title: s35, BMDM, AhR-KO, unstimulated


title: s32, BMDM, AhR-KO, LPS

status: Public on Feb 09 2023

type: SRA

city: Neuherberg

first: Caspar

last: Ohnmacht

address: Ingolstaedter Landstrasse 1

department: Center of Allergy and Environment

country: Germany

institute: Helmholtz Center Munich

library_source: transcriptomic

data_processing:
[basecalling]  Basecalls were done with Illumina bcl2fastq version 2.20.0.
[mapping]  Reads were aligned to the mouse reference genome mm10 using the aligner gsnap (v2020-12-16) with Ensembl 98 human splice sites as support (parameter: --gunzip -A sam -t 11 --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000 -B 5 -n 1 -m 0.6 -s EnsemblGene-92.ss.hg38.iit -N 0 --action-if-cigar-error noprint).
[counts per feature]  Uniquely mapped reads were compared based on their overlap to Ensembl 98 mouse gene annotations using featureCounts (v2.0.1) to create a table of fragments per mouse gene and sample (parameter: featureCounts -a EnsemblGene-98.mm10.TR.gtf -s 2 -p -o bfx1781.mm10.e98.txt -Q 1 -T 8).
Assembly: mm10
Supplementary files format and content: bfx1781.mm10.e98.txt.gz is a tab-separated file with the output from featureCounts. Each row represents a gene and the columns contain the gene information followed by the sample counts.

molecule: polyA RNA

organism: Mus musculus

source_name: BMDM

growth_protocol: AhR-KO and wildtype bone marrow was cultured in RPMI supplemented with 10 ng/ml GM-CSF, 2 ng/ml TGF-ß, 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using Rneasy plus mini kit (Qiagen).
mRNA enrichment,  reverse-transcription into cDNA and library preparation was done with the NEBNext Ultra II Directional RNA Lib Prep Kit for Illumina (NEB) following manufacturer's protocol.

treatment_protocol: On the 6th day of differentiation cells where stimulated with 97 EU/ml LPS. After 24 h of stimulation 5 µM Ca2+-ionophore A23187 was added for 10 min to ensure full release of lipid mediators.

tag: cell type

value: BMDM

tag: genotype

value: AhR-KO

tag: treatment

value: LPS


title: III_G4_S76

city: Wurzburg

first: Regan

last: Hayward

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

library_source: transcriptomic single cell

data_processing:
Read trimming and quality control of MATQ-seq reads was executed using BBDuk. To efficiently remove primer and  adapter sequences located at both ends of a read, we ran BBDuk in a two-pass procedure using the default adapter sequence database augmented with MATQ-seq specific sequences. The first pass focused on the 5’ end, with parameters: minlen=18 qtrim=rl trimq=20 ktrim=l k=17 mink=11 hdist=1 trimpolya=30; while the second pass focused on the 3’ end with parameters: minlen=18 qtrim=rl trimq=20 ktrim=r k=17 mink=11 hdist=1.
Read alignment and counting was performed with Bowtie2 (Langmead & Salzberg 2012) and featureCounts (Liao et al. 2014), allowing a single mismatch and run-in --local mode. BigWig files were generated using deepTools (Ramírez et al. 2014), passing additional parameters: --binSize 5 --normalizeUsing BPM. We have employed the same gene detection method from the original MATQ-seq analyses (Imdahl et al. 2020), requiring a detected gene to have > 5 reads.
DESeq2 (Love et al. 2014) was used for normalization and differential expression analysis, using size factors calculated by the computeSumFactors function in Scran (Lun et al. 2016) and other recommended parameters for DESeq2 single cell analysis, which included using the likelihood ratio test (LRT), useT=TRUE, minmu=1e-6, and minReplicatesForReplace=Inf.
Assembly: NC_016810.1
Supplementary files format and content: Unprocessed count matrix from all samples
Supplementary files format and content: sc_counts.tsv

molecule: total RNA

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: bacterial cell

extract_protocol:
Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer’s recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer’s recommendation using 100ng total RNA as input per sample.
cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer’s recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio

value: bacterial cell

tag: media

value: Lennox broth media

tag: od

tag: condition

value: MEP


title: MCF7_FLAG_cMYCMAX_0250nM_HisMYC_0000nM_CUTaRUN_b

city: NIJMEGEN

first: Hannah

last: Neikes

state: Gelderland

address: Geert Grooteplein Zuid 28

country: Netherlands

institute: Radboud University

library_source: genomic

data_processing:
Sequence data processing was performed automatically with automated processing pipeline seq2science, v 0.7.2
Read alignment to target and spike-in genome with bwa-mem2 v2.1, options -M
Filtering out MAPQ <30, multimapper and map to the ENCODE blacklist
Duplicates removed with PICARD v2.23.8
Peak calling with macs2 v2.2.7, options --keep-dup 1 --buffer-size 10000 --call-summits -BAMPE
Total read counts per sample determined with samtools v1.9
Read normalisation in R v4.0.3 to reads per million spike-in reads and to highest signal per binding site and experiment. Fit signal-over-concentration to hill equation at bound sites to determine genome-wide binding affinities (apparent Kds).
Assembly: hg38, S.cerevisiae-74-D694-2.0
Library strategy: CUT&RUN

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Isolated nuclei of MCF-7, R1 mESC, NPC or F121 cells were incubated with a titration series of FLAG-tagged transcription factor of interest, which was followed up by either ChIP-seq or CUT&RUN with anti-FLAG antibody, including heterologous spike-in DNA (dm6 or S.cerevisiae for ChIP-seq or CUT&RUN-based follow-up, resp.). Released DNA fragments were column purified and used for preparation of sequencing libraries.
Libraries were prepared using the Kapa Hyper Prep Kit (Kapa Biosystems) according to manufacturer’s protocol, with the following modifications. All input material was used to prepare libraries and 2.5 μl of the NEXTflex adapter stock (600nM, Bioo Scientific) was used for adapter ligation of each sample. Libraries were amplified with 12 PCR cycles and a double post-amplification clean-up was used to ensure proper removal of adapters.
Samples were analyzed for purity using a High Sensitivity DNA Chip on a Bioanalyzer 2100 system (Agilent). Libraries were paired-end sequenced on a Illumina NextSeq500.

tag: banc-seq follow up method

value: CUT&RUN

tag: spike in genome


title: III_F6_S66


title: s30, BMDM, WT, LPS

value: WT


title: MCF7_FLAG_cMYCMAX_0100nM_HisMYC_0000nM_CUTaRUN_b


title: SUM149 Cells Treated by Ricolinostat for 24 hours Replicate 2

type: RNA

city: Memphis

first: Qingfei

last: Pan

state: TN

address: 262 Danny Thomas Place

department: Department of Computational Biology

country: USA

institute: St. Jude Children's Research Hospital

description: SurePrint G3 Human Gene Expression v3 8x60K Microarray Kit

hyb_protocol: Labeled cRNA was hybridized using Gene Expression Hybridization Kit.

scan_protocol: Scanned on an Agilent G2600D scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1.1.1).

data_processing: The data normalization was performed by limma R package (v-3.42.2) with LOESS method within array and QUANTILE between arrays.

source_name: breast cancer cell line: SUM149PT

label_protocol: Sample labeling and array hybridization were performed according to the Two-Color Microarray-Based Gene Expression Analysis—Low Input Quick Amp Labeling—protocol (Agilent Technologies).

extract_protocol: Total RNA of three sensitive cell lines (MDA-MB-453, SK-BR-3 and SUM-149) and mouse model (MMTV- Neu) was extracted using the RNAeasy Kit (Qiagen). The samples with the optical density 260/280 ratio greater than 1.8 and the total RNA yield greater than 1 μg were considered qualified.

tag: agent

value: Ricolinostat

tag: time point

value: 24 hours

tag: replicate

tag: subtype

value: Basal B

tag: response

value: Sensitive

source_name: Universal Human Reference RNA

tag: catalog#


title: s29, BMDM, WT, LPS


title: III_F5_S65


title: s33, BMDM, WT, unstimulated

value: unstimulated


title: s28, BMDM, AhR-KO, unstimulated


title: SUM149 Cells Treated by Ricolinostat for 24 hours Replicate 1


title: s27, BMDM, AhR-KO, unstimulated


title: III_F4_S64


title: s26, BMDM, WT, unstimulated


title: III_E6_S54


title: MCF7_FLAG_cMYCMAX_0010nM_HisMYC_0000nM_CUTaRUN_b


title: MCF7_FLAG_cMYCMAX_0001nM_HisMYC_0000nM_CUTaRUN_b


title: MCF7_FLAG_cMYCMAX_0000nM_HisMYC_0000nM_CUTaRUN_b


title: SUM149 Cells Treated by Ricolinostat for 12 hours Replicate 1

value: 12 hours


title: III_E5_S53


title: MCF7_FLAG_cMYCMAX_1000nM_HisMYC_1000nM_CUTaRUN_a


title: s25, BMDM, WT, unstimulated


title: III_E4_S52


title: s24, BMDM, AhR-KO, LPS


title: MCF7_FLAG_cMYCMAX_0500nM_HisMYC_1000nM_CUTaRUN_a


title: SUM149 Cells Treated by Ricolinostat for 6 hours Replicate 2

value: 6 hours


title: s23, BMDM, AhR-KO, LPS


title: SUM149 Cells Treated by Ricolinostat for 6 hours Replicate 1


title: III_D6_S42


title: SUM149 Cells Treated by Vehicle Replicate 2

value: Vehicle


title: III_D5_S41


title: SUM149 Cells Treated by Vehicle Replicate 1


title: SUM149 Cells Treated by Ricolinostat for 12 hours Replicate 2


title: s22, BMDM, WT, LPS


title: MCF7_FLAG_cMYCMAX_0010nM_HisMYC_1000nM_CUTaRUN_a


title: III_D4_S40


title: SKBR3 Cells Treated by Ricolinostat for 24 hours Replicate 2

source_name: breast cancer cell line: SK-BR-3

value: Luminal


title: MCF7_FLAG_cMYCMAX_0000nM_HisMYC_1000nM_CUTaRUN_a


title: s20, BMDM, AhR-KO, unstimulated

value: BMDM


title: III_C6_S30


title: s21, BMDM, WT, LPS


title: III_C5_S29


title: SKBR3 Cells Treated by Ricolinostat for 12 hours Replicate 2


title: s19, BMDM, AhR-KO, unstimulated

value: AhR-KO


title: III_C4_S28


title: MCF7_FLAG_cMYCMAX_0100nM_HisMYC_1000nM_CUTaRUN_a


title: s17, BMDM, WT, unstimulated


title: MCF7_FLAG_cMYCMAX_0010nM_HisMYC_0000nM_CUTaRUN_a


title: MCF7_FLAG_cMYCMAX_0100nM_HisMYC_0000nM_CUTaRUN_a


title: MCF7_FLAG_cMYCMAX_0500nM_HisMYC_0000nM_CUTaRUN_a


title: III_B6_S18


title: III_B5_S17


title: s18, BMDM, WT, unstimulated


title: MCF7_FLAG_cMYCMAX_1000nM_HisMYC_0000nM_CUTaRUN_a


title: III_B4_S16


title: s19, BMDM, AhR-KO, unstimulated (ATAC-seq)

data_processing:
[basecalling]  Basecalls were done with Illumina bcl2fastq version 2.20.0.
The nf-core/atacseq pipeline (version v1.2.1; Patel et al., 2020; 10.5281/zenodo.3965985) was used to perform the primary analysis of the samples. The command used was "nextflow run nf-core/atacseq --input samples.csv --genome mm10 --outdir results -with-singularity atacseq_latest.sif -r 1.2.1". All data was processed relative to the mouse genome mm10. Gene annotation files in GTF format were downloaded from Ensembl (v98). For a condensed overview of the pipeline, the bioinformatics tools used in each step and an extensive list of citations please see the pipeline homepage (https://github.com/nf-core/atacseq).
Assembly: mm10
Supplementary files format and content: bfx1782.consensus_peaks.mLb.clN.featureCounts.txt.gz: Tab-separated file with the output from featureCounts. Each row represents a consensus peak (produced by combining the individual sample peaks) and the columns contain the consensus peak information followed by the sample counts.
Supplementary files format and content: bigWig files: Normalised bigWig files scaled to 1 million mapped reads.
Supplementary files format and content: narrowPeak files: Peak calling files produced by MACS2. BED format with the following columns: chromosome, start, end, name, score, strand, signalValue, pValue, qValue and peak.

extract_protocol:
RNA was harvested using Rneasy plus mini kit (Qiagen).
Tagmentation of genomic DNA and library preparation was done with the Nextera DNA Library Preparation Kit (Illumina).


