title: PPMS_NAWM_08

city: Broadway

first: Alessandro

last: Castorina

state: NSW

address: PO box 123

country: Australia

institute: University of Technology Sydney

data_processing:
Sequencing reads were provided by the Ramaciotti Centre for Genomics (Sydney, NSW).
Sequencing reads were trimmed for adaptor sequences/low quality sequences using trimmomatic (version0.39).
Trimmed reads were aligned to GRCh38 (Ensembl) using STAR (version 2.7.10a) in default mode.
Quality control was performed using FastQC and summarized counts were obtained using FeatureCounts (v2.0.1)
Assembly: GRCh38.p13
Supplementary files format and content: Summarized raw count matrix as text file for each sample

source_name: Brain white matter

extract_protocol:
Normal-appearing white matter was dissected from the obtained tissue block and total RNA was subsequently harvested using the TriReagent RNA extraction protocol. 1ug of total RNA per sample was subsequently used for the contructio of the sequencing library.
Library preparation was performed at the Ramaciotti Centre for Genomics (Sydney,NSW) using Illumina® Stranded Total RNA with Ribo-Zero Plus.

value: Brain white matter

value: PPMS


title: PSPPH_5171-ChIP-1

status: Public on Oct 04 2022

type: SRA

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-5171-ChIP-1_combined

library_source: genomic

data_processing:
ChIP-seq reads were mapped to the Pseudomonas sringae 1448A (NC_005773.3) using Bowtie2 (version 2.3.4.3). Only the uniquely mapped reads were kept for the subsequent analyses. Bam files were transformed into bigWig files by deeptools (version 3.1.3)
RNA-seq reads were mapped to the Pseudomonas sringae 1448A (NC_005773.3) using STAR (version STAR_2.6.1). Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using DESeq2 R package.
Genome_build: Pseudomonas sringae 1448A NC_005773.3
Supplementary_files_format_and_content: narrowPeak files were generated from ChIP-seq, containing significant peaks. xlsx files were generated from RNA-seq, containing the differential expressional genes.

molecule: genomic DNA

organism: Pseudomonas savastanoi pv. phaseolicola 1448A

source_name: liquid culture in KB (King's B)  medium

growth_protocol: ChIP-(KB with Rif and Spec) ; RNA-seq(KB or MM with Rif)

extract_protocol:
NEXTflex™ ChIP-Seq Kit (Bioo Scientific)
The ChIP assay was performed as previously described.For the FLAG-tagged plasmids, the open reading frame of each regulator coding gene was amplified by PCR from Psph1448A genome and cloned into pHM1 plasmid. Wild-type Psph1448A containing empty pHM1 or pHM1-RR-FLAG was cultured in 20 ml KB medium until mid-log phase (OD600 = 0.6). Cultured bacteria were then reated with 1% formaldehyde for 10 min at 28 ℃. Cross-linking was stopped by the addition of 125 mM glycine. Bacterial pellets were washed twice with a Tris buffer (20 mM Tris-HCl [pH 7.5] and 150 mM NaCl), re-suspended in 500 μl IP buffer (50 mM HEPES–KOH [pH 7.5], 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, and mini-protease inhibitor cocktail (Roche), and then subjected to sonication to produce 100-300 bp DNA fragments. Insoluble cellular debris was removed by centrifugation at 4 ℃ and the supernatant was used as the input sample in IP experiments. Both control and IP samples were washed with protein A beads (General Electric) and then incubated with 50 μl agarose- conjugated anti-FLAG antibodies (Sigma) in IP buffer. Washing, crosslink reversal, and purification of the ChIP DNA were conducted. DNA fragments (150-250 bp) were selected for library construction and sequencing libraries were prepared using the NEXTflex™ ChIP-Seq Kit (Bioo Scientific). The libraries were sequenced using the HiSeq 2000 system (Illumina). Two biological replications have been performed for all ChIP-seq experiments. ChIP-seq reads were mapped to the Pseudomonas syringae pv. phaseolicola 1448A genome (NC_005773.3) using Bowtie2 (version 2.3.4.3). Uniquely mapped reads were retained for the subsequent analyses. Binding peaks (q < 0.01) were identified using MACS2 software (version 2.1.0). Reproducible binding sites in both replicates were identified by BEDtools software (version 2.27.1)and used for the following analysis. Subsequently, the enriched loci for each regulator were annotated using the R package ChIPpeakAnno (version 3.18.2) . Target genes were annotated by peaks located in gene promoters defined as upstream of transcription start site (TSS), overlapping with TSS or encompassing the whole gene.
To examine the effect of histidine kinases on the transcriptome, 2 ml of mid-log-phase (OD600 = 0.6) bacterial cultures or 2 ml cultures of mid-log-phase induced in MM with 6 hours (Psph1448A and transcriptional regulator mutant strains) were collected by centrifugation (12,000 rpm, 4 ℃). A RNeasy mini kit (Qiagen) was used for subsequent RNA purification with DNaseI (NEB) treatment. After removing rRNA by using the MICROBExpress kit (Ambion), mRNA was used to generate the cDNA library according to the NEBNext® UltraTM II RNA Library Prep Kit protocol (Illumina), which was then sequenced using the HiSeq 2000 system (Illumina). Two biological replications have been performed for all RNA-seq experiments. For each RNA-seq sample, raw reads were mapped to the Pseudomonas sringae pv. phaseolicola 1448A genome (NC_005773.3) using STAR (version 2.6.1), and uniquely mapped reads were kept for further analyses. Differentially expressed genes were identified using DESeq2 (BH-adjusted P < 0.05 and log2 Fold Change| > 0.5).

treatment_protocol:
grow until mid-log phase in KB
grow until mid-log phase

tag: strain/genotype

tag: condition

value: virulence suppressing (King’s B medium, KB) condition

tag: chip antibody

value: monoclonal Anti-FLAG-Agarose antibody (SigmaAldrich, A2220, SLBX3759)


title: PPMS_NAWM_07

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: disease state


title: Tcf7_CD4_WT

city: Ann Arbor

first: Marina

last: Pasca di Magliano

state: MI

address: 1500 E Medical Center Dr

country: USA

institute: University of Michigan

description: Orthotopic pancreatic tumor digested to single cell suspension and submitted for single cell RNA sequencing

data_processing:
Sample was run using paired-end 50 cycle reads on NovaSeq 6000 (Illumina) to a depth of 100,000 reads.
Raw Data was processed and aligned by the University of Michigan Advanced Genomics Core. Files were demulitplexed into FASTQ files using cellranger mkfastq v4.0.0.
FASTQ files were aligned, filtered, and counted by cellranger count v4.0.0 (sample 2038-WD-1) or cellranger count v6.0.1 (3421-WD-1 or 3421-WD-2) for samples and formed into feature-barcode matrices.
Feature-barcode matrices were read into R using the package Seurat version 4.0.1 and package SeuratObject version 4.0.2 and were analyzed according to the Seurat pipeline, including normalizing, scaling, filtering based on read counts and mitochondrial gene percentage, and manually labeling cells according to gene expression profiles.
Assembly: mm10-2020-A
Supplementary files format and content: H5 files containing aligned single cell sequencing data output by CellRanger

organism: Mus musculus

source_name: Orthotopic pancreatic tumor

extract_protocol:
Samples were mechanically and enzymatically digested (Collagenase V; 1 mg/mL in RPMI) under constant agitation. Single cell suspensions were obtained by filtering consecutively through 500 µm, 100 µm, and 40 µm cell strainers. Dead cells were removed using MACS Dead Cell Removal Kit (Miltenyi Biotec).
Single cell cDNA libraries were prepared and sequenced using the 10x Genomics platform at the University of Michigan Advanced Genomics Core.

treatment_protocol: Mice were treated with tamoxifen (4mg/day in 5 consecutive days) via oral gavage to induce depletion of Tcf7 in CD4+ T cells. The mice were then on tamoxifen chow (400mg/kg) until the end of the experiment.

tag: strain

tag: genotype

tag: number of mice pooled

tag: run date


title: Tcf7_CD4_KO


title: U87-MG_Hi-C

city: La Jolla

first: Jesse

middle: R

last: Dixon

state: CA

address: 10010 N. Torrey Pines Rd.

institute: Salk Institute for Biological Studies

data_processing:
Hi-C reads were aligned to the hg38 reference genome using BWA and processed with custom perl scripts (available from https://github.com/dixonlab/HiC_alignment_basic_scripts).
Processed Hi-C files were generated by first converting aligned bam files to contact files using custom perl scripts (available from https://github.com/dixonlab/HiC_alignment_basic_scripts). *.hic or *.cool files were generated using juicer (*.hic files) or cooler (*.cool files).
RNA-seq data was aligned using STAR to the hg38 reference genome. PCR duplicate reads identified using STAR.
Processed RNA-seq files (bigWig) were generated by first generating bedGraph files from STAR. Separate bedGraph files were generated for reads aligning to the positive and negative strands. These were normalized for read depth (reads per million). Negative stranded bedGraph values were multiplied by -1 for display purposed. Bedgraphs were converted to bigwig files using wigToBigWig from UCSC.
Processed RNA-seq files (*rpkm.txt) were generated by first generating gene counts over Gencode genes using HTSeq. Expression was then normalized for gene length and total read counts (RPKM).
Genome_build: hg38
Supplementary_files_format_and_content: *hic files
*cool files
bigWig files
text files (gene model RPKM)

source_name: U87-MG cell line

growth_protocol: Cell lines were grown in recommended media and passaged with TrypLE.

extract_protocol:
For Hi-C, cells were fixed with 1% formaldehyde for 10 minutes at room temperture, quenched with 0.2M Glycine for 5 minutes. Adherent cells were fixed on the tissue culture plate and removed using a cell scraper. Suspension cells were fixed in suspension. After fixation and quenching, cells were pelleted, washed 1X with DPBS, pelleted again, and frozen on dry ice. Samples were stored in -80C until further processing.
For RNA, cells were harvested in Trizol according to the manufacturers instrutions. After homogenization, samples were stored at -80C until further processing. RNA was isolate using the Purelink RNA mini kit with on column Dnase I treatment. RNA integrity was evaluated using RNA tapestation.
In situ Hi-C was performed accoring to Rao et al. Cell 2014 using the MboI restriction enzyme. Libraries were sequenced on the NextSeq 500 platform.
Stranded mRNA-seq libraries were constructed using the Illumina stranded mRNA seq kit according to the manufacturers instructions. Libaries were sequenced on the NextSeq 500 platform.

treatment_protocol: No treatments were performed

tag: cell line

tag: experiment type

value: MboI in situ Hi-C

value: Wild-type

tag: media

value: EMEM + 10% FBS + P/S


title: PPMS_NAWM_06


title: Tcf7_CD4_Merged


title: PSPPH_5118-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-5118-ChIP-2_combined


title: U118-MG_Hi-C

source_name: U118-MG cell line

value: DMEM + 10% FBS + P/S


title: TKO_LG_3

city: Boston

first: Michelle

last: Prew

state: MA

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

description:
STAR_Gene_Counts.csv
Gene_TPM.csv
LG_TKOvDKO.deseq.csv

data_processing:
Sequenced reads were aligned to the UCSC mm10 reference genome assembly and gene counts were quantified using STAR v2.7.3a.
Differential gene expression testing was performed by DESeq2 v1.22.1.
RNA-seq analysis was performed using the VIPER snakemake pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: File with raw counts for each sample
Supplementary_files_format_and_content: File with normalized counts (TPM) for each sample
Supplementary_files_format_and_content: File with differential expression data for TKO v. DKO in regular media
Supplementary_files_format_and_content: File with differential expression data for TKO v. DKO in low glucose media

source_name: B-ALL cell line

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Mini Kit following the manufacturer’s instructions.
Libraries were prepared using the Roche Kapa mRNA HyperPrep strand specific sample preparation kit from 200ng of purified total RNA according to the manufacturer’s protocol on a Beckman Coulter Biomek i7.

