title: THP-1 sgSUV39H1/2 DKO Cells, Replicate 2

description: Library name: THP-1-DKO-Rep2


title: Ctrl_NON_S_3

status: Public on Jun 17 2026

type: SRA

city: Guangzhou

first: Jinwen

last: Kang

state: Guangdong

address: 483 Wushan Road, Tianhe District

country: China

institute: South China Agricultural University

description: Library name: A3

library_source: transcriptomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Uterus

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 ug oftotal RNA was used forthe construction ofsequencing libraries.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.

tag: tissue

value: Uterus

tag: cell line

value: Primary cell

tag: cell type

value: Stromal Cells

tag: genotype

value: WT


title: THP-1 sgSUV39H1/2 DKO Cells, Replicate 1

city: Chicago

first: Feng

last: Yue

address: 420 E. Superior St.

country: USA

institute: Northwestern University

description: Library name: THP-1-DKO-Rep1

data_processing:
RNA-Seq raw pair-end FASTQ files underwent quality control using fastp (version 0.23.4) with default settings to remove low-quality reads and trim adapters.
Cleaned RNA-Seq data were aligned to the reference genome hg38 using STAR (version 2.7.11b) with default parameters. Gene expression quantification was determined with featureCounts from the subread package (version 2.0.6), considering only the properly mapped pair-end read counts
Assembly: hg38
Supplementary files format and content: tab-delimited file including raw reads

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: U937 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS). THP-1 cells were maintained in RPMI-1640 supplemented with 10% FBS and 50nM BME. All cell cultures were supplemented with 1X Antibiotic-Antimycotic and were grown in 37°C with 5% CO2.

extract_protocol:
One million cells were stabilized in RNAprotect (Qiagen, 76526) and were stored in -80C prior to extraction. Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen, 75134) and the RNA integrity was evaluated using RNA ScreenTape Analysis (Agilent, 5067-5576).
Library preparation was then performed using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina, in conjunction with NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs #E7490) following manufacturer’s protocol.

value: AML


title: MDA-2

city: IOWA CITY

first: Shanshan

last: Liu

state: IA

address: 431 Newton Road

institute: The University of Iowa

description:
Library name: Sample2
MDA.2

data_processing:
1. Evaluate sequence quality, trim reads and map reads to genome 2. Generate hit counts for genes/exons 3. Compare gene/exon hit counts and analyze gene ontology
Assembly: hg38
Supplementary files format and content: tab delimited text file includes raw counts for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug pf total RNA was used for the construction of sequencing libraries.
1. Ribosomal RNA depletion; 2. RNA Fragmentation and random priming; 3. First and second strand cDNA synthesis; 4. End repair, 5’Phosphorylation, and dA-Tailing; 5. Adaptor ligation, PCR enrichment, and sequencing

tag: group

value: FABP4 non-binding

value: breast cancer cells

tag: treatment

value: cell sorting


title: Ctrl_NON_S_2

description: Library name: A2


title: THP-1 sgSUV39H1 SKO Cells, Replicate 3

description: Library name: THP-1-SKO-Rep3


title: Ctrl_NON_S_1

description: Library name: A1


title: THP-1 sgSUV39H1 SKO Cells, Replicate 2

description: Library name: THP-1-SKO-Rep2


title: C4-2B, QDT_rep3

city: Shanghai

first: Fuwen

last: Yuan

state: 上海

address: Cailun Road #1200, Pudong New area

institute: Shanghai University of Traditional Chinese Medicine

description: Library name: Sample 6

data_processing:
Majorbio Cloud Platform, https://cloud.majorbio
Sequence reads were trimmed for adaptor sequence/low quality sequece (Quality lomit : 0.5)
Trimmed sequence reads were mapped to GRCh38.p13 (parameters-mismatch cost: 2 insertion cost: 3 deletion cost 3 legtn faction: 0.8 semilarity fractions: 0.8)
Read count extraction and normalization were performed using Majorbio Cloud Platform
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes TPM for each sample

growth_protocol: C4-2B cells were mantined in RMPI-1640 supplemented with 10% fetal bovine serum (FBS) in humidified atmshpore with 5% CO2 at 37℃.

extract_protocol:
The total RNA was isolated using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme RC112-01; China). The RNA quality was assessed using a Bioanalyzer 2100 (Agilent, USA), 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit fellowing manufaturer's protocols.

treatment_protocol: Cells were treated with 10 uM QDT or vehicle and cluture for 24 h followed with RNA extraction and sequencing.

value: prostate cancer

value: QDT


title: Input control hypothalamus, MOR-SAL, female

city: la jolla

first: Yanmiao

last: Du

state: CA

address: 4254 Urey Hall, 9500 Gilman Drive

department: Department of Chemistry and Biochemistry/Cellular and Molecular Medicine

institute: UCSD

description:
Library name: Input_Hypothalamus_MOR-SAL_F
Input control (pooled)

library_source: genomic

data_processing:
Adapters and low-quality bases were trimmed using Trim Galore (v0.6.7, --paired --fastqc).
Reads were aligned to Mus musculus mm10 using Bowtie2 (v2.4.5). PCR duplicates were removed with SAMtools (v1.15.1) markdup. Reads overlapping ENCODE mm10 blacklist (v2) were excluded with BEDTools subtract (v2.30.0). Coverage profiles were generated with bedtools genomecov and converted to BigWig with bedGraphToBigWig.
Peak calling: MACS2 (v2.2.7.1; -q 0.05 -g mm) against matched pooled Input controls.
Differential H3K27ac analysis: consensus peak set constructed in DiffBind (v3.10.1) with condition-aware merging. Read counts quantified with DiffBind (dba.count, summarizeOverlaps); peaks retained if >= 15 reads in >= 80% of samples within any condition. Differential peaks identified via DESeq2 (dba.analyze); FDR < 0.05. Peaks annotated with ChIPpeakAnno (v3.32.1) and EnsDb.Mmusculus.v79.
Transcription factor regulatory influence assessed with Taiji (v1.2.0) integrating H3K27ac enhancers and RNA-seq expression. TF activity quantified as personalized PageRank scores (z-score normalized, capped at +/-2).
Assembly: mm10
Supplementary files format and content: narrowPeak files (MACS2 peak calls); bigWig coverage tracks (bedtools genomecov + bedGraphToBigWig)

molecule: genomic DNA

source_name: hypothalamus

growth_protocol: Male and female C57BL/6NTac mice (Taconic, Hudson, NY) were bred at the University of Pennsylvania and group-housed (3-5/cage) under a 12-h light/dark cycle (lights on at 0700) with ad libitum access to food and water. All procedures were approved by the University of Pennsylvania Animal Care and Use Committee.

extract_protocol:
Brain tissues (PFC, hippocampus, hypothalamus, striatum) were collected by bilateral punch (2.0 mm) and flash-frozen at -80C. Nuclei were isolated in cold extraction buffer using a Dounce tissue grinder, filtered (40 um), and enriched by iodixanol gradient centrifugation. NeuN+ neuronal nuclei were labeled with anti-NeuN Alexa Fluor 488 (MAB377X, EMD Millipore) at 4C for 1 h, then sorted by FACS (BD Biosciences). ~10,000 NeuN+ nuclei per replicate were lysed and digested with MNase (88216, Thermo Fisher) in the presence of CaCl2; reaction quenched with EDTA. Chromatin IP was performed using 0.125 ug anti-H3K27ac antibody (39135, Active Motif) coupled to 5 uL protein A Dynabeads (10001D, Thermo Fisher), following the MOWChIP-seq protocol.
ChIP-seq libraries were constructed from purified ChIP DNA (~10,000 NeuN+ nuclei) and input DNA (~2,000 nuclei). PFC libraries used xGen 2S DNA Library Prep Kit (10009877, IDT); hippocampus, hypothalamus, and striatum libraries used ThruPLEX DNA-Seq kit (R400674, Takara Bio). Fragment size verified on TapeStation (Agilent) with High Sensitivity DNA Analysis Kit; primer-dimers removed with SPRIselect beads. Libraries quantified with KAPA Library Quantification Kit (4824, Roche), pooled, and sequenced on an Illumina NovaSeq X Plus platform (paired-end 150 nt, ~15 million reads per library).

treatment_protocol: Perinatal morphine exposure: 8-12-week-old female mice were implanted with osmotic minipumps (Alzet model 1004) delivering morphine sulfate (10 mg/kg/day, NIDA Drug Supply) or saline, then co-housed with drug-naive males. Pups were transferred to drug-naive surrogates within 4-8 hours of birth. Postnatal morphine (10 mg/kg SC, 10 mL/kg) or saline was administered twice daily (09:00 and 17:00) from PND1 through the morning of PND14, after which mice underwent spontaneous opioid withdrawal. In adulthood, mice were assigned to four groups: SAL-SAL (saline/saline), SAL-LPS (saline/LPS challenge), MOR-SAL (morphine/saline), or MOR-LPS (morphine/LPS challenge). Brain tissues were collected 2 hours after adult LPS or saline injection.

value: hypothalamus

value: wild type

value: MOR-SAL


title: THP-1 sgSUV39H1 SKO Cells, Replicate 1

description: Library name: THP-1-SKO-Rep1


title: C4-2B, QDT_rep2

description: Library name: Sample 5


title: yeast cells expressing nonsense control in YjiE,YdaG,SecB experiment, low adenine media, bio-rep2

city: Irvine

first: Alireza

last: Tanoori

address: 419 South Circle View Dr.

institute: University of California, Irvine

description:
Library name: Nonsense-control-YjiE,YdaG,SecB-selective-2
8BDQYS-raw-counts.txt

data_processing:
Quality of the fastq files was assessed using FastQC v0.12.1. Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp. Quality-filtered reads were aligned to the reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, followed by coordinate sorting using samtools v1.22.1. PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0. Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3, with results aggregated into a comprehensive quality control report using MultiQC v1.32. Gene-level expression quantification was performed using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers,  and grouped by gene_id. Final gene counts were annotated with gene biotype and  other metadata extracted from the reference GTF file.  Sample-sample correlations for sample-sample heatmap and PCA were calculated on normalized counts (TMM, trimmed mean of M-values) using Pearson correlation. Differential expression was done with edgeR v4.0.16 using standard practice including filtering for low-expressed genes with edgeR::filterByExprwith default values.
Assembly: R64
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Yeast strains encoding the evolved gene or a nonsense gene were passaged twice in nonselective(adenine-rich) media.

extract_protocol:
Total RNA was extracted using the RNeasy Kit (Qiagen). Cells were harvested at mid-log phase (OD600 = 0.5 - 1) from 700 ul of culture.
RNA libraries were prepared by Plasmidsaurus using their standard 3' counting workflow. 3 ug of total RNA was used for construction of the libraries

treatment_protocol: Cultures were then grown overnight in either nonselective (80 mg/L adenine) or selective (2.5 mg/L adenine) media, testing two to three biological replicates per condition.

