title: S. Heidelberg 18-9079+ E. coli 47-1826 in media_3

city: Gainesville

first: Yasir Razzaq

last: khan

state: Florida

address: 2015 SW 16th Ave

department: Large Animals Clinical Sciences

institute: university of Florida

description:
processed data files:
raw_counts.txt

data_processing:
CLC Genomics workbench v.23.0.4
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC-genomics bench work
Read count extraction and normalization were performed using CLC genomics workbench
Assembly: NC_008563.1, NZ_CP051310.1, NZ_MW349106.1
Supplementary files format and content: 9070-S and 47-9079-S files ( processed data file _1) contain data processed with  Salmonella enterica subsp. enterica serovar Heidelberg strain CVM 35161 as reference
Supplementary files format and content: 47-E and 47-9079-E  files ( processed data file _2)  contain data processed with Escherichia coli APEC O1 as reference
Supplementary files format and content: 9079-P and 47-9079-P  files ( processed data file _3)  contain data  processed with Escherichia coli strain 18-9079 plasmid P18-9079S as reference

organism:
Escherichia coli
Salmonella enterica subsp. enterica serovar Heidelberg

source_name: bacterial cells

growth_protocol: S. Heidelberg 189079 and E. coli 471826 grown  in Luria Bertani (LB) (BD, Difco, Franklin Lakes, NJ, USA) broth  at an equal concentration of 0.01 OD600 (Spectrophotometer, Thermo Fischer Scientific, USA) and incubated for 24 h at 37°C under anaerobic conditions.

extract_protocol:
Total RNA was extracted using RiboPure™ RNA Purification Kit (Invitrogen™). The samples further processed for rRNA depletion to enrich bacterial mRNA using using MICROBExpress™ Bacterial mRNA Enrichment Kit (Invitrogen™). All steps were carried out according to the manufacturer’s instructions. Quality and concentration of RNA samples in each step was measured using NanoDrop™ 2000/2000c Spectrophotometer (Thermo Scientific™).
Library preparation was done using TruSeq® Stranded mRNA library kit (Illumina Inc., San Diego, CA, USA) as per manufacturer’s recommendations

treatment_protocol: S. Heidelberg 189079 co-cultured with E. coli 471826 co  in Luria Bertani (LB) (BD, Difco, Franklin Lakes, NJ, USA)  broth  at an equal concentration of 0.01 OD600 (Spectrophotometer, Thermo Fischer Scientific, USA)  and incubated for 24 h at 37°C under anaerobic conditions.

value: bacterial cells

tag: strain

tag: genotype

value: WT

value: co-culture


title: S. Heidelberg 18-9079+ E. coli 47-1826 in media_2

status: Public on Sep 17 2024

type: SRA

country: USA

description:
processed data files:
raw_counts.txt

library_source: transcriptomic

molecule: total RNA

tag: cell type

tag: treatment


title: E_Untreated_1_A_NEAT1

city: Würzburg

first: Redmond

last: Smyth

state: Bayern

address: Josef-Schneider-Straße 2, D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
Basecalling
Demuliplexing
Alignment with last against Neat1 transcript
Mutations counted with rf_count
Assembly: Neat1 transcript
Supplementary files format and content: Binary file containing mutation counts (https://rnaframework-docs.readthedocs.io/en/latest/rf-count/)

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
RNAhot extract with Trizol
Reverse transcribed with MarathonRT and amplified with specific primers
Nanopore DNA sequencing (with barcoding)

tag: cell line

value: Untreated

tag: replicate

tag: dms treatment


title: cytosol, 120min, rep6

city: Berlin

first: Markus

last: Landthaler

address: Hannoversche Str. 28

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrueck Center

data_processing:
Alignment of raw reads was done with STAR (v2.7.6).
Reads in exons were counted with HTSeq-count (v0.11.1) and exon and TPM values were obtained by RSEM (v.1.3.3) using default parameters.
Based on a binomial mixture model by Juerges et al. (2018) we determined the conversion rate per sample. With the conversion rates, T and T2C conversion counts the fraction of new to total RNA was calculated on intron/exon level, which was used later on as input for the kinetic model.
Gene set enrichment analyses were performed with fgsea (v1.28.0) with the GSEA parameter set to 0 and gene set sizes limited from 30 to 900.
Fitting was performed throughout with the python package lmfit (v1.0.3) using the Levenberg-Marquardt “least-squares” algorithm to minimize the chi-squared unless otherwise specified. Summarizing different models and genes, the following kinetic rates were estimated: transcript elongation rate, intron removal rate, nuclear export rate, nuclear degradation rate, cytosolic degradation rate, cytosolic transport rate and membrane degradation rate.
Assembly: mm10
Supplementary files format and content: {sample}.txt files provide raw read counts per gene, reads counted in exons with HTSeq-count
Supplementary files format and content: {sample}_t2c_counts.txt files give gene and exon-wise T2C metrics: conversion probability (p_conv), number of Ts in gene/exon/intron (T_exon, T_intron), number of T2C transitions in gene/exon/intron (T2C_exon, T2C_intron) and share of T2C vs total T counts divided by conversion probability per gene/exon/intron (T2C_over_T_exon, T2C_over_T_intron).

organism: Mus musculus

growth_protocol: E14TG2a mESCs [Iacovino, M., Roth, M. E. & Kyba, M. Rapid genetic modification of mouse embryonic stem cells by Inducible Cassette Exchange recombination. Methods Mol. Biol. 1101, 339–351 (2014)] were cultured in 0.1% gelatin [w/v] coated plates in “2i + LIF” ES medium [Advanced DMEM/F12 (12634028, Thermo Fisher Scientific) – Neurobasal (21103049, Thermo Fisher Scientific) – Knockout™ DMEM (10829018, Thermo Fisher Scientific) (1 : 1 : 0.5), 14% Fetal Bovine Serum qualified for ES cells (16141079, Life Technologies), 1X N2 (17502048, Thermo Fisher Scientific), 1X B27 (17504001, Thermo Fisher Scientific), 1X GlutaMax (35050061, ThermoFisher Scientific), 1X MEM Non-Essential Amino Acid (11140050, Thermo Fisher Scientific), 1X Nucleosides (ES-008-D, Merck Millipore), 100 µM β-mercaptoethanol (21985023, Thermo Fisher Scientific), 3 μM CHIR99021 (SML1046-5MG, Invitrogen) and 1 μM PD0325901 (PZ0162-5MG, Invitrogen), 1000 U/ml Leukemia inhibitory factor (ESG1107, Merck Millipore)], under a controlled atmosphere at 5% CO2 and 37°C. mESCs were seeded the day before the experiments at a density of 3× 105 cells/ml.

extract_protocol:
Briefly, medium was aspirated, 5 ml of ice-cold PBS supplemented with 100 µM cycloheximide (A0879,0001, Biochemika) was added to the plates, cells were scraped from the plates, transferred to 15ml falcon and spun down. Pellet was resuspended in 500 µl of ice-cold permeabilization buffer (110 mM KOAc, 25 mM K-HEPES pH 7.2, 2.5 mM Mg(OAc)2, 1 mM EGTA with freshly added 0.015% digitonin, 1 mM DTT, 100 μg/ml cycloheximide, 1X Complete Protease Inhibitor Cocktail and 40 U/mL RNaseOUT™). 100 µl of the sample was taken aside as Total extract and rest was incubated for 10 min at 4°C with rotation, followed by centrifugation at 3000 g 5 min at 4°C. Supernatant (corresponding to the Cytosolic fraction) was transferred to new tube while the pellet was resuspended in 5ml of wash buffer (110 mM KOAc, 25 mM K-HEPES pH 7.2, 2.5 mM Mg(OAc)2, 1 mM EGTA with freshly added 0.004% digitonin, 1mM DTT, 100μg/ml cycloheximide) and spun down again at 3000 g 5 min at 4°C. After centrifugation washed pellet was mixed with 500 µl of ice-cold lysis buffer (400 mM KOAc, 25 mM K-HEPES pH 7.2, 15 mM Mg(OAc)2, 0.5% (v/v) NP-40 and freshly added 1 mM DTT, 100 μg/ml cycloheximide, 1X Complete Protease Inhibitor Cocktail, 40 U/mL RNase Out) and incubated for 5 min on ice followed by centrifugation at 3000 g 5 min at 4°C to collect the supernatant (corresponding to the Membrane fraction) and the pellet (insoluble and the nuclear fraction). For additional purity nuclei were loaded on 10% sucrose cushion in lysis buffer and centrifuged at 200 g 5 min at 4°C. The cytosolic and membrane fractions were clarified at 7500 g 10 min at 4°C to remove cell debris. 20 µl of all fractions were taken for Western analysis while rest were mixed with Trizol LS (10296028, Thermo Fisher Scientific) for subsequent RNA isolation.
One microgram of total RNA was used as an input for TruSeq Stranded mRNA Library Prep Kit according to the instructions of the manufacturer.
TruSeq Stranded mRNA Library Paired-End

treatment_protocol: Two independently passaged biological replicates of mESCs (~3.5 × 107 cells per replicate) were separately labelled in “2i + LIF” ES medium supplemented with 500 µM (for 0, 15, 20, 30, 40 min) or 100 µM (for 60, 120 and 180 min) 4-thiouridine (4sU, RP-2304, ChemGenes) and fractionated by sequential detergent extraction, as described previously [Jagannathan et al. 2011] with minor modifications.

value: mESC

value: 100uM 4-thiouridine


title: D_Etoposide_1_A_NEAT1

value: Etoposide

value: DMS


title: S. Heidelberg 18-9079+ E. coli 47-1826 in media_1

description:
processed data files:
raw_counts.txt


title: cytosol, 120min, rep5


title: cytosol, 15min, rep1

value: 500uM 4-thiouridine


title: cytosol, 180min, rep3


title: cytosol, 120min, rep4


title: ZNF274KO_2

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

country: Switzerland

institute: EPFL

library_source: genomic

data_processing:
Data were mapped to the hg19 genome using Msuite2 with aligner hisat2
The Msuite2 pipeline was also used to make the methylation calls
Assembly: hg19
Supplementary files format and content: Methylation call from the Msuite2 pipeline
Library strategy: EM-seq

molecule: genomic DNA

extract_protocol:
GeneJET Genomic DNA Purification Kit (Ref.C5042) and NEBNext Enzymatic Methyl-seq Kit (Ref. E7120S)
NEBNext Ultra II (Ref. E7120S)

value: EM-seq


title: control3

city: St. Louis

first: Michelle

last: Brennan

state: MO

address: 1100 South Grand Blvd

department: Biochemistry & Molecular Biology

institute: Saint Louis University School of Medicine

data_processing:
Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned with STAR version 2.7.9a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32.
Assembly: Human Ensembl GRCh38.101
Supplementary files format and content: tab separated value file containing log2 normalized gene counts and differential expression values

source_name: THH

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Invitrogen, OR).
Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

value: THH

value: vehicle


title: cytosol, 120min, rep3


title: control1


title: control2


title: treatment2

value: 10 μM cabozantinib and 10 μM silmitasertib


title: J-Lat 10.6_WT_DMSO_RPB3_R2

city: Seattle

first: Michael

last: Emerman

state: Washington

address: 1110 Fairview Ave N

institute: Fred Hutch Cancer Research Center

description: RPB3 Ab

data_processing:
Fastq files were aligned to the custom genome assembly prepared by Hsieh et al. 2023 (PLoS Pathogens) in which chr9:136468439–136468594 of hg38 is replaced with the integrated HIV-1 sequence from MN989412.1 (Chung et al. 2020 Microbiol Resour Announc), and the second 634 bp copy of the LTR is masked by ‘N’s. Bowtie2 version 2.4.2 was used for alignments with the following parameters: —very-sensitive-local—soft-clipped-unmapped-tlen—dovetail—no-mixed—no-discordant -q—phred33 -I 10 -X 1000. For each target protein and each condition 3-5 technical replicates were profiled. We removed duplicate reads from each replicate, and the combined reads for all replicates were pooled and used to generate the coverage-normalized bigwig files shown as genome-browser tracks.
Assembly: hg38 with HIV sequence inserted on chr9.
Supplementary files format and content: genome coverage profiles in bigwig format
Library strategy: AutoCUT&Tag

source_name: Peripheral blood

growth_protocol: J-Lat 10.6 cells were cultured with RPMI 1640 media (ThermoFisher, 11875093) supplemented with 10% Fetal Bovine Serum (FBS), Penicillin/Streptomycin, and 10 mM HEPES (ThermoFisher, 15630080). AAVS1 KO and INTS12 KO cells were seeded at a density of 5e5 cells/ml in 96 well plates with 200 ul/well or in flasks. LRA treatments were performed in triplicate. Cells were treated with 10 nM AZD5582 & 100 nM I-BET151 for 48 hrs.

