bc_matrix.h5,  atac_fragments.tsv.gz

molecule: polyA RNA

organism: Homo sapiens

source_name: Central Amygdala

extract_protocol:
Nuclei were isolated from fresh-frozen human central amygdala tissue and purified to generate single-nucleus suspensions for simultaneous chromatin accessibility and gene-expression profiling.
Single-nucleus multiome libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression workflow, which constructs matched ATAC-seq (genomic DNA accessibility) and gene-expression (polyA nuclear RNA) libraries from the same nucleus.

value: Central Amygdala

tag: treatment

value: alcohol use disorder

tag: batch


title: NT4

city: Boston

first: Ke

last: Zhang

state: MA

address: 360 Huntington Ave

institute: Northeastern University

description:
Library name: Sample 9
Column name in raw_counts_all_samples.csv: NT_G_3

data_processing:
Index of the reference genome was built usingHisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome (GRCm39/mm39) with Hisat2 v2.0.5. using standard workflows (Novogene)
Additional analysis was conducted in Rstudio using the DEseq2, clusterProfiler, fgsea, and gsva packages
Assembly: mm39
Supplementary files format and content: csv file of raw counts for each sample titled raw_counts_all_samples.csv

source_name: quadricep

extract_protocol:
Individual muscle sections were homogenized in a lysis buffer containing 10% BME on a Beadblaster 24R Microtube Homogenizer (Benchmark scientific, NJ, USA.). Total cellular RNA was extracted using the RNeasy® Fibrous Tissue Mini Kit (Qiagen), and RNA quality and quantity were assessed on a NanoDrop® ND-1000 UV-Vis Spectrophotometer.
Messenger RNA was purified from total RNA using poly-T oligo-attachedmagnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNAsynthesis After polyA enrichment and quality control, libraries were sequenced on an Illumina NovaSeq6000 PE150 system to obtain paired-end reads of 150 bp.

treatment_protocol: 8 week old HSA-LR20b or FVB/N wildtype mice were injected by tail vein with drug or control. Mice were humanely sacrificed by carbon dioxide two weeks after the final injection and muscle sections were immediately harvested and flash frozen in liquid nitrogen.

value: quadricep

tag: strain

value: FVB/N

tag: genotype

value: no treatment


title: 14 day SeV infected, AT2 cells, replicate 03, ATAC

city: Cincinnati

first: Jichao

last: Chen

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: Library name: 14dpi_SeV_03, ATAC

library_source: genomic

data_processing:
Fastq files were generated through demultiplexing using BCL2Fastq and quality checked using FastQC
Poor quality bases were removed using Trimmomatic and filtered reads were aligned to the UCSC mm10 reference genome with Bowtie2
Aligned reads were converted from sam files to bam files using Samtools and filtered for poor alignment and unmapped reads using Picard, MarkDuplicates, and Samtools with the following parameters: –f 3 –F 4 –F 256 –F 1024 –F 2048 –q 30
Peak calling was conducted using MACS2 with the following parameters: -q 0.05 –nomodel –shift -100 –extsize 200 –broad and filtered for a−log10 q value greater than 5 and removal of mm10 blacklist sites
Assembly: mm10
Supplementary files format and content: MACS2 output peak files as .broadpeak
Supplementary files format and content: MACS2 output peak files as .gappedpeak
Supplementary files format and content: MACS2 output peak files as .txt

molecule: genomic DNA

source_name: lung

extract_protocol:
Mouse lungs were harvested, dissociated and sorted for 100,000 tdT+ AT2 cells. Cells were centrifuged in 4°C at 1098 rcf  for 5 minutes in a fixed angle centrifuge. The supernatant was discarded, and the pellets were resuspended in 50 µL of cold ATAC-RSB lysis buffer (0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin, 10 mM Tris-HCl pH 8.1, 10 mM NaCl, 3 mM MgCl2). The resuspension was incubated on ice for 3 minutes followed by the addition of 1mL of cold ATAC-RSB+Tween (10 mM Tris-HCl pH 8.1, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) and inverted 3 times to mix. Nuclei were pelleted through centrifugation in 4°C at 1098 rcffor 10 minutes in a fixed angle centrifuge. The supernatant was discarded, and the pellet was resuspended in 50 µL of transposition buffer that included the following: 22.5 µL of Tn5 Reaction Mix (PBS, 2.2% Digitonin, 2.2% Tween-20), 25 µL of Tn5 Buffer (10 mM MgCl2, 20 mM Tris-HCl, 20% Dimethyl Formamide), and 2.5 µL of Tn5 Enzyme (NX#-TDE1, Tagment DNA Enzyme, 15027865, Illumina). The reaction was incubated in a thermocycler at 37°C for 30 minutes. DNA was purified using the Qiagen MinElute PCR Purification Kit (29004) following the manufacturer instructions with one modification of eluting with 10 µL of distilled water.
Sample barcoding and PCR amplification was performed using the Greenleaf ATAC primers (Buenrostro et al., 2013) following the OMNI-ATAC protocol PCR parameters.  To assess amplification efficiency, 5 µL of each sample was saved and set aside while the remainder of each sample continued to size selection purification using SPRIselect beads (Beckman Coulter, B23318). Following the manufacturer instructions for double size selection, the sample was incubated for upper size selection with 0.5X the volume and for lower size selection at 1.8X the volume. Size selection was verified using agarose gel electrophoresis with 1 µL of final sample as well as the previously saved pre size selection sample. Final DNA quantification was measured using the Qubit HS dsDNA assay (Thermo Fisher Scientific, Q32851).

value: lung

tag: cell type

value: SftpcCreER/+;RosatdT/+

value: Sendai virus infected


title: Multiome, central amygdala, RT00293NRP, AUD, human, ATAC

description: Library name: RT00293NRP_ATAC

library_source: genomic single cell


title: 49 day mock PBS, AT2 cells, repliate 01, ATAC

description: Library name: 49dpi_PBScontrol_01, ATAC


title: NT3

description:
Library name: Sample 8
Column name in raw_counts_all_samples.csv: NT_C_DM1_69


title: Multiome, central amygdala, RT00269N, AUD, human, ATAC

description: Library name: RT00269N_ATAC


title: NT2

description:
Library name: Sample 7
Column name in raw_counts_all_samples.csv: NT_DM1_29


title: NT1

description:
Library name: Sample 6
Column name in raw_counts_all_samples.csv: NT_DM1_8


title: Multiome, central amygdala, RT00269N, AUD, human, GEX

description: Library name: RT00269N_GEX


title: Multiome, central amygdala, RT00265NRP, CON, human, GEX

description: Library name: RT00265NRP_GEX

value: control


title: Multiome, central amygdala, RT00265NRP, CON, human, ATAC

description: Library name: RT00265NRP_ATAC


title: WT4

description:
Library name: Sample 4
Column name in raw_counts_all_samples.csv: WT_H_3

value: WT


title: WT5

description:
Library name: Sample 5
Column name in raw_counts_all_samples.csv: WT1_1


title: Multiome, central amygdala, RT00264N, CON, human, GEX

description: Library name: RT00264N_GEX


title: WT3

description:
Library name: Sample 3
Column name in raw_counts_all_samples.csv: WT_G_3


title: WT2

description:
Library name: Sample 2
Column name in raw_counts_all_samples.csv: FVBN_49


title: WT1

description:
Library name: Sample 1
Column name in raw_counts_all_samples.csv: FVBN_64


title: Multiome, central amygdala, RT00263N, AUD, human, ATAC

description: Library name: RT00263N_ATAC


title: Multiome, central amygdala, RT00263N, AUD, human, GEX

description: Library name: RT00263N_GEX


title: Multiome, central amygdala, RT00264N, CON, human, ATAC

description: Library name: RT00264N_ATAC


title: Multiome, central amygdala, RT00262N, AUD, human, ATAC

description: Library name: RT00262N_ATAC


title: EpiTFM3

city: Groningen

first: Reinoud

last: Gosens

address: Antonius Deusinglaan 1

department: Molecular Pharmacology

country: Netherlands

institute: University of Groningen

description: Library name: Sample23

data_processing:
Library preparation was checked by calculating ribosomal (and globin) content.
Checks for possible sample and barcode contamination were performed and a set of standard quality metrics for the raw dataset was determined using quality control tools (FstQC v0.34 and FastQA).
Prior to alignment, the reads were trimmed for adapter sequences using Trimmomatic v0.30.
Assembly: To align the reads of each sample, the  human reference mCh39 was used. Data was analyzed with DESEQ2 package in R studio
Supplementary files format and content: xlsx

source_name: Lung organoid

growth_protocol: The organoid assay was based on published protocols with slight modifications 3. Briefly,  CCL206 fibroblasts were mixed with  freshly isolated mouse lung epithelial cells and seeded into transwell inserts (Thermo Fischer Scientific, Waltham, MA, USA) in 100 μL growth factor-reduced Matrigel (Fisher Scientific, Landsmeer, The Netherlands) diluted 1:1 with DMEM/Ham’s F12 medium containing 10% (v/v) FBS, penicillin/streptomycin (100 U/ml), 2 mM l-glutamine, and 1% amphotericin B. Cultures were maintained in DMEM/ Ham’s F12 medium supplemented with 5% (v/v) FBS, penicillin/streptomycin (100 U/ml), 2 mM L-glutamine, 1% amphotericin B, insulin-transferrin-selenium (X1, Gibco, cat no. 15290018), recombinant mouse epidermal growth factor (EGF) (0.025 μg/ml, Sigma, cat. no. SRP-3196) and bovine pituitary extract (BPE) (30 μg/ml, Sigma, cat. no. P-1476). Organoids were cultured in a humidified atmosphere under 5% CO2/95% air at 37°C, and medium was refreshed every 2 to 3 days. On day 14, the number and size of organoids were evaluated by light microscopy. In some experiments, an extended organoid culture was used to model the effect of initial cigarette smoke exposure on the subsequent Tanimilast and Formoterol treatment. In the first window, primary mouse epithelial cells isolated from naïve mouse lungs were co-cultured with CCL206 fibroblasts and maintained in culture for 14 days. From day 0 to 14, organoids were exposed to either 5% cigarette smoke extract (CSE) or vehicle. On day 14, organoids were disrupted and dissociated into single cells again to re-initiate lung organoid growth. Equal numbers of epithelial cells with fresh CCL206 were then replated and treated with Tanimilast (100 nM) and/or Formoterol (100 nM). On day 28, the number and size of organoids were evaluated to assess the effects of pharmacological intervention on organoid growth

extract_protocol:
Total RNA was isolated using the RNA purification NucleoSpin RNA XS kit (#740902 Macherey-Nagel, Germany) according to the manufacturer’s guide. The yield of the isolated RNA was then measured using the NanoDrop 1000 spectrophotometer.
RNA-seq was conducted using the Illumina NovaSeq 6000 sequencer by BMK (https://www.bmkgene.com/). The procedure included data quality control, adapter trimming, alignment of short reads and feature counting. Library preparation was checked by calculating ribosomal (and globin) content. Checks for possible sample and barcode contamination were performed and a set of standard quality metrics for the raw dataset was determined using quality control tools (FstQC v0.34 and FastQA). Prior to alignment, the reads were trimmed for adapter sequences using Trimmomatic v0.30. To align the reads of each sample, the the  mouse reference GRCh38.p14 was used. Data was analyzed with DESEQ2 in R studio

treatment_protocol: An extended organoid culture was used to model the effect of initial cigarette smoke exposure on the subsequent Tanimilast and Formoterol treatment. In the first window, primary mouse epithelial cells isolated from naïve mouse lungs were co-cultured with CCL206 fibroblasts and maintained in culture for 14 days. From day 0 to 14, organoids were exposed to either 5% cigarette smoke extract (CSE) or vehicle. On day 14, organoids were disrupted and dissociated into single cells again to re-initiate lung organoid growth. Equal numbers of epithelial cells with fresh CCL206 were then replated and treated with Tanimilast (100 nM) and/or Formoterol (100 nM). On day 28, the organoids were harvested for RNA isolation.