value: yeast cells

value: Nonsense control

value: 2.5 mg/L Adenine media


title: H3K27ac ChIP-seq hypothalamus, MOR-SAL, female, replicate 12-1

description:
Library name: ChIP_Hypothalamus_MOR-SAL_F_12-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: THP-1 sgControl Cells, Replicate 3

description: Library name: THP-1-sgControl-Rep3


title: C4-2B, QDT_rep1

description: Library name: Sample 4


title: yeast cells expressing nonsense control in YjiE,YdaG,SecB experiment, low adenine media, bio-rep1

description:
Library name: Nonsense-control-YjiE,YdaG,SecB-selective-1
8BDQYS-raw-counts.txt


title: H3K27ac ChIP-seq hypothalamus, MOR-LPS, male, replicate 6-0

description:
Library name: ChIP_Hypothalamus_MOR-LPS_M_6-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: MOR-LPS


title: THP-1 sgControl Cells, Replicate 2

description: Library name: THP-1-sgControl-Rep2


title: C4-2B, vehicle_rep3

description: Library name: Sample 3

value: vehicle


title: yeast cells expressing SecB Variant1, low adenine media, bio-rep3

description:
Library name: SecB-selective-3
8BDQYS-raw-counts.txt


title: H3K27ac ChIP-seq hypothalamus, MOR-SAL, female, replicate 18-0

description:
Library name: ChIP_Hypothalamus_MOR-SAL_F_18-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: H3K27ac ChIP-seq hypothalamus, MOR-LPS, male, replicate 14-4

description:
Library name: ChIP_Hypothalamus_MOR-LPS_M_14-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: MDA-3

description:
Library name: Sample3
MDA.3


title: THP-1 sgControl Cells, Replicate 1

description: Library name: THP-1-sgControl-Rep1


title: C4-2B, vehicle_rep2

description: Library name: Sample 2


title: H3K27ac ChIP-seq hypothalamus, MOR-SAL, female, replicate 16-3

description:
Library name: ChIP_Hypothalamus_MOR-SAL_F_16-3
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: yeast cells expressing SecB Variant1, low adenine media, bio-rep2

description:
Library name: SecB-selective-2
8BDQYS-raw-counts.txt


title: MDA-1

description:
Library name: Sample1
MDA.1


title: U937 sgSUV39H1/2 DKO Cells, Replicate 3

description: Library name: U937-DKO-Rep3


title: C4-2B, vehicle_rep1

description: Library name: Sample 1


title: H3K27ac ChIP-seq hypothalamus, MOR-LPS, male, replicate 14-0

description:
Library name: ChIP_Hypothalamus_MOR-LPS_M_14-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: yeast cells expressing SecB Variant1, low adenine media, bio-rep1

description:
Library name: SecB-selective-1
8BDQYS-raw-counts.txt


title: H3K27ac ChIP-seq hypothalamus, MOR-SAL, female, replicate 15-4

description:
Library name: ChIP_Hypothalamus_MOR-SAL_F_15-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: yeast cells expressing nonsense control in YjiE,YdaG,SecB experiment, low adenine media, bio-rep3

description:
Library name: Nonsense-control-YjiE,YdaG,SecB-selective-3
8BDQYS-raw-counts.txt


title: Input control hypothalamus, MOR-LPS, male

description:
Library name: Input_Hypothalamus_MOR-LPS_M
Input control (pooled)


title: U937 sgSUV39H1/2 DKO Cells, Replicate 2

description: Library name: U937-DKO-Rep2


title: GTC_CAR-T

city: West Haven

first: Sidi

last: Chen

state: CT

address: 850 West Campus Drive

institute: Yale University

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were pre-processed and aligned to a human transcriptome reference (GRCh38 Gencode V37) using CellRanger v4.3.0 (default settings).
Spliced and unspliced single-cell RNAseq data were aligned to a human genome reference (STAR-solo GRCh38) using STAR v2.7.4a (parameters: --clipAdapterType CellRanger4 --outFilterScoreMin 30 --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIfiltering MultiGeneUMI_CR --soloUMIdedup 1MM_CR --soloType CB_UMI_Simple --soloFeatures Gene Velocyto ).
Assembly: GRCh38 Gencode V37
Supplementary files format and content: Processed data is in the standard CellRanger output format, which includes barcodes.tsv (cell barcodes), features.tsv (genes), and matrix.mtx (feature count matrix). We also included  additional matrix files, where the counts were separated by spliced or unspliced transcripts.

source_name: CAR-T cell

extract_protocol:
Live human CD45+ tumor-infiltrating CAR-T cells expressing mScarlet were sorted from processed and stained tumor samples. Cells were sorted from each tumor in similar cell numbers within treatment group, and cells from same group were combined. After sorting, cells were washed with PBS, and cell number and viability were quantified by Trypan blue (Lonza) staining.
For scRNA-seq, 5 - 10 × 10^3 mScarlet+ CAR-T cells were used to prepare the library with Chromium Next GEM Sign Cell 5’ Regent kits V2 (10x Genomics), according to the manufacturer’s instructions. The scRNA-seq libraries were sequenced on the NovaSeq 6000 system (Illumina) using a paired-end 150 bp read length.

value: CAR-T cell

value: in vivo tumor model


title: yeast cells expressing YdaG Variant1, low adenine media, bio-rep3

description:
Library name: YdaG-selective-3
8BDQYS-raw-counts.txt


title: H3K27ac ChIP-seq hypothalamus, MOR-LPS, male, replicate 13-2

description:
Library name: ChIP_Hypothalamus_MOR-LPS_M_13-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: U937 sgSUV39H1/2 DKO Cells, Replicate 1

description: Library name: U937-DKO-Rep1


title: SOCS3-SKO_CAR-T


title: yeast cells expressing YdaG Variant1, low adenine media, bio-rep2

description:
Library name: YdaG-selective-2
8BDQYS-raw-counts.txt


title: H3K27ac ChIP-seq hypothalamus, MOR-LPS, female, replicate 7-1

description:
Library name: ChIP_Hypothalamus_MOR-LPS_F_7-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: U937 sgSUV39H1 SKO Cells, Replicate 3

description: Library name: U937-SKO-Rep3


title: yeast cells expressing YdaG Variant1, low adenine media, bio-rep1

description:
Library name: YdaG-selective-1
8BDQYS-raw-counts.txt


title: NR4A1-SKO_CAR-T


title: H3K27ac ChIP-seq hypothalamus, MOR-LPS, female, replicate 18-1

description:
Library name: ChIP_Hypothalamus_MOR-LPS_F_18-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: U937 sgSUV39H1 SKO Cells, Replicate 2

description: Library name: U937-SKO-Rep2


title: yeast cells expressing YjiE Variant1, low adenine media, bio-rep3

description:
Library name: YjiE-selective-3
8BDQYS-raw-counts.txt


title: DKO_CAR-T


title: H3K27ac ChIP-seq hypothalamus, MOR-LPS, female, replicate 16-4

description:
Library name: ChIP_Hypothalamus_MOR-LPS_F_16-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: U937 sgSUV39H1 SKO Cells, Replicate 1

description: Library name: U937-SKO-Rep1


title: G_72_3

data_processing:
For data processing, raw demultiplexed Fastq sequencing files had adapters trimmed using cutadapt v3.4 (parameters: --pair-filter=any -m20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT). Trimmed reads were aligned to a human reference genome (GRCh38 Gencode v44) using kallisto v0.48.0 with 100 bootstraps (seed = 42).
Assembly: GRCh38 Gencode v44
Supplementary files format and content: Processed data is a tab-delimited file of the estimated transcript counts

extract_protocol:
On day 7, different CAR-T groups were cocultured with U87-GL-EGFRvIII cells at E:T = 1:4 ( defined as 0-hour stimulation), and repeated challenged after 36 hours with same E:T ratio. mScarlet+ CAR-T cells were sorted at the time point of 0-hour, 6-hour, 24-hour, and 72-hour stimulation. >90% sorting purity was verified, and at least 0.5 million cells were sorted and collected for each RNA sequencing sample. mRNAs were extracted using RNeasy Mini Kit (QIAGEN).
RNA sequencing library was prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB), following manufacturers’ instructions. The RNA sequencing library was sequenced using the NovaSeq 6000 system (Illumina) with paired-end 150 bp reads.

value: 72hr Cancer co-culture


title: yeast cells expressing YjiE Variant1, low adenine media, bio-rep2

description:
Library name: YjiE-selective-2
8BDQYS-raw-counts.txt


title: H3K27ac ChIP-seq hypothalamus, MOR-LPS, female, replicate 16-0

description:
Library name: ChIP_Hypothalamus_MOR-LPS_F_16-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: U937 sgControl Cells, Replicate 3

description: Library name: U937-sgControl-Rep3

value: AML


title: G_72_2


title: yeast cells expressing YjiE Variant1, low adenine media, bio-rep1

description:
Library name: YjiE-selective-1
8BDQYS-raw-counts.txt


title: U937 sgControl Cells, Replicate 2

description: Library name: U937-sgControl-Rep2


title: H3K27ac ChIP-seq hypothalamus, MOR-LPS, female, replicate 15-3

description:
Library name: ChIP_Hypothalamus_MOR-LPS_F_15-3
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: G_72_1


title: yeast cells expressing nonsense control in YjiE,YdaG,SecB experiment, high adenine media, bio-rep3

description:
Library name: Nonsense-control-YjiE,YdaG,SecB-nonselective-3
8BDQYS-raw-counts.txt

value: 80 mg/L Adenine media


title: Input control hypothalamus, MOR-LPS, female

description:
Library name: Input_Hypothalamus_MOR-LPS_F
Input control (pooled)


title: U937 sgControl Cells, Replicate 1

description: Library name: U937-sgControl-Rep1


title: G_24_3

value: 24hr Cancer co-culture


title: yeast cells expressing nonsense control in YjiE,YdaG,SecB experiment, high adenine media, bio-rep2

description:
Library name: Nonsense-control-YjiE,YdaG,SecB-nonselective-2
8BDQYS-raw-counts.txt


title: H3K27ac ChIP-seq hypothalamus, MOR-LPS, female, replicate 15-1

description:
Library name: ChIP_Hypothalamus_MOR-LPS_F_15-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: U937 DKO HiC

description: Library name: U937-DKO-HiC

data_processing:
HiC raw pair-end FASTQ files were trimmed using trimGalore (v.0.6.10) to remove adaptor sequences and quality control was subsequently performed using FastQC (v.0.12.1).
Trimmed Hi-C data was processed using our in-house runHiC pipeline (v.0.8.7), detailed at (https://xiaotaowang.github.io/HiC_pipeline/quickstart.html). In short, hg38 genome alignment was performed using BWA-MEM (v.0.7.17). Aligned read pairs underwent filtering, deduplication and assembly. Identical restriction fragment mappings were removed. Read pairs were binned at multiple resolutions (5kb to 50Mb) with simultaneous ICE normalization. The process yielded ICE-normalized matrices in .mcool format for subsequent analysis. Hi-C contact maps were converted from aligned read pairs using Juicer Tools (v1.22.01) and were used for visualization with KR normalization.
Assembly: hg38
Supplementary files format and content: mcool

extract_protocol:
In-situ Hi-C was performed using the Arima-HiC+ Kit (Arima, A51008-ARI) following manufacturer protocol. In brief, one million cells were crosslinked with 2% formaldehyde as described above. Cell lysis, nuclear permeabilization, chromatin digestion and biotin ligation were all performed according to manufacturer protocol. DNA shearing was performed using Vibra-Cell (Sonics & Maerials, VCX750) in 32% Amplitude for in total 1 minute to produce ~400-600bp of fragments.
Biotin enrichment was then performed using streptavidin-coated enrichment beads supplied in the Arima Hi-C kit according to the manufacturer’s protocol. On-bead library preparation was performed using KAPA HyperPrep (Roche, 7962363001) following the adjusted protocol supplied by Arima.