title: SKBR3 Cells Treated by Ricolinostat for 6 hours Replicate 2


title: GUCY2C Medium Intestinal cell transcriptome [GCC_Lo15]

city: Philadelphia

first: Scott

last: Waldman

state: PA

address: 1020 Locust St

department: Pharmacology and Experimental Therapeutics

institute: Thomas Jefferson University

data_processing:
For analysis, only genes with counts per million (cpm) >0.5 in at least 3 of the samples were included (15,689 genes)
Limma (v3.40.6) and edgeR (v3.26.8) packages were used to determine differential gene expression (adj P value <0.01).
Assembly: mm9
Supplementary files format and content: csv files with differentially expressed genes ranked by upregulation in either GUCY2C-GFP High, or GUCY2C-GFP Medium groups

source_name: GUCY2C-GFP CD1

extract_protocol:
mRNA was extracted using Qiagen RNeasy Micro Plus kit
Libraries were prepared using NEBNext Ultra™ II RNA Library Prep Kit (New England Biosciences (NEB), Ipswich, MA, E7760)
STAR software was then used to align and map clean reads to the mouse reference genome (mm9)

treatment_protocol: 5, 10-week-old litter-matched Gucy2c-GFP mice that were FACS sorted into GUCY2CHigh and GUCY2CMed groups at 20,000 cells per group.

tag: tissue

value: Small Intestinal

tag: sequencing

value: transcriptome

tag: mouse strain

value: GUCY2C-GFP Medium cells


title: GUCY2C Medium Intestinal cell transcriptome [GCC_Lo14]

tag: cell type


title: SKBR3 Cells Treated by Ricolinostat for 12 hours Replicate 1


title: SKBR3 Cells Treated by Ricolinostat for 24 hours Replicate 1


title: SKBR3 Cells Treated by Ricolinostat for 6 hours Replicate 1


title: SKBR3 Cells Treated by Vehicle Replicate 2


title: MDAMB453 Cells Treated by Ricolinostat for 24 hours Replicate 2

source_name: breast cancer cell line: MDA-MB-453


title: MCF_7_FLAG_YY1_FLAG_cMYCMAX_ChIP_0000_nM

description:
MCF_7_FLAG_YY1_ChIP_relEnr_Kds_noOutliers.txt
MCF_7_FLAG_cMYCMAX_ChIP_relEnr_Kds_noOutliers.txt

data_processing:
Sequence data processing was performed automatically with automated processing pipeline seq2science, v 0.5.4.
Read alignment to target and spike-in genome with bwa-mem2 v2.1, options -M
Filtering out MAPQ <30, multimapper and map to the ENCODE blacklist
Duplicates removed with PICARD v2.23.8
Peak calling with macs2 v2.2.7, options --keep-dup 1 --buffer-size 10000 --call-summits -BAMPE
Total read counts per sample determined with samtools v1.9
Read normalisation in R v4.0.3 to reads per million spike-in reads and to highest signal per binding site and experiment. Fit signal-over-concentration to hill equation at bound sites to determine genome-wide binding affinities (apparent Kds).
Genome_build: mm10, hg38, CAST/EiJ, 129S1/SvImJ, dm6, E.coli_C142, S.cerevisiae-74-D694-2.0
Supplementary_files_format_and_content: Tab delimited .txt file containing relative signal per concentration as well as KdApps and additional values

extract_protocol:
Isolated nuclei of MCF-7 or F121 cells were incubated with a titration series of FLAG-tagged transcription factor of interest, which was followed up by either ChIP-seq or CUT&RUN with anti-FLAG antibody, including heterologous spike-in DNA (dm6 or S.cerevisiae for ChIP-seq or CUT&RUN-based follow-up, resp.). Released DNA fragments were column purified and used for preparation of sequencing libraries.
Libraries were prepared using the Kapa Hyper Prep Kit (Kapa Biosystems) according to manufacturer’s protocol, with the following modifications. All input material was used to prepare libraries and 2.5 μl of the NEXTflex adapter stock (600nM, Bioo Scientific) was used for adapter ligation of each sample. Libraries were amplified with 12 PCR cycles and a double post-amplification clean-up was used to ensure proper removal of adapters.
Samples were analyzed for purity using a High Sensitivity DNA Chip on a Bioanalyzer 2100 system (Agilent). Libraries were paired-end sequenced on a Illumina NextSeq500.

tag: strain

value: ChIP-seq


title: MDAMB453 Cells Treated by Ricolinostat for 24 hours Replicate 1


title: SKBR3 Cells Treated by Vehicle Replicate 1


title: GUCY2C Medium Intestinal cell transcriptome [GCC_Lo12]


title: III_A5_S5

value: bacterial cell

value: Lennox broth media

value: MEP


title: III_A6_S6


title: MCF_7_FLAG_YY1_CUTaRUN_1000nM_YY1

description: MCF_7_FLAG_YY1_CUTaRUN_relEnr_Kds_noOutliers.txt

value: WT

value: CUT&RUN


title: MCF_7_FLAG_YY1_CUTaRUN_0100nM_YY1


title: II_H9_S381


title: MCF7_FLAG_cMYCMAX_0000nM_HisMYC_0000nM_CUTaRUN_a


title: II_H8_S380


title: GUCY2C Medium Intestinal cell transcriptome [GCC_Lo7]


title: GUCY2C Medium Intestinal cell transcriptome [GCC_Lo2]


title: GUCY2C High Intetinal cell transcriptome [GCC_Hi15]

value: GUCY2C-GFP High cells


title: MCF_7_FLAG_YY1_CUTaRUN_0010nM_YY1


title: MCF_7_FLAG_YY1_CUTaRUN_0001nM_YY1


title: MDAMB453 Cells Treated by Ricolinostat for 12 hours Replicate 2

value: Ricolinostat

value: Sensitive


title: GUCY2C High Intetinal cell transcriptome [GCC_Hi12]


title: MCF_7_FLAG_YY1_ChIP_1000nM

description: MCF_7_FLAG_YY1_ChIP_relEnr_Kds_noOutliers.txt


title: II_G9_S369


title: II_H7_S379


title: IV_A2_S98


title: II_G8_S368


title: MCF_7_FLAG_YY1_ChIP_0100nM


title: MDAMB453 Cells Treated by Ricolinostat for 12 hours Replicate 1

value: 12 hours


title: MDAMB453 Cells Treated by Ricolinostat for 6 hours Replicate 1

value: 6 hours


title: MDAMB453 Cells Treated by Vehicle Replicate 1

value: Vehicle

value: Luminal


title: MCF_7_FLAG_YY1_CUTaRUN_0000nM_YY1


title: GUCY2C High Intetinal cell transcriptome [GCC_Hi2]


title: MDAMB453 Cells Treated by Vehicle Replicate 2


title: MCF_7_FLAG_YY1_ChIP_0010nM


title: II_G7_S367


title: MDAMB453 Cells Treated by Ricolinostat for 6 hours Replicate 2


title: Clear-cell Renal cell carcinoma, patient 4, frozen

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

description: 10x Genomics

data_processing:
Pre-processing, quality controls, integration and normalization. Demultiplexed raw sequencing reads were processed, mapped to the GRCh38 human reference genome and quantified based on unique molecular identifiers (UMIs) with the Cell Ranger pipeline (v3.0.2, 10x Genomics). The resulting raw count matrices from the 7 individual samples were then merged (from RCC1-5 patients). The cell-calling algorithm from Cell Ranger, which relies on the EmptyDrops method, was also used to establish a first set of potential valid cells. Subsequently, the scater R package. (v1.10.1) was used to remove outlier cells by using several cell features including the proportions of reads mapping to mitochondrial and ribosomal genes. In parallel, doublets were filtered out independently in each individual matrix by using the DoubletFinder R package (v.2.0.2). Next, raw count matrix files from the scRNA-seq dataset published by Young and colleagues were downloaded from their online supplementary data (RCC6-8). Cells with fewer than 200 detected genes and genes detected in fewer than 10 cells were removed. Cells from both datasets were assigned a cell cycle phase by using both the Scran R package (v1.10.2) and the Seurat v3.1.5 package. Each dataset was individually normalized using the NormalizeData function implemented in Seurat. The two datasets were merged and batch-effect corrected using the CCA method implemented in the Seurat package to regress out technical covariates between datasets. This procedure is based on the FindIntegrationAnchors and IntegrateData functions with the following parameters: anchor.features=3000 and dims=30.
Reduction of dimensionality and clustering: The 3000 integration anchors identified by the FindIntegrationAnchors function were used to perform a principal component analysis with the RunPCA function implemented in Seurat. Cells were then clustered by using the FindNeighbors and FindClusters functions on the top-30 principal components, with default parameters. Finally, we used the uniform manifold approximation and projection (UMAP) method implemented in Seurat to project single cells in a reduced 2D space.
Cluster annotation and differential gene expression analysis: Cell clusters were annotated using a set of known marker genes complemented with genes that were significantly differentially expressed between cell clusters. Differentially expressed genes were identified with the FindAllMarkers function implemented in Seurat, with default parameters.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: ccRCC

extract_protocol:
Fresh tumor samples, ranging from pT1a to pT3b and ISUP 2 to 4, were collected from a total of five untreated patients who underwent either radical or partial nephrectomy for ccRCC at the urology department of the Rennes university-hospital center. For each tumor, ~2-9 punches were pooled and dissociated. Briefly, samples were first subjected to enzymatic and mechanical disaggregation (tumor dissociation kit, Miltenyi Biotec) before undergoing red blood cell lysis and low-speed centrifugation steps to remove debris and dead cells while maintaining tumor cells. Partial depletion of CD45 (an immune cell marker) positive cells was performed using the Miltenyi kit (CD45 MicroBeads, human) to enrich the samples in malignant/stromal cells and remove circulating and tumor-infiltrating immune cells.
Construction of single-cell libraries (Chromium™ Single Cell 3’ Library & Gel Bead Kit v2) was carried out according to the manufacturer’s instructions (10x Genomics). Single-cell libraries were quality-controlled using the Agilent 2100 Bioanalyzer system and sequenced on an Illumina HiSeq 4000 instrument using a 2x100 paired-end sequencing protocol (Illumina, San Diego, CA).

value: ccRCC

tag: developmental stage

value: Adult

tag: age

tag: Sex

value: Female

tag: ptnm stage

tag: isup grade

tag: vhl status

value: deleted

tag: nephrectomy

value: radical


title: Clear-cell Renal cell carcinoma, patient 5

description: 10x Genomics


title: Cerebellum, mouse 3, replicate 2

city: München

first: Johannes

last: Wirth

address: Trogerstrasse 18

department: Institute of Pathology

institute: Technical University Munich

data_processing:
ReadsToCounts pipeline: This script takes two FASTQ files (Read 1 and Read 2) and barcode-coordinate information as input and processes them as follows: Read 1 sequences are trimmed and filtered using cutadapt v3.7 (Martin, 2011) and mapped against the mm10 (GRCm38.p6) mouse genome using STAR-2.7.4a (Dobin et al., 2013). Unique molecular identifiers (UMIs) and spatial barcodes are extracted from Read 2 using the Drop-seq tool TagBamWithReadSequenceExtended and a custom Python 3 pipeline assigns coordinates using barcode information provided in a CSV file. The DigitalExpression function is used to collaps the UMIs and generate a spot-count matrix. RNA metrics are calculated using CollectRnaSeqMetrics.
CountsToAnndata pipeline: In this stage the spot-count matrix and imaging data are aligned and integrated. In brief, the positions of the alignment marker vertices are extracted semi-automatically from the alignment images using napari (Sofroniew et al., 2022) and Squidpy (Palla et al., 2022). The coordinates of the vertices are used to register alignment image and xDbit spots by performing an affine transformation using OpenCV (Bradski, 2000). In order to align the high-resolution images of the first imaging round with the xDbit spots, the SIFT algorithm (Lowe, 2004) is used to extract common features between the alignment DAPI image and the high-resolution DAPI image. Based on the coordinates of these features an affine transformation matrix is determined which is used to align the xDbit spots to the high-resolution image. The dataset is saved in the AnnData format (Virshup et al., 2021). In this study we included intronic reads (Supp. Fig. 2 C) into the analysis.
Assembly: mm10 (GRCm38.p6)
Supplementary files format and content: gzipped tar archive containing gene expression matrix in txt.gz format and metadata file from ReadsToCounts pipeline
Supplementary files format and content: h5ad file containing anndata object with xDbit spatial transcriptomic data and aligned images
Library strategy: xDbit

source_name: Cerebellum

extract_protocol:
The amplified cDNA was purified using SPRIselectTM beads (Beckman Coulter) following a left sided size selection with a bead-to-sample ratio of 0.8X. In brief, 160 µL of sample were mixed with 128 µL of resuspended SPRIselect beads and incubated for 5 min at rt. Beads were washed two times in 85% ethanol and air-dried for 3 min. The cDNA was eluted in 20 µL ultrapure water by incubation at 37 °C for 10 min. The supernatants were transferred to a fresh tube resulting in 9 tubes of purified cDNA. The quality of the cDNA was analyzed using the Bioanalyzer High Sensitivity DNA chip (Agilent) and samples were stored at -20 °C.
The concentration of the cDNA was determined using a Qubit 1X dsDNA assay (Invitrogen) and the sequencing library was generated using the Nextera XT DNA Library Preparation Kit (Illumina). The quality of the library was assessed using the Bioanalyzer High Sensitivity DNA chip (Agilent). Samples were sequenced on a NovaSeq 6000 system (Illumina) at a sequencing depth of minimum 50,000 reads per spot using a 100 cycles kit in paired-end mode. Following read length configurations were used: R1: 7 cycles, i7: 6 cycles, R2: 58 cycles.