value: Lung organoid

tag: cell line

value: Epcam+ cells

value: Epithelial cell

value: Tanimilast+Formoterol

value: Mouse 3


title: EpiCSEM3

description: Library name: Sample22

value: CSE+Vehicle


title: Multiome, central amygdala, RT00262N, AUD, human, GEX

description: Library name: RT00262N_GEX


title: Multiome, central amygdala, RT00261NRP, CON, human, ATAC

description: Library name: RT00261NRP_ATAC


title: EpiVehM3

description: Library name: Sample21

value: Vehicle


title: FibCSETFM3

description: Library name: Sample20

value: Epcam- cells

value: Fibroblast

value: CSE+Tanimilast+Formoterol


title: Multiome, central amygdala, RT00260N, CON, human, ATAC

description: Library name: RT00260N_ATAC

value: Central Amygdala


title: Multiome, central amygdala, RT00261NRP, CON, human, GEX

description: Library name: RT00261NRP_GEX


title: FibTFM3

description: Library name: Sample19


title: FibCSEM3

description: Library name: Sample18


title: Multiome, central amygdala, RT00260N, CON, human, GEX

description: Library name: RT00260N_GEX


title: Multiome, central amygdala, RT00259N, AUD, human, ATAC

description: Library name: RT00259N_ATAC

value: alcohol use disorder


title: Multiome, central amygdala, RT00259N, AUD, human, GEX

description: Library name: RT00259N_GEX


title: Multiome, central amygdala, RT00258N, CON, human, ATAC

description: Library name: RT00258N_ATAC


title: EpiCSETFM2

description: Library name: Sample16

value: Mouse 2


title: Bulk RNAseq of iAstros exposed to Interferon-Beta or PBS_PBS1

city: Dublin

first: Michael John

last: Dolan

state: Dublin 2

address: Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin

country: Ireland

institute: Trinity College Dublin

description: Library name: PBS_1

data_processing:
iAstrocyte: FastQC (v.0.12.1) and MultiQC (v.1.23) were to generate initial quality control (QC) reports. STAR (v.2.7.10b) was used to build the reference index (based on GRCh38) and align reads, then the quality of the generated BAM files was assessed with Samtools (v.1.6) quickcheck (all samples had greater than 94% alignment). The count matrix was generated using featureCounts (v.2.0.6). R (v.4.3.1) was used for subsequent analyses.  iMGL scRNAseq: Cellranger (version 6, 10X Genomics) was used for demultiplexing, barcode preprocessing, generation of fastq files, alignment and the counting of unique molecular identifiers (UMI). We applied Cellranger’s aggr function to all samples to merge and normalize by sequencing depth. We then applied CellBender to remove ambient RNA and technical artifacts due to barcode swapping (Fleming et al. 2023).
Assembly: GRCh38
Supplementary files format and content: Seurat object of iMGL scRNAseq data

source_name: cell line

growth_protocol: iMGL Differentiation: Human H1 embryonic stem cells were cultured in Essential 8 media on Matrigel, dissociated with Accutase, and aggregated in low-adherence plates with ROCK inhibitor. Cells were differentiated through sequential exposure to hematopoietic cytokines (FGF2, BMP4, VEGF, TPO, SCF, IL6, IL3) in HPC medium under hypoxic and then normoxic conditions. By day 10, cells were cryopreserved and later thawed for microglia maturation in iMG media containing M-CSF, IL-34, and TGF-β1. Final maturation occurred between days 30–45 with additional supplementation of CD200 and CX3CL1.  iAstro Differentiation: H1 hESCs were genetically engineered to express doxycycline-inducible NFIB and SOX9 from the AAVS1 locus. After transfection, cells were selected with geneticin and expanded. iAstrocyte induction was initiated with doxycycline in E8 medium, followed by sequential exposure to expansion, FGF, and maturation media containing BMP4, CNTF, and dbcAMP. Cells were dissociated on day 7, replated, and matured in MM medium until day 20 before use.

extract_protocol:
RNA was extracted either with Qiagen RNeasy Mini extraction kit (iAstrocytes) or subjected to single-cell RNA sequencing (iMGLs)
iAstrocye RNA underwent library preparation based on PolyA sequencing. iMGL underwent single-cell library preparation according to 10X Genomics protocol

treatment_protocol: Cells were treated with PBS or 25ng/ml Interferon Beta

value: stemcell astrocyte


title: Multiome, central amygdala, RT00258N, CON, human, GEX

description: Library name: RT00258N_GEX


title: EpiVehM2

description: Library name: Sample13


title: Phgdh WT with Serine/Glycine in medium with hepatocytes rep1

city: New York

first: Jason

middle: Rodencal

last: Terrell

state: NY

address: 530 1st Avenue

institute: NYU Langone Health

description: Library name: WT_10

data_processing:
File RNAseq_Exp1-gene_fpkm.txt was generated using the standard Novogene RNA-seq analysis pipeline. Raw paired-end reads were produced on an Illumina NovaSeq 6000 platform. Adapter sequences and low-quality reads were removed to obtain clean reads. Clean reads were aligned to the reference genome using HISAT2, and gene-level read counts were quantified. Gene expression levels were normalized and reported as FPKM values.
Assembly: GRCm38 (mm10)
Supplementary files format and content: RNAseq_Exp1-gene_fpkm.txt

extract_protocol:
RNA was extracted using RNeasy mini kit per manufacturer's protcols and RNA quality was validated.
As per Novogene protocols

value: PDAC

value: Phgdh WT

value: hepatocyte coculture


title: Multiome, central amygdala, RT00257N, CON, human, GEX

description: Library name: RT00257N_GEX

value: control


title: FibCSETFM2

description: Library name: Sample12

value: Lung organoid

value: WT


title: Multiome, central amygdala, RT00256N, CON, human, ATAC

description: Library name: RT00256N_ATAC


title: FibTFM2

description: Library name: Sample11

value: Tanimilast+Formoterol


title: FibCSEM2

description: Library name: Sample10


title: Multiome, central amygdala, RT00255N, AUD, human, ATAC

description: Library name: RT00255N_ATAC


title: FibVehM2

description: Library name: Sample9


title: Multiome, central amygdala, RT00255N, AUD, human, GEX

description: Library name: RT00255N_GEX


title: EpiCSETFM1

description: Library name: Sample8

value: Epcam+ cells

value: Epithelial cell

value: Mouse 1


title: Multiome, central amygdala, RT00254N, CON, human, ATAC

description: Library name: RT00254N_ATAC


title: Multiome, central amygdala, RT00254N, CON, human, GEX

description: Library name: RT00254N_GEX


title: EpiCSEM1

description: Library name: Sample6

value: CSE+Vehicle


title: G401-i cells, SMARCB1-reexpression, day 10, rep3

city: Paris

first: Franck

last: Bourdeaut

address: 26 rue d'ulm

country: France

institute: Institut Curie

description:
Library name: G401_SMARCB1_J10_3
Column name in raw counts and TPM matrixes : P118T554
raw_counts_G401i_RNAseq.txt
TPM_G401i_RNAseq.txt

data_processing:
Raw data were processed using an in-house pipeline developed at the Institut Curie Bioinformatics Core Facility, following standard analysis in the field and available at https://github.com/bioinfo-pf-curie/RNA-seq.
Sequencing adaptors were trimmed using TrimGalore!
read QC were performed using fastqc
read mapping on GRCh39/hg19 reference genome were performed using STAR (version 2.5.3a) and the refFlat gene annotation downloaded from UCSC
duplicated reads were marked with picard and then removed
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: a single tab-delimited text file includes matrix of TPM values with sample in columns and genes on rows

growth_protocol: I2A cells were maintained in RPMI containing 10% fetal bovine serum (FBS) and supplemented with 50 ng/mL doxycycline, 50 μg/mL hygromycin B and 300 μg/mL geneticin. G401-i cells were maintained in RPMI containing 10% FBS and supplemented with 50 ng/mL doxycycline. For both inducible cell lines, medium was changed every 3-4 days to renew drugs and cells were washed three times in Phosphate Buffer Saline (PBS) to completely remove doxycycline in order to induce SMARCB1 expression.

extract_protocol:
Total RNAs from cell line samples were extracted using the Nucleospin II kit (Macherey-Nagel). Total RNAs from frozen human tumors were extracted using the QIAamp RNAeasy kit (Qiagen)
Barcoded Illumina compatible libraries were generated from 750 ng of total RNA for each sample using TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, California, U.S.,).

treatment_protocol: For low-dose decitabine (DAC) experiments, I2A cells were treated with DAC at 100 nM or DMSO as a control for 21 days.

value: Rhabdoid tumor cells


title: Caco-2.batch2.DIQ.rep1.H01

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

description: Library name: Caco2_Batch2_DIQ_1_H01

library_source: other

data_processing:
Reads were aligned using STAR alignment on QIAGEN's CLC workbench software (v25.0.1) and Kallisto alignment on ExpressAnalyst
Raw counts were logCPM normalized and filtered for low abundance (5) and variance (15) using ExpressAnalyst
Normalized counts were analyzed for differential expression using DESeq2
Assembly: CLC workbench used hg38.p14 Ensembl v113 GCA_000001405.29; ExpressAnalyst used hg38.p14 GCA_000001405
Supplementary files format and content: raw files and count files are provided as fastq.gz files and .txt files, respectively.

molecule: other

source_name: cell lysate

growth_protocol: from ms

extract_protocol:
cells were lysed in Qiagen's proprietary lysis buffer and used directly for library preparation
ultraplex 3' transcriptome library preparation following Qiagen's UPXome protocol

treatment_protocol: cells were exposed to various concentrations of 6ppd-quinone for 24 hours after seeding at 35,000 cells per well

value: colon

value: epithelial

value: cell line


title: FibCSETFM1

description: Library name: Sample4

value: Epcam- cells

value: Fibroblast

value: CSE+Tanimilast+Formoterol


title: Caco-2.batch2.DIQ.rep1.G01

description: Library name: Caco2_Batch2_DIQ_1_G01


title: FibTFM1

description: Library name: Sample3


title: FibCSEM1

description: Library name: Sample2


title: Caco-2.batch2.DIQ.rep1.F01

description: Library name: Caco2_Batch2_DIQ_1_F01


title: FibVehM1

description: Library name: Sample1

value: Vehicle


title: Caco-2.batch2.DIQ.rep1.D01

description: Library name: Caco2_Batch2_DIQ_1_D01


title: Caco-2.batch2.DIQ.rep1.E01

description: Library name: Caco2_Batch2_DIQ_1_E01


title: 24L012738_FO_Vehicle_iset4

city: Leipzig

first: Bilal

last: Sheikh

state: Sachsen

address: Philipp-Rosenthal-Str. 27

department: HI-MAG

country: Germany

institute: Helmholtz Zentrum München

description:
Library name: Sample_24L012738_FO_17_13_iset4
>27.5 × 103 reads per cell

data_processing:
Reads were demultiplexing and mapped to the mm10 mouse genome build (GENCODE vM23/Ensembl98) using CellRanger v8.0.1 (10x Genomics) with default parameters.
Assembly: mm10 mouse genome build (GENCODE vM23/Ensembl98)
Supplementary files format and content: Filtered features, barcodes and matrix

molecule: nuclear RNA

source_name: Abdomnal aorta

growth_protocol: The experiment was performed in accordance with the animal ethics laws of Saxony, Baden Württemberg and Hessen, Germany, and were approved by the state animal ethics committee. Female C57BL/6N mice at 8 weeks old were injected intravenously with 1 x 1011 vector genome copies of rAAV8-PCSK9D377Y. After 7 days, the mice were kept on a high fat diet (Ssniff Spezialdiäten, V1534) and treated with fluoxetine or vehicle for 10 weeks. Fluoxetine (Sigma, 56296-78-7) was offered in the drinking water ad libitum at 160 mg/ml with 0.1% saccharine (109185, Sigma). After 10 weeks, mice were sacrificed and perfused with PBS. The abdominal aorta and surrounding perivascular adipose tissue  was dissected and snap frozen.

extract_protocol:
Frozen abdominal aortas were dissociated in 2 ml ice-cold lysis buffer. Lysis buffer was prepared with 5 mM CaCl, 3 mM MgAc, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM Tris (pH 8), 10 mM sodium butyrate, 1 mM Dithiothreitol, cOmplete™ Protease Inhibitor Cocktail (11836145001, Roche) and 1.2U/ml RNAseOUT (10777019, Invitrogen). Aortas were dissociated in the gentleMACS Octo Dissociator system with heaters (MACS Technology, Miltenyi Biotec) using the program “Protein_01.01”. After dissociation, an additional 2 ml lysis buffer (supplemented with 0.4% Triton-X) was added to the gentleMACS tube and the solution was mixed by inversion. Samples were briefly centrifuged and strained through a 70 µm BD-cell strainer. The gentleMACS tube was rinsed with 2 ml lysis buffer (0.2% Triton-X) and the wash was also strained. After centrifugation (4 °C, 1000 xg, 5 min), the supernatant was discarded, and the dissociated tissue was washed with 1 ml PBS. Samples were stained with DAPI (A3672, AppliChem PanReac) and strained into a FACS tube (CLS352235, Corning). Nuclei were sorted on a FACS Aria (BD Biosciences).
snRNA-seq was performed with the 10x Next GEM Single-Cell 3′ GEM kit v3.1 (10x Genomics) according to the instructions from the manufacturer. The nuclei were FACS sorted two samples at a time and ~12,000 nuclei from each aorta were pooled. After centrifugation (4 °C, 300 xg, 5 min), nuclei were resuspended at ~1,000 cells/µl and loaded into the 10x Chromium controller. Fluoxetine and vehicle samples were processed in separate 10x Genomics reactions. Libraries were sequenced on an Illumina NovaSeq with >27.5 × 103 reads per cell.