title: yeast cells expressing nonsense control in YjiE,YdaG,SecB experiment, high adenine media, bio-rep1

description:
Library name: Nonsense-control-YjiE,YdaG,SecB-nonselective-1
8BDQYS-raw-counts.txt


title: G_24_2


title: U937 SKO HiC

description: Library name: U937-SKO-HiC


title: H3K27ac ChIP-seq hippocampus, SAL-SAL, male, replicate 5-1

description:
Library name: ChIP_Hippo_SAL-SAL_M_5-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

source_name: hippocampus

value: hippocampus

value: SAL-SAL


title: G_24_1


title: H3K27ac ChIP-seq hippocampus, SAL-SAL, male, replicate 3-4

description:
Library name: ChIP_Hippo_SAL-SAL_M_3-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: U937 WT HiC

description: Library name: U937-WT-HiC


title: G_6_3

value: 06hr Cancer co-culture


title: yeast cells expressing SecB Variant1, high adenine media, bio-rep2

description:
Library name: SecB-nonselective-2
8BDQYS-raw-counts.txt


title: H3K27ac ChIP-seq hippocampus, SAL-SAL, male, replicate 3-0

description:
Library name: ChIP_Hippo_SAL-SAL_M_3-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: U937 WT Cells Input

description: Library name: U937-WT-input

data_processing:
ChIP-Seq raw pair-end FASTQ files were trimmed using trimGalore (v.0.6.10) to remove adaptor sequences and quality control was subsequently performed using FastQC (v.0.12.1).
Trimmed ChIP-Seq data was processed using the ENCODE ChIP-Seq pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2). In short, trimmed reads were aligned to hg38, duplicates and unmapped reads were then removed. Peak calling was performed, and IDR filtering was performed to obtain highly reproducible peaks. For downstream analysis and visualization, read counts were normalized to counts per million (CPM) with bamCoverage function in deeptools (v.3.5.6).
Spike-in ChIP-Seq data were also processed using the ENCODE ChIP-Seq pipeline with slight adjustments for performing spike-in normalization.  Peak calling was performed using epic2 (v.0.052), with parameters --bin-size 800 -g 4. To perform spike-in normalization, trimmed reads were also aligned to dm6 genome and were processed as the same way as human reads. Number of reads aligned to dm6 for each library was then used to generate scale factors as described in ChIP-Rx. Normalized bigwig files were then generated with bamCoverage function in deeptools with the calculated scale factors.
Assembly: hg38
Supplementary files format and content: Bed (Peaks called, except for Input sample)

extract_protocol:
Cells were cross-linked in 2% formaldehyde for 20 mins and quenched in glycine for 10 mins. Cells were subsequently lysed and sonicated using Vibra-Cell (Sonics & Materials, VCX750) in 37% Amplitude for in total 3.5 minutes. Sheared chromatin was then quantified and evaluated.
[spike-in protocol] Drosophila S2 cells were processed by the same method. For the immunoprecipitation step in ChIP-Rx, the weight of human, drosophila chromatin and antibody were maintained the same across conditions: H3K9me3 ChIP-Rx, 5ug human, 0.25ug S2, 5ug antibody; H3K27me3 ChIP-Rx, 10ug human, 0.3ug S2, 2ug antibody
ChIP libraries were then prepared using Nextera XT DNA Library Preparation Kit (Illumina, GA09115), and size selection was performed to select fragment sizes at 300-500bp.

tag: chip antibody


title: yeast cells expressing SecB Variant1, high adenine media, bio-rep1

description:
Library name: SecB-nonselective-1
8BDQYS-raw-counts.txt


title: G_6_2


title: H3K27ac ChIP-seq hippocampus, SAL-SAL, male, replicate 11-1

description:
Library name: ChIP_Hippo_SAL-SAL_M_11-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: G_6_1


title: U937 WT Cells SETDB1 ChIP, Replicate 2

description: Library name: U937-WT-SETDB1-Rep2

value: SETDB1 (Proteintech, #11231-1-AP)


title: yeast cells expressing YdaG Variant1, high adenine media, bio-rep3

description:
Library name: YdaG-nonselective-3
8BDQYS-raw-counts.txt


title: U937 sgSUV39H1/2 DKO Cells, ATAC Replicate 2

description: Library name: U937-DKO-ATAC-Rep2

data_processing:
ATAC-Seq raw pair-end FASTQ files were trimmed using trimGalore (v.0.6.10) to remove adaptor sequences and quality control was subsequently performed using FastQC (v.0.12.1).
Trimmed ATAC-Seq reads were processed using the ENCODE ATAC-Seq pipeline. Trimmed reads were aligned to the hg38 reference genome, followed by removal of duplicates and unmapped. Peak calling was performed, and IDR filtering was performed across the duplicates to identify highly reproducible peaks.
Assembly: hg38
Supplementary files format and content: IDR peaks

extract_protocol:
ATAC-Seq was performed as described previously with slight adjustments. Quarter of a million cells were used and lysed on ice for total of 20 minutes under 0.1% Tween-20, 0.1% NP-40 and 0.01% Digitonin. The intact nuclei were then collected for tagmentation using 5uL of Tagment DNA TDE1 Enzyme (Illumina).
Total DNA were extracted and library preparation was then performed using Nextera XT DNA Library Preparation Kit (Illumina). All ATAC-Seq experiments were performed in duplicates.


title: H3K27ac ChIP-seq hippocampus, SAL-SAL, male, replicate 1-3

description:
Library name: ChIP_Hippo_SAL-SAL_M_1-3
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: wild type


title: U937 WT Cells SETDB1 ChIP, Replicate 1

description: Library name: U937-WT-SETDB1-Rep1


title: G_0_3

value: No cancer co-culture


title: U937 DKO Cells Input

description: Library name: U937-DKO-input


title: Input control hippocampus, SAL-SAL, male

description:
Library name: Input_Hippo_SAL-SAL_M
Input control (pooled)


title: yeast cells expressing YdaG Variant1, high adenine media, bio-rep2

description:
Library name: YdaG-nonselective-2
8BDQYS-raw-counts.txt

value: yeast cells


title: H3K27ac ChIP-seq hypothalamus, MOR-SAL, male, replicate 6-1

description:
Library name: ChIP_Hypothalamus_MOR-SAL_M_6-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: hypothalamus

value: MOR-SAL


title: yeast cells expressing YdaG Variant1, high adenine media, bio-rep1

description:
Library name: YdaG-nonselective-1
8BDQYS-raw-counts.txt


title: G_0_2


title: H3K27ac ChIP-seq hippocampus, SAL-SAL, male, replicate 1-1

description:
Library name: ChIP_Hippo_SAL-SAL_M_1-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: U937 sgSUV39H1 SKO Cells, ATAC Replicate 1

description: Library name: U937-SKO-ATAC-Rep1


title: G_0_1


title: U937 SKO Cells Input

description: Library name: U937-SKO-input


title: yeast cells expressing YjiE Variant1, high adenine media, bio-rep3

description:
Library name: YjiE-nonselective-3
8BDQYS-raw-counts.txt


title: U937 sgControl Cells Input

description: Library name: U937-sgControl-input


title: S_72_3


title: H3K27ac ChIP-seq hippocampus, SAL-SAL, female, replicate 9-2

description:
Library name: ChIP_Hippo_SAL-SAL_F_9-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: yeast cells expressing YjiE Variant1, high adenine media, bio-rep2

description:
Library name: YjiE-nonselective-2
8BDQYS-raw-counts.txt


title: H3K27ac ChIP-seq hippocampus, SAL-SAL, female, replicate 9-0

description:
Library name: ChIP_Hippo_SAL-SAL_F_9-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: S_72_2


title: U937 DKO Cells H3K27me3 ChIP, Replicate 2

description: Library name: U937-DKO-H3K27me3-Rep2

value: H3K27me3 (Cell Signaling Technology, #13969)


title: yeast cells expressing YjiE Variant1, high adenine media, bio-rep1

description:
Library name: YjiE-nonselective-1
8BDQYS-raw-counts.txt


title: S_72_1


title: U937 DKO Cells H3K27me3 ChIP, Replicate 1

description: Library name: U937-DKO-H3K27me3-Rep1


title: H3K27ac ChIP-seq hippocampus, SAL-SAL, female, replicate 4-3

description:
Library name: ChIP_Hippo_SAL-SAL_F_4-3
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: yeast cells expressing nonsense control in YdfC experiment, low adenine media, bio-rep3

description:
Library name: Nonsense-control-YdfC-selective-3
JZJMR8-raw-counts.txt

value: Nonsense control

value: 2.5 mg/L Adenine media


title: S_24_3

value: CAR-T cell


title: U937 SKO Cells H3K27me3 ChIP, Replicate 2

description: Library name: U937-SKO-H3K27me3-Rep2


title: H3K27ac ChIP-seq hippocampus, SAL-SAL, female, replicate 4-1

description:
Library name: ChIP_Hippo_SAL-SAL_F_4-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: yeast cells expressing nonsense control in YdfC experiment, low adenine media, bio-rep2

description:
Library name: Nonsense-control-YdfC-selective-2
JZJMR8-raw-counts.txt


title: Input control hippocampus, SAL-SAL, female

description:
Library name: Input_Hippo_SAL-SAL_F
Input control (pooled)


title: S_24_2


title: U937 SKO Cells H3K27me3 ChIP, Replicate 1

description: Library name: U937-SKO-H3K27me3-Rep1


title: yeast cells expressing SecB Variant1, high adenine media, bio-rep3

description:
Library name: SecB-nonselective-3
8BDQYS-raw-counts.txt


title: yeast cells expressing nonsense control in YdfC experiment, low adenine media, bio-rep1

description:
Library name: Nonsense-control-YdfC-selective-1
JZJMR8-raw-counts.txt


title: U937 sgControl Cells H3K27me3 ChIP, Replicate 2

description: Library name: U937-sgControl-H3K27me3-Rep2


title: S_24_1


title: H3K27ac ChIP-seq hippocampus, SAL-SAL, female, replicate 10-3

description:
Library name: ChIP_Hippo_SAL-SAL_F_10-3
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: yeast cells expressing YdfC-GFP Variant1, low adenine media, bio-rep3

description:
Library name: YdfC-selective-3
JZJMR8-raw-counts.txt


title: U937 sgControl Cells H3K27me3 ChIP, Replicate 1

description: Library name: U937-sgControl-H3K27me3-Rep1


title: H3K27ac ChIP-seq hippocampus, SAL-LPS, male, replicate 5-2

description:
Library name: ChIP_Hippo_SAL-LPS_M_5-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: SAL-LPS


title: S_6_3


title: yeast cells expressing YdfC-GFP Variant1, low adenine media, bio-rep2

description:
Library name: YdfC-selective-2
JZJMR8-raw-counts.txt


title: H3K27ac ChIP-seq hippocampus, SAL-LPS, male, replicate 5-0

description:
Library name: ChIP_Hippo_SAL-LPS_M_5-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: U937 DKO Cells H3K9me3 ChIP, Replicate 2

description: Library name: U937-DKO-H3K9me3-Rep2

value: AML

value: H3K9me3 (Abcam, #ab8898)


title: yeast cells expressing YdfC-GFP Variant1, low adenine media, bio-rep1

description:
Library name: YdfC-selective-1
JZJMR8-raw-counts.txt


title: S_6_2


title: H3K27ac ChIP-seq hippocampus, SAL-LPS, male, replicate 3-3

description:
Library name: ChIP_Hippo_SAL-LPS_M_3-3
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: U937 DKO Cells H3K9me3 ChIP, Replicate 1

description: Library name: U937-DKO-H3K9me3-Rep1


title: S_6_1


title: yeast cells expressing nonsense control in YdfC experiment, high adenine media, bio-rep3

description:
Library name: Nonsense-control-YdfC-nonselective-3
JZJMR8-raw-counts.txt

value: 80 mg/L Adenine media


title: H3K27ac ChIP-seq hippocampus, SAL-LPS, male, replicate 11-0

description:
Library name: ChIP_Hippo_SAL-LPS_M_11-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: hippocampus


title: S_0_3


title: H3K27ac ChIP-seq hippocampus, SAL-LPS, male, replicate 1-2

description:
Library name: ChIP_Hippo_SAL-LPS_M_1-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: U937 SKO Cells H3K9me3 ChIP, Replicate 2

description: Library name: U937-SKO-H3K9me3-Rep2


title: yeast cells expressing nonsense control in YdfC experiment, high adenine media, bio-rep2

description:
Library name: Nonsense-control-YdfC-nonselective-2
JZJMR8-raw-counts.txt


title: U937 SKO Cells H3K9me3 ChIP, Replicate 1

description: Library name: U937-SKO-H3K9me3-Rep1


title: S_0_2


title: yeast cells expressing nonsense control in YdfC experiment, high adenine media, bio-rep1

description:
Library name: Nonsense-control-YdfC-nonselective-1
JZJMR8-raw-counts.txt


title: Input control hippocampus, SAL-LPS, male

description:
Library name: Input_Hippo_SAL-LPS_M
Input control (pooled)


title: U937 sgControl Cells H3K9me3 ChIP, Replicate 2

description: Library name: U937-sgControl-H3K9me3-Rep2


title: Donor3, WT Group, 48 Hour Timepoint

city: Bethesda

first: Skyler

middle: Alexander

last: Kuhn

state: Maryland

address: 9000 Rockville Pike, BG 29B RM 1NN20

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

description:
Library name: Donor3_WT_T48_S23
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor3_WT_T48_S23

data_processing:
Sequencing adapters and low-quality bases were trimmed using Cutadapt v1.18.
Trimmed reads were aligned to the GENCODE (9) GRCh38.p13 primary human reference genome with STAR v2.7.6a in two-pass basic mode.
PCR duplicates were marked using Picard’s MarkDuplicate utility.
Gene expression levels were quantified with RSEM v1.3.3 using v41 of GENCODE's comprehensive annotation.
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited text file containing raw counts for each sample.