value: Cerebellum

value: 4 months

value: male

tag: genotype

value: wild-type


title: MCF_7_FLAG_YY1_ChIP_0001nM

value: WT

tag: banc-seq follow up method

value: ChIP-seq

tag: spike in genome


title: II_F9_S357

value: bacterial cell

tag: media

value: Lennox broth media

tag: od

tag: condition

value: MEP


title: Clear-cell Renal cell carcinoma, patient 4

description: 10x Genomics

tag: tissue


title: Clear-cell Renal cell carcinoma, patient 3

description: 10x Genomics

value: Male


title: Thrombus, patient 5

description: 10x Genomics


title: Cerebellum, mouse 3, replicate 1


title: Kidney, mouse 2, replicate 2

source_name: Kidney

value: Kidney

value: 3 months


title: GUCY2C High Intetinal cell transcriptome [GCC_Hi7]

value: Small Intestinal

tag: sequencing

value: transcriptome

tag: mouse strain

value: GUCY2C-GFP High cells


title: II_F8_S356

tag: cell type


title: MCF_7_FLAG_SP1_CUTaRUN_0250nM

description: MCF_7_FLAG_SP1_CUTaRUN_relEnr_Kds_noOutliers.txt

tag: strain

value: CUT&RUN


title: Clear-cell Renal cell carcinoma, patient 2

description: 10x Genomics

value: ccRCC

tag: developmental stage

value: Adult

tag: age

value: deleted

value: radical


title: MCF_7_FLAG_SP1_CUTaRUN_0500nM


title: MCF_7_FLAG_SP1_CUTaRUN_0150nM


title: II_E9_S345


title: Kidney, mouse 2, replicate 1

tag: Sex

value: male

value: wild-type


title: Clear-cell Renal cell carcinoma, patient 1

description: 10x Genomics

tag: ptnm stage

tag: isup grade

value: partial


title: Liver, mouse 2, replicate 1

source_name: Liver

value: Liver


title: MCF_7_FLAG_SP1_CUTaRUN_0100nM

value: WT


title: II_E8_S344

value: bacterial cell

value: Lennox broth media

value: MEP


title: II_E7_S343


title: MCF_7_FLAG_SP1_CUTaRUN_0050nM


title: II_D9_S333


title: Heart, mouse 2, replicate 2

source_name: Heart

value: Heart

value: 3 months


title: Heart, mouse 2, replicate 1


title: MCF_7_FLAG_SP1_CUTaRUN_0025nM


title: MCF_7_FLAG_SP1_CUTaRUN_0005nM


title: Spleen, mouse 2, replicate 2

source_name: Spleen

value: Spleen


title: II_D8_S332


title: II_F7_S355


title: MCF_7_FLAG_FOXA1_CUTaRUN_0500nM

description: MCF_7_FLAG_FOXA1_CUTaRUN_relEnr_Kds_noOutliers.txt


title: II_D7_S331


title: Kidney, mouse 1, replicate 2

value: Kidney


title: II_C9_S321


title: MCF_7_FLAG_SP1_CUTaRUN_0000nM

value: CUT&RUN


title: MCF_7_FLAG_FOXA1_CUTaRUN_0250nM


title: Liver, mouse 1, replicate 1


title: Kidney, mouse 1, replicate 1


title: GUCY2C High Intetinal cell transcriptome [GCC_Hi14]

value: Small Intestinal

value: transcriptome

value: GUCY2C-GFP High cells


title: MCF_7_FLAG_FOXA1_CUTaRUN_0150nM


title: Heart, mouse 1, replicate 2


title: II_C7_S319


title: II_C8_S320


title: MCF_7_FLAG_FOXA1_CUTaRUN_0125nM


title: Spleen, mouse 2, replicate 1


title: II_B9_S309


title: Heart, mouse 1, replicate 1


title: II_B8_S308


title: MCF_7_FLAG_FOXA1_CUTaRUN_0050nM


title: II_B7_S307


title: Spleen, mouse 1, replicate 2


title: Spleen, mouse 1, replicate 1


title: MCF_7_FLAG_FOXA1_CUTaRUN_0025nM


title: II_A9_S297


title: MCF_7_FLAG_FOXA1_CUTaRUN_0005nM


title: BMDMB2-WT-Rep3

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

data_processing:
Reads were first trimmed for adapters using fastp (v0.20.0)(Chen et al., 2018),  then counted in two ways at gene exons either by pseudoalignment approach kallisto(v0.46.1, parameters “quant --fr-stranded  --plaintext --bias ”) or alignment to the mouse genome mm10(Gencode GRCm38) by STAR (version 2.7.1a, parameters: "--outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJstitchMismatchNmax 5 -1 5 5 --alignSJDBoverhangMin 10 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 100000 --outSAMmapqUnique 60 --outSAMmultNmax 1 --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM NM MD --outSAMunmapped Within --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --chimMultimapNmax 10 --chimMultimapScoreRange 10 --chimNonchimScoreDropMin 10 --chimOutJunctionFormat 1 --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic --peOverlapNbasesMin 12 --peOverlapMMp 0.1")(Dobin et al., 2013) and counted by HTSeq(v0.11.2)(Anders et al.) based on GENCODE mouse gene annotation (vM22) (Harrow et al., 2012).
STAR results were chosen for following analysis since they got more reads counts that all samples achieved 1.5M reads counts.
After normalization by trimmed mean of M-values normalization (edgeR v3.34.0) (Robinson and Oshlack, 2010), Voom (limma v3.48.3) (Law et al.) was used to identify differential expressed genes. Pathway enrichment analysis were then performed at Enrichr server (Kuleshov et al., 2016) on significant differential expressed genes.
Assembly: mm10
Supplementary files format and content: txt file of exon counts by gene using HTSeq

source_name: Bone marrow-derived macrophages(BMDM)

extract_protocol:
Total RNA was isolated using the PureLink™ RNA Mini Kit (Invitrogen, 12183025). RNA sequencing was performed by the University of Texas Genomic Sequencing and Analysis Facility. Poly(A) enrichement was performed.  mRNA was isolated from total RNA using the Poly(A) Purist-MAG kit (ThermoFisher). Briefly, total RNA was combined in a 96-well plate with washed and resuspended Oligo (dT) MagBeads. The mixture was heated in a thermocycler set to 70°C for 5 minutes, followed by incubation at room temperature with gentle vortexing for 30 minutes. Subsequently, the beads were captured and washed, and bound poly(A) RNA was eluted in water.  mRNA quality was assessed on the Agilent Bioanalyzer using the Agilent RNA 6000 Pico kit (Agilent).
Libraries were prepared at the University of Texas Genomic Sequencing and Analysis Facility according to manufacturer’s instructions for the NEBNext Ultra II Directional RNA kit (NEB, product number E7760). The resulting libraries tagged with unique dual indices were checked for size and quality using the Agilent High Sensitivity DNA Kit (Agilent). Library concentrations were measured using the KAPA SYBR Fast qPCR kit and loaded for sequencing on the NovaSeq 6000 instrument (paired end 2X150).

value: Wild Type

value: Bone marrow-derived macrophages(BMDM)


title: MCF_7_FLAG_FOXA1_CUTaRUN_0000nM


title: BMDMB2-WT-Rep2


title: II_A8_S296


title: III_A4_S4


title: BMDMB2-PP2A-KO-Rep3

value: PP2A KO


title: BMDMB2-WT-Rep1


title: MCF_7_FLAG_cMYCMAX_ChIP_0100nM

description: MCF_7_FLAG_cMYCMAX_ChIP_relEnr_Kds_noOutliers.txt

value: ChIP-seq


title: II_A7_S295


title: I_H11_S287


title: BMDMB2-PP2A-KO-Rep2


title: I_H10_S286


title: MCF_7_FLAG_cMYCMAX_ChIP_0010nM


title: I_G12_S276


title: MCF_7_FLAG_cMYCMAX_ChIP_0001nM


title: xzl.gga.xianju.testis.wt.adult.unox.rep5.small-RNA.R1

city: Yiwu

first: Jiafei

last: Shen

address: N1 Shangcheng Road

country: China

institute: International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine

data_processing:
Analyses were performed using piPipes v1.4. All data from the small RNA-seq, RNA sequencing, were analyzed using the latest mouse genome release galGal6 (GCA_000002315.5). Generally, one mismatch is allowed for genome mapping.
For RNA-seq reads, the expression per transcript was normalized to the top quartile of expressed transcripts per library calculated by Cuffdiff, and the tpm (transcripts per million) value was quantified using the Salmon software.
For small RNA-seq analysis, uniquely mapping reads excluding rRNA and miRNA  between 26 nt and 32 nt were selected for further analysis.
For ONT, the ONT Sequencing data collected in this experiment were obtained as fast5 files, and after conversion of electric signals into base calls via the guppy (Oxford Nanopore Technologies, UK), the reads with mean qScore greater or equal to 7 were kept to continue subsequent bioinformatic analysis. The filtered data were aligned with the chicken genome (galGal6) using NGMLR (v0.27). The SVs were detected using Sniffles (v1.0.8). We also independently used SVIM (v1.4.2 ) to call SVs with default settings.
Assembly: Gallus gallus: galGal6 (GCA_000002315.5)
Supplementary files format and content: For small RNA-seq, processed data files are unique genome alignment results in bigWig result format. RNAseq quantification results are .sf files output by Salmon software. For ONT, processed data files are performed a shuffling test in .txt format.

organism: Gallus gallus

source_name: testis

growth_protocol: Chickens were used according to guidelines for animal care of the NIH and the University Committee on Animal Resources at the University of Rochester.

extract_protocol:
Total RNAs were extracted using mirVana miRNA Isolation Kit (ThermoFisher, AM1560). Genomic DNA was size selected using the Pippin HT DNA Size Selection System (Sage Science, Beverly, MA, USA).
1, Strand-specific RNA-seq: libraries were constructed following the TruSeq RNA sample preparation protocol. rRNAs were depleted from total RNAs by Ribo-Zero Gold (Epicentre Biotechnologies, Madison, WI, USA).  2, Small RNA-seq: Testes samples were lysed and treated with sodium periodate for library constrution. The 3'-adapter is TGGAATTCTCGGGTGCCAAGG and has been trimmed in the raw data.
1, Strand-specific RNA-seq; 2, Small RNA-seq

value: whole testis

tag: breed

value: Xianju

value: adult

value: wildtype

tag: fraction

value: unoxidized small RNA


title: MCF_7_FLAG_cMYCMAX_ChIP_1000nM

value: WT

tag: banc-seq follow up method


title: MCF_7_FLAG_FOXA1_CUTaRUN_0100nM

tag: spike in genome


title: WT-M-Brain

data_processing:
Single-cell gene expression was obtained using kits from 10x Genomics (Single Cell 3' v3). Libraries were sequenced on the Illumina NovaSeq platform at 28bp by 90bp setting to obtain at least 35,000 reads per cell. Read processing, read alignment, cell-barcode demultiplexing, and gene-specific UMI counting was performed with CellRanger (v3.0.2)(Zheng et al., 2017) using the mouse references mm10(ensemble version r97, MH029771.1-sfGFP and GQ357182.1-eGFP CDS sequences were downloaded from Genbank and added to the references, see DOI:10.6084/m9.figshare.19342418 for details).
Distinct samples were processed independently and reviewed for quality that each sample achieved ~8000 cells, > 1200 expressed genes, > 90% reads in cells. All 4 samples were then aggregated by CellRanger for downstream analyses. Seurat (version 4.0.6)(Stuart et al., 2019) were then used for analysis based on filtered feature barcode matrices. Briefly, cells with < 200 expressed genes or genes expressed in < 3 cells were filtered out from analysis. SCTransform (Seurat function) were used to normalize the data using top 3000 variable genes and regressing out the effect of mitochondrial expression percentage and cell cycle scores(Tirosh et al., 2016).
We then performed Principal Component Analysis (PCA) on the scaled genes and selecting the top 10 PCs for following analysis because the standard deviation plateaued after top 10 PCs in ElbowPlot (Seurat function). tSNE and UMAP have been ran and clusters have been identified using default parameters from Seurat. Cd45+eGFP- cell/clusters (Clusters 6, 10-15, 17, 21-23 or Ptprc > 0, exclude eGFP > 0) were then selected for downstream analysis separately by tissues (Details command lines used, QC files, UMAP/tSNE projection and clustering meta data could be found at DOI:10.6084/m9.figshare.19342418).
barcode suffix "-1" to "-4" were WT-T-KO-M-Brain, WT-T-WT-M-SC, WT-T-WT-M-Brain, WT-T-KO-M-SC
Assembly: mm10
Supplementary files format and content: filtered 10x h5 file

source_name: tumor tissue inoculated SB28 tumors

extract_protocol:
Single cell suspensions were obtained using Tumor Dissociation Kit (Miltenyi™, 130-096-730) and the gentleMACS Octo Dissociator (Miltenyi™) per manufacture instruction.
Single cell suspensions were processed in the University of Texas Genomic Sequencing and Analysis Facility. Cell suspensions were loaded on the Chromium Controller (10X Genomics) and processed for cDNA library generation following the manufacturer’s instructions for the Chromium NextGEM Single Cell 3’ Reagent Kit v3.1 (10X Genomics).