treatment_protocol: Cells were cultured in regular or low glucose media for 24 hours.

tag: treatment

value: Low glucose media


title: SPMS_NAWM_15

value: SPMS


title: TKO_LG_2


title: SPMS_NAWM_13


title: TKO_LG_1


title: Patient 104 post-1 year 1

city: Dallas

first: Sangeetha

last: Reddy

state: Texas

address: 2280 Inwood Road

institute: UT Southwestern Medical Center

data_processing:
FASTQ files were processed through the GeoMx ngs pipeline, uploaded to the Geomx, and standard QC applied to flag individual collections with <1000 raw reads, <80% aligned reads, <50% sequencing saturation, nuclei count <100, or No Template control counts are >1000. Additionally, segments were filtered out if they contained fewer than 10% of probes above threshold LOQ (=2*neg probe geomean or 2, whichever is higher), and probes were filtered out if they were above the LOQ in 10% of the segments or more.
save-interim-files = false
quality-trim-score = 20
2color-trimming = True
adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
adapter-trim-match-length = 10
adapter-trim-max-mismatch = 3
barcode-max-mismatch = 1
stitching-max-mismatch = 2
dedup-hd = 1
threads = 4
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached PKC file (Hs_R_NGS_WTA_v1.0.pkc)
Supplementary files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Library strategy: GeoMx Seq

source_name: primary RCC cancer

extract_protocol:
On average, 5 um-thick cryostat sections were prepared for the extraction of total RNA from tumor cell-rich areas from pre- and post-tumor biopsy tissue after ROI selection based on H&E and CAIX markers, which were identified by a surgical pathologist (PK)  stained by H&E
Each collection of oligo tags from one well (representing an ROI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

value: RCC

tag: individual

value: Patient 104

value: primary RCC cancer

tag: age

tag: tumor stage

tag: status after 1 year

value: controlled

tag: histology

value: clear cell

tag: time

value: post


title: PSPPH_5114-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-5114-ChIP-1_combined

tag: strain/genotype

tag: condition

tag: chip antibody


title: PSPPH_3362-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
N-PSPH-3362-1_combined


title: MOLM13_Hi-C

source_name: MOLM13 cell line

value: RPMI + 10% FBS + P/S


title: PPMS_NAWM_09

tag: tissue

value: Brain white matter

tag: disease state


title: PSPPH_4828-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-4828-ChIP-2_combined


title: TKO_Reg_3

description:
STAR_Gene_Counts.csv
Gene_TPM.csv
Reg_TKOvDKO.deseq.csv

tag: genotype

value: Regular media


title: Capan-1_Hi-C

source_name: Capan-1 cell line

value: IMDM + 20% FBS + P/S


title: SPMS_NAWM_12


title: A172_Hi-C

source_name: A172 cell line


title: MG-63_Hi-C

source_name: MG-63 cell line


title: A2058_Hi-C

source_name: A2058 cell line


title: PSPPH_5118-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-5118-ChIP-1_combined

value: virulence suppressing (King’s B medium, KB) condition

value: monoclonal Anti-FLAG-Agarose antibody (SigmaAldrich, A2220, SLBX3759)


title: TKO_Reg_2


title: PSPPH_4828-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-4828-ChIP-1_combined


title: PSPPH_4420-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-4420-ChIP-2_combined


title: SK-OV-3_Hi-C

source_name: SK-OV-3 cell line

value: MboI in situ Hi-C

value: Wild-type


title: RRMS_NAWM_05

value: RRMS


title: TKO_Reg_1


title: RRMS_NAWM_03


title: PSPPH_4420-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-4420-ChIP-1_combined


title: SW1088_Hi-C

source_name: SW1088 cell line

value: DMEM + 10% FBS + P/S


title: DKO_LG_3

value: Low glucose media


title: RRMS_NAWM_02


title: DKO_LG_2


title: SW626_Hi-C

source_name: SW626 cell line


title: CTL_NAWM_09

value: Control


title: Caov-3_Hi-C

source_name: Caov-3 cell line


title: DKO_LG_1


title: PSPPH_4255-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-4255-ChIP-2_combined


title: SPMS_NAWM_10

value: SPMS


title: PSPPH_3962-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3962-ChIP-2_combined


title: PSPPH_4255-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-4255-ChIP-1_combined


title: DKO_Reg_3


title: HS578T_Hi-C

source_name: HS578T cell line

value: EMEM + 10% FBS + P/S


title: CTL_NAWM_07

source_name: Brain white matter


title: BT-20_Hi-C

source_name: BT-20 cell line


title: PSPPH_3962-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3962-ChIP-1_combined

source_name: liquid culture in KB (King's B)  medium


title: CTL_NAWM_08


title: DKO_Reg_2


title: BT-549_Hi-C

source_name: BT-549 cell line


title: PSPPH_3876-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3876-ChIP-2_combined


title: DKO_Reg_1


title: DJ40_Heart_RNA_AAV-Osm_S45

city: Portland

first: Teresa

last: Zimmers

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Cell, Developmental & Cancer Biology

institute: Oregon Health & Science University

data_processing:
FASTQ files were aligned with STAR v.2.5.2b using parameter "--outSAMmapqUnique 60"
Aligned reads in BAM files were counted with featureCounts from the subread package v.1.5.1 with parameters "-s 2 -p -Q 10"
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text file with raw gene counts

source_name: apex heart

growth_protocol: Ten week old wildtype mice were injected with AAV-Osm and ten week old wildtype mice were injected with AAV-Null in the right gastrocnemius. The mice were monitored over the course of 12 weeks and euthanized according to IACUC protocol. The apex of the heart was harvested and frozen in cryovial tubes placed in liquid nitrogen then stored in -80C until RNA was extracted.

extract_protocol:
Tissues that were snap frozen in liquid nitrogen were removed from -80C. Tissues were homogenized in trizol with the bullet blender at 4C. RNA extraction was done with Qiagen RNeasy Kit. Samples were DNAse treated with the ThermoFisher Turbo DNA Free.
The concentration and quality of the RNA of the samples was first assesed with the Agilent 2100 BioAnalyzer. An RNA Integrity Number (RIN) of 5 or higher was required to pass the quality control but a RIN of 9 or higher was desired. The 100ng of RNA was used for cDNA library preparation which included mRNA purification/enrichment, RNA fragmentation, cDNA synthesis, ligation of index adaptors, and application following KAPA mRNA Hyperprep Kit prep (KK8581). Each resulting indexed library was quantified and its quality accessed by NovaSeq 6000; 5µL of 2nM pooled libraries per lane were denatured, neutralized, and applied to the cBot for flow cell deposition and cluster amplification before loading to HiSeq 3000/4000 for 75bp paired-end sequencing (Illumnia, Inc). Approximately 50M reads per library were generated. A Phred quality score (Q score) was used to measure the quality of sequencing. More than 90% of the sequencing reads reached Q30 (99.9% base call accuracy). The sequence reads were mapped to the designated reference genome using STAR (Spliced Transcripts Alignment to a Reference).

treatment_protocol: Intramuscular injection of either AAV-Null or AAV-Osm was performed on wildtype mice at 10 weeks of age.

value: cardiac muscle

tag: strain

value: AAV-Osm

tag: Sex

value: male


title: MDA-MD-436_Hi-C

source_name: MDA-MD-436 cell line

tag: cell line

tag: experiment type


title: PSPPH_3876-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3876-ChIP-1_combined


title: HCC2157_Hi-C

source_name: HCC2157 cell line

tag: media

value: RPMI + 10% FBS + P/S


title: CTL_NAWM_03

value: Brain white matter


title: PSPPH_3737-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3737-ChIP-2_combined


title: CTL_NAWM_01


title: DJ37_Heart_RNA_AAV-Osm_S43

tag: treatment


title: DJ38_Heart_RNA_AAV-Osm_S44


title: MDA-MD-231_Hi-C

source_name: MDA-MD-231 cell line


title: PSPPH_3547-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3547-ChIP-1_combined


title: PSPPH_3737-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3737-ChIP-1_combined


title: CTL_NAWM_05


title: MDA-MB-468_Hi-C

source_name: MDA-MB-468 cell line


title: HCC70_Hi-C

source_name: HCC70 cell line


title: DJ32_Heart_RNA_AAV-Osm_S42


title: DJ31_Heart_RNA_AAV-Osm_S41


title: HCC38_Hi-C

source_name: HCC38 cell line


title: DJ30_Heart_RNA_AAV-Null_S40

value: AAV-Null


title: PSPPH_3547-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3547-ChIP-2_combined


title: CTL_NAWM_04


title: PDO003, scRNAseq

city: Beijing

first: Kai

last: Chen

address: 8th Xishiku Street

department: General Surgery

country: China

institute: Peking University First Hospital

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The Cell Ranger software was downloaded from 10x Genomics website (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest). Alignment (GRCh38 reference for human samples), filtering, barcode counting, and UMI counting were performed with cell ranger count module to generate gene-cell matrix (v6.1.2, 10x Genomics).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Pancreatic cancer organoid

extract_protocol: The concentration of single cell suspension was determined using the Count Star instrument and adjusted to 1000 cells/μl. The cell suspension was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion using single cell 3’ Library and Gel Bead Kit v3.1 and Chromium Next GEM Chip G Single Cell Kit according to the manufacturer’s instructions. About 6,000 cells were loaded to each channel. Captured cells were lysed and the released RNA were barcoded by reverse transcription in each GEM. Reverse transcription was completed on a S1000TM Touch Thermal Cycler (Bio Rad). The cDNA libraries were generated, amplified, and quality assessed using the Agilent 4200. Finally, the cDNA libraries were sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with paired-end 150 bp (PE150) reading strategy.

value: Pancreatic cancer organoid

value: No treatment


title: DJ29_Heart_RNA_AAV-Null_S39


title: PDO001, scRNAseq

description: 10x Genomics


title: PSPPH_3453-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3453-ChIP-1_combined

value: virulence suppressing (King’s B medium, KB) condition

value: monoclonal Anti-FLAG-Agarose antibody (SigmaAldrich, A2220, SLBX3759)


title: PDO002, scRNAseq

description: 10x Genomics


title: Primary003, scRNAseq

description: 10x Genomics

source_name: Pancreatic cancer primary tumor

value: Pancreatic cancer primary tumor


title: HCC2218_Hi-C

source_name: HCC2218 cell line

value: MboI in situ Hi-C

value: Wild-type


title: PSPPH_3377-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3377-ChIP-2_combined


title: DJ27_Heart_RNA_AAV-Null_S38


title: HCC1569_Hi-C

source_name: HCC1569 cell line


title: HCC1937_Hi-C

source_name: HCC1937 cell line


title: Primary001, scRNAseq

description: 10x Genomics


title: PSPPH_3377-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3377-ChIP-1_combined


title: DJ26_Heart_RNA_AAV-Null_S37


title: HCC1806_Hi-C

source_name: HCC1806 cell line


title: PSPPH_3453-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3453-ChIP-2_combined


title: PSPPH_3359-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3359-ChIP-2_combined


title: Day0, Day5, Day10, with and without XAV939, multiplexed samples, scRNAseq

city: Helsinki

first: Yafei

last: Wang

state: Finland

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description:
10x Genomics
CMO ID: 301 = Day0, un differentiating sample
CMO ID: 302 = Day5, no XAV939 treatment sample
CMO ID: 303 = Day5, XAV939 treatment sample
CMO ID: 304 = Day10, no XAV939 treatment sample
CMO ID: 305 = Day10, XAV939 treatment sample

