title: XO9_iPSC_p11

description:
3' polyA RNA
d141


title: XO8_iPSC_p14_1

status: Public on Oct 04 2022

type: SRA

city: Farmington

first: Stefan

middle: F

last: Pinter

state: CT

address: 263 Farmington Avenue

department: Genetics and Genome Sciences

country: USA

institute: University of Connecticut, UConn Health

description:
3' polyA RNA
d138

library_source: transcriptomic

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

molecule: polyA RNA

organism: Homo sapiens

source_name: hIPSC

growth_protocol: hiPSCs were grown on Geltrex in mTeSR media.

extract_protocol:
RNA was extracted using the PureLink RNA Minit Kit (Thermo Fisher).
3'mRNA hiPSC libraries were prepared using the Quant-seq 3’ mRNA Library Prep Kit FWD (Lexogen).
For the hiPSCs, 75bp single-end reads were sequenced on the NextSeq500.

tag: cell type

value: hIPSC

tag: chromosome composition

value: XO


title: XO8_iPSC_p11

description:
3' polyA RNA
d136


title: E18-1

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

data_processing:
Basecalls/demultiplexing performed using Illumina CASAVA 1.8.2
Aligned to mm10 using STAR2.4.0
Count read using HT-seq0.6.1 using mm10 RefSeq as reference
Normalization (TMM), and differential expression analysis using EdgeR
Genome_build: mm10

organism: Mus musculus

source_name: Immunopanned retinal ganglion cells

extract_protocol:
RGCs were purified from mouse retinas by sequential immunopanning. Retinas were dissociated with papain, cleared of macrophages by anti-macrophage antibodies, and RGCs purified by anti-CD90 antibodies as described previously ( Meyer-Franke et al, 1995).
RNA libraries were prepared for sequencing using standard Illumina protocols
TrueSeq +RiboZero gold

value: embryonic mouse RGCs

tag: strain


title: XO2_iPSC_p14

description:
3' polyA RNA
d134


title: XO8_iPSC_p12

description:
3' polyA RNA
d137


title: XO2_iPSC_p16

description:
3' polyA RNA
d135


title: XO2_iPSC_p13

description:
3' polyA RNA
d133


title: XO2_iPSC_p12

description:
3' polyA RNA
d132


title: XX6_iPSC_p16

description:
3' polyA RNA
d129

value: XX


title: XX6_iPSC_p15

description:
3' polyA RNA
d130


title: XX6_iPSC_p14

description:
3' polyA RNA
d128


title: XO2_iPSC_p11

description:
3' polyA RNA
d131


title: XX6_iPSC_p12

description:
3' polyA RNA
d127


title: Contrl_5_KB-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

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
(KB) WT control for PSPPH_2083 PSPPH_2377 PSPPH_3961 PSPPH_4481 PSPPH_4827 PSPPH_1479
Contrl_5_KB-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.

molecule: total RNA

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:
TruSeq RNA sample prep kit protocol (Illumina)
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


title: Contrl_5_KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
(KB) WT control for PSPPH_2083 PSPPH_2377 PSPPH_3961 PSPPH_4481 PSPPH_4827 PSPPH_1479
Contrl_5_KB-1_combined


title: Contrl_7_KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
(KB) WT control for PSPPH_2483 PSPPH_1874
Contrl_7_KB-2_combined


title: Contrl_6_KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
(KB) WT control for PSPPH_1907 PSPPH_2601 PSPPH_3454 PSPPH_3550 PSPPH_4256 PSPPH_5115 PSPPH_5172 PSPPH_3736 PSPPH_1568 PSPPH_1905 PSPPH_3360 PSPPH_0070 PSPPH_2604 PSPPH_3446 PSPPH_3877
Contrl_6_KB-1_combined


title: Contrl_6_KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
(KB) WT control for PSPPH_1907 PSPPH_2601 PSPPH_3454 PSPPH_3550 PSPPH_4256 PSPPH_5115 PSPPH_5172 PSPPH_3736 PSPPH_1568 PSPPH_1905 PSPPH_3360 PSPPH_0070 PSPPH_2604 PSPPH_3446 PSPPH_3877
Contrl_6_KB-2_combined


title: Contrl_4_KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
(KB) WT control for PSPPH_2262
Contrl_4_KB-2_combined


title: Contrl_4_KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
(KB) WT control for PSPPH_2262
Contrl_4_KB-1_combined


title: Contrl_3_KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
(KB) WT control for PSPPH_1194 PSPPH_2021 PSPPH_3041 PSPPH_3276 PSPPH_3628 PSPPH_4001 PSPPH_4074
Contrl_3_KB-1_combined


title: Contrl_3_KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
(KB) WT control for PSPPH_1194 PSPPH_2021 PSPPH_3041 PSPPH_3276 PSPPH_3628 PSPPH_4001 PSPPH_4074
Contrl_3_KB-2_combined


title: Contrl_2_KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
(KB) WT control for PSPPH_0147 PSPPH_0805 PSPPH_1371 PSPPH_1480 PSPPH_2185 PSPPH_3906 PSPPH_0483 PSPPH_4852
Contrl_2_KB-2_combined


title: Contrl_2_KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
(KB) WT control for PSPPH_0147 PSPPH_0805 PSPPH_1371 PSPPH_1480 PSPPH_2185 PSPPH_3906 PSPPH_0483 PSPPH_4852
Contrl_2_KB-1_combined


title: Contrl_1_KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
(KB) WT control for PSPPH_0253 PSPPH_0641 PSPPH_2510 PSPPH_2606 PSPPH_3295 PSPPH_3386 PSPPH_3473 PSPPH_4003 PSPPH_4095 PSPPH_4381 PSPPH_4416 PSPPH_4451 PSPPH_1729
Contrl_1_KB-1_combined


title: Contrl_1_KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
(KB) WT control for PSPPH_0253 PSPPH_0641 PSPPH_2510 PSPPH_2606 PSPPH_3295 PSPPH_3386 PSPPH_3473 PSPPH_4003 PSPPH_4095 PSPPH_4381 PSPPH_4416 PSPPH_4451 PSPPH_1729
Contrl_1_KB-2_combined


title: Contrl_7_KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
(KB) WT control for PSPPH_2483 PSPPH_1874
Contrl_7_KB-1_combined


title: Shoot 5 DAD_EtOH_1

type: RNA

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

country: Japan

institute: RIKEN

hyb_protocol: 600 ng of cRNAs  were hybridized to the microarray (GPL19830) at 65 degree for 17 hours, using Gene Expression Hybridization kit. After hybridization, the microarray was washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer  (Agilent), and then dried immediately by brief centrifugation.

scan_protocol: The microarray was scanned by Agilent DNA Microarray Scanner G2539A and  raw data was extracted using Feature Extraction program ver 10.7.3.

data_processing: Data were processed using Greenspring GX (v.14.9, Agilent Technologies) with quantile normalization as described previously. Statistical significance was assessed using a one-way ANOVA with BH correction and a 95% confidence interval (Corrected P-value < 0.1). Genes with false discovery rate (FDR) values less than 0.1 and at least 2-fold change were regarded as differentially expressed.

organism: Arabidopsis thaliana

source_name: Ethanol treated and drought stressed Shoots

label_protocol: Fluorescent-labeled (Cy3) cRNAs were prepared from 200 ng total RNA from each sample using a Quick Amp labeling kit (Agilent Technologies).

growth_protocol: Gene expression profiles of ethanol treated drought-stressed roots and shoots was performed at 3, 24, and 72 h after ethanol treatment and 1, 3, and 5 days after drought stress were analyzed using the custom microarray Agilent-034592.

extract_protocol: RNA was extracted from at least three biological replicates with the mirVana miRNA Isolation Kit (Ambion, USA) according to the manufacturer’s instructions.

treatment_protocol: 10 mM ethanol was applied through roots. Water treated plants were used as control. The drought treatment was commenced by removing excess water from the trays and ceasing any subsequent watering. Roots and shoots were harvested separately.

tag: tissue

value: Shoot

tag: treatment

value: Ethanol treatment followed by drought

tag: ecotype


title: Shoot 5 DAD_EtOH_3


title: Shoot 5 DAD_EtOH_2


title: Shoot 3 DAD_EtOH_3


title: Shoot 3 DAD_EtOH_4


title: Shoot 3 DAD_EtOH_2


title: Shoot 3 DAD_EtOH_1


title: Shoot 72 H_EtOH_3

source_name: Ethanol treated shoot

value: Ethanol treatment


title: Shoot 72 H_EtOH_1


title: Shoot 1 DAD_EtOH_2


title: Shoot 1 DAD_EtOH_3


title: Shoot 72 H_EtOH_2


title: Shoot 24 H_EtOH_3


title: Shoot 1 DAD_EtOH_1


title: Shoot 24 H_EtOH_1


title: Shoot 3 H_EtOH_3


title: PSPPH_1874-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-OX1874-KB-2_combined

value: over-expressed PSPPH_1874


title: PSPPH_2483-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-OX2483-KB-2_combined

value: over-expressed PSPPH_2483


title: PSPPH_2483-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-OX2483-KB-1_combined


title: PSPPH_1874-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-OX1874-KB-1_combined


title: Shoot 24 H_EtOH_2


title: PSPPH_3877-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-3877-KB-1_combined

value: PSPPH_3877 mutant


title: PSPPH_3446-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-3446-KB-2_combined

value: PSPPH_3446 mutant


title: PSPPH_3877-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-3877-KB-2_combined


title: PSPPH_3446-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-3446-KB-1_combined


title: Shoot 5 DAD_Water_3

source_name: Water treated and drought stressed Shoots

value: Water treatment followed by drought


title: Shoot 3 DAD_Water_3


title: Shoot 3 H_EtOH_1


title: Shoot 72 H_Water_3

source_name: Water treated shoot

value: Water treatment


title: Shoot 3 H_EtOH_2


title: Shoot 1 DAD_Water_3


title: Shoot 5 DAD_Water_2


title: Shoot 3 DAD_Water_2


title: Shoot 5 DAD_Water_1


title: PSPPH_0070-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-0070-KB-2_combined

