title: WT_H3K9_CnT_3

data_processing:
Raw reads were mapped with bowtie2 to the human hg19 genome
Peak calling was done with MACS2 for transcription factor and EPIC for histone marks. For Cut&Tag samples, SEACR was used
Assembly: hg19
Supplementary files format and content: Peaks in bed format
Library strategy: Cut&Tag

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.  CuT&Tag was performed as described previously (Kaya-Okur et al., 2019). For each mark, 200’000 cells were used per sample using the anti-H3K9me3 primary antibody (Active Motif, AB_2532132). A homemade purified ProtA-Tn5 protein (3XFlag-pA-Tn5-Fl, addgene #124601) was produced and coupled with MEDS oligos by the Protein Production and Purification of EPFL, as previously described (Bryson T, Henikoff S. 3XFlag-PATn5 Protein Purification and MEDS-Loading; 2019. doi:10.17504/protocols.io.8yrhxv6). Purified recombinant protein was used at a final concentration of 700 ng/uL. Libraries were sequenced with 75 bp paired end on the NextSeq 500 (Illumina).
NextSeq v2.5 (with Illumina protocol #15048776)

value: anti-H3K9me3 Active motif, ref. AB_2532132


title: Day_07_rep_B

status: Public on Sep 17 2024

type: SRA

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

country: USA

institute: University of Michigan

library_source: transcriptomic

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

molecule: polyA RNA

organism: Mus musculus

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

tag: tissue

value: Kidney

tag: cell line

value: Primary cells

tag: cell type

value: Proximal tubule

tag: genotype

value: wild type

tag: strain

tag: age

value: 6 weeks

tag: Sex

value: female

tag: treatment

tag: time

value: Day 7

tag: biological replicate

value: B


title: sample125, oral flora, 16s rRNA, non-hypertension

city: Shanghai

first: Xin

last: Chen

address: Zhangheng Rd

country: China

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: 192_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

molecule: total RNA

organism: Homo sapiens

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

value: Astrocytes

tag: replicate

value: C

value: F

tag: diagnosis

value: CN

tag: rnaseq batch


title: Day_04_rep_B

value: Day 4


title: Day_04_rep_C


title: sample124, oral flora, 16s rRNA, hypertension

value: hypertension


title: WT_H3K9_CnT_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

molecule: genomic DNA

tag: chip antibody

value: anti-H3K9me3 Active motif, ref. AB_2532132

value: WT


title: 191_Astrocytes_IDO1i_B


title: WT_H3K9_CnT_1


title: Day_02_rep_B

value: Kidney

value: Primary cells

value: Proximal tubule

value: Day 2


title: Day_00_rep_C

value: wild type

value: 6 weeks

value: female

value: Day 0


title: sample126, oral flora, 16s rRNA, hypertension

value: salivary

value: oral flora


title: WT_H3K9_CnT_4


title: Day_01_rep_B

value: Day 1

value: B


title: ZNF274KO_H3K9_CnT_4


title: sample122, oral flora, 16s rRNA, hypertension


title: ZNF274KO_H3K9_CnT_3


title: Day_00_rep_B


title: 188_Neurons_IDO1i_B

description: Neurons exposed to IDO1i Astrocytes

value: Neurons

value: F

value: CN


title: sample121, oral flora, 16s rRNA, non-hypertension

value: non-hypertension


title: ZNF274KO_H3K9_CnT_2

value: anti-H3K9me3 Active motif, ref. AB_2532132


title: 187_Neurons_IDO1i_A

description: Neurons exposed to IDO1i Astrocytes

value: A


title: Day_14_rep_A

value: Kidney

value: Primary cells

value: Day 14


title: sample120, oral flora, 16s rRNA, non-hypertension


title: ZNF274KO_H3K9_CnT_1


title: Day_07_rep_A

value: Proximal tubule

value: wild type

value: Day 7


title: sample119, oral flora, 16s rRNA, non-hypertension


title: Day_04_rep_A

value: 6 weeks

value: female

value: Day 4


title: 186_Astrocytes_VEH_C

value: Astrocytes

value: VEH

value: C


title: sample118, oral flora, 16s rRNA, hypertension

value: salivary

value: hypertension

value: oral flora


title: ZNF274KO_CTCF_WCE_3

description: IP_CTCF_8716_3-12-20_S11_vs_WCE_8716_3-12-20_S5_peaks.bed.gz

data_processing:
Raw reads were mapped with bowtie2 to the human hg19 genome
Peak calling was done with MACS2 for transcription factor and EPIC for histone marks. For Cut&Tag samples, SEACR was used
Assembly: hg19
Supplementary files format and content: Peaks in bed format


title: 185_Astrocytes_VEH_B

value: B

value: F

value: CN


title: sample123, oral flora, 16s rRNA, hypertension


title: 190_Astrocytes_IDO1i_A

value: A


title: ZNF274KO_CTCF_WCE_4

description: IP_CTCF_8718_3-12-20_S12_vs_WCE_8718_3-12-20_S6_peaks.bed.gz


title: sample117, oral flora, 16s rRNA, hypertension


title: 189_Neurons_IDO1i_C

description: Neurons exposed to IDO1i Astrocytes

value: Neurons


title: Day_02_rep_A

value: Kidney

value: Primary cells

value: Proximal tubule

value: Day 2


title: 184_Astrocytes_VEH_A


title: sample116, oral flora, 16s rRNA, hypertension


title: sample115, oral flora, 16s rRNA, hypertension


title: WT_CTCF_WCE_3

description: IP_CTCF_7586_3-12-20_S7_vs_WCE_7586_3-12-20_S1_peaks.bed.gz

value: WT


title: 183_Neurons_VEH_C

description: Neurons exposed to DMSO treated Astrocytes


title: Day_00_rep_A

value: wild type

value: 6 weeks

value: female

value: Day 0


title: 182_Neurons_VEH_B

value: VEH


title: ZNF274KO_CTCF_4

description: ChIP-CTCF-8718_S20_vs_Ti-8718_S26_peaks.bed.gz

value: anti-CTCF Millipore, ref. 07-729


title: sample114, oral flora, 16s rRNA, hypertension

value: salivary

value: hypertension

value: oral flora


title: Ddit3

city: Kunming

first: Yaying

last: Zhu

state: Yunnan

address: Chenggong district of yunnan university in kunming, yunnan province

institute: yunnan university

data_processing:
Reads were aligned to the mm10 mouse genome with bowtie2 v2.2.5 tool --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700
Reads were filtered by best quality reads with samtools
Signal coverage files BigWig were obtained with bamCoverage from deeptools package
Peaking calling was perfomed with MACS2 v2.2.7 with the significance cut-off q-value <= 0.1 and default settings
Assembly: mm10
Supplementary files format and content: BigWig
Supplementary files format and content: narrowPeak except for Input sample
Library strategy: Cut&Run

source_name: liver

extract_protocol:
1 mg of fresh tissue was weighed for each antibody/MNase reaction, with an additional 1 mg for the input sample. Reactions included positive and negative controls. Tissues were fixed with 1 ml of 0.1% formaldehyde for 10 minutes and quenched with glycine for 5 minutes.
Cut&Run was conducted on mouse liver tissue samples from mice injected with APAP for 6 hours using the Cut&Run assay kit (CST, 86652). For Cut&Run, purified DNA was used to prepare sequencing libraries with the NEB Next Ultra II DNA Library Prep Kit for Illumina (7645S and 7335L)

value: liver

value: Acetaminophen


title: WT_CTCF_WCE_4

description: IP_CTCF_8713_3-12-20_S8_vs_WCE_8713_3-12-20_S2_peaks.bed.gz


title: ZNF274KO_CTCF_3

description: ChIP-CTCF-8716_S19_vs_Ti-8716_S25_peaks.bed.gz


title: Day_01_rep_A

value: Day 1

value: A


title: Input


title: 181_Neurons_VEH_A

value: Neurons

value: F

value: CN


title: sample113, oral flora, 16s rRNA, hypertension


title: 180_Astrocytes_IDO1i_C

value: Astrocytes

value: C

value: M


title: WT_CTCF_4

description: ChIP-CTCF-8713_S16_vs_Ti-8713_S24_peaks.bed.gz

value: WT


title: WT_CTCF_3

description: ChIP-CTCF-7586_S15_vs_Ti-7586_S23_peaks.bed.gz


title: 179_Astrocytes_IDO1i_B

value: B


title: sample112, oral flora, 16s rRNA, non-hypertension

value: non-hypertension


title: APAP6h

description: Fresh frozen Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed with 10X Genomics Space Ranger pipleline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Gene expression level of coding genes were quantifiied using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expresssion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Liver