value: Abdomnal aorta


title: Caco-2.batch2.DIQ.rep1.C01

description: Library name: Caco2_Batch2_DIQ_1_C01


title: CUTTAG_H3K27m3_KMS11_NSD2KO#12_Rep1

city: Miami

first: sanxiong

last: liu

state: FL

address: 1501 NW 10th Avenue

department: Human Genetics

institute: University of Miami Miller School of Medicine

description: Library name: Sample 31

data_processing:
Raw paired-end sequencing reads (FASTQ) were first assessed for quality and cleaned using fastp (v0.24.0). Cleaned reads were then aligned to the human reference genome (hg38) using Bowtie2 with parameters --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. The resulting alignments were converted to BAM format, sorted, and indexed using Samtools. PCR duplicates were marked using Picard MarkDuplicates. Alignments were subsequently filtered using Samtools to retain properly paired reads and exclude reads mapping to ENCODE blacklisted regions. For visualization and downstream analysis, signal tracks in bigWig format were generated using deepTools (v3.5.1) bamCoverage, normalizing signal to Reads Per Kilobase per Million mapped reads (RPKM) with a bin size of 50 bp. Peak calling for the H3K27me3 modification was performed using MACS3 (v3.0.2) callpeak with parameters --format BAMPE -g hs --broad --broad-cutoff 0.1 --keep-dup all. Consensus peak sets were generated by merging reproducible peaks across replicates. Differential binding analysis between conditions was performed using DESeq2 on read counts within the consensus peak set (obtained via chromVAR), and resulting differentially bound regions were annotated using the ChIPseeker R package (v 1.42.1).
Assembly: hg38
Supplementary files format and content: Processed data files are provided for each H3K27me3 CUTTAG sample in two formats: 1) bigWig (.bw) files containing genome-wide signal enrichment, normalized as Reads Per Kilobase per Million mapped reads (RPKM) using deepTools, suitable for visualization; and 2) BED (.broadPeak) files generated by MACS3 (using --broad --broad-cutoff 0.1), defining genomic regions significantly enriched for the H3K27me3 mark.
Library strategy: CUT&Tag

growth_protocol: KMS-11 cells are cultured in RPMI-1640 supplemented with 10% FBS and 1% Penicillin-Streptomycin.

extract_protocol:
CUTTAG was performed starting with 50,000 nuclei per sample. Nuclei were isolated, resuspended in Wash Buffer, and loaded onto a silica column. On-column incubations were performed sequentially with primary antibody (anti-H3K27me3, Cell Signaling Technology #9733), secondary antibody (Antibodies-Online ABIN101961), and pAG-Tn5 transposase complex (Epicypher #15-1017), with buffer washes performed after antibody and transposase incubation steps. Tagmentation was carried out on-column by adding MgCl2 in Wash Buffer and incubating at 4°C for 1 hour. Following tagmentation, nuclei were lysed using SDS and Proteinase K. DNA fragments were then extracted and purified using the DNA Clean & Concentrator-5 kit (Zymo Research #D4014) and eluted in H2O.
Sequencing libraries were prepared from the purified tagmented DNA obtained via the Extract Protocol. Library amplification was performed by PCR for 13 cycles using NEBNext HiFi 2 × PCR Master mix (NEB #M0541). Following PCR amplification, the libraries were purified using HighPrep beads (MagBio genomics #AC-60500).

treatment_protocol: NSD2dTAG KMS-11 cells were treated with dTAGV-1 (100 nM) to induce NSD2 degradation.The specific duration of each treatment varied according to the experimental condition and is indicated in the metadata associated with each sample.

value: NSD2 KO

value: No


title: Caco-2.batch2.DIQ.rep1.B01

description: Library name: Caco2_Batch2_DIQ_1_B01


title: Caco-2.batch2.DIQ.rep1.A01

description: Library name: Caco2_Batch2_DIQ_1_A01


title: 24L012738_FO_Vehicle_iset2

description:
Library name: Sample_24L012738_FO_17_13_iset2
>27.5 × 103 reads per cell


title: 24L012738_FO_Vehicle_iset1

description:
Library name: Sample_24L012738_FO_17_13_iset1
>27.5 × 103 reads per cell


title: 24L012737_FO_Vehicle_iset4

description:
Library name: Sample_24L012737_FO_14_15_iset4
>27.5 × 103 reads per cell


title: Caco-2.batch2.DIP.rep3.H07

description: Library name: Caco2_Batch2_DIP_3_H07


title: Caco-2.batch2.DIP.rep3.F07

description: Library name: Caco2_Batch2_DIP_3_F07


title: 24L012737_FO_Vehicle_iset3

description:
Library name: Sample_24L012737_FO_14_15_iset3
>27.5 × 103 reads per cell


title: 24L012737_FO_Vehicle_iset2

description:
Library name: Sample_24L012737_FO_14_15_iset2
>27.5 × 103 reads per cell


title: 24L012733_FO_Fluoxetine_iset4

description:
Library name: Sample_24L012733_FO_10_11_iset4
>27.5 × 103 reads per cell

value: Fluoxetine


title: Caco-2.batch2.DIP.rep3.C07

description: Library name: Caco2_Batch2_DIP_3_C07


title: 24L012733_FO_Fluoxetine_iset3

description:
Library name: Sample_24L012733_FO_10_11_iset3
>27.5 × 103 reads per cell


title: Caco-2.batch2.DIP.rep3.A07

description: Library name: Caco2_Batch2_DIP_3_A07


title: Caco-2.batch2.DIP.rep2.H07

description: Library name: Caco2_Batch2_DIP_2_H07


title: 24L012733_FO_Fluoxetine_iset2

description:
Library name: Sample_24L012733_FO_10_11_iset2
>27.5 × 103 reads per cell


title: 24L012733_FO_Fluoxetine_iset1

description:
Library name: Sample_24L012733_FO_10_11_iset1
>27.5 × 103 reads per cell


title: Caco-2.batch2.DIP.rep2.G07

description: Library name: Caco2_Batch2_DIP_2_G07


title: 24L012729_FO_Fluoxetine_iset4

description:
Library name: Sample_24L012729_FO_7_9_iset4
>27.5 × 103 reads per cell

value: 7 and 9


title: Caco-2.batch2.DIP.rep2.F07

description: Library name: Caco2_Batch2_DIP_2_F07


title: Caco-2.batch2.DIP.rep2.E07

description: Library name: Caco2_Batch2_DIP_2_E07


title: 24L012729_FO_Fluoxetine_iset1

description:
Library name: Sample_24L012729_FO_7_9_iset1
>27.5 × 103 reads per cell


title: 24L012729_FO_Fluoxetine_iset2

description:
Library name: Sample_24L012729_FO_7_9_iset2
>27.5 × 103 reads per cell


title: Caco-2.batch2.DIP.rep2.D07

description: Library name: Caco2_Batch2_DIP_2_D07


title: Caco-2.batch2.DIP.rep2.C07

description: Library name: Caco2_Batch2_DIP_2_C07


title: Caco-2.batch2.DIP.rep2.B07

description: Library name: Caco2_Batch2_DIP_2_B07


title: M3-CKO, Input MeRIP-seq

city: Guangzhou

first: Kechen

state: Guangdong

address: Shatai South Road

country: China

institute: Southern Medical University

description: Library name: M3CKO_Input_MeRIP

data_processing:
Raw reads were trim adapter using trim_galore, mapped to the reference genome using hisat2, deduplicated using sambamba and gene counting using FeatureCounts
Assembly: mm39
Supplementary files format and content: Feature Count file for RNA-seq and bedgraph for MeRIP-seq
Library strategy: MeRIP-Seq

source_name: Trachea

growth_protocol: Freshly isolated basal cells were resuspended in mouse tracheal epithelial cell (MTEC)/Plus culture medium (DMEM/F12 (Gibco; 1130032) supplemented with 10 μg ml-1 insulin (GlpBio; GC31303), 5 μg ml-1 transferrin (Sigma; T8158), 100 ng ml-1 cholera toxin (Sigma; C8052), 25 ng ml-1 epidermal growth factor (Sigma; E4127), 30 μg ml-1 bovine pituitary extract (MACGEE; CC203), 50 nM all-trans retinoic acid (ATRA, Sigma; R2625), 1 μM A83-01 (Beyotime; SF7917), 1 μM DMH-1 (MedChemExpress; HY-12273), and 5% FBS). Cells were mixed with growth factor-reduced Matrigel (Corning; 356237) at a 1:1 ratio, and three to five 20 μl droplets of the mixture were seeded per well in 12-well plates, with approximately 5-10 × 103 epithelial cells per well. After Matrigel solidification, droplets were overlaid with 1.5 ml MTEC/Plus culture medium and the organoids were maintained at 37°C with 5% CO2. Culture medium was replaced every 2-3 days. The ROCK inhibitor Y-27632 (10 μM, MedChemExpress; HY-101069) was added in the medium for the first 3 days of culture. For basal cell differentiation, organoids were changed into MTEC/SF differentiation medium (DMEM/F12 supplemented with 5 μg ml-1 insulin, 5 μg ml-1 transferrin, 25 ng ml-1 cholera toxin, 5 ng ml-1 epidermal growth factor, 30 μg ml-1 bovine pituitary extract, 50 nM retinoic acid and 0.1% bovine serum albumin).

extract_protocol:
tracheal from Ctrl and M3-CKO mice were dissected, cleaned of connective tissue, and minced into pieces. The tissue were then incubated in DMEM/F12 medium containing 2mg/mL dispase (Sigma; D4693) at 37°C for 30 minutes. Subsequently, tracheas were incubated in 0.5mg/mL DNase I (Solarbio; D8071) for additional 30 minutes at 37°C. The epithelial sheets were delicately peeled using forceps and further digested in 0.25% Trypsin-EDTA (Thermo Fisher Scientific; 25200056) at 37°C for 5 minutes to obtain single cells. The resulting cells suspension was gently pipetted and passed through a 70 μm cell strainer to removed any remaining tissue fragments. Cells were buried in metrigel and culture immediately in mouse tracheal epithelial cell culture medium for 14 day. On day 14, organoids were harvested for  RNA extraction.
Total RNA was extracted using Trizol reagent. Briefly, purified mRNAs were fragmented using an RNA fragmentation kit. A portion of the fragmented mRNA (~4%) was reserved as input control, while the remaining fragmented RNA was incubated with an anti-m6A antibody and subjected to m6A immunoprecipitation (IP) using the EpiMark N6-Methyladenosine Enrichment Kit according to the manufacturer’s protocol. Both the IP-purified fragmented mRNA and input RNA were used to construct libraries with the SMARTer Stranded Total RNA-seq Kit v2-Pico Input Mammalian, following the manufacturer’s instructions.

value: Trachea


title: Ctrl, IP MeRIP-seq

description: Library name: Ctrl_IP_MeRIP


title: Caco-2.batch2.DIP.rep2.A07

description: Library name: Caco2_Batch2_DIP_2_A07


title: Caco-2.batch2.DIP.rep1.H08

description: Library name: Caco2_Batch2_DIP_1_H08


title: Ctrl, Input MeRIP-seq

description: Library name: Ctrl_Input_MeRIP


title: M3-CKO, replicate 3,RNA-seq

description: Library name: M3CKO_Rep3_RNA

data_processing:
Raw reads were trim adapter using trim_galore, mapped to the reference genome using hisat2, deduplicated using sambamba and gene counting using FeatureCounts
Assembly: mm39
Supplementary files format and content: Feature Count file for RNA-seq and bedgraph for MeRIP-seq


title: Caco-2.batch2.DIP.rep1.G08

description: Library name: Caco2_Batch2_DIP_1_G08


title: 24L012738_FO_Vehicle_iset3

description:
Library name: Sample_24L012738_FO_17_13_iset3
>27.5 × 103 reads per cell


title: M3-CKO, replicate 2,RNA-seq

description: Library name: M3CKO_Rep2_RNA


title: Caco-2.batch2.DIP.rep1.F08

description: Library name: Caco2_Batch2_DIP_1_F08


title: Caco-2.batch2.DIP.rep1.E08

description: Library name: Caco2_Batch2_DIP_1_E08


title: M3-CKO, replicate 1,RNA-seq

description: Library name: M3CKO_Rep1_RNA


title: Ctrl, replicate 3, RNA-seq

description: Library name: Ctrl_Rep3_RNA


title: Caco-2.batch2.DIP.rep1.D08

description: Library name: Caco2_Batch2_DIP_1_D08


title: Ctrl, replicate 2, RNA-seq

description: Library name: Ctrl_Rep2_RNA


title: Caco-2.batch2.DIP.rep3.B07

description: Library name: Caco2_Batch2_DIP_3_B07


title: Ctrl, replicate 1, RNA-seq

description: Library name: Ctrl_Rep1_RNA


title: Caco-2.batch2.DIP.rep1.C08

description: Library name: Caco2_Batch2_DIP_1_C08


title: Caco-2.batch2.DIP.rep1.A08

description: Library name: Caco2_Batch2_DIP_1_A08


title: S. Typhimurium infected and RV-treated cells, replicate 3

city: changchun

first: Jiayang

state: 柳加洋

address: xian road

institute: jlu

description: Library name: D3

data_processing:
Data quality control was performed using fastp software. Adapters, reads containing poly-N, and low-quality reads were removed to obtain clean reads. Q20, Q30, and GC content were calculated for the clean data.
An index of the reference genome was built and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
Read counts mapped to each gene were quantified using featureCounts (v1.5.0-p3). Subsequently, FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values were calculated for each gene based on its length and read count.
Differential expression analysis was performed using the DESeq2 R package (v1.20.0).
Assembly: GRCm38
Supplementary files format and content: The processed data file (gene_fpkm.xls) is a table where rows represent genes and columns represent samples. The values indicate FPKM (Fragments Per Kilobase of transcript per Million mapped reads) for each gene in each sample.