value: PSPPH_0070 mutant


title: Shoot 3 DAD_Water_1


title: Shoot 1 DAD_Water_2


title: PSPPH_0070-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-0070-KB-1_combined


title: PSPPH_3736-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-3736-KB-2_combined

value: PSPPH_3736 mutant


title: Shoot 24 H_Water_3


title: Shoot 72 H_Water_1


title: Shoot 24 H_Water_2


title: PSPPH_3736-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-3736-KB-1_combined


title: Shoot 72 H_Water_2


title: Shoot 24 H_Water_1


title: Shoot 3 H_Water_3


title: PSPPH_1905-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-1905-KB-2_combined

value: PSPPH_1905 mutant


title: PSPPH_1905-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-1905-KB-1_combined


title: Shoot 3 H_Water_2


title: Shoot 1 DAD_Water_1


title: Shoot 3 H_Water_1


title: PSPPH_3360-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-3360-KB-1_combined

value: PSPPH_3360 mutant


title: Root 5 DAD_EtOH_3

source_name: Ethanol treated and drought stressed roots

value: Root


title: Root 5 DAD_EtOH_2


title: Root 5 DAD_EtOH_1


title: PSPPH_1568-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-1568-KB-1_combined

value: PSPPH_1568 mutant


title: Root 3 DAD_EtOH_2


title: Root 1 DAD_EtOH_3


title: Root 3 DAD_EtOH_4


title: PSPPH_3360-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-3360-KB-2_combined


title: Root 3 DAD_EtOH_3


title: Root 72 H_EtOH_3

source_name: Ethanol treated root


title: Root 1 DAD_EtOH_2


title: Root 3 DAD_EtOH_1


title: Root 1 DAD_EtOH_1


title: PSPPH_5172-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-5172-KB-2_combined

value: PSPPH_5172 mutant


title: PSPPH_1568-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-1568-KB-2_combined

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


title: PSPPH_5172-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-5172-KB-1_combined


title: Root 24 H_EtOH_3


title: PSPPH_5115-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-5115-KB-2_combined

value: PSPPH_5115 mutant


title: Root 72 H_EtOH_2


title: Root 24 H_EtOH_2


title: chpseq-FA71xAsnSer-2

city: La Jolla

first: Alain

last: Domissy

address: 10550 North Torrey Pines Road

department: Immunology

institute: The Scripps Research Institute

library_source: genomic

data_processing:
rna-seq processing with the nf-core rnaseq version 3.3 pipeline
pathway analysis with the advaitabio ipathwayguide platform
chip-seq processing with the nf-core chipseq version 1.2.2 pipeline
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files with raw rnaseq gene counts for every gene and every sample
Supplementary files format and content: comma-delimited text file with raw chipseq peak regions with value and fold change for AsnSer vs AsnXxx

molecule: genomic DNA

source_name: patient FA71x chipseq technical replicate 2

growth_protocol: iPSCs grown on Matrigel (Corning, Coming, NY) and mTeSR (Stem Cell Technologies, Vancouver, Canada) were treated for 10 days in E6 medium (Stem Cell Technologies, Vancouver, Canada) with 0.5μM LDN-193189, 10μM SB431542 and 20μg/ml FGF2. iPSC colonies were dissociated with Accutase (Innovative Cell Technologies, San Diego, CA) and plated in AggreWell plates (Stem Cell Technologies, Vancouver, Canada) at a density of 1000 cells per microwell. Neurospheres were grown in suspension for one week in  Neurobasal A medium (Thermo Fisher Scientific, Waltham, MA), supplemented with N2 and B27 supplements (Thermo Fisher Scientific, Waltham, MA) and FGF2 and EGF, both at 20μg/ml. Neurospheres were then plated on Matrigel and grown in the same medium as above until rosettes appeared. Rosettes were manually isolated, grown for 4 to 7 days in suspension, then dissociated with Accutase and plated on Matrigel at 200,000 cells/cm2. To induce neuronal differentiation, cells were grown in the same medium as above without FGF2 and EGF for 14 days.

extract_protocol:
CHIPseq libraries were prepared for sequencing using standard Illumina protocols
RNA was isolated using the RNeasy mini kit (QIAgen, Hilden, Gemany). For ChIPseq cells were crosslinked with 1% formaldehyde directly added to tissue culture media and lysed in 5mM PIPES pH 8.0, 85 mM KCL and 0.5% NP40 and cell nuclei recovered. Nuclei were lysed in 1% SDS, 10 mM EDTA pH 8.0 and  50 mM Tris-HCL, pH 8.0. Nuclei were sonicated to a DNA average size of 300bp. IP was performed with Sirt6 antibody from Abcam (Cambridge UK) ab191385

tag: disease status

value: Friedreich Ataxia

tag: genotype

value: AsnSer

tag: antibody


title: Root 72 H_EtOH_1

value: Ethanol treatment


title: Root 3 H_EtOH_3


title: Root 3 H_EtOH_2


title: Root 5 DAD_Water_3

source_name: Water treated and drought stressed roots


title: chpseq-FA272AsnSer-2

source_name: patient FA272 chipseq technical replicate 2


title: PSPPH_5115-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-5115-KB-1_combined


title: chpseq-FA71xAsnSer-1

source_name: patient FA71x chipseq technical replicate 1


title: chpseq-4078xAsnXxx-2

source_name: patient 4078x chipseq technical replicate 2

value: Asn


title: chpseq-FA272AsnSer-1

source_name: patient FA272 chipseq technical replicate 1


title: c6_iPSC_p7

type: genomic

hyb_protocol: manufacturer's standard protocol

scan_protocol: Beadchips were imaged on an Illumina instrument (Illumina). using standard recommended Illumina scanner settings

data_processing: GenomeStudio Methylation Module

label_protocol: Genomic DNA was bisulfite-converted using the EZ DNA Methylation Kit (Zymo Research), then labeled and hybridized using the Infinium Methylation EPIC BeadChip Kit (Illumina) following standard protocol of each manufacturer.

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

tag: Sex

value: female

tag: passage


title: PSPPH_4256-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-4256-KB-2_combined

value: PSPPH_4256 mutant


title: PSPPH_3550-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-3550-KB-2_combined

value: PSPPH_3550 mutant


title: PSPPH_4256-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-4256-KB-1_combined


title: PSPPH_3550-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-3550-KB-1_combined


title: Root 3 H_EtOH_1


title: chpseq-3816xAsnXxx-2

source_name: patient 3816x chipseq technical replicate 2


title: chpseq-4078xAsnXxx-1

source_name: patient 4078x chipseq technical replicate 1


title: chpseq-3816xAsnXxx-1

source_name: patient 3816x chipseq technical replicate 1


title: PSPPH_3454-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-3454-KB-2_combined

value: PSPPH_3454 mutant


title: Root 5 DAD_Water_2

value: Water treatment followed by drought


title: Root 24 H_EtOH_1


title: Root 5 DAD_Water_1


title: Root 1 DAD_Water_3


title: Root 3 DAD_Water_1


title: c6_iPSC_p22


title: PSPPH_2604-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-2604-KB-2_combined

value: PSPPH_2604 mutant


title: Root 3 DAD_Water_2


title: Root 72 H_Water_2

source_name: Water treated root

value: Water treatment


title: Root 72 H_Water_3

value: Root


title: Root 1 DAD_Water_1


title: Root 72 H_Water_1


title: Root 1 DAD_Water_2


title: Root 3 DAD_Water_3


title: Root 24 H_Water_2


title: rnaseq-FA71xAsnSer-2

source_name: patient FA71X rnaseq technical replicate 2

extract_protocol:
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA was isolated using the RNeasy mini kit (QIAgen, Hilden, Gemany). For ChIPseq cells were crosslinked with 1% formaldehyde directly added to tissue culture media and lysed in 5mM PIPES pH 8.0, 85 mM KCL and 0.5% NP40 and cell nuclei recovered. Nuclei were lysed in 1% SDS, 10 mM EDTA pH 8.0 and  50 mM Tris-HCL, pH 8.0. Nuclei were sonicated to a DNA average size of 300bp. IP was performed with Sirt6 antibody from Abcam (Cambridge UK) ab191385


title: rnaseq-FA71xAsnSer-3

source_name: patient FA71X rnaseq technical replicate 3


title: PSPPH_2604-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-2604-KB-1_combined

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


title: PSPPH_3454-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-3454-KB-1_combined


title: rnaseq-FA71xAsnSer-4

source_name: patient FA71X rnaseq technical replicate 4


title: PSPPH_2601-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-2601-KB-1_combined

value: PSPPH_2601 mutant


title: rnaseq-FA272AsnSer-3

source_name: patient FA272 rnaseq technical replicate 3


title: rnaseq-FA272AsnSer-4

source_name: patient FA272 rnaseq technical replicate 4


title: Root 24 H_Water_1


title: Root 3 H_Water_3


title: Root 3 H_Water_2


title: Shoot 0H_ Ethanol_3

source_name: Ethanol treated shoot

value: Shoot


title: Root 24 H_Water_3


title: PSPPH_1907-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-1907-KB-2_combined

value: PSPPH_1907 mutant

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


title: Root 3 H_Water_1


title: Shoot 0H_ Ethanol_2


title: PSPPH_2601-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-2601-KB-2_combined


title: rnaseq-FA272AsnSer-2

source_name: patient FA272 rnaseq technical replicate 2

value: Friedreich Ataxia


title: PSPPH_1907-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
L12-1907-KB-1_combined


title: FBSA, Treatment, Replicate 1, 3' RNA-seq

city: Corvallis

first: Christopher

middle: Michael

last: Sullivan

state: OR

address: Sinnhuber Aquatic Research Laboratory, 28645 East HWY 34

department: Environmental & Molecular Toxicology

institute: Oregon State University

data_processing:
Alignment was conducted against the Genome Reference Consortium Zebrafish Build 11 (GRCz11) using the STAR aligner using the following parameters: STAR --runThreadN 10 --genomeDir ./genomeLex --readFilesIn <file1>.fastq.gz --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype SAM --outFileNamePrefix Lexogen_Control_1_LexPipeline2
All files were converted to SAM format and gene counts were obtained using HTSeq and the following parameters: python -m HTSeq.scripts.count -m intersection-nonempty -s yes -f sam -r pos $sams/<file1>.sam $ref > $out/<file1>.txt
Raw counts files were normalized and differential expression analysis performed using DESeq2 and default parameters.
Assembly: Genome Reference Consortium Zebrafish Build 11 (GRCz11)
Supplementary files format and content: Norm_Count_Data.csv

organism: Danio rerio

source_name: whole embryo

growth_protocol: Zebrafish (Tropical 5D wild-type line) embryos were developmentally staged, dechorionated at 4 hours post fertilization (hpf), placed in 96-well plates in buffered embryo medium, and maintained at 28° ± 1°C.