extract_protocol:
Freshly harvested liver tissues were frozen using isopentane and liquid nitrogen, embedded in OCT, sectioned into 10 μm slices.
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatal Gene Expression Sides & Reagert kit acording to manlacturer's corstucion

value: Liver

tag: model

value: Acetaminophen induced liver injury model


title: 178_Astrocytes_IDO1i_A


title: sample111, oral flora, 16s rRNA, non-hypertension

value: salivary


title: APAP24h


title: ZNF274KO_CTCF_WCE_2


title: sample110, oral flora, 16s rRNA, non-hypertension

value: oral flora


title: APAP3h


title: ZNF274KO_CTCF_WCE_1


title: 177_Neurons_IDO1i_C

description: Neurons exposed to IDO1i Astrocytes


title: APAP0h


title: sample109, oral flora, 16s rRNA, hypertension

value: hypertension


title: WT_CTCF_WCE_2


title: 176_Neurons_IDO1i_B

description: Neurons exposed to IDO1i Astrocytes


title: sample108, oral flora, 16s rRNA, non-hypertension


title: Naïve AM-4

city: Newark

first: Adriana

last: Messyasz

address: 185 South Orange Avenue

institute: Rutgers-New Jersey Medical School

data_processing:
nf-core RNAseq workflow
Raw transcriptome reads were assessed for quality control (FASTQC v0.11.8) and trimmed for quality and adapter contaminant (cutadapt v 2.5)
Trimmed reads were aligned to the Mus Musculus genome using STAR (v2.6.1)
Transcript abundance calculation and hit count extraction with StringTie (v2.0) and featureCounts (v1.6.4) respectively
Hit count normalization and differential gene expression group cross-comparisons were performed using DESeq2 (v1.26.0)
Assembly: Mmul_10
Supplementary files format and content: Plain-text, tab-separated file with a single header line (which names all of the columns), includes Salmon quantification values for each Sample

source_name: lung

extract_protocol:
RNA was extracted using Rneasy kit from Qiagen.
Total RNA is turned into cDNA and reversed back to RNA for amplification by MessageAmP II aRNA Amplification kit

treatment_protocol: We injected mice with 2.5mg tamoxifen on day -1 on CX3CR1CreER x RosaR26TdTomato mice (monocyte fate mapper), and immunized mice with HK-fbp1 on day 0. On day 30 post vaccination, we sacrificed mice, and sorted tissue-derived alveolar macrophage (TD-AMs, CD45+DAPI-CD11c+SiglecFhi TdTomato-) and monocyte-derived AMs (Mo-AMs, CD45+DAPI-CD11c+SiglecFhi TdTomato+) the lung.

value: lung

value: CX3CR1CreER x RosaR26TdTomato mice


title: 214_Astrocytes_IDO1i_A

value: A


title: sample107, oral flora, 16s rRNA, hypertension


title: 175_Neurons_IDO1i_A

description: Neurons exposed to IDO1i Astrocytes

value: Neurons


title: 174_Astrocytes_VEH_C

value: VEH


title: ZNF274KO_CTCF_2

value: anti-CTCF Millipore, ref. 07-729


title: Naïve AM-3


title: sample106, oral flora, 16s rRNA, non-hypertension


title: Naïve AM-2


title: ZNF274KO_CTCF_1


title: sample105, oral flora, 16s rRNA, hypertension


title: 172_Astrocytes_VEH_A

value: Astrocytes

value: CN


title: Naïve AM-1


title: WT_CTCF_2


title: sample104, oral flora, 16s rRNA, hypertension


title: 173_Astrocytes_VEH_B

value: M


title: Fall, spleen, rep 05

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: spleen

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: spleen

value: Fall


title: WT_CTCF_1

value: WT


title: 171_Neurons_VEH_C

value: C


title: Mo-AM-2, Day 30

value: HK-fbp1 immunization


title: sample103, oral flora, 16s rRNA, non-hypertension

value: salivary

value: non-hypertension


title: 170_Neurons_VEH_B

value: B


title: ZNF274KO_H3K9_WCE_4

description: IP_H3K9_8718_15-10-20_S13_vs_WCE_H3K9_8718_15-10-20_S8.bed.gz


title: WT_CTCF_WCE_1


title: ZNF274KO_H3K9_WCE_3

description: IP_H3K9_8716_15-10-20_S3_vs_WCE_H3K9_8716_15-10-20_S2.bed.gz


title: TD-AM-3, Day 30

value: lung


title: sample101, oral flora, 16s rRNA, non-hypertension

value: oral flora


title: 169_Neurons_VEH_A

value: A


title: 168_Astrocytes_IDO1i_C

value: F

value: AD


title: WT_H3K9_WCE_4

description: IP_H3K9_8714_15-10-20_S2_vs_WCE_H3K9_8714_15-10-20_S1.bed.gz


title: sample100, oral flora, 16s rRNA, non-hypertension


title: TD-AM-2, Day 30

value: CX3CR1CreER x RosaR26TdTomato mice


title: WT_H3K9_WCE_3

description: IP_H3K9_7586_15-10-20_S12_vs_WCE_H3K9_7586_15-10-20_S7.bed.gz


title: TD-AM-1, Day 30


title: ZNF274KO_H3K9_4

value: anti-H3K9me3 Diagenode, ref. C15410056


title: Mo-AM-3, Day 30


title: 167_Astrocytes_IDO1i_B

value: Astrocytes


title: 166_Astrocytes_IDO1i_A


title: sample98, oral flora, 16s rRNA, hypertension

value: hypertension


title: 165_Neurons_IDO1i_C

description: Neurons exposed to IDO1i Astrocytes

value: Neurons


title: D27-LSK-W2_HTO

city: Barcelona

first: Daniel

last: Fernandez-Perez

state: Choose State

address: Carrer Baldiri Reixac 12

department: Aging and Metabolism

country: Spain

institute: IRB Barcelona

description:
10xGenomics
Following the reverse transcription of mRNA and first-strand cDNA amplification, 100 ng of the cDNA libraries were used as templates to amplify LARRY barcodes by nested PCR similar to the protocol described in (Weinreb et al. 2020). The first PCR used forward primer CTGAGCAAAGACCCCAACGAGAA together with the corresponding 10x Genomics dual index TruSeq reverse primer using the following programs 1, 98 C, 3 min; 2, 98 C, 20 s; 3, 58 C, 15 s; 4, 72 C, 20 s; 5, repeat steps 2–4 08 times; 6, 72 C, 3 min; 7, 4 C, hold. The PCR products were then purified with a 0.8:1 ratio of Ampure XP beads. Purified PCR products were then subjected to a second PCR using the forward primer GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC TGC TAG GAG AGA CCA TAT GGG ATC and the corresponding 10x dual index Truseq reserve primer, following program 1, 98 C, 3 min; 2, 98 C, 20 s; 3, 58 C, 15 s; 4, 72 C, 20 s; 5, repeat steps 2–4 08 times; 6, 72 C, 3 min; 7, 4 C, hold. The final PCR products were then purified by a 0.8:1 ratio of Ampure XP bead: PCR products, were indexed using the 10x dual index TruSeq kit, and sequenced using Illumina NovaSeq or NextSeq.