source_name: RAW264.7 cells

growth_protocol: RAW264.7 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS) in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol™ Reagent (Thermo Fisher Scientific) according to the manufacturer's instructions.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Cells were seeded in 6-well plates at a density of 1x10^6 cells/well and grown to approximately 80% confluency. For the infection groups, cells were infected with Salmonella Typhimurium at an MOI of 20 for 1 hour, followed by a gentamicin protection assay to eliminate extracellular bacteria. For the treatment groups, cells were exposed to 32 µg/mL resveratrol. Specific treatments for each group were maintained for 6 hours.

value: RAW264.7 cells


title: S. Typhimurium infected and RV-treated cells, replicate 2

description: Library name: D2


title: Caco-2.batch2.DIC.rep3.H06

description: Library name: Caco2_Batch2_DIC_3_H06


title: S. Typhimurium infected and RV-treated cells, replicate 1

description: Library name: D1


title: S. Typhimurium-infected RAW264.7 cells, replicate 3

description: Library name: X3


title: Caco-2.batch2.DIC.rep3.F06

description: Library name: Caco2_Batch2_DIC_3_F06


title: S. Typhimurium-infected RAW264.7 cells, replicate 2

description: Library name: X2


title: Caco-2.batch2.DIC.rep3.G06

description: Library name: Caco2_Batch2_DIC_3_G06


title: M3-CKO, IP MeRIP-seq

description: Library name: M3CKO_IP_MeRIP


title: Caco-2.batch2.DIC.rep3.E06

description: Library name: Caco2_Batch2_DIC_3_E06


title: S. Typhimurium-infected RAW264.7 cells, replicate 1

description: Library name: X1


title: Caco-2.batch2.DIC.rep3.D06

description: Library name: Caco2_Batch2_DIC_3_D06


title: Resveratrol-treated RAW264.7 cells, replicate 3

description: Library name: Y3


title: Resveratrol-treated RAW264.7 cells, replicate 2

description: Library name: Y2


title: Caco-2.batch2.DIC.rep3.C06

description: Library name: Caco2_Batch2_DIC_3_C06


title: Caco-2.batch2.DIC.rep3.B06

description: Library name: Caco2_Batch2_DIC_3_B06


title: Resveratrol-treated RAW264.7 cells, replicate 1

description: Library name: Y1


title: Caco-2.batch2.DIC.rep3.A06

description: Library name: Caco2_Batch2_DIC_3_A06


title: Untreated RAW264.7 cells, replicate 3

description: Library name: B3


title: Caco-2.batch2.DIC.rep2.H06

description: Library name: Caco2_Batch2_DIC_2_H06


title: Caco-2.batch2.DIC.rep2.G06

description: Library name: Caco2_Batch2_DIC_2_G06


title: Untreated RAW264.7 cells, replicate 2

description: Library name: B2


title: Caco-2.batch2.DIC.rep2.F06

description: Library name: Caco2_Batch2_DIC_2_F06


title: Untreated RAW264.7 cells, replicate 1

description: Library name: B1


title: DCW_gex

first: Andrés

last: Hidalgo

address: 10 Amistad Street

description: Library name: gex

data_processing:
R packages Signac v1.14.0 and Seurat v5.2.1 were used to analyze single cell chromatin data and gene expression, respectively.
Full genome sequences for Mus musculus (Mouse) were used as provided by UCSC (mm10, based on GRCm38.p6), and annotated using Ensembl Mus musculus annotations v.79.
Assembly: mm10
Supplementary files format and content: seurat object containg peaks and RNA counts per cell

source_name: mixed sample (non-demultiplexed spleen, lps, lung llc and healthy blood)

extract_protocol:
DIG permeabilization – The pooled cell suspension is washed, resuspended in 100ul of cold DIG lysis buffer, and incubated for 5min on ice. 1ml of cold DIG wash buffer is then added to the suspension and spun down for 5min at 500g. The pellet is resuspended in 100ul of 1x Nuclei buffer (2000207, 10X Genomics) supplemented with 1mM DTT (10708984001, Sigma) and 2U/l RNAse inhibitor (3335399001, Roche), at a final concentration of 3,400 cells/ul.
The library was prepared following the CG000338_ChromiumNextGEM_Multiome_ATAC_GEX_User_Guide_RevE user guide.The sequencing has been performed on a NovaSeq instrument, HiSeq paired-end 150 bp, 75 million reads.

value: FACS neutrophils (CD11b+Ly6G+)


title: Caco-2.batch2.DIC.rep2.E06

description: Library name: Caco2_Batch2_DIC_2_E06


title: EpiCSETFM3

description: Library name: Sample24

value: Lung organoid

value: Epcam+ cells

value: Epithelial cell

value: WT

value: Mouse 3


title: Caco-2.batch2.DIC.rep2.D06

description: Library name: Caco2_Batch2_DIC_2_D06

value: colon

value: epithelial

value: cell line


title: RNA-Seq of mus musculus:P90 male 3671 Smo WT microglia

city: Le Kremlin-Bicêtre

first: Elisabeth

last: TRAIFFORT

address: 80 Rue du Général Leclerc

institute: Inserm

description: Library name: 3671TAM_P90

data_processing:
All RNA-seq reads were aligned onto the mm10 reference genome using Tophat2, gene expression levels were quantified with featureCounts
RNA-seq reads were aligned onto the mm10 reference transcriptome using bowtie and quantified using eXpress
The edgeR R-package was used to perform both data normalization and differential expression analyses
Assembly: mm10
Supplementary files format and content: genes were considered regulated when p-value < 0.05 and Fold change > 1.2

source_name: Brain

growth_protocol: In vivo Magnetic-activated cell sorting of CD11b+ microglial cells from P7 and P90 SmoWT or SmoiKO mouse brain

extract_protocol:
RNAs were extracted from MACsorted CD11b+ cells from P7 and P90 SmoiKO and SmoWT mice, using Nucleospin RNA kit (Macherey-Nagel, 740990)
RNA-seq libraries from P7 SmoWT (n=4) and SmoiKO (n=4) and P90 SmoWT (n=4) and SmoiKO (n=4) CD11b+cells were prepared using TruSeq Stranded mRNA (Illumina 20020594)

treatment_protocol: Tamoxifen was administered by gavage to the mother (P1-P4; 30 mg/ml-100ul) or injected subcutaneously for 5 days (at P90; 10mg/ml-100ul) in SmoWT and SmoiKO animals.

value: Brain

value: Microglia

value: Tamoxifen


title: DCW_atac

description: Library name: atac

value: mixed sample (non-demultiplexed spleen, lps, lung llc and healthy blood)


title: Caco-2.batch2.DIC.rep2.C06

description: Library name: Caco2_Batch2_DIC_2_C06


title: RNA-Seq of mus musculus:P90 male 3670 Smo WT microglia

description: Library name: 3670TAM_P90


title: Caco-2.batch2.DIC.rep2.B06

description: Library name: Caco2_Batch2_DIC_2_B06


title: Caco-2.batch2.DIP.rep1.B08

description: Library name: Caco2_Batch2_DIP_1_B08


title: RNA-Seq of mus musculus:P90 male 3667 Smo WT microglia

description: Library name: 3667TAM_P90


title: FibVehM3

description: Library name: Sample17

value: Epcam- cells

value: Fibroblast

value: Vehicle


title: Caco-2.batch2.DIC.rep1.H06

description: Library name: Caco2_Batch2_DIC_1_H06


title: EpiTFM2

description: Library name: Sample15

value: Tanimilast+Formoterol

value: Mouse 2


title: Caco-2.batch2.DIC.rep2.A06

description: Library name: Caco2_Batch2_DIC_2_A06


title: RNA-Seq of mus musculus:P90 male 3714 Smo Lox  microglia

description: Library name: 3714LOX_P90

value: Lox


title: RNA-Seq of mus musculus:P90 male 3666 Smo WT microglia

description: Library name: 3666TAM_P90


title: EpiCSEM2

description: Library name: Sample14

value: Lung organoid

value: Epcam+ cells

value: CSE+Vehicle


title: Multiome, central amygdala, RT00257N, CON, human, ATAC

description: Library name: RT00257N_ATAC

value: Central Amygdala

value: control


title: RNA-Seq of mus musculus:P90 male 3657 Smo Lox microglia

description: Library name: 3657LOX_P90


title: Caco-2.batch2.DIC.rep1.G06

description: Library name: Caco2_Batch2_DIC_1_G06

value: colon

value: epithelial


title: Caco-2.batch2.DIC.rep1.F06

description: Library name: Caco2_Batch2_DIC_1_F06

value: cell line


title: RNA-Seq of mus musculus:P90 male 3655 Smo Lox microglia

description: Library name: 3655LOX_P90

value: Brain

value: Microglia


title: Multiome, central amygdala, RT00256N, CON, human, GEX

description: Library name: RT00256N_GEX


title: Caco-2.batch2.DIC.rep1.E06

description: Library name: Caco2_Batch2_DIC_1_E06


title: RNA-Seq of mus musculus:P90 male 3654 Smo Lox microglia

description: Library name: 3654LOX_P90

value: Tamoxifen


title: RNA-Seq of mus musculus:P7 male 8 Smo WT  microglia

description: Library name: 8TAM_P7

value: WT


title: EpiTFM1

description: Library name: Sample7

value: Epithelial cell

value: Mouse 1


title: Caco-2.batch2.DIC.rep1.D06

description: Library name: Caco2_Batch2_DIC_1_D06


title: Caco-2.batch2.DIC.rep1.C06

description: Library name: Caco2_Batch2_DIC_1_C06


title: RNA-Seq of mus musculus:P7 male 7 Smo WT microglia

description: Library name: 7TAM_P7


title: Caco-2.batch2.DIC.rep1.B06

description: Library name: Caco2_Batch2_DIC_1_B06


title: RNA-Seq of mus musculus:P7 male 6 Smo WT microglia

description: Library name: 6TAM_P7


title: Caco-2.batch2.DIC.rep1.A06

description: Library name: Caco2_Batch2_DIC_1_A06


title: RNA-Seq of mus musculus:P7 male 5 Smo WT microglia

description: Library name: 5TAM_P7


title: RNA-Seq of mus musculus:P7 male 4 Smo Lox microglia

description: Library name: 4LOX_P7


title: Caco-2.batch2.Control.rep3.D09

description: Library name: Caco2_Batch2_Control_3_D09


title: Caco-2.batch2.Control.rep3.C09

description: Library name: Caco2_Batch2_Control_3_C09


title: EpiVehM1

description: Library name: Sample5

value: Vehicle


title: Caco-2.batch2.Control.rep3.B09

description: Library name: Caco2_Batch2_Control_3_B09


title: RNA-Seq of mus musculus:P7 male 3 Smo Lox microglia

description: Library name: 3LOX_P7


title: RNA-Seq of mus musculus:P7 male 2 Smo Lox microglia

description: Library name: 2LOX_P7


title: RNA-Seq of mus musculus:P7 male 1 Smo Lox microglia

description: Library name: 1LOX_P7


title: Caco-2.batch2.Control.rep3.A09

description: Library name: Caco2_Batch2_Control_3_A09


title: Caco-2.batch2.Control.rep2.D08

description: Library name: Caco2_Batch2_Control_2_D08


title: Caco-2.batch2.Control.rep2.C08

description: Library name: Caco2_Batch2_Control_2_C08


title: Cre-WT

city: Taichung

first: Hieu-Huy

last: Nguyen-Tran

state: Taichung

address: Xueshi

department: Graduate Institute of Biomedical Sciences

country: Taiwan

institute: China Medical University

description: Library name: Sample 2

data_processing:
Raw sequencing reads were processed using Cell Ranger software (v6.1.2, 10x Genomics). Reads were aligned to the mouse reference genome (mm10/GRCm38) using STAR aligner integrated in Cell Ranger. Gene-barcode matrices were generated using the cellranger count pipeline with default settings. The outputs include the filtered feature-barcode matrix, unfiltered matrix, and accompanying quality control metrics. Downstream analysis, including filtering, normalization, dimensionality reduction, clustering, and annotation, was conducted in R using the Seurat package (v5.0.1).
Assembly: mm10/GRCm38
Supplementary files format and content: VhlhKO&WT.rds

source_name: Kidney tissue

extract_protocol:
The sorted cells from Cre-Vhlh-KO and Cre-WT were centrifuged and resuspended in 1X PBS with 0.04% BSA. Cell viability and concentration were assessed using trypan blue staining and an automated cell counter ensuring >90% viability. Single-cell suspensions were loaded into the 10x Genomics Chromium Single Cell A Chip according to the manufacturer’s protocol (Chromium Single Cell 3' Reagent Kits v3 User Guide, CG000183).
Single-cell RNA libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 (10x Genomics, PN-1000075), following the manufacturer’s protocol. Briefly, single cells were encapsulated into droplets along with barcoded gel beads using the Chromium Controller. Following reverse transcription and cDNA amplification, libraries were constructed by fragmentation, end repair, A-tailing, adapter ligation, and PCR amplification. The resulting libraries were quantified and quality-checked using a Bioanalyzer (Agilent Technologies) and sequenced on an Illumina NovaSeq 6000 platform with paired-end 150 bp reads.