data_processing:
The Cell Ranger v3.1 mkfastq and count pipelines (10x Genomics, Pleasanton, CA) were used to demultiplex and convert Chromium single-cell 3’ RNA-sequencing barcodes and read data to FASTQ files and to generate aligned reads and gene-cell matrices.
Assembly: human genome GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: WA09 ESC

extract_protocol:
Medium was removed and cells were washed one time with DMEM/F12 and one time with sterile PBS, and incubated in 2 mg/mL Papain solution (STEMCELLTM, Cat. 07465) for 7 minutes at 37 ℃. An equal volume of 1% BSA in PBS without Ca2+ and Mg2+ was added to the cell suspension, and cells were suspended by pipetting up and down approximately 15 times using a 1 mL pipette tip. The suspension was moved to a 2 mL Eppendorf tube, and centrifuged at 300 x g for 3 minutes. The supernatant was removed and cells were resuspended in 1% BSA + 2 µM EDTA in PBS without Ca2+ and Mg2+, where volume was adjusted based on a viable cell count of approximately 1000 cells/µL using LUNA-FLTM Dual Fluorescence Cell Counter. The cell suspension was filtered 2-4 times through a 35 µm cell strainer tube cap (Falcon, Cat. 352235), and processed for scRNA-seq library construction and sequencing.
Single-cell RNA-sequencing was performed using the Chromium Single-Cell 3′RNA-sequencing system (10x Genomics, Pleasanton, CA) with the Reagent Kit v3 according to the manufacturer’s instructions. Briefly, the cells were loaded into Chromium Single Cell B Chip (10x Genomics, Pleasanton, CA) and gel beads in emulsion (GEM) generation were performed aiming at 10,000 cell capture per sample. Subsequent cDNA purification, amplification, and library construction was performed as instructed. Sample libraries were sequenced on Illumina NovaSeq 6000 system using following read lengths: 28bp (Read 1), 8bp (i7 Index), 0 bp (i5 Index) and 89bp (Read 2) aiming at 50 000 reads per cell sequencing depth.

value: WA09 ESC

tag: cell type

value: neural progenitor

value: Wild Type

value: multiplexed sample:D0, D5 and D10

value: multiplexed sample:with or without XAV939 treatment


title: HCC1599_Hi-C

source_name: HCC1599 cell line


title: Day0, Day5, Day10, with and without XAV939, multiplexed samples, CMO


title: PSPPH_3359-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3359-ChIP-1_combined

source_name: liquid culture in KB (King's B)  medium


title: Primary002, scRNAseq

description: 10x Genomics


title: Day26, differentiating sample, scRNAseq

description: 10x Genomics

value: neuron


title: DU4475_Hi-C

source_name: DU4475 cell line


title: Day24, differentiating sample, scRNAseq

description: 10x Genomics


title: HCC1187_Hi-C

source_name: HCC1187 cell line


title: PSPPH_3294-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3294-ChIP-1_combined


title: PSPPH_3294-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3294-ChIP-2_combined


title: ZNF148_repeat2

city: Austin

first: Mijeong

last: Kim

address: 2500 Speedway

institute: The University of Texas at Austin

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to hg38 genome using BWA version 0.5.9-r16.
Peaks were called using MACS peak caller with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include information regarding chromosome, peak start, peak end, peak score, and peak center for each peak

source_name: MDA-MB-231 cells stably expressing the bacterial biotin ligase Bir A

growth_protocol: MDA-MB-231 cells were cultured in RPMI with 10% FCS, 2mM Glutamine and 2% penicillin-streptomycin (P/S) at 37 degrees Celsius, 5% CO2.

extract_protocol:
ChIP was performed by cross-linking proteins to DNA using 1% formaldehyde solution in MDA-MB-231 cells. Immunoprecipitated DNA was sequenced using Illumina sequencers.
Pull-downed DNA was applied for the generation of sequencing libraries using the NEB ChIP-seq library prep. kit (E6200L) following by manufacturer’s instructions.

value: basal subtype triple negative breast cancer cell line

tag: experiment

value: Chromatin IP against biotinylated ZNF128


title: ZNF148_repeat1


title: Day22, differentiating sample, scRNAseq

description: 10x Genomics


title: 48hr_H1_Mock_rep_3

city: Cambridge

first: Rudolf

last: Jaenisch

address: 455 Main St.

institute: Whitehead Institute for Biomedical Research

data_processing:
Fifty one nt long paired end reads were mapped with STAR (PMID 23104886 ) limiting the intron length (--alignIntronMax) to 95000. We used human genome version hg38 with ENSEMBL annotation GRCh38.93. We added the SARS-CoV2 sequence (GenBank ID: MN988713.1) and annotation to the genome fasta and gtf files before making a genome index.
We assigned reads to genes using featureCounts (PMID 24227677)  with options “-p -s 2” and the same gtf file used for mapping.
Assembly: hg38, gene annotation GRCh38.93
Supplementary files format and content: Text file containing gene counts.

source_name: hPSC derived liver organoid

extract_protocol: Total RNA libraries were prepared using the Swift RNA library prep kit (Swift Biosciences).

value: hPSC derived liver organoid

value: conditioned media (mock infected)

value: 48 hrs

tag: replicate

value: Replicate 3


title: PSPPH_3040-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3040-ChIP-2_combined

value: virulence suppressing (King’s B medium, KB) condition


title: BirA_control_repeat 2

value: input


title: PSPPH_3040-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3040-ChIP-1_combined

value: monoclonal Anti-FLAG-Agarose antibody (SigmaAldrich, A2220, SLBX3759)


title: 48hr_H1_Mock_rep_2

value: Replicate 2


title: BirA_control_repeat 1


title: PSPPH_2995-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-2995-ChIP-2_combined


title: 48hr_H1_Mock_rep_1

value: Replicate 1


title: PSPPH_2995-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-2995-ChIP-1_combined


title: 48hr_H1_HI_rep2

value: heat-inactivated SARS-CoV-2


title: PSPPH_2605-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-2605-ChIP-2_combined


title: 48hr_H1_HI_rep_1


title: shZnf148, repeat 3

city: Nedlands

first: Andrew

middle: Jonghan

last: Woo

state: WA

address: 6 Verdun Street

department: UWA Centre for Medical Research

institute: University of Western Australia

data_processing:
Image analysis and base-calling was perfromed by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3. Sequence data are generated by bcl2fastq 2.17.1.14 pipeline.
Sequence data were aligned to the hg18 genome build using Tophat (v2.0.14)
Expression at the gene level (FPKM values) was estimated and normalized by Cufflinks (v2.2.1), Cuffmerge (v1.0.0) and Cuffnorm (v2.2.1).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample

growth_protocol: MDA-MB-231 cells were transduced with shControl or shZnf148 lentiviruses for 48 hours. The cells with stably integrated shRNAs were selected with 0.5 micrograms/mL of puromycin for 24 hours.  Total RNA was extracted with SV Total RNA kit (Promega).

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subtype

value: Basal

tag: transduced


title: shZnf148, repeat 1


title: PSPPH_2605-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-2605-ChIP-1_combined

tag: strain/genotype


title: shZnf148, repeat 2


title: 48hr_H1_CoV2_rep_3

value: live SARS-CoV-2

tag: time


title: 48hr_H1_CoV2_rep_2


title: shControl, repeat 3

value: LKO short-hairpin (sh) luciferase control


title: daf-2_d11_3

city: Daejeon

first: Seung-Jae

middle: V

last: Lee

address: 291 Daehak-ro

department: Biological Sciences

country: South Korea

institute: KAIST

description: mRNA

data_processing:
Sequenced reads were aligned to the C. elegans genome WBcel235 (ce11) and Ensembl transcriptome (release 98) by using STAR (v.2.7.0e). The aligned reads to genes and transcripts were quantified by using RSEM (v.1.3.1). Detailed parameters of the alignment and quantification were calculated by following guidelines of ENCODE long RNA-Seq processing pipeline.
Genome_build: WBcel235 (ce11)
Supplementary_files_format_and_content: Text files with read counts were generated by using RSEM (v.1.3.1).

organism: Caenorhabditis elegans

source_name: Whole body

growth_protocol: Worms were grown on nematode growth medium (NGM) plates as previously described in 'Maintenance of C. elegans (Stiernagle T, WormBook, 2006)'.

extract_protocol:
RNA extraction was performed as previously described with minor modifications (Jeong et al., 2020). Total RNA was extracted using RNAiso plus (Takara, Shiga, Japan) following the manufacturer’s instruction.
Libraries were constructed with TruSeq Stranded Total RNA with Ribo-Zero H/M/R_Gold (Illumina, CA, USA) by Macrogen Inc. (Seoul, South Korea) following the manufacture’s instruction.

treatment_protocol: To synchronize the stages of worms, embryos were obtained by a bleaching method (Hwang et al. 2014) and incubated in S-basal buffer for 16 hrs at 20°C with gentle rotation. Worms were placed and cultured on OP50-seeded NGM plates until they reached L4 larval stage. The worms were then treated with 50 µM 5-fluoro-2′-deoxyuridine (FUDR; SigmaAldrich, MO, USA) to prevent progeny from hatching. The animals were subsequently harvested with M9 buffer at days 1, 4, 7, and 11 of adulthoods.

tag: developmental stage

value: Day 11 adult

value: Whole body


title: daf-2_d11_2

description: mRNA

tag: tissue


title: PSPPH_2600-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-2600-ChIP-1_combined

tag: condition

tag: chip antibody


title: PSPPH_2600-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-2600-ChIP-2_combined


title: PSPPH_2022-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-2022-ChIP-2_combined


title: daf-2_d11_1

description: mRNA

tag: strain

tag: genotype


title: shControl, repeat 2

tag: cell line


title: shControl, repeat 1


title: PSPPH_5114-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-5114-ChIP-2_combined


title: 48hr_H1_CoV2_rep_1


title: 48hr_1016_Mock_rep_2

value: DiPS 1016 SevA


title: daf-2_d7_3

description: mRNA

value: Day 7 adult


title: daf-2_d7_2

description: mRNA


title: 48hr_1016_HI_rep_2

value: hPSC derived liver organoid


title: 48hr_1016_Mock_rep_1

value: conditioned media (mock infected)


title: PSPPH_1904-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-1904-ChIP-1_combined


title: PSPPH_1904-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-1904-ChIP-2_combined


title: daf-2_d7_1

description: mRNA


title: Hu blood mono, replicate 4, scRNAseq

city: Rozzano, Milan

first: Sara

last: Terzoli

address: Via Alessandro Manzoni, 56

country: Italy

institute: Humanitas Clinical and Research Center

description:
10x Genomics
The barcode appendix number matches the replicate number. e.g., Replicate 1 barcodes are identified by NNNNN_1, Replicate 2 barcodes are identifed by NNNNN_2.