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software 7.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrices

source_name: exvivo HSC PVA culture

growth_protocol: Ex-vivo cultures of HSCs were done under self-renewing F12-PVA-based conditions as described previously ((Wilkinson et al. 2019)). To this end, cell-culture activated 96-well flat-bottom plates were coated with a layer of 100 ng/ml fibronectin (Bovine Fibronectin Protein, CF Catalog: 1030-FN) for 30 minutes at room temperature. Following the sorting process, HSCs were transferred into 200 µl of complete HSC media supplemented with 100ng/ml recombinant mouse TPO and 10ng/ml recombinant mouse SCF (PeproTech Recombinant Murine TPO Catalogue Number: 315-14; PeproTech Recombinant Murine SCF, Catalogue Number: 250-03) and grown at 37°C with 5% CO2. During lentiviral library transduction, the first media change took place 24 hours post-transduction. All other protocol steps followed the guidelines provided in (Wilkinson et al. 2020)

extract_protocol:
Following euthanasia, bone marrow was harvested from the femur, tibia, pelvis, and sternum through mechanical crushing, ensuring the retrieval of most HSCs. The collected bone marrow cells were then sieved through a 100-μm strainer and cleansed with a cold 'Easy Sep' buffer containing PBS with 2% fetal bovine serum (FBS), followed by lysis of red blood cells using RBC lysis buffer (Biolegend, Catalog no. 420302). At first, mature lineage cells were selectively depleted through the Lineage Cell Depletion Kit, mouse (Miltenyi Biotec, Catalog no. 130-110-470), while the resulting Lin- (lineage-negative) fraction was then enriched for c-Kit expression using CD117 MicroBeads (Miltenyi Biotec, Catalog no: 130-091-224). These cKit-enriched cells were washed, blocked with FcX and stained with following fluorescently labeled antibodies: APC anti-mouse CD117, clone ACK2 (Biolegend catalog no. 105812), PE/Cy7 anti-mouse Ly6a (Sca-1) (Biolegend, catalog no. 108114); Pacific Blue anti-mouse Lineage Cocktail (Biolegend, catalog no. 133310); PE anti-mouse CD201 (EPCR) (Biolegend, catalog no. 141504); PE/Cy5 anti-mouse CD150 (SLAM) (Biolegend, catalog no. 115912); APC/Cyanine7 anti-mouse CD48 (Biolegend, catalog no. 103432).
For scRNA sequencing and subsequent plating, cells were pipetted up and down gently a few times to be dissociated into single cells and transferred to a 1.5 mL microtube. The well was then washed with prewarmed PBS to collect all the possible remaining cells. Cells were then concentrated by centrifugation at 800 g for 8 minutes. Washed cells were then blocked with FcX, and stained with the E-SLAM stem cell antibodies panel, to confirm expansion of E-SLAM cells. Live cells were then sorted based on fluorescent reporter expression. Part of the sample as specified in text was then taken for constructing a single-cell library using Chromium Single Cell 3’ Reagent Kits (v3) following the manufacturer’s guidelines (10X Genomics). The remaining part was then plated back for further expansion in culture. To minimize the impact of batch effects on sequencing, we multiplexed different conditions leveraging the unique barcode pattern of our libraries together with Biolegend TotalSeq™ anti-mouse hashing antibodies, enabling the simultaneous preparation of libraries representing all experimental conditions in a single reaction for each day of sampling.