value: Kidney tissue

value: Whole tissue

value: Cre-WT


title: Cre-Vhlh-KO

description: Library name: Sample 1

value: Cre-Vhlh-KO


title: Caco-2.batch2.Control.rep2.B08

description: Library name: Caco2_Batch2_Control_2_B08


title: BAL, MHV1 infection, ZT6 time point, collected post-infection day 8, replicate 4

city: St Louis

first: Jeffery

last: Haspel

state: MO

address: 660 S Euclid Avenue

institute: Washington University, St Louis

description:
Library name: Sample90
all.gene_moderated_log2cpm_BAL.tsv
BAL_5667_RNA

data_processing:
RNA-seq reads were aligned to the Ensembl release 76 assembly with STAR version 2.0.4b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5
Transcript counts were produced by Sailfish version 0.6.3
Sequencing performance was assessed for total number of aligned reads, total number of uniquely aligned reads, genes and transcripts detected, ribosomal fraction known junction saturation, and read distribution over known gene models with RSeQC version 2.3
Gene-level and transcript counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for sample differences in library size.
The TMM size factors and the matrix of counts were imported into R/Bioconductor package Limma, and weighted likelihoods based on the observed mean-variance relationship of every gene/transcript were then calculated for all samples with the Voom function
Assembly: mm10
Supplementary files format and content: tab-delimited text files include log2 counts per million (CPM) values for each Sample.

source_name: BAL

growth_protocol: Mice were maintained and propagated in shoebox-sized cages in a 12-hour light-dark cycle with food available ad lib. To shift the circadian phases of mice, they were acclimated in custom light-tight enclosures (Gorilla Grow Tenet) for two weeks with the light cycle controlled by a programmable timer

extract_protocol:
To obtain BALs, mice were euthanized and their tracheas were cannulated with a 20G flexible catheter, 1-2 mm distal to the larynx.   The lungs were then slowly lavaged in 2 passes with a total of 1 ml sterile phosphate buffered saline (PBS).
Whole lungs were manually excised and immersed in RNAlater solution
Total RNA was isolated from lung homogenates using RNeasy Mini Kits (Qiagen)
RNA from whole lung homogenates or BAL cell pellets were converted to cDNA libraries for sequencing using the the SMARTer kit following manufacturer protocols

treatment_protocol: Mice were anesthetized with 3% isoflurane and then intranasally treated with 30ul of virus diluted in PBS. After viral infection, mice were housed in constant dark conditions until the end of the experiment.

value: BAL

tag: tissue type

value: BAL cell pellet

value: Wild type

value: MHV1 infection, collected post-infection day 8, ZT6


title: BAL, MHV1 infection, ZT6 time point, collected post-infection day 14, replicate 4

description:
Library name: Sample91
all.gene_moderated_log2cpm_BAL.tsv
BAL_5668_RNA

value: MHV1 infection, collected post-infection day 14, ZT6


title: Caco-2.batch2.Control.rep1.D07

description: Library name: Caco2_Batch2_Control_1_D07

value: colon

value: epithelial

value: cell line


title: Caco-2.batch2.Control.rep2.A08

description: Library name: Caco2_Batch2_Control_2_A08


title: 3-004

city: DIJON

first: François

last: Ghiringhelli

address: 1 rue du Professeur Marion

institute: UMR INSERM 1231

description:
Library name: 3-004
TPM_exp.txt

data_processing:
Raw FASTQ data were pseudo-aligned, and gene counts were quantified using Kallisto software (Bray et al). Kallisto transcript index used as reference was built from merged human cDNA and ncDNA files from the GRCh37 assembly Ensembl. Gene-level count and transcripts matrices were then created with the DESeq2 library
Assembly: GRCh37
Supplementary files format and content: tabulated txt file containing TPM values

source_name: Tumor

extract_protocol:
By using the Maxwell RNA FFPE kit (Promega), fifty nanograms of total RNA were ribodepleted with the RiboCop rRNA Depletion kit (Lexogen) by following manufacturer’s protocol, and then purified using NEB kit by following manufacturer’s instructions.
By using the Maxwell RNA FFPE kit (Promega), fifty nanograms of total RNA were ribodepleted with the RiboCop rRNA Depletion kit (Lexogen) by following manufacturer’s protocol, and then purified using NEB kit by following manufacturer’s instructions.

treatment_protocol: Following dissection, tumor tissue was placed in formaldehyde for 24 hours, followed by ethanol dehydration, cleared with xylene, and embedded in paraffin wax at 60ºC to create FFPE samples

value: Tumor

value: exp


title: Caco-2.batch2.Control.rep1.C07

description: Library name: Caco2_Batch2_Control_1_C07


title: BAL, MHV1 infection, ZT12 time point, collected post-infection day 8, replicate 4

description:
Library name: Sample89
all.gene_moderated_log2cpm_BAL.tsv
BAL_5665_RNA

value: MHV1 infection, collected post-infection day 8, ZT12


title: Caco-2.batch2.Control.rep1.B07

description: Library name: Caco2_Batch2_Control_1_B07


title: BAL, MHV1 infection, ZT12 time point, collected post-infection day 6, replicate 4

description:
Library name: Sample88
all.gene_moderated_log2cpm_BAL.tsv
BAL_5664_RNA

value: MHV1 infection, collected post-infection day 6, ZT12


title: Caco-2.batch2.DIP.rep3.G07

description: Library name: Caco2_Batch2_DIP_3_G07


title: BAL, MHV1 infection, ZT12 time point, collected post-infection day 8, replicate 3

description:
Library name: Sample87
all.gene_moderated_log2cpm_BAL.tsv
BAL_5663_RNA


title: Caco-2.batch2.Control.rep1.A07

description: Library name: Caco2_Batch2_Control_1_A07


title: BAL, MHV1 infection, ZT12 time point, collected post-infection day 6, replicate 2

description:
Library name: Sample85
all.gene_moderated_log2cpm_BAL.tsv
BAL_5661_RNA


title: Caco-2.batch2.CAR.rep3.G04

description: Library name: Caco2_Batch2_CAR_3_G04


title: BAL, MHV1 infection, ZT12 time point, collected post-infection day 14, replicate 4

description:
Library name: Sample84
all.gene_moderated_log2cpm_BAL.tsv
BAL_5618_RNA

value: MHV1 infection, collected post-infection day 14, ZT12


title: Caco-2.batch2.CAR.rep3.F04

description: Library name: Caco2_Batch2_CAR_3_F04


title: Caco-2.batch2.CAR.rep3.E04

description: Library name: Caco2_Batch2_CAR_3_E04


title: BAL, MHV1 infection, ZT12 time point, collected post-infection day 8, replicate 2

description:
Library name: Sample83
all.gene_moderated_log2cpm_BAL.tsv
BAL_5617_RNA


title: BAL, MHV1 infection, ZT12 time point, collected post-infection day 14, replicate 2

description:
Library name: Sample81
all.gene_moderated_log2cpm_BAL.tsv
BAL_5614_RNA


title: BAL, MHV1 infection, ZT6 time point, collected post-infection day 8, replicate 3

description:
Library name: Sample80
all.gene_moderated_log2cpm_BAL.tsv
BAL_5612_RNA


title: Caco-2.batch2.CAR.rep3.B04

description: Library name: Caco2_Batch2_CAR_3_B04


title: Caco-2.batch2.CAR.rep3.A04

description: Library name: Caco2_Batch2_CAR_3_A04


title: BAL, MHV1 infection, ZT12 time point, collected post-infection day 4, replicate 4

description:
Library name: Sample78
all.gene_moderated_log2cpm_BAL.tsv
BAL_5570_RNA

value: MHV1 infection, collected post-infection day 4, ZT12


title: BAL, MHV1 infection, ZT6 time point, collected post-infection day 6, replicate 4

description:
Library name: Sample79
all.gene_moderated_log2cpm_BAL.tsv
BAL_5611_RNA

value: MHV1 infection, collected post-infection day 6, ZT6


title: Caco-2.batch2.CAR.rep2.H04

description: Library name: Caco2_Batch2_CAR_2_H04


title: Caco-2.batch2.CAR.rep2.G04

description: Library name: Caco2_Batch2_CAR_2_G04


title: Caco-2.batch2.CAR.rep2.F04

description: Library name: Caco2_Batch2_CAR_2_F04


title: BAL, MHV1 infection, ZT6 time point, collected post-infection day 14, replicate 1

description:
Library name: Sample75
all.gene_moderated_log2cpm_BAL.tsv
BAL_5477_RNA


title: BAL, MHV1 infection, ZT6 time point, collected post-infection day 14, replicate 2

description:
Library name: Sample76
all.gene_moderated_log2cpm_BAL.tsv
BAL_5478_RNA


title: Caco-2.batch2.CAR.rep2.E04

description: Library name: Caco2_Batch2_CAR_2_E04


title: BAL, MHV1 infection, ZT6 time point, collected post-infection day 8, replicate 2

description:
Library name: Sample72
all.gene_moderated_log2cpm_BAL.tsv
BAL_5473_RNA


title: Caco-2.batch2.CAR.rep2.B04

description: Library name: Caco2_Batch2_CAR_2_B04


title: BAL, MHV1 infection, ZT6 time point, collected post-infection day 4, replicate 4

description:
Library name: Sample71
all.gene_moderated_log2cpm_BAL.tsv
BAL_5472_RNA

value: MHV1 infection, collected post-infection day 4, ZT6


title: Caco-2.batch2.CAR.rep2.A04

description: Library name: Caco2_Batch2_CAR_2_A04


title: Caco-2.batch2.CAR.rep3.H04

description: Library name: Caco2_Batch2_CAR_3_H04


title: BAL, Control, ZT12 time point, replicate 2

description:
Library name: Sample68
all.gene_moderated_log2cpm_BAL.tsv
BAL_5460_RNA

value: Control, ZT12


title: BAL, MHV1 infection, ZT12 time point, collected post-infection day 8, replicate 1

description:
Library name: Sample67
all.gene_moderated_log2cpm_BAL.tsv
BAL_5413_RNA

value: BAL


title: Caco-2.batch2.CAR.rep1.D04

description: Library name: Caco2_Batch2_CAR_1_D04


title: BAL, MHV1 infection, ZT6 time point, collected post-infection day 2, replicate 4

description:
Library name: Sample65
all.gene_moderated_log2cpm_BAL.tsv
BAL_5409_RNA

value: BAL cell pellet

value: MHV1 infection, collected post-infection day 2, ZT6


title: Caco-2.batch2.CAR.rep1.C04

description: Library name: Caco2_Batch2_CAR_1_C04


title: Caco-2.batch2.CAR.rep1.B04

description: Library name: Caco2_Batch2_CAR_1_B04


title: BAL, MHV1 infection, ZT6 time point, collected post-infection day 6, replicate 2

description:
Library name: Sample73
all.gene_moderated_log2cpm_BAL.tsv
BAL_5474_RNA

value: Wild type


title: BAL, Control, ZT12 time point, replicate 1

description:
Library name: Sample63
all.gene_moderated_log2cpm_BAL.tsv
BAL_5359_RNA


title: Caco-2.batch2.CAR.rep1.H04

description: Library name: Caco2_Batch2_CAR_1_H04


title: BAL, Control, ZT12 time point, replicate 3

description:
Library name: Sample69
all.gene_moderated_log2cpm_BAL.tsv
BAL_5461_RNA