source_name: blood

growth_protocol: Human monocyte-derived dendritic cells (MDDCs) were generated from cryopreserved human monocytes obtained from 5 donors. After thawing, monocytes were washed with PBS and cultured at 1 x 10^6 cells/mL in DC medium consisting of RPMI + Glutamax, 5% FBS, 15 mM HEPES, 0.1 mM nonessential amino acids, 1 mM sodium pyruvate, 100 U/mL penicillin, and 100 ug/mL streptomycin, supplemented with IL-4 (20 ng/mL) and GM-CSF (20 ng/mL). Cells were cultured for 5 days with replacement of half of the medium and addition of fresh cytokines every other day. Nonadherent dendritic cells were harvested by centrifugation and resuspended in DC medium. Resulting cells were >95% CD11c+/CD209+ by flow cytometry. For RNA-seq experiments, MDDCs were plated at 1 x 10^6 cells/well in 12-well plates.

extract_protocol:
Cells were harvested by centrifugation and lysed in 1 mL TRIzol reagent per sample, then stored at -80 C until extraction. For RNA isolation, samples were mixed with 200 uL 1-bromo-3-chloropropane and centrifuged at 4 C for 15 minutes at 16,000 x g. The aqueous phase was collected and passed through a QIAshredder column at 21,000 x g for 2 minutes. RNA was purified using the Qiagen AllPrep DNA/RNA system with an additional on-column DNase I treatment. RNA quality was assessed using the Agilent 2100 Bioanalyzer RNA 6000 Pico kit and quantified using the Quant-iT RiboGreen RNA assay.
Sequencing libraries were prepared from 200 ng total RNA using the Illumina Stranded mRNA Prep, Ligation kit according to the manufacturer’s protocol. Libraries were quality checked by Agilent Bioanalyzer, quantified by KAPA SYBR FAST qPCR, pooled, and sequenced as paired-end reads on Illumina platforms, with final sequencing performed on a NovaSeq 6000 (2 x 100 bp).

treatment_protocol: Human MDDCs were mock-infected or infected with Powassan virus (POWV) at an MOI of 0.1 in a small volume for 1 hour at 37 C and 5% CO2 with occasional gentle rocking. In experiments involving inhibitor treatment, MDDCs were pretreated with ruxolitinib (10 ug/mL) for 1 hour prior to infection and maintained in the culture for the duration of the experiment.

value: blood

value: monocyte-derived dendritic cells

value: WT

tag: time

value: Hour 48


title: yeast cells expressing YdfC-GFP Variant1, high adenine media, bio-rep3

description:
Library name: YdfC-nonselective-3
JZJMR8-raw-counts.txt


title: S_0_1

value: No cancer co-culture


title: U937 sgControl Cells H3K9me3 ChIP, Replicate 1

description: Library name: U937-sgControl-H3K9me3-Rep1


title: H3K27ac ChIP-seq hippocampus, SAL-LPS, male, replicate 1-0

description:
Library name: ChIP_Hippo_SAL-LPS_M_1-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: wild type


title: N_72_3

value: 72hr Cancer co-culture


title: Donor2, WT Group, 48 Hour Timepoint

description:
Library name: Donor2_WT_T48_S22
Column name in raw counts file, "RSEM_genes_expected_counts.tsv": Donor2_WT_T48_S22


title: yeast cells expressing YdfC-GFP Variant1, high adenine media, bio-rep2

description:
Library name: YdfC-nonselective-2
JZJMR8-raw-counts.txt

value: yeast cells


title: H3K27ac ChIP-seq hippocampus, SAL-LPS, female, replicate 4-2

description:
Library name: ChIP_Hippo_SAL-LPS_F_4-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Terra_CMO_library2

city: New York

first: Maria

middle: Antonietta

last: Tosches

state: NY

address: 1212 Amsterdam Ave

department: Biological Sciences

institute: Columbia University

description:
Library name: Terra_M2
CMO tag sequencing for library 2 |CMO305|CMO306|CMO307

data_processing:
Reads were assigned to the  Pleurodeles waltl genome using cellranger (v8.0.1). Reference index was built from Pleurodeles waltl genome aPleWal1.hap1.20221129 modified to include mitochondiral genes and the EGFP gene. Count parameters were set as default. Multiplex tag reads were also assigned using cellranger.
Assembly: GCF_031143425.1_aPleWal1.hap1.20221129_genomic.fa
Supplementary files format and content: raw count matrix

organism: Pleurodeles waltl

source_name: Telencephalon

extract_protocol:
Tissue pieces were dissociated for 30 min at room temperature using the Papain dissociation kit (Worthington) in calcium-free Hibernate A (BrainBits). After processing and concentration, cells were resuspended in calcium and magnesium-free HibernateA (BrainBits) at a concentration of 1000 cells/µl. Cells were counted in a haemocytometerchamber and immediately processed for single-cell GEM formation (10x Genomics, single cellRNA sequencing 3’, Chromium V3.1). Cells  were resuspended at ~1000 cells/µl and multiplexed using distinct Cell Multiplexing Oligos from the 10x Genomics 3’ CellPlex Multiplexing kit prior to GEM formation.
The cells were loaded into a 10x Chromium Chip G with a targeted cell recovery of 14,000-18,000 cells for GEM Generation and cell barcoding. Single-cell RNA-seq libraries were prepared with 10x Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 (Dual Index)

value: Telencephalon

tag: library type

value: CMO


title: 508-RL-mKO-sol

city: Boston

first: Masanori

last: Fujimoto

state: MA

address: Center for Life Sciences 3 Blackfan Circle, Room CLS730

department: Division of Endocrinology

institute: Beth Israel Deaconess Medical Center, Harvard Medical School

description:
Library name: 508-RL-mKO-sol
2x150 Paired-End

data_processing:
Sequencing was performed on the Illumina NovaSeq platform using a 2x150 Paired-End configuration
Raw sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The reads were then mapped to the reference genome (mm10) using the STAR aligner v.2.5.2b.
Assembly: mm10
Supplementary files format and content: raw_counts.csv
Supplementary files format and content: TPM_values.csv

source_name: Muscle

growth_protocol: Mice were housed at 23˚C or 30˚C in ventilated cages under a 12 h – 12 h light/dark cycle. Mice were fed a standard diet (Lab Diet 5008) with free access to food and water unless specified.

extract_protocol:
Total RNA were extracted using Rneasy kit (QIAGEN)
ERCC RNA Spike-In Mix (ThermoFisher) was added to normalized total RNA prior to library preparation following manufacturer’s protocol. The next steps included performing rRNA depletion using QIAGEN FastSelect rRNA HMR Kit (Qiagen). RNA sequencing libraries were constructed with the NEBNext Ultra II RNA Library Preparation Kit for Illumina according to manufacturer’s instructions.

value: Muscle

tag: batch


title: N_72_2

value: CAR-T cell


title: yeast cells expressing YdfC-GFP Variant1, high adenine media, bio-rep1

description:
Library name: YdfC-nonselective-1
JZJMR8-raw-counts.txt


title: H3K27ac ChIP-seq hippocampus, SAL-LPS, female, replicate 4-0

description:
Library name: ChIP_Hippo_SAL-LPS_F_4-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: SAL-LPS


title: Terra_transcript_library2

description: Library name: Terra_T2

value: GEX


title: N_72_1


title: Terra_CMO_library1

description:
Library name: Terra_M1
CMO tag sequencing for library 1 |CMO305|CMO306|CMO307


title: H3K27ac ChIP-seq hippocampus, SAL-LPS, female, replicate 2-2

description:
Library name: ChIP_Hippo_SAL-LPS_F_2-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: N_24_3

value: 24hr Cancer co-culture


title: yeast cells expressing nonsense control in YeiG experiment, low adenine media, bio-rep1

description:
Library name: Nonsense-control-YieG-selective-1
ZRSM94-raw-counts.txt

value: Nonsense control

value: 2.5 mg/L Adenine media


title: yeast cells expressing nonsense control in YeiG experiment, low adenine media, bio-rep2

description:
Library name: Nonsense-control-YieG-selective-2
ZRSM94-raw-counts.txt


title: Terra_transcript_library1

description: Library name: Terra_T1


title: H3K27ac ChIP-seq hippocampus, SAL-LPS, female, replicate 2-0

description:
Library name: ChIP_Hippo_SAL-LPS_F_2-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: hippocampus


title: N_24_2


title: yeast cells expressing nonsense control in YeiG experiment, high adenine media, bio-rep2

description:
Library name: Nonsense-control-YieG-nonselective-2
ZRSM94-raw-counts.txt

value: 80 mg/L Adenine media


title: E7_CMO_library1

description:
Library name: E7_M
CMO tag sequencing for library 1 |CMO301|CMO302


title: N_24_1


title: yeast cells expressing nonsense control in YeiG experiment, high adenine media, bio-rep1

description:
Library name: Nonsense-control-YieG-nonselective-1
ZRSM94-raw-counts.txt


title: N_6_3

value: 06hr Cancer co-culture


title: H3K27ac ChIP-seq hippocampus, SAL-LPS, female, replicate 10-4

description:
Library name: ChIP_Hippo_SAL-LPS_F_10-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: E7_transcript_library1

description: Library name: E7_T


title: yeast cells expressing YeiG Variant1, low adenine media, bio-rep2

description:
Library name: YeiG-selective-2
ZRSM94-raw-counts.txt


title: Input control hippocampus, SAL-LPS, female

description:
Library name: Input_Hippo_SAL-LPS_F
Input control (pooled)


title: N_6_2


title: yeast cells expressing YeiG Variant1, low adenine media, bio-rep1

description:
Library name: YeiG-selective-1
ZRSM94-raw-counts.txt


title: H3K27ac ChIP-seq hippocampus, SAL-LPS, female, replicate 10-0

description:
Library name: ChIP_Hippo_SAL-LPS_F_10-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: maize_leaf, Zip1 treated, 6 hpi, rep3

city: Köln

first: Gunther

last: Doehlemann

address: Zülpicherstrasse 47a

department: Institute for Plant Sciences

country: Germany

institute: University of Cologne

description:
Library name: (F3) GB_Zip1_R3
total RNA

data_processing:
alignment: HISAT2 (version 2.0.5)
featureCounts (version 1.5.0-p3)
R package DESeq2 (version 1.20.0)
Assembly: Z. mays (Hufford et al., 2021)
Supplementary files format and content: count files

organism: Zea mays

source_name: leaf

growth_protocol: Maize kernels were sown into soil and grown for 8 days.