tag: genotype/variation

tag: inoculated site

value: Brain


title: xzl.gga.xianju.testis.wt.adult.unox.rep4.small-RNA.R1

tag: genotype


title: xzl.gga.xianju.testis.wt.adult.unox.rep3.small-RNA.R1

tag: tissue


title: KO-M-SC

value: Flank


title: KO-M-Brain


title: I_H12_S288

value: bacterial cell

tag: media

value: Lennox broth media

tag: od

tag: condition

value: MEP


title: I_G11_S275

tag: cell type


title: I_F12_S264


title: WT-M-SC

tag: strain


title: I_G10_S274


title: I_F11_S263


title: xzl.gga.xianju.testis.wt.adult.unox.rep2.small-RNA.R1

tag: age


title: I_F10_S262


title: I_E12_S252


title: BMDMB2-PP2A-KO-Rep1


title: BALs, p20097-s100

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were aligned using STAR v2.7.3.(Dobin et al.)
The STAR index was built by combining genome sequences for Macaca mulatta (Mmul10 Ensembl release 100), SARS-CoV2 (strain MN985325.1 - NCBI) and ERCC sequences. The gffread utility (https://github.com/gpertea/gffread) was used to convert gff3 file for SARS-CoV2 and the resulting gtf file for SARS-CoV2 was edited to include exon entries which had the same coordinates as CDS to get counts with STAR. The combined genomic and gtf files were used for generating the STAR index.
Transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count(Sandler et al., 2014).
Assembly: Macaca mulatta Mmul10 Ensembl release 100
Assembly: SARS-CoV2 (strain MN985325.1 - NCBI)
Supplementary files format and content: tab delimited text file containing raw read counts for each sample (in columns) and each annotated transcript (in rows).

organism: Macaca mulatta

source_name: BAL

extract_protocol:
50,000 cells were lysed directly into 700 ul of QIAzol reagent.  RNA was isolated using RNeasy Mini or Micro kits (Qiagen) with on-column DNase digestion. RNA quality was assessed using an Agilent Bioanalyzer
total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using the NexteraXT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on an Agilent 4200 TapeStation, pooled at equimolar concentrations, and sequenced on an Illumina NovaSeq6000 at 100SR, yielding 20-25 million reads per sample.

treatment_protocol: RMs were infected with 1.1x106 plaque forming units (PFU) SARS-CoV-2 via both the intranasal (1 mL) and intratracheal (1 mL) routes concurrently. Four RMs were administered 4 mg Baricitinib starting at day 2 post-infection (DPI) for 8-9 consecutive days. Baricitinib was supplied as a powder that was folded into food items (i.e. honey, yogurt, etc.) or distilled water, which was delivered either orally or as a gavage when animals were being anesthetically accessed, respectively.

value: BAL

tag: animal id

tag: infection

tag: treatment

value: Baricitinib

tag: time


title: BALs, p20097-s101

value: Necropsy


title: xzl.gga.xianju.testis.wt.adult.ox.rep5.small-RNA.R1

tag: breed

tag: fraction

value: oxidized small RNA


title: xzl.gga.xianju.testis.wt.adult.unox.rep1.small-RNA.R1


title: I_E11_S251


title: BALs, p20097-s098


title: xzl.gga.xianju.testis.wt.adult.ox.rep4.small-RNA.R1


title: BALs, p20097-s097

value: prior to SARS-CoV-2 inoculation


title: xzl.gga.xianju.testis.wt.adult.ox.rep3.small-RNA.R1


title: I_D12_S240


title: BALs, p20097-s096

value: untreated


title: xzl.gga.xianju.testis.wt.adult.ox.rep1.small-RNA.R1

value: whole testis


title: I_D11_S239


title: I_C12_S228


title: I_D10_S238


title: xzl.gga.WhiteLeghorn.testis.wt.adult.unox.rep4.small-RNA

value: White Leghorn


title: BALs, p20097-s093


title: BALs, p20097-s094


title: I_C11_S227


title: xzl.gga.WhiteLeghorn.testis.wt.adult.ox.rep4.small-RNA

value: adult


title: BALs, p20097-s092


title: BALs, p20097-s099


title: I_E10_S250


title: xzl.gga.WhiteLeghorn.testis.wt.adult.unox.rep3.small-RNA

value: wildtype


title: I_C10_S226


title: I_B12_S216


title: BALs, p20097-s091


title: xzl.gga.WhiteLeghorn.testis.wt.adult.unox.rep2.small-RNA

value: unoxidized small RNA


title: BALs, p20097-s090


title: xzl.gga.WhiteLeghorn.testis.wt.adult.ox.rep3.small-RNA


title: xzl.gga.WhiteLeghorn.testis.wt.adult.ox.rep2.small-RNA


title: xzl.gga.wenchang.testis.wt.adult.unox.rep5.small-RNA.R1

value: Wenchang


title: BALs, p20097-s089


title: I_B11_S215


title: I_B10_S214


title: xzl.gga.wenchang.testis.wt.adult.unox.rep4.small-RNA.R1


title: xzl.gga.xianju.testis.wt.adult.ox.rep2.small-RNA.R1

value: Xianju


title: BALs, p20097-s095


title: xzl.gga.wenchang.testis.wt.adult.unox.rep3.small-RNA.R1


title: BALs, p20097-s087


title: BALs, p20097-s086


title: I_A11_S203


title: I_A10_S202


title: BALs, p20097-s085


title: xzl.gga.wenchang.testis.wt.adult.unox.rep2.small-RNA.R1


title: A_WTCtrl_3

city: London

first: Goran

last: Tomic

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
The RSEM package (version 1.3.0) in conjunction with the STAR alignment algorithm (version 2.5.2)  was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to Ensembl GRCm38-release-89 transcriptome
Differential expression analysis was performed with the DESeq2 package (version 1.10.1) within the R programming environment (version 3.3.2)
Assembly: GRCm38
Supplementary files format and content: Tab delimited text files containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.

source_name: Control cells (PDA530 Met, single cell clone, failed KO)

growth_protocol: Mouse metastatic pancreatic ductal adenocarcinoma PDA530 Met cell line, derived from a liver metastasis of a male KPC mouse (kindly provided by David Tuveson, Cold Spring Harbor Laboratory) was grown in Dulbecco’s Modified Eagle Medium (DMEM) with L-glutamine, 10% foetal bovine serum (FBS) and antibiotics (Penicillin/Streptomycin, 100 U/mL)

extract_protocol:
Total RNA was isolated using GenElute™ Mammalian Total RNA Miniprep Kit (Sigma-Aldrich) from approximately 5 million cells per biological sample of PDA530Met cells, control and KO clones (n=3). Sample quality of isolated RNA was assessed using 2100 Bioanalyzer (Agilent).
The libraries were prepared using KAPA mRNA HyperPrep kit (Roche).

treatment_protocol: No treatment. The cells were harvested under normal growth conditions.

value: Mixed 129/SvJae/C57Bl/6 background

value: PDAC cell line


title: xzl.gga.wenchang.testis.wt.adult.ox.rep5.small-RNA.R1


title: A_WTCtrl_2


title: xzl.gga.wenchang.testis.wt.adult.unox.rep1.small-RNA.R1


title: BALs, p20097-s088


title: A_WTCtrl_1


title: IV_H11_S191

source_name: bacterial cell

value: bacterial cell

value: Lennox broth media

value: EEP


title: IV_H12_S192


title: xzl.gga.wenchang.testis.wt.adult.ox.rep4.small-RNA.R1


title: IV_H10_S190


title: A_WT_3

source_name: Parental cells (PDA530 Met)


title: A_WT_2


title: BALs, p20097-s083

value: BAL


title: A_WT_1


title: BALs, p20097-s084


title: IV_G12_S180


title: xzl.gga.wenchang.testis.wt.adult.ox.rep3.small-RNA.R1


title: I_A12_S204

value: MEP


title: IV_G11_S179


title: A_E4_3

source_name: Zdhhc20 KO cells (single cell clone)


title: BALs, p20097-s081

value: Baricitinib

value: Necropsy


title: BALs, p20097-s080


title: A_E4_2


title: xzl.gga.wenchang.testis.wt.adult.ox.rep1.small-RNA.R1

value: oxidized small RNA


title: IV_G10_S178


title: xzl.gga.wenchang.testis.wt.adult.ox.rep2.small-RNA.R1

value: whole testis


title: xzl.gga.tibetan.testis.wt.adult.unox.rep5.small-RNA.R1

value: Tibetan


title: BALs, p20097-s078


title: IV_F10_S166


title: IV_F11_S167


title: BALs, p20097-s077

value: prior to SARS-CoV-2 inoculation


title: xzl.gga.tibetan.testis.wt.adult.unox.rep4.small-RNA.R1

value: adult

value: wildtype


title: BALs, p20097-s076

value: untreated


title: BALs, p20097-s082


title: xzl.gga.tibetan.testis.wt.adult.unox.rep3.small-RNA.R1

value: unoxidized small RNA


title: IV_E12_S156


title: BALs, p20097-s075


title: BALs, p20097-s074


title: SRE_Elk_High_R2

city: Berlin

first: Oriana

last: Genolet

address: Ihnestrasse 63

department: OWL Schulz

institute: Max Planck Institute for Molecular Genetics

description:
Normalized_counts.txt, Raw_counts.txt
Same as SRE_Elk_High, second replicate

data_processing:
Tab delimited text files with raw and normalized counts were generated on the public Galaxy server usegalaxy.eu (Afgan et al., 2016) with the MAGeCK CRISPR screen analysis tools (Li et al., 2014, 2015). Alignment and read counting was performed with MAGeCK_count and statistical analysis was performed with MAGeCK_mle.
Genome_build: GRCm38 mm10
Supplementary_files_format_and_content: Tab delimited text files include raw and normalized counts for each sample
Supplementary_files_format_and_content: Phosphatase sgRNA library (tab delimited text files provided)

source_name: mESCs

growth_protocol: All mESC lines were grown without feeder cells on gelatin-coated flasks (Millipore, 0.1%) in serum-containing ES cell medium (DMEM (Sigma), 15% FBS (PanBiotech), 0.1 mM ß-Mercaptoethanol (Sigma), 1000 U/ml leukemia inhibitory factor (LIF, Merck)). mESCs were passaged every second day at a density of 4*104 cells/cm2 and medium was changed daily. For stable expression of the Cas9 endonuclease, cells were transduced with virus carrying Cas9 and selected for cells with stable integration. Cells were then transduced with the respective sgRNA library with a MOI (multiplicity of infection) of 0.3 and selected for stable sgRNA cassette integration. Cells were then grown for seven days prior to sorting.