title: BAL, MHV1 infection, ZT12 time point, collected post-infection day 14, replicate 1

description:
Library name: Sample62
all.gene_moderated_log2cpm_BAL.tsv
BAL_5348_RNA


title: Caco-2.batch2.CAR.rep1.E04

description: Library name: Caco2_Batch2_CAR_1_E04


title: BAL, MHV1 infection, ZT12 time point, collected post-infection day 6, replicate 1

description:
Library name: Sample66
all.gene_moderated_log2cpm_BAL.tsv
BAL_5411_RNA


title: BAL, MHV1 infection, ZT12 time point, collected post-infection day 4, replicate 3

description:
Library name: Sample61
all.gene_moderated_log2cpm_BAL.tsv
BAL_5347_RNA


title: BAL, Control, ZT6 time point, replicate 3

description:
Library name: Sample60
all.gene_moderated_log2cpm_BAL.tsv
BAL_5341_RNA

value: Control, ZT6


title: Caco-2.batch2.AMPA.rep3.F05

description: Library name: Caco2_Batch2_AMPA_3_F05

value: colon


title: BAL, Control, ZT6 time point, replicate 2

description:
Library name: Sample59
all.gene_moderated_log2cpm_BAL.tsv
BAL_5339_RNA


title: Caco-2.batch2.AMPA.rep3.E05

description: Library name: Caco2_Batch2_AMPA_3_E05

value: epithelial


title: BAL, Control, ZT6 time point, replicate 1

description:
Library name: Sample58
all.gene_moderated_log2cpm_BAL.tsv
BAL_5310_RNA


title: Caco-2.batch2.AMPA.rep3.D05

description: Library name: Caco2_Batch2_AMPA_3_D05

value: cell line


title: BAL, MHV1 infection, ZT6 time point, collected post-infection day 4, replicate 2

description:
Library name: Sample57
all.gene_moderated_log2cpm_BAL.tsv
5609_RNA


title: Caco-2.batch2.AMPA.rep3.C05

description: Library name: Caco2_Batch2_AMPA_3_C05


title: BAL, MHV1 infection, ZT6 time point, collected post-infection day 6, replicate 1

description:
Library name: Sample56
all.gene_moderated_log2cpm_BAL.tsv
5571_RNA


title: Caco-2.batch2.AMPA.rep3.B05

description: Library name: Caco2_Batch2_AMPA_3_B05


title: BAL, MHV1 infection, ZT12 time point, collected post-infection day 4, replicate 2

description:
Library name: Sample55
all.gene_moderated_log2cpm_BAL.tsv
5569_RNA


title: Caco-2.batch2.CAR.rep1.A04

description: Library name: Caco2_Batch2_CAR_1_A04


title: Caco-2.batch2.AMPA.rep3.A05

description: Library name: Caco2_Batch2_AMPA_3_A05


title: BAL, MHV1 infection, ZT6 time point, collected post-infection day 8, replicate 1

description:
Library name: Sample54
all.gene_moderated_log2cpm_BAL.tsv
5474_RNA

value: MHV1 infection, collected post-infection day 8, ZT6


title: Caco-2.batch2.AMPA.rep2.H05

description: Library name: Caco2_Batch2_AMPA_2_H05


title: Caco-2.batch2.AMPA.rep3.G05

description: Library name: Caco2_Batch2_AMPA_3_G05


title: Caco-2.batch2.AMPA.rep3.H05

description: Library name: Caco2_Batch2_AMPA_3_H05


title: BAL, MHV1 infection, ZT6 time point, collected post-infection day 2, replicate 2

description:
Library name: Sample53
all.gene_moderated_log2cpm_BAL.tsv
5470_RNA


title: Caco-2.batch2.AMPA.rep2.G05

description: Library name: Caco2_Batch2_AMPA_2_G05


title: BAL, MHV1 infection, ZT6 time point, collected post-infection day 2, replicate 1

description:
Library name: Sample52
all.gene_moderated_log2cpm_BAL.tsv
5469_RNA


title: BAL, MHV1 infection, ZT12 time point, collected post-infection day 2, replicate 4

description:
Library name: Sample51
all.gene_moderated_log2cpm_BAL.tsv
5463_RNA

value: MHV1 infection, collected post-infection day 2, ZT12


title: Caco-2.batch2.AMPA.rep2.E05

description: Library name: Caco2_Batch2_AMPA_2_E05


title: Caco-2.batch2.AMPA.rep2.F05

description: Library name: Caco2_Batch2_AMPA_2_F05


title: BAL, MHV1 infection, ZT12 time point, collected post-infection day 2, replicate 3

description:
Library name: Sample50
all.gene_moderated_log2cpm_BAL.tsv
5462_RNA


title: BAL, MHV1 infection, ZT12 time point, collected post-infection day 6, replicate 3

description:
Library name: Sample86
all.gene_moderated_log2cpm_BAL.tsv
BAL_5662_RNA


title: Caco-2.batch2.AMPA.rep2.D05

description: Library name: Caco2_Batch2_AMPA_2_D05


title: Caco-2.batch2.CAR.rep3.D04

description: Library name: Caco2_Batch2_CAR_3_D04


title: Caco-2.batch2.CAR.rep3.C04

description: Library name: Caco2_Batch2_CAR_3_C04


title: BAL, MHV1 infection, ZT12 time point, collected post-infection day 14, replicate 3

description:
Library name: Sample82
all.gene_moderated_log2cpm_BAL.tsv
BAL_5616_RNA


title: BAL, MHV1 infection, ZT6 time point, collected post-infection day 4, replicate 1

description:
Library name: Sample49
all.gene_moderated_log2cpm_BAL.tsv
5410_RNA


title: Caco-2.batch2.AMPA.rep2.C05

description: Library name: Caco2_Batch2_AMPA_2_C05


title: Caco-2.batch2.AMPA.rep2.B05

description: Library name: Caco2_Batch2_AMPA_2_B05


title: BAL, MHV1 infection, ZT12 time point, collected post-infection day 4, replicate 1

description:
Library name: Sample48
all.gene_moderated_log2cpm_BAL.tsv
5346_RNA


title: BAL, MHV1 infection, ZT6 time point, collected post-infection day 14, replicate 3

description:
Library name: Sample77
all.gene_moderated_log2cpm_BAL.tsv
BAL_5541_RNA

value: MHV1 infection, collected post-infection day 14, ZT6


title: BAL, MHV1 infection, ZT12 time point, collected post-infection day 2, replicate 2

description:
Library name: Sample47
all.gene_moderated_log2cpm_BAL.tsv
5345_RNA


title: Caco-2.batch2.AMPA.rep2.A05

description: Library name: Caco2_Batch2_AMPA_2_A05


title: BAL, MHV1 infection, ZT12 time point, collected post-infection day 2, replicate 1

description:
Library name: Sample46
all.gene_moderated_log2cpm_BAL.tsv
5344_RNA


title: Caco-2.batch2.AMPA.rep1.H05

description: Library name: Caco2_Batch2_AMPA_1_H05


title: Lung, MHV1 infection, ZT6 time point, collected post-infection day 14, replicate 4

description:
Library name: Sample45
all.gene_moderated_log2cpm_lung.tsv
5668_LUNG_RNA_DAY_14

source_name: Lung

value: Lung

value: Mouse whole lung


title: Caco-2.batch2.AMPA.rep1.G05

description: Library name: Caco2_Batch2_AMPA_1_G05


title: Caco-2.batch2.CAR.rep2.D04

description: Library name: Caco2_Batch2_CAR_2_D04


title: Caco-2.batch2.CAR.rep2.C04

description: Library name: Caco2_Batch2_CAR_2_C04


title: BAL, MHV1 infection, ZT6 time point, collected post-infection day 6, replicate 3

description:
Library name: Sample74
all.gene_moderated_log2cpm_BAL.tsv
BAL_5475_RNA


title: Caco-2.batch2.AMPA.rep1.F05

description: Library name: Caco2_Batch2_AMPA_1_F05


title: Lung, MHV1 infection, ZT12 time point, collected post-infection day 8, replicate 4

description:
Library name: Sample43
all.gene_moderated_log2cpm_lung.tsv
5665_LUNG_RNA_DAY_8

value: MHV1 infection, collected post-infection day 8, ZT12


title: Lung, MHV1 infection, ZT6 time point, collected post-infection day 8, replicate 4

description:
Library name: Sample44
all.gene_moderated_log2cpm_lung.tsv
5667_LUNG_RNA_DAY_8


title: Caco-2.batch2.AMPA.rep1.E05

description: Library name: Caco2_Batch2_AMPA_1_E05


title: Caco-2.batch2.AMPA.rep1.D05

description: Library name: Caco2_Batch2_AMPA_1_D05


title: Lung, MHV1 infection, ZT12 time point, collected post-infection day 6, replicate 3

description:
Library name: Sample42
all.gene_moderated_log2cpm_lung.tsv
5664_LUNG_RNA_DAY_6

value: MHV1 infection, collected post-infection day 6, ZT12


title: Lung, MHV1 infection, ZT12 time point, collected post-infection day 8, replicate 3

description:
Library name: Sample41
all.gene_moderated_log2cpm_lung.tsv
5663_LUNG_RNA_DAY_8


title: Caco-2.batch2.AMPA.rep1.C05

description: Library name: Caco2_Batch2_AMPA_1_C05


title: Caco-2.batch2.AMPA.rep1.B05

description: Library name: Caco2_Batch2_AMPA_1_B05


title: Caco-2.batch1.THX.rep3.H08

description: Library name: Caco2_Batch1_THX_3_H08


title: Lung, MHV1 infection, ZT12 time point, collected post-infection day 14, replicate 4

description:
Library name: Sample38
all.gene_moderated_log2cpm_lung.tsv
5618_LUNG_RNA_DAY_14

value: MHV1 infection, collected post-infection day 14, ZT12


title: Lung, MHV1 infection, ZT12 time point, collected post-infection day 8, replicate 2

description:
Library name: Sample37
all.gene_moderated_log2cpm_lung.tsv
5617_LUNG_RNA_DAY_8


title: Lung, MHV1 infection, ZT12 time point, collected post-infection day 14, replicate 3

description:
Library name: Sample36
all.gene_moderated_log2cpm_lung.tsv
5616_LUNG_RNA_DAY_14


title: Caco-2.batch1.THX.rep3.F08

description: Library name: Caco2_Batch1_THX_3_F08


title: Lung, MHV1 infection, ZT12 time point, collected post-infection day 6, replicate 1

description:
Library name: Sample39
all.gene_moderated_log2cpm_lung.tsv
5661_LUNG_RNA_DAY_6


title: Lung, MHV1 infection, ZT12 time point, collected post-infection day 14, replicate 2

description:
Library name: Sample35
all.gene_moderated_log2cpm_lung.tsv
5614_LUNG_RNA_DAY_14


title: Lung, MHV1 infection, ZT6 time point, collected post-infection day 8, replicate 3

description:
Library name: Sample34
all.gene_moderated_log2cpm_lung.tsv
5612_LUNG_RNA_DAY_8


title: Caco-2.batch1.THX.rep3.E08

description: Library name: Caco2_Batch1_THX_3_E08


title: Caco-2.batch1.THX.rep3.D08

description: Library name: Caco2_Batch1_THX_3_D08


title: Lung, MHV1 infection, ZT6 time point, collected post-infection day 6, replicate 5

description:
Library name: Sample33
all.gene_moderated_log2cpm_lung.tsv
5611_LUNG_RNA_DAY_6

value: MHV1 infection, collected post-infection day 6, ZT6


title: Lung, MHV1 infection, ZT6 time point, collected post-infection day 4, replicate 4

description:
Library name: Sample32
all.gene_moderated_log2cpm_lung.tsv
5609_LUNG_RNA_DAY_4

value: MHV1 infection, collected post-infection day 4, ZT6


title: Caco-2.batch1.THX.rep3.C08

description: Library name: Caco2_Batch1_THX_3_C08


title: Caco-2.batch1.THX.rep3.B08

description: Library name: Caco2_Batch1_THX_3_B08


title: Lung, MHV1 infection, ZT6 time point, collected post-infection day 6, replicate 4

description:
Library name: Sample31
all.gene_moderated_log2cpm_lung.tsv
5571_LUNG_RNA_DAY_6


title: Caco-2.batch1.THX.rep3.A08

description: Library name: Caco2_Batch1_THX_3_A08


title: Lung, MHV1 infection, ZT12 time point, collected post-infection day 4, replicate 3

description:
Library name: Sample30
all.gene_moderated_log2cpm_lung.tsv
5570_LUNG_RNA_DAY_4