extract_protocol:
RNA was harvested from frozen and homogenized samples using TRIzol reagent (Invitrogen, Darmstadt, Germany). The Turbo DNA-Free Kit from Ambion (Ambion Life TechnologiesTM, Carlsbad, USA) was used to exclude DNA contamination.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: The 2nd leaf of seedlings was cut and mock, 2mM SA, 5µM Zip1 peptide soultion was infiltrated using 60mbar vacuum

value: leaf

value: Golden Bantam


title: N_6_1


title: yeast cells expressing YeiG Variant1, high adenine media, bio-rep2

description:
Library name: YeiG-nonselective-2
ZRSM94-raw-counts.txt


title: H3K27ac ChIP-seq hippocampus, MOR-SAL, male, replicate 8-2

description:
Library name: ChIP_Hippo_MOR-SAL_M_8-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: wild type

value: MOR-SAL


title: maize_leaf, Zip1 treated, 6 hpi, rep2

description:
Library name: (E3) GB_Zip1_R2
total RNA


title: N_0_3

value: No cancer co-culture


title: H3K27ac ChIP-seq hippocampus, SAL-LPS, female, replicate 10-2

description:
Library name: ChIP_Hippo_SAL-LPS_F_10-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: yeast cells expressing YeiG Variant1, high adenine media, bio-rep1

description:
Library name: YeiG-nonselective-1
ZRSM94-raw-counts.txt

value: yeast cells


title: H3K27ac ChIP-seq hippocampus, MOR-SAL, male, replicate 8-0

description:
Library name: ChIP_Hippo_MOR-SAL_M_8-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: maize_leaf, Zip1 treated, 6 hpi, rep1

description:
Library name: (D3) GB_Zip1_R1
total RNA


title: Healthy human donor (2), CAR T cells, GFP, Input, Rep1

city: Stanford

first: Oliver

last: Takacsi-Nagy

address: 234 Pasteur Dr. (BMI 4600)

department: Pathology

institute: Stanford University School of Medicine

description: Library name: Acute-2E-GFP-N-Rep-1

data_processing:
Basecalls were performed using bcl-convert Version 4.4.6 from Illumina
Adapters were trimmed from reads prior to mapping to the hg38 reference with  the Burrow-Wheeler Aligner [bwa (v0.7.17-r1188)] and removal of duplicate reads and alignments to artifactual/high signal regions using the nf-core/chipseq pipeline (v2.0.0, doi: 10.5281/zenodo.3240506) with default parameters.
Peaks were called using MACS3 callpeak (v3.0.3) with the following parameters: --gsize 2913022398 -s 150 –nomodel –extsize 200 --bdg. We empirically determined optimal peak calling parameters by examining sites resulting from (1) pooling data from replicates together prior to peak detection with permissive MACS3 q-value of 0.1 (‘oracle peaks’) with post-filtering on q-value and/or signal fold enrichment (FE) and (2) calling peaks separately for each replicate at permissive MACS3 p-value of 1 with post-filtering on p-value (range: 10-3 to 1) and irreducible discovery rate (IDR, v2.0.3) threshold of 1% or 5% with or without restricting to oracle peaks. This analysis identified an acceptable tradeoff between specificity and sensitivity for peaks called from pooled data at MACS3 p-value threshold of 0.1 with post-filtering to retain sites with q-value of 10-3 and FE > 8. The number of unique alignments within peaks for each ChIP dataset was tabulated using subread featureCounts (v2.1.1) with the following parameters: -p –countReadPairs –primary –ignoreDup.
Fold enrichment tracks were generated from ChIP and input signal bedgraph files using MACS3 (v3.0.3) bdgcmp with default parameters.
For visualization, bedgraphs were converted to bigwig using UCSC bedGraphToBigWig (v2.10).
To define a unified set of binding sites across ChIP datasets, peaks were merged using bedtools merge (v2.31.1) with default parameters.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input samples). A consensus peak set for each TF was generated as described above such that the same peak set is applicable to different human donors/technical replicates.

source_name: Primary Human T Cell

growth_protocol: Primary human T cells were negatively selected from PBMCs isolated from leukoreduction chambers from two healthy blood donors and activated by CD3/28 agonism in X-VIVO 15 supplemented with 5% FBS and 50 IU/mL recombinant human IL-2. 48 hours post-activation, T cells were electroporated with Cas9 ribonucleoprotein and a plasmid homology-directed repair template to enable integration of a multicistronic cassette encoding tNGFR, CD19-28z and variable natural and engineered FLAG-tagged AP-1 transcription factors within the continuous reading frame of the TRAC locus. Pre- and post-editing cells were maintained at 0.5-1e6/ml. Six days post-editing, CAR T cells were challenged with CD19-expressing Nalm6 targets (leukemia cell line, 1:8 Effector:Target ratio, 72-hour co-culture).

extract_protocol:
Up to 1e7 live CAR T cells (NGFR+) were enriched magnetically and cross-linked at RT first in 2 mM disuccinimidyl glutarate in PBS for 30 min and then in 1% methanol-free formaldehyde in PBS for 10 min. Formaldehyde was quenched by adding glycine to 125 mM final concentration. Cross-linked cells were pelleted, snap-frozen in liquid nitrogen, stored at –80ºC. Nuclei were isolated from cryopreserved pellet (1.5 x 1e6 cells) by sequential lysis in LB1 (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% IGEPAL CA-630, and 0.25% Triton X-100), LB2 (10 mM Tris-HCl pH 8, 200 mM NaCl, 1 mM EDTA, and 0.5 mM EGTA), and LB3 (10 mM Tris-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% sodium deoxycholate [NaDOC], and 0.5% N-laurylsarcosine) supplemented with 0.5 mM phenylmethylsulfonyl fluoride and 0.5X protease inhibitor cocktail. Chromatin was fragmented to 200-700 bp on a Covaris E220 focused ultrasonicator in microTubes with the following parameters: 140W peak incident power, 5% duty factor, 200 cycles per burst, 6ºC temperature setpoint (range 3-9ºC), run level 6, and time 12-14 min. Triton X-100 was added to final concentration of 1% to clarified chromatin prior to immunoprecipitation for 16h at 4ºC with 2.5 uL of 1 mg/mL mouse monoclonal anti-FLAG M2 antibody bound to a 1:1 mixture of protein A and G magnetic beads. Immunoprecipitated, bead-bound chromatin was washed sequentially with the following buffers supplemented with 0.5 mM PMSF and 0.5X PIC: three times with WB1 (20 mM Tris pH 8, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% sodium dodecyl sulfate [SDS], and 0.1% NaDOC); twice with WB2 (20 mM Tris-HCl pH8, 500 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, and 0.1% NaDOC); twice with WB3 (20 mM Tris-HCl pH 8, 250 mM LiCl, 1 mM EDTA, 0.5% IGEPAL CA-630, and 0.5% NaDOC); twice with TET (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.2% Tween-20); and once with TE0.1 (10 mM Tris-HCl pH 8, 0.1 mM EDTA). This mirrors the methods used previously (Umhoefer, et al., Immunity, 2025 and Arce, et al., Nature, 2025).
Beads were brought up in TT (10 mM Tris-HCl pH 8, 0.05% Tween-20) prior to on-bead library preparation using the NEBNext Ultra II DNA Library Prep Kit as previously described (Texari, et al., STAR Protocols, 2021).

treatment_protocol: All T cells in this sample were treated the same, the only difference between the T cells is which healthy human donor they were isolated from and which transcription factor they were edited to express.

value: Primary Human T Cell

tag: individual

value: Healthy Donor 2

tag: tf expressed

value: GFP


title: N_0_2

value: CAR-T cell


title: Toxoplasma gondii RH strain, TGGT1_245740 knockout tachyzoite, biological replicate 3

city: China

first: Jing

last: Li

address: No. 182, Tianmu Mountain Road, Xihu District, Hangzhou City, Zhejiang Province, Hangzhou Medical College

institute: Laboratory of Pathogenic Biology, School of Basic Medicine and Forensic Medicine, Hangzhou Medical College, China.

description: Library name: KO245740_Rep3

data_processing:
Illumina Casava 1.8 software used for basecalling
Assembly: https://toxodb.org/common/downloads/Current_Release/TgondiiRH88/fasta/data/ToxoDB-68_TgondiiRH88_Genome.fasta
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

organism: Toxoplasma gondii

source_name: tachyzoite

growth_protocol: Toxoplasma gondii RH wild-type, TGGT1_245740 knockout tachyzoites were routinely cultured in HFF-1 human foreskin fibroblasts maintained in DMEM medium supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin at 37°C, 5% CO₂. Freshly egressed extracellular tachyzoites were collected, filtered through 5μm membrane, washed twice with cold PBS for RNA extraction.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using Fast RNA-seq Lib Prep Kit V2 （Cat.No.RK20306） following manufacturer's protocols.

value: tachyzoite

value: TGGT1_245742 knockout RH strain

value: untreated


title: Toxoplasma gondii RH strain, TGGT1_245740 knockout tachyzoite, biological replicate 2

description: Library name: KO245740_Rep2

value: TGGT1_245741 knockout RH strain


title: N_0_1


title: maize_leaf, SA treated, 6 hpi, rep2

description:
Library name: (E2) GB_SA_R2
total RNA

value: SA


title: H3K27ac ChIP-seq hippocampus, MOR-SAL, male, replicate 17-4

description:
Library name: ChIP_Hippo_MOR-SAL_M_17-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: hippocampus


title: H3K27ac ChIP-seq hippocampus, MOR-SAL, male, replicate 6-1

description:
Library name: ChIP_Hippo_MOR-SAL_M_6-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: maize_leaf, SA treated, 6 hpi, rep3

description:
Library name: (F2) GB_SA_R3
total RNA


title: D_72_3

value: 72hr Cancer co-culture


title: Toxoplasma gondii RH strain, TGGT1_245740 knockout tachyzoite, biological replicate 1

description: Library name: KO245740_Rep1

value: TGGT1_245740 knockout RH strain


title: maize_leaf, SA treated, 6 hpi, rep1

description:
Library name: (D2) GB_SA_R1
total RNA

value: leaf

value: Golden Bantam


title: H3K27ac ChIP-seq hippocampus, MOR-SAL, male, replicate 14-1

description:
Library name: ChIP_Hippo_MOR-SAL_M_14-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: wild type

value: MOR-SAL


title: D_72_2


title: Toxoplasma gondii RH strain, wild-type tachyzoite, biological replicate 3

description: Library name: RH_WT_Rep3

value: Wild-type RH strain


title: maize_leaf, mock treated, 6 hpi, rep3

description:
Library name: (F1) GB_M_R3
total RNA

value: mock


title: D_72_1


title: Input control hippocampus, MOR-SAL, male

description:
Library name: Input_Hippo_MOR-SAL_M
Input control (pooled)


title: Toxoplasma gondii RH strain, wild-type tachyzoite, biological replicate 2

description: Library name: RH_WT_Rep2


title: maize_leaf, mock treated, 6 hpi, rep2

description:
Library name: (E1) GB_M_R2
total RNA


title: H3K27ac ChIP-seq hippocampus, MOR-SAL, male, replicate 13-1

description:
Library name: ChIP_Hippo_MOR-SAL_M_13-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Toxoplasma gondii RH strain, wild-type tachyzoite, biological replicate 1

description: Library name: RH_WT_Rep1


title: maize_leaf, mock treated, 6 hpi, rep1

description:
Library name: (D1) GB_M_R1
total RNA


title: H3K27ac ChIP-seq hippocampus, MOR-SAL, female, replicate 7-3

description:
Library name: ChIP_Hippo_MOR-SAL_F_7-3
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: D_24_3

value: 24hr Cancer co-culture


title: D_24_2


title: IT50

first: Xiaoli

last: Wei

address: Dongan Road 130

institute: Fudan University

description: Library name: Sample2

data_processing:
Raw sequencing data generated on the Illumina platform were converted to FASTQ files and processed using the Cell Ranger software (v7.1.0) with default parameters. Reads were aligned to the mouse reference genome using the STAR algorithm. Unique molecular identifiers (UMIs) were counted, and cell barcodes not corresponding to real cells were filtered out, resulting in a filtered gene expression matrix.
Assembly: GRCm39
Supplementary files format and content: matrix files

source_name: lung

extract_protocol:
The tissues were immediately transferred into tissue storage buffer on ice, then washed in 10 mL of chilled 1× Dulbecco’s Phosphate-Buffered Saline (DPBS) to remove residual buffer. Tissues were finely minced on ice and enzymatically digested in a solution containing Collagenase (1 mg/mL), Dispase (1 mg/mL), and DNase I (10 μg/mL) at 37 °C for 30 minutes with gentle agitation. The resulting cell suspensions were filtered through 40 μm cell strainers and subjected to red blood cell (RBC) lysis56. After lysis, cells were washed with 1× DPBS supplemented with 0.4% fetal bovine serum (FBS). Cell viability was assessed using 0.4% acridine orange/propidium iodide (AO/PI) staining and analyzed on the Countstar Rigel S2 system. Viable single-cell suspensions were submitted to Majorbio Biopharm Technology Co., Ltd. (Shanghai, China) for single-cell RNA sequencing.
Sequencing libraries were prepared using randomlyinterrupted whole-transcriptome amplification products to enrich the 3' end of the transcriptslinked with the cell barcode and UMI. All the remaining procedures including the libraryconstruction were performed according to the standard manufacturer's protocol (Chromium SingleCell 3' v3.1) Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent)on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific)The libraries were sequenced on Xplus (llumina) /MGI DNBSEQ-T7 using 2x150 chemistry. These quencing and bioinformatic analysis were performed on platform of Majorbio Co., Ltd(Shanghai, China)