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2
Assembly: GRCh38 – hg 38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: blood

extract_protocol:
Peripheral blood was obtained from 5 adult male healthy donors. Samples were collected in EDTA-coated tubes (BD Vacutainer K2E), and peripheral blood mononuclear cells (PBMCs) were isolated by Lympholyte® Cell Separation density gradient solution (Cederlane). Any residual erythrocytes were removed via ammonium-chloride-potassium (ACK) Lysing Buffer (Lonza) treatment for 60 sec at room temperature (RT). To assess PBMCs vitality, cells were stained with viability dye (Zombie NIR; Biolegend) for 15 min at RT and Fc-block was performed with 1% human serum for 10 min at RT. PBMCs were then stained for 15 min at RT with fluorophore-conjugated antibodies. Finally, cells were washed in 2% fetal bovine serum/PBS and live CD45pos/HLA-DRpos/lineageneg (CD3, CD19, CD56) were immediately FACS sorted on a FACSAria III (BD Biosciences). Cells resuspended in 0.5 ml PBS 1X plus 0.04% BSA were washed once by centrifugation and counted with an automatic cell counter (ThermoFisher; Countess II).
About 20.000 cells per sample were loaded into one channel of the Chromium Chip B using the Chromium Single Cell 3' Reagent Kits (v3 Chemistry) (10X Genomics). 50 ng per sample of the barcoded and amplified cDNA was used then for constructing the sequencing libraries. Sequencing was performed on the NextSeq550 Illumina Platform, generating on average about 477 million reads per sample (on average about 67.000 reads per single cell recovered) following the configuration of the sequencing RUN indicated by the Single Cell 3' scRNAseq v3 protocol.

value: CD45pos/HLA-DRpos/lineage neg (CD3, CD19, CD56)

value: blood

tag: age

value: 18-60 years old

tag: Sex

value: male


title: 48hr_1016_HI_rep_1

tag: treatment

value: 48 hrs


title: PSPPH_1867-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-1867-ChIP-2_combined

value: virulence suppressing (King’s B medium, KB) condition

value: monoclonal Anti-FLAG-Agarose antibody (SigmaAldrich, A2220, SLBX3759)


title: PSPPH_1867-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-1867-ChIP-1_combined


title: PSPPH_2022-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-2022-ChIP-1_combined


title: daf-2_d4_2

description: mRNA

value: Day 4 adult


title: PSPPH_1207-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-1207-ChIP-2_combined


title: Hu blood mono, replicate 5, scRNAseq

tag: cell type


title: daf-2_d4_1

description: mRNA


title: Hu blood mono, replicate 2, scRNAseq


title: daf-2_d1_2

description: mRNA

value: Day 1 adult


title: 48hr_1016_CoV2_rep_1

value: live SARS-CoV-2

value: Replicate 1


title: 48hr_1016_CoV2_rep_2

value: Replicate 2


title: Hu blood mono, replicate 1, scRNAseq


title: 120hr_Mock_w_MAC_rep_2

value: conditioned media (mock infected) and macrophage exposure

value: 120 hrs


title: Stimulated memory CD4+ T effector cells

city: Oxford

first: David

last: Flores Santa Cruz

state: Oxfordshire

address: Roosevelt Drive

department: Diabetes and Inflammation Laboratory

country: United Kingdom

institute: Wellcome Centre for Human Genetics

data_processing:
Map sample reads to the human reference genome with mm2
Merge the different lanes per sample
Remove duplicates, each replicate separately
Merge both replicates
Create the bigwig files with bamCoverage
Genome_build: GRCh38
Supplementary_files_format_and_content: Genome coverage per sample in bigwig format, with a bin size of 1

source_name: Whole blood

growth_protocol: Enriched CD4+ T cells (1–2 × 10^6 CD4s/well) were cultured in a 24-well flat-bottom cell culture plate at 37 °C + 5% CO2 resuspended in X-VIVO-15 (Lonza) + 5% heat-inactivated, filtered human AB serum.

extract_protocol: OMNI-ATAC   Corces et al: doi: 10.1038/nmeth.4396

treatment_protocol: Phorbol myristate acetate (PMA), ionomycin, and protein transport inhibitors (brefeldin A and monensin). 1 × eBioscience Cell Stimulation Cocktail.

value: CD4+ T cell subsets

value: Stimulated


title: daf-2_d1_3

description: mRNA

value: Whole body


title: Unstimulated memory CD4+ T effector cells

value: Unstimulated


title: 120hr_Mock_w_MAC_rep_1

value: hPSC derived liver organoid

value: DiPS 1016 SevA


title: genomic DNA from Sella turcica tumor

type: genomic

city: New York

first: Varshini

last: Vasudevaraja

state: New York

address: 240 East 38th street

institute: NYU Langone Health

description: tumor tissue sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Ilumina iScan

data_processing: R BioConductor minfi average beta values

label: Cy3 and Cy5

source_name: Sella turcica mass

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from formalin fixed parafin embedded tissue using Maxwell 16 FFPE Plus LEV DNA Purification Kit according to standard instructions

tag: gender

value: female


title: daf-2_d4_3

description: mRNA


title: PSPPH_1195-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-1195-ChIP-2_combined


title: daf-2_d1_1

description: mRNA


title: PSPPH_1195-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-1195-ChIP-1_combined


title: 120hr_Mock_No_MAC_rep_2

value: conditioned media (mock infected)

tag: replicate


title: Unstimulated Foxp3+ Helios+ naive regulatory T cells

value: blood


title: Hu blood mono, replicate 3, scRNAseq

value: CD45pos/HLA-DRpos/lineage neg (CD3, CD19, CD56)

value: 18-60 years old

value: male


title: Stimulated Foxp3+ Helios+ naive regulatory T cells


title: PSPPH_1207-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-1207-ChIP-1_combined

value: virulence suppressing (King’s B medium, KB) condition

value: monoclonal Anti-FLAG-Agarose antibody (SigmaAldrich, A2220, SLBX3759)


title: 120hr_Mock_No_MAC_rep_1

value: Replicate 1


title: Unstimulated Foxp3+ Helios+ memory regulatory T cells


title: 120hr_HI_w_MAC_rep_2

value: heat-inactivated SARS-CoV-2 and macrophage exposure

value: Replicate 2


title: PSPPH_1179-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-1179-ChIP-1_combined


title: N2_d11_2

description: mRNA

value: wild type

value: Day 11 adult


title: PSPPH_0923-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-0923-ChIP-1_combined


title: Stimulated Foxp3+ Helios+ memory regulatory T cells

value: CD4+ T cell subsets

value: Stimulated


title: 120hr_HI_No_MAC_rep_2

value: hPSC derived liver organoid

value: heat-inactivated SARS-CoV-2

value: 120 hrs


title: N2_d7_2

description: mRNA

value: Day 7 adult

value: Whole body


title: N2_d11_1

description: mRNA


title: 120hr_HI_w_MAC_rep_1

value: DiPS 1016 SevA


title: PSPPH_1179-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-1179-ChIP-2_combined


title: N2_d7_3

description: mRNA


title: BMDM_pbs_SREBP_N2

city: Amsterdam

first: Lisa

last: Willemsen

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC - locatie AMC

data_processing:
Reads were aligned to mouse genome mm10 using Bowtie2 (Langmead & Salzberg, 2012).
SREBP1/2 binding sites were called with MACS2 using -q 1e-6.
Genomic distribution of SREBP1/2 binding sites was determined using an in-house script yielding a list of 8056 genes with SREBP1/2 bound at the promoter (between 500 and -250 bp of the TSS).
Significance of overlap between SREBP1/2 bound and down regulated genes after DOT1L inhibition was computed using a hypergeometric test.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Bone marrow-derived macrophages

extract_protocol:
30 million BMDMs were crosslinked in 2mM Disuccinimmidyl Glutarate (Pierce) and 1% formaldehyde. BMDMs were resuspended in swelling buffer (10 mM HEPES/KOH pH7.9, 85 mM KCl, 1 mM EDTA, 0.5% IGEPAL CA-630, 1x protease inhibitor cocktail, 1 mM PMSF) and incubated on ice for 5 minutes. Cells were spun down and lysed in 130 µl RLNR1 lysis buffer (20 mM Tris/HCl pH7.5, 1 mM EDTA, 0.5 mM EGTA, 0.1% SDS, 0.4% Na-Deoxycholate, 1% NP-40 alternative, 0.5 mM DTT, 1x protease inhibitor cocktail, 1 mM PMSF) and chromatin was sheared by sonication in a 96 Place microTUBE Rack (Covaris cat#500282) using a Covaris E220 for 18 cycles with the following setting: time, 60 seconds; duty, 5.0; PIP, 140; cycles, 200; amplitude, 0.0; velocity, 0.0; dwell, 0.0. Samples were recovered and spun down at max speed, 4°C for 10 minutes. 1% supernatant was taken as input DNA and remaining supernatant was transferred to PCR strips and brought up to a volume of 200 µl using RLNR1 lysis buffer (20 mM Tris/HCl pH7.5, 1 mM EDTA, 0.5 mM EGTA, 0.1% SDS, 0.4% Na-Deoxycholate, 1% NP-40 alternative, 0.5 mM DTT, 1x protease inhibitor cocktail, 1 mM PMSF). 30 µl Dynabeads Protein A/G coated with the indicated antibodies for SREBP1/2 (antibody details in Supplementary Table 1) were added to the sample, and immunoprecipitation was carried out at 4°C overnight. Beads were then collected using a magnet and washed with 175 µl ice-cold buffer as indicated by incubating samples on ice for 3 minutes: 3 times RLNR1 lysis buffer (20 mM Tris/HCl pH7.5, 1 mM EDTA, 0.5 mM EGTA, 0.1% SDS, 0.4% Na-Deoxycholate, 1% NP-40 alternative, 0.5 mM DTT, 1x protease inhibitor cocktail, 1 mM PMSF), 6 times LiCl-NR1 buffer (10 mM Tris/HCl pH7.5, 250 mM LiCl, 1 mM EDTA, 0.7% Na-Deoxycholate, 1% NP-40 alternative, 1x protease inhibitor cocktail, 1 mM PMSF), 3 times TET (10 mM Tris/HCl pH 8.0, 1 mM EDTA, 0.2% Tween-20, 1x protease inhibitor cocktail, 1 mM PMSF), and 1 time IDTET (10 mM Tris/HCl pH 8.0, 0.1 mM EDTA, 0.2% Tween-20, 1x protease inhibitor cocktail, 1 mM PMSF). Bead complexes were resuspended in 25 µl TT (10 mM Tris/HCl pH 8.0, 0.05% Tween-20, 1x protease inhibitor cocktail) and sequencing libraries were prepared on-bead as described below. ChIP libraries were prepared while bound to Dynabeads using NEBNext Ultra II DNA Library preparation kit. Libraries were eluted and crosslinks reversed by adding to the 46.5 µl NEB reaction, 20 µl water, 4 µl 10% SDS, 4.5 µl 5 M NaCl, 3 µl 0.5 M EDTA, and 1 µl 20 mg/ml proteinase K, 1 µl RNase E, followed by incubation at 55°C for 1 hour and 65°C for 2 hours to overnight in a thermal cycler. Dynabeads were removed from the library using a magnet and libraries cleaned by adding 2 µl SpeedBeads 3 EDAC in 61 µl 20% PEG 8000/1.5 M NaCl, mixing well, then incubating at RT for 10 minutes. SpeedBeads were collected on a magnet and washed two times with 150 µl 80% ethanol for 30 seconds. Beads were collected and ethanol removed following each wash. After ethanol wash, beads were air-dried and DNA eluted in 13 µl 10 mM Tris/HCl pH 8.0 and 0.05% Tween-20.
DNA was amplified by PCR for 14 cycles in a 25 µl reaction volume using NEBNext Ultra II PCR master mix and 0.5 µM each Solexa 1GA and Solexa 1GB primers. PCR amplified libraries were size selected 200-500 bp using gel extraction using 10% TBE acrylamide gels.