value: MHV1 infection, collected post-infection day 4, ZT12


title: Caco-2.batch1.THX.rep2.H08

description: Library name: Caco2_Batch1_THX_2_H08


title: Caco-2.batch1.THX.rep2.G08

description: Library name: Caco2_Batch1_THX_2_G08


title: Lung, MHV1 infection, ZT12 time point, collected post-infection day 4, replicate 2

description:
Library name: Sample29
all.gene_moderated_log2cpm_lung.tsv
5569_LUNG_RNA_DAY_4


title: Lung, MHV1 infection, ZT6 time point, collected post-infection day 14, replicate 3

description:
Library name: Sample28
all.gene_moderated_log2cpm_lung.tsv
5541_LUNG_RNA_DAY_14


title: Caco-2.batch1.THX.rep2.F08

description: Library name: Caco2_Batch1_THX_2_F08


title: Lung, MHV1 infection, ZT6 time point, collected post-infection day 14, replicate 1

description:
Library name: Sample26
all.gene_moderated_log2cpm_lung.tsv
5477_LUNG_RNA_DAY_14


title: Caco-2.batch1.THX.rep2.E08

description: Library name: Caco2_Batch1_THX_2_E08


title: Lung, MHV1 infection, ZT6 time point, collected post-infection day 14, replicate 2

description:
Library name: Sample27
all.gene_moderated_log2cpm_lung.tsv
5478_LUNG_RNA_DAY_14


title: Caco-2.batch1.THX.rep2.D08

description: Library name: Caco2_Batch1_THX_2_D08


title: Lung, MHV1 infection, ZT6 time point, collected post-infection day 6, replicate 3

description:
Library name: Sample25
all.gene_moderated_log2cpm_lung.tsv
5476_LUNG_RNA_DAY_6


title: Caco-2.batch1.THX.rep2.C08

description: Library name: Caco2_Batch1_THX_2_C08


title: Lung, MHV1 infection, ZT6 time point, collected post-infection day 6, replicate 2

description:
Library name: Sample24
all.gene_moderated_log2cpm_lung.tsv
5475_LUNG_RNA_DAY_6


title: Caco-2.batch1.THX.rep2.B08

description: Library name: Caco2_Batch1_THX_2_B08


title: Lung, MHV1 infection, ZT6 time point, collected post-infection day 8, replicate 2

description:
Library name: Sample23
all.gene_moderated_log2cpm_lung.tsv
5474_LUNG_RNA_DAY_8


title: Lung, MHV1 infection, ZT6 time point, collected post-infection day 4, replicate 3

description:
Library name: Sample21
all.gene_moderated_log2cpm_lung.tsv
5472_LUNG_RNA_DAY_4


title: Caco-2.batch1.THX.rep1.G08

description: Library name: Caco2_Batch1_THX_1_G08


title: Caco-2.batch1.THX.rep1.H08

description: Library name: Caco2_Batch1_THX_1_H08


title: Lung, MHV1 infection, ZT6 time point, collected post-infection day 4, replicate 2

description:
Library name: Sample20
all.gene_moderated_log2cpm_lung.tsv
5471_LUNG_RNA_DAY_4


title: Caco-2.batch1.THX.rep1.F08

description: Library name: Caco2_Batch1_THX_1_F08


title: Lung, MHV1 infection, ZT6 time point, collected post-infection day 2, replicate 3

description:
Library name: Sample18
all.gene_moderated_log2cpm_lung.tsv
5469_LUNG_RNA_DAY_2

value: MHV1 infection, collected post-infection day 2, ZT6


title: Caco-2.batch1.THX.rep1.D08

description: Library name: Caco2_Batch1_THX_1_D08


title: Lung, MHV1 infection, ZT12 time point, collected post-infection day 2, replicate 3

description:
Library name: Sample16
all.gene_moderated_log2cpm_lung.tsv
5462_LUNG_RNA_DAY_2

value: Wild type


title: Lung, Control, ZT12 time point, replicate 3

description:
Library name: Sample15
all.gene_moderated_log2cpm_lung.tsv
5461_LUNG_RNA_CTRL

value: Control, ZT12


title: Caco-2.batch1.THX.rep1.B08

description: Library name: Caco2_Batch1_THX_1_B08

value: colon


title: Caco-2.batch1.THX.rep1.C08

description: Library name: Caco2_Batch1_THX_1_C08

value: epithelial


title: Lung, Control, ZT12 time point, replicate 2

description:
Library name: Sample14
all.gene_moderated_log2cpm_lung.tsv
5460_LUNG_RNA_CTRL


title: Caco-2.batch1.THX.rep1.A08

description: Library name: Caco2_Batch1_THX_1_A08

value: cell line


title: Lung, MHV1 infection, ZT12 time point, collected post-infection day 6, replicate 2

description:
Library name: Sample40
all.gene_moderated_log2cpm_lung.tsv
5662_LUNG_RNA_DAY_6


title: Caco-2.batch2.AMPA.rep1.A05

description: Library name: Caco2_Batch2_AMPA_1_A05


title: Caco-2.batch1.THX.rep3.G08

description: Library name: Caco2_Batch1_THX_3_G08


title: Lung, Control, ZT12 time point, replicate 1

description:
Library name: Sample13
all.gene_moderated_log2cpm_lung.tsv
5459_LUNG_RNA_CTRL


title: Caco-2.batch1.MET.rep3.H07

description: Library name: Caco2_Batch1_MET_3_H07


title: Caco-2.batch1.MET.rep3.G07

description: Library name: Caco2_Batch1_MET_3_G07


title: Lung, MHV1 infection, ZT12 time point, collected post-infection day 8, replicate 1

description:
Library name: Sample12
all.gene_moderated_log2cpm_lung.tsv
5413_LUNG_RNA_DAY_8


title: Caco-2.batch1.MET.rep3.F07

description: Library name: Caco2_Batch1_MET_3_F07


title: Lung, MHV1 infection, ZT6 time point, collected post-infection day 6, replicate 1

description:
Library name: Sample11
all.gene_moderated_log2cpm_lung.tsv
5411_LUNG_RNA_DAY_6


title: Caco-2.batch1.MET.rep3.E07

description: Library name: Caco2_Batch1_MET_3_E07


title: Lung, MHV1 infection, ZT6 time point, collected post-infection day 4, replicate 1

description:
Library name: Sample10
all.gene_moderated_log2cpm_lung.tsv
5410_LUNG_RNA_DAY_4


title: Caco-2.batch1.MET.rep3.D07

description: Library name: Caco2_Batch1_MET_3_D07


title: Caco-2.batch1.MET.rep3.C07

description: Library name: Caco2_Batch1_MET_3_C07


title: Lung, MHV1 infection, ZT6 time point, collected post-infection day 2, replicate 2

description:
Library name: Sample9
all.gene_moderated_log2cpm_lung.tsv
5409_LUNG_RNA_DAY_2


title: Caco-2.batch1.MET.rep3.B07

description: Library name: Caco2_Batch1_MET_3_B07


title: Lung, MHV1 infection, ZT6 time point, collected post-infection day 2, replicate 1

description:
Library name: Sample8
all.gene_moderated_log2cpm_lung.tsv
5408_LUNG_RNA_DAY_2


title: Lung, MHV1 infection, ZT12 time point, collected post-infection day 14, replicate 1

description:
Library name: Sample7
all.gene_moderated_log2cpm_lung.tsv
5348_LUNG_RNA_DAY_4


title: Caco-2.batch1.MET.rep3.A07

description: Library name: Caco2_Batch1_MET_3_A07


title: Lung, MHV1 infection, ZT12 time point, collected post-infection day 4, replicate 1

description:
Library name: Sample6
all.gene_moderated_log2cpm_lung.tsv
5346_LUNG_RNA_DAY_4


title: Caco-2.batch1.MET.rep2.H07

description: Library name: Caco2_Batch1_MET_2_H07


title: Lung, MHV1 infection, ZT12 time point, collected post-infection day 2, replicate 2

description:
Library name: Sample5
all.gene_moderated_log2cpm_lung.tsv
5345_LUNG_RNA_DAY_2


title: Lung, MHV1 infection, ZT12 time point, collected post-infection day 2, replicate 1

description:
Library name: Sample4
all.gene_moderated_log2cpm_lung.tsv
5344_LUNG_RNA_DAY_2


title: Lung, Control, ZT6 time point, replicate 3

description:
Library name: Sample3
all.gene_moderated_log2cpm_lung.tsv
5341_LUNG_RNA_CTRL

value: Control, ZT6


title: Caco-2.batch1.MET.rep2.F07

description: Library name: Caco2_Batch1_MET_2_F07


title: Caco-2.batch1.THX.rep2.A08

description: Library name: Caco2_Batch1_THX_2_A08


title: Caco-2.batch1.MET.rep2.G07

description: Library name: Caco2_Batch1_MET_2_G07


title: Caco-2.batch1.MET.rep2.E07

description: Library name: Caco2_Batch1_MET_2_E07


title: Lung, Control, ZT6 time point, replicate 2

description:
Library name: Sample2
all.gene_moderated_log2cpm_lung.tsv
5340_LUNG_RNA_CTRL


title: Caco-2.batch1.MET.rep2.D07

description: Library name: Caco2_Batch1_MET_2_D07


title: Lung, MHV1 infection, ZT6 time point, collected post-infection day 2, replicate 4

description:
Library name: Sample19
all.gene_moderated_log2cpm_lung.tsv
5470_LUNG_RNA_DAY_2


title: Lung, MHV1 infection, ZT6 time point, collected post-infection day 8, replicate 1

description:
Library name: Sample22
all.gene_moderated_log2cpm_lung.tsv
5473_LUNG_RNA_DAY_8

value: MHV1 infection, collected post-infection day 8, ZT6


title: Caco-2.batch1.MET.rep2.C07

description: Library name: Caco2_Batch1_MET_2_C07


title: Lung, Control, ZT6 time point, replicate 1

description:
Library name: Sample1
all.gene_moderated_log2cpm_lung.tsv
5339_LUNG_RNA_CTRL


title: Caco-2.batch1.THX.rep1.E08

description: Library name: Caco2_Batch1_THX_1_E08


title: A0042_VV(2e6)+OXP: oxaliplatin ip, hIL-7/mIL-12-VV 2E6 pfu it, rep3

city: Ibaraki

first: Kentaro

last: Ikegami

address: 21 Miyukigaoka, Tsukuba

country: Japan

institute: Astellas Pharma Inc.

description: Library name: A0042

data_processing:
The sequencing reads were aligned onto the mm10 genome sequence using open-source software (Spliced Transcripts Alignment to a Reference, ver. 2.7.10b). Reads were counted for each gene for each sample using Rotational Scanning Electron Micrographs.
Assembly: mm10
Supplementary files format and content: The TSV file is an output file from RSEM and contains values such as raw read counts and TPM for each gene.

source_name: LLC1 tumor

extract_protocol:
Tumor tissues were harvested and quickly suspended in an RNA extraction solution (ISOGEN). Total RNA was isolated according to the manufacturer’s instructions. Total RNA (>1 ug) was used as input for mRNA enrichment using a sequencing kit (SMART-Seq v4 Ultra Low Input RNA Kit).
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA Library Prep Kit following manufacturer's protocols.

value: LLC1 tumor

tag: time


title: Caco-2.batch1.MET.rep2.B07

description: Library name: Caco2_Batch1_MET_2_B07


title: A0041_VV(2e6)+OXP: oxaliplatin ip, hIL-7/mIL-12-VV 2E6 pfu it, rep2

description: Library name: A0041


title: A0040_VV(2e6)+OXP: oxaliplatin ip, hIL-7/mIL-12-VV 2E6 pfu it, rep1

description: Library name: A0040


title: Caco-2.batch1.MET.rep1.H07

description: Library name: Caco2_Batch1_MET_1_H07


title: Caco-2.batch1.MET.rep2.A07

description: Library name: Caco2_Batch1_MET_2_A07


title: A0039_VV(2e6)-mono: 5%glucose ip, hIL-7/mIL-12-VV 2E6 pfu it, rep3

description: Library name: A0039


title: Caco-2.batch1.MET.rep1.G07

description: Library name: Caco2_Batch1_MET_1_G07


title: Lung, MHV1 infection, ZT12 time point, collected post-infection day 2, replicate 4

description:
Library name: Sample17
all.gene_moderated_log2cpm_lung.tsv
5463_LUNG_RNA_DAY_2

value: Lung

value: MHV1 infection, collected post-infection day 2, ZT12


title: Caco-2.batch1.MET.rep1.F07

description: Library name: Caco2_Batch1_MET_1_F07


title: A0038_VV(2e6)-mono: 5%glucose ip, hIL-7/mIL-12-VV 2E6 pfu it, rep2

description: Library name: A0038


title: Caco-2.batch1.MET.rep1.E07

description: Library name: Caco2_Batch1_MET_1_E07


title: A0036_OXP: oxaliplatin ip, PBS it. rep3

description: Library name: A0036


title: Xenopus laevis stage 40 brain and spinal cord, wild type

city: Houston

first: Amy

last: Sater

state: Texas

address: 3455 Cullen Blvd, SR2 421F

department: Biology and Biochemistry

institute: University of Houston

description:
Library name: Sample 1
10X Genomics

data_processing:
Demultiplexing, barcode processing, reads alignment to the reference genome, gene quantification, and sample aggregation were performed using Cell Ranger v8.0.
Assembly: Xenopus_laevis_v10.1
Supplementary files format and content: Tab-separted values and matrix files

organism: Xenopus laevis

source_name: Neural tissues

growth_protocol: Embryos were raised in 1/3 MMR at 18˚C.