treatment_protocol: J-Lat cells were knocked out for INTS12 or AAVS1 with single guides cloned in the HIV-CRISPR vector. Transduced cells were selected with 0.4 μg/mL puromycin selection for 10–14 days to generate CRISPR/Cas9-edited knockout pools. Knockout scores were generated by amplifying PCR products including the edited and non edited region and then using Synthego ICE analysis software to generate a knockout score. The knockout score of J-lats used in this experiment for INTS12 was 80%. AZD5582 (MedChemExpress, HY-12600) and I-BET151 (SelleckChem, S2780) were resuspended in DMSO to make 1 mM stocks stored at -80 °C. Stocks were then diluted down to single-use working concentrations for experiments with RPMI. AAVS1 KO and INTS12 KO cells were seeded at a density of 5e5 cells/ml in 96 well plates with 200 ul/well or in flasks. LRA treatments were performed in triplicate. Cells were treated with 10 nM AZD5582 & 100 nM I-BET151 for 48 hrs.

tag: tissue

value: Peripheral blood

value: Jurkat

value: AAVS1 knockout cell

value: DMSO


title: cytosol, 0min, rep4


title: ZNF274KO_1


title: treatment1


title: WT_1


title: treatment3


title: J-Lat 10.6_WT_DMSO_INTS12_2_R4

description: INTS12 Ab #2


title: WT_2


title: cytosol, 0min, rep3


title: scRNA-seq NPC ZNF274KO

description: 10X 5'GE  v2.0

library_source: transcriptomic single cell

data_processing:
The 10x standard cellranger pipeline was run to map the data and produce counttables in h5 format
Assembly: hg19
Supplementary files format and content: Raw fastq data (barcode and read sequence) and count matrix as outputed by cellranger in h5 format

source_name: NPC

extract_protocol:
RNA was extracted using the Chromium Single Cell 5' Reagent Kit.
10X 5'GE  v2.0

value: NPC


title: J-Lat 10.6_WT_DMSO_INTS12_2_R2

description: INTS12 Ab #2


title: J-Lat 10.6_WT_DMSO_INTS12_2_R1

description: INTS12 Ab #2


title: HiC_NPC_ZNF274KO_1

description: HiC rep1 in ZNF274KO

data_processing:
The HiC pro pipeline was run on the raw data with detault parameters to extract 20KB contact matrices
Assembly: hg19
Supplementary files format and content: HiC: Raw contact matrices at 20kb resolution

extract_protocol:
Arima Genome-Wide Hi-C Kit
NovaSeq v1.5 STD (Illumina protocol #1000000106351 v03)

value: Hi-C


title: ZNF274KO_HEK_293T_S20

description:
RNA-seq  ZNF274KO HEK293T
ZNF274_KO_HEK293.csv

data_processing:
Raw reads were mapped with hisat2 with -k5 optino to the human hg19 genome
Gene summaziation performed with featureCounts using -Q 10 as option
Assembly: hg19
Supplementary files format and content: countTable raw unique read counts

extract_protocol:
RNA was extracted using the High Pure RNA Isolation Kit from ROCHE (Ref. 11828665001)
Illumina Truseq stranded mRNA(Ref 20040534)


title: HiC_NPC_ZNF274KO_2

description: HiC re2  in ZNF274KO


title: cytosol, 0min, rep1


title: J-Lat 10.6_WT_DMSO_INTS12_1_R4

description: INTS12 Ab #1


title: HiC_NPC_WT_2

description: HiC rep2 in WT cells

value: WT


title: J-Lat 10.6_WT_DMSO_RPB3_R3

description: RPB3 Ab


title: HiC_NPC_WT_1

description: HiC rep1 in WT cells


title: J-Lat 10.6_WT_DMSO_RPB3_R1

description: RPB3 Ab


title: ZNF274KO_HEK_293T_S19


title: J-Lat 10.6_WT_DMSO_INTS12_1_R2

description: INTS12 Ab #1


title: J-Lat 10.6_WT_DMSO_INTS12_1_R3

description: INTS12 Ab #1


title: ZNF274KO_HEK_293T_S18


title: C4-2B, L14-8_2

city: Shanghai

first: Fuwen

last: Yuan

state: 上海

address: Cailun Road #1200, Pudong New area

country: China

institute: Shanghai University of Traditional Chinese Medicine

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

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

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

treatment_protocol: Cells were treated with 10 uM L14-8 or vehicle and cluture for 24 h followed with RNA extraction and sequencing.

value: prostate cancer cells


title: C4-2B, L14-8_1


title: C4-2B, L14-8_3


title: WT_HEK_293T_S17

description:
RNA-seq WT HEK293T
ZNF274_KO_HEK293.csv


title: C4-2B, Vehicle_3


title: scRNA-seq NPC WT

description: 10X 5'GE  v2.0


title: C4-2B, Vehicle_1


title: J-Lat 10.6_WT_AZD5582andIBET-151_RPB3_R3

description: RPB3 Ab


title: J-Lat 10.6_WT_DMSO_INTS12_1_R1

description: INTS12 Ab #1


title: J-Lat 10.6_ AAVS1 KO_PMAi_R3

data_processing:
A custom reference was built on the combined genome of human and HIV. HIV genome sequence (MN989412) was inserted into human chr9 at the known integrated site. 3' LTR of HIV was masked. GENCODE annotation v38 and HIV gene annotation were combined and genome coordinates were modified accordingly. STAR v2.7.7a with 2-pass mapping was used to align paired-end reads to the custom reference. FastQC 0.11.9, RNA-SeQC 2.3.4, RSeQC 4.0.0 were used to check various QC metrics including insert fragment size, read quality, read duplication rates, rRNA rates, gene body coverage and read distribution in different genomic regions. featureCounts in Subread 2.0.0 was used to quantify gene-level fragment counts in second-stranded fashion.  Bioconductor package edgeR 3.36.0 was used to detect differential gene expression between sample groups. Genes with low expression were excluded using edgeR function filterByExpr with min.count = 10 and min.total.count = 15. The filtered expression matrix was normalized by TMM method and subject to significance testing using quasi-likelihood pipeline implemented in edgeR. A gene was deemed differentially expressed if absolute log2 fold change was above 1 (i.e. fold change > 2 in either direction) and Benjamini-Hochberg adjusted p-values was less than 0.05.
Assembly: hg38 with HIV sequence inserted on chr9.
Supplementary files format and content: A text file of gene-by-sample read counts. Gene symbols and sum of non-overlapping exon lengths are provided.

growth_protocol: J-Lat 10.6 cells were cultured with RPMI 1640 media (ThermoFisher, 11875093) supplemented with 10% Fetal Bovine Serum (FBS), Penicillin/Streptomycin, and 10 mM HEPES (ThermoFisher, 15630080).

extract_protocol:
Cells were lysed with 700 µl of QIAzol (Qiagen, 1023537). Samples were spun through a QIAshredder (Qiagen, 79654) and then frozen at -80°C. Cells were then processed with a miRNeasy kit (Qiagen, 217004), DNase treated with RNase-Free DNase Set (Qiagen, 79254), and then re-processed through the RNeasy Mini Kit (Qiagen, 74104) with the EtOH wash modified to 700 µL for small RNAs.
rRNA was removed with the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit (20040525) followed by indexing with IDT for Illumina RNA UD Indexes Set A Ligation (20040553).

treatment_protocol: J-Lat cells were knocked out for INTS12 or AAVS1 with single guides cloned in the HIV-CRISPR vector. Transduced cells were selected with 0.4 μg/mL puromycin selection for 10–14 days to generate CRISPR/Cas9-edited knockout pools. Knockout scores were generated by amplifying PCR products including the edited and non edited region and then using Synthego ICE analysis software to generate a knockout score. The knockout score of J-lats used in this experiment for INTS12 was 75%. AZD5582 (MedChemExpress, HY-12600) and I-BET151 (SelleckChem, S2780) were resuspended in DMSO to make 1 mM stocks stored at -80 °C. Stocks were then diluted down to single-use working concentrations for experiments with RPMI. AAVS1 KO and INTS12 KO cells were seeded at a density of 5e5 cells/ml in 96 well plates with 200 ul/well or in flasks. LRA treatments were performed in triplicate. Cells were treated with 10 nM AZD5582 & 100 nM I-BET151 for 48 hrs.

value: AAVS1 knockout cells

value: PMA & ionomycin


title: WT_HEK_293T_S16

description:
RNA-seq WT HEK293T
ZNF274_KO_HEK293.csv


title: C4-2B, Vehicle_2


title: J-Lat 10.6_WT_AZD5582andIBET-151_RPB3_R2

description: RPB3 Ab


title: MP3-719-TCR

city: Atlanta

first: Christian

last: Larsen

state: Georgia

address: 101 Woodruff Circle

department: Department of Surgery

institute: Emory University

description: VDJ TCR

data_processing:
VDJ TCR alignment and filtering for single-cell TCR sequencing samples were performed using Cell Ranger v3.1
VDJ TCR alignment and filtering for non-paired TCR sequencing samples were performed using MIXCR
Assembly: A genome build is generally not required for TCR sequencing, as it focuses on the rearranged TCR genes using V(D)J reference libraries
Supplementary files format and content: The processed data for single-cell TCR sequencing samples include filtered contig annotations, consensus annotations, clonotypes, and all contig annotations. For bulk TCR sequencing, the processed data contain clonotype information for both TCRα and TCRβ chains.
Library strategy: VDJ TCR

source_name: PBMC

extract_protocol:
Cells were FACS sorted and used to generate single cell suspensions. Samples were loaded onto the 10X Genomics Chromium Controller according to manufacturer's protocol.
Library construction was performed using the Chromium Single Cell 5’ Library Construction Kit

tag: Sex

value: Female

value: PBMC

value: CD4 T cells

value: In vitro peptide stimulation


title: J-Lat 10.6_ AAVS1 KO_DMSO_R3


title: At_ EVs_Mock_2

city: Irapuato

first: Obed

middle: Ramirez

last: Sanchez

state: Guanajuato

address: Km. 9.6 Libramiento NorteCarr. Irapuato-León

department: langebio

country: Mexico

institute: cinvestav

description: mRNAs isolated from EVs purified from 4 week-old  A.thaliana leaves, biological repeat 2

data_processing:
Fastq libraries were aligned to a concatenated genome composed of A. thaliana (TAIR10) and B. cinerea B05 (ASM83294v1) using STAR parameters --outFilterMismatchNoverLmax 0.3,  and --outFilterMismatchNoverReadLmax 0.1
Gene quantifciation was obtanied with featureCounts using default parameters
Assembly: TAIR10/ASM83294v1
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Arabidopsis thaliana

source_name: plant leaves

growth_protocol: All A. thaliana lines used were 4 week-old in the Columbia background (Col-0). A. thaliana plants were grown in a controlled environment glasshouse at 23°C with 55% humidity and 12 h light d-1 . B. cinerea was cultured on Potato Dextrose Agarat (PDA) at room temperature.

extract_protocol:
Total RNAs were extracted from the above samples using the TRIzol reagent and treated with DNase I.
NEB Next Poly(A) mRNA Magnetic Isolation Module kit (NEB #E7490) coupled with NEBNext® Ultra™ Directional RNA Library Prep Kit (NEB #E7420) were used to make the libraries for Illumina sequencing based on the manufacturer’s protocols.

tag: ecotype


title: J-Lat 10.6_ AAVS1 KO_PMAi_R1


title: J-Lat 10.6_WT_AZD5582andIBET-151_INTS12_2_R5

description: INTS12 Ab #2


title: J-Lat 10.6_ AAVS1 KO_DMSO_R2


title: At_ EVs_Mock_1

description: mRNAs isolated from EVs purified from 4 week-old  A.thaliana leaves, biological repeat 1


title: At_ EVs_Mock_3

description: mRNAs isolated from EVs purified from 4 week-old  A.thaliana leaves, biological repeat 3


title: J-Lat 10.6_ AAVS1 KO_AZDIBET_R2


title: J-Lat 10.6_ AAVS1 KO_DMSO_R1


title: J-Lat 10.6_WT_AZD5582andIBET-151_INTS12_2_R4

description: INTS12 Ab #2


title: WT_HEK_293T_S15

description:
RNA-seq WT HEK293T
ZNF274_KO_HEK293.csv


title: J-Lat 10.6_ AAVS1 KO_AZDIBET_R1


title: J-Lat 10.6_WT_AZD5582andIBET-151_INTS12_2_R3

description: INTS12 Ab #2


title: J-Lat 10.6_ INTS12 KO_PMAi_R3

value: INTS12 knockout cells


title: J-Lat 10.6_ AAVS1 KO_AZDIBET_R3


title: J-Lat 10.6_WT_AZD5582andIBET-151_INTS12_2_R2

description: INTS12 Ab #2


title: J-Lat 10.6_ INTS12 KO_DMSO_R3


title: B16F10_S127A3

city: Chongqing

first: Fanxuan

last: Tian

address: No. 10, Changjiang Zhi Road, Daping Street, Yuzhong District

institute: Department of Gastroenterology, Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University

data_processing:
The sequencing data was filtered with SOAPnuke by Removing reads containing sequencing adapter
Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format
Assembly: mm10
Supplementary files format and content: tab-delimited text file include TPM values for each sample

source_name: Melanoma

extract_protocol:
Total RNA was extracted from normal or mutated B16F10 cells using TRIzol reagent (15596018CN, Invitrogen). Total RNA was quantified using a NanoDrop spectrophotometer and an Agilent 2100 bioanalyzer (Thermo Fisher Scientific).
RNA library construction and subsequent RNA sequencing were performed using BGI-Shenzhen (Shenzhen, China) software. First-strand cDNA was generated by random hexamer-primed reverse transcription followed by second-strand cDNA synthesis. Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubation for end repair. The cDNA fragments obtained from the previous step were amplified by PCR and the products were purified using Ampure XP Beads and dissolved in an EB solution. The product was validated using an Agilent Technologies 2100 Bioanalyzer for quality control. Double-stranded PCR products from the previous step were denatured and circularized using splint oligo sequences to obtain the final library. Single-stranded circular DNA used as the final library.