extract_protocol:
Genomic DNA from frozen cell pellets was isolated via Phenol/Chloroform extraction due to higher yields. Briefly, cell pellets were thawed and resuspended in 250µl of Lysis buffer (1% SDS (Thermo Fisher Scientific), 0.2M NaCl and 5mM DTT (Roth) in TE Buffer) and incubated over night at 65°C. 200µg of RNAse A (Thermo Fisher Scientific) was added to the sample and incubated at 37°C for 1h. 100µg of Proteinase K (Sigma) were subsequently added followed by a 1h incubation at 50°C. Phenol/Chloroform/Isoamyl alcohol (Roth) was added to each sample in a 1:1 ratio, the mixture was vortexed at RT for 1 min and subsequently centrifuged at 16000 xg for 10 min at room temperature. The aqueous phase was transferred to a new tube, 1 ml 100% EtOH, 90 µl 5 M NaCl and 1µl Pellet Paint (Merck) was added to each sample, mixed, and incubated at -80°C for 1 hr. DNA was pelleted by centrifugation for 16000 xg for 15 min at 4°C, pellets were washed twice with 70% EtOH, air-dried and resuspended in 50µl H2O.
The PCR amplification of the sgRNA cassette was performed in two PCR steps as described previously with minor modifications (Shalem et al. 2014).

treatment_protocol: No treatment was carried out.

tag: gdna isolation

value: Phenol/Chloroform

tag: molecule

value: DNA PCR Amplicon


title: IV_E11_S155

value: bacterial cell


title: SRE_Elk_Input_R2

description:
Normalized_counts.txt, Raw_counts.txt
Same as SRE_Elk_Input, second replicate


title: xzl.gga.tibetan.testis.wt.adult.unox.rep1.small-RNA.R1


title: xzl.gga.tibetan.testis.wt.adult.ox.rep5.small-RNA.R1


title: IV_E10_S154

value: Lennox broth media


title: SRE_Elk_Low_R2

description:
Normalized_counts.txt, Raw_counts.txt
Same as SRE_Elk_Low, second replicate


title: BALs, p20097-s073


title: BALs, p20097-s079


title: IV_F12_S168

value: EEP


title: IV_D12_S144


title: xzl.gga.tibetan.testis.wt.adult.ox.rep4.small-RNA.R1


title: A_E4_1

value: Mixed 129/SvJae/C57Bl/6 background

value: PDAC cell line


title: SRE_Elk_Input_R1

description:
Normalized_counts.txt, Raw_counts.txt
Unsorted population of cells 7 days after transduction with GeCKOx sgRNA library (cells were previous to sgRNA library transduction transduced with the Cas9 endonuclease)


title: xzl.gga.tibetan.testis.wt.adult.unox.rep2.small-RNA.R1


title: SRE_Elk_Low_R1

description:
Normalized_counts.txt, Raw_counts.txt
15% of cells with the lowest reporter activity (based on GFP levels whose expression was driven by a MAPK sensitive promoter) were FACS-sorted.


title: pMek_High_R2

description:
Normalized_counts.txt, Raw_counts.txt
Same as pMek_High, second replicate


title: SRE_Elk_High_R1

description:
Normalized_counts.txt, Raw_counts.txt
15% of cells with the highest reporter activity (based on GFP levels whose expression was driven by a MAPK sensitive promoter) were FACS-sorted.


title: xzl.gga.tibetan.testis.wt.adult.ox.rep2.small-RNA.R1


title: xzl.gga.tibetan.testis.wt.adult.ox.rep1.small-RNA.R1


title: IV_C12_S132


title: IV_D11_S143


title: pMek_Low_R2

description:
Normalized_counts.txt, Raw_counts.txt
Sample as pMek_Low, second replicate


title: pMek_Input_R2

description:
Normalized_counts.txt, Raw_counts.txt
Same a pMek_Input, second replicate


title: BALs, p20097-s070

value: BAL

value: Baricitinib


title: BALs, p20097-s069


title: BALs, p20097-s067


title: pMek_Low_R1

description:
Normalized_counts.txt, Raw_counts.txt
15% cells with the lowest pMek signal (based on an intracellular staining with an anti-pMek primary antibody and a secondary Alexa-647 coupled antibody) were FACS sorted


title: BALs, p20097-s072


title: xzl.gga.Sweden.testis.wt.adult.unox.rep4.small-RNA

value: Sweden


title: BALs, p20097-s068


title: IV_C10_S130


title: xzl.gga.Sweden.testis.wt.adult.unox.rep5.small-RNA

value: whole testis


title: IV_B12_S120


title: xzl.gga.Sweden.testis.wt.adult.ox.rep5.small-RNA

value: oxidized small RNA


title: IV_C11_S131


title: BALs, p20097-s066

value: Necropsy


title: pMek_High_R1

description:
Normalized_counts.txt, Raw_counts.txt
15% cells with the highest pMek signal (based on an intracellular staining with an anti-pMek primary antibody and a secondary Alexa-647 coupled antibody) were FACS sorted


title: xzl.gga.Sweden.testis.wt.adult.ox.rep4.small-RNA

value: adult


title: IV_D10_S142


title: BALs, p20097-s071


title: xzl.gga.tibetan.testis.wt.adult.ox.rep3.small-RNA.R1

value: Tibetan

value: wildtype


title: BALs, p20097-s065

value: untreated


title: Nanog_Live_Low_R2

description:
Normalized_counts.txt, Raw_counts.txt
Same as Nanog_Live_Low, second replicate

value: Phenol/Chloroform


title: Nanog_Live_High_R2

description:
Normalized_counts.txt, Raw_counts.txt
Same as Nanog_Live_High, second replicate

value: DNA PCR Amplicon


title: IV_B10_S118

value: bacterial cell


title: xzl.gga.silkie.testis.wt.adult.unox.rep5.small-RNA

value: Silkie

value: unoxidized small RNA


title: IV_A12_S108

value: Lennox broth media

value: EEP


title: xzl.gga.silkie.testis.wt.adult.unox.rep4.small-RNA


title: xzl.gga.silkie.testis.wt.adult.unox.rep3.small-RNA


title: Nanog_Live_Input_R2

description:
Normalized_counts.txt, Raw_counts.txt
Same as Nanog_Live_Input, second replicate


title: BALs, p20097-s063

value: BAL


title: IV_A11_S107


title: pMek_Input_R1

description:
Normalized_counts.txt, Raw_counts.txt
Unsorted population of cells 7 days after transduction with the Phosphatase sgRNA library (cells were previous to sgRNA library transduction transduced with the Cas9 endonuclease). Cells were fixed with PFA and Methanol.


title: BALs, p20097-s062

value: prior to SARS-CoV-2 inoculation


title: xzl.gga.silkie.testis.wt.adult.unox.rep2.small-RNA


title: xzl.gga.silkie.testis.wt.adult.unox.rep1.small-RNA


title: Nanog_Live_High_R1

description:
Normalized_counts.txt, Raw_counts.txt
15% of cells with the highest mCherry fluorescence were FACS-sorted (These cells carry a C-terminally tagged Nanog locus with mCherry linked via a P2A peptide).


title: Nanog_Live_Input_R1

description:
Normalized_counts.txt, Raw_counts.txt
Unsorted population of cells 7 days after transduction with Phosphatase sgRNA library (cells were previous to sgRNA library transduction transduced with the Cas9 endonuclease). These cells carry a C-terminally tagged Nanog locus with mCherry linked via a P2A peptide.


title: Nanog_Live_Low_R1

description:
Normalized_counts.txt, Raw_counts.txt
15% of cells with the lowest mCherry fluorescence were FACS-sorted (These cells carry a C-terminally tagged Nanog locus with mCherry linked via a P2A peptide).


title: xzl.gga.silkie.testis.wt.adult.ox.rep5.small-RNA


title: III_H3_S87


title: III_H2_S86


title: PBMCs, p20097-s061

source_name: PBMC

value: PBMC

value: Baricitinib


title: IV_A10_S106


title: III_H1_S85


title: Nanog_FISH_High_R2

description:
Normalized_counts.txt, Raw_counts.txt
Same as Nanog_FISH_High, second replicate


title: Nanog_FISH_Low_R2

description:
Normalized_counts.txt, Raw_counts.txt
Same as Nanog_FISH_Low, second replicate


title: PBMCs, p20097-s060


title: PBMCs, p20097-s058


title: xzl.gga.silkie.testis.wt.adult.ox.rep4.small-RNA

value: whole testis

value: oxidized small RNA


title: PBMCs, p20097-s059


title: III_G3_S75


title: BALs, p20097-s064


title: xzl.gga.silkie.testis.wt.adult.ox.rep3.small-RNA

value: adult


title: xzl.gga.silkie.testis.wt.adult.ox.rep2.small-RNA


title: PBMCs, p20097-s057


title: Transduced_Library_R2

description:
Normalized_counts.txt, Raw_counts.txt
Sample as Transduces_Library, second replicate


title: III_G2_S74


title: xzl.gga.silkie.testis.wt.adult.ox.rep1.small-RNA


title: III_G1_S73


title: PBMCs, p20097-s056


title: PBMCs, p20097-s055


title: Nanog_FISH_Low_R1

description:
Normalized_counts.txt, Raw_counts.txt
15% of cells with the lowest fluorescence were FACS-sorted. These cells were labelled with probes against Nanog mRNA coupled to an Alexa647 fluorophore (Prime-Flow).


title: IV_B11_S119


title: III_F3_S63


title: Nanog_FISH_High_R1

description:
Normalized_counts.txt, Raw_counts.txt
15% of cells with the highest fluorescence were FACS-sorted. These cells were labelled with probes against Nanog mRNA coupled to an Alexa647 fluorophore (Prime-Flow).


title: xzl.gga.dongxianglvke.testis.wt.adult.unox.rep5.small-RNA.R1

value: Dongxianglvke


title: PBMCs, p20097-s054

value: Necropsy


title: III_F2_S62


title: Nanog_FISH_Input_R1

description:
Normalized_counts.txt, Raw_counts.txt
Unsorted population of cells 7 days after transduction with Phosphatase sgRNA library (cells were previous to sgRNA library transduction transduced with the Cas9 endonuclease). These cells carry a C-terminally tagged Nanog locus linked via a P2A peptide. Cells were fixed according to the PrimeFlow protocol.


title: Nanog_FISH_Input_R2

description:
Normalized_counts.txt, Raw_counts.txt
Same as Nanog_FISH_Input, second replicate


title: PBMCs, p20097-s053

value: untreated


title: Transduced_Library_R1

description:
Normalized_counts.txt, Raw_counts.txt
Cells were transduced with Phosphatase Library and harvested the next day

value: Phenol/Chloroform


title: III_F1_S61


title: xzl.gga.dongxianglvke.testis.wt.adult.unox.rep4.small-RNA.R1

value: wildtype


title: III_E3_S51

value: bacterial cell


title: xzl.gga.dongxianglvke.testis.wt.adult.unox.rep2.small-RNA.R1


title: PBMCs, p20097-s051


title: xzl.gga.dongxianglvke.testis.wt.adult.unox.rep3.small-RNA.R1


title: PBMCs, p20097-s052


title: III_E2_S50


title: xzl.gga.dongxianglvke.testis.wt.adult.unox.rep1.small-RNA.R1


title: PBMCs, p20097-s050


title: xzl.gga.dongxianglvke.testis.wt.adult.ox.rep5.small-RNA.R1


title: PBMCs, p20097-s049


title: xzl.gga.dongxianglvke.testis.wt.adult.ox.rep4.small-RNA.R1


title: III_D3_S39


title: Longissimus, D 42 postnatal, rep 2

city: Clemson

first: Susan

last: Duckett

state: South Carolina

address: 105 Collings ST, RM 112 BRC

department: Animal and Veterinary Science

institute: Clemson University

data_processing:
FastQC v.0.11.9
TrimGalore v0.6.6
RSEM v1.3.3
Subread's feature Counts v2.0.2
EdgeR v3.34.1
Assembly: ftp://ftp.ensembl.org/pub/release-96/fasta/ovis_aries/
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Ovis aries

source_name: Longissimus

extract_protocol:
Total RNA was extracted with Trizol according to manufactures specifications. Qantificatioon and qualification were checked by 1% agarose gel, NanoPhotometer spectrophotometer, and Agilent Bioanalyzer 2100 system.
NEBNext Poly(A) Magnetic Isolation Module was used to purify, fragment, and add random primers to mRNA according to the manufacturer. MEBNext Ultra II RNA Library Prep Kit for Illumina was used according to the manufacturer for library preparation.