value: Bone marrow-derived macrophages

value: WT

tag: antibody


title: 120hr_HI_No_MAC_rep_1


title: PSPPH_0807-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-0807-ChIP-2_combined

value: virulence suppressing (King’s B medium, KB) condition


title: BMDM_pbs_input_i5


title: 120hr_CoV2_w_MAC_rep_2

value: live SARS-CoV-2 and macrophage exposure


title: KO_input

city: Seville

first: Jose

middle: Antonio

last: Guerrero-Martinez

state: Seville

address: Av. Americo Vespucio, N 24

department: Genome Biology

country: Spain

institute: CABIMER

description: KO, Input

data_processing:
One biological replicate of the ChIP-seq data for each condition (NMuMG control cells and NMuMG KO cells) were primarily filtered using the FASTQ Toolkit v1.0.0 program. Data were aligned using align function from Rsubread package, to map reads to the mm10 mouse reference genome using type = 1, TH1=2 and unique=TRUE parameters. The downstream analysis was performed on bamfiles with duplicates removed using the samtools rmdup command.
BamCoverage from Deeptools suite was used to create bigWig files using RPKM normalization.
Assembly: mm10 mouse reference genome
Supplementary files format and content: bigWig files

source_name: NMuMG cell line

growth_protocol: Normal murine mammary gland NMuMG epithelial cells were cultured in Dulbecco's modified Eagle's medium containing 10% serum and 10 μg/ml insulin, until reaching 70–80% confluency.

extract_protocol: Cells were crosslinked in 1% formaldehyde for 10 min at room temperature followed by addition of glycine (125 mM final concentration) for 5 min. Nuclei were isolated using lysis buffer 1 (5 mM Pipes pH 8, 85 mM KCl, 0.5% NP40, and complete protease inhibitor cocktail (Roche)) and were lysed using lysis buffer 2 (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.1, and complete protease inhibitor cocktail (Roche)). Chromatin was sheared into an average size of 500 bp by 8 s pulses (30 s pause between pulses) at 4 °C in the water bath sonicator Bioruptor (Diagenode, Liège, Belgium). Thirty micrograms of chromatin were incubated overnight at 4 °C in rotation, diluted 1:10 in IP buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.1, and 167 mM NaCl, 1% sodium deoxycholate) and with the respective antibodies: 3 µg of anti-H3K27ac (Ab4729, Abcam.), 3 µg of anti-H3K4me1 (Ab8895, Abcam) and 3 µg of anti-K3m4me3 (Ab8580, Abcam). Immunoprecipitations were incubated for 2 h at 4 °C in rotation with protein A Dynabeads (Invitrogen) and then washed with wash buffer 1 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, and 150 mM NaCl, 1% sodium deoxycholate), wash buffer 2 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, and 500 mM NaCl, 1% sodium deoxycholate), wash buffer 3 (0.25 M LiCl, 1% NP40, 1% sodium deoxycholate, 1 mM EDTA, and 10 mM Tris-HCl pH 8.1), and twice with TE buffer (10 mM Tris-HCl pH 8.0 and 1 mM EDTA). The complexes were eluted from the beads with elution buffer (1% SDS in TE buffer) by incubating twice 10 min at 65 °C. The eluates and the inputs were incubated overnight at 65 °C for de-crosslinking and chipped DNA was purified with phenol:chloroform extraction followed by ethanol precipitation and resuspended in miliQ water.

value: NMuMG

value: KO

tag: tissue origin

value: mammary gland


title: N2_d7_1

description: mRNA

value: wild type


title: N2_d11_3

description: mRNA

value: Day 11 adult


title: PSPPH_0479-ChIP-2

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

institute: City University of Hong Kong

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-0479-ChIP-2_combined

data_processing:
ChIP-seq reads were mapped to the Pseudomonas sringae 1448A (NC_005773.3) using Bowtie2 (version 2.3.4.3). Only the uniquely mapped reads were kept for the subsequent analyses. Bam files were transformed into bigWig files by deeptools (version 3.1.3)
RNA-seq reads were mapped to the Pseudomonas sringae 1448A (NC_005773.3) using STAR (version STAR_2.6.1). Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using DESeq2 R package.
Genome_build: Pseudomonas sringae 1448A NC_005773.3
Supplementary_files_format_and_content: narrowPeak files were generated from ChIP-seq, containing significant peaks. xlsx files were generated from RNA-seq, containing the differential expressional genes.

extract_protocol:
NEXTflex™ ChIP-Seq Kit (Bioo Scientific)
The ChIP assay was performed as previously described.For the FLAG-tagged plasmids, the open reading frame of each regulator coding gene was amplified by PCR from Psph1448A genome and cloned into pHM1 plasmid. Wild-type Psph1448A containing empty pHM1 or pHM1-RR-FLAG was cultured in 20 ml KB medium until mid-log phase (OD600 = 0.6). Cultured bacteria were then reated with 1% formaldehyde for 10 min at 28 ℃. Cross-linking was stopped by the addition of 125 mM glycine. Bacterial pellets were washed twice with a Tris buffer (20 mM Tris-HCl [pH 7.5] and 150 mM NaCl), re-suspended in 500 μl IP buffer (50 mM HEPES–KOH [pH 7.5], 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, and mini-protease inhibitor cocktail (Roche), and then subjected to sonication to produce 100-300 bp DNA fragments. Insoluble cellular debris was removed by centrifugation at 4 ℃ and the supernatant was used as the input sample in IP experiments. Both control and IP samples were washed with protein A beads (General Electric) and then incubated with 50 μl agarose- conjugated anti-FLAG antibodies (Sigma) in IP buffer. Washing, crosslink reversal, and purification of the ChIP DNA were conducted. DNA fragments (150-250 bp) were selected for library construction and sequencing libraries were prepared using the NEXTflex™ ChIP-Seq Kit (Bioo Scientific). The libraries were sequenced using the HiSeq 2000 system (Illumina). Two biological replications have been performed for all ChIP-seq experiments. ChIP-seq reads were mapped to the Pseudomonas syringae pv. phaseolicola 1448A genome (NC_005773.3) using Bowtie2 (version 2.3.4.3). Uniquely mapped reads were retained for the subsequent analyses. Binding peaks (q < 0.01) were identified using MACS2 software (version 2.1.0). Reproducible binding sites in both replicates were identified by BEDtools software (version 2.27.1)and used for the following analysis. Subsequently, the enriched loci for each regulator were annotated using the R package ChIPpeakAnno (version 3.18.2) . Target genes were annotated by peaks located in gene promoters defined as upstream of transcription start site (TSS), overlapping with TSS or encompassing the whole gene.
To examine the effect of histidine kinases on the transcriptome, 2 ml of mid-log-phase (OD600 = 0.6) bacterial cultures or 2 ml cultures of mid-log-phase induced in MM with 6 hours (Psph1448A and transcriptional regulator mutant strains) were collected by centrifugation (12,000 rpm, 4 ℃). A RNeasy mini kit (Qiagen) was used for subsequent RNA purification with DNaseI (NEB) treatment. After removing rRNA by using the MICROBExpress kit (Ambion), mRNA was used to generate the cDNA library according to the NEBNext® UltraTM II RNA Library Prep Kit protocol (Illumina), which was then sequenced using the HiSeq 2000 system (Illumina). Two biological replications have been performed for all RNA-seq experiments. For each RNA-seq sample, raw reads were mapped to the Pseudomonas sringae pv. phaseolicola 1448A genome (NC_005773.3) using STAR (version 2.6.1), and uniquely mapped reads were kept for further analyses. Differentially expressed genes were identified using DESeq2 (BH-adjusted P < 0.05 and log2 Fold Change| > 0.5).

tag: strain/genotype

value: monoclonal Anti-FLAG-Agarose antibody (SigmaAldrich, A2220, SLBX3759)


title: 120hr_CoV2_w_MAC_rep_1

tag: time

value: Replicate 1


title: PSPPH_0807-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-0807-ChIP-1_combined


title: N2_d4_2

description: mRNA

tag: developmental stage

value: Day 4 adult


title: N2_d4_3

description: mRNA

tag: tissue


title: NmuMG_input

description: Control, Input

value: Control


title: PSPPH_0479-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-0479-ChIP-1_combined

tag: condition


title: N2_d4_1

description: mRNA


title: PSPPH_0923-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-0923-ChIP-2_combined

tag: chip antibody


title: PSPPH_4853-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-4853-CHIP-2_combined


title: 120hr_CoV2_w_MAC_and_T_rep_2

value: hPSC derived liver organoid

value: live SARS-CoV-2 plus, macrophage exposure and tocilizumab

value: 120 hrs

value: Replicate 2


title: N2_d1_3

description: mRNA

tag: strain

value: Day 1 adult

value: Whole body


title: PSPPH_4853-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-4853-CHIP-1_combined

value: virulence suppressing (King’s B medium, KB) condition


title: N2_d1_2

description: mRNA

tag: genotype


title: KO_rep2

description: KO cells

data_processing:
RNA-Seq data were primarily filtered using the FASTQ Toolkit v1.0.0 program.
Data were aligned using HISAT2 software from Galaxy, to map reads to the mm10 mouse reference genome, specifying strand information as reverse (R). Limma-voom from galaxy was used to study differential expression of each gene.
Assembly: mm10 mouse reference genome
Supplementary files format and content: raw_counts.txt: Raw counts per ENSEMBL GENCODE genes at exon level for all treatments.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen).
The libraries were prepared with the TruSeq Stranded TOTAL RNA kit (Illumina, San Diego, CA, USA) and the sequencing was performed with the Illumina NextSeq 500 Mid Output 2x75 bp.

treatment_protocol: For TGFβ treatment, cells were washed with phosphate-buffered saline (PBS), and then treated with 10 ng/ml TGFβ1 diluted in 4 mM HCl, 1 mg/ml BSA (240-B, R&D Systems) for the indicated time.

tag: cell line


title: KO_TGFb2h_rep1

description: KO cells treated with 10 ng/mL TGFβ1 for 2 hours.

value: 10 ng/mL TGFbeta1 for 2 hours


title: 120hr_CoV2_No_MAC_rep_1

value: DiPS 1016 SevA

value: live SARS-CoV-2


title: N2_d1_1

description: mRNA


title: PSPPH_4737-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-4737-CHIP-2_combined


title: KO_TGFb2h_rep2

value: NMuMG

value: KO

value: mammary gland


title: FBP1 GS

city: hangzhou

first: zhimin

last: lu

address: 258kaixuan rd

institute: zhejiang university

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: Cells were cultured at 37C at 5% CO2, in DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a ultrasonicator (Covaris).
DNA fragments were end-repaired, 3’A-tail added, and ligated to Illumina sequencing adapters. Libraries were amplified and post amplification libraries were size selected at 100-300bp in length using Agencourt AMPure XP beads from Beckman Coulter.

treatment_protocol: treated with DMEM without glucose, 10% fetal bovine serum, 1x penicillin/streptomycin for 2h.