value: Melanoma

value: tumor cells

value: TNFα treatment with amino acid-limitation


title: B16F10_S127A2


title: J-Lat 10.6_ INTS12 KO_DMSO_R2

value: Peripheral blood

value: Jurkat


title: J-Lat 10.6_WT_AZD5582andIBET-151_INTS12_2_R1

description: INTS12 Ab #2

value: AAVS1 knockout cell


title: J-Lat 10.6_WT_AZD5582andIBET-151_RPB3_R1

description: RPB3 Ab


title: B16F10_S127A1


title: J-Lat 10.6_ AAVS1 KO_PMAi_R2


title: B16F10_WT3


title: B16F10_WT2


title: J-Lat 10.6_WT_AZD5582andIBET-151_INTS12_1_R5

description: INTS12 Ab #1


title: J-Lat 10.6_ INTS12 KO_PMAi_R1


title: J-Lat 10.6_ INTS12 KO_DMSO_R1

value: DMSO


title: J-Lat 10.6_ INTS12 KO_AZDIBET_R1


title: J-Lat 10.6_WT_AZD5582andIBET-151_INTS12_1_R4

description: INTS12 Ab #1


title: J-Lat 10.6_WT_AZD5582andIBET-151_INTS12_1_R3

description: INTS12 Ab #1


title: J-Lat 10.6_WT_AZD5582andIBET-151_INTS12_1_R2

description: INTS12 Ab #1


title: J-Lat 10.6_WT_AZD5582andIBET-151_INTS12_1_R1

description: INTS12 Ab #1


title: sample204, oral flora, 16s rRNA, non-hypertension

first: Xin

last: Chen

address: Zhangheng Rd

institute: SHUTCM

library_source: other

data_processing:
QIIME2 2022.11
Assembly: SILVA Release 138.1 /UNITE Release 9.0 Database
Supplementary files format and content: txt file includes raw counts for each sample
Library strategy: 16s rRNA-seq

molecule: other

organism: human oral metagenome

source_name: salivary

extract_protocol:
Total genomic DNA samples were extracted using the OMEGA Soil DNA Kit (M5635-02) (Omega Bio-Tek, Norcross, GA, USA), following the manufacturer’s instructions, and stored at -20 °C prior to further analysis. The quantity and quality of extracted DNAs were measured using a NanoDrop NC2000 spectrophotometer(Thermo Fisher Scientific, Waltham, MA, USA) and agarose gel electrophoresis, respectively.
PCR amplification of the bacterial 16S rRNA genes V3–V4 region was performed using the forward primer 338F (5'-ACTCCTACGGGAGGCAGCA-3') and the reverse primer 806R (5'-GGACTACHVGGGTWTCTAAT-3'). Sample-specific 7-bp barcodes were incorporated into the primers for multiplex sequencing. The PCR components contained 5 μl of buffer (5×), 0.25 μl of Fast pfu DNA Polymerase (5U/μl), 2 μl (2.5 mM) of dNTPs, 1 μl (10 uM) of each Forward and Reverse primer, 1 μl of DNA Template, and 14.75 μl of ddH2O. Thermal cycling consisted of initial denaturation at 98 °C for 5 min, followed by 25 cycles consisting of denaturation at 98 °C for 30 s, annealing at 53 °C for 30 s, and extension at 72 °C for 45 s, with a final extension of 5 min at 72 °C. PCR amplicons were purified with Vazyme VAHTSTM DNA Clean Beads (Vazyme, Nanjing, China) and quantified using the Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen, Carlsbad, CA, USA). After the individual quantification step, amplicons were pooled in equal amounts, and pair-end 2250 bp sequencing was performed using the Illlumina NovaSeq platform with NovaSeq 6000 SP Reagent Kit (500 cycles) at Shanghai Personal Biotechnology Co., Ltd (Shanghai,  China).

value: salivary

tag: condition

value: non-hypertension

value: oral flora


title: sample205, oral flora, 16s rRNA, hypertension

value: hypertension


title: J-Lat 10.6_ INTS12 KO_PMAi_R2

value: PMA & ionomycin


title: sample203, oral flora, 16s rRNA, hypertension


title: MEL-300-B, 72h, High GF Media, PF-07038124, Plate6, Rep1

city: Aurora

first: Stanca

last: Birlea

state: CO

department: Dermatology

institute: University of Colorado, Anschutz Medical Campus

description:
Normalized_count_matrix_all_samples
PDE4_vs_DMSO_72h_CSV
MEL300B_57

data_processing:
FASTQ files were scrutinized for quality using FastQC, while STAR was utilized to align and map raw reads to the human genome. The initial count matrix included transcripts undetected or barely expressed across samples, contributing negligible information regarding gene expression levels. To refine the data, genes with total counts below 100 across all samples were excluded, as were those with counts surpassing 5 million, to mitigate the influence of outliers. Additionally, genes with subtle or no variation-determined by a standard deviation threshold of 20 across subjects-were also excluded to ensure robustness in subsequent analysis. Although potential batch effects, such as plate variation, were assessed via principal component analysis, our rigorous evaluation revealed no significant effects.
For differential expression analysis, DESeq2 was employed, utilizing the Benjamini-Hochberg procedure to adjust for the false discovery rate amidst multiple tests. During RNA-seq data processing in DESeq2 analysis, normalization is conducted via size factor estimation to adjust for sequencing depth across samples. Our analytical model was designed to dissect the primary effects of 'Drug', 'Media', and 'Hours', along with the interaction between 'Drug' and 'Hours'. This approach allowed us to dissect the influence of drug treatment, media type, and treatment duration on gene expression. The DMSO-treated group and the initial time point (time "0") were established as baseline references for analyzing drug and temporal effects, respectively. In addition, by including the interaction term 'Drug:Hours', the model will assess whether the effect of the drug treatment on gene expression changes over time. This interaction term is crucial as it can reveal time-dependent effects of the drug that would not be apparent if only main effects were considered.
To generate the processed data files displaying fold changes for the marginal drug effects, all samples treated with a given drug (DMSO, Crisaborole, or PF-07038127) were combined regardless of media type (Low and High Growth Factor samples were combined).
Assembly: Human GRCh38.p14
Supplementary files format and content: "Normalized_count_matrix_all_samples" is a .CSV file showing gene counts that were prepared using the median-of-ratios normalization method in DESeq2, for all samples included in this study.
Supplementary files format and content: "Crisa_vs_DMSO_72h_CSV" is a .CSV file showing baseline-sample-adjusted values (base means and fold changes) for Crisaborole vs DMSO after 72 hours treatment, combining all Crisaborole-treated and DMSO-treated samples regardless of media type (marginal drug effect).
Supplementary files format and content: "PDE4_vs_DMSO_72h_CSV" is a .CSV file showing baseline-sample-adjusted values (base means and fold changes) for PF-07038124 vs DMSO after 72 hours treatment, combining all PF-07038124-treated and DMSO-treated samples regardless of media type (marginal drug effect).

source_name: MelanoDermTM

growth_protocol: The MelanoDermTM 3D in vitro co-culture skin model (MatTek Corp., Ashland, MA) incorporates normal human epidermal melanocytes (NHM) into a well differentiated epidermal tissue composed of non-matched normal human epidermal keratinocytes (NHEK), both derived from neonatal foreskin (Passeron et al., 2009). Tissues containing melanocytes from a Black donor (MEL-300-B) were equilibrated for 24 hours after arrival, in a 37°C, 5% CO2 incubator, using EPI-100-NMM-113 media (MatTek Corp., Ashland, MA).  The next day, media was changed (on Day 0 of the experiment) to the desired media type and drug treatment, as well as once every 48 hours until culture duration was complete (72 hours for MEL-300-B). Tissues were cultured in proprietary 12-well hang-top plates (MatTek Corp., Ashland MA) according to the recommended protocol. Sterile technique was used when handling tissues, and all media changes were performed in a laminar flow biosafety cabinet. Culture plates were only removed from the incubator as necessary to lower tissue exposure and the risk of contamination.

extract_protocol:
To isolate RNA, MelanoDermTM tissues were allowed to warm to room temperature for 15 minutes, removed from plastic inserts using straight fine-point tweezers, carefully blotted dry on clean Kimwipes, and transferred to 1.5 ml microcentrifuge tubes containing 300 μL buffer RLT from the RNeasy® Fibrous Tissue Mini Kit (#74704; Qiagen, Redwood City, CA) containing 1% β-mercaptoethanol (#M3148; Sigma-Aldrich, St. Louis, MO). Tissues (still adhered to culture membranes) were homogenized for 2 minutes each using a tissue homogenizer apparatus (#749540-0000; Kontes Pellet Pestle mixer motor; DWK Life Sciences, Wertheim, Germany) and disposable Pellet Pestle mixers (#74952-0000; DWK Life Sciences, Wertheim, Germany). A new pestle mixer was used for each sample and discarded. The culture membrane remained intact after homogenization and was separated from the tissue lysate after the initial centrifugation step and discarded. RNA was isolated using the RNeasy® Fibrous Tissue Mini Kit (#74704; Qiagen, Redwood City, CA) using the manufacturer’s recommended protocol. Next, 20 μL of isolated RNA from each sample (ranging between 6-10 μg) was further purified using the RNeasy® PowerClean® Pro Cleanup Kit (#13997-50; Qiagen, Redwood City, CA) to remove melanin and other impurities that may interfere with RNA sequencing.
RNA purity, quantity and integrity was determined using a NanoDropTM spectrophotometer (Thermo-Fisher Scientific, Waltham, MA) and TapeStation 4200 (Agilent Technologies, Inc., Santa Clara, CA) analysis prior to RNA-seq library preparation. The Universal Plus mRNA-Seq library preparation kit with NuQuant® was used (Tecan Genomics, Inc., Redwood City, CA) with an input of 200ng of total RNA to generate RNA-Seq libraries. Paired-end sequencing reads of 150bp were generated on NovaSeq 6000 (Illumina Inc., San Diego, CA) sequencer at a target depth of 80 million paired-end reads per sample. Raw sequencing reads were de-multiplexed using bcl2fastq.

treatment_protocol: MEL-300-B (Black donor) MelanoDermTM tissues were cultured according to the same methods described above, and tissues were treated with crisaborole at 10 μM (Pfizer Corp., New York, NY), PF-07038124 at 100 nM (Pfizer Corp., New York, NY) and DMSO vehicle control (#D265; Sigma-Aldrich, St. Louis, MO) at the same v/v concentration as crisaborole in low GF media.  To preserve RNA, each tissue was collected in 5ml RNAlater™ Stabilization Solution (#AM7020; Thermo-Fisher Scientific, Waltham, MA) in a 50 ml conical tube and allowed to equilibrate for 24 hr at 4C, followed by long-term storage at -20C. Tissues were collected in triplicate for each treatment group at 72 hr after initiating drug treatments. In addition, 6 baseline tissues were collected before the start of treatment, which were used as baseline references for treated samples grown in matching culture plates (see plate number).