value: exvivo HSC PVA culture

value: LSK cells

value: WT, Dnmt3aR878H, Npm1cA

tag: library type

value: HTO


title: sample97, oral flora, 16s rRNA, hypertension

tag: tissue

value: salivary


title: D27-LSK-W1_HTO


title: ZNF274KO_H3K9_3

tag: cell line


title: WT_H3K9_4

value: WT


title: sample102, oral flora, 16s rRNA, non-hypertension

value: non-hypertension

tag: cell type


title: Mo-AM-1, Day 30

value: lung

tag: genotype

value: HK-fbp1 immunization


title: sample96, oral flora, 16s rRNA, hypertension

value: oral flora


title: WT_H3K9_3


title: 163_Neurons_IDO1i_A

description: Neurons exposed to IDO1i Astrocytes

value: A

value: F


title: sample95, oral flora, 16s rRNA, hypertension


title: ZNF274KO_H3K9_WCE_2

description: ChIP_H3K9_8718_S8_vs_Ti_H3_8718_S4.bed.gz


title: 162_Astrocytes_VEH_C

value: VEH

value: C

value: AD


title: sample99, oral flora, 16s rRNA, non-hypertension


title: ZNF274KO_H3K9_WCE_1

description: ChIP_H3K9_8716_S7_vs_Ti_H3_8716_S3.bed.gz


title: D14-W2_HTO


title: D14-W1_HTO


title: sample93, oral flora, 16s rRNA, non-hypertension


title: D27-LK-W1_HTO

value: LK cells


title: WT_H3K9_WCE_2

description: ChIP_H3K9_8714_S6_vs_Ti_H3_8714_S2.bed.gz


title: 159_Neurons_VEH_C

value: Neurons


title: 160_Astrocytes_VEH_A

value: Astrocytes


title: sample92, oral flora, 16s rRNA, hypertension

value: hypertension


title: 164_Neurons_IDO1i_B

description: Neurons exposed to IDO1i Astrocytes

value: B


title: 161_Astrocytes_VEH_B


title: sample90, oral flora, 16s rRNA, hypertension


title: sample91, oral flora, 16s rRNA, hypertension


title: D7-rep1_LARRY

value: exvivo HSC PVA culture

value: LSK cells

value: WT, Dnmt3aR878H, Npm1cA

value: Feature Barcode


title: 158_Neurons_VEH_B


title: 157_Neurons_VEH_A


title: ZNF274KO_H3K9_2

value: anti-H3K9me3 Diagenode, ref. C15410056


title: sample94, oral flora, 16s rRNA, hypertension

value: salivary


title: D27-LSK-W1_LARRY


title: WT_H3K9_WCE_1

description: ChIP_H3K9_7586_S5_vs_Ti_H3_7586_S1.bed.gz

value: WT


title: D7-rep2_LARRY


title: D27-LSK-W2_LARRY


title: ZNF274KO_H3K9_1


title: WT_H3K9_2


title: 156_Astrocytes_IDO1i_C

value: M

value: CN


title: D27-LK-W2_LARRY


title: D27-LK-W2_HTO

value: HTO


title: WT_H3K9_1


title: 155_Astrocytes_IDO1i_B


title: Input_ZNF274KO_2

description: H3K4me3_6784_B_ChIP_vs_Mix_Ti_6784_B_Ti.bed.gz


title: D27-LK-W1_LARRY


title: sample87, oral flora, 16s rRNA, hypertension

value: oral flora


title: D14-W2_LARRY


title: sample86, oral flora, 16s rRNA, non-hypertension

value: non-hypertension


title: 154_Astrocytes_IDO1i_A

value: A


title: 153_Neurons_IDO1i_C

description: Neurons exposed to IDO1i Astrocytes

value: Neurons

value: C


title: sample85, oral flora, 16s rRNA, hypertension

value: hypertension


title: sample84, oral flora, 16s rRNA, non-hypertension


title: D14-W1_LARRY


title: D7-rep2_GEX

value: GEX


title: sample83, oral flora, 16s rRNA, hypertension


title: Input_ZNF274KO_1

description: H3K4me3_6781_B_ChIP_vs_Mix_Ti_6781_B_Ti.bed.gz


title: 152_Neurons_IDO1i_B

description: Neurons exposed to IDO1i Astrocytes

value: B


title: H3K4me3_ZNF274KO_2

value: anti-H3K4me3 Cell Signaling, ref. 9751S


title: sample82, oral flora, 16s rRNA, hypertension


title: 151_Neurons_IDO1i_A

description: Neurons exposed to IDO1i Astrocytes


title: 150_Astrocytes_VEH_C

value: Astrocytes

value: VEH


title: sample88, oral flora, 16s rRNA, non-hypertension


title: D7-rep1_GEX

value: exvivo HSC PVA culture

value: LSK cells

value: WT, Dnmt3aR878H, Npm1cA


title: sample81, oral flora, 16s rRNA, hypertension

value: salivary


title: Input_ZNF274WT_1

description: H3K4me3_6781_A_ChIP_vs_Mix_Ti_6781_A_Ti.bed.gz

value: WT


title: D27-LSK-W2_GEX


title: D27-LSK-W1_GEX


title: 149_Astrocytes_VEH_B

value: M

value: CN


title: Input_ZNF274WT_2

description: H3K4me3_6784_A_ChIP_vs_Mix_Ti_6784_A_Ti.bed.gz


title: H3K4me3_ZNF274KO_1


title: 148_Astrocytes_VEH_A


title: D27-LK-W2_GEX

value: LK cells


title: 147_Neurons_VEH_C

description: Neurons exposed to DMSO treated Astrocytes


title: sample80, oral flora, 16s rRNA, hypertension

value: oral flora


title: D27-LK-W1_GEX


title: sample79, oral flora, 16s rRNA, non-hypertension

value: non-hypertension


title: ZNF274_dSCAN_WCE_H3K9_2

description: IP_H3K9_9550_15-10-20_S16_vs_WCE_H3K9_9550_15-10-20_S11.bed.gz

value: ZNF274 dSCAN overexpression


title: D14-W2_GEX


title: 146_Neurons_VEH_B

value: Neurons


title: sample78, oral flora, 16s rRNA, hypertension

value: hypertension


title: 145_Neurons_VEH_A

value: A


title: ZNF274_dSCAN_H3K9_2

value: anti-H3K9me3 Diagenode, ref. C15410056


title: H3K4me3_ZNF274WT_2

value: anti-H3K4me3 Cell Signaling, ref. 9751S


title: sample77, oral flora, 16s rRNA, hypertension


title: ZNF274_dKRAB_WCE_H3K9_2

description: IP_H3K9_9549_15-10-20_S15_vs_WCE_H3K9_9549_15-10-20_S10.bed.gz

value: ZNF274 dKRAB overexpression


title: sample76, oral flora, 16s rRNA, hypertension


title: 143_Astrocytes_IDO1i_B

value: Astrocytes

value: B

value: F

value: AD


title: D14-W1_GEX

value: exvivo HSC PVA culture

value: LSK cells

value: WT, Dnmt3aR878H, Npm1cA

value: GEX


title: ZNF274_WT_WCE_H3K9_2

description: IP_H3K9_9548_15-10-20_S14_vs_WCE_H3K9_9548_15-10-20_S9.bed.gz

value: ZNF274 WT overexpression


title: ZNF274_dKRAB_H3K9_2


title: sample75, oral flora, 16s rRNA, non-hypertension

value: salivary

value: non-hypertension

value: oral flora


title: Young_Control_Female6

city: Madison

first: Chung-Yang

last: Yeh

state: WI

address: 2500 Overlook Ter

department: Department of Medicine

institute: University of Wisconsin-Madison

data_processing:
Data processing follows protocol described by Law et al. 2017, ISCB Comm "RNA-seq analysis easy as 1-2-3 with limma, Glimma and edgeR
Assembly: mm10
Supplementary files format and content: The process file is expressed as individual gene expression in log(cpm) format after filtering and the removal of one outlier.

extract_protocol:
RNA extraction was performed with Invitrogen PureLink RNA Mini Kit following manufacturer instructions.
TruSeq Stranded mRNA