value: immortalized human hepatocyte cell line


title: NmuMG_lamin

description: Control, ChIP

value: Lamin A/C


title: KO_lamin

description: KO, ChIP


title: KO_rep1

description: KO cells


title: 120hr_CoV2_w_MAC_and_T_rep_1

value: Replicate 1


title: PSPPH_4737-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-4737-CHIP-1_combined

value: monoclonal Anti-FLAG-Agarose antibody (SigmaAldrich, A2220, SLBX3759)


title: PPARa GS

value: PPARa  (Abcam, #ab227074)


title: PSPPH_4419-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-4419-CHIP-1_combined


title: PSPPH_4419-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-4419-CHIP-2_combined


title: S1008

city: GUANGZHOU

first: YISI

last: LIU

address: SHATAI ROAD

institute: SOUTH MEDICAL UNIVERSITY

description: CamkⅡα- cre(C57BL/6)

data_processing:
Base-calling performed using Bcl2fastq (v2.17.1.14)
To remove technical sequences from raw data, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof and quality of bases lower than 20, raw data in the fastq format were processed by Trimmomatic (v 0.30) to obtain high quality reads(Bolger et al., 2014). All libraries were aligned to UCSC mm10 using Hisat2 (v 2.0.1)(Kim et al., 2015). The clean data were monitored by quality control (QC) criteria. QC-qualified samples were included for each group (Q30 > 85%, total mapped > 70%). Raw counts of the number of tags on each gene  were generated by using HTSeq (v 0.6.1), and the Fragments Per Kilobase of exon model per Million reads mapped (FPKM) is a normalized estimation of gene expression based on read ccount.
Genome_build: UCSCmm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Hippo Pyramidal neruon

extract_protocol:
Mice were perfused with artificial cerebrospinal fluid under anesthesia state which may cool the brain more rapidly(Zeisel et al., 2018). We slightly modified their protocol. ACSF consisting of 87 mM NaCl, 2.5 mM KCl, 1.25 mM NaH2PO4, 26 mM NaHCO3, 75 mM sucrose, 20 mM glucose, 1 mM CaCl2, 7 mM MgSO4 and 0.1 µM tetrodotoxin was equilibrated in 95% O2 /5% CO2 before use. Mice were anesthetized with 1% pentobarbital sodium, followed by transcardial perfusion through the left ventricle with ice-cold ACSF. The brain was removed, and 300-μm vibratome sections were collected using Vibroslice (VT 1000S; Leica) in ice-cold ACSF.  The hippocampus was microdissected and transferred to 100-mm dishes containing 7 mL digestion solution (2 mg/mL papain, Worthington, LS003119; 0.5 mM EDTA-2Na; 2.5 mL/L Glutamax 100X, ThermoFisher; resolved in Hibernate A, ThermoFisher) with 30-40 min enzymatic digestion at 30 ℃. The digestion solution was weakly acidic after the addition of papain, and 300-μL neruobasal A (ThermoFisher, 10888022) was required to adjust the pH to 7.4. After incubation, the tissue was transferred to a 15-mL tube containing 5 mL ice-cold HABG (60 mL Hibernate A; 20 mL/L B27 50X, ThermoFisher; 2.5 mL/L Glutamax 100X). The tissue pieces were gently triturated through Pasteur pipettes with polished tip openings of 0.6 mm, 0.3 mm and 0.15 mm diameter. The supernatant was transferred to a 15-mL tube after settling for 1 min. The sediment was resuspended in 2 mL HABG, and the supernatant was transferred. The procedures were repeated until the sediment was almost dissociated. The cells were enriched by centrifugation (800 g, 5 min, 4 ℃), resuspended in 1 mL HABG containing 1 mg/mL DNase I (Roche, 11284932001), and filtered with a 40-μm cell strainer (Falcon). To exclude dead cells, 0.1 μg/mL DAPI (Invitrogen) was added to the single-cell suspension. Then, the cells were immediately loaded into the Beckman MoFlo XDP Cell Sorter system for fluorescence-activated cell sorting (FACS). The high mCherry and low DAPI fluorescent cells were isolated into 1.5-mL tubes containing 5.4 µL sample buffer, 0.6 µL RNase inhibitor and 4 µL RNase-free water (Discover-sc WTA Kit V2, N711, Vazyme). Oxygenation and a short time of dissection were crucial to keep a high rate of survival in the cell suspension. For cell sorting experiments, ∼500 - 1,000 cells were isolated from 2 - 3 mice, and this represented 1 biological sample in our analysis. For each group, 3-5 biological replicates were obtained.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Three different doses (2.88×10^8, 2.88×10^9, 2.88×10^10 vector genomes) of rAAV5 vectors carrying cre-dependent mCherry mRNA (rAAV5-DIO-mCherry) were chosen in this study, and the lower rAAV5 was used as a default control. To isolate the fluorescent cells for transcriptional profiling, slices of the hippocampus were sectioned three weeks after rAAV5-DIO-mCherry injection, and a single-cell suspension was generated.

value: brain

value: Hippo Pyramidal neruon


title: S1009

description: CamkⅡα- cre(C57BL/6)


title: control_TGFb2h_rep2

description: Cells treated with 10 ng/mL TGFβ1 for 2 hours.

value: Control


title: control_TGFb2h_rep1


title: S1007

description: CamkⅡα- cre(C57BL/6)


title: HSC.RNA

first: Sai

last: Ma

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The data is processed using share-seq alignment v2 pipeline (https://github.com/masai1116/SHARE-seq-alignmentV2)
Assembly: hg19 or mm10
Supplementary files format and content: Counts.csv file contains sumamried information for each cell barcode. Column 1-4 are cell barcodes, column 5 is filtered read count, column 6 is sequencing depth, column 7 is duplciation rate, column 8 is estimated library size
Supplementary files format and content: fragments file contains Tn5 corrected cut sites per cell. Column 1-3 are genomic coordinates, column 4 is cell barcode, column 5 is frequency of the fragment.
Supplementary files format and content: count.matrix file is a sparse matrix file of the filtered ATAC count matrix.
Supplementary files format and content: peak file contain peak range of ATAC count matrix
Supplementary files format and content: metadata table contains cell type annotation, barcode translation table and umap coordiantes
Supplementary files format and content: h5 is the unfiltered RNA count matrix

molecule: polyA RNA

source_name: bone marrow

extract_protocol:
For colonic epithelial cell collection, ten C57BL/6J male mice at 9 weeks of age were sacrificed and cardiac perfusion was performed using normal saline to deplete circulating immune cells and colonic tissue between the rectum and cecum was isolated. Colonic waste content was flushed and the lumen was exposed. Tissue was then placed in EDTA Dissociation Buffer (4 mM EDTA, 10 mM HEPES pH 7.2, 10% FBS) and rotated at RT for 30 minutes. The epithelial surface was then scraped four to five times with a glass coverslip to collect the mucosa and the remaining tissue was minced finely with scissors. The mucosal and muscle wall tissue were each transferred to Advanced DMEM/F12 (Fisher, 12-634-028 ) containing collagenase 0.4 mg/mL (Sigma, C9263-25MG), dispase II 1.25 U/mL (Sigma, D4693-1G), DNase 1 U/mL (Worthington, LS002004), 10 mM HEPES pH 7.2 and 5 µM Y-27632 (MedChem Express, HY-10071). Following an initial 30 minute incubation, both sets of tissue were triturated every 10 to 15 minutes until dissociated fully to single cells. Both sets of tissue were pooled, washed once with PBS and stained with Calcein Red-AM (BioLegend, 425205) for 15 minutes at room temperature. Cells were then stained with anti-Epcam  PE/Cy7 (Thermo, 14-5791-81), anti-CD45 APC-Cy7 (BioLegend, 103116), anti-Ly6G APC (BioLegend, 127613), anti-SiglecF APC (BioLegend, 155507) and DAPI. Live cells were identified as Calcein+DAPI- events. Both epithelial cells (Epcam+CD45-) and non-granulocytic immune cells (CD45+Ly6G-SiglecF-) were isolated using a BD FACSAria by sorting into Advanced DMEM/F12 with 0.2% RNase-free BSA (AmericanBio, AB01243-00050), RNase inhibitor 0.1 U/µL (Enzymatics, Y9240L) and 15 µM Y-27632.   Human bone marrow samples were purchased from AllCells (BM, CR,MNC, 10M). CD34+ selection was performed using CD34 microbead kit (Miltenyi Biotech, 130-046-703) and FACS- purified for long term HSCs (CD45+Lin-CD34+CD38-CD45RA-CD90+). The following antibodies were used for long term HSC sorting: CD45 PE Dazzle 594 (Biolegend, 304050), Lin FITC (Biolegend, 348801), CD34 APC-Cy7 (Biolegend, 343514), CD38 PE-Cy7 (Biolegend, 303516), CD45RA APC (BD, 564442) and CD90 BV421 (Biolegend cat# 328122). About 5,000 FACS sorted long term HSCs were cultured in expansion medium consisting of StemSpan SFEM II (STEMCELL Technologies) supplemented with StemSpan CD34+ expansion supplement (STEMCELL Technologies, 02691), UM171 (STEMCELL Technologies, 72912) and Stemregenin 1 (STEMCELL Technologies, 72342) in 96 well plates coated with fibronectin (Corning, 354409). After two weeks of culture in the expansion media, about 300,000 cells were harvested and profiled using SHARE-seq V2 protocol.  Frozen human Bone Marrow Mononuclear Cells (BMMCs, Allcells) are thawed in a 37 °C water bath for 1 min and transferred to a 15 ml centrifuge tube. 10 ml of pre-warmed DMEM with 10% FBS was added to cells drop-wisely. The cells were spun at 400g for 3 minutes at room temperature. After removing supernatant, the cells are washed twice in 0.5 ml PBS with 0.04% BSA. To deplete neutrophils, the cells were resuspended in 100 μl chilled DPBS with 0.2% BSA and 10 μl of human TrueStain FcX (BioLegend, 422302) and incubated on ice for 10 min to reduce non-specific labeling. The cells were then incubated on ice for another 30 min after adding 0.5 μl of biotin anti-human CD15 antibody (BioLegend, 301913). After immunostaining, 25 μl of MyOne T1 beads were added to the sample to capture the neutrophils for 5 min at room temperature. We then added 900 μl of DPBS with 0.2% BSA to dilute the sample. The sample was placed on a magnet for 3 minutes and 1 ml of the sample was transferred to a new tube while the sample was on the magnet. The cells were ready for fixation and SHARE-seqV2 experiment.
The libraries are contructed using SHARE-seqV2 procotol.
SHARE-seqV2

value: bone marrow


title: PSPPH_3907-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3907-CHIP-2_combined


title: control_rep2

description: Control cells


title: 120hr_CoV2_No_MAC_rep_2

value: hPSC derived liver organoid

value: 120 hrs

value: Replicate 2


title: PSPPH_3907-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3907-CHIP-1_combined

value: virulence suppressing (King’s B medium, KB) condition


title: BMMC.ATAC


title: control_rep1

description: Control cells


title: PSPPH_3428-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3428-CHIP-1_combined


title: XX23_TBL_4

city: Farmington

first: Stefan

middle: F

last: Pinter

state: CT

address: 263 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut, UConn Health

data_processing:
Adapters were trimmed using cutadapt v2.7
Reads were aligned to the human genome (hg38) using hisat v2.2.1
Reads were quantified against GENCODE version 36 using featureCounts v2.0 from the Rsubread package.
Assembly: hg38
Supplementary files format and content: raw counts for each gene for each sample of hiPSCs and TBLs

source_name: hiPSC-derived TBL

extract_protocol:
RNA was extracted using the PureLink RNA Minit Kit (Thermo Fisher).
TBL mRNA libraries were prepared using the  Illumina Strand mRNA Kit.
For the TBLs, 150bp paired-end reads were sequenced on the NovaSeq.

treatment_protocol: hiPSCs were differentiated to TBLs using the BAP method. hiPSCs were singlized with Accutase and plated at 50,000 cells/well of a 6well plate in mTeSR with 10uM Y-27632  for one day. Then media was changed to mouse embryonic fibroblast conditioned media (MEF-CM), supplemented with 8ng/uL human basic FGF and 10uM Y-27632. The following day, media was switched to BAP differentiation media, which consisted of MEF-CM with 10ng/mL BMP4 and 0.1uM PD173074. Media was changed daily until day 8 when cells were harvested for RNA collection.