value: lung

value: neutrophil

value: mRNA-LNP


title: L327P/WT forebrain organoids, scRNA-seq, library 2

city: San Francisco

first: Kelsey

last: Hennick

address: 1651 4th St room 521A

institute: UCSF

description:
Library name: L327P-scRNAseq-rep2
HET18, L327P/WT clone 2

data_processing:
scRNA-seq data was first processed using PIPseeker for quality control, and then following the Seurat pipeline.
Assembly: hg38
Supplementary files format and content: scRNA-seq: csv file with cell metadata

source_name: hiPSC-derived forebrain organoid

extract_protocol:
RNA was extracted following the Fluent PIP-seq protocol (PMID: 36879006)
Libraries were constructed using the Fluent PIP-seq reagents (PMID: 36879006)

value: hiPSC-derived forebrain organoid

value: CRISPR isogenic 13234 clone

value: hiPSC

value: forebrain organoid differentiation

value: total RNA


title: H3K27ac ChIP-seq hippocampus, MOR-SAL, female, replicate 7-2

description:
Library name: ChIP_Hippo_MOR-SAL_F_7-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: hippocampus


title: D_24_1

value: CAR-T cell


title: blank

description: Library name: Sample1

value: control


title: H3K27ac ChIP-seq hippocampus, MOR-SAL, female, replicate 16-1

description:
Library name: ChIP_Hippo_MOR-SAL_F_16-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: L327P/WT forebrain organoids, scRNA-seq, library 1

description:
Library name: L327P-scRNAseq-rep1
HET15, L327P/WT clone1


title: D_6_3

value: 06hr Cancer co-culture


title: WT_Cort_MCAO_Rep4

city: Granada

first: Jose

middle: Luis

last: Ruiz Rodriguez

state: Granada

address: Avda. del Conocimiento 17. P. T. Ciencias de la Salud

country: Spain

institute: IPBLN-CSIC

description: Library name: WT_Cort_MCAO_Rep4

data_processing:
Given the low expression levels of cortistatin, we implemented the reanalyzerGSE software (v3.0.0) in the RNA-seq analysis to identify differentially expressed genes (DEGs) and to prevent the exclusion of low expressed genes with potential biological relevance.
Multidimensional scaling  (Principal Coordinates Analysis, PCoA) and unsupervised hierarchical clustering of normalized samples were performed to assess the divergence and the replicability of samples from each independent comparison
DEGs with a False Discovery Rate (FDR) ≤ 0.05 were calculated by comparing: i) Cort-/- vs Cort+/+ samples for each condition (CL and MCAO); ii) MCAO vs CL for each genotype (Cort-/- and Cort+/+). The log2 fold change (log2FC) was used to quantify gene expression changes. To explore the functional significance of DEGs, Gene Ontology (GO)-based enrichment analyses were performed
Assembly: GRCm39
Supplementary files format and content: Tab delimited file with normalized counts for each sample

source_name: brain

growth_protocol: The experimental protocols employed in this study were approved by the Animal Care and Use Board and the Ethical Committee of the Spanish National Research Council (Animal Care Unit Committee IPBLN-CSIC # protocol CEEA OCT/2017.EGR), and were conducted in accordance with Directive 2010/63/EU of the European Parliament on the protection of animals used for scientific purposes. Transgenic mice deficient in the cortistatin gene (Cort-/-), generously provided by Dr Luis de Lecea (Stanford University, United States), were generated and maintained on a C57BL/6J background as previously described. Mice were housed in groups of ten per cage under controlled environmental conditions (22 ± 1 ºC, 60-70 % relative humidity) with a 12 h light/dark cycle (lights on at 7:00 a.m.), and were provided ad libitum access to food and water.

extract_protocol:
After MCAO, brains were collected at the specified time points and separated into contralateral and ipsilateral hemispheres. For RNA isolation, brain tissues were placed in TriPure reagent (Roche).
RNA (200 ng) from contralateral (CL, healthy) and ischemic (MCAO) brain hemispheres isolated from Cort+/+ and Cort-/- mice 48 h post-stroke was used to prepare mRNA libraries with the Illumina stranded mRNA Prep Ligation kit (Illumina, San Diego, CA, USA). Three (CL) and five (MCAO) independent biological replicates were used with RNA Integrity Number coefficients >8.7 (Bioanalyzer RNA 6000 Nano-chip, from Agilent, Santa Clara, CA, USA). Quality and size distribution of mRNA libraries were validated using the Bioanalyzer High Sensitivity DNA assay and their concentrations were measured on a Qubit fluorometer (ThermoFisher). Final dsDNA libraries were pooled in equimolecular ratios and converted to single stranded circular DNA with MGIEasy Universal Library Conversion kit (MGI Tech, Shenzhen, China) for sequencing on MGI platforms .

treatment_protocol: Young (12 weeks old) and middle-aged (6 months old) Cort+/+ and Cort-/- mice were subjected to the MCAO model as previously described. Anaesthesia was induced using isoflurane (1.5-2 % in 70 % N2O / 30 % O2) via a facemask and meloxicam (2 mg/kg, subcutaneously, Norbrook) was administered for post-surgical analgesia. Body temperature was maintained constant throughout the procedure using a heating pad. Regional cerebral blood flow (rCBF) was continuously monitored by laser Doppler flowmetry (moorVMS-LDF1, Moor Instruments) fixing a probe on the skull over the core area supplied by the middle cerebral artery (MCA) (approximately 1 mm posterior and 6 mm lateral to the bregma). Transient focal ischemia was induced by introducing a silicon-coated filament (701756PK5Re, Doccol) through the left common carotid artery into the internal carotid artery to occlude the MCA. The occlusion was maintained for 20 min in young mice (considered as a mild MCAO model) and 35 min in middle-aged mice, after which the filament was withdrawn to allow reperfusion. The surgery was considered successful if the rCBF decreased to < 20 % of the baseline during occlusion and recovered to > 50 % of the baseline upon reperfusion. Following surgery, mice were returned to their cages with ad libitum access to food and water. Each cage was supplied with water-softened chow and recovery gel.

value: brain

value: MCAO


title: WT forebrain organoids for L327P experiment, scRNA-seq, library 2

description:
Library name: WT-scRNAseq-L327P-rep2
WT2, WT/WT clone 2

value: WT/WT


title: D_6_2


title: KPC

city: Austin

first: Bryan

last: McClellan

state: TX

address: 1601B Trinity St, Hdb 6.302

institute: University of Texas at Austin

description: Library name: KPC

data_processing:
Data was processed using spaceranger count v4.0.1
Assembly: GRCm39 2024-A
Supplementary files format and content: tissue_hires_image.png: high resolution H & E tissue image
Supplementary files format and content: tissue_lowres_image.png: low resolution H & E tissue image
Supplementary files format and content: detected_tissue_image.jpg: detected tissue image
Supplementary files format and content: cytassist_image.tiff: cytassist tissue image
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of tissue image
Supplementary files format and content: aligned_tissue_image.jpg: aligned tissue image
Supplementary files format and content: matrix.mtx.gz: gene expression count data
Supplementary files format and content: features.tsv.gz: list of genes
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: scalefactors_json.json: scale factors in json format
Library strategy: Spatial Transcriptomics

source_name: Pancreas Tumor

growth_protocol: 50,000 mT4-2D cells were injected into the tail of the pancreas

extract_protocol:
Three days post treatment, tumors were isolated and frozen in OCT as fresh frozen tumors.
Libraries were constructed using Visium HD 3' library construction kit CG000805

treatment_protocol: Pancreas tumors were treated with five million anti-mesothelin CAR T-cells

value: Pancreas Tumor

value: mT4-2D orthotpically injected

value: Pancreas cancer cell

tag: strain


title: H3K27ac ChIP-seq hippocampus, MOR-SAL, female, replicate 15-0

description:
Library name: ChIP_Hippo_MOR-SAL_F_15-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

data_processing:
Adapters and low-quality bases were trimmed using Trim Galore (v0.6.7, --paired --fastqc).
Reads were aligned to Mus musculus mm10 using Bowtie2 (v2.4.5). PCR duplicates were removed with SAMtools (v1.15.1) markdup. Reads overlapping ENCODE mm10 blacklist (v2) were excluded with BEDTools subtract (v2.30.0). Coverage profiles were generated with bedtools genomecov and converted to BigWig with bedGraphToBigWig.
Peak calling: MACS2 (v2.2.7.1; -q 0.05 -g mm) against matched pooled Input controls.
Differential H3K27ac analysis: consensus peak set constructed in DiffBind (v3.10.1) with condition-aware merging. Read counts quantified with DiffBind (dba.count, summarizeOverlaps); peaks retained if >= 15 reads in >= 80% of samples within any condition. Differential peaks identified via DESeq2 (dba.analyze); FDR < 0.05. Peaks annotated with ChIPpeakAnno (v3.32.1) and EnsDb.Mmusculus.v79.
Transcription factor regulatory influence assessed with Taiji (v1.2.0) integrating H3K27ac enhancers and RNA-seq expression. TF activity quantified as personalized PageRank scores (z-score normalized, capped at +/-2).
Assembly: mm10
Supplementary files format and content: narrowPeak files (MACS2 peak calls); bigWig coverage tracks (bedtools genomecov + bedGraphToBigWig)

extract_protocol:
Brain tissues (PFC, hippocampus, hypothalamus, striatum) were collected by bilateral punch (2.0 mm) and flash-frozen at -80C. Nuclei were isolated in cold extraction buffer using a Dounce tissue grinder, filtered (40 um), and enriched by iodixanol gradient centrifugation. NeuN+ neuronal nuclei were labeled with anti-NeuN Alexa Fluor 488 (MAB377X, EMD Millipore) at 4C for 1 h, then sorted by FACS (BD Biosciences). ~10,000 NeuN+ nuclei per replicate were lysed and digested with MNase (88216, Thermo Fisher) in the presence of CaCl2; reaction quenched with EDTA. Chromatin IP was performed using 0.125 ug anti-H3K27ac antibody (39135, Active Motif) coupled to 5 uL protein A Dynabeads (10001D, Thermo Fisher), following the MOWChIP-seq protocol.
ChIP-seq libraries were constructed from purified ChIP DNA (~10,000 NeuN+ nuclei) and input DNA (~2,000 nuclei). PFC libraries used xGen 2S DNA Library Prep Kit (10009877, IDT); hippocampus, hypothalamus, and striatum libraries used ThruPLEX DNA-Seq kit (R400674, Takara Bio). Fragment size verified on TapeStation (Agilent) with High Sensitivity DNA Analysis Kit; primer-dimers removed with SPRIselect beads. Libraries quantified with KAPA Library Quantification Kit (4824, Roche), pooled, and sequenced on an Illumina NovaSeq X Plus platform (paired-end 150 nt, ~15 million reads per library).

value: wild type

value: MOR-SAL


title: WT forebrain organoids for L327P experiment, scRNA-seq, library 1

description:
Library name: WT-scRNAseq-L327P-rep1
WT1, WT/WT clone 1

value: hiPSC-derived forebrain organoid


title: Input control hippocampus, MOR-SAL, female

description:
Library name: Input_Hippo_MOR-SAL_F
Input control (pooled)


title: WT_Cort_MCAO_Rep3

description: Library name: WT_Cort_MCAO_Rep3


title: WT_Cort_MCAO_Rep2

description: Library name: WT_Cort_MCAO_Rep2


title: D_6_1


title: H3K27ac ChIP-seq hippocampus, MOR-SAL, female, replicate 12-1

description:
Library name: ChIP_Hippo_MOR-SAL_F_12-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: 22Rv1_M253K_xeno_rep5

city: Valhalla

first: Shuai

last: Gao

address: 40 Sunshine Cottage Rd

institute: New York Medical College

description: Library name: Sample 9

data_processing:
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were aligned to the human reference genome (hg19) using STAR (version 2.7.2) followed by counting with featureCounts (version 1.6.4) from GRCh37 Ensembl reference.
Assembly: hg19
Supplementary files format and content: tab-deliminted text file includes raw count for each sample

extract_protocol:
RNeasy Kit (Qiagen) were used for tumor RNA extraction per manufacture’s instruction.
The TruSeq Strand Total RNA LT kit (Illumina) was used for library preparation.