extract_protocol:
10 embryos were pooled per replicate, euthanized via ice bath, homogenized in RNA-zol, and stored at -80°C until processing. Samples were then extracted using a Zymo Research Direct-zol RNA MiniPrep kit.
Libraries were prepared by the Center for Quantitative Life Sciences (CQLS) at Oregon State University using the Lexogen QuantSeq 3' FWD kit (100 bp, single end).
3' RNA-seq

treatment_protocol: Embryos were statically exposed to chemical treatments beginning 8 hpf (0 or 47 uM PFAS, 0.5% methanol normalization). 96-well plates were then sealed and shaken overnight on an orbital shaker at 235 rpm. Embryos were sampled at 48 hpf.

value: whole embryo

tag: line

value: Tropical 5D Wildtype

tag: time of harvest of rna

value: 48 hours post fertilization

tag: number of embryos used per sample

value: exposed to 47 uM FBSA at 8 hours post fertilization


title: PSPPH_4827-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
Psph-4827-KB-2_combined

value: PSPPH_4827 mutant


title: FBSA, Treatment, Replicate 2, 3' RNA-seq


title: Shoot 0H_ Ethanol_1

value: Ethanol treatment


title: FBSA, Treatment, Replicate 3, 3' RNA-seq


title: Control, Replicate 1, 3' RNA-seq

value: untreated (methanol control)


title: Control, Replicate 2, 3' RNA-seq


title: PSPPH_4827-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
Psph-4827-KB-1_combined


title: Control, Replicate 3, 3' RNA-seq


title: rnaseq-4078xAsnXxx-3

source_name: patient 4078x rnaseq technical replicate 3

value: Asn


title: Root 0H_ Ethanol_1

source_name: Ethanol treated root


title: rnaseq-4078xAsnXxx-4

source_name: patient 4078x rnaseq technical replicate 4


title: rnaseq-4078xAsnXxx-2

source_name: patient 4078x rnaseq technical replicate 2


title: PSPPH_4481-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
Psph-4481-KB-2_combined

value: PSPPH_4481 mutant


title: D5-9

city: Tarrytown

first: Kaitlyn

last: Gayvert

state: NY

address: 777 Old Saw Mill River Rd

department: Molecular Profiling & Data Science

institute: Regeneron Pharmaceuticals

description:
4871.14009.1318684.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

data_processing:
FASTQ files were aligned and quantified using Omicsoft ArrayStudio
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include read counts and TPM for each Sample

source_name: Donor D5, no stim, no stim+REGN7257

extract_protocol:
Tissues/Cells were homogenized in TRIzol and chloroform was used for phase separation. The aqueous phase, containing total RNA, was purified using MagMAX™-96 for Microarrays Total RNA Isolation Kit (Ambion by Life Technologies) according to manufacturer’s specifications. Genomic DNA was removed using RNase-Free DNase Set (Qiagen) on the Kingfisher Flex machine (Thermofisher).
mRNA-seq libraries were generated using KAPA® mRNA HyperPrep Kit (Roche Sequencing.) Starting material was 500 ng RNA and fragmentation was done at 85°C for 6 minutes. cDNA was ligated with 1.5 µM xGen Dual Index UMI Adapters (Integrated DNA Technologies) and amplified using 12 PCR cycles, also respective to RNA input. Sequencing of the resulting libraries was done on NovaSeq 6000 (Illumina) using a 51 cycle, single-end sequencing recipe.

tag: donor

value: PBMCs

value: no stim+REGN7257


title: D5-12

description:
4871.14009.1318687.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D5, stim, stim+REGN7257


title: rnaseq-3816xAsnXxx-4

source_name: patient 3816x rnaseq technical replicate 4


title: D5-10

description:
4871.14009.1318685.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt


title: D5-8

description:
4871.14009.1318683.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D5, stim, stim+REGN1945


title: D5-6

description:
4871.14009.1318681.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D5, no stim, no stim+REGN1945

value: no stim+REGN1945


title: PSPPH_4481-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
Psph-4481-KB-1_combined


title: D5-7

description:
4871.14009.1318682.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt


title: rnaseq-3816xAsnXxx-3

source_name: patient 3816x rnaseq technical replicate 3


title: D5-5

description:
4871.14009.1318680.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt


title: PSPPH_3961-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
Psph-3961-KB-2_combined

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

value: PSPPH_3961 mutant


title: Root 0H_ Ethanol_3

value: Root


title: D5-4

description:
4871.14009.1318679.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D5, stim, stim+no mab

value: stim+no mab


title: rnaseq-3816xAsnXxx-2

source_name: patient 3816x rnaseq technical replicate 2


title: D5-2

description:
4871.14009.1318677.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D5, no stim, no stim+no mab

value: no stim+no mab


title: PSPPH_3961-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
Psph-3961-KB-1_combined

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


title: U87-MG_RNA

first: Jesse

middle: R

last: Dixon

address: 10010 N. Torrey Pines Rd.

institute: Salk Institute for Biological Studies

data_processing:
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: bigWig files
Supplementary_files_format_and_content: 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 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.
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.
Stranded mRNA-seq

treatment_protocol: No treatments were performed

tag: cell line

tag: experiment type

value: Stranded mRNA-seq

value: Wild-type

tag: media

value: EMEM + 10% FBS + P/S


title: U118-MG_RNA

source_name: U118-MG cell line

value: DMEM + 10% FBS + P/S


title: D5-1

description:
4871.14009.1318676.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt


title: D4-11

description:
4871.14009.1318674.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D4, stim, stim+REGN7257


title: D4-12

description:
4871.14009.1318675.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt


title: D4-9

description:
4871.14009.1318672.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D4, no stim, no stim+REGN7257


title: SW626_RNA

source_name: SW626 cell line


title: Root 0H_ Ethanol_2

source_name: Ethanol treated root


title: PSPPH_2083-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
Psph-2083-KB-2_combined

tag: strain/genotype

value: PSPPH_2083 mutant


title: D4-10

description:
4871.14009.1318673.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt


title: D4-7

description:
4871.14009.1318670.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D4, stim, stim+REGN1945


title: SW1088_RNA

source_name: SW1088 cell line

tag: condition


title: PSPPH_2083-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
Psph-2083-KB-1_combined


title: SNU-C1_RNA

source_name: SNU-C1 cell line

value: RPMI + 10% FBS + P/S


title: D4-6

description:
4871.14009.1318669.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D4, no stim, no stim+REGN1945

tag: tissue


title: D4-4

description:
4871.14009.1318667.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D4, stim, stim+no mab

tag: treatment


title: PSPPH_1479-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
Psph-1479-KB-2_combined

value: PSPPH_1479 mutant


title: D4-3

description:
4871.14009.1318666.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt


title: PSPPH_1479-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
Psph-1479-KB-1_combined


title: D4-2

description:
4871.14009.1318665.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D4, no stim, no stim+no mab


title: SK-OV-3_RNA

source_name: SK-OV-3 cell line


title: NCI-H596_RNA

source_name: NCI-H596 cell line


title: PSPPH_2377-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
Psph-2377-KB-2_combined

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

value: PSPPH_2377 mutant


title: D3-12

description:
4871.14009.1318663.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D3, stim, stim+REGN7257


title: D3-10

description:
4871.14009.1318661.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D3, no stim, no stim+REGN7257


title: PSPPH_2262-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-2262-KB-2_combined

value: PSPPH_2262 mutant


title: NCI-H1975_RNA

source_name: NCI-H1975 cell line


title: NCI-H1573_RNA

source_name: NCI-H1573 cell line


title: D3-8

description:
4871.14009.1318659.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D3, stim, stim+REGN1945

value: PBMCs


title: PSPPH_2377-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
Psph-2377-KB-1_combined


title: D3-9

description:
4871.14009.1318660.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

value: no stim+REGN7257


title: D3-7

description:
4871.14009.1318658.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt


title: PSPPH_4074-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-4074-KB-2_combined

value: PSPPH_4074 mutant


title: D3-6

description:
4871.14009.1318657.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D3, no stim, no stim+REGN1945

value: no stim+REGN1945


title: D3-1

description:
4871.14009.1318652.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D3, no stim, no stim+no mab


title: NCI-H1563_RNA

source_name: NCI-H1563 cell line


title: D2-12

description:
4871.14009.1318651.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D2, stim, stim+REGN7257


title: NCI-H1437_RNA

source_name: NCI-H1437 cell line


title: PSPPH_4001-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-4001-KB-2_combined

value: PSPPH_4001 mutant


title: D2-11

description:
4871.14009.1318650.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt


title: D4-1

description:
4871.14009.1318664.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt


title: MV411_RNA

source_name: MV411 cell line


title: PSPPH_4001-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-4001-KB-1_combined


title: PSPPH_4074-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-4074-KB-1_combined


title: D2-8

description:
4871.14009.1318647.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D2, stim, stim+REGN1945


title: MOLM13_RNA

source_name: MOLM13 cell line


title: PSPPH_3628-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-3628-KB-2_combined

value: PSPPH_3628 mutant


title: PSPPH_2262-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-2262-KB-1_combined


title: D2-5

description:
4871.14009.1318644.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D2, no stim, no stim+REGN1945


title: D2-10

description:
4871.14009.1318649.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D2, no stim, no stim+REGN7257


title: D2-9

description:
4871.14009.1318648.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt


title: D2-3

description:
4871.14009.1318642.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D2, stim, stim+no mab

value: stim+no mab


title: PSPPH_3628-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-3628-KB-1_combined