extract_protocol:
Dissociated cells were processed for single-cell RNA sequencing by standard methods in accordance with 10X Genomics protocols.
Sequencing libraries from individual cells were prepared in accordance will 10X Genomics protocolsand sequenced using an Illumina NextSeq 500 instrument.

treatment_protocol: Central Nervous System (CNS) isolates, consisting of the brain and spinal cord, were isolated in 2 mg/ml liberase (Roche), as described in Ritter et al., (2020) from pre-feeding tadpoles at st. 40.  The optic vesicles were removed, and the neural tubes were incubated in papain solution (0.5 µg/ml papain in 1 ml containing 15 µl Trypsin LE (GIBCO), 5 mM Cysteine, 1 mM EDTA, prepared 35 minutes before use to allow preactivation of papain). The isolated neural tubes from st. 40 tadpoles required 75 minutes in papain, followed by 10-12 rounds of pipetting, to bring about dissociation.

value: Neural tissues

value: Untreated


title: A0037_VV(2e6)-mono: 5%glucose ip, hIL-7/mIL-12-VV 2E6 pfu it, rep1

description: Library name: A0037


title: Rings_KS_rep4

city: Nijmegen

first: Martijn

middle: van den

last: Broek

address: Geert Grooteplein 24, route 846

department: Molecular Biology

institute: Radboud university - RIMLS Science

description: Library name: KS_2110

data_processing:
UMI-tools (v1.1.5) was used to extract barcode and UMI information from read 2 and append it to read 1. Read 1 was subsequently trimmed using trim_galore (v0.6.10) and alignment using STAR (2.7.10b) to the P. falciparum, Human and ERCC combined genome. Reads were seperated based on their origin and split into reads from P. falciparum, human and ERCC. Reads were attributed to features using featureCounts (v2.0.6) and UMI-tools was used again to count features with unique UMIs per cell and produce the raw count matrix .tsv files.
Assembly: For Plasmodium falciparum the PlasmoDB-68 pfalciparum3D7 genome build was used. For human the Homo sapiens GRCh38 genome was used
Supplementary files format and content: Processed data files are available as .tsv containing the raw count matrices per 384-wells plate.

organism: Plasmodium falciparum

source_name: Plasmodium infected red blood cells

extract_protocol:
Infected red blood cells were selected based on episomally expressed mCherry expression by the Plasmodium parasite. mCherry positive cells were sorted in 384-wells plates for single-cell sequencing
scRNA sequencing libraries were prepared according to the CELseq2 protocol. Briefly, infected red blood cells were sorted in 384-wells plates containing CELseq2 primers (containing an unique cell barcodes in each well). Next, cell were lysed using tritonX100 and after 5 minutes at 65°C, first strand reaction material were added (using Superscript II), and first strand reaction was performed (10m at 35°C, 60m at 42°C and 10m at 70°C). Then, second strand syntehsis was performed for 2 hours at 16°C. Double stranded barcoded DNA was collected in a single tube per plate, and purified using Ampure Beads XP cleanup. In vitro transcription was performed overnight (14 hours) at 37°C using the MEGAScript T7 transcription kit. The amplified RNA was treated with rSAP/ExoI to remove NTPs and the DNA template, fragmented for 1.5 minutes at 94°C and purified using Ampure Beads XP bead clean up. All the RNA was used as input in a second first-strand reverse transcription reaction using Superscript II (10m at 25°C, 60m at 42°C and 10m at 70°C). Plate barcode primers were added together with the library preparation forward primer and PCR was performed using Phusion High Fidelity mix (98°C for 30s, 11 cycles of 98°C for 10s, 60°C for 30s and 65°C for 60s, and ended with 65°C for 5m). Afterwards two library cleanups were performed using Ampure Beads XP (0.8 ratio) and then libraries were ready for sequencing.

value: Plasmodium infected red blood cells

value: Knock sideways / Mislocalized


title: Rings_KS_rep3

description: Library name: KS_2109


title: Caco-2.batch1.MET.rep1.C07

description: Library name: Caco2_Batch1_MET_1_C07


title: Caco-2.batch1.MET.rep1.D07

description: Library name: Caco2_Batch1_MET_1_D07


title: Rings_KS_rep2

description: Library name: KS_2108


title: A0035_OXP: oxaliplatin ip, PBS it. rep2

description: Library name: A0035


title: Rings_KS_rep1

description: Library name: KS_2107


title: A0034_OXP: oxaliplatin ip, PBS it. rep1

description: Library name: A0034


title: Caco-2.batch1.MET.rep1.B07

description: Library name: Caco2_Batch1_MET_1_B07


title: Rings_control_rep3

description: Library name: Control_2112

value: Control


title: A0033_vehicle: 5%glucose ip, PBS it, rep3

description: Library name: A0033


title: Rings_control_rep2

description: Library name: Control_2105


title: Caco-2.batch1.MET.rep1.A07

description: Library name: Caco2_Batch1_MET_1_A07


title: Rings_control_rep1

description: Library name: Control_2104


title: A0032_vehicle: 5%glucose ip, PBS it, rep2

description: Library name: A0032


title: Caco-2.batch1.IMZ.rep3.H05

description: Library name: Caco2_Batch1_IMZ_3_H05


title: XBP1_KO_Tm_H3K27ac_HiChIP_SET2_rep1

city: Seoul

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

department: Department of Tropical Medicine

country: South Korea

institute: Yonsei University College of Medicine

description: Library name: XBP1_KO_Tm_H3K27ac_HiChIP_SET2_rep1

data_processing:
Paired-end Hi-C sequencing reads were processed using HiC-Pro (v2.11.4).
Chromatin loops from HiChIP data were identified using FitHiChIP (v8.0). Loop calling was performed in peak-to-all mode (IntType=3) using paired ChIP-seq peaks as input. The bin size was set to 5kb (default), with interaction distance range defined as 10kb to 2Mb. Bias correction was enabled using coverage normalization, and peak-to-all background was used for contact probability estimation (UseP2PBackgrnd = 0). Loops were identified at a threshold of Q-value < 0.00001 for H3K27Ac HiChIP data, Q-value < 0.01 for ATF4 HiChIP data.
Assembly: hg19
Supplementary files format and content: hic contaning validpairs
Library strategy: HiChIP

growth_protocol: The human colorectal cancer cell line HCT116 was cultured in RPMI-1640 medium (Welgene) supplemented with 10% fetal bovine serum (FBS; HyClone) and 1% penicillin–streptomycin (Welgene) at 37 ℃ in a humidified incubator containing 5% CO2. Cells were subcultured every 48–72 h.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min at room temperature and quenched using 0.125 M glycine for 5 min, followed by washing with cold PBS. After cell lysis, cross-linked chromatin was digested with the DpnII restriction enzyme, with enzyme amounts adjusted in proportion to the number of cells, followed by fill-in with biotin-14-dATP (Jena Bioscience) and proximity ligation. The resulting ligation products were sheared by sonication using a Qsonica sonicator (30 s ON/30 s OFF, 10 cycles) and incubated overnight at 4 ℃ with either an H3K27ac antibody (Abcam, ab4729) or an ATF4 antibody (Cell Signaling Technology, 11815). After sequential washes with standard ChIP wash buffers, chromatin–antibody complexes were reverse cross-linked overnight. De-cross-linked DNA was purified and quantified using Qubit dsDNA HS Assay Kit (Invitrogen, Q32854) and 5 ng of DNA was subjected to biotin pull-down using a streptavidin C-1 magnetic beads.
Tagmentation was directly performed on bead-bound DNA with Tn5 transposase with enzyme amounts adjusted according to the DNA input, followed by washing with appropriate buffers. Tagmented DNA was released from the beads by a simplified PCR procedure and further amplified using Nextera PCR primers. Amplified libraries were size-selected and purified using AMPure XP beads (0.5x–0.75x).

treatment_protocol: Cells were treated with tunicamycin (Sigma-Aldrich) at a final concentration of 0.5 µg ml-1 for 6 h. Cells treated with 0.1% DMSO for the same duration served as vehicle controls.

tag: chip antibody

value: H3K27ac (Abcam #Ab4729)

value: Human colorectal cancer

value: 0.5 μg/ml tunicamycin


title: XBP1_KO_Tm_H3K27ac_HiChIP_SET2_rep2

description: Library name: XBP1_KO_Tm_H3K27ac_HiChIP_SET2_rep2


title: XBP1_KO_Con_H3K27ac_HiChIP_SET2_rep2

description: Library name: XBP1_KO_Con_H3K27ac_HiChIP_SET2_rep2

value: 0.1% DMSO


title: A0031_vehicle: 5%glucose ip, PBS it, rep1

description: Library name: A0031


title: XBP1_KO_Con_H3K27ac_HiChIP_SET2_rep1

description: Library name: XBP1_KO_Con_H3K27ac_HiChIP_SET2_rep1


title: Caco-2.batch1.IMZ.rep3.G05

description: Library name: Caco2_Batch1_IMZ_3_G05

value: colon


title: ATF6_KO_Tm_H3K27ac_HiChIP_SET2_rep2

description: Library name: ATF6_KO_Tm_H3K27ac_HiChIP_SET2_rep2


title: ATF6_KO_Tm_H3K27ac_HiChIP_SET2_rep1

description: Library name: ATF6_KO_Tm_H3K27ac_HiChIP_SET2_rep1


title: ATF6_KO_Con_H3K27ac_HiChIP_SET2_rep2

description: Library name: ATF6_KO_Con_H3K27ac_HiChIP_SET2_rep2


title: Caco-2.batch1.IMZ.rep3.F05

description: Library name: Caco2_Batch1_IMZ_3_F05

value: epithelial


title: VV(2e7)-mono: 5%glucose ip, hIL-7/mIL-12-VV 2E7 pfu it, rep2, day7

description: Library name: A0029


title: Caco-2.batch1.IMZ.rep3.E05

description: Library name: Caco2_Batch1_IMZ_3_E05

value: cell line


title: ATF6_KO_Con_H3K27ac_HiChIP_SET2_rep1

description: Library name: ATF6_KO_Con_H3K27ac_HiChIP_SET2_rep1


title: VV(2e7)-mono: 5%glucose ip, hIL-7/mIL-12-VV 2E7 pfu it, rep1, day7

description: Library name: A0028


title: ATF4_KO_Tm_H3K27ac_HiChIP_SET2_rep2

description: Library name: ATF4_KO_Tm_H3K27ac_HiChIP_SET2_rep2


title: VV(2e7)-mono: 5%glucose ip, hIL-7/mIL-12-VV 2E7 pfu it, rep3, day7

description: Library name: A0030


title: ATF4_KO_Tm_H3K27ac_HiChIP_SET2_rep1

description: Library name: ATF4_KO_Tm_H3K27ac_HiChIP_SET2_rep1


title: Caco-2.batch1.IMZ.rep3.D05

description: Library name: Caco2_Batch1_IMZ_3_D05


title: VV(2e6)+OXP: oxaliplatin ip, hIL-7/mIL-12-VV 2E6 pfu it, rep3, day7

description: Library name: A0027


title: ATF4_KO_Con_H3K27ac_HiChIP_SET2_rep2

description: Library name: ATF4_KO_Con_H3K27ac_HiChIP_SET2_rep2


title: Caco-2.batch1.IMZ.rep3.C05

description: Library name: Caco2_Batch1_IMZ_3_C05


title: ATF4_KO_Con_H3K27ac_HiChIP_SET2_rep1

description: Library name: ATF4_KO_Con_H3K27ac_HiChIP_SET2_rep1


title: VV(2e6)+OXP: oxaliplatin ip, hIL-7/mIL-12-VV 2E6 pfu it, rep2, day7

description: Library name: A0026


title: WT_Tm_H3K27ac_HiChIP_SET2_rep2

description: Library name: WT_Tm_H3K27ac_HiChIP_SET2_rep2

value: WT


title: Caco-2.batch1.IMZ.rep3.B05

description: Library name: Caco2_Batch1_IMZ_3_B05


title: WT_Tm_H3K27ac_HiChIP_SET2_rep1

description: Library name: WT_Tm_H3K27ac_HiChIP_SET2_rep1