value: FKHD mutant overexpression


title: H3K27ac ChIP-seq hippocampus, MOR-LPS, male, replicate 8-3

description:
Library name: ChIP_Hippo_MOR-LPS_M_8-3
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: MOR-LPS


title: WT_Cort_CL_Rep3

description: Library name: WT_Cort_CL_Rep3


title: D_0_3

value: No cancer co-culture


title: 22Rv1_M253K_xeno_rep4

description: Library name: Sample 8


title: D_0_2


title: H3K27ac ChIP-seq hippocampus, MOR-LPS, male, replicate 6-4

description:
Library name: ChIP_Hippo_MOR-LPS_M_6-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: 22Rv1_M253K_xeno_rep3

description: Library name: Sample 7


title: WT_Cort_CL_Rep2

description: Library name: WT_Cort_CL_Rep2


title: D_0_1


title: H3K27ac ChIP-seq hippocampus, MOR-LPS, male, replicate 6-0

description:
Library name: ChIP_Hippo_MOR-LPS_M_6-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Donor6_Tumor3

data_processing:
The dual-sgRNA CRISPR screen data were pre-processed to acquire paired spacer sequences of each guide via Cutadapt v3.4 92. Briefly, reads were trimmed in paired-end mode to remove flanking sequences of the sgRNA spacers, first removing the 5’ adaptors (Read 1:  5’-GTTTCAGAGCTATGCTGG; Read 2: 5’-CAAGGCTTTTCTCCAAGG) and then 3’ adaptors (Read 1:  5’-GGAAAGGACGAAACACCG; Read 2: 5’-TATTTCTAGCTCTAAAAC). The paired spacers were then filtered to include those with a length of > 18 nt. The pre-processed spacer sequences were then aligned to the paired sgRNA library reference, comprised of joined spacer sequences without gaps, using Bowtie v1.3.0 93 (parameters: -v2 -m2 --suppress 1,4,5,6,7 -I 26 --chunkmbs 2000 --fr -X 100 --best ).
Assembly: Custom CRISPR library sequences were used for alignment
Supplementary files format and content: Processed data is in a tab-delimited file, where the first column = sgRNA name, second column = gene name, and every other column are the CRISPR library counts for each sample.

extract_protocol:
Method 1: for cells less than 1 × 105, cells were directly resuspended in 100 μL QuickExtract solution (Epicenter), incubated at 65 °C for 30 min to lyse the cell, and 95 °C for 5 min to denature proteins.
Method 2: for cell number between 1 × 105 to 2 × 106, QIAmp Fast DNA Tissue Kit (QIAGEN) was used in accordance with manufacturer’s protocol.
Genomic DNA of whole tumor or spleen samples were harvested for library readout PCR. CRISPR screen sample sgRNA library readout was performed by a two-step PCR. For PCR #1, two primers were used to pre-amplify the dual-sgRNA containing region:
Forward: AATGGACTATCATATGCTTACCGTAACTTGAAAGTATTTTCG
Reverse: GGCTGCAGGAATTCGATATCAAGC
In a 100 μL readout PCR system, 1 μg spleen or cell sample gDNA, or 2 μg tumor gDNA was used as input. 20 PCR reactions were used to ensure the coverage of the library. gDNA was PCR amplified using Phusion Flash 2× PCR Master Mix (ThermoFisher) according to manufacturer’s protocol, in 28 cycles with Tm = 62.4 °C.
The products from PCR #1 were pooled for each sample, then used for a second amplification using barcoded PCR primers (Supplementary information - Oligos). In a 50 μL readout PCR system, at least four PCR #2 reactions were carried out for each sample, using 2 µL of the pooled PCR #1 product for each reaction, in 28 cycles with Tm = 67.2 °C. PCR #2 products were pooled, normalized, and pooled together. The pooled PCR product was purified through a 2% E-gel EX (Life Technologies) and the QiaQuick kit (QIAGEN). The purified, pooled library was quantified using BioAnalyzer (Agilent), and then sequenced by Illumina NovaSeq 6000 system.

value: wt


title: 22Rv1_M253K_xeno_rep2

description: Library name: Sample 6


title: WT_Cort_CL_Rep1

description: Library name: WT_Cort_CL_Rep1


title: KO_Cort_MCAO_Rep5

description: Library name: KO_Cort_MCAO_Rep5


title: 22Rv1_M253K_xeno_rep1

description: Library name: Sample 5


title: Donor6_Tumor2


title: H3K27ac ChIP-seq hippocampus, MOR-LPS, male, replicate 14-2

description:
Library name: ChIP_Hippo_MOR-LPS_M_14-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: hippocampus


title: H3K27ac ChIP-seq hippocampus, MOR-LPS, male, replicate 17-1

description:
Library name: ChIP_Hippo_MOR-LPS_M_17-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: KO_Cort_MCAO_Rep4

description: Library name: KO_Cort_MCAO_Rep4


title: 22Rv1_WT_xeno_rep4

description: Library name: Sample 4

value: wild-type FOXA1 overexpression


title: KO_Cort_MCAO_Rep3

description: Library name: KO_Cort_MCAO_Rep3


title: Donor6_Tumor1

value: CAR-T cell


title: Input control hippocampus, MOR-LPS, male

description:
Library name: Input_Hippo_MOR-LPS_M
Input control (pooled)


title: KO_Cort_MCAO_Rep2

description: Library name: KO_Cort_MCAO_Rep2


title: Donor5_Tumor3


title: 22Rv1_WT_xeno_rep3

description: Library name: Sample 3


title: Donor5_Tumor2


title: KO_Cort_MCAO_Rep1

description: Library name: KO_Cort_MCAO_Rep1


title: 22Rv1_WT_xeno_rep2

description: Library name: Sample 2


title: H3K27ac ChIP-seq hippocampus, MOR-LPS, male, replicate 13-2

description:
Library name: ChIP_Hippo_MOR-LPS_M_13-2
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: H3K27ac ChIP-seq hippocampus, MOR-LPS, female, replicate 18-1

description:
Library name: ChIP_Hippo_MOR-LPS_F_18-1
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: 22Rv1_WT_xeno_rep1

description: Library name: Sample 1


title: KO_Cort_CL_Rep3

description: Library name: KO_Cort_CL_Rep3


title: H3K27ac ChIP-seq hippocampus, MOR-LPS, female, replicate 16-4

description:
Library name: ChIP_Hippo_MOR-LPS_F_16-4
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Puck_230913_14

city: New Haven

first: Hattie

last: Chung

address: 300 George St

description: Library name: 2025-03-13_Puck_230913_14

data_processing:
Raw sequencing data were processed using the Slide-seq pipeline following Stickels et al. Nat Biotech 2021.
Assembly: mm10
Supplementary files format and content: [puck_name].h5ad: processed raw counts of beads (rows) and genes (columns)
Library strategy: Spatial Transcriptomics

source_name: Ovary

growth_protocol: Female C57BL/6 mice were maintained under SPF conditions on a 12-hour light-dark cycle with standard chow and water provided ad libitum.

extract_protocol:
10µm frozen sections were cut on the cryostat
Spatial transcriptome libraries were prepared using the Slide-seq V2 protocol

treatment_protocol: Mice were staged near-daily for their estrous cycle and harvested at the estrus or metestrus stage via intracardial perfusion with PBS. Ovaries were fresh frozen embedded in OCT.

value: Ovary

tag: Stage

value: Metestrus

value: Yale

value: Young


title: Donor5_Tumor1


title: Donor6_Control

value: control


title: KO_Cort_CL_Rep2

description: Library name: KO_Cort_CL_Rep2

value: brain


title: H3K27ac ChIP-seq hippocampus, MOR-LPS, female, replicate 15-3

description:
Library name: ChIP_Hippo_MOR-LPS_F_15-3
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)


title: Input, AM, REP1

city: Pittsburgh

first: Issam

last: Al Diri

state: PA

address: 1622 Locust St

department: Ophthalmology

institute: University of Pittsburgh School of Medicine

description: Library name: Input

data_processing:
Raw FASTQ reads were trimmed by Trimmomatic
Reads were aligned to mouse refenrence genome mm10 by BWA
BAM filtering was performed by samtools and markduplicate by Picard tool
Peaks were called by MACS broadPeak with a cutoff of < 0.0005.
bigWig files was generated by deeptools bamCoverage
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Retina

extract_protocol:
Frozen tissue was sent to Active Motif Services (Carlsbad, CA) for ChIP-Seq. Active Motif prepared chromatin, performed ChIP reactions, generated libraries, sequenced the libraries and performed data analysis. In brief, tissue was submersed in PBS + 1% formaldehyde, cut into small pieces and incubated at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycine (final). Chromatin was isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer, washing and sonication using the PIXUL® Multi-Sample Sonicator (Active Motif, Catalog #53130) to shear DNA to an average fragment size of 200–1000 bp. To determine chromatin yield, an aliquot of the sheared chromatin was reverse crosslinked at 65°C, treated with RNase and proteinase K, and subjected to DNA purification using SPRI beads (Beckman Coulter). DNA concentrations were measured using a Qubit Fluorometer (Thermo Fisher), and total chromatin yield was extrapolated based on the original chromatin volume.
ChIP DNA was then purified using phenol-chloroform extraction and ethanol precipitation. ChIP DNA libraries were prepared using either the PrepX DNA Library Kit (Takara Bio) on the Apollo automation platform or the NEB DNA Library Prep Kit, following the manufacturers' protocols. Libraries were sequenced on the Illumina platform and the resulting data were analyzed using standard ChIP-Seq workflows.

value: Retina

tag: developmental stage

value: WT


title: KO_Cort_CL_Rep1

description: Library name: KO_Cort_CL_Rep1


title: Donor5_Control


title: Input control hippocampus, MOR-LPS, female

description:
Library name: Input_Hippo_MOR-LPS_F
Input control (pooled)

value: wild type


title: Donor3_Control


title: H3K27me3, AM, REP2

description: Library name: H3K27me3_R2, ChIP


title: CRC_CD45_N_deltaMYL

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

description: EgfrΔMYL

data_processing:
cellRanger (v3.0.2) was run on the raw data using the mm10 annotation. cellRanger aggr was used to aggregate samples.
Assembly: mm10
Supplementary files format and content: Tab-separated annotation files and matrix file

source_name: CD45- non-immune TME

growth_protocol: Female mice were injected intraperitoneally (IP) with 12.5 mg/kg AOM (A5486; Sigma-Aldrich, St. Louis, MO) followed by regular diet and water for 5 days. After that, mice received 2.5% DSS (Dextran-Sulphate-Sodium; 02160110-CF; MP Biomedicals, Santa Ana, CA) in autoclaved water for 5 days, followed by maintenance on regular autoclaved water for  16 days and 2 additional DSS cycles (5 days of 2.5% DSS and 5 days of 2% DSS). Mice were sacrificed 30 days after the last DSS treatment.

extract_protocol:
AOM/DSS-induced colon polyps were cut into pieces and digested in RPMI medium supplemented with 10% fetal calf serum (FCS), 1% penicillin/streptomycin, 1.5 mg/mL Collagenase VIII (Sigma-Aldrich, St. Louis, MO) and 0.5 mg/mL DNase I (Sigma-Aldrich) for 1 hour at 37°C shaking at 300 rpm. Samples were filtered through a 70-μm cell strainer and washed once with Hank’s balanced salt solution containing 10% FCS, 1% penicillin/streptomycin, and 5 mM EDTA and twice with PBS containing 5% FCS, 5 mM EDTA, and 20 μg/mL DNase I. Single cell suspensions were initially blocked with Fc-block (CD16/CD32, Biolegend) following staining with fluorescent CD45 and EPCAM antibodies for 30 min at 4 °C. Subsequent FACS-sorting was performed on a BD Aria III instrument.
Single cell suspensions of sorted CD45-pos and CD45-neg cells were loaded into one well for single-cell capture using the Chromium Single Cell 3’ Reagent Kit V3 (10X Genomics). Library preparation for each sample was also performed using the Chromium Single Cell 3’ Reagent Kit V3, and each sample was given a unique i7 index. Libraries were pooled and subjected to sequencing.