value: Longissimus

value: SuffolkxTexel

value: Postnatal d 42


title: Longissimus, D 42 postnatal, rep 1


title: Longissimus, D 42 postnatal, rep 3


title: Longissimus, gestational d 133, rep 3

value: d 133 of gestation


title: xzl.gga.dongxianglvke.testis.wt.adult.ox.rep3.small-RNA.R1


title: Longissimus, gestational d 133, rep 2


title: III_D1_S37

value: Lennox broth media

value: EEP


title: III_D2_S38


title: Longissimus, gestational d 133, rep 1


title: III_C3_S27


title: PBMCs, p20097-s048

value: PBMC

value: prior to SARS-CoV-2 inoculation


title: PBMCs, p20097-s046

value: Baricitinib


title: Longissimus, gestational d 85, rep 3

value: d 85 of gestation


title: xzl.gga.dongxianglvke.testis.wt.adult.ox.rep1.small-RNA.R1

value: whole testis

value: adult

value: oxidized small RNA


title: Longissimus, gestational d 85, rep 2


title: III_C2_S26


title: PBMCs, p20097-s044


title: xzl.gga.Davis.testis.wt.adult.unox.rep3.small-RNA

value: Davis

value: unoxidized small RNA


title: Longissimus, gestational d 85, rep 1


title: III_C1_S25


title: PBMCs, p20097-s043


title: xzl.gga.Davis.testis.wt.adult.unox.rep2.small-RNA

value: wildtype


title: xzl.gga.Davis.testis.wt.adult.unox.rep1.small-RNA


title: III_E1_S49

value: bacterial cell


title: III_B3_S15


title: Longissimus, D 243 postnatal, rep 3

value: Longissimus

value: Postnatal d 243


title: PBMCs, p20097-s047

value: Necropsy


title: Longissimus, D 243 postnatal, rep 2

value: SuffolkxTexel


title: xzl.gga.dongxianglvke.testis.wt.adult.ox.rep2.small-RNA.R1

value: Dongxianglvke


title: xzl.gga.Davis.testis.wt.adult.ox.rep2.small-RNA


title: PBMCs, p20097-s045


title: xzl.gga.Davis.testis.wt.adult.ox.rep1.small-RNA


title: Longissimus, D 243 postnatal, rep 1


title: xzl.gga.Davis.testis.wt.adult.ox.rep3.small-RNA


title: xzl.gga.aracucana.testis.wt.adult.unox.rep4+rept4.small-RNA

value: Aracucana


title: PBMCs, p20097-s041

value: PBMC


title: PBMCs, p20097-s039

value: untreated


title: PBMCs, p20097-s042

value: Baricitinib


title: PBMCs, p20097-s040


title: PBMCs, p20097-s037


title: PPB_M6

city: Cambridge

first: Michelle

last: Ramseier

state: MA

address: 400 Main St

department: Harvard-MIT Health Sciences and Technology

institute: Massachusetts Institute of Technology

description:
Seq-Well S3
pi3k_merged_counts.txt
pi3k_merged_metadata.txt

data_processing:
Cell barcode and UMI tagging of transcript reads was performed using DropSeqTools v1.12 (Macosko et al., 2015)
Assembly: mm10
Supplementary files format and content: Tab-separated .txt files

source_name: Tumor immune infiltrate

extract_protocol:
Individual mouse tumors were enzymatically dissociated using collagenase, hyaluronidase, and DNAse I. Live CD45+ and CD3+ cells from the dissociated single-cell suspensions were stained and flow sorted to co-load onto Seq-Well arrays.
CD45+ (whole immune) and CD45+CD3+ (T cell) single-cell suspensions from each tumor were loaded in a 1:1 ratio onto Seq-Well arrays and processed using the second-strand synthesis protocol described in Hughes et al., Immunity (2020) and Gierahn et al., Nature Methods (2017).

value: Tumor immune infiltrate

value: K14-Cre; Pten L/L ; Trp53 L/L ; Pik3cb L/L (PPB)


title: PPA_M8

value: K14-Cre; Pten L/L ; Trp53 L/L ; Pik3ca L/L (PPA)


title: PP_M7

value: K14-Cre; Pten L/L ; Trp53 L/L (PP)


title: PPA_M5


title: PPB_M9


title: PP_M4


title: PBMCs, p20097-s038


title: PBMCs, p20097-s034


title: PBMCs, p20097-s036


title: PBMCs, p20097-s035


title: PBMCs, p20097-s033

value: prior to SARS-CoV-2 inoculation


title: PPB_M3


title: PPA_M2


title: II_H5_S377

value: Lennox broth media

value: EEP


title: II_H6_S378

value: bacterial cell


title: III_B1_S13


title: II_H4_S376


title: III_A2_S2


title: III_A1_S1


title: II_G6_S366


title: III_B2_S14


title: III_A3_S3


title: PBMCs, p20097-s031


title: II_G4_S364


title: II_F6_S354


title: MEL cells, CTRL, H3K27me3

city: Basel

first: Jonathan

last: Seguin

address: Spitalstrasse 33

country: Switzerland

institute: UKBB-DBM

data_processing:
Reads were mapped to the mouse genome assembly, version mm10, with bowtie2 (version 2. 4.2) using the option '--wrapper basic-0 --maxins 2000 --no-mixed --no-discordant --local'.
The output was sorted and indexed with samtools (version 1.11). Picard markDuplicates (version 2.23.4) was used to collapse samples run on different sequencing lanes.
Coverage tracks per sample were generated by tiling the genome in 20bp windows, counting overlapping reads per window using the function bamCount from the bioconductor package bamsignals (bioconductor version 3.6) and exporting these window counts in bigWig format using the export function of the bioconductor package rtracklayer.
Regions of accessible chromatin were called with macs2 (version 2.2.7.1) using the option '--nomodel --format=BAM --keep-dup=all --bdg --SPMR -g 2652783500 --extsize 155 --qvalue 0.05'. The peak-calling was performed for the HA tag in NFIA-ETO2 MEL sample without using the input as control (nevertheless, the peak calling result with the use of the input is provided in the HA-HA-131R_fdr0.05_narrowPeak.bed.gz file).
Assembly: mm10
Supplementary files format and content: bigWig, bed

source_name: murine erythroleukemia

growth_protocol: Murine erythroleukemia (MEL) cells were obtained from DSMZ (cultured in suspension in DMEM (Dulbecco's Modified Eagle Medium) (Gibco, Lubio, Thermo Fisher Scientific, Reinach, Switzerland), 5% FCS (Fetal Calf Serum), 1% P/S  (Penicillin-Streptomycin) (Reddy and Shen 1992).

extract_protocol:
MEL cells were crosslinked in 1% formaldehyde at room temperature for 10 minutes, followed by lysis in SDS lysis buffer. Precipitation for all samples was performed with ChIP grade protein A/G coupled magnetic beads. After the overnight incubation, washing steps were performed, followed by the elution in fresh elution buffer.
Libraries were prepared following the manufacturer protocols for Chipseq sequencing with Illumina NextSeq 550DX sequencer (ILLUMINA).

treatment_protocol: Cells were transduced with viral supernatants, containing the vector to express NFIA-ETO2 gene fusion, in presence of 5ug/ml polybrene (Sigma Aldrich, Buchs, Switzerland) 90min, 1800 rpm at 30°C. Cells were incubated overnight with the cells, and washed with PBS and plated in DMEM.

value: murine erythroleukemia

tag: chip antibody


title: PBMCs, p20097-s032


title: II_G5_S365

data_processing:
Read trimming and quality control of MATQ-seq reads was executed using BBDuk. To efficiently remove primer and  adapter sequences located at both ends of a read, we ran BBDuk in a two-pass procedure using the default adapter sequence database augmented with MATQ-seq specific sequences. The first pass focused on the 5’ end, with parameters: minlen=18 qtrim=rl trimq=20 ktrim=l k=17 mink=11 hdist=1 trimpolya=30; while the second pass focused on the 3’ end with parameters: minlen=18 qtrim=rl trimq=20 ktrim=r k=17 mink=11 hdist=1.
Read alignment and counting was performed with Bowtie2 (Langmead & Salzberg 2012) and featureCounts (Liao et al. 2014), allowing a single mismatch and run-in --local mode. BigWig files were generated using deepTools (Ramírez et al. 2014), passing additional parameters: --binSize 5 --normalizeUsing BPM. We have employed the same gene detection method from the original MATQ-seq analyses (Imdahl et al. 2020), requiring a detected gene to have > 5 reads.
DESeq2 (Love et al. 2014) was used for normalization and differential expression analysis, using size factors calculated by the computeSumFactors function in Scran (Lun et al. 2016) and other recommended parameters for DESeq2 single cell analysis, which included using the likelihood ratio test (LRT), useT=TRUE, minmu=1e-6, and minReplicatesForReplace=Inf.
Assembly: NC_016810.1
Supplementary files format and content: Unprocessed count matrix from all samples
Supplementary files format and content: sc_counts.tsv

extract_protocol:
Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer’s recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer’s recommendation using 100ng total RNA as input per sample.
cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer’s recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio


title: PBMCs, p20097-s030


title: II_F5_S353


title: PBMCs, p20097-s029


title: MEL cells, CTRL, input (H3K27me3, H3K4me1)

tag: genotype


title: PBMCs, p20097-s028


title: MEL cells, CTRL, H3K9me1


title: II_F4_S352


title: MEL cells, CTRL, input (H3K9me1)


title: II_E6_S342


title: xzl.gga.1995.testis.wt.30week.ox.rep1+rept1.small-RNA

tag: tissue

value: whole testis

value: wildtype

value: oxidized small RNA


title: xzl.gga.2015.testis.wt.30week.ox.rep1+rept1.small-RNA


title: xzl.gga.aracucana.testis.wt.adult.unox.rep2+rept2.small-RNA

value: adult

value: unoxidized small RNA


title: xzl.gga.aracucana.testis.wt.adult.ox.rep4+rept4.small-RNA

value: Aracucana


title: xzl.gga.aracucana.testis.wt.adult.ox.rep1+rept1.small-RNA


title: xzl.gga.aracucana.testis.wt.adult.ox.rep3+rept3.small-RNA


title: xzl.gga.1995.testis.wt.30week.unox.rep1+rept1.small-RNA


title: xzl.gga.aracucana.testis.wt.adult.ox.rep2+rept2.small-RNA


title: xzl.gga.aracucana.testis.wt.adult.unox.rep3+rept3.small-RNA


title: xzl.gga.2015.testis.wt.30week.unox.rep1+rept1.small-RNA


title: xzl.gga.aracucana.testis.wt.adult.unox.rep1+rept1.small-RNA


title: PBMCs, p20097-s027

value: PBMC


title: II_E5_S341

tag: media


title: xzl.gga.1950.testis.wt.30week.unox.rep1+rept1.small-RNA


title: MEL cells, NFIA-ETO2, H3K4me1


title: PBMCs, p20097-s026

value: Baricitinib


title: II_E4_S340

tag: od


title: xzl.gga.1950.testis.wt.30week.ox.rep1+rept1.small-RNA


title: 48hr treated astrocytes, Ribo-seq, batch C

city: Tel Aviv

first: Shir

last: Mandelboum

address: chaim levanon

department: Sagol School of Neuroscience

country: Israel

institute: Tel Aviv University

description: Ribosome-protected-fragmantes (RPF)

data_processing:
Sequenced reads were aligned to mm10 reference genome using TopHat2 , followed by generation of gene count data using FeatureCounts.
Only genes with at least 20 counts in all replicate samples of at least one condition were included in the analysis.
Changes in Translation efficiency (TE) of the coupled Ribo-seq and RNA-seq data was calculated using DTEG analysis
Assembly: mm10
Supplementary files format and content: excel file containing data with an overall coverage of 12,206 genes.  For each gene, Ensemble ID and symbol is specified.
Supplementary files format and content: The first tab of the excel file presents the log2 fold change value of each mRNA and RPF upon (24-hr-treated vs untreated), and (48-hr-treated vs untreated)
Supplementary files format and content: together with the TE value of each gene.
Supplementary files format and content: The 2nd-6th tabs of the excel file present specific GO term and KEGG group lists that were diffrentially expressed within the tested samples
Supplementary files format and content: The 7th tab of the excel file presents specific examples and p-values shown in the published manuscript
Library strategy: Ribo-seq

source_name: Primary astrocytes

growth_protocol: Freshly thawed primary astrocytes seeded at a density of 1.3x10^6 cells per 15-cm plate and grown in ‘astrocyte medium’ (#1801; ScienCell Research Labs, Carlsbad, CA, USA)

extract_protocol:
After thorough removal of PBS 230ul of lysis buffer were added to each 15 cm plate. The lysis buffer, composed of 25mM K-HEPES pH=7.2, 10mM MgCl2, 200mM KCl
and freshly added 2% DDM, 1mM DTT, 1X complete EDTA-free protease inhibitor (Roche), 100 μg/ml cycloheximide, and 25U/ml Turbo DNase-I (Thermo Scientific, AM2238),
was added directly onto the cells for 5 min incubation on ice. Cell lysates were scraped and collected, then incubated on ice for additional 10 min.
A portion of each sample was treated with RNase-I (Thermo Scientific, AM2295) to generate ribosome footprints, while an undigested portion was used to isolate total RNA.
Following RNase treatment, the footprint samples were layered on 1M sucrose cushion, following ultracentrifugation at 78,000 rpm for 2 h at 4°C in a Beckman Coulter TLA120.2 rotor.
RNA extracted from sucrose cushion pellets were subjected to size selection, by separation of the footprint samples on a 15% PolyAcrylamide TBE-urea gel
followed by purification of 26-34 nt fragments from the gel.
libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Gold kit (Illumina #20020598) following manufacturer's protocols.
libraries for Ribo-seq were generated with NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, #E7300L),
then size selected by gel electrophoresis on 8% PolyAcrylamide Gel, with ~155 bp sized product purified from the gel.