value: Liver

value: 10 mo Female, after Control Diet 4 mo


title: sample74, oral flora, 16s rRNA, non-hypertension


title: ZNF274_WT_H3K9_2

value: anti-H3K9me3 Diagenode, ref. C15410056


title: Young_Control_Female5


title: sample73, oral flora, 16s rRNA, non-hypertension


title: Young_Control_Female4


title: 144_Astrocytes_IDO1i_C

value: C


title: 141_Neurons_IDO1i_C

description: Neurons exposed to IDO1i Astrocytes

value: Neurons


title: Young_Control_Female3


title: ZNF274_dSCAN_WCE_H3K9_1

description: IP_H3K9_9547_15-10-20_S6_vs_WCE_H3K9_9547_15-10-20_S1.bed.gz

value: ZNF274 dSCAN overexpression


title: 140_Neurons_IDO1i_B

description: Neurons exposed to IDO1i Astrocytes

value: B


title: Young_Control_Female2


title: 142_Astrocytes_IDO1i_A

value: Astrocytes

value: A

value: F


title: sample72, oral flora, 16s rRNA, non-hypertension


title: 139_Neurons_IDO1i_A

description: Neurons exposed to IDO1i Astrocytes

value: AD


title: H3K4me3_ZNF274WT_1

value: anti-H3K4me3 Cell Signaling, ref. 9751S

value: WT


title: sample71, oral flora, 16s rRNA, non-hypertension


title: Young_Control_Female1


title: 138_Astrocytes_VEH_C

value: VEH


title: ZNF274_dKRAB_WCE_H3K9_1

description: IP_H3K9_9546_15-10-20_S5_vs_WCE_H3K9_9546_15-10-20_S4.bed.gz

value: ZNF274 dKRAB overexpression


title: Aged_Low_Ile_Female6

value: 24 mo Female, after Low Ile Diet 4 mo


title: ZNF274_dKRAB_H3K9_1


title: sample69, oral flora, 16s rRNA, hypertension

value: salivary

value: hypertension

value: oral flora


title: sample70, oral flora, 16s rRNA, hypertension


title: Aged_Low_Ile_Female5

value: Liver


title: Aged_Low_Ile_Female4


title: sample68, oral flora, 16s rRNA, hypertension


title: 137_Astrocytes_VEH_B


title: 136_Astrocytes_VEH_A


title: 135_Neurons_VEH_C

value: C


title: sample67, oral flora, 16s rRNA, hypertension


title: ZNF274_WT_H3K9_1

description: IP_H3K9_9545_15-10-20_S4_vs_WCE_H3K9_9545_15-10-20_S3.bed.gz

value: anti-H3K9me3 Diagenode, ref. C15410056

value: ZNF274 WT overexpression


title: ZNF274_WT_WCE_H3K9_1


title: Aged_Low_Ile_Female2


title: sample66, oral flora, 16s rRNA, non-hypertension

value: non-hypertension


title: 134_Neurons_VEH_B

value: Neurons

value: B


title: ZNF274_dSCAN_WCE_2

description: IP_9550_HA_IP_S10_vs_WCE_9550_WCE_S16_peaks.bed.gz

value: ZNF274 dSCAN overexpression


title: ZNF274_dSCAN_H3K9_1


title: ZNF274_dSCAN_HA_2

value: anti-HA.11 BioLegend ref:901503


title: ZNF274_dKRAB_WCE_2

description: IP_9549_HA_IP_S9_vs_WCE_9549_WCE_S15_peaks.bed.gz


title: Aged_Low_Ile_Female1


title: Aged_Control_Female6

value: 24 mo Female, after Control Diet 4 mo


title: sample64, oral flora, 16s rRNA, non-hypertension


title: sample65, oral flora, 16s rRNA, non-hypertension


title: ZNF274_dKRAB_HA_2


title: 131_Astrocytes_IDO1i_B

value: Astrocytes

value: M

value: AD


title: sample63, oral flora, 16s rRNA, hypertension


title: Aged_Low_Ile_Female3

value: 24 mo Female, after Low Ile Diet 4 mo


title: sample62, oral flora, 16s rRNA, non-hypertension

value: salivary


title: ZNF274_WT_WCE_2

description: IP_9548_HA_IP_S8_vs_WCE_9548_WCE_S14_peaks.bed.gz


title: 129_Neurons_IDO1i_C

description: Neurons exposed to IDO1i Astrocytes


title: Aged_Control_Female3


title: sample61, oral flora, 16s rRNA, non-hypertension


title: ZNF274_WT_HA_2


title: 133_Neurons_VEH_A

value: VEH

value: A

value: F


title: ZNF274_dSCAN_WCE_1

description: IP_9547_HA_IP_S7_vs_WCE_9547_WCE_S13_peaks.bed.gz.gz


title: Aged_Control_Female1

value: Liver


title: Aged_Control_Female2


title: ZNF274_dSCAN_HA_1

description: IP_9547_HA_IP_S7_vs_WCE_9547_WCE_S13_peaks.bed.gz


title: 127_Neurons_IDO1i_A

description: Neurons exposed to IDO1i Astrocytes


title: sample60, oral flora, 16s rRNA, non-hypertension

value: oral flora


title: sample59, oral flora, 16s rRNA, non-hypertension


title: 132_Astrocytes_IDO1i_C

value: C


title: Young_Control_Male6

value: 10 mo Male, after Control Diet 4 mo


title: 126_Astrocytes_VEH_C


title: 125_Astrocytes_VEH_B


title: sample58, oral flora, 16s rRNA, hypertension

value: hypertension


title: Aged_Control_Female5


title: Young_Control_Male5


title: ZNF274_dKRAB_WCE_1

description: IP_9546_HA_IP_S6_vs_WCE_9546_WCE_S12_peaks.bed.gz

value: ZNF274 dKRAB overexpression


title: sample57, oral flora, 16s rRNA, non-hypertension

value: non-hypertension


title: 124_Astrocytes_VEH_A


title: 130_Astrocytes_IDO1i_A


title: Aged_Control_Female4


title: Young_Control_Male4


title: 128_Neurons_IDO1i_B

description: Neurons exposed to IDO1i Astrocytes

value: Neurons

value: B


title: 123_Neurons_VEH_C


title: ZNF274_WT_WCE_1

description: IP_9545_HA_IP_S5_vs_WCE_9545_WCE_S11_peaks.bed.gz

value: ZNF274 WT overexpression


title: Young_Control_Male3


title: ZNF274_WT_HA_1

value: anti-HA.11 BioLegend ref:901503


title: 122_Neurons_VEH_B

value: M

value: AD


title: MC38 cells, P2ry6, UDP, rep2

city: Beijing

first: Xilong

last: Xu

address: 7 Science Park Road ZGC Life Science Park, Beijing

institute: National Institute of Biological Sciences, Beijing

data_processing:
Paired-end read adaptors were trimmed using fastp (v0.23.2)
The resulting clean reads were aligned to the mouse reference genome (mm10) using Bowtie2 (v2.3.5.1).
Peaks were called using MACS2 (v2.2.7.1) with the parameter 'macs2 callpeak -g mm --broad --bdg -f BAMPE'
To generate bigwig files, deepTools (v3.4.3) and the function bamCoverage were employed, using BAM files.
Read coverage in the bigwig files was normalized as Counts Per Million mapped reads (CPM). ATAC-seq results were visualized in the bigwig format using IGV (v2.12.3)
Assembly: mm10
Supplementary files format and content: BigWig file includes genome data for each sample

source_name: Colon

growth_protocol: MC38 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
After treatment, 2×105 cells from each sample were lysed using 50 μl of cold cell lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.5% NP40)
ATAC-seq libraries were prepared using a commercial ATAC kit (Chromatin Profile Kit for Illumina, Novoprotein Inc., Tianjin, China) following the manufacturer's instructions.

treatment_protocol: Cells were treated with 100 μM UDP for 12 hours

value: Colon

value: Tumor cell

value: UDP


title: Young_Control_Male2


title: ZNF274_dKRAB_HA_1


title: Young_Control_Male1


title: sample53, oral flora, 16s rRNA, hypertension

value: salivary


title: SUDHL5, RNA-seq, 30 nM Neg2 (BAK_04_066) treated, 4hr, rep2

first: Sai

last: Gourisankar

address: 240 Pasteur Dr, Rm 4700

department: Chemical Systems Biology

institute: Stanford

data_processing:
Raw reads were checked for quality using fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed from adapters using cutadapt(59) using parameters cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -b AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --nextseq-trim=20 --minimum-length 1. Transcripts were quantified using kallisto(60) against the human Gencode v33 indexed transcriptome and annotations. Differential gene analysis was performed using DESeq2(61) using apeglm(62) to shrink log2FoldChanges and pathway and enrichment analyses using Enrichr(63) and ChIP-Atlas(64). GSEA analysis was performed on an in-house dataset consisting of LymphDB (L. Staudt, NIH, https://lymphochip.nih.gov/signaturedb/), MSigDB pathways, and an in-house dataset generated at MD Anderson of lymphoma-specific signaling.
Assembly: Human Gencode v33
Supplementary files format and content: For RNA-seq: transcripts per million quantified from kallisto as .tsv files

growth_protocol: SUDHL5 cells were cultured in 10% FBS/RPMI-1640 + PenStrep

extract_protocol:
Cells were plated at 1M/mL and harvested in TRIsure (Bioline #38033). RNA was extracted using Direct-zol RNA MicroPrep columns (Zymo #R2062) treated with DNAseI.
For sequencing library preparation, polyA-containing transcripts were enriched, prepared into paired-end libraries, and sequenced on an Illumina NovaSeq (Novogene).

treatment_protocol: SUDHL5 cells were plated at 1M/mL and treated with DMSO or compound at indicated concentrations at final 0.1% DMSO concentrations.

value: DLBCL


title: 121_Neurons_VEH_A

value: VEH

value: A


title: Aged_Low_Ile_Male6

value: Liver

value: 24 mo Male, after Low Ile Diet 4 mo


title: MC38 cells, Vector, UDP, rep2

value: Vector control


title: sample52, oral flora, 16s rRNA, non-hypertension

value: non-hypertension

value: oral flora


title: Aged_Low_Ile_Male5


title: MC38 cells, Vector, UDP, rep1


title: sample51, oral flora, 16s rRNA, non-hypertension


title: SUDHL5, RNA-seq, 30 nM Neg2 (BAK_04_066) treated, 4hr, rep1


title: sample55, oral flora, 16s rRNA, non-hypertension


title: Aged_Low_Ile_Male4


title: SUDHL5, RNA-seq, 30 nM Neg1 (BAK_04_054) treated, 4hr, rep2


title: sample89, oral flora, 16s rRNA, hypertension

value: hypertension


title: sample50, oral flora, 16s rRNA, non-hypertension


title: SUDHL5, RNA-seq, 30 nM Neg1 (BAK_04_054) treated, 4hr, rep1


title: Aged_Low_Ile_Male3


title: sample54, oral flora, 16s rRNA, non-hypertension


title: sample49, oral flora, 16s rRNA, non-hypertension


title: MC38 cells, P2ry6, UDP, rep1


title: sample48, oral flora, 16s rRNA, non-hypertension


title: SUDHL5, RNA-seq, 30 nM CDK-TCIP1 treated, 4hr, rep2

value: 30 nM CDK-TCIP1, 4hr


title: Aged_Low_Ile_Male1


title: Aged_Low_Ile_Male2


title: sample47, oral flora, 16s rRNA, hypertension


title: MDA231OpA_B2

city: Waco

first: Joe

last: Taube

state: Texas

address: One Bear Place #97388

institute: Baylor University

data_processing:
We used Salmon (Patro et al. Nature Methods 2017) to quantify the expression of transcripts from FASTQ files.
We indexed the reads using the GRCh38 human genome with the following options: --threads 8 --gcBias –validate Mappings. Quantifications were imported to DESeq2 (v1.32.0) using the tximeta (v1.10.0) package in R (v4.1.1)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts

extract_protocol:
RNA was harvested using Trizol according to manufacturer's instuctions
Library was prepared using commercial services of Novogene Inc.

value: human breast adenocarcinoma

value: WT

value: OpA 250 nM, 3h


title: MDA231OpA_B3


title: MDA_231_B3

value: Vehicle


title: MDA231OpA_B1


title: MDA_231_B2


title: sample46, oral flora, 16s rRNA, non-hypertension


title: SUDHL5, RNA-seq, 30 nM CDK-TCIP1 treated, 4hr, rep1


title: MDA_231_B1


title: SUDHL5, RNA-seq, 30 nM Neg2 (BAK_04_066) treated, 2hr, rep2


title: Aged_Control_Male5

value: 24 mo Male, after Control Diet 4 mo


title: sample45, oral flora, 16s rRNA, hypertension


title: Aged_Control_Male4


title: Neuron, 81 CAG repeat HTT, rep3

city: Singapore

first: Vincent

last: Tano

address: 14 Medical Dr

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

description:
Neu_81Q_3
gene_counts_matrix.tsv.gz
junction_counts_matrix.tsv.gz
junction_ratio_matrix.tsv.gz