value: MelanoDermTM

value: MEL-300-B; Black donor MCs

value: Keratinocytes and Melanocytes

value: PF-07038124 (0.1 μM) for 72h in High GF Media

tag: culture plate

value: Culture Plate 6


title: MEL-300-B, 72h, High GF Media, PF-07038124, Plate6, Rep2

description:
Normalized_count_matrix_all_samples
PDE4_vs_DMSO_72h_CSV
MEL300B_58


title: MEL-300-B, 72h, High GF Media, Crisaborole, Plate5, Rep1

description:
Normalized_count_matrix_all_samples
Crisa_vs_DMSO_72h_CSV
MEL300B_47

value: Crisaborole (10 μM) for 72h in High GF Media

value: Culture Plate 5


title: MEL-300-B, 0h, High GF Media, DMSO, Plate4, Baseline

description:
Normalized_count_matrix_all_samples
Crisa_vs_DMSO_72h_CSV
PDE4_vs_DMSO_72h_CSV
MEL300B_40

value: None; baseline

value: Culture Plate 4


title: MEL-300-B, 72h, High GF Media, Crisaborole, Plate5, Rep2

description:
Normalized_count_matrix_all_samples
Crisa_vs_DMSO_72h_CSV
MEL300B_48


title: sample206, oral flora, 16s rRNA, non-hypertension


title: J-Lat 10.6_ INTS12 KO_AZDIBET_R3

value: Peripheral blood

value: Jurkat

value: INTS12 knockout cells


title: MEL-300-B, 0h, High GF Media, DMSO, Plate6, Baseline

description:
Normalized_count_matrix_all_samples
Crisa_vs_DMSO_72h_CSV
PDE4_vs_DMSO_72h_CSV
MEL300B_60


title: J-Lat 10.6_INTS12KO_DMSO_RPB3_R3

description: RPB3 Ab

value: INTS12 knockout cell

value: DMSO


title: MEL-300-B, 72h, High GF Media, DMSO, Plate4, Rep3

description:
Normalized_count_matrix_all_samples
Crisa_vs_DMSO_72h_CSV
PDE4_vs_DMSO_72h_CSV
MEL300B_39

value: DMSO (10 μM) for 72h in High GF Media


title: J-Lat 10.6_ INTS12 KO_AZDIBET_R2


title: MEL-300-B, 72h, High GF Media, PF-07038124, Plate6, Rep3

description:
Normalized_count_matrix_all_samples
PDE4_vs_DMSO_72h_CSV
MEL300B_59


title: B16F10_WT1

value: Melanoma

value: tumor cells

value: WT

value: TNFα treatment with amino acid-limitation


title: J-Lat 10.6_INTS12KO_DMSO_RPB3_R2

description: RPB3 Ab


title: MEL-300-B, 0h, High GF Media, DMSO, Plate5, Baseline

description:
Normalized_count_matrix_all_samples
Crisa_vs_DMSO_72h_CSV
PDE4_vs_DMSO_72h_CSV
MEL300B_50

value: MelanoDermTM

value: MEL-300-B; Black donor MCs

value: Keratinocytes and Melanocytes


title: MEL-300-B, 72h, High GF Media, DMSO, Plate4, Rep2

description:
Normalized_count_matrix_all_samples
Crisa_vs_DMSO_72h_CSV
PDE4_vs_DMSO_72h_CSV
MEL300B_38


title: MEL-300-B, 72h, High GF Media, Crisaborole, Plate5, Rep3

description:
Normalized_count_matrix_all_samples
Crisa_vs_DMSO_72h_CSV
MEL300B_49

value: Crisaborole (10 μM) for 72h in High GF Media


title: MEL-300-B, 72h, High GF Media, DMSO, Plate4, Rep1

description:
Normalized_count_matrix_all_samples
Crisa_vs_DMSO_72h_CSV
PDE4_vs_DMSO_72h_CSV
MEL300B_37


title: sample202, oral flora, 16s rRNA, non-hypertension

value: salivary

value: non-hypertension

value: oral flora


title: J-Lat 10.6_INTS12KO_DMSO_RPB3_R1

description: RPB3 Ab

value: Peripheral blood


title: sample201, oral flora, 16s rRNA, non-hypertension


title: MEL-300-B, 72h, Low GF Media, PF-07038124, Plate3, Rep3

description:
Normalized_count_matrix_all_samples
PDE4_vs_DMSO_72h_CSV
MEL300B_29

value: PF-07038124 (0.1 μM) for 72h in Low GF Media

value: Culture Plate 3


title: MEL-300-B, 0h, Low GF Media, DMSO, Plate3, Baseline

description:
Normalized_count_matrix_all_samples
Crisa_vs_DMSO_72h_CSV
PDE4_vs_DMSO_72h_CSV
MEL300B_30

value: None; baseline


title: J-Lat 10.6_INTS12KO_DMSO_INTS12_2_R4

description: INTS12 Ab #2

value: Jurkat

value: INTS12 knockout cell

value: DMSO


title: MEL-300-B, 72h, Low GF Media, PF-07038124, Plate3, Rep2

description:
Normalized_count_matrix_all_samples
PDE4_vs_DMSO_72h_CSV
MEL300B_28


title: sample200, oral flora, 16s rRNA, non-hypertension


title: J-Lat 10.6_INTS12KO_DMSO_INTS12_2_R2

description: INTS12 Ab #2


title: MEL-300-B, 72h, Low GF Media, PF-07038124, Plate3, Rep1

description:
Normalized_count_matrix_all_samples
PDE4_vs_DMSO_72h_CSV
MEL300B_27


title: J-Lat 10.6_INTS12KO_DMSO_INTS12_2_R3

description: INTS12 Ab #2


title: MEL-300-B, 72h, Low GF Media, Crisaborole, Plate2, Rep3

description:
Normalized_count_matrix_all_samples
Crisa_vs_DMSO_72h_CSV
MEL300B_19

value: Crisaborole (10 μM) for 72h in Low GF Media

value: Culture Plate 2


title: J-Lat 10.6_INTS12KO_DMSO_INTS12_2_R1

description: INTS12 Ab #1


title: MEL-300-B, 0h, Low GF Media, DMSO, Plate2, Baseline

description:
Normalized_count_matrix_all_samples
Crisa_vs_DMSO_72h_CSV
PDE4_vs_DMSO_72h_CSV
MEL300B_20


title: sample198, oral flora, 16s rRNA, non-hypertension


title: sample197, oral flora, 16s rRNA, non-hypertension


title: sample199, oral flora, 16s rRNA, hypertension

value: hypertension


title: MEL-300-B, 72h, Low GF Media, Crisaborole, Plate2, Rep2

description:
Normalized_count_matrix_all_samples
Crisa_vs_DMSO_72h_CSV
MEL300B_18

value: MelanoDermTM


title: J-Lat 10.6_INTS12KO_DMSO_INTS12_1_R4

description: INTS12 Ab #1


title: Emergence, ventral skin, rep06

city: STORRS MANSFIELD

first: Grace

last: Vaziri

state: CT

address: 77 Forest Rd., Apt A

institute: University of Connecticut

data_processing:
We  used Trimmomatic (v. 0.39) to remove remaining adapter sequences and sequences shorter than 45 bp. We also used a sliding window for sequence quality to trim sequences at the point that a sequence’s average quality over any four-base pair window dropped below 25.
We assembled a transcriptome and generated a structural genome annotation using StringTie
Trimmed reads were aligned to the wood frog genome (GenBank Accession: JAQSEC000000000.1) using HISAT2
These alignments were used to make sample-level transcriptome assemblies and then merged across samples into a single representative transcriptome using Stringtie
From the merged assembly annotation file, ‘agat’ was used to extract coding region [35].
We used the Transdecoder Predict function with the flag ‘single_best_only’ to first find open reading frames at least 100bp long, translate them to peptide sequences for the centroid of each clustered coding region, and retain the single best (longest and with greatest homology to centroid) open reading frame for each coding region
Assembly: GenBank Accession: JAQSEC000000000.1, FASTA file with transcript sequence is available on the series record.
Supplementary files format and content: tab delimited text file including raw count data for sample by transcript
Supplementary files format and content: .count files are tab-delimited text files containing counts for each transcript in each sample

organism: Lithobates sylvaticus

source_name: ventral skin

extract_protocol:
We extracted and purified total RNA using a modified protocol for phase separation using TRI-reagent (Ambion, Invitrogen, Carlsbad, CA, USA) and the Direct-zol RNA Miniprep Plus Kit (Zymo Research, Irvine, CA, USA) for purification. Briefly, after thawing samples, we pipetted off the RNAlater preservative and immediately added 500 mL TRI-Reagent and a sterile steel bead. We briefly vortexed the sample, bead, and reagent before adding 500 mL more TRI-reagent and vortexing again for 10 min. Following vortexing we added 100 mL of cold 1-Bromo-3-chloropropane to each sample, shook each sample by hand for 20 s, and incubated for 15 min at room temperature. We then centrifuged samples at -2°C for 60 min at 16,000xg. After centrifuging, we checked samples to confirm that phase separation had occurred and transferred the aqueous (upper) RNA-containing phase to a sterile microcentrifuge tube for purification and DNase treatment, which we performed according to the manufacturer’s suggested protocol.
Total RNA samples were prepared for mRNA-sequencing using the Illumina Stranded mRNA Sample Preparation kit following the manufacturer’s protocol (Illumina, San Diego, CA, USA). Libraries were validated for length and adapter dimer removal using the Agilent TapeStation 4200 D1000 High Sensitivity assay (Agilent Technologies, Santa Clara, CA, USA) then quantified and normalized using the dsDNA High Sensitivity Assay for Qubit 3.0 (Life Technologies, Carlsbad, CA, USA).

value: ventral skin

tag: time

value: Emergence


title: Winter, ventral skin, rep05

value: Winter


title: Winter, ventral skin, rep03


title: J-Lat 10.6_INTS12KO_DMSO_INTS12_1_R3

description: INTS12 Ab #1


title: sample196, oral flora, 16s rRNA, non-hypertension

value: salivary


title: sample195, oral flora, 16s rRNA, hypertension


title: MEL-300-B, 0h, Low GF Media, DMSO, Plate1, Baseline

description:
Normalized_count_matrix_all_samples
Crisa_vs_DMSO_72h_CSV
PDE4_vs_DMSO_72h_CSV
MEL300B_10

value: MEL-300-B; Black donor MCs

value: Keratinocytes and Melanocytes

value: Culture Plate 1


title: Fall, ventral skin, rep 05

value: Fall


title: J-Lat 10.6_INTS12KO_DMSO_INTS12_1_R2

description: INTS12 Ab #1

value: Peripheral blood


title: MEL-300-B, 72h, Low GF Media, Crisaborole, Plate2, Rep1

description:
Normalized_count_matrix_all_samples
Crisa_vs_DMSO_72h_CSV
MEL300B_17


title: Winter, ventral skin, rep06


title: Spring, spleen, rep12

source_name: spleen

value: spleen

value: Spring


title: sample194, oral flora, 16s rRNA, non-hypertension

value: non-hypertension

value: oral flora


title: MEL-300-B, 72h, Low GF Media, DMSO, Plate1, Rep3

description:
Normalized_count_matrix_all_samples
Crisa_vs_DMSO_72h_CSV
PDE4_vs_DMSO_72h_CSV
MEL300B_9

value: DMSO (10 μM) for 72h in Low GF Media


title: J-Lat 10.6_INTS12KO_DMSO_INTS12_1_R1

description: INTS12 Ab #1

value: Jurkat

value: INTS12 knockout cell

value: DMSO


title: Emergence,spleen, rep06


title: Winter, spleen, rep06


title: MEL-300-B, 72h, Low GF Media, DMSO, Plate1, Rep2

description:
Normalized_count_matrix_all_samples
Crisa_vs_DMSO_72h_CSV
PDE4_vs_DMSO_72h_CSV
MEL300B_8

value: MelanoDermTM


title: sample193, oral flora, 16s rRNA, non-hypertension


title: J-Lat 10.6_INTS12KO_AZD5582andIBET-151_RPB3_R3

description: RPB3 Ab


title: MEL-300-B, 72h, Low GF Media, DMSO, Plate1, Rep1

description:
Normalized_count_matrix_all_samples
Crisa_vs_DMSO_72h_CSV
PDE4_vs_DMSO_72h_CSV
MEL300B_7


title: J-Lat 10.6_INTS12KO_AZD5582andIBET-151_RPB3_R2

description: RPB3 Ab


title: sample192, oral flora, 16s rRNA, hypertension

value: hypertension


title: Winter, spleen, rep05

value: Winter


title: SK.N.SH GEX

city: Boston

first: Allan

middle: M

last: Goldstein

state: MA

address: 185 Cambridge St

department: Pediatric Surgery

institute: Massachusetts General Hospital

data_processing:
Sequencing performed using Illumina NextSeq or NovaSeq platforms
Genome alignment and counts matrices generated using 10X Genomics Cell Ranger pipeline
Assembly: hg38
Supplementary files format and content: CSV
Supplementary files format and content: GEX and ATAC raw count matrices

source_name: Neuroblastoma tumor

extract_protocol:
Single nuclei
10X Genomics Cell Ranger pipeline

value: Neuroblastoma tumor

value: Tumor cells


title: J-Lat 10.6_INTS12KO_AZD5582andIBET-151_RPB3_R1

description: RPB3 Ab


title: Fall, spleen, rep 10


title: SK.N.SH ATAC


title: sample190, oral flora, 16s rRNA, hypertension

value: salivary


title: Spring, ventral skin, rep12

value: ventral skin


title: J-Lat 10.6_INTS12KO_AZD5582andIBET-151_INTS12_2_R4

description: INTS12 Ab #2


title: J-Lat 10.6_INTS12KO_AZD5582andIBET-151_INTS12_2_R2

description: INTS12 Ab #2


title: SK.N.DZ GEX


title: Spring, ventral skin, rep09


title: sample189, oral flora, 16s rRNA, non-hypertension


title: sample188, oral flora, 16s rRNA, non-hypertension


title: sample187, oral flora, 16s rRNA, non-hypertension


title: Spring, spleen, rep09


title: J-Lat 10.6_INTS12KO_AZD5582andIBET-151_INTS12_1_R4

description: INTS12 Ab #1


title: sample191, oral flora, 16s rRNA, non-hypertension


title: SK.N.AS GEX


title: Spring, spleen, rep07


title: SHSY5Y GEX


title: sample184, oral flora, 16s rRNA, non-hypertension


title: SK.N.AS ATAC


title: J-Lat 10.6_INTS12KO_AZD5582andIBET-151_INTS12_1_R3

description: INTS12 Ab #1


title: sample185, oral flora, 16s rRNA, non-hypertension


title: J-Lat 10.6_INTS12KO_AZD5582andIBET-151_INTS12_1_R2

description: INTS12 Ab #1


title: Spring, ventral skin, rep07


title: Spring, ventral skin, rep02


title: sample183, oral flora, 16s rRNA, hypertension


title: SHSY5Y ATAC


title: J-Lat 10.6_INTS12KO_AZD5582andIBET-151_INTS12_2_R1

description: INTS12 Ab #2


title: Spring, spleen, rep02


title: CHP134 ATAC


title: SK.N.DZ ATAC


title: CHP134 GEX


title: Be2c GEX


title: Spring, spleen, rep01


title: sample182, oral flora, 16s rRNA, hypertension


title: Spring, ventral skin, rep08


title: Spring, ventral skin, rep01


title: sample181, oral flora, 16s rRNA, hypertension


title: sample186, oral flora, 16s rRNA, non-hypertension


title: Emergence, ventral skin, rep08

value: Emergence


title: MCF-7 cells, siCDK4-2-2

city: shanghai

first: Fan

last: Wei

address: 501 haike road

department: Divison of Anti-Tumor Pharmacology

institute: Shanghai Institute of Materia Medica, Chinese Academy of Sciences

description: gene.fpkm.matrix.annot

data_processing:
Cleandata for each sample were first mapped to a reference genome hg38 with the software STAR
HTSeq was used to count the reads numbers mapped to each gene
the expression level of each transcript was calculated according to the number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) method
Differential expression analysis was performed using the DESeq2
Assembly: hg38
Supplementary files format and content: fpkm values for each sample
Supplementary files format and content: transcriptome fpkm values for each sample

growth_protocol: MCF-7 cells were maintained in complete medium containg 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37 ℃

extract_protocol:
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparation
The RNA-seq transcriptome library was prepared following Illumina Stranded mRNA Prep, Ligation from Illumina according to the manufacturer’s instructions.