treatment_protocol:
Untreated cells were incubated for 120 hr, while trated cells were incubated for 72 hr or 96 hr followed by treatment with 20ng/ml TNFα (Peprotech #315-01A)
and 0.25ng/ml IL-1β (Peprotech #211-11B) for 48 hr or 24 hr, respectively.

value: Primary astrocytes

tag: developmental stage

value: newborn (P0-P2)

tag: Sex

value: pooled male and female

value: WT

value: TNFalpha+ IL-1Beta

tag: time point

value: 48 hr


title: PBMCs, p20097-s025

tag: cell type

value: prior to SARS-CoV-2 inoculation


title: xzl.gga.1950.testis.wt.18week.unox.rep1+rept1.small-RNA

tag: age


title: II_D6_S330

value: bacterial cell

value: Lennox broth media

tag: condition

value: EEP


title: 48hr treated astrocytes, Ribo-seq, batch A

description: Ribosome-protected-fragmantes (RPF)

tag: strain

tag: treatment


title: PBMCs, p20097-s024

tag: animal id

tag: infection

value: untreated

tag: time

value: Necropsy


title: xzl.gga.1950.testis.wt.18week.ox.rep1+rept1.small-RNA

value: whole testis

tag: breed

value: wildtype

tag: fraction

value: oxidized small RNA


title: 48hr treated astrocytes, Ribo-seq, batch B

description: Ribosome-protected-fragmantes (RPF)

tag: genotype


title: xzl.gga.1950.testis.wt.14wk.unox.rep1.small-RNA

tag: tissue

value: unoxidized small RNA


title: 24hr treated astrocytes, Ribo-seq, batch B

description: Ribosome-protected-fragmantes (RPF)

value: 24 hr


title: II_D5_S329

tag: media


title: II_D4_S328

tag: od


title: PBMCs, p20097-s023

value: PBMC


title: PBMCs, p20097-s022


title: 24hr treated astrocytes, Ribo-seq, batch C

description: Ribosome-protected-fragmantes (RPF)

value: Primary astrocytes

tag: developmental stage

value: newborn (P0-P2)


title: 24hr treated astrocytes, Ribo-seq, batch A

description: Ribosome-protected-fragmantes (RPF)

tag: Sex

value: pooled male and female

value: WT


title: PBMCs, p20097-s021


title: PBMCs, p20097-s020


title: PBMCs, p20097-s019


title: II_B6_S306


title: Untreated astrocytes, Ribo-seq, batch C

description: Ribosome-protected-fragmantes (RPF)

value: Untreated


title: II_C5_S317


title: xzl.gga.1950.testis.wt.12wk.ox.rep1.small-RNA


title: II_C4_S316


title: Untreated astrocytes, Ribo-seq, batch B

description: Ribosome-protected-fragmantes (RPF)


title: xzl.gga.1950.testis.wt.12wk.unox.rep1.small-RNA


title: xzl.gga.1950.testis.wt.14wk.ox.rep1.small-RNA


title: xzl.gga.1950.testis.wt.10wk.unox.rep1.small-RNA


title: xzl.gga.1950.testis.wt.10wk.ox.rep1.small-RNA


title: PBMCs, p20097-s018


title: Untreated astrocytes, Ribo-seq, batch A

description: Ribosome-protected-fragmantes (RPF)


title: II_C6_S318


title: PBMCs, p20097-s017

value: prior to SARS-CoV-2 inoculation


title: xzl.gga.1950.testis.wt.8week.unox.rep1+rept1.small-RNA


title: II_B5_S305

value: bacterial cell


title: 48hr treated astrocytes, RNA-seq, batch C

data_processing:
Sequenced reads were aligned to mm10 reference genome using TopHat2 , followed by generation of gene count data using FeatureCounts.
Only genes with at least 20 counts in all replicate samples of at least one condition were included in the analysis.
Changes in Translation efficiency (TE) of the coupled Ribo-seq and RNA-seq data was calculated using DTEG analysis
Assembly: mm10
Supplementary files format and content: excel file containing data with an overall coverage of 12,206 genes.  For each gene, Ensemble ID and symbol is specified.
Supplementary files format and content: The first tab of the excel file presents the log2 fold change value of each mRNA and RPF upon (24-hr-treated vs untreated), and (48-hr-treated vs untreated)
Supplementary files format and content: together with the TE value of each gene.
Supplementary files format and content: The 2nd-6th tabs of the excel file present specific GO term and KEGG group lists that were diffrentially expressed within the tested samples
Supplementary files format and content: The 7th tab of the excel file presents specific examples and p-values shown in the published manuscript

value: TNFalpha+ IL-1Beta

tag: time point

value: 48 hr


title: II_B4_S304

tag: cell type

value: Lennox broth media

value: EEP


title: xzl.gga.1950.testis.wt.8week.ox.rep1+rept1.small-RNA

value: whole testis

tag: age


title: 48hr treated astrocytes, RNA-seq, batch A


title: PBMCs, p20097-s015

value: Baricitinib


title: II_A6_S294

tag: condition


title: II_A5_S293


title: 48hr treated astrocytes, RNA-seq, batch B

tag: strain


title: II_A4_S292


title: 24hr treated astrocytes, RNA-seq, batch C

tag: treatment


title: PBMCs, p20097-s013

tag: animal id


title: 24hr treated astrocytes, RNA-seq, batch A


title: xzl.gga.1950.testis.wt.Day1.unox.rep1+rept1.small-RNA

value: wildtype


title: xzl.gga.1950.testis.wt.6wk.ox.rep1.small-RNA

value: oxidized small RNA


title: PBMCs, p20097-s016

tag: infection

value: Necropsy


title: 24hr treated astrocytes, RNA-seq, batch B

value: 24 hr


title: xzl.gga.1950.testis.wt.Day1.ox.rep1+rept1.small-RNA


title: I_H7_S283


title: I_H8_S284


title: PBMCs, p20097-s012

value: PBMC

tag: time


title: PBMCs, p20097-s011


title: Untreated astrocytes, RNA-seq, batch C

value: Primary astrocytes

value: newborn (P0-P2)


title: xzl.gga.1950.testis.wt.6wk.unox.rep1.small-RNA

tag: breed

value: unoxidized small RNA


title: xzl.gga.tibetan.testis.wt.adult.rep3.RNAseq

value: Tibetan

value: adult

tag: fraction

value: rRNA depleted RNA


title: PBMCs, p20097-s010


title: PBMCs, p20097-s014


title: xzl.gga.tibetan.testis.wt.adult.rep2.RNAseq

tag: genotype


title: Untreated astrocytes, RNA-seq, batch B

value: pooled male and female

value: WT

value: Untreated


title: I_H9_S285

value: bacterial cell

value: Lennox broth media

value: EEP


title: xzl.gga.tibetan.testis.wt.adult.rep1.RNAseq

tag: tissue

value: whole testis

value: wildtype


title: PBMCs, p20097-s009

value: prior to SARS-CoV-2 inoculation

value: Baricitinib


title: PBMCs, p20097-s008

value: PBMC

value: untreated

value: Necropsy


title: I_G8_S272

tag: media


title: xzl.gga.silkie.testis.wt.adult.rep3.RNAseq

value: Silkie


title: I_G7_S271

tag: od


title: Primary astrocytes,  optimized-extraction, batch C

data_processing:
Sequenced reads were aligned to mm10 reference genome using TopHat2 , followed by generation of gene count data using FeatureCounts.
Only genes with at least 20 counts in all replicate samples of at least one condition were included in the analysis.
Conditional quantile normalization (CQN) was performed to correct for sample-specific gene length effect
Assembly: mm10
Supplementary files format and content: excel file containing data with an overall coverage of 13,970 genes, out of which ‘shared-genes’ (N = 13,278; 1st tab in the excel file) were detected by both extraction methods
Supplementary files format and content: 75 genes were exclusively detected by ‘standard’ extraction (‘ST-genes’; 2nd tab of the excel file), and 617 genes were exclusively detected by ‘optimized’ extraction (‘OP-genes’; 3rd tab of the excel file).
Supplementary files format and content: For each gene, Ensemble ID and symbol is specified, together with 'named’ or ‘un-named’ specification; Genes with the ending ‘Rik’, the beginning GM, or the symbol ‘NA’ were considered as unnamed genes.
Supplementary files format and content: For each of the ‘shared-genes’ the log2 fold change value of each transcript abundance upon ‘optimized’ vs ‘standard’ extraction is presented.
Supplementary files format and content: The 4th-9th tabs of the excel file contain specific GO term and KEGG group lists that were diffrentially expressed within the tested samples

extract_protocol:
‘Standard’ extraction: Cells were scraped in PBS containing 100 μg/ml CHX and collected on ice, followed by pelleting and storing at -80°C for future use. Frozen cell pellets were thawed on ice,
resuspended in 500 ul of lysis buffer containing 18 mM Tris-HCl pH 7.5, 50 mM KCl, 10 mM MgCl2, 10mM NaF, and freshly added 1% Triton X-100, 1% sodium deoxycholate, 1.25 mM DTT,
1X completeTM EDTA-free protease inhibitor cocktail (42364500 Roche), 100 μg/ml cycloheximide, and 1 U/ul RiboLock RNase inhibitor (Thermo Scientific), followed by incubation on ice for further 15 min.
200ul (12 ug RNA) of each lysate were layered onto a 900μl cushion of 1 M sucrose, followed by ultracentrifugation at 75,000 rpm for 2 h at 4°C in a Beckman Coulter TLA120.2 rotor.
‘Optimized’ extraction: After thorough removal of PBS 230ul of lysis buffer were added to each 15 cm plate. The lysis buffer, composed of 25mM K-HEPES pH=7.2, 10mM MgCl2, 200mM KCl
and freshly added 2% DDM, 1mM DTT, 1X complete EDTA-free protease inhibitor (Roche), 100 μg/ml cycloheximide, and 1 U/μl RiboLock RNase inhibitor (Thermo Scientific),
was added directly onto the cells for 5 min incubation on ice. Cell lysates were scraped and collected, then incubated on ice for additional 10 min.
200ul (12 ug RNA) of each lysate were layered onto a 900μl cushion of 1 M sucrose, followed by ultracentrifugation at 75,000 rpm for 2 h at 4°C in a Beckman Coulter TLA120.2 rotor.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Gold kit (Illumina #20020598) following manufacturer's protocols.