data_processing:
Quality control of RNA-seq libraries was performed using FastQC to control at least 80 million reads per library
For gene expression analysis, reads alignment and counting were performed using RSEM (B. Li & Dewey, 2011) `rsem-calculate-expression` with options for STAR (v2.7.0f) (Dobin & Gingeras, 2015) paired end alignment to the Ensembl hg38 reference genome assembly and gene annotation gtf (GRCh38 release 96 Homo sapiens).
For alternative splicing (AS) and custom peptide proteomics analyses, reads were aligned using STAR (v2.7.0f) with options for the basic two-pass mode (`--twopassMode Basic`) and filtering of non-canonical splice sites (`--outFilterIntronMotifs RemoveNoncanonicalUnannotated`) to improve discovery of novel splice sites.
Alignments were filtered to retain only uniquely mapped reads aligned to the chromosomal DNA using SAMBAMBA (v0.6.6) (Tarasov et al., 2015). Splice site read counting and annotation for each sample were then performed using RegTools.
A unified splice site junction database was generated by summarizing sample junction read counts using bedtools (Quinlan & Hall, 2010). Splice junctions were then annotated using the Ensembl hg38 genome assembly and gtf as reference.
Only splice junctions that have a splice site base sequence that are not repeat-masked and were identified in at least 3 samples were retained for downstream analysis.
Splice junction clustering and read counting were performed using the `leafcutter_cluster_regtools.py` script with the `-C` option to include constitutively spliced junctions.
Assembly: hg38
Supplementary files format and content: tab-delimited text files containing raw gene-level read counts for each sample
Supplementary files format and content: tab-delimited text files containing raw splice junction-spanning read counts for each sample

source_name: 81Q Neuron

growth_protocol: TALEN-edited isogenic IsoHD hESC cells (Ooi et al., 2019) were cultured on matrigel-coated plates (BD Biosciences) in mTeSR1 medium (STEMCELL Technologies) in a humidified environment with 5% CO2 at 37°C.

extract_protocol:
RNA samples were prepared using an RNeasy mini kit (QIAGEN)
Sequencing libraries were prepared using TruSeq Stranded mRNA sample preparation kit (Illumina)
Paired-end 150-bp RNA-sequencing

treatment_protocol:
For NPC differentiation, hESCs were cultured in N2B27 medium supplemented with 100 nM LDN193189 (Stemgent), 10 μM SB-431542 (Sigma Aldrich), 2 μM XAV929 (Stemgent) and 200 ng/mL SHH (R&D).
For forebrain neuron differentiation, NPCs were cultured in N2B27 medium supplemented with 20 ng/mL BDNF and 20 ng/mL GDNF, 0.5 mM cAMP (Sigma Aldrich) and 0.2 M ascorbic acid (STEMCELL Technologies).

value: Forebrain neuron

value: 81Q/81Q HTT

value: Forebrain neuron differentiation


title: SUDHL5, RNA-seq, 30 nM Neg1 (BAK_04_054) treated, 2hr, rep2

value: DLBCL


title: SUDHL5, RNA-seq, 30 nM CDK-TCIP1 treated, 4hr, rep3


title: Neuron, 81 CAG repeat HTT, rep2

description:
Neu_81Q_2
gene_counts_matrix.tsv.gz
junction_counts_matrix.tsv.gz
junction_ratio_matrix.tsv.gz


title: Aged_Control_Male3


title: sample43, oral flora, 16s rRNA, non-hypertension

value: salivary


title: Aged_Control_Male2

value: Liver


title: SUDHL5, RNA-seq, 30 nM Neg1 (BAK_04_054) treated, 2hr, rep1


title: sample42, oral flora, 16s rRNA, hypertension


title: Neuron, 81 CAG repeat HTT, rep1

description:
Neu_81Q_1
gene_counts_matrix.tsv.gz
junction_counts_matrix.tsv.gz
junction_ratio_matrix.tsv.gz


title: Neuron, 45 CAG repeat HTT, rep3

description:
Neu_45Q_3
gene_counts_matrix.tsv.gz
junction_counts_matrix.tsv.gz
junction_ratio_matrix.tsv.gz

source_name: 45Q Neuron

value: 45Q/45Q HTT


title: Aged_Control_Male6


title: SUDHL5, RNA-seq, 100 nM CDK-TCIP1 treated, 2hr, rep3

value: 100 nM CDK-TCIP1, 2hr


title: Aged_Control_Male1


title: SUDHL5, RNA-seq, 100 nM CDK-TCIP1 treated, 2hr, rep1


title: Neuron, 45 CAG repeat HTT, rep2

description:
Neu_45Q_2
gene_counts_matrix.tsv.gz
junction_counts_matrix.tsv.gz
junction_ratio_matrix.tsv.gz


title: SUDHL5, RNA-seq, 100 nM CDK-TCIP1 treated, 2hr, rep2


title: SUDHL5, RNA-seq, 30 nM Neg2 (BAK_04_066) treated, 2hr, rep1


title: sample44, oral flora, 16s rRNA, non-hypertension

value: non-hypertension


title: sample41, oral flora, 16s rRNA, non-hypertension

value: oral flora


title: sample39, oral flora, 16s rRNA, non-hypertension


title: Heart BAF-2

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: includ gene expression

source_name: Heart

extract_protocol:
Heart were removed, quikly frozen in luquid nitrogen, and RNA was harvested using Trizol reagent. PurelinkTM RNA Mini Kit (Cat#12183018A) was used tp abtain 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: ICR

value: Heart

value: 10 weeks


title: sample56, oral flora, 16s rRNA, non-hypertension


title: Neuron, H9 control, rep3

description:
Neu_30Q_3
gene_counts_matrix.tsv.gz
junction_counts_matrix.tsv.gz
junction_ratio_matrix.tsv.gz

source_name: H9 Neuron

value: control


title: Heart BAF-3

tag: age


title: sample38, oral flora, 16s rRNA, non-hypertension


title: Heart BAF-1


title: SUDHL5, RNA-seq, 30 nM CDK-TCIP1 treated, 2hr, rep3

value: 30 nM CDK-TCIP1, 2hr


title: sample37, oral flora, 16s rRNA, hypertension

value: hypertension


title: SUDHL5, RNA-seq, 30 nM CDK-TCIP1 treated, 2hr, rep4


title: Neuron, H9 control, rep2

description:
Neu_30Q_2
gene_counts_matrix.tsv.gz
junction_counts_matrix.tsv.gz
junction_ratio_matrix.tsv.gz


title: Heart BCF-3

value: B+Con-FMT


title: Neuron, H9 control, rep1

description:
Neu_30Q_1
gene_counts_matrix.tsv.gz
junction_counts_matrix.tsv.gz
junction_ratio_matrix.tsv.gz

value: Forebrain neuron


title: sample40, oral flora, 16s rRNA, non-hypertension


title: Heart BCF-2


title: sample36, oral flora, 16s rRNA, hypertension


title: SUDHL5, RNA-seq, 30 nM CDK-TCIP1 treated, 2hr, rep2


title: Neuron, 45 CAG repeat HTT, rep1

description:
Neu_45Q_1
gene_counts_matrix.tsv.gz
junction_counts_matrix.tsv.gz
junction_ratio_matrix.tsv.gz


title: NPC, 81 CAG repeat HTT, rep3

description:
NPC_81Q_3
gene_counts_matrix.tsv.gz
junction_counts_matrix.tsv.gz
junction_ratio_matrix.tsv.gz

source_name: 81Q NPC

value: Neural progenitor cell

value: 81Q/81Q HTT

value: NPC differentiation


title: SUDHL5, RNA-seq, 30 nM CDK-TCIP1 treated, 2hr, rep1

value: DLBCL


title: SUDHL5, RNA-seq, 10 nM CDK-TCIP1 treated, 2hr, rep2

value: 10 nM CDK-TCIP1, 2hr


title: NPC, 81 CAG repeat HTT, rep2

description:
NPC_81Q_2
gene_counts_matrix.tsv.gz
junction_counts_matrix.tsv.gz
junction_ratio_matrix.tsv.gz


title: Heart BCF-1


title: sample35, oral flora, 16s rRNA, non-hypertension

value: salivary


title: Heart BA0-3

value: Busulfan 20mg/kg


title: Heart BA0-2


title: SUDHL5, RNA-seq, 10 nM CDK-TCIP1 treated, 2hr, rep1


title: sample33, oral flora, 16s rRNA, hypertension


title: Heart BA0-1


title: SUDHL5, RNA-seq, DMSO treated, 4hr, rep3

value: 0.1% DMSO 4hr


title: sample32, oral flora, 16s rRNA, hypertension

value: oral flora


title: SUDHL5, RNA-seq, DMSO treated, 4hr, rep2


title: sample34, oral flora, 16s rRNA, hypertension


title: Heart Con-3

value: ICR


title: NPC, 81 CAG repeat HTT, rep1

description:
NPC_81Q_1
gene_counts_matrix.tsv.gz
junction_counts_matrix.tsv.gz
junction_ratio_matrix.tsv.gz