tag: round of differentiation

value: H

value: hiPSC-derived TBL

tag: chromosome composition

value: XX


title: HSC.ATAC


title: PSPPH_3413-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3413-CHIP-2_combined


title: Grpel1 flox/flox control mice WT4_S4

first: Jouni

middle: Antero

last: Kvist

state: Uusimaa

department: Research Program for Molecular Neurology

description: Grpel1 flox/flox control mice

data_processing:
Raw data (bcl-files) was demultiplexed with bcl2fastq2 (v2.20.0.422; Illumina), removing adapter sequences and excluding reading reads that were too short (<35bp).
Additional trimming for remaining adapter sequences, ambiguous (N) and low quality bases (Phred score < 25) was done using cutadapt (Martin, 2011).
The filtered read pair were mapped to the mouse reference genome (GRCm38) with STAR (v. 2.5.4b) (Dobin et al., 2013).
Read pairs mapping to exons were used to extract gene expression counts using Rsubreads (v.2.6.4) (Liao, Smyth, & Shi, 2019). Duplicates, chimeric and multimapping reads were excluded, as well as reads with low mapping score (MAPQ < 10).
The read count data was analyzed with DESeq2 (v.1.32.0) (Love, Huber, & Anders, 2014), comparing knockout to wild type. Genes with low read depth (<50 reads in total) were excluded.
Assembly: GRCm38
Supplementary files format and content: csv (Gene annotations, DESeq2 expression results, FPKM-values and count data)

source_name: Quadriceps femoris

growth_protocol: Standard rodent housing

extract_protocol:
Total RNA using TRIZol reagent
NEBNext Ultra II Directional RNA Library Prep Kit

value: Skeletal Muscle

tag: gene knockout

value: WT (Grpel1 flox/flox)


title: Grpel1 flox/flox control mice WT3_S3

description: Grpel1 flox/flox control mice


title: S1004

description: CamkⅡα- cre(C57BL/6)

tag: cell type


title: XX23_TBL_3

value: G


title: S1003

description: CamkⅡα- cre(C57BL/6)


title: Grpel1 flox/flox control mice WT1_S1

description: Grpel1 flox/flox control mice


title: PSPPH_3413-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3413-CHIP-1_combined


title: XX19_TBL_4


title: Grpel1 flox/flox control mice WT2_S2

description: Grpel1 flox/flox control mice


title: XX23_TBL_2

value: F


title: PSPPH_3385-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3385-CHIP-2_combined

value: monoclonal Anti-FLAG-Agarose antibody (SigmaAldrich, A2220, SLBX3759)


title: AG04381_XO15

hyb_protocol: see  label protocol

scan_protocol: Bead chips were images on a NextSeq 550 instrument (Illumina) using standard recommended Illumina scanner settings

data_processing:
BlueFuse Multi analysis software
Processed data files include: Median log2 ratio (as calculated by BlueFuse Multi)

source_name: hiPSC

label_protocol: Genomic DNA was labeled and hybridized to an 850K version 1.2 bead chip following the Infinium CytoSNP 850K assay reference guide

growth_protocol: hiPSCs were cultured on mitotically inactive mouse embryonic fibroblasts in standard hiPSC media (80% DMEM/F12, 20% Knockout Serum Replacement, 1% Glutamax, 1% Non-Essential Amino Acids, 0.1% β-Mercaptoethanol, and 8ng/mL bFGF),  and passaged weekly by manual disruption of  10-20 representative colonies.

extract_protocol: For DNA extraction, cells were pelleted and resuspended in cell lysis buffer (10 mM Tris-HCl, pH 8.0; 100 mM NaCl; 10 mM EDTA, pH 8.0; 1% SDS; 200 μg/ml Proteinase K) and incubated at 55°C overnight. DNA was isolated using Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v), precipitated with isopropanol, washed with 70% ethanol, and resuspended in TE buffer.

value: hiPSC

value: XO


title: XX23_TBL_1

value: E


title: PSPPH_3385-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3385-CHIP-1_combined


title: S1006

description: CamkⅡα- cre(C57BL/6)

value: brain

value: Hippo Pyramidal neruon


title: AG04381_XO7


title: Skeletal muscle specific Grpel1 knockout mice KO3_S7

value: KO (Grpel1 smk -/-)


title: S1005

description: CamkⅡα- cre(C57BL/6)


title: XX19_TBL_3


title: PSPPH_3428-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3428-CHIP-2_combined


title: PSPPH_1374-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-1374-CHIP-2_combined


title: S1002

description: CamkⅡα- cre(C57BL/6)


title: AG04381_XY69

value: XY


title: XX19_TBL_2


title: PSPPH_1374-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-1374-CHIP-1_combined


title: PSPPH_1363-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-1363CHIP-2_combined


title: S1001

description: CamkⅡα- cre(C57BL/6)


title: AG05278_XX23


title: Skeletal muscle specific Grpel1 knockout mice KO1_S5


title: PSPPH_1363-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-1363-CHIP-1_combined


title: XO8_TBL_4

value: D


title: AG05278_XO9


title: PSPPH_1166-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-1166-CHIP-2_combined

value: virulence suppressing (King’s B medium, KB) condition


title: XO9_TBL_4


title: AG05278_XX19


title: GN1

city: Melbourne

first: Janith

last: Seneviratne

state: VIC

address: Peter MacCallum Cancer Centre, 305 Grattan Street

institute: Peter MacCallum Cancer Centre

data_processing:
Fastq read pairs from sequencing runs of each cell plate (following the Smart-seq2 protocol) were parsed using the DrSeq2 pipeline (v2.2.0) implemented in python 2.7.0. DrSeq2 was ran in "simple" mode with the following run parameters (DrSeq simple -b $plate"_combined_R1.fastq" -r $plate"_combined_R2.fastq" -n $samplename --cellbarcoderange 9:16 --umirange 17:26 -g hg38_genes.genePred --maptool STAR --mapindex star_index_hg38 --thread 8 -f). The STAR version used internally for index generation, read alignment and counting was v2.7.5c.Read alignments were made to the human genome (hg38, ensembl release 93 GRCh38).
Resulting UMI count matrices from different plates corresponding to different patient samples were then bound using a custom R script with base R functions (R version 3.5.1).
Genome_build: hg38
Supplementary_files_format_and_content: The processed files are in a tab-dellimited text format. Each file contains the raw/unfiltered UMI count matrices of single cells (columns) and genes (rows) corresponding to each sample.

source_name: Peripheral neuroblastic tumor (PNT)

extract_protocol:
Following surgical resection of peripheral neuroblastic tumors, fresh tissue samples were immediately transferred to DMEM/F12 medium (MULTICELL), supplemented with 2% FBS (Gemini Bio-Products) and were delivered on ice within 60 minutes to the laboratory to be processed. Tissue processing was completed within 90 minutes of collection. Samples were first rinsed in ice cold PBS (MULTICELL) with 2% penicillin-streptomycin (BBI life science) and then minced into 1mm3 pieces using curved scissors under sterile conditions. The fragments were further enzymatically dissociated into single cells using LiberaseTM (Roche) with a final concentration of 0.26 U/mL and a final volume of 25ml Liberase solution/0.5g tissue on a shaker with a speed of 85 rpm for 45 min at 37℃. The Liberase was diluted in Hyclone L-15 Leibovitz media. DMEM/F12 media supplemented with 10% FBS was used to stop dissociation. The resulting single-cell suspension was filtered through a 70µm nylon cell strainer (BD Falcon) and then centrifuged for 5 min at 300g at room temperature. The cell pellet was resuspended in 500µL of PBS supplemented with 0.1% BSA (BBI life science) and passed through a 40µm nylon cell strainer (BIOFIL). This cell suspension was stained with Calcein-Blue (Invitrogen) and DRAQ5 (CST) prior to fluorescence activated cell sorting (FACS) in order to isolate live and nucleated cells (Calcein-Blue+ DRAQ+). Single cells were sorted using a BD Becton Dickinson FACSAriaII into 96-well PCR plates. Each well of the 96-well plate contained 3µL lysis buffer (10U Recombinant RNase Inhibitor (Takara Bio), 0.2% Triton X-100 (Sigma- Aldrich), 3mM dNTP mix (Takara Bio)), and reverse transcription reagents (see below). Immediately following FACS, plates were briefly centrifuged and stored at -80℃.
scRNA-seq was conducted using the Smart-seq2 protocol with some modifications being made to incorporate unique molecular identifiers (UMIs) into the 3’ end of transcripts. Reverse transcription was performed directly in the 96-well plates by incubation at 72℃ for 5 min, after which the plate was replaced on ice to allow the oligo-DT primer to hybridize to the poly(A) tail of the mRNA molecules. The oligo(dT) primer used in reverse transcription included an additional 8bp cell barcode, 9bp unique molecular identifiers (UMIs) and template-switching oligo sequence. PCR amplification was performed by adding 15µL PCR mix containing 0.5U KAPA HiFi HotStart (Kapa Biosystems), 1x KAPA Buffer (Kapa Biosystems), 12.5mM MgCl2 (Kapa Biosystems), 5µM ISPCR Primer and 7.5mM dNTP mix (Takara Bio). PCR amplification was performed in a thermal cycler (BIORAD C1000 Touch Thermal Cycler) at 98℃ for 3 min, 24 cycles of 98℃ for 20s, 67℃ for 15s, and 72℃ for 6 min, and a final incubation at 72℃ for 5 min. PCR products were purified using 1X AMPure XP bead (Beckman, Cat. #A63882) and Qubit dsDNA HS Assay Kit (Invitrogen, Cat. #Q32854). TN5 tagmentation and library amplification realized 3’end fragments by Nextera XT DNA Sample Preparation Kit (Illumina, Cat # FC- 131-1024) according to the manufacturer’s instructions while P5_TSO and Nextera_N7xx took the place of the custom primers. Pooled single cell libraries were sequenced at an average depth of 0.5 million reads per cell on an Illumina HiSeqX10 instrument using a 2 x 150bp paired end sequencing kit (Genewiz).
scRNA-seq of primary neuroblastic tumor using the Smartseq2-UMI platform.
OTHER: Modified Smart-seq2

value: Peripheral neuroblastic tumor (PNT)

tag: histological subtype

value: ganglioneuroma

tag: sequencing batch

value: B

tag: age at diagnosis in months

tag: Sex

value: Female

tag: inss disease stage

tag: inrg risk stratification

tag: chromosome 1p deletion

tag: chemotherapy

value: no

tag: primary site

tag: histology

tag: inrc therapy response

value: complete response

tag: vital status

value: Alive

tag: time of last follow up in months


title: Skeletal muscle specific Grpel1 knockout mice KO4_S8

tag: tissue

value: Skeletal Muscle


title: GNB3

value: ganglioneuroblastoma intermixed

value: C

value: Male

value: Low

value: mediastiunum


title: GNB4

value: E

value: Intermediate

value: yes

value: retroperitoneum


title: AG05278_XO8

value: hiPSC

tag: chromosome composition

value: XO


title: XO2_TBL_4

tag: round of differentiation

value: D

value: hiPSC-derived TBL


title: XX6_TBL_4

tag: cell type

value: XX


title: AG04381_XY70

value: XY


title: AG05278_XX6


title: Skeletal muscle specific Grpel1 knockout mice KO2_S6

tag: gene knockout

value: KO (Grpel1 smk -/-)


title: XO_TBL_4


title: PSPPH_0642-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-0642-CHIP-2_combined

source_name: liquid culture in KB (King's B)  medium

tag: strain/genotype

tag: condition

value: virulence suppressing (King’s B medium, KB) condition

tag: chip antibody

value: monoclonal Anti-FLAG-Agarose antibody (SigmaAldrich, A2220, SLBX3759)


title: GNB1

value: Peripheral neuroblastic tumor (PNT)

tag: histological subtype

value: ganglioneuroblastoma nodular

tag: sequencing batch

value: B

tag: age at diagnosis in months

tag: Sex

value: Female

tag: inss disease stage

value: High

value: no

value: progressive disease

value: Alive


title: GNB2

value: A

value: Male

tag: inrg risk stratification

value: Intermediate

tag: chromosome 1p deletion

tag: chemotherapy

tag: primary site

tag: histology

value: ganglioneuroblastoma nodular poorly differentiated

value: complete response


title: XX19_TBL_1

value: E

value: hiPSC-derived TBL

tag: chromosome composition

value: XX


title: PSPPH_0642-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-0642-CHIP-1_combined

value: virulence suppressing (King’s B medium, KB) condition

value: monoclonal Anti-FLAG-Agarose antibody (SigmaAldrich, A2220, SLBX3759)