treatment_protocol: siRNA of CDK4 for 48 hours

value: breast cancer cells

value: CDK4 knockdown


title: Be2c ATAC


title: J-Lat 10.6_INTS12KO_AZD5582andIBET-151_INTS12_1_R1

description: INTS12 Ab #1

value: Peripheral blood


title: Emergence,spleen, rep08

value: spleen


title: Emergence, ventral skin, rep07


title: MCF-7 cells, siCDK4-1-2

description: gene.fpkm.matrix.annot


title: Emergence,spleen, rep07


title: MCF-7 cells, siCDK4-1-1

description: gene.fpkm.matrix.annot


title: Emergence, ventral skin, rep05


title: MCF-7 cells, siNC-2

description: gene.fpkm.matrix.annot

value: WT


title: Emergence,spleen, rep05


title: Emergence, ventral skin, rep02


title: MCF-7 cells, siNC-1

description: gene.fpkm.matrix.annot


title: Emergence,spleen, rep02


title: 240_Astrocytes_IDO1i_C

city: Stanford

first: Katrin

middle: I

last: Andreasson

state: CA

address: 1201 Welch Road MSLS P250

department: 1Dept of Neurology & Neurological Sciences

institute: Stanford University

data_processing:
FASTQC
TrimGalore
Star aligner
RSEM
DESEQ2
Assembly: Hg38

extract_protocol:
Trizol
low input RNA (121-180) and Ultra Low input RNA-Seq cDNA Prep (SMART-seq) (181-240)

value: Astrocytes

value: C

value: F

tag: diagnosis

value: CN

tag: rnaseq batch


title: 239_Astrocytes_IDO1i_B

value: B


title: Emergence, ventral skin, rep01


title: 238_Astrocytes_IDO1i_A

value: A


title: MCF-7 cells, siCDK4-2-1

description: gene.fpkm.matrix.annot


title: Emergence,spleen, rep01


title: healthy donor 2

city: TOULOUSE

first: Pauline

last: Gravelle

address: 1 Avenue Irène Joliot Curie

department: Anatomy-Pathology

country: France

institute: IUCT-ONCOPOLE

data_processing:
bcl2 files conversion to FASTQ format using spaceranger-mkfastq™ algorithm (10x Genomics)
align to the GRCh38 reference transcriptome using cellranger-count
Preprocessing, normalization of UMI, and QC were performed using the R package Seurat
The integrated (cell x gene) matrices of all samples are provided.
Assembly: GRCh38
Supplementary files format and content: Matrix_SMZL_spatial_GEX.tsv (Spatial transcriptomic datasets gene expression of 3 SMZL  and 1 healthy donor samples)
Supplementary files format and content: Matrix_SMZL_spatial_Annotations.tsv (Annotation matrix for all spatial transcriptomic of each sample included in this study)
Supplementary files format and content: Matrix_SMZL_tissue_positions_coordinates.tsv (Annotation matrix for tissue position coordinates for all spatial transcriptomic)
Supplementary files format and content: .png files (Images of tissues in high resolution for spatial representation )
Library strategy: Spatial Transcriptomics

growth_protocol: Tissues were processed before sequencing without growth protocol.

extract_protocol:
Tissues were then permeabilized and reverse transcription was performed on the slide.
Second-strand synthesis, denaturation, DNA amplification, libraries construction and sequencing were performed following the manufacturer's instructions (Visium Spatial Gene Expression Reagent Kits User Guide - Rev C).
Visium Spatial chemistry

treatment_protocol: After surgery, human spleen samples were snap-frozen in isopentane bath and stored at -80°C. On the day of the experiment, spleen tissues were embedded in OCT and cut with a cryostat. Sections were placed on the Visium spatial slide following the manufacturer's instructions (Visium Spatial Protocols - Tissue Preparation Guide - Rev A). Methanol fixation was performed and followed by staining with Haematoxylin, several washes in Ultrapure water, and aqueous eosin coloration. Imaging was done with LSM 710 videomicroscope, under a 10X magnification.

tag: age

value: Male

tag: disease

value: healthy control

tag: disease stage


title: 237_Neurons_IDO1i_C

description: Neurons exposed to IDO1i Astrocytes

value: Neurons


title: splenic marginal zone lymphoma sample 3

source_name: splenic marginal zone lymphoma

value: 66 yrs

value: Female

value: SMZL

value: diagnosis


title: healthy donor 1 blood

data_processing:
bcl2 files conversion to FASTQ format using cellranger-mkfastq™ algorithm (10x Genomics)
align to the GRCh38 reference transcriptome using cellranger-count
Preprocessing, normalization of UMI, and QC for discarding cell doublets and dying cells were performed using the R package Seurat
The integrated (cell x gene) matrices of all single cells are provided.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and sample
Supplementary files format and content: Matrix_SMZL_GEX.txt: All 5’ single-cell datasets gene expression of 3 SMZL samples
Supplementary files format and content: Matrix_SMZL_T.txt: All single-cell T-cell receptors data from 3 SMZL samples
Supplementary files format and content: Matrix_SMZL_B.txt: All single-cell B-cell receptors data from 3 SMZL samples

source_name: blood

growth_protocol: Cells were thawed before sequencing without growth protocol.

extract_protocol:
For the experiment, 10 000 cells of each sample were loaded in Chromium device for emulsion-based production of single cell mRNA libraries with the 10XGenomics platform chemistry 5’ V3. Reverse transcription was performed on the C1000 Touch Thermal Cycler, and cDNA were amplified for 12 cycles. cDNA quality control and dosage were performed on Fragment Analyzer, and then by PCR.
Chromium Controller Single-Cell Instrument and Chromium Single Cell 5 Library & Gel Bead Kit (V3) were used to prepare individually barcoded single-cell RNA-Seq libraries. Double sided size selection of PCR products was performed with SPRIselect Reagent Kit (Beckman Coulter, France). The sequencing-ready library was cleaned up with SPRIselect beads and the sequencing was performed on a NextSeq 550 instrument (Illumina).

treatment_protocol: Dead Cell Removal Kit was used to improve cell viability

value: blood

value: not collected

tag: description


title: Winter, ventral skin, rep09

value: ventral skin

value: Winter


title: 236_Neurons_IDO1i_B

description: Neurons exposed to IDO1i Astrocytes

tag: cell type


title: splenic marginal zone lymphoma sample 2

value: spleen

value: 75 yrs


title: sample176, oral flora, 16s rRNA, non-hypertension

value: salivary

value: non-hypertension

value: oral flora


title: sample179, oral flora, 16s rRNA, non-hypertension


title: Winter, spleen, rep07


title: sample178, oral flora, 16s rRNA, hypertension

value: hypertension


title: sample171, oral flora, 16s rRNA, non-hypertension


title: Winter, spleen, rep09


title: sample172, oral flora, 16s rRNA, hypertension


title: sample180, oral flora, 16s rRNA, hypertension


title: sample175, oral flora, 16s rRNA, hypertension


title: Winter, ventral skin, rep08


title: sample170, oral flora, 16s rRNA, non-hypertension


title: sample174, oral flora, 16s rRNA, non-hypertension


title: sample173, oral flora, 16s rRNA, non-hypertension


title: sample169, oral flora, 16s rRNA, hypertension


title: sample177, oral flora, 16s rRNA, non-hypertension


title: sample168, oral flora, 16s rRNA, non-hypertension


title: Winter, ventral skin, rep07


title: 235_Neurons_IDO1i_A

description: Neurons exposed to IDO1i Astrocytes

tag: treatment

value: A

value: F

value: CN


title: splenic marginal zone lymphoma sample 1

value: 59 yrs

value: Male


title: sample167, oral flora, 16s rRNA, non-hypertension


title: 234_Astrocytes_VEH_C

tag: cell line

value: Astrocytes

value: VEH

value: C


title: sample166, oral flora, 16s rRNA, hypertension


title: healthy donor 2 spleen

value: not collected


title: splenic marginal zone lymphoma sample 3 blood

value: blood

value: 66 yrs

value: Female


title: 233_Astrocytes_VEH_B

tag: replicate

value: B


title: sample165, oral flora, 16s rRNA, non-hypertension

value: salivary


title: Winter, spleen, rep04

value: spleen

value: Winter


title: sample163, oral flora, 16s rRNA, non-hypertension

value: non-hypertension

value: oral flora


title: 230_Neurons_VEH_B

description: Neurons exposed to DMSO treated Astrocytes

value: Neurons

value: F


title: sample161, oral flora, 16s rRNA, non-hypertension


title: splenic marginal zone lymphoma sample 2 blood

value: 75 yrs


title: 229_Neurons_VEH_A

value: A

value: CN


title: Winter, ventral skin, rep02

value: ventral skin


title: 231_Neurons_VEH_C

value: VEH

value: C


title: splenic marginal zone lymphoma sample 1 blood

value: blood

value: 59 yrs

value: Male


title: sample164, oral flora, 16s rRNA, non-hypertension


title: 232_Astrocytes_VEH_A

value: Astrocytes


title: splenic marginal zone lymphoma sample 3 spleen

value: 66 yrs

value: Female


title: Winter, spleen, rep03

value: spleen

value: Winter


title: sample160, oral flora, 16s rRNA, hypertension

value: salivary

value: hypertension

value: oral flora


title: sample162, oral flora, 16s rRNA, non-hypertension

value: non-hypertension


title: Winter, ventral skin, rep01


title: 228_Astrocytes_IDO1i_C

value: M

value: AD


title: 227_Astrocytes_IDO1i_B

value: B


title: splenic marginal zone lymphoma sample 2 spleen

value: 75 yrs


title: Fall, spleen, rep 11

value: Fall


title: splenic marginal zone lymphoma sample 1 spleen


title: nucleus, 0min, rep4

data_processing:
Alignment of raw reads was done with STAR (v2.7.6).
Reads in exons were counted with HTSeq-count (v0.11.1) and exon and TPM values were obtained by RSEM (v.1.3.3) using default parameters.
Based on a binomial mixture model by Juerges et al. (2018) we determined the conversion rate per sample. With the conversion rates, T and T2C conversion counts the fraction of new to total RNA was calculated on intron/exon level, which was used later on as input for the kinetic model.
Gene set enrichment analyses were performed with fgsea (v1.28.0) with the GSEA parameter set to 0 and gene set sizes limited from 30 to 900.
Fitting was performed throughout with the python package lmfit (v1.0.3) using the Levenberg-Marquardt “least-squares” algorithm to minimize the chi-squared unless otherwise specified. Summarizing different models and genes, the following kinetic rates were estimated: transcript elongation rate, intron removal rate, nuclear export rate, nuclear degradation rate, cytosolic degradation rate, cytosolic transport rate and membrane degradation rate.
Assembly: mm10
Supplementary files format and content: {sample}.txt files provide raw read counts per gene, reads counted in exons with HTSeq-count
Supplementary files format and content: {sample}_t2c_counts.txt files give gene and exon-wise T2C metrics: conversion probability (p_conv), number of Ts in gene/exon/intron (T_exon, T_intron), number of T2C transitions in gene/exon/intron (T2C_exon, T2C_intron) and share of T2C vs total T counts divided by conversion probability per gene/exon/intron (T2C_over_T_exon, T2C_over_T_intron).