title: Heart Con-2

value: Heart


title: NPC, 45 CAG repeat HTT, rep3

description:
NPC_45Q_3
gene_counts_matrix.tsv.gz
junction_counts_matrix.tsv.gz
junction_ratio_matrix.tsv.gz

source_name: 45Q NPC

value: 45Q/45Q HTT


title: SUDHL5, RNA-seq, DMSO treated, 4hr, rep1


title: NPC, 45 CAG repeat HTT, rep1

description:
NPC_45Q_1
gene_counts_matrix.tsv.gz
junction_counts_matrix.tsv.gz
junction_ratio_matrix.tsv.gz


title: NPC, 45 CAG repeat HTT, rep2

description:
NPC_45Q_2
gene_counts_matrix.tsv.gz
junction_counts_matrix.tsv.gz
junction_ratio_matrix.tsv.gz


title: KARPAS422, Input, ChIP-seq, 30 nM CDK-TCIP1 treated, 2hr, rep2

data_processing:
The data quality was checked using fastqc. The raw reads were trimmed from adapters with trim_galore (parameters: --paired –illumina) and raw reads were aligned to hg38 human genome assembly and the dm6 fly genome assembly (spike in of Drosophila chromatin was used only for CDK9 ChIPs) using bowtie2 (parameters: --local --maxins 1000). Low quality reads, duplicated reads and reads with multiple alignments were removed using samtools and Picard (https://broadinstitute.github.io/picard/). macs2 was used to map position of peaks with FDR cutoff of 0.05. Bedtools was used to find consensus set of peaks by merging peaks across multiple conditions (bedtools merge), count number of reads in peaks (bedtools intersect -c) and generate genome coverage (bedtools genomecov -bga). deepTools was used to generate coverage densities across multiple experimental conditions (deeptools computeMatrix and deeptools plotProfile) and to generate bigwig files (deeptools bamCoverage), where reads mapping to ENCODE blacklist regions were excluded..
Assembly: hg38

growth_protocol: Cells were cultured in 10% FBS/RPMI-1640 + PenStrep

extract_protocol:
25-30 million cells were treated with CDK-TCIP1 or DMSO for indicated timepoints. Cells were washed in PBS containing CDK-TCIP1 and crosslinked for 12 min in CiA Fix Buffer (50mM HEPES pH 8.0, 1mM EDTA, 0.5mM EGTA, 100mM NaCl) with addition of formaldehyde to a final concentration of 1%. The crosslinking reaction was quenched by glycine added at 0.125M final concentration. Crosslinked cells were centrifuged at 1,000 x g for 5min. Nuclei were prepared by 10 min incubation of resuspended pellet in CiA NP-Rinse 1 buffer (50mM HEPES pH 8.0, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% IPEGAL CA-630, 0.25% Triton X100) followed by wash in CiA NP-Rinse 2 buffer (10mM Tris pH 8.0, 1mM EDTA, 0.5mM EGTA, 200mM NaCl). The pellet was resuspended in CiA Covaris Shearing Buffer (0.1% SDS,1mM EDTA pH 8.0, 10mM Tris HCl pH 8.0) with 1000x protease inhibitors (Roche) and sonicated for 40 min with Covaris E220 sonicator (Peak Power 140, Duty Factor 5.0, Cycles/Burst 200). The distribution of fragments was confirmed with D1000 Tapestation. 50 µg of chromatin per ChIP was used with anti-CDK9 antibodies (Cell Signaling CST2361S, abcam ab239364), with 40ng Drosophila chromatin (53083, ActiveMotif) spiked in. 50µg of chromatin was used with anti-Pol II ser 2 phos (2 µg, Abcam ab5095) and anti-Pol II ser 5 phos (2 µg, Abcam ab5131) antibodies, and anti-Pol II (5 µg, Santa Cruz 8WG16) antibodies. After overnight incubation at 4OC in IP buffer (50mM HEPES pH 7.5, 300mM NaCl, 1mM EDTA, 1% Triton X100, 0.1% sodium deoxycholic acid salt (DOC), 0.1% SDS), IPs were washed twice with IP buffer, once with DOC buffer (10mM Tris pH 8, 0.25M LiCl, 0.5% IPEGAL CA-630, 0.5% sodium deoxycholic acid salt (DOC), 1mM EDTA), and once with 10mM Tris/1mM EDTA buffer (TE) pH 8. IPs and inputs were reverse-crosslinked in TE/0.5% SDS/0.5µg/µL proteinase K for 55°C/3 hrs then 65OC/18 hrs, then DNA was purified using a PCR cleanup spin column (Takara #74609).
The sequencing library preparation was performed using NEBNext Ultra II DNA kit (#E7645S).

treatment_protocol: Cells were plated at 1M/mL and treated with DMSO or compound at indicated concentrations at final 0.1% DMSO concentrations.

value: 30 nM CDK-TCIP1 2hr


title: sample30, oral flora, 16s rRNA, hypertension


title: sample31, oral flora, 16s rRNA, hypertension


title: Heart Con-1

value: 10 weeks

value: control


title: sample29, oral flora, 16s rRNA, hypertension

value: hypertension


title: KARPAS422, Input, ChIP-seq, 30 nM CDK-TCIP1 treated, 2hr, rep1


title: NPC, H9 control, rep2

description:
NPC_H9_2
gene_counts_matrix.tsv.gz
junction_counts_matrix.tsv.gz
junction_ratio_matrix.tsv.gz

source_name: H9 NPC


title: NPC, H9 control, rep3

description:
NPC_H9_3
gene_counts_matrix.tsv.gz
junction_counts_matrix.tsv.gz
junction_ratio_matrix.tsv.gz


title: sample28, oral flora, 16s rRNA, hypertension


title: KARPAS422, Input, ChIP-seq, DMSO treated, 2hr, rep2

value: 0.1% DMSO 2hr


title: NPC, H9 control, rep1

description:
NPC_H9_1
gene_counts_matrix.tsv.gz
junction_counts_matrix.tsv.gz
junction_ratio_matrix.tsv.gz

value: Neural progenitor cell


title: 37 Planktonic M9 0.5%Rha Rep3

city: Oberlin

first: Lisa

last: Ryno

state: Ohio

address: 119 Woodland St

department: Chemistry and Biochemistry

institute: Oberlin College

data_processing:
RNA-Seq data quality control, alignment, quantification, and statistics calculations were done using the workflow, using the reference genome and annotation of E. coli strain MG1655 from NCBI (genome sequence GenBank ID U00096.3; assembly ID GCA_000005845.2). Adapter sequences were trimmed with scythe v0.994, and low-quality ends were trimmed with sickle v1.33.5,17 HISAT2 v2.2.2.1 was used to align reads to the reference genome.20 Salmon v1.10.2 was used to quantify the expression of transcripts.35
Assembly: GCA_000005845
Supplementary files format and content: Tab-delimited text file of raw counts for each sample

organism: Escherichia coli

growth_protocol: PHL628 E coli cells were grown in either LB or M9 media supplemented with rhamnose or no additional sugar or 0.5% glucose, respectively. Cells were grown at 28 or 37 C for 48 h and harvested as biofilm cells or planktonic (swimming) cells.