title: AG09270_XO

value: hiPSC

value: XO


title: AG05278_XO2


title: PSPPH_0499-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-0499-CHIP-2_combined


title: XY_TBL_4

tag: round of differentiation

value: D

value: XY


title: NB5

tag: tissue

value: Peripheral neuroblastic tumor (PNT)

value: neuroblastoma

value: F

value: High

value: yes

value: retroperitoneum

value: neuroblastoma differentiating

tag: inrc therapy response

tag: vital status

value: Dead

tag: time of last follow up in months


title: NB4

value: Female

value: Intermediate

value: no

value: neuroblastoma poorly differentiated

value: complete response

value: Alive


title: XO9_TBL_3

value: C

tag: cell type

value: hiPSC-derived TBL

value: XO


title: PSPPH_0499-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-0499-CHIP-1_combined

tag: strain/genotype

tag: condition

value: virulence suppressing (King’s B medium, KB) condition

tag: chip antibody

value: monoclonal Anti-FLAG-Agarose antibody (SigmaAldrich, A2220, SLBX3759)


title: NB3

value: Peripheral neuroblastic tumor (PNT)

tag: histological subtype

value: neuroblastoma

tag: sequencing batch

value: B

tag: age at diagnosis in months

tag: Sex

value: Male

value: partial response


title: AG09270_XY

value: hiPSC

value: XY


title: PSPPH_0480-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-0480-CHIP-2_combined


title: PSPPH_1166-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-1166-CHIP-1_combined


title: PSPPH_0480-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-0480-CHIP-1_combined


title: NB2

value: A

tag: inss disease stage

tag: inrg risk stratification

value: High

tag: chromosome 1p deletion

tag: chemotherapy

value: yes


title: NB1

value: Female

value: Intermediate

value: no

tag: primary site

tag: histology

value: neuroblastoma poorly differentiated

value: complete response


title: XO2_TBL_3

tag: round of differentiation

value: C

value: hiPSC-derived TBL

tag: chromosome composition

value: XO


title: XX6_TBL_3

value: XX


title: Sample 2E_Rep2

city: Miami

first: Chaitanya

last: Jain

state: FL

address: 1011 NW 15th St

department: Biochemistry and Molecular Biology

institute: University Of Miami

description: PAR-CLIP

data_processing:
Reads were trimmed using Cutadapt
Reads were aligned using Bowtie 2
Read counts and variants were identified by using Naïve Variants Caller
Read counts and variants were counted by using Variants Annotator
Assembly: NC_000913.3
Supplementary files format and content: Base reads by genome coordinate

organism: Escherichia coli

source_name: WT strain

growth_protocol: Wild-type and mutant cells were grown at 37C in rich defined medium containing 4-thiouridine and harvested in mid log phase

extract_protocol:
Cells were lysed by sonication and cell extracts were incubated with anti-FLAG beads. After purification, proteins were gel-fractionated and transferred to nitrocellulose. RNA was released by using proteinase K treatment.
Libraries were constructed from the RNAs by using the NEBNext Small RNA prep kit (New England Biolabs).

tag: cell line

value: MG1655 rph+

value: Bacteria

tag: genotype

value: Wild-type

tag: treatment

value: Growth at 37C with 4-thiouridine


title: Sample 2D_Rep2

description: PAR-CLIP

tag: cell type


title: PSPPH_0252-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-0252-CHIP-2_combined

tag: strain/genotype

tag: condition

value: virulence suppressing (King’s B medium, KB) condition

tag: chip antibody

value: monoclonal Anti-FLAG-Agarose antibody (SigmaAldrich, A2220, SLBX3759)


title: Sample 2C_Rep2

description: PAR-CLIP


title: XO_TBL_3


title: species mixing.RNA

organism:
Homo sapiens
Mus musculus

source_name: HEK293 and NIH/3T3

value: HEK293 and NIH/3T3


title: Sample 2B_Rep2

description: PAR-CLIP


title: XY_TBL_3

value: XY


title: PSPPH_0252-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-0252-CHIP-1_combined


title: species mixing.ATAC


title: Sample 2A_Rep2

description: PAR-CLIP


title: PSPPH_3800-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3800-CHIP-2_combined


title: XO9_TBL_2

value: B


title: Wheat Root RNA-seq Rep 2

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
Sequences were quality trimmed and adaptors were identified and filtered using CutAdapt v2.8
UMI sequences were extracted from processed fasta files using UMI-tools v1.0.1
Sequences were aligned to their respective genome using STAR v2.7.2
Sequences were deduplicated using the UMI and mapping location using UMI-tools v1.0.1
Transcriptoinal start sites were determined using the R library TSRchitect v1.2.0 in R v4.0.0
Genome_build: Maize genome = AGPv4.38, Sorghum genome = NCBIv3.52, Rice genome = IRGSP-1.0.51, Wheat genome = IWGSC.51, Soy genome = Wm82.a4.v1
Supplementary_files_format_and_content: Text file containing single nucleotide position of transcription start site, read count, and strand

organism: Triticum aestivum

source_name: Wheat root

growth_protocol: Plants grown for four weeks with standard 16H daylight conditions at room temperature

extract_protocol:
RNA was extracted using Monarch Total RNA Extraction and Purification kit (NEB #T2010)
Libraries where prepared using the novel smar2C2 method described in the related manuscript

tag: strain

value: Chinese spring

tag: technique

value: RNA-seq

tag: tissue

value: Root


title: PSPPH_3800-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3800-CHIP-1_combined


title: Sample 1E_Rep2

description: PAR-CLIP

source_name: FLAG-tagged Hfq strain


title: XO8_TBL_3


title: XO8_TBL_2


title: XO2_TBL_2


title: Wheat Shoot RNA-seq Rep 2

source_name: Wheat shoot

value: Shoot


title: Sample 1D_Rep2

description: PAR-CLIP


title: PSPPH_3220-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3220-CHIP-2_combined


title: Wheat Shoot RNA-seq Rep 1


title: Sample 1C_Rep2

description: PAR-CLIP


title: Wheat Root smar2C2 Rep 2


title: Sample 1B_Rep2

description: PAR-CLIP


title: PSPPH_1906-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-1906-CHIP-2_combined


title: PSPPH_1906-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-1906-CHIP-1_combined


title: Sample 1A_Rep2

description: PAR-CLIP


title: Wheat Root smar2C2 Rep 1


title: XY_TBL_2


title: PSPPH_1364-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-1364-CHIP-2_combined


title: Sample 2E_Rep1

description: PAR-CLIP


title: XO9_TBL_1

value: A


title: PSPPH_1364-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-1364-CHIP-1_combined


title: Wheat Root RNA-seq Rep 1


title: Sample 2D_Rep1

description: PAR-CLIP


title: Wheat Shoot smar2C2 Rep 1


title: PSPPH_0800-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-0800-CHIP-2_combined


title: XO8_TBL_1

value: hiPSC-derived TBL


title: PSPPH_3220-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-3220-CHIP-1_combined


title: Sample 2C_Rep1

description: PAR-CLIP


title: PSPPH_0800-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-0800-CHIP-1_combined


title: Maize Root RNA-seq Rep 1

organism: Zea mays

source_name: Maize root


title: Sample 2B_Rep1

description: PAR-CLIP


title: XO2_TBL_1

value: XO


title: XX6_TBL_1

value: XX


title: PSPPH_4431-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-4431-CHIP-2_combined


title: XX6_TBL_2


title: Sample 2A_Rep1

description: PAR-CLIP

value: MG1655 rph+


title: Maize Shoot RNA-seq Rep 2

source_name: Maize shoot


title: XO_TBL_2


title: XO_TBL_1


title: Sample 1E_Rep1

description: PAR-CLIP

value: Bacteria


title: PSPPH_4431-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-4431-CHIP-1_combined


title: Wheat Shoot smar2C2 Rep 2


title: Maize Shoot RNA-seq Rep 1


title: XY_TBL_1


title: PSPPH_0094-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-0094-CHIP-2_combined


title: Sample 1D_Rep1

description: PAR-CLIP


title: Maize Root smar2C2 Rep 2


title: PSPPH_0094-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-0094-CHIP-1_combined


title: Maize Root RNA-seq Rep 2


title: Maize Root smar2C2 Rep 1


title: MRC5-veh-A

first: Genomics-core-facility

last: WCM

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
RNA was prepared using TruSeq Stranded mRNA Sample Library Preparation kit (Illumina, San Diego, CA), according to the manufacturer’s instructions.
The normalized cDNA libraries were pooled and sequenced on Illumina NovaSeq6000 sequencer with pair-end 50 cycles. The raw sequencing reads in BCL format were processed through
The RNA reads were aligned and mapped to the GRCm38 human reference genome by STAR (Version2.5.2).
The transcriptome reconstruction was performed by Cufflinks (Version 2.1.1). The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include normalized abundance measurements(FPKM) at gene level for each samples

source_name: lung fibroblast

growth_protocol: MRC5 were maintained in EMEM (ATCC) supplemented with 10% FBS (Sigma-Aldrich) and 1% penicillin-streptomycin (Gibco).

extract_protocol:
RNA was extracted from cells using the Ambion PureLink RNA Mini Kit (Life Technologies) according to manufacturer’s instructions and treated with DNase I (Amplification grade, Sigma-Aldrich). Total RNA integrity was checked using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). RNA concentrations were measured using the NanoDrop system (Thermo Fisher Scientific, Inc., Waltham, MA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1mM MMA was added into medium, the cells were treated for 5days

value: lung

value: fibroblast

value: vehicle


title: MRC5-veh-C


title: PSPPH_0069-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
PSPPH-0069-CHIP-2_combined

value: virulence suppressing (King’s B medium, KB) condition

value: monoclonal Anti-FLAG-Agarose antibody (SigmaAldrich, A2220, SLBX3759)


title: Sample 1B_Rep1

description: PAR-CLIP

value: Growth at 37C with 4-thiouridine


title: Maize Shoot smar2C2 Rep 2


title: MRC5-MMA-C

value: MMA


title: Sample 1C_Rep1

description: PAR-CLIP


title: MRC5-MMA-A


title: ful PI rep1

status: Public on Oct 03 2022

city: Berlin

middle: M.

last: Muino

address: Max-Dohrn-Str. 8-10

country: Germany

institute: German Federal Institute for Risk Assessment

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using STAR_2.7.0b with parameters --outMultimapperOrder Random --outSAMtype BAM SortedByCoordinate
Count reads  were calculated using with featureCounts v1.6.0 with parameters  -t exon -g gene_id -T 20 -O -s 0  -M
Genome_build: TAIR10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample. Samples are listed in sequential order. i.e,. rep1, rep2, rep3

organism: Arabidopsis thaliana

source_name: Pistil

growth_protocol: Arabidopsis plants were grown on rockwool blocks watered with 1.3g/l hyponex in a growth chamber at 21C and long days (16h/8h)

extract_protocol:
The RNA was extracted with a CTAB/LiCL protocol. The samples contained each about 20 pistils/siliques or 20 dissected inflorescence meristems. RNA was extracted using CTAB/LiCL.
RNA libraries were prepared for sequencing using standard Illumina protocols. The total RNA was enriched for mRNA and processed into cDNA libraries using the Illumina TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina). After quality control (Qubit and Fragment Analyzer), samples were sequenced using Illumina NovaSeq 2x150 nt Paired End sequencing.

treatment_protocol: No treatment

value: Pistil/silique stages 12-16 (Smyth et al., 1990)

tag: ecotype

value: Ler


title: ful PI rep3


title: ful PI rep2


title: Ler PI rep3

value: wild type


title: Maize Shoot smar2C2 Rep 1

value: Shoot


title: Ler PI rep1