extract_protocol:
Briefly, medium was aspirated, 5 ml of ice-cold PBS supplemented with 100 µM cycloheximide (A0879,0001, Biochemika) was added to the plates, cells were scraped from the plates, transferred to 15ml falcon and spun down. Pellet was resuspended in 500 µl of ice-cold permeabilization buffer (110 mM KOAc, 25 mM K-HEPES pH 7.2, 2.5 mM Mg(OAc)2, 1 mM EGTA with freshly added 0.015% digitonin, 1 mM DTT, 100 μg/ml cycloheximide, 1X Complete Protease Inhibitor Cocktail and 40 U/mL RNaseOUT™). 100 µl of the sample was taken aside as Total extract and rest was incubated for 10 min at 4°C with rotation, followed by centrifugation at 3000 g 5 min at 4°C. Supernatant (corresponding to the Cytosolic fraction) was transferred to new tube while the pellet was resuspended in 5ml of wash buffer (110 mM KOAc, 25 mM K-HEPES pH 7.2, 2.5 mM Mg(OAc)2, 1 mM EGTA with freshly added 0.004% digitonin, 1mM DTT, 100μg/ml cycloheximide) and spun down again at 3000 g 5 min at 4°C. After centrifugation washed pellet was mixed with 500 µl of ice-cold lysis buffer (400 mM KOAc, 25 mM K-HEPES pH 7.2, 15 mM Mg(OAc)2, 0.5% (v/v) NP-40 and freshly added 1 mM DTT, 100 μg/ml cycloheximide, 1X Complete Protease Inhibitor Cocktail, 40 U/mL RNase Out) and incubated for 5 min on ice followed by centrifugation at 3000 g 5 min at 4°C to collect the supernatant (corresponding to the Membrane fraction) and the pellet (insoluble and the nuclear fraction). For additional purity nuclei were loaded on 10% sucrose cushion in lysis buffer and centrifuged at 200 g 5 min at 4°C. The cytosolic and membrane fractions were clarified at 7500 g 10 min at 4°C to remove cell debris. 20 µl of all fractions were taken for Western analysis while rest were mixed with Trizol LS (10296028, Thermo Fisher Scientific) for subsequent RNA isolation.
One microgram of total RNA was used as an input for TruSeq Stranded mRNA Library Prep Kit according to the instructions of the manufacturer.
TruSeq Stranded mRNA Library Paired-End

value: mESC

value: 500uM 4-thiouridine


title: sample159, oral flora, 16s rRNA, non-hypertension


title: 226_Astrocytes_IDO1i_A

value: A


title: Fall, ventral skin, rep 10

value: ventral skin


title: Fall, ventral skin, rep 11


title: Fall, ventral skin, rep 09


title: CC-1690 cells, vip1-1, nutritional stress, biol rep 3

city: Sevilla

first: Rodrigo

last: Bedera-García

state: Sevilla

address: Américo Vespucio 49

department: Plant Biochemistry and Molecular Biology

country: Spain

institute: Universidad de Sevilla

data_processing:
Sequence reads were mapped using Hisat2
Transcript assembly and expression quantification was done using Stringtie
Ballgown was used to generate the processed data with FPKM values and prepDE.py from Stringtie to generate the processed data with raw counts
Assembly: Chlamydomonas_reinhardtii_v5.5 from EnsemblPlants
Supplementary files format and content: comma-delimited text file (.csv) includes FPKM values for each sample
Supplementary files format and content: comma-delimited text file (.csv) includes raw counts for each sample

organism: Chlamydomonas reinhardtii

growth_protocol: Cells were grown in liquid TAP medium at 25ºC under 50 μmol m-2 s-1 photon flux density.

extract_protocol:
RNA was purified using ISOLATE II RNA Plant Kit (Bioline) following manufacturer’s instructions
Sequencing libraries were generated according to Illumina TruSeq Stranded mRNA protocol

treatment_protocol: Both the wild-type strain and the vip1-1 strain were grown for 24 h for control conditions, and grown for 14 days for nutritional stress conditions.

tag: strain

tag: genotype

value: nutritional stress


title: CC-1690 cells, vip1-1, nutritional stress, biol rep 2


title: sample157, oral flora, 16s rRNA, non-hypertension

tag: tissue


title: Fall, spleen, rep 09


title: sample155, oral flora, 16s rRNA, non-hypertension


title: Fall, ventral skin, rep 08


title: sample156, oral flora, 16s rRNA, non-hypertension


title: CC-1690 cells, vip1-1, control, biol rep 3

value: control


title: 224_Neurons_IDO1i_B

description: Neurons exposed to IDO1i Astrocytes

value: Neurons

tag: Sex


title: CC-1690 cells, vip1-1, control, biol rep 2


title: 223_Neurons_IDO1i_A

description: Neurons exposed to IDO1i Astrocytes


title: sample154, oral flora, 16s rRNA, non-hypertension

tag: condition


title: Fall, spleen, rep 08

value: spleen


title: CC-1690 cells, vip1-1, nutritional stress, biol rep 1


title: CC-1690 cells, vip1-1, control, biol rep 1


title: 222_Astrocytes_VEH_C

value: Astrocytes

value: VEH

value: C


title: Fall, ventral skin, rep 07


title: 221_Astrocytes_VEH_B


title: sample153, oral flora, 16s rRNA, non-hypertension

value: salivary

value: non-hypertension

value: oral flora


title: 220_Astrocytes_VEH_A

value: M

value: AD


title: CC-1690 cells, wild-type, nutritional stress, biol rep 3

value: wild-type


title: sample158, oral flora, 16s rRNA, hypertension

value: hypertension


title: sample152, oral flora, 16s rRNA, non-hypertension


title: 219_Neurons_VEH_C


title: 225_Neurons_IDO1i_C

description: Neurons exposed to IDO1i Astrocytes


title: Fall, ventral skin, rep 06

value: Fall


title: Fall, spleen, rep 07


title: sample151, oral flora, 16s rRNA, hypertension


title: 218_Neurons_VEH_B

value: B


title: Fall, spleen, rep 06


title: CC-1690 cells, wild-type, control, biol rep 3


title: CC-1690 cells, wild-type, nutritional stress, biol rep 1


title: 216_Astrocytes_IDO1i_C

value: CN


title: sample148, oral flora, 16s rRNA, hypertension


title: sample150, oral flora, 16s rRNA, hypertension


title: H3k4me3_TaDRIM-Seq-293T-rep2

city: Wuhan

first: guoting

last: chen

address: 1 Shizishan Street, Hongshan District

institute: National Key Laboratory of Crop Genetic Improvement

data_processing:
Raw reads were filtered for adapter and low quality reads by Trimmomatic
splitting data into DNA-end and RNA-end data, mapping DNA-end data to the reference genome by BWA
RNA-end data to the reference genome by HISAT2 and Bowtie2
Extracting the uniquely matched reads
Converting bam files to BigWig files
Assembly: genome build by BWA and assembly by HISAT2 and Bowtie2
Supplementary files format and content: Download the genome from http://rice.hzau.edu.cn/
Supplementary files format and content: The hic format file was converted by juicer_tools

molecule: nuclear RNA

growth_protocol: Human K562 cells (ATCC) were cultured in DMEM containing 10% FBS (Gibco) and 1% penicillin-streptomycin (Gibco) and growing at 37 °C and 5% CO2 in a cellmate CO2 incubator (Esco Scientific). Cells were cross-linked with 1% formaldehyde (Sigma-Aldrich) in 1×PBS (Thermo Fisher) for 10 min with rotation at room temperature, followed by quenching with 0.2M glycine for 5 min at room temperature with rotation. Cells were washed three times with 1×PBS and stored at -80 °C.Rice Xian/indica cv. Minghui 63 (MH63) seeds were used and sown in May. Germinated seedlings were transplanted into a paddy field (Huazhong Agricultural University at Wuhan, China), and grown under normal agricultural conditions. Mature leaves were collected on July, and were immediately single cross-linked with 1% formaldehyde and stored at -80 °C.

extract_protocol:
Approximately1×106- 1×107 crosslinked cells were used per replicate. Cell nuclei were isolated in 1 mL lysis buffer (10mM Tris pH 7.5, 10mM NaCl, 0.2% NP40, 1×protease inhibitors, 0.2 U/μl RiboLock RNase) (Thermo Fisher), and incubated for 10min on ice followed by centrifugation for 3min at 2500g and 4°C. The nuclei were washed twice with 300µl 1×wash buffer A (20mM HEPES pH 7.6, 150mM NaCl, 0.5mM Spermidine, 1×protease inhibitors, 0.2U/μl RiboLock RNase) (Thermo Fisher), and nuclei were collected by centrifugation for 3min at 2500g and 4 °C. Nuclei were then resuspended in Antibody buffer (495μl 1×wash buffer A, 5μl 5% digitonin, 2μl 0.5M EDTA, 1.6μl 30%BSA, 10μg antibody (H3K4me3, Abcam, ab8580; H3K9ac, Abcam, ab10812; CTCF, Abcam, ab188408), and incubated at 4°C for 2h with rotation. Nuclei were pelleted for 3 min at 2500g and washed five times with 300μl 1×wash buffer A, resuspended 500µl 1×transposase incubation buffer (20mM HEPES pH 7.6, 300mM NaCl, 0.5mM Spermidine, 0.01% digitonin, 1×protease inhibitors, 0.2U/μl RiboLock RNase) (Thermo Fisher), followed by adding 5μl TTE Mix, and incubated at 4°C for 1h with rotation. Nuclei were collected and washed five times with 300µl 1×transposase incubation buffer and resuspended in tagmentation buffer (500µl 1×transposase incubation buffer, 5µl 1M MgCl2), and incubated at 37°C for 1h. Next, 500µl of 40mM EDTA (Thermo Fisher) was added to stop the reaction. The isolated nuclei were washed twice with 500µl 1×PBS (Thermo Fisher) and then incubated in 200µl permeabilization buffer (190µl nuclease-free water, 10µl 10% SDS) (Thermo Fisher) at 62°C for 10min, and immediately quenched the SDS reaction by adding add 580μl of nuclease-free water and 100μl of 10% (vol/vol) Triton X-100 (Sigma-aldrich), and incubated at 37°C for 15min with rotation.The isolated nuclei were washed twice with 500µl 1×wash buffer B (20mM Tris-HCl, pH 7.5, 10mM MgCl2 and 0.2% Tween 20) and resuspended in 500µl 1× CutSmart buffer (NEB), followed by adding 1.6µl RNase If (NEB) with dilution tenfold in 1× PBS, and incubated at 37°C for 3min with rotation followed by incubation for 5min on ice. Nuclei were collected by centrifugation, then resuspended by 400µl PNK solution containing 1×T4 PNK reaction buffer, 1mM ATP, 1U/μl RiboLock RNase and 1U/μl T4 PNK (Thermo Fisher) at 37°C for 40min with rotation. The specific bridge linker was designed containing 5ʹ phosphorylation [5Phos] and Internal Biotin dT [ibiodT] chemical modifications. The forward strand is: 5′-[5APP]CCTCGATAC/iBIOdT/TGAGCTGAC-3′, and reverse strand is 5′-[5Phos]GTCAGC/iBIOdT/CAAGTATCGAG-3′. The 5′App ends of forward strand was treated by using a DNA 5′ Adenylation Kit (NEB). The isolated nuclei were washed twice with 500µl 1×wash buffer B and resuspended in 400µl of RNA ligation solution (1×T4 RNA ligase reaction buffer, 1U/μl RiboLock RNase, 10U/μl T4 RNA Ligase 2 truncated, 1.5pmol/μl bridge linker, 15% (w/v) PEG 8000, 0.1% Triton X-100) (NEB), and incubated overnight at 16 °C with rotation. The nuclei were pelleted by centrifugation, resuspended in 400 μl reverse transcription solution (1×MMLV buffer, 0.5mM dNTP, 8U/μl MMLV (RNase H-), 1U/μl RiboLock RNase) (Promega), and then incubated at 42 °C for 1 h. The isolated nuclei were washed five times with 500μl 1×wash buffer B, resuspended in T4 DNA ligation solution (1×DNA ligase reaction buffer with 10mM ATP, 4U/μl T4 DNA ligase, 0.1% (vol/vol) Triton X-100 and 0.1 mg/mLBSA) (NEB), incubated overnight at 16 °C with rotation. The isolated nuclei were resuspended in proteinase K solution (50 mM Tris-HCl, pH 7.5, 1% SDS, 100mM NaCl, 1mM EDTA and 1mg/mL proteinase K) at 65 °C for 3h with shaking at 800 rpm. RNA/DNA complex was extracted and dissolved in nuclease-free water (Thermo Fisher). The purified RNA/DNA complexes were incubated with gap-filling solution (10×NEBuffer r2.1,1mM dNTP and 0.18U/μl T4 DNA polymerase) (NEB) at room temperature for 40min to repair the pG-Tn5 transposition gap, followed by second-strand cDNA synthesis.
DNA-cDNA complexes were converted to DNA library according to the TruePrep DNA Library Prep Kit for Illumina (Vazyme, cat. no. TD501). The fragments containing biotinylated bridge-linker were enriched by M280 beads (Thermo Fisher) before PCR, and enriched library DNA is size-selected by using AMPure XP beads (Beckman), and sequenced (2×150 bp) using Illumina Hiseq X-Ten (Annoroad Gene Technology).