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

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


title: D2-2

description:
4871.14009.1318641.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D2, no stim, no stim+no mab

value: no stim+no mab


title: D2-1

description:
4871.14009.1318640.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt


title: PSPPH_3276-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-3276-KB-2_combined

value: PSPPH_3276 mutant


title: D2-4

description:
4871.14009.1318643.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt


title: Maver-1_RNA

source_name: Maver-1 cell line

value: Stranded mRNA-seq

value: Wild-type


title: Mino-1_RNA

source_name: Mino-1 cell line


title: D3-4

description:
4871.14009.1318655.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D3, stim, stim+no mab


title: ML2_RNA

source_name: ML2 cell line


title: PSPPH_3276-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-3276-KB-1_combined


title: D1-12

description:
4871.14009.1318639.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D1, stim, stim+REGN7257


title: D1-8

description:
4871.14009.1318635.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D1, stim, stim+REGN1945


title: D1-11

description:
4871.14009.1318638.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt


title: D1-7

description:
4871.14009.1318634.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt


title: D1-10

description:
4871.14009.1318637.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D1, no stim, no stim+REGN7257


title: HL-60_RNA

source_name: HL-60 cell line

value: IMDM + 20% FBS + P/S


title: PSPPH_3041-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-3041-KB-1_combined

value: PSPPH_3041 mutant


title: D1-9

description:
4871.14009.1318636.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt


title: D1-5

description:
4871.14009.1318632.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D1, no stim, no stim+REGN1945


title: D1-6

description:
4871.14009.1318633.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt


title: DU-145_RNA

source_name: DU-145 cell line

value: EMEM + 10% FBS + P/S


title: CESS_RNA

source_name: CESS cell line

value: CESS

value: RPMI + 10% FBS + P/S


title: Jeko1_RNA

source_name: Jeko1 cell line


title: D1-2

description:
4871.14009.1318629.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D1, no stim, no stim+no mab

value: PBMCs


title: PSPPH_3041-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-3041-KB-2_combined


title: PSPPH_2021-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-2021-KB-2_combined

value: PSPPH_2021 mutant


title: D1-1

description:
4871.14009.1318628.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt


title: D1-4

description:
4871.14009.1318631.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D1, stim, stim+no mab


title: PSPPH_2021-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-2021-KB-1_combined


title: Caov-3_RNA

source_name: Caov-3 cell line

value: DMEM + 10% FBS + P/S


title: A2058_RNA

source_name: A2058 cell line


title: Capan-1_RNA

source_name: Capan-1 cell line


title: PSPPH_1194-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-1194-KB-2_combined

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

value: PSPPH_1194 mutant


title: PSPPH_1194-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-1194-KB-1_combined


title: decidua8, Recurrent miscarriage, replicate 1, scRNAseq

city: Nanning

first: Peiru

last: Wei

address: Shuangyong Road, 22

country: China

institute: Guangxi Medical University

description:
RM_D8
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, genes.tsv, matrix.mtx).

source_name: decidua

extract_protocol:
Decidual and placental tissue was washed in phosphate-buffered saline with 100 IU/mL penicillin/streptomycin and sheared into tiny pieces. Decidual tissue were digested with collagenase Type IV (0.5 mg/ml, Invitrogen) for 30 min when the resultant villous tissue was enzymatically digested with EDTA (Sigma) with stirring at 37 °C for 9 min. The disaggregated cell suspension was passed through 70 and 40 µm mesh sieves (Biologix), centrifuged, and resuspended in 3 ml of red blood cell lysis buffer (Invitrogen) for 3 min to exclude any remaining red blood cells. Finally, the pelleted decidual cells and placental cells were resuspended in PBS and then were used for single‐cell 3′ cDNA library preparation followed by 10× Genomics Chromium Single‐Cell 3′ reagent Kits protocol.
Library was performed according to the manufacturer’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriately sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: decidua

value: Recurrent miscarriage


title: villi7, Recurrent miscarriage, replicate 1, scRNAseq

description:
RM_V7
10x Genomics

source_name: villi

value: villi


title: decidua7, Recurrent miscarriage, replicate 1, scRNAseq

description:
RM_D7
10x Genomics


title: villi8, normal, replicate 1, scRNAseq

description:
NC_V8-1
10x Genomics

value: Normal pregnancy


title: decidua6, Recurrent miscarriage, replicate 1, scRNAseq

description:
RM_D6
10x Genomics


title: villi7, normal, replicate 1, scRNAseq

description:
NC_V7-1
10x Genomics


title: villi7, normal, replicate 2, scRNAseq

description:
NC_V7-2
10x Genomics


title: villi8, normal, replicate 2, scRNAseq

description:
NC_V8-2
10x Genomics


title: PSPPH_3906-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-3906-KB-1_combined

value: PSPPH_3906 mutant

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


title: decidua8, normal, replicate 2, scRNAseq

description:
NC_D8-2
10x Genomics


title: villi8, Recurrent miscarriage, replicate 1, scRNAseq

description:
RM_V8
10x Genomics


title: PSPPH_3906-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-3906-KB-2_combined


title: PSPPH_2185-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-2185-KB-2_combined

value: PSPPH_2185 mutant


title: villi6, Recurrent miscarriage, replicate 1, scRNAseq

description:
RM_V6
10x Genomics


title: decidua7, normal, replicate 2, scRNAseq

description:
NC_D7-2
10x Genomics


title: SK-N-DZ_WT_rep2_RNA

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: SK-N-DZ cell line

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.

value: SK-N-DZ

value: Stranded mRNA-seq

value: Wild-type

value: DMEM + 10% FBS + P/S + NEAA


title: decidua7, normal, replicate 1, scRNAseq

description:
NC_D7-1
10x Genomics


title: SK-N-DZ_C7C8E2_RNA

source_name: Engineered SK-N-DZ cell line

value: Engineered t(7;8)


title: SK-N-DZ_C7C8D9_RNA


title: decidua8, normal, replicate 1, scRNAseq

description:
NC_D8-1
10x Genomics


title: decidua6, normal, replicate 1, scRNAseq

description:
NC_D6-1
10x Genomics


title: SK-N-DZ_C6BC81A1_RNA

value: Engineered t(6;8)


title: villi6, normal, replicate 1, scRNAseq

description:
NC_V6-1
10x Genomics


title: PSPPH_4852-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-4852-KB-1_combined

value: PSPPH_4852 mutant


title: PSPPH_2185-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-2185-KB-1_combined


title: SK-N-DZ_C6BC81F2_RNA


title: MTA2-GFP11 ApaLI, Dox, sorted GFP+, replicate 2

city: New York

first: Yi

last: Fu

state: New York

address: 430 E 67th Street – RRL 1141

institute: MSKCC

description:
MTA2-counts.raw.csv
MTA2-deseq2.dds.rds
MTA2-4-12C-iA-DoxD3-GFPpos-2_IGO_12747_D_7

data_processing:
Fastq files were analyzed directly with Seq-N-Slide pipeline designed for NYU HPC cluster (https://doi.org/10.5281/zenodo.5550459)
Standard RNA-seq analysis using STAR (command: sns/run rna-star)
Differential expression analysis using DESeq2 (Command: sns/run rna-star-groups-dge)
Supplementary files format and content: RRBP1-counts.raw.csv and MTA2-counts.raw.csv are raw counts.
Supplementary files format and content: RRBP1-deseq2.dds.rds and MTA2-deseq2.dds.rds are DESeq2 objects (dds) that can be loaded and modified in R.

extract_protocol:
Frozen cells were lysed in 1 ml TRIzol Reagent (Thermo Fisher 15596018) and phase separation was induced with 200 μl chloroform. RNA was extracted from 350 μl of the aqueous phase using the miRNeasy Mini Kit (Qiagen 217004) on the QIAcube Connect (Qiagen) according to the manufacturer’s protocol. Samples were eluted in 33 μl RNase-free water.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500 ng of total RNA with RIN values of 8.9 - 10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, RS-122-2102), with 8 cycles of PCR.