treatment_protocol: Cells remained untreated

value: Primary astrocytes

tag: developmental stage

value: newborn (P0-P2)

tag: rnp complexes_extraction

value: astrocyte-optimized


title: PBMCs, p20097-s007


title: Untreated astrocytes, RNA-seq, batch A

tag: Sex

value: pooled male and female


title: I_F9_S261

tag: cell type


title: Primary astrocytes, optimized-extraction, batch B


title: xzl.gga.silkie.testis.wt.adult.rep2.RNAseq

tag: age

value: adult

value: rRNA depleted RNA


title: PBMCs, p20097-s006


title: Primary astrocytes, optimized-extraction, batch A

value: Untreated


title: I_F8_S260

value: bacterial cell

value: Lennox broth media

tag: condition


title: PBMCs, p20097-s005


title: I_G9_S273

value: EEP


title: I_F7_S259


title: xzl.gga.White.Leghorn.testis.wt.adult.rep4.RNAseq

value: whole testis

value: White Leghorn

value: wildtype


title: PBMCs, p20097-s004

value: PBMC


title: xzl.gga.White.Leghorn.testis.wt.adult.rep3.RNAseq


title: Primary astrocytes, standard-extraction, batch C

tag: strain

value: standard


title: I_E9_S249


title: Primary astrocytes, standard-extraction, batch B

tag: treatment


title: PBMCs, p20097-s003

tag: animal id

value: untreated


title: xzl.gga.White.Leghorn.testis.wt.adult.rep2.RNAseq


title: xzl.gga.Sweden.testis.wt.adult.rep6.RNAseq

value: Sweden


title: PBMCs, p20097-s001

tag: infection

value: prior to SARS-CoV-2 inoculation


title: PBMCs, p20097-s002

tag: time


title: I_E8_S248


title: Primary astrocytes, standard-extraction, batch A

value: Primary astrocytes

value: newborn (P0-P2)


title: MEL cells, CTRL, HA

data_processing:
Reads were mapped to the mouse genome assembly, version mm10, with bowtie2 (version 2. 4.2) using the option '--wrapper basic-0 --maxins 2000 --no-mixed --no-discordant --local'.
The output was sorted and indexed with samtools (version 1.11). Picard markDuplicates (version 2.23.4) was used to collapse samples run on different sequencing lanes.
Coverage tracks per sample were generated by tiling the genome in 20bp windows, counting overlapping reads per window using the function bamCount from the bioconductor package bamsignals (bioconductor version 3.6) and exporting these window counts in bigWig format using the export function of the bioconductor package rtracklayer.
Regions of accessible chromatin were called with macs2 (version 2.2.7.1) using the option '--nomodel --format=BAM --keep-dup=all --bdg --SPMR -g 2652783500 --extsize 155 --qvalue 0.05'. The peak-calling was performed for the HA tag in NFIA-ETO2 MEL sample without using the input as control.
Assembly: mm10
Supplementary files format and content: bigWig, bed

value: murine erythroleukemia

value: CTRL

tag: chip antibody


title: I_D9_S237


title: MEL cells, CTRL, input


title: I_E7_S247


title: I_D8_S236


title: xzl.gga.Sweden.testis.wt.adult.rep5.RNAseq

tag: breed

value: adult

tag: fraction

value: rRNA depleted RNA


title: xzl.gga.silkie.testis.wt.adult.rep1.RNAseq

tag: tissue

value: Silkie

tag: genotype


title: xzl.gga.Davis.testis.wt.adult.rep3.RNAseq

value: Davis


title: xzl.gga.Sweden.testis.wt.adult.rep4.RNAseq


title: I_C9_S225

value: bacterial cell

tag: media

value: Lennox broth media

tag: od

value: EEP


title: xzl.gga.Davis.testis.wt.adult.rep2.RNAseq

value: whole testis

value: wildtype


title: MEL cells, NFIA-ETO2, HA


title: MEL cells, NFIA-ETO2, IGG


title: xzl.gga.Davis.testis.wt.adult.rep1.RNAseq


title: I_B9_S213


title: I_C7_S223


title: xzl.gga.1950.testis.wt.30week.rep1.RNAseq


title: Lung adenocarcinoma cells no treatment

city: Elizabeth City

first: Hirendranath

last: Banerjee

state: North Carolina

address: 1704 Weeksville Rd,

department: Department of Natural, Pharmacy and Health sciences

institute: Elizabeth City State University

description:
3841_Normal
Ampliseq Transcriptome

data_processing:
Torrent Suite Software v. 5.12.1.
Adapters were trimmed and low quality reads filtered by the Torrent Suite Software v. 5.12.1.
StrandNGS software v. 3.4.
Raw reads were mapped to hg19 human reference genome using a proprietary algorithm named computationally-optimized Burrows Wheeler Transformed (COBWeb) by the Strand.
Read count extraction and Normalization was performed by StrandNGS using DESeq algorithm.
Assembly: hg19
Supplementary files format and content: Banerjee_Ampliseq_Transcriptome_raw_coumts.tsv: Tab-separated value (TSV) text file containing raw counts for each sample.

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 10 ng of total RNA was used for the construction of sequencing libraries.
Ampliseq Transcriptome libraries were constructed using the Ampliseq Transcriptome kit (Thermofisher) and manufacturer's recommended protocol.

tag: cell line

value: Lung adenocarcinoma cells

value: WT


title: MEL cells, NFIA-ETO2, H3K27ac


title: I_C8_S224


title: xzl.gga.Red.jungle.fowl.testis.Red.jungle.fowl.adult.rep4.RPF

data_processing:
Analyses were performed using piPipes v1.4. All data from the small RNA-seq, RNA sequencing, were analyzed using the latest mouse genome release galGal6 (GCA_000002315.5). Generally, one mismatch is allowed for genome mapping.
For RNA-seq reads, the expression per transcript was normalized to the top quartile of expressed transcripts per library calculated by Cuffdiff, and the tpm (transcripts per million) value was quantified using the Salmon software.
For small RNA-seq analysis, uniquely mapping reads excluding rRNA and miRNA  between 26 nt and 32 nt were selected for further analysis.
For ONT, the ONT Sequencing data collected in this experiment were obtained as fast5 files, and after conversion of electric signals into base calls via the guppy (Oxford Nanopore Technologies, UK), the reads with mean qScore greater or equal to 7 were kept to continue subsequent bioinformatic analysis. The filtered data were aligned with the chicken genome (galGal6) using NGMLR (v0.27). The SVs were detected using Sniffles (v1.0.8). We also independently used SVIM (v1.4.2 ) to call SVs with default settings.
Assembly: Gallus gallus: galGal6 (GCA_000002315.5)
Supplementary files format and content: For small RNA-seq, processed data files are unique genome alignment results in bigWig result format. RNAseq quantification results are .sf files output by Salmon software. For ONT, processed data files are performed a shuffling test in .txt format.
Library strategy: RPF

value: Red Jungle Fowl

value: ribosome protected fragments


title: I_B8_S212


title: I_B7_S211


title: I_D7_S235


title: Input

city: Montreal

first: Terence

last: Hébert

state: Quebec

address: 3655 Promenade Sir William Osler

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University

data_processing:
Fastq files were trimmed with TrimGalore (v0.6.0)  with the settings --phred33 --length 36 -q 5 --stringency 1 -e 0.1
Processed reads were aligned to the custom combined rat and S. pombe genome with Bowtie2 (v2.3.5)
Low-quality mapped reads (MAPQ < 10) and reads mapped to non-standard chromosomes were removed wtih SAMtools (v1.9)
Duplicate reads were removed with Picard tools (v2.20.6, Broad Institute)
Aligned reads were separated into individual files for the rat or S. pombe genome respectively
Input reads subtracted with the deepTools (v3.3.1) function bamCompare (--scaleFactorsMethod SES) and negative values set to 0
Values were converted to RPM with library size adjusted by the total number of reads aligned to the S. pombe genome
Genome_build: Rattus_norvegicus.Rnor_6.0.94 and Schizosaccharomyces_pombe.ASM294v2
Supplementary_files_format_and_content: bigwig file of merged biological replicates

organism: Rattus norvegicus

source_name: cardiac fibroblasts

growth_protocol: Cardiac fibroblasts were isolated from 1-3 day old Sprague-Dawley rats.

extract_protocol:
Cardiac fibroblasts were fixed with 1% formaldehyde and the fixed chromatin sonicated for 18 cycles (30 seconds on/30 seconds off) in a Diagenode BioRuptor UCD-200
Libraries were prepared with the NEBNext® UltraTM II DNA Library Prep kit for Illumina

treatment_protocol: Cardiac fibroblasts were treated for 75 min with 1 μM Ang II

value: Neonatal


title: I_A9_S201

first: Regan

last: Hayward

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research


title: Flag_Gβ1_AngII_2

description:
Sheared chromain
Cardiac fibroblasts were treated 96 h after transduction with AAV1-FLAG-Gβ1. Chromatin from a S. pombe strain expressing FLAG-Bdf2 was added and immunoprecipated alongside FLAG-Gβ1 with an anti-FLAG M2 antibody
Flag_Gβ1_AngII.bw

value: 1 uM AngII


title: PP_M1

value: Tumor immune infiltrate

value: K14-Cre; Pten L/L ; Trp53 L/L (PP)


title: Flag_Gβ1_DMEM_2

description:
Sheared chromain
Cardiac fibroblasts were treated 96 h after transduction with AAV1-FLAG-Gβ1. Chromatin from a S. pombe strain expressing FLAG-Bdf2 was added and immunoprecipated alongside FLAG-Gβ1 with an anti-FLAG M2 antibody
Flag_Gβ1_DMEM.bw

value: DMEM


title: xzl.gga.Red.jungle.fowl.testis.Red.jungle.fowl.adult.rep6.RPF

value: adult


title: TGF beta induced EMT model lung adenocarcinoma

description:
3840_EMT
Ampliseq Transcriptome

value: EMT


title: RNAPII_AngII_siGβ1_3

description:
Sheared chromain
Cardiac fibroblasts were treated 72 h after transfection with 50 nM siRNA. S. pombe chromatin was combined with the rat chromatin and immunoprecipitated with an anti-Rpb1 (8WG16) antibody
RNAPII_AngII_siGβ1.bw

value: 1 uM AngII/50 nM siGβ1


title: xzl.gga.Red.jungle.fowl.testis.Red.jungle.fowl.adult.rep5.RPF


title: OD_2.0_r3

data_processing:
Read trimming and quality control of was executed using BBDuk using the the default adapter sequence database
Read alignment and counting was performed with Bowtie2 (Langmead & Salzberg 2012) and featureCounts (Liao et al. 2014)
Assembly: NC_016810.1
Supplementary files format and content: Unprocessed count matrix from all samples
Supplementary files format and content: bulk_counts.tsv

extract_protocol:
Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer’s recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer’s recommendation using 100ng total RNA as input per sample.
DNA libraries suitable for sequencing were prepared using CORALL Total RNA-Seq Library Prep protocol (Lexogen) according to the manufacturer's recommendation with 13 PCR cycles. Library quality was checked using a 2100 Bioanalyzer DNA High Sensitivity kit.

value: bacterial cell

value: ESP


title: Flag_Gβ1_AngII_1


title: RNAPII_AngII_siGβ1_2


title: OD_2.0_r2

value: Lennox broth media


title: OD_2.0_r1


title: WT N2 C. elegans, input

first: Francesco Nicola

last: Carelli

address: Henry Wellcome Building of Cancer and Developmental Biology,  Tennis Court Road

institute: University of Cambridge

data_processing:
Reads were preprocessed using trim-galore (version 0.6.7) and then mapped on the C. elegans genome (wormbase release WS285) using bwa-mem (version 0.7.17).
Reads with mapping quality (MAPQ) higher than 10 were extracted using Samtools, and bigwig tracks generated using bamCoverage (from DeepTools, version 3.5.1) with parameters: "--binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 100286401 --extendReads".
Assembly: WS285
Supplementary files format and content: BigWig tracks, RPGC-normalized, 1bp resolution

organism: Caenorhabditis elegans

source_name: WT N2 synchronised adults

growth_protocol: Worms were grown at 20C on 1xNGM plates with HB101 bacteria.

extract_protocol:
Worms were ground and fixed with EGS solution (final 1.5mM concentration) for 8 minutes, followed by crosslinking with 1% methanol-free formaldehyde for 8 minutes. Chromatin was sonicated to 100-300bp length with a Bioruptor sonicator. 20ug of chromatin was used per IP reaction.
The library preparation was performed as previously described (Janes et al. 2018 eLife) using a modified Illumina TruSeq protocol. Briefly, TruSeq adaptors were ligated using NB Quick Ligase (M2200) and libraries were amplified with a KAPA HiFi Hot Start polymerase mix. Aftr PCR amplification, size selection was performed with AMPure beads (Beckman Coulter) to obtain fragments between 250-370bp, and size distribution was validated with a Agilent Tapestation.

treatment_protocol: Synchronised worms were collected as gravid adults.

tag: evelopmental stage

value: WT N2 synchronised adults

value: whole woms


title: GFP-SPT-2 C. elegans, input

source_name: gfp::spt-2 synchronised adults

value: gfp::spt-2 synchronised adults

tag: cell type


title: I_A8_S200

value: EEP


title: I_A7_S199


title: RNAPII_DMEM_siGβ1_3

description:
Sheared chromain
Cardiac fibroblasts were treated 72 h after transfection with 50 nM siRNA. S. pombe chromatin was combined with the rat chromatin and immunoprecipitated with an anti-Rpb1 (8WG16) antibody
RNAPII_DMEM_siGβ1.bw

tag: age

value: DMEM/50 nM siGβ3


title: WT N2 C. elegans, GFP, replicate 2

value: GFP (Abcam, ab290)


title: OD_1.0_r3

tag: condition

value: LEP


title: WT N2 C. elegans, GFP, replicate 1


title: Flag_Gβ1_DMEM_1

value: Neonatal


title: RNAPII_DMEM_siGβ1_2

value: DMEM/50 nM siGβ2


title: OD_1.0_r2


title: gfp::spt-2 C. elegans, GFP, replicate 2


title: RNAPII_DMEM_siGβ1_1

value: DMEM/50 nM siGβ1


title: OD_1.0_r1