treatment_protocol: Approximately1×106- 1×107 crosslinked cells were used per replicate. Cell nuclei were isolated in 1 mL lysis buffer (10mM Tris pH 7.5, 10mM NaCl, 0.2% NP40, 1×protease inhibitors, 0.2 U/μl RiboLock RNase) (Thermo Fisher), and incubated for 10min on ice followed by centrifugation for 3min at 2500g and 4°C. The nuclei were washed twice with 300µl 1×wash buffer A (20mM HEPES pH 7.6, 150mM NaCl, 0.5mM Spermidine, 1×protease inhibitors, 0.2U/μl RiboLock RNase) (Thermo Fisher), and nuclei were collected by centrifugation for 3min at 2500g and 4 °C. Nuclei were then resuspended in Antibody buffer (495μl 1×wash buffer A, 5μl 5% digitonin, 2μl 0.5M EDTA, 1.6μl 30%BSA, 10μg antibody (H3K4me3, Abcam, ab8580)), and incubated at 4°C for 2h with rotation. Nuclei were pelleted for 3 min at 2500g and washed five times with 300μl 1×wash buffer A, resuspended 500µl 1×transposase incubation buffer (20mM HEPES pH 7.6, 300mM NaCl, 0.5mM Spermidine, 0.01% digitonin, 1×protease inhibitors, 0.2U/μl RiboLock RNase) (Thermo Fisher), followed by adding 5μl TTE Mix, and incubated at 4°C for 1h with rotation. Nuclei were collected and washed five times with 300µl 1×transposase incubation buffer and resuspended in tagmentation buffer (500µl 1×transposase incubation buffer, 5µl 1M MgCl2), and incubated at 37°C for 1h. Next, 500µl of 40mM EDTA (Thermo Fisher) was added to stop the reaction. The isolated nuclei were washed twice with 500µl 1×PBS (Thermo Fisher) and then incubated in 200µl permeabilization buffer (190µl nuclease-free water, 10µl 10% SDS) (Thermo Fisher) at 62°C for 10min, and immediately quenched the SDS reaction by adding add 580μl of nuclease-free water and 100μl of 10% (vol/vol) Triton X-100 (Sigma-aldrich), and incubated at 37°C for 15min with rotation.The isolated nuclei were washed twice with 500µl 1×wash buffer B (20mM Tris-HCl, pH 7.5, 10mM MgCl2 and 0.2% Tween 20) and resuspended in 500µl 1× CutSmart buffer (NEB), followed by adding 1.6µl RNase If (NEB) with dilution tenfold in 1× PBS, and incubated at 37°C for 3min with rotation followed by incubation for 5min on ice. Nuclei were collected by centrifugation, then resuspended by 400µl PNK solution containing 1×T4 PNK reaction buffer, 1mM ATP, 1U/μl RiboLock RNase and 1U/μl T4 PNK (Thermo Fisher) at 37°C for 40min with rotation. The specific bridge linker was designed containing 5ʹ phosphorylation [5Phos] and Internal Biotin dT [ibiodT] chemical modifications. The forward strand is: 5′-[5APP]CCTCGATAC/iBIOdT/TGAGCTGAC-3′, and reverse strand is 5′-[5Phos]GTCAGC/iBIOdT/CAAGTATCGAG-3′. The 5′App ends of forward strand was treated by using a DNA 5′ Adenylation Kit (NEB). The isolated nuclei were washed twice with 500µl 1×wash buffer B and resuspended in 400µl of RNA ligation solution (1×T4 RNA ligase reaction buffer, 1U/μl RiboLock RNase, 10U/μl T4 RNA Ligase 2 truncated, 1.5pmol/μl bridge linker, 15% (w/v) PEG 8000, 0.1% Triton X-100) (NEB), and incubated overnight at 16 °C with rotation. The nuclei were pelleted by centrifugation, resuspended in 400 μl reverse transcription solution (1×MMLV buffer, 0.5mM dNTP, 8U/μl MMLV (RNase H-), 1U/μl RiboLock RNase) (Promega), and then incubated at 42 °C for 1 h. The isolated nuclei were washed five times with 500μl 1×wash buffer B, resuspended in T4 DNA ligation solution (1×DNA ligase reaction buffer with 10mM ATP, 4U/μl T4 DNA ligase, 0.1% (vol/vol) Triton X-100 and 0.1 mg/mLBSA) (NEB), incubated overnight at 16 °C with rotation. The isolated nuclei were resuspended in proteinase K solution (50 mM Tris-HCl, pH 7.5, 1% SDS, 100mM NaCl, 1mM EDTA and 1mg/mL proteinase K) at 65 °C for 3h with shaking at 800 rpm. RNA/DNA complex was extracted and dissolved in nuclease-free water (Thermo Fisher). The purified RNA/DNA complexes were incubated with gap-filling solution (10×NEBuffer r2.1,1mM dNTP and 0.18U/μl T4 DNA polymerase) (NEB) at room temperature for 40min to repair the pG-Tn5 transposition gap, followed by second-strand cDNA synthesis.


title: sample149, oral flora, 16s rRNA, hypertension


title: CC-1690 cells, wild-type, control, biol rep 1


title: sample146, oral flora, 16s rRNA, non-hypertension


title: KO-R3

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Samples were sequenced using Novaseq 6000(Illumina) using 100 cycles. 200M reads were targeted for each sample, targeting20,000 reads per nuclei. Samples were analyzed using Cell Ranger and Loupe (10x Genomics).
Raw reads were aligned to the mouse genome (mm10), and the digital expression matrix was generated using cellranger count.
Assembly: mm10
Supplementary files format and content: Raw count expression matrix for snRNA-seq.

source_name: heart

extract_protocol:
Hearts were harvested on day 7 post injury and used for single nuclei preparation for 10X genomics sequencing. Briefly, the heart tissue was minced with razor blade and gently homogenized by Dounce homogenizer containing 1.5 ml of chilled lysis buffer (in mM) (10 Tris-HCl (pH 7.4), 10 NaCl, 3 MgCl2, 0.1% NP-40). Then the homogenate was filtered through a 40 µm cell strainer and centrifuged at 500 g for 5 min at 4 °C. The pellet was resuspended in 1 ml nuclei wash buffer (1x PBS with 2% BSA and 0.2 U/mL RNase inhibitor). The suspension was filtered through a 20 µm cell strainer and centrifuged at 500 g for 5 min at 4 °C. The nuclei pellet was resuspended in 300 mL nuclei wash buffer followed by library preparation. Equal number of cells from 3 mouse hearts were mixed for each group.
Single nuclei gene expression libraries were created using Chromium Next GEM Single Cell 3' (v3.1 Chemistry) (10x Genomics), Chromium Next GEM Chip G Single Cell Kit (10x Genomics), and Single Index Kit T Set A (10x Genomics) according to the manufacturer’s instructions. Briefly, samples were loaded to target10,000nuclei to form GEMs and barcode individual cells. GEMs were then cleaned cDNA and libraries were also created according to manufacturer’s instructions. Library quality was assessed using 4200 TapeStation System and D1000 ScreenTape (both from Agilent) and Qubit 2.0 (Invitrogen) for concentration and size distribution.

value: heart

value: heart cell

value: GPNMB KO

value: Myocardial infarction


title: KO-R2


title: H3k4me3_TaDRIM-Seq-293T-rep1


title: sample147, oral flora, 16s rRNA, non-hypertension


title: 215_Astrocytes_IDO1i_B

value: Astrocytes


title: CC-1690 cells, wild-type, nutritional stress, biol rep 2

value: nutritional stress


title: 217_Neurons_VEH_A

value: Neurons

value: VEH

value: A


title: 213_Neurons_IDO1i_C

description: Neurons exposed to IDO1i Astrocytes

value: C


title: CC-1690 cells, wild-type, control, biol rep 2

value: control


title: KO-R1


title: sample145, oral flora, 16s rRNA, hypertension

value: salivary

value: oral flora


title: 1%formaldehyde-5min-H3k4me3_TaDRIM-Seq-K562-rep2


title: 1%formaldehyde-5min-H3k4me3_TaDRIM-Seq-K562-rep1


title: sample144, oral flora, 16s rRNA, hypertension

value: hypertension


title: p23158-s004

description: VDJ TCR

source_name: Lymph node

value: Female

value: Lymph node

value: CD4 T cells

value: Skin-graft rejection pooled from 5 mice


title: sample143, oral flora, 16s rRNA, hypertension


title: 211_Neurons_IDO1i_A

description: Neurons exposed to IDO1i Astrocytes

value: M

value: CN


title: 210_Astrocytes_VEH_C


title: 1%formaldehyde-30s-H3k4me3_TaDRIM-Seq-K562-rep2


title: p23045-s006_Sample-6

description: VDJ TCR

value: Skin-graft rejection


title: sample141, oral flora, 16s rRNA, non-hypertension

value: non-hypertension


title: sample142, oral flora, 16s rRNA, hypertension


title: 209_Astrocytes_VEH_B

value: Astrocytes

value: B


title: p23045-s005_Sample-5

description: VDJ TCR


title: 208_Astrocytes_VEH_A

value: VEH


title: sample140, oral flora, 16s rRNA, non-hypertension


title: 212_Neurons_IDO1i_B

description: Neurons exposed to IDO1i Astrocytes

value: Neurons


title: 207_Neurons_VEH_C

value: C


title: 206_Neurons_VEH_B


title: ZNF274KO_H3K36me3_ChIP_1

first: Julien

last: Duc

institute: EPFL

data_processing:
Raw reads were mapped with bowtie2 to the human hg19 genome
EPIC was used for peak calling with default parameters
Assembly: hg19
Supplementary files format and content: Peaks in bed format

extract_protocol:
ChIP was performed as described previously (Imbeault et al., 2017). Briefly, cells were cross-linked for 10 minutes at room temperature in PBS + 1% methanol-free formaldehyde solution, followed by quenching with 250 mM Tris pH 8. Nuclei were sonicated with Covaris E220 sonicatior (settings: 5% duty, 200 cycle, 140 PIP, 20 min) to yield genomic DNA fragments with a bulk size 200-500bp. IP was performed overnight at 4º C using 5 μg antibody (anti-H3K9me3 Diagenode, ref. C15410056; anti-HA.11 BioLegend ref: 901503; anti-H3K4me3 Cell Signaling, ref. 9751S; anti-CTCF Millipore, ref. 07-729; anti-Rad21 Abcam, ref. ab993) coupled to 50µl Protein G Dynabeads (Invitrogen ref: 10009D). Final DNA was purified with QIAGEN Elute Column.
Up to 10 ng of material for both total inputs and chromatin immunoprecipitated samples were used for library preparation. After end-repair and A-tailing, Illumina IDT indexes were ligated to the samples. Libraries were size-selected using Ampure XP beads (Beckman Coulter), quality-checked on a Bioanalyzer DNA high sensitivity chip (Agilent) and quantified with a Qubit dsDNA HS assay.

tag: chip antibody

value: anti-H3K36me3 Diagenode, ref. C15410192


title: sample139, oral flora, 16s rRNA, non-hypertension

value: salivary


title: WT_H3K36me3_ChIP_2

value: WT


title: BV2 cells,10panx1-3(9h)

city: Hubei

first: zhang

middle: tian

last: tianhao

state: Hubei

address: sdggvsdv

institute: Department of Anesthesiology, Union Hospital of Tongji Medical College of Huazhong University of Science and Technology

data_processing:
Quality Control: FastQC was used to assess the quality of raw sequence data.
Trimming: Trimmomatic was employed to trim adaptors and low-quality bases.
Alignment: Cleaned reads were aligned to the mouse reference genome using STAR aligner.
Quantification: FeatureCounts was used to count read mappings to genomic features.
Normalization and Analysis: DESeq2 was utilized for differential expression analysis to identify genes significantly regulated under glucose deprivation.
Assembly: The reference genome used for alignment and analysis was GRCm38 (Mouse).
Supplementary files format and content: CSV: Normalized and raw read count files generated by FeatureCounts and DESeq2. Includes log2 fold changes, p-values, and adjusted p-values for differential expression analysis.

growth_protocol: BV2  lines were cultured in Dulbecco's Modified Eagle's Medium (DMEM) containing high glucose (Gibco, USA) with 10% fetal bovine serum (Gibco, USA) to promote cell growth and proliferation. Additionally, 1% penicillin-streptomycin (Solarbio, China) was added to minimize bacterial contamination and maintain sterility. Cells were seeded in T75 tissue culture flasks and kept in a humidified incubator with an atmosphere of 5% CO2 at 37 °C. The medium was refreshed every 2-3 days, and once 80% confluency was achieved, cells were passaged using a 0.25% trypsin-EDTA solution (Solarbio, China).

extract_protocol:
For RNA extraction, BV2 microglial cells were subjected to glucose deprivation followed by RNA isolation using the TRIzol reagent (Invitrogen). Cells were lysed directly in the culture dish, and total RNA was extracted according to the manufacturer's instructions. The RNA integrity was assessed using an Agilent 2100 Bioanalyzer, ensuring an RNA integrity number (RIN) greater than 8.0.
Library preparation for sequencing was conducted using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. Following manufacturer’s protocols, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Subsequently, second strand cDNA synthesis was performed using DNA Polymerase I and RNase H. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure was ligated to prepare for hybridization. Library fragments were purified with the AMPure XP system and enriched with PCR to create the final cDNA library.
The library strategy used is RNA-Seq, which involves direct sequencing of cDNA fragments. This method is utilized to capture a comprehensive snapshot of the transcriptomic profile of glucose-deprived BV2 microglial cells, focusing on both coding and non-coding RNA to investigate cellular responses to glucose deprivation at the molecular level.