tag: cell type

value: retinal pigment epithelia

value: mito-mCherry-GFP1-10 overexpressed, endogenous MTA2 homozygously tagged with 4xGFP11 at the C-terminus, inducible ApaLI integrated

value: Doxycycline for 3 days, GFP+ cells sorted


title: SK-N-DZ_WT_rep1_RNA


title: SK-N-DZ_C7C8E10_RNA


title: PSPPH_1480-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-1480-KB-2_combined

value: PSPPH_1480 mutant


title: PSPPH_4852-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-4852-KB-2_combined


title: MTA2-GFP11 ApaLI, Dox, sorted GFP+, replicate 1

description:
MTA2-counts.raw.csv
MTA2-deseq2.dds.rds
MTA2-4-12C-iA-DoxD3-GFPpos-1_IGO_12747_D_3


title: PSPPH_1480-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-1480-KB-1_combined


title: MTA2-GFP11 ApaLI, Dox, sorted GFP-, replicate 2

description:
MTA2-counts.raw.csv
MTA2-deseq2.dds.rds
MTA2-4-12C-iA-DoxD3-GFPneg-2_IGO_12747_D_8

value: Doxycycline for 3 days, GFP- cells sorted


title: MTA2-GFP11 ApaLI, Dox, sorted GFP-, replicate 1

description:
MTA2-counts.raw.csv
MTA2-deseq2.dds.rds
MTA2-4-12C-iA-DoxD3-GFPneg-1_IGO_12747_D_4


title: PSPPH_1371-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-1371-KB-2_combined

value: PSPPH_1371 mutant


title: SK-N-DZ_C5BC89D4_RNA

value: Engineered t(5;8)


title: MTA2-GFP11 ApaLI, Dox, unsorted, replicate 2

description:
MTA2-counts.raw.csv
MTA2-deseq2.dds.rds
MTA2-4-12C-iA-DoxD3-2_IGO_12747_D_6

value: Doxycycline for 3 days


title: SK-N-DZ_C1C84E12_RNA

value: Engineered t(1;8)


title: MTA2-GFP11 ApaLI, Dox, unsorted, replicate 1

description:
MTA2-counts.raw.csv
MTA2-deseq2.dds.rds
MTA2-4-12C-iA-DoxD3-1_IGO_12747_D_2


title: MTA2-GFP11 ApaLI*, Dox, unsorted, replicate 2

description:
MTA2-counts.raw.csv
MTA2-deseq2.dds.rds
MTA2-4-12C-iAd-DoxD3-2_IGO_12747_D_5

value: mito-mCherry-GFP1-10 overexpressed, endogenous MTA2 homozygously tagged with 4xGFP11 at the C-terminus, inducible catalytically inactive ApaLI integrated


title: SK-N-DZ_C12BC83A5_RNA

value: SK-N-DZ

value: Engineered t(12;8)


title: MTA2-GFP11 ApaLI*, Dox, unsorted, replicate 1

description:
MTA2-counts.raw.csv
MTA2-deseq2.dds.rds
MTA2-4-12C-iAd-DoxD3-1_IGO_12747_D_1


title: PSPPH_1371-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-1371-KB-1_combined

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


title: PSPPH_0805-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-0805-KB-1_combined

value: PSPPH_0805 mutant


title: RRBP1-GFP11 ApaLI, Dox, sorted GFP+, replicate 2

description:
RRBP1-counts.raw.csv
RRBP1-deseq2.dds.rds
3-4F-iA-DoxD3-Gpos-Rep2_IGO_12747_B_7

value: mito-mCherry-GFP1-10 overexpressed, endogenous RRBP1 homozygously tagged with 4xGFP11 at the C-terminus, inducible ApaLI integrated


title: PSPPH_0805-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-0805-KB-2_combined


title: PSPPH_0483-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-0483-KB-2_combined

value: PSPPH_0483 mutant


title: RRBP1-GFP11 ApaLI, Dox, sorted GFP+, replicate 1

description:
RRBP1-counts.raw.csv
RRBP1-deseq2.dds.rds
3-4F-iA-DoxD3-Gpos-Rep1_IGO_12747_B_3


title: SK-N-DZ_C12AC83E1_RNA

value: Stranded mRNA-seq

value: DMEM + 10% FBS + P/S + NEAA


title: RRBP1-GFP11 ApaLI, Dox, unsorted, replicate 2

description:
RRBP1-counts.raw.csv
RRBP1-deseq2.dds.rds
3-4F-iA-DoxD3-Rep2_IGO_12747_B_6

value: retinal pigment epithelia


title: RRBP1-GFP11 ApaLI, Dox, sorted GFP-, replicate 1

description:
RRBP1-counts.raw.csv
RRBP1-deseq2.dds.rds
3-4F-iA-DoxD3-Gneg-Rep1_IGO_12747_B_4


title: RRBP1-GFP11 ApaLI, Dox, sorted GFP-, replicate 2

description:
RRBP1-counts.raw.csv
RRBP1-deseq2.dds.rds
3-4F-iA-DoxD3-Gneg-Rep2_IGO_12747_B_8


title: SK-N-DZ_C7C8B1_RNA

value: Engineered t(7;8)


title: PSPPH_0147-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-0147-KB-2_combined

value: PSPPH_0147 mutant


title: SK-N-DZ_C12AC84G1_RNA


title: MDA-MB-231 H3K27ac

city: Beijing

first: Wanliang

last: Lu

address: No.38 Xueyuan Road, Haidian District

institute: Peking University

data_processing:
ChIP-Seq raw reads were firstly filtered to remove low-quality or adaptor sequence by SOAPnuke with parameters: filter -1 5 –q 0.5 –n 0.1 –Q 2 -5 1 –c 50.
Cleaned reads were mapped to the reference genome of NCBI hg38 using SOAPaligner/SOAP2 (version: 2.2.5), whose parameters was –v 2 –s 35.
MACS2 (version: 2.1.2) was used to call peaks (open chromatin regions), in which ‘—bw 200 –g NCBI –s 50 –p le-5 –m 10 30 –broad –B –trackline’ was used.
The overlapped enrichment peaks between H3K4me1 and H3K27ac data in the same cell type were identified by bedtools intersect mode with overlap 50%.
Genome_build: hg 38
Supplementary_files_format_and_content: WIG files

growth_protocol: MDA-MB-231 cells and MCF-7 cells  were cultured in the Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS; PAN, Beijing local agent, Germany), 100 U/mL penicillin, and 100 μg/mL streptomycin (Macgene, Beijing, China) at 37°C under 5% CO2 circumstance.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature, and quenched by the addition of glycine to a final concentration of 125 mM for 5 min. The fixed cells were re-suspended in SDS lysis buffer in the presence of protease inhibitor Cocktail II, then subjected to 12 cycles (turn on for 20 s and turn off for 10 s) of sonication (Biorupter, Ningbo, China) to generate chromatin fragments of 200-1000 bp in length. Lysates were centrifuged at 14000 g for 10 min at 4°C to remove insoluble material. Supernatant was diluted in ChIP Dilution Buffer. For immunoprecipitation, the diluted chromatin was incubated with specific antibodies overnight at 4 °C with constant rotation, followed by incubation with protein G agarose for 1 h. Beads were washed continuously with buffers. The pulled-down chromatin complex was de-crosslinked at 65 °C for 5 h in elution buffer. Eluted DNA was digested with RNase at 37 °C for 30 min, and with proteinase K at 45 °C for 2 h to further purify. Purified DNA was enriched by spin columns.
To construct the ChIP-Seq library, DNA was combined with end repair mix, and incubated at 20 °C for 30 min. The end-repaired DNA was purified with QIAquick PCR-purification kit (Qiagen, Beijing local agent, China), then added with A-Tailing mix, incubated at 37 °C for 30 min. the purified Adenylate 3’ ends DNA, adapter and ligation mix were combined, and incubated the ligation reaction at 20 °C for 15 min. the Adapter-ligated DNA was purified with QIAquick PCR Purification Kit. Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix were performed to enrich the Adapter-ligated DNA fragments. Then the PCR products were selected (about 100-300 bp, including adaptor sequence) by running a 2% agarose gel to recover the target fragments. The gel was purified with QIAquick Gel Extraction Kit (Qiagen, Beijing local agent, China). The final library was quantified in two ways: the average molecule length and sample integrity as well as purity were quantified using Agilent 2100 bioanalyzer instrument (Agilent DNA 1000 Reagents), and quantified using real-time quantitative PCR.   The double-stranded PCR products were heat-denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formulated as the final library. The library was qualified by Qubit ssDNA kit. The sequencing was performed with the BGISEQ-500 sequencing system, featuring combinatorial probe-anchor synthesis (cPAS) and DNA Nanoballs (DNB) technology for superior data quality (BGI-Shenzhen, China). For Illumina, the qualified libraries were amplified on cBot to generate the cluster on the flowcell (TruSeq PE Cluster Kit V3-cBot-HS, Illumina). And the amplified flowcell was sequenced pair end on the HiSeq 2000 System (TruSeq SBS Kit-HS V3, Illumina).

treatment_protocol: Cells were under no treatments.

tag: disease state

value: breast cancer

tag: disease subtype

value: Triple negative

tag: chip antibody


title: MDA-MB-231 H3K4me1


title: RRBP1-GFP11 ApaLI, Dox, unsorted, replicate 1

description:
RRBP1-counts.raw.csv
RRBP1-deseq2.dds.rds
3-4F-iA-DoxD3-Rep1_IGO_12747_B_2

tag: genotype


title: PSPPH_0483-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-0483-KB-1_combined


title: MCF-7 H3K27ac

value: Estrogen receptor positive


title: SK-N-DZ_C6C83G1_RNA

value: Engineered t(6;8)


title: RRBP1-GFP11 ApaLI*, Dox, unsorted, replicate 2

description:
RRBP1-counts.raw.csv
RRBP1-deseq2.dds.rds
3-4F-iAd-DoxD3-Rep2_IGO_12747_B_5

value: mito-mCherry-GFP1-10 overexpressed, endogenous RRBP1 homozygously tagged with 4xGFP11 at the C-terminus, inducible catalytically inactive ApaLI integrated

value: Doxycycline for 3 days


title: MCF-7 H3K4me1


title: SK-N-DZ_C6C81G10_RNA

value: SK-N-DZ


title: PSPPH_0147-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-0147-KB-1_combined


title: REGN7257, sample 10

description:
5090.15475.1374195.S33.W101102
EAE_counts.txt
EAE_TPM.txt

source_name: REGN7257, sample 10

value: spinal cord


title: SK-N-DZ_C12AC82B6_RNA

value: Engineered t(12;8)


title: SK-N-DZ_C5C83G2_RNA

value: Engineered t(5;8)


title: PSPPH_4451-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-4451-KB-2_combined

value: PSPPH_4451 mutant

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


title: REGN7257, sample 9

description:
5090.15475.1374194.S33.W101102
EAE_counts.txt
EAE_TPM.txt

source_name: REGN7257, sample 9


title: PSPPH_4451-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-4451-KB-1_combined


title: SK-N-DZ_C5C81F11_RNA

value: Stranded mRNA-seq


title: PSPPH_4416-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-4416-KB-1_combined