value: CD45- non-immune TME

value: Egfr{delta}MYL

value: AOM/DSS


title: H3K27ac ChIP-seq hippocampus, MOR-LPS, female, replicate 12-0

first: Yanmiao

last: Du

address: 4254 Urey Hall, 9500 Gilman Drive

description:
Library name: ChIP_Hippo_MOR-LPS_F_12-0
ChIP antibody: anti-H3K27ac (Active Motif cat. 39135)

value: MOR-LPS


title: H3K27me3, AM, REP1

description: Library name: H3K27me3_R1, ChIP


title: CRC_CD45_N_WT

description: Egfr fl/fl

value: Egfr fl/fl


title: EZH2, CST, REP2

description: Library name: EZH2_CST_R2, ChIP


title: 18N2KOVNSLPS

city: Charlottesville

first: Vikram

last: Sabapathy

state: Virginia

address: 1340 Jefferson Park Ave., Pinn Hall, Room No: 4043

department: Center for Immunity, Inflammation and Regenerative Medicine

institute: University of Virginia

description: Library name: Sample 18

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using fastp v.0.23.1.
Trimmed and de-duplicated reads were then mapped to the Mus musculus GRCm38 ERCC reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed.
Assembly: Mus musculus GRCm38
Supplementary files format and content: CSV file include featurecounts for all the sample

source_name: Kidney

extract_protocol:
RNA was isolated from FACS-sorted cells using RNeasy Plus mini kit (Qiagen) and the quality was assessed with an HS-RNA Agilent Tape Station
mRNA sequencing with Twist UMI system

value: Kidney

value: Cx3cr1-Cre; Notch2flox/flox

value: VNS + LPS


title: Donor3_Tumor5

first: Sidi

last: Chen

address: 850 West Campus Drive

value: CAR-T cell

value: wt


title: Donor3_Tumor4


title: 17N2KOVNSLPS

description: Library name: Sample 17


title: EZH2, CST, REP1

description: Library name: EZH2_CST_R1, ChIP


title: CRC_CD45_P_deltaMYL

description: EgfrΔMYL

source_name: CD45+ immune TME

value: CD45+ immune TME


title: Donor3_Tumor3

source_name: CAR-T cell


title: EZH2, AM, 106, REP2

description: Library name: EZH2_106_R2, ChIP


title: MUC20720_GLPG3974

city: Munich

first: Stefanie

last: Eyerich

address: Biedersteinerstr. 29

institute: TUM

description: Library name: MUC20720

data_processing:
Sequence alignment was performed using STAR aligner with human genome reference hg38. Raw count data for 60,666 genes was processed using the DESeq2 R package version 1.32.0 (Love et al. 2014)
Assembly: hg38
Supplementary files format and content: csv with metadata of the patient, including treatment (group), Biobank_ID and age
Supplementary files format and content: csv with count data

source_name: skin punch biopsies

extract_protocol:
Biopsies were stored in RNAprotect Tissue Reagent (Qiagen) at -80°C until RNA was isolated using QIAzol Lysis Reagent (Qiagen) and miRNeasy Mini Kit (Qiagen) according to manufacturer’s protocol.
RNASeq libraries were generated using the TruSeq Stranded Total RNA Kit (Illumina) according to the manufacturer’s high sample protocol.

treatment_protocol: One part of the biopsy was stimulated with 100 μM GLPG3970, the other part with vehicle (1% DMSO) for 24 h.

value: skin punch biopsies

value: tissue

value: 6 mm skin biopsies


title: 15N2WTVNSLPS

description: Library name: Sample 15


title: CRC_CD45_P_WT

description: Egfr fl/fl


title: Donor3_Tumor1


title: Donor3_Tumor2


title: 16N2KOVNSLPS

description: Library name: Sample 16


title: EZH2, AM, 106, REP1

description: Library name: EZH2_106_R1, ChIP

value: Retina


title: MUC20719_vehicle

description: Library name: MUC20719

value: vehicle


title: 14N2WTVNSLPS

description: Library name: Sample 14


title: MUC20718_GLPG3973

description: Library name: MUC20718


title: DM1_DM2_AO_ALVO

city: Utrecht

first: Gijs

middle: Jacob Fransiscus

last: van Son

address: Heidelberglaan 25

country: Netherlands

institute: Prinses maxima centrum

description: Library name: TX935_to_938

data_processing:
Cellranger
Assembly: Custom
Supplementary files format and content: conversion of gene numbers to gene symbols
Supplementary files format and content: conversion of gene numbers to gene mouse symbols
Supplementary files format and content: conversion of gene numbers to gene human symbols
Supplementary files format and content: Annotated seurat object

organism: Python regius

source_name: Airway

extract_protocol: 10X 3' OCM gene expression library preparation

value: Airway

value: Various

value: WT


title: SP_12_ON_DOX

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: Library name: SP_12_ON_DOX

data_processing:
Reads were aligned to the mouse genome (GRCm38) using STAR aligner with default parameters. Featurecounts was used to produce gene count for entrez gene information
Assembly: GRCm38
Supplementary files format and content: Gene expression counts for genes with Entrez IDs across samples

source_name: spleen

extract_protocol:
Total RNA was extracted from the splenic leukemia cells in BM transplanted mice using Trizol reagent (Invitrogen, 15596026), according to the manufacturer’s protocol.
Whole RNA was treated with DNaseI for 30 min; and 500 ng RNA was used to prepare 3’mRNA-Seq libraries with the QuantSeq 3’mRNA-Seq V2 Library Prep Kit FWD with UDI (UDI12A_0001-0096; Lexogen) for Illumina according to manufacturer protocol

value: spleen

value: Dox


title: 13N2WTVNSLPS

description: Library name: Sample 13


title: Tis_airway

description: Library name: Tis_airway

data_processing:
Mapping using STAR
assigning readcounts using featurecounts
https://github.com/Hubrecht-Clevers/Python_regius_project
Assembly: Custom
Supplementary files format and content: count table in csv format

extract_protocol:
Rneasy kit
Truseq RNA polyA library prep


title: SP_11_ON_DOX

description: Library name: SP_11_ON_DOX


title: MUC20717_vehicle

description: Library name: MUC20717


title: 12N2KOShamLPS

description: Library name: Sample 12

value: LPS


title: MUC20716_GLPG3972

description: Library name: MUC20716


title: SP_10_ON_DOX

description: Library name: SP_10_ON_DOX


title: 11N2KOShamLPS

description: Library name: Sample 11

value: Kidney


title: Org_NI2

description: Library name: Org_NI2


title: SP_6_NO_DOX

description: Library name: SP_6_NO_DOX

value: no


title: Org_BP2

description: Library name: Org_BP2


title: 10N2KOShamLPS

description: Library name: Sample 10

value: Cx3cr1-Cre; Notch2flox/flox


title: SP_5_NO_DOX

description: Library name: SP_5_NO_DOX


title: MUC20715_vehicle

description: Library name: MUC20715


title: Org_NI1

description: Library name: Org_NI1


title: 9N2WTShamLPS

description: Library name: Sample 9


title: MUC20714_GLPG3971

description: Library name: MUC20714


title: Org_BP1

description: Library name: Org_BP1


title: MUC20713_vehicle

description: Library name: MUC20713


title: SP_4_NO_DOX

description: Library name: SP_4_NO_DOX


title: 7N2WTShamLPS

description: Library name: Sample 7


title: 8N2WTShamLPS

description: Library name: Sample 8


title: MUC20712_GLPG3970

description: Library name: MUC20712


title: 6N2WTVNSSaline

description: Library name: Sample 6

value: VNS + Saline


title: 4N2WTVNSSaline

description: Library name: Sample 4


title: MUC20711_vehicle

description: Library name: MUC20711


title: 5N2WTVNSSaline

description: Library name: Sample 5


title: SSV1-infected Saccharolobus solfataricus S441 middle post-UV-induction; control

city: Brussels

first: Wouter

last: Magnus

address: Pleinlaan 2

country: Belgium

institute: Vrije Universiteit Brussel

description:
Library name: PROM14_BC4
TSS_enr_ratios_SSV1-v2_middle.plus.csv
TSS_enr_ratios_SSV1-v2_middle.minus.csv
TTS_eff_ratios_SSV1-v2_middle.plus.drop.coverage
TTS_eff_ratios_SSV1-v2_middle.minus.drop.coverage

library_source: other

data_processing:
Real time basecalling and demultiplexing by the Guppy software (v3.2.10) in high accuracy mode.
read processing, mapping and identification of the viral transcription start sites (TSS) and termination sites (TTS) was performed according to the ONT-cappable-seq v2.0.0 automated data-analysis workflow (https://github.com/LoGT-KULeuven/ONT-cappable-seq/releases/tag/v2.0.0)
Assembly: SSV1 (NC_001338.1)
Supplementary files format and content: .csv files contain information on the location of transcription start sites of SSV1
Supplementary files format and content: .drop.coverage files contain information on the efficiency of transcription termination sites of SSV1

molecule: other

organism:
Saccharolobus solfataricus
Sulfolobus spindle-shaped virus 1

source_name: archaeal cells infected with virus

growth_protocol: SSV1-infected Saccharolobus solfataricus S441 was cultivated in liquid DT medium to OD600 of 0.5 (mid-exponential phase). For studying carrier state infection, culture samples were taken, while for studying infection post-UV-induction, which 20 mL aliquots were transferred to 95 mm diameter Petri dishes for UV-irradiation, after which samples were collected at 1, 2, 3, 4, 5, 6, 7, 8.5 and 12 hours post-UV-induction.

extract_protocol:
For every post-UV-induction RNA sample, RNA was extracted using hot phenol treatment and ethanol precipitation to extract and purify the RNA.
Total RNA was enriched for primary transcripts using the ONT-cappable-seq enrichment protocol. In parallel, control samples were subjected to similar environmental conditions. The RNA was reverse transcribed, PCR amplified and barcoded accoriding to Oxford Nanopore Technology cDNA-PCR protocol (SQK-PCB109)

treatment_protocol: Total RNA was extracted using hot-phenol extraction, followed by DNAse treatment. The enriched samples were subjected to an enrichment procedure based on streptavidin beads to enrich for primary transcripts. For the control samples the enrichment steps were omitted.

value: archaeal cells infected with virus

value: no enrichment

tag: infection stage

value: middle time points (6, 7 hours) post-UV-induction


title: SSV1-infected Saccharolobus solfataricus S441 middle post-UV-induction; enriched

description:
Library name: PROM14_BC3
TSS_enr_ratios_SSV1-v2_middle.plus.csv
TSS_enr_ratios_SSV1-v2_middle.minus.csv
TTS_eff_ratios_SSV1-v2_middle.plus.drop.coverage
TTS_eff_ratios_SSV1-v2_middle.minus.drop.coverage

value: enriched for primary transcripts


title: SSV1-infected Saccharolobus solfataricus S441 late post-UV-induction; enriched

description:
Library name: PROM14_BC5
TSS_enr_ratios_SSV1-v2_late.plus.csv
TSS_enr_ratios_SSV1-v2_late.minus.csv
TTS_eff_ratios_SSV1-v2_late.plus.drop.coverage
TTS_eff_ratios_SSV1-v2_late.minus.drop.coverage

value: late time points (8.5, 12 hours) post-UV-induction


title: SSV1-infected Saccharolobus solfataricus S441 late post-UV-induction; control

description:
Library name: PROM14_BC6
TSS_enr_ratios_SSV1-v2_late.plus.csv
TSS_enr_ratios_SSV1-v2_late.minus.csv
TTS_eff_ratios_SSV1-v2_late.plus.drop.coverage
TTS_eff_ratios_SSV1-v2_late.minus.drop.coverage


title: SSV1-infected Saccharolobus solfataricus S441 early post-UV-induction; control

description:
Library name: PROM14_BC2
TSS_enr_ratios_SSV1-v2_early.minus.csv
TTS_eff_ratios_SSV1-v2_early.plus.drop.coverage
TTS_eff_ratios_SSV1-v2_early.minus.drop.coverage

value: early time points (1-5 hours) post-UV-induction


title: SSV1-infected Saccharolobus solfataricus S441 early post-UV-induction; enriched

description:
Library name: PROM14_BC1
TSS_enr_ratios_SSV1-v2_early.minus.csv
TTS_eff_ratios_SSV1-v2_early.plus.drop.coverage
TTS_eff_ratios_SSV1-v2_early.minus.drop.coverage