treatment_protocol: To mimic the in vivo hypoxic-ischemic condition of stroke in vitro, an OGD/reoxygenation (OGD/R) model was implemented. Cells were subjected to hypoxic conditions in an incubator set to 1% O2, 5% CO2, and 94% N2. During this OGD phase, the regular growth medium was replaced with glucose-free DMEM (Gibco, USA), and the cells were maintained under these conditions for a duration of 9 hours. Subsequently, to simulate reperfusion, the OGD-treated cells were reintroduced to normal culture conditions. The glucose-free DMEM was replaced with regular growth medium, and the cells were shifted back to the normoxic environment (37 °C; 5% CO2) for recovery.

value: microglia

value: Oxygen–Glucose Deprivation and Reperfusion+10panx1


title: BV2 cells,10panx1-2(9h)


title: BV2 cells,10panx1-1(9h)


title: p23226-s003_S3

description: VDJ TCR

data_processing:
VDJ TCR alignment and filtering for single-cell TCR sequencing samples were performed using Cell Ranger v3.1
VDJ TCR alignment and filtering for non-paired TCR sequencing samples were performed using MIXCR
Assembly: A genome build is generally not required for TCR sequencing, as it focuses on the rearranged TCR genes using V(D)J reference libraries
Supplementary files format and content: The processed data for single-cell TCR sequencing samples include filtered contig annotations, consensus annotations, clonotypes, and all contig annotations. For bulk TCR sequencing, the processed data contain clonotype information for both TCRα and TCRβ chains.
Library strategy: VDJ TCR

extract_protocol:
Cells were FACS sorted and used to generate single cell suspensions. Samples were loaded onto the 10X Genomics Chromium Controller according to manufacturer's protocol.
Library construction was performed using the Chromium Single Cell 5’ Library Construction Kit

value: Female

value: Lymph node

value: Skin-graft rejection pooled from 7 mice


title: WT_H3K36me3_ChIP_1

city: Lausanne

address: Station 19 CH-1015 Lausanne


title: 204_Astrocytes_IDO1i_C

value: F


title: 1%formaldehyde-30s-H3k4me3_TaDRIM-Seq-K562-rep1


title: sample136, oral flora, 16s rRNA, non-hypertension

value: oral flora


title: ZNF274 UMI4C in ZNF274KO 3

description:
UMI4C in ZNF274KO rep3
HEK293T_KO_DS2_HS16_20_raw.bedGraph.gz
HEK293T_KO_DS2_HS5_1_raw.bedGraph.gz
HEK293T_KO_DS2_Peak1_PCDH_raw.bedGraph.gz
HEK293T_KO_DS3_Peak2A_PCDH_raw.bedGraph.gz

data_processing:
For HiC, the HiC pro pipeline was run on the raw data. For UMI4C, the pipeline from umi4cPackage
Assembly: hg19
Supplementary files format and content: HiC: Raw contact matrices at 20kb resolution, UMI4C: Bedgraph with average contact between selected probes and genomes
Library strategy: UMI4C

extract_protocol:
The Hi-C libraries were prepared using Arima-HiC (Arima Genomics), following the manufacturer’s protocol. For all samples, 5 million cells were fixed in 1% methanol-free formaldehyde solution for 10min at RT and the reaction was quenched for 5min with glycine to a final concentration of 125 mM. UMI-4C experiments were performed as described previously (Schwartzman et al. 2016). Briefly, 5 million cells were fixed in 1% methanol-free formaldehyde solution for 10min at RT and the reaction was quenched for 5min with glycine to a final concentration of 125 mM. Cells were lysed in ice-cold Lysis Buffer (10mM Tris HCl pH 8,10mM NaCl, 0.2% NP-40), chromatin was digested with 800U DpnII (NEB), and digested ends were marked with biotin
UMI- 4C (https://pubmed.ncbi.nlm.nih.gov/27376768/) is a 3D technique involving  primers and biotinilation/ligation to infer the contacts points of regions of interest. It's very similar to a 4C with the addition of UMI for deduplication.


title: ZNF274KO_H3K36me3_ChIP_2


title: ZNF274 UMI4C in ZNF274KO 2

description:
UMI4C in ZNF274KO rep2
HEK293T_KO_DS2_HS16_20_raw.bedGraph.gz
HEK293T_KO_DS2_HS5_1_raw.bedGraph.gz
HEK293T_KO_DS2_Peak1_PCDH_raw.bedGraph.gz
HEK293T_KO_DS3_Peak2A_PCDH_raw.bedGraph.gz


title: 203_Astrocytes_IDO1i_B

value: CN


title: BV2 cells,control-2(9h)

value: Oxygen–Glucose Deprivation and Reperfusion


title: 202_Astrocytes_IDO1i_A

value: Astrocytes

value: A


title: 205_Neurons_VEH_A

value: VEH

value: M


title: BV2 cells,10panx1(6h)


title: sample133, oral flora, 16s rRNA, non-hypertension

value: non-hypertension


title: ZNF274 UMI4C in ZNF274KO 1

description:
UMI4C in ZNF274KO rep1
HEK293T_KO_DS2_HS16_20_raw.bedGraph.gz
HEK293T_KO_DS2_HS5_1_raw.bedGraph.gz
HEK293T_KO_DS2_Peak1_PCDH_raw.bedGraph.gz
HEK293T_KO_DS3_Peak2A_PCDH_raw.bedGraph.gz


title: ZNF274 UMI4C in WT 3

description:
UMI4C in WT rep3
HEK293T_WT_DS2_HS16_20_raw.bedGraph.gz
HEK293T_WT_DS2_HS5_1_raw.bedGraph.gz
HEK293T_WT_DS2_Peak1_PCDH_raw.bedGraph.gz
HEK293T_WT_DS3_Peak2A_PCDH_raw.bedGraph.gz


title: BV2 cells,control-1(9h)


title: 201_Neurons_IDO1i_C

description: Neurons exposed to IDO1i Astrocytes

value: Neurons

value: C


title: 200_Neurons_IDO1i_B

description: Neurons exposed to IDO1i Astrocytes

value: B


title: sample134, oral flora, 16s rRNA, hypertension

value: salivary

value: hypertension


title: Day_14_rep_C

city: Ann Arbor

first: Jeffrey

middle: A

last: Beamish

state: MI

address: 1500 E. Medical Center Drive, SPC 5364

department: Department of Internal Medicine, Division of Nephrology

institute: University of Michigan

data_processing:
The reads were trimmed using Cutadapt v2.3. FastQC v0.11.8 was used to ensure the quality of data. Fastq Screen v was used to screen for various types of contamination. Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a and assigned count estimates to genes with RSEM v1.3.3. Alignment options followed ENCODE standards for RNA-seq.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

source_name: Kidney

growth_protocol: Proximal tubules were obtained by collagenase digestion of minced kidneys from 6-week-old female C57BL/6J mice and purified by centrifugation on a Percoll gradient. Tubules were plated in standard tissue culture plastic culture plates and cultured for 14 days without subculture. Medium was changed daily for the first 3 days after seeding, then every other day or as needed for a total of 14 days.

extract_protocol:
RNA was extracted using RNEasy kits (Qiagen)
University of Michigan Advanced Genomics Core for polyA cDNA library preparation

treatment_protocol: no additional treatments

value: Kidney

value: Primary cells

value: Proximal tubule

value: wild type

value: 6 weeks

value: female

tag: time

value: Day 14

tag: biological replicate


title: sample132, oral flora, 16s rRNA, hypertension

data_processing:
QIIME2 2022.11
Assembly: SILVA Release 138.1 /UNITE Release 9.0 Database
Supplementary files format and content: txt file includes raw counts for each sample
Library strategy: 16s rRNA-seq

extract_protocol:
Total genomic DNA samples were extracted using the OMEGA Soil DNA Kit (M5635-02) (Omega Bio-Tek, Norcross, GA, USA), following the manufacturer’s instructions, and stored at -20 °C prior to further analysis. The quantity and quality of extracted DNAs were measured using a NanoDrop NC2000 spectrophotometer(Thermo Fisher Scientific, Waltham, MA, USA) and agarose gel electrophoresis, respectively.
PCR amplification of the bacterial 16S rRNA genes V3–V4 region was performed using the forward primer 338F (5'-ACTCCTACGGGAGGCAGCA-3') and the reverse primer 806R (5'-GGACTACHVGGGTWTCTAAT-3'). Sample-specific 7-bp barcodes were incorporated into the primers for multiplex sequencing. The PCR components contained 5 μl of buffer (5×), 0.25 μl of Fast pfu DNA Polymerase (5U/μl), 2 μl (2.5 mM) of dNTPs, 1 μl (10 uM) of each Forward and Reverse primer, 1 μl of DNA Template, and 14.75 μl of ddH2O. Thermal cycling consisted of initial denaturation at 98 °C for 5 min, followed by 25 cycles consisting of denaturation at 98 °C for 30 s, annealing at 53 °C for 30 s, and extension at 72 °C for 45 s, with a final extension of 5 min at 72 °C. PCR amplicons were purified with Vazyme VAHTSTM DNA Clean Beads (Vazyme, Nanjing, China) and quantified using the Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen, Carlsbad, CA, USA). After the individual quantification step, amplicons were pooled in equal amounts, and pair-end 2250 bp sequencing was performed using the Illlumina NovaSeq platform with NovaSeq 6000 SP Reagent Kit (500 cycles) at Shanghai Personal Biotechnology Co., Ltd (Shanghai,  China).

value: oral flora


title: BV2 cells,control1(6h)

value: microglia

value: WT

value: Oxygen–Glucose Deprivation and Reperfusion


title: ZNF274 UMI4C in WT 2

description:
UMI4C in WT rep2
HEK293T_WT_DS2_HS16_20_raw.bedGraph.gz
HEK293T_WT_DS2_HS5_1_raw.bedGraph.gz
HEK293T_WT_DS2_Peak1_PCDH_raw.bedGraph.gz
HEK293T_WT_DS3_Peak2A_PCDH_raw.bedGraph.gz


title: 199_Neurons_IDO1i_A

description: Neurons exposed to IDO1i Astrocytes

value: A

value: F

tag: diagnosis

value: CN

tag: rnaseq batch


title: BV2 cells,control-3(9h)


title: ZNF274 UMI4C in WT 1

description:
UMI4C in WT rep1
HEK293T_WT_DS2_HS16_20_raw.bedGraph.gz
HEK293T_WT_DS2_HS5_1_raw.bedGraph.gz
HEK293T_WT_DS2_Peak1_PCDH_raw.bedGraph.gz
HEK293T_WT_DS3_Peak2A_PCDH_raw.bedGraph.gz


title: sample138, oral flora, 16s rRNA, hypertension


title: sample135, oral flora, 16s rRNA, hypertension


title: Day_07_rep_C

tag: age

value: Day 7

value: C


title: sample137, oral flora, 16s rRNA, hypertension

value: salivary

value: hypertension


title: sample131, oral flora, 16s rRNA, non-hypertension

value: non-hypertension


title: ZNF274KO_NPC_S2

description:
RNA-seq ZNF274 KO in NPC
ZNF274KO_NPC.csv

data_processing:
Raw reads were mapped with hisat2 with -k5 optino to the human hg19 genome
Gene summaziation performed with featureCounts using -Q 10 as option
Assembly: hg19
Supplementary files format and content: countTable raw unique read counts

extract_protocol:
RNA was extracted using the High Pure RNA Isolation Kit from ROCHE (Ref. 11828665001)
Illumina Truseq stranded mRNA(Ref 20040534)

value: NPC


title: KO-R4

value: heart

value: heart cell

value: GPNMB KO

value: Myocardial infarction


title: 198_Astrocytes_VEH_C

value: Astrocytes

value: VEH


title: sample130, oral flora, 16s rRNA, hypertension

value: oral flora


title: 197_Astrocytes_VEH_B

value: B


title: ZNF274KO_NPC_S1


title: sample129, oral flora, 16s rRNA, non-hypertension


title: 196_Astrocytes_VEH_A

value: A


title: 195_Neurons_VEH_C

value: Neurons

value: F


title: Day_01_rep_C

value: Kidney

value: Primary cells

value: Proximal tubule

value: wild type

value: 6 weeks

value: female

value: Day 1


title: sample128, oral flora, 16s rRNA, non-hypertension

value: salivary

value: non-hypertension


title: WT_NPC_S5

description:
RNA-seq WT NPC
ZNF274KO_NPC.csv

value: NPC

value: WT


title: sample127, oral flora, 16s rRNA, hypertension

value: hypertension


title: Day_02_rep_C

value: Day 2

value: C


title: WT_NPC_S3

description:
RNA-seq WT NPC
ZNF274KO_NPC.csv


title: Day_14_rep_B

value: Day 14

value: B


title: 193_Neurons_VEH_A

value: Neurons

value: VEH

value: A

value: F

value: CN


title: 194_Neurons_VEH_B