value: PSPPH_4416 mutant


title: REGN7257, sample 7

description:
5090.15475.1374192.S33.W101102
EAE_counts.txt
EAE_TPM.txt

source_name: REGN7257, sample 7


title: REGN7257, sample 8

description:
5090.15475.1374193.S33.W101102
EAE_counts.txt
EAE_TPM.txt

source_name: REGN7257, sample 8


title: PSPPH_4416-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-4416-KB-2_combined


title: PSPPH_4381-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-4381-KB-2_combined

value: PSPPH_4381 mutant


title: D4-5

description:
4871.14009.1318668.S33.W111102
PBMCs_counts.txt
PBMCs_TPM.txt

source_name: Donor D4, no stim, no stim+REGN1945

value: PBMCs

value: no stim+REGN1945


title: SK-N-DZ_C1C89F4_RNA

value: Engineered t(1;8)

value: DMEM + 10% FBS + P/S + NEAA


title: REGN7257, sample 6

description:
5090.15475.1374191.S33.W101102
EAE_counts.txt
EAE_TPM.txt

source_name: REGN7257, sample 6


title: PSPPH_4381-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-4381-KB-1_combined


title: SK-N-DZ_WT_rep3_Hi-C

value: MboI in situ Hi-C

value: Wild-type


title: siha, oa3

city: St. Louis

first: Jin

last: Zhang

address: 4511 Forest Park Parkway

department: Radiation Oncology

institute: Washington University School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCh38.76
Supplementary files format and content: Gene counts with CPM in tab-delimited text format

source_name: SiHa

extract_protocol: KAPA RiboErase, RNeasy Plus Micro Kit, Poly-A selection

value: SiHa

value: WT

value: Treatment with oleic acid


title: siha, oa+ir2

value: Treatment with oleic acid and single fraction dose of 6 Gy


title: siha, oa2


title: siha, oa+ir1


title: siha, oa1


title: SK-N-DZ_WT_rep1_Hi-C

value: SK-N-DZ


title: RRBP1-GFP11 ApaLI*, Dox, unsorted, replicate 1

description:
RRBP1-counts.raw.csv
RRBP1-deseq2.dds.rds
3-4F-iAd-DoxD3-Rep1_IGO_12747_B_1

value: retinal pigment epithelia

value: mito-mCherry-GFP1-10 overexpressed, endogenous RRBP1 homozygously tagged with 4xGFP11 at the C-terminus, inducible catalytically inactive ApaLI integrated

value: Doxycycline for 3 days


title: PSPPH_4095-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-4095-KB-2_combined

value: PSPPH_4095 mutant

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


title: REGN7257, sample 4

description:
5090.15475.1374189.S33.W101102
EAE_counts.txt
EAE_TPM.txt

source_name: REGN7257, sample 4

value: spinal cord


title: SK-N-DZ_C7C8E2_Hi-C

value: Engineered t(7;8)


title: siha, oa+ir3


title: REGN7257, sample 3

description:
5090.15475.1374188.S33.W101102
EAE_counts.txt
EAE_TPM.txt

source_name: REGN7257, sample 3


title: SK-N-DZ_WT_rep2_Hi-C


title: SK-N-DZ_C7C8E10_Hi-C


title: SK-N-DZ_C7C8D9_Hi-C


title: REGN1945, sample 10

description:
5090.15475.1374185.S33.W101102
EAE_counts.txt
EAE_TPM.txt

source_name: REGN1945, sample 10


title: siha, ir1

value: Single fraction dose of 6 Gy


title: SK-N-DZ_C6BC81F2_Hi-C

value: Engineered t(6;8)


title: REGN7257, sample 1

description:
5090.15475.1374186.S33.W101102
EAE_counts.txt
EAE_TPM.txt

source_name: REGN7257, sample 1


title: siha, ir3


title: REGN7257, sample 5

description:
5090.15475.1374190.S33.W101102
EAE_counts.txt
EAE_TPM.txt

source_name: REGN7257, sample 5


title: PSPPH_3473-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-3473-KB-2_combined

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

value: PSPPH_3473 mutant


title: PSPPH_4095-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-4095-KB-1_combined


title: siha, ir2


title: REGN7257, sample 2

description:
5090.15475.1374187.S33.W101102
EAE_counts.txt
EAE_TPM.txt

source_name: REGN7257, sample 2


title: PSPPH_4003-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-4003-KB-2_combined

value: PSPPH_4003 mutant


title: SK-N-DZ_C6BC81A1_Hi-C

value: MboI in situ Hi-C

value: DMEM + 10% FBS + P/S + NEAA


title: PSPPH_3386-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-3386-KB-2_combined

value: PSPPH_3386 mutant


title: siha, ctrl3

value: SiHa

value: WT

value: No treatment


title: PSPPH_4003-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-4003-KB-1_combined


title: SK-N-DZ_C6C81G10_Hi-C

value: SK-N-DZ


title: Patient 110 baseline 9

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 110

value: primary RCC cancer

tag: age

tag: tumor stage

tag: status after 1 year

value: controlled

tag: histology

value: clear cell

tag: time

value: pre


title: PSPPH_3473-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-3473-KB-1_combined

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


title: REGN1945, sample 9

description:
5090.15475.1374184.S33.W101102
EAE_counts.txt
EAE_TPM.txt

source_name: REGN1945, sample 9

tag: donor

value: spinal cord


title: REGN1945, sample 8

description:
5090.15475.1374183.S33.W101102
EAE_counts.txt
EAE_TPM.txt

source_name: REGN1945, sample 8


title: REGN1945, sample 6

description:
5090.15475.1374181.S33.W101102
EAE_counts.txt
EAE_TPM.txt

source_name: REGN1945, sample 6


title: SK-N-DZ_C5C83G2_Hi-C

source_name: Engineered SK-N-DZ cell line

tag: cell line

tag: experiment type

value: Engineered t(5;8)

tag: media


title: SK-N-DZ_C6C83G1_Hi-C

tag: condition

value: Engineered t(6;8)


title: PSPPH_3386-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-3386-KB-1_combined

tag: strain/genotype


title: siha, ctrl2

tag: treatment


title: siha, ctrl1


title: Patient 110 baseline 8

tag: disease state

tag: tissue


title: REGN1945, sample 5

description:
5090.15475.1374180.S33.W101102
EAE_counts.txt
EAE_TPM.txt

source_name: REGN1945, sample 5


title: PSPPH_3295-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-3295-KB-2_combined

value: PSPPH_3295 mutant


title: SK-N-DZ_C5C81F11_Hi-C

value: MboI in situ Hi-C

value: DMEM + 10% FBS + P/S + NEAA


title: REGN1945, sample 4

description:
5090.15475.1374179.S33.W101102
EAE_counts.txt
EAE_TPM.txt

source_name: REGN1945, sample 4


title: Patient 110 baseline 7


title: Patient 110 baseline 6


title: PSPPH_2606-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-2606-KB-2_combined

value: PSPPH_2606 mutant


title: REGN1945, sample 2

description:
5090.15475.1374177.S33.W101102
EAE_counts.txt
EAE_TPM.txt

source_name: REGN1945, sample 2


title: Patient 110 baseline 5


title: Patient 110 baseline 4


title: PSPPH_2606-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-2606-KB-1_combined


title: REGN1945, sample 1

description:
5090.15475.1374176.S33.W101102
EAE_counts.txt
EAE_TPM.txt

source_name: REGN1945, sample 1


title: Patient 110 post-1 year 3

value: post


title: SK-N-DZ_C1C89F4_Hi-C

value: Engineered t(1;8)


title: SK-N-DZ_C1C84E12_Hi-C

value: SK-N-DZ


title: Patient 110 post-1 year 2

value: RCC


title: PBS, sample 9

description:
5090.15475.1374174.S33.W101102
EAE_counts.txt
EAE_TPM.txt

source_name: PBS, sample 9

value: PBS


title: SK-N-DZ_C12AC84G1_Hi-C

value: Engineered t(12;8)


title: Patient 110 post-1 year 1

value: Patient 110

value: primary RCC cancer

value: controlled


title: PBS, sample 10

description:
5090.15475.1374175.S33.W101102
EAE_counts.txt
EAE_TPM.txt

source_name: PBS, sample 10


title: PSPPH_2510-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-2510-KB-2_combined

value: PSPPH_2510 mutant

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


title: PSPPH_2510-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-2510-KB-1_combined


title: PSPPH_3295-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-3295-KB-1_combined


title: SK-N-DZ_C5BC89D4_Hi-C

value: Engineered t(5;8)


title: PSPPH_1729-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-1729-KB-2_combined

value: PSPPH_1729 mutant


title: SK-N-DZ_C12AC84E1_Hi-C


title: PBS, sample 8

description:
5090.15475.1374173.S33.W101102
EAE_counts.txt
EAE_TPM.txt

source_name: PBS, sample 8

value: spinal cord


title: REGN1945, sample 3

description:
5090.15475.1374178.S33.W101102
EAE_counts.txt
EAE_TPM.txt

source_name: REGN1945, sample 3


title: Patient 112 baseline 12

value: Patient 112

value: clear cell

value: pre


title: SK-N-DZ_C12AC82B6_Hi-C

value: MboI in situ Hi-C

value: DMEM + 10% FBS + P/S + NEAA


title: PSPPH_1729-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-1729-KB-1_combined


title: PSPPH_0641-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-0641-KB-2_combined

value: PSPPH_0641 mutant


title: SK-N-DZ_C7C8B1_Hi-C

value: SK-N-DZ

value: Engineered t(7;8)


title: PBS, sample 7

description:
5090.15475.1374172.S33.W101102
EAE_counts.txt
EAE_TPM.txt

source_name: PBS, sample 7

value: PBS


title: SK-N-DZ_C12BC83A5_Hi-C

value: Engineered t(12;8)


title: PSPPH_0641-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-0641-KB-1_combined


title: PBS, sample 5

description:
5090.15475.1374170.S33.W101102
EAE_counts.txt
EAE_TPM.txt

source_name: PBS, sample 5


title: PSPPH_0253-KB-2

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-0253-KB-2_combined

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

value: PSPPH_0253 mutant


title: U343_Hi-C

source_name: U343 cell line

value: Wild-type

value: DMEM + 10% FBS + P/S


title: Patient 112 baseline 10

source_name: primary RCC cancer

value: RCC

value: primary RCC cancer

value: controlled


title: Patient 112 baseline 11


title: Patient 112 baseline 9


title: PSPPH_0253-KB-1

description:
paired-end RNA-seq data of Pseudomonas sringae 1448A
psph-0253-KB-1_combined

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


title: DU-145_Hi-C

source_name: DU-145 cell line

value: EMEM + 10% FBS + P/S


title: PBS, sample 3

description:
5090.15475.1374168.S33.W101102
EAE_counts.txt
EAE_TPM.txt

source_name: PBS, sample 3

value: spinal cord


title: NCI-H1975_Hi-C

source_name: NCI-H1975 cell line

value: RPMI + 10% FBS + P/S


title: L12-CHIP-pHM1-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
Input for L12-CHIP-0146-1 L12-CHIP-0146-2 L12-CHIP-4002-1 L12-CHIP-4002-2 L12-CHIP-2376-1 L12-CHIP-2376-2 L12-CHIP-3387-1 L12-CHIP-3387-2 L12-CHIP-3875-1 L12-CHIP-3875-2
L12-CHIP-pHM1-2_combined

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).


title: L12-CHIP-pHM1-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
Input for L12-CHIP-0146-1 L12-CHIP-0146-2 L12-CHIP-4002-1 L12-CHIP-4002-2 L12-CHIP-2376-1 L12-CHIP-2376-2 L12-CHIP-3387-1 L12-CHIP-3387-2 L12-CHIP-3875-1 L12-CHIP-3875-2
L12-CHIP-pHM1-1_combined


title: pHM1-CHIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
Input for PSPPH_0069-ChIP-1 PSPPH_0069-ChIP-2 PSPPH_0094-ChIP-1 PSPPH_0094-ChIP-2 PSPPH_4431-ChIP-1 PSPPH_4431-ChIP-2 PSPPH_0800-ChIP-1 PSPPH_0800-ChIP-2 PSPPH_1364-ChIP-1 PSPPH_1364-ChIP-2 PSPPH_1906-ChIP-1 PSPPH_1906-ChIP-2 PSPPH_3220-ChIP-1 PSPPH_3220-ChIP-2 PSPPH_3800-ChIP-1 PSPPH_3800-ChIP-2 PSPPH_0252-ChIP-1 PSPPH_0252-ChIP-2 PSPPH_0480-ChIP-1 PSPPH_0480-ChIP-2 PSPPH_0499-ChIP-1 PSPPH_0499-ChIP-2 PSPPH_0642-ChIP-1 PSPPH_0642-ChIP-2 PSPPH_1166-ChIP-1 PSPPH_1166-ChIP-2 PSPPH_1363-ChIP-1 PSPPH_1363-ChIP-2 PSPPH_1374-ChIP-1 PSPPH_1374-ChIP-2 PSPPH_3385-ChIP-1 PSPPH_3385-ChIP-2 PSPPH_3413-ChIP-1 PSPPH_3413-ChIP-2 PSPPH_3428-ChIP-1 PSPPH_3428-ChIP-2 PSPPH_3907-ChIP-1 PSPPH_3907-ChIP-2 PSPPH_4419-ChIP-1 PSPPH_4419-ChIP-2 PSPPH_4737-ChIP-1 PSPPH_4737-ChIP-2 PSPPH_4853-ChIP-1 PSPPH_4853-ChIP-2 PSPPH_0479-ChIP-1 PSPPH_0479-ChIP-2 PSPPH_0807-ChIP-1 PSPPH_0807-ChIP-2 PSPPH_0923-ChIP-1 PSPPH_0923-ChIP-2 PSPPH_1179-ChIP-1 PSPPH_1179-ChIP-2 PSPPH_1195-ChIP-1 PSPPH_1195-ChIP-2 PSPPH_1207-ChIP-1 PSPPH_1207-ChIP-2 PSPPH_1867-ChIP-1 PSPPH_1867-ChIP-2 PSPPH_1904-ChIP-1 PSPPH_1904-ChIP-2 PSPPH_2022-ChIP-1 PSPPH_2022-ChIP-2 PSPPH_2600-ChIP-1 PSPPH_2600-ChIP-2 PSPPH_2605-ChIP-1 PSPPH_2605-ChIP-2 PSPPH_2995-ChIP-1 PSPPH_2995-ChIP-2 PSPPH_3040-ChIP-1 PSPPH_3040-ChIP-2 PSPPH_3294-ChIP-1 PSPPH_3294-ChIP-2 PSPPH_3359-ChIP-1 PSPPH_3359-ChIP-2 PSPPH_3377-ChIP-1 PSPPH_3377-ChIP-2 PSPPH_3453-ChIP-1 PSPPH_3453-ChIP-2 PSPPH_3547-ChIP-1 PSPPH_3547-ChIP-2 PSPPH_3737-ChIP-1 PSPPH_3737-ChIP-2 PSPPH_3876-ChIP-1 PSPPH_3876-ChIP-2 PSPPH_3962-ChIP-1 PSPPH_3962-ChIP-2 PSPPH_4255-ChIP-1 PSPPH_4255-ChIP-2 PSPPH_4420-ChIP-1 PSPPH_4420-ChIP-2 PSPPH_4828-ChIP-1 PSPPH_4828-ChIP-2 PSPPH_5114-ChIP-1 PSPPH_5114-ChIP-2 PSPPH_5118-ChIP-1 PSPPH_5118-ChIP-2 PSPPH_5171-ChIP-1 PSPPH_5171-ChIP-2 PSPPH_3362-ChIP-1 PSPPH_3362-ChIP-2 PSPPH_4075-ChIP-1 PSPPH_4075-ChIP-2
pHM1-CHIP-2_combined


title: Nudt15R138C/R138C HSCs rep3 [PR2649_08_a]

city: Otsu

first: Noriaki

last: Yamashita

state: Shiga

address: seta-tsukinowa

department: Department of Medicine

institute: Shiga University of Medical Science

data_processing:
DRAGEN Bio-IT Platform v 3.7.5 (illumina)
Transcriptome sequence data were mapped to the mouse genome (GRCm38) and expression levels were normalized as transcripts per kilobase million (TPM) using DRAGEN Bio-IT platform v 3.7.5 (Illumina).
Assembly: GRCm38
Supplementary files format and content: PR2649_transcript_expression_TPM.xlsx

source_name: hematopoietic stem cells

extract_protocol:
Total RNA of sorted HSCs from mice 24h after peritoneal administration of 5 mg/kg 6-MP was extracted using a RNeasy Micro (QIAGEN) according to the manufacturer’s instruction.
cDNA were synthesized using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio USA), the libraries were prepared using Nextera XT DNA Library Prep Kit (Illumine) according to the manufacturer’s instruction.

tag: cell type

value: hematopoietic stem cells


title: Nudt15+/+ HSCs rep3 [PR2649_07_a]

tag: genotype


title: Patient 112 post-1 year 6

tag: individual

value: Patient 112

value: clear cell

value: post


title: pHM1-CHIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
Input for PSPPH_0069-ChIP-1 PSPPH_0069-ChIP-2 PSPPH_0094-ChIP-1 PSPPH_0094-ChIP-2 PSPPH_4431-ChIP-1 PSPPH_4431-ChIP-2 PSPPH_0800-ChIP-1 PSPPH_0800-ChIP-2 PSPPH_1364-ChIP-1 PSPPH_1364-ChIP-2 PSPPH_1906-ChIP-1 PSPPH_1906-ChIP-2 PSPPH_3220-ChIP-1 PSPPH_3220-ChIP-2 PSPPH_3800-ChIP-1 PSPPH_3800-ChIP-2 PSPPH_0252-ChIP-1 PSPPH_0252-ChIP-2 PSPPH_0480-ChIP-1 PSPPH_0480-ChIP-2 PSPPH_0499-ChIP-1 PSPPH_0499-ChIP-2 PSPPH_0642-ChIP-1 PSPPH_0642-ChIP-2 PSPPH_1166-ChIP-1 PSPPH_1166-ChIP-2 PSPPH_1363-ChIP-1 PSPPH_1363-ChIP-2 PSPPH_1374-ChIP-1 PSPPH_1374-ChIP-2 PSPPH_3385-ChIP-1 PSPPH_3385-ChIP-2 PSPPH_3413-ChIP-1 PSPPH_3413-ChIP-2 PSPPH_3428-ChIP-1 PSPPH_3428-ChIP-2 PSPPH_3907-ChIP-1 PSPPH_3907-ChIP-2 PSPPH_4419-ChIP-1 PSPPH_4419-ChIP-2 PSPPH_4737-ChIP-1 PSPPH_4737-ChIP-2 PSPPH_4853-ChIP-1 PSPPH_4853-ChIP-2 PSPPH_0479-ChIP-1 PSPPH_0479-ChIP-2 PSPPH_0807-ChIP-1 PSPPH_0807-ChIP-2 PSPPH_0923-ChIP-1 PSPPH_0923-ChIP-2 PSPPH_1179-ChIP-1 PSPPH_1179-ChIP-2 PSPPH_1195-ChIP-1 PSPPH_1195-ChIP-2 PSPPH_1207-ChIP-1 PSPPH_1207-ChIP-2 PSPPH_1867-ChIP-1 PSPPH_1867-ChIP-2 PSPPH_1904-ChIP-1 PSPPH_1904-ChIP-2 PSPPH_2022-ChIP-1 PSPPH_2022-ChIP-2 PSPPH_2600-ChIP-1 PSPPH_2600-ChIP-2 PSPPH_2605-ChIP-1 PSPPH_2605-ChIP-2 PSPPH_2995-ChIP-1 PSPPH_2995-ChIP-2 PSPPH_3040-ChIP-1 PSPPH_3040-ChIP-2 PSPPH_3294-ChIP-1 PSPPH_3294-ChIP-2 PSPPH_3359-ChIP-1 PSPPH_3359-ChIP-2 PSPPH_3377-ChIP-1 PSPPH_3377-ChIP-2 PSPPH_3453-ChIP-1 PSPPH_3453-ChIP-2 PSPPH_3547-ChIP-1 PSPPH_3547-ChIP-2 PSPPH_3737-ChIP-1 PSPPH_3737-ChIP-2 PSPPH_3876-ChIP-1 PSPPH_3876-ChIP-2 PSPPH_3962-ChIP-1 PSPPH_3962-ChIP-2 PSPPH_4255-ChIP-1 PSPPH_4255-ChIP-2 PSPPH_4420-ChIP-1 PSPPH_4420-ChIP-2 PSPPH_4828-ChIP-1 PSPPH_4828-ChIP-2 PSPPH_5114-ChIP-1 PSPPH_5114-ChIP-2 PSPPH_5118-ChIP-1 PSPPH_5118-ChIP-2 PSPPH_5171-ChIP-1 PSPPH_5171-ChIP-2 PSPPH_3362-ChIP-1 PSPPH_3362-ChIP-2 PSPPH_4075-ChIP-1 PSPPH_4075-ChIP-2
pHM1-CHIP-1_combined


title: NCI-H1563_Hi-C

source_name: NCI-H1563 cell line

value: MboI in situ Hi-C


title: NCI-H1573_Hi-C

source_name: NCI-H1573 cell line


title: Patient 112 post-1 year 5

tag: age


title: Nudt15R138C/R138C HSCs rep1 [PR2649_04_a]


title: Nudt15R138C/R138C HSCs rep2 [PR2649_05_a]


title: Patient 112 post-1 year 4

tag: tumor stage


title: NCI-H596_Hi-C

source_name: NCI-H596 cell line


title: NCI-H1437_Hi-C

source_name: NCI-H1437 cell line


title: Patient 112 post-1 year 3

tag: status after 1 year


title: TT_Hi-C

source_name: TT cell line

value: TT


title: PBS, sample 6

description:
5090.15475.1374171.S33.W101102
EAE_counts.txt
EAE_TPM.txt

source_name: PBS, sample 6

value: PBS


title: PSPPH_3875-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
L12-CHIP-3875-2_combined

tag: chip antibody

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


title: Patient 112 baseline 8

tag: histology

tag: time

value: pre


title: PSPPH_3387-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
L12-CHIP-3387-2_combined


title: Patient 112 post-1 year 2


title: PBS, sample 4

description:
5090.15475.1374169.S33.W101102
EAE_counts.txt
EAE_TPM.txt

source_name: PBS, sample 4

tag: donor


title: Nudt15+/+ HSCs rep1 [PR2649_01_a]


title: Patient 112 baseline 7


title: Patient 112 post-1 year 1


title: RPMI-8402_Hi-C

source_name: RPMI-8402 cell line

tag: cell line

tag: experiment type

value: Wild-type

value: RPMI + 15% FBS + 2 mM L-glutamine


title: PSPPH_3387-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
L12-CHIP-3387-1_combined

tag: condition


title: Female Morphine 8

city: Philadelphia

first: Julie

last: Blendy

state: PA

address: 125 S 31st St Room 2109A

department: Pharmacology

institute: University of Pennsylvania

data_processing:
RUM v 2.05_06 35 was used to align the reads to mm10. In our analyses we used the RUM counts derived from the uniquely mapped reads
Raw counts for RefSeq transcripts from uniquely mapped reads were the input for the Differential Expression (DE) analysis, which was done with DESeq2. RefSeqs with less than 10 counts across samples were filtered out.
Assembly: mm10
Supplementary files format and content: tab files with counts for each sample

source_name: Brain- paraventricular nucleus of thalamus

extract_protocol:
We used both control mice and mice exposed to chronic morphine for TRAP. Mice were sacrificed and, for each mouse, a gross dissection targeted at the PVT was used to generate tissue for the translating ribosome affinity purification. Due to the small amount of brain tissue, 2 PVT dissections were pooled together to create each biological sample – males were only pooled with males and females were only pooled with females, for a total of 4 biological replicates for each of the morphine and control groups. Tissue was homogenized with lysis buffer and incubated overnight with magnetic beads (Dynabeads Protein G, ThermoFisher Scientific, Waltham, MA, cat. No. 10004D) and anti-GFP antibodies (htz-GFP-19f and htz-GFP-19C8, Memorial Sloan-Kettering Monoclonal Antibody Facility, New York, NY) to complete the affinity purification bound by the EGFP-L10a fusion protein. RNA was isolated from the cells in each sample expressing EGFP-L10a 26,34 with the Absolutely RNA Nanoprep RNA isolation kit (Agilent Technologies, cat. No. 400753).
RNA was processed, assessed for quality control, and prepared and sequenced by the University of Pennsylvania’s Next Generation Sequencing Core (https://ngsc.med.upenn.edu). Briefly, libraries were sequenced as 50PE and samples had between 37 and 58 million reads. RNA-Seq library prep using the NEBNext Ultra II Directional RNA library prep kit, E7760S. Labor NOT included.

value: PVT neurons

tag: cell subset

value: Mu opioid receptor+

value: OPRM1cre X EGFP-L10a

value: Morphine


title: Patient 104 baseline 10

value: RCC

value: Patient 104

value: primary RCC cancer

value: controlled


title: MOLT-4_Hi-C

source_name: MOLT-4 cell line

tag: media


title: PSPPH_2376-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
L12-CHIP-2376-2_combined

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

tag: strain/genotype

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


title: Patient 104 baseline 9

tag: disease state

tag: tissue

value: clear cell


title: Jurkat_Hi-C

source_name: Jurkat cell line

value: Jurkat

value: MboI in situ Hi-C

value: RPMI + 10% FBS + P/S


title: Female Morphine 7

value: Brain- paraventricular nucleus of thalamus

tag: cell type

tag: genotype

tag: treatment


title: PSPPH_3875-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
L12-CHIP-3875-1_combined

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


title: PSPPH_2376-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
L12-CHIP-2376-1_combined


title: CCRF-CEM_Hi-C

source_name: CCRF-CEM cell line

value: CCRF-CEM

value: Wild-type


title: Male Morphine 4

value: PVT neurons


title: HL-60_Hi-C

source_name: HL-60 cell line

value: IMDM + 20% FBS + P/S


title: Male Morphine 3

value: Mu opioid receptor+

value: OPRM1cre X EGFP-L10a


title: CESS_Hi-C

source_name: CESS cell line

value: CESS


title: PSPPH_4002-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
L12-CHIP-4002-1_combined


title: Mino-1_Hi-C

source_name: Mino-1 cell line


title: Patient 104 baseline 7

source_name: primary RCC cancer

value: RCC

tag: individual

value: Patient 104

tag: age

tag: tumor stage

value: pre


title: PSPPH_4002-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
L12-CHIP-4002-2_combined

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

tag: chip antibody


title: Patient 104 baseline 8

value: primary RCC cancer

tag: status after 1 year

value: controlled

tag: histology

value: clear cell

tag: time


title: Patient 104 baseline 6


title: Female Control 6

value: Control drinking water


title: PSPPH_0146-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
L12-CHIP-0146-2_combined


title: Maver-1_Hi-C

source_name: Maver-1 cell line

tag: cell line

tag: experiment type

value: MboI in situ Hi-C

value: RPMI + 10% FBS + P/S


title: PSPPH_0146-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
L12-CHIP-0146-1_combined

tag: condition

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


title: Nudt15+/+ HSCs rep2 [PR2649_02_a]

source_name: hematopoietic stem cells

value: hematopoietic stem cells


title: Patient 104 baseline 5


title: Female Control 5

value: Brain- paraventricular nucleus of thalamus

value: PVT neurons

tag: cell subset


title: Male Control 2

value: Mu opioid receptor+


title: Rec-1_Hi-C

source_name: Rec-1 cell line

value: Wild-type

tag: media


title: Patient 104 post-1 year 4

tag: disease state

value: post


title: Male Control 1

tag: tissue

value: OPRM1cre X EGFP-L10a


title: Granta_Hi-C

source_name: Granta cell line

value: Granta


title: Patient 104 post-1 year 3

value: RCC

value: Patient 104


title: PSPPH_4075-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
N-PSPH-4075-2_combined

tag: strain/genotype

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


title: Jeko1_Hi-C

source_name: Jeko1 cell line


title: PSPPH_4075-ChIP-1

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
N-PSPH-4075-1_combined


title: PSPPH_3362-ChIP-2

description:
paired-end ChIP-seq data of Pseudomonas sringae 1448A
N-PSPH-3362-2_combined


title: Patient 104 baseline 2

value: primary RCC cancer

value: controlled

value: pre


title: ML2_Hi-C

source_name: ML2 cell line

value: MboI in situ Hi-C


title: colon.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

source_name: colon

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: colon

tag: strain


title: colon.ATAC


title: KPC_6mo

city: Ann Arbor

first: Marina

last: Pasca di Magliano

state: MI

address: 1500 E Medical Center Dr

institute: University of Michigan Medical School

description: Spontaneous 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 demultiplexed into FASTQ files using cellranger mkfastq v4.0.0.
FASTQ files were aligned, filtered, and counted by cellranger count v3.1.0 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: mm10-3.0.0
Supplementary files format and content: H5 files containing aligned single cell sequencing data output by CellRanger.

source_name: Spontaneous pancreatic tumor

growth_protocol: KPC mouse grew to 6 months of age before being euthanized and having its tumor harvested for single-cell RNA sequencing.

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.

value: Mixed

tag: genotype

value: KrasLSL-G12D; Trp53LSL-R172H; Ptf1a-Cre

value: 6 months

value: Spontaneous pancreatic tumor

tag: number of mice pooled


title: MV411_Hi-C

source_name: MV411 cell line

value: RPMI + 10% FBS + P/S


title: PSPPH_5171-ChIP-2

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

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