extract_protocol:
RNA was harvested using RNAprotect (Qiagen) and Rneasy Plus kit (Qiagen). 1 µg or greater was sent for sequencing. rRNA removal by using Ribo-Zero Plus rRNA Depletion Kit (Illumina)
rRNA depleted samples were quantified and used for library preparation using the KAPA mRNA HyperPrep Kits (Roche). Following the library preparation, the final concentration of all of the libraries was measured using the Qubit dsDNA HS Assay Kit (Life Technologies), and the average library size was determined using the Agilent 2100 Bioanalyzer (Agilent Technologies)

value: planktonic

tag: media type

tag: temperature

value: 37 °C

value: rhamnose


title: sample27, oral flora, 16s rRNA, hypertension


title: KARPAS422, Input, ChIP-seq, DMSO treated, 2hr, rep1

value: DLBCL

tag: treatment


title: 28 Planktonic M9 0.5%Rha Rep3

value: 28 °C


title: hESC, 81 CAG repeat HTT, rep3

description:
ESC_81Q_3
gene_counts_matrix.tsv.gz
junction_counts_matrix.tsv.gz
junction_ratio_matrix.tsv.gz

source_name: 81Q hESC

value: Embryonic stem cell

value: 81Q/81Q HTT


title: KARPAS422, CDK9, CST2316S, ChIP-seq, 30 nM CDK-TCIP1 treated, 2hr, rep2


title: sample25, oral flora, 16s rRNA, non-hypertension

value: salivary

value: non-hypertension

value: oral flora


title: 28 Planktonic M9 0.5%Glu Rep3


title: sample26, oral flora, 16s rRNA, hypertension


title: hESC, 81 CAG repeat HTT, rep2

description:
ESC_81Q_2
gene_counts_matrix.tsv.gz
junction_counts_matrix.tsv.gz
junction_ratio_matrix.tsv.gz


title: KARPAS422, CDK9, CST2316S, ChIP-seq, 30 nM CDK-TCIP1 treated, 2hr, rep1


title: KARPAS422, CDK9, CST2316S, ChIP-seq, DMSO treated, 2hr, rep2


title: sample24, oral flora, 16s rRNA, non-hypertension


title: hESC, 81 CAG repeat HTT, rep1

description:
ESC_81Q_1
gene_counts_matrix.tsv.gz
junction_counts_matrix.tsv.gz
junction_ratio_matrix.tsv.gz


title: sample23, oral flora, 16s rRNA, hypertension


title: 37 Planktonic M9 0.5%Rha Rep2


title: hESC, 45 CAG repeat HTT, rep2

description:
ESC_45Q_2
gene_counts_matrix.tsv.gz
junction_counts_matrix.tsv.gz
junction_ratio_matrix.tsv.gz

source_name: 45Q hESC

value: 45Q/45Q HTT


title: 28 Planktonic M9 0.5%Rha Rep2


title: KARPAS422, CDK9, CST2316S, ChIP-seq, DMSO treated, 2hr, rep1


title: 37 Planktonic M9 0.5%Glu Rep2


title: hESC, 45 CAG repeat HTT, rep3

description:
ESC_45Q_3
gene_counts_matrix.tsv.gz
junction_counts_matrix.tsv.gz
junction_ratio_matrix.tsv.gz


title: sample22, oral flora, 16s rRNA, hypertension


title: 28 Planktonic M9 0.5%Glu Rep2


title: SUDHL5, Input, ChIP-seq, 30 nM CDK-TCIP1 treated, 2hr, rep1

value: 30 nM CDK-TCIP1 2hr


title: 37 Planktonic M9 0.5%Rha Rep1


title: sample20, oral flora, 16s rRNA, non-hypertension


title: 37 Planktonic M9 0.5%Glu Rep3


title: SUDHL5, Input, ChIP-seq, 30 nM CDK-TCIP1 treated, 2hr, rep2


title: sample21, oral flora, 16s rRNA, hypertension


title: SUDHL5, Input, ChIP-seq, DMSO treated, 2hr, rep2


title: 37 Planktonic M9 0.5%Glu Rep1


title: SUDHL5, Input, ChIP-seq, DMSO treated, 2hr, rep1


title: sample19, oral flora, 16s rRNA, hypertension


title: hESC, H9 control, rep1

description:
ESC_H9_1
gene_counts_matrix.tsv.gz
junction_counts_matrix.tsv.gz
junction_ratio_matrix.tsv.gz

source_name: H9 hESC


title: 28 Planktonic M9 0.5%Rha Rep1


title: sample18, oral flora, 16s rRNA, hypertension

source_name: salivary


title: 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

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

value: WT


title: SUDHL5, CDK9, CST2316S, ChIP-seq, 30 nM CDK-TCIP1 treated, 2hr, rep2


title: 28 Planktonic M9 0.5%Glu Rep1

value: control


title: hESC, 45 CAG repeat HTT, rep1

description:
ESC_45Q_1
gene_counts_matrix.tsv.gz
junction_counts_matrix.tsv.gz
junction_ratio_matrix.tsv.gz


title: sample17, oral flora, 16s rRNA, non-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


title: SUDHL5, CDK9, CST2316S, ChIP-seq, 30 nM CDK-TCIP1 treated, 2hr, rep1


title: sample15, oral flora, 16s rRNA, hypertension

value: hypertension


title: hESC, H9 control, rep3

description:
ESC_H9_3
gene_counts_matrix.tsv.gz
junction_counts_matrix.tsv.gz
junction_ratio_matrix.tsv.gz


title: SUDHL5, CDK9, CST2316S, ChIP-seq, DMSO treated, 2hr, rep1

value: 0.1% DMSO 2hr


title: E. coli 47-1826 in media_2

description:
processed data files:
raw_counts.txt


title: sample16, oral flora, 16s rRNA, non-hypertension


title: E. coli 47-1826 in media_1

description:
processed data files:
raw_counts.txt


title: p24174-s010-S10_S10

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: Lymph node

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: Male

value: Lymph node

value: CD4 T cells

value: Skin-graft rejection


title: 37 Biofilm M9 0.5%Rha Rep3

value: biofilm

value: 37 °C

value: rhamnose


title: sample14, oral flora, 16s rRNA, hypertension

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


title: SUDHL5, CDK9, CST2316S, ChIP-seq, DMSO treated, 2hr, rep2

value: DLBCL


title: SUDHL5, CDK9, ab239364, ChIP-seq, 30 nM CDK-TCIP1 treated, 2hr, rep2


title: p24174-s009-S9_S9

description: VDJ TCR


title: sample13, oral flora, 16s rRNA, non-hypertension

value: non-hypertension

value: oral flora


title: 28 Biofilm M9 0.5%Glu Rep3

value: 28 °C


title: hESC, H9 control, rep2

description:
ESC_H9_2
gene_counts_matrix.tsv.gz
junction_counts_matrix.tsv.gz
junction_ratio_matrix.tsv.gz

value: Embryonic stem cell


title: SUDHL5, CDK9, ab239364, ChIP-seq, 30 nM CDK-TCIP1 treated, 2hr, rep1

value: 30 nM CDK-TCIP1 2hr


title: p24174-s008-S8_S8

description: VDJ TCR


title: 37 Biofilm M9 0.5%Rha Rep2


title: 37 Biofilm M9 0.5%Glu Rep3

value: control


title: SUDHL5, CDK9, ab239364, ChIP-seq, DMSO treated, 2hr, rep2


title: 37 Biofilm M9 0.5%Glu Rep2


title: sample12, oral flora, 16s rRNA, hypertension

value: hypertension


title: p24174-s007-S7_S7

description: VDJ TCR


title: SUDHL5, CDK9, ab239364, ChIP-seq, DMSO treated, 2hr, rep1

value: 0.1% DMSO 2hr


title: sample11, oral flora, 16s rRNA, hypertension


title: SUDHL5, Input, ChIP-seq, DMSO treated, 4hr, rep2

value: 0.1% DMSO 4hr


title: p24174-s006-S6_S6

description: VDJ TCR

value: Male

value: Lymph node


title: sample9, oral flora, 16s rRNA, hypertension


title: p24174-s011-S11_S11

description: VDJ TCR

value: CD4 T cells

value: H2-Kd peptides+Tacrolimus+anti-CD8


title: p24174-s005-S5_S5

description: VDJ TCR


title: p24174-s004-S4_S4

description: VDJ TCR


title: SUDHL5, Input, ChIP-seq, DMSO treated, 4hr, rep1


title: SUDHL5, Pol II, ChIP-seq, 30 nM CDK-TCIP1 treated, 4hr, rep3

value: 30 nM CDK-TCIP1 4hr


title: 37 Biofilm M9 0.5%Glu Rep1

value: biofilm

value: 37 °C


title: 28 Biofilm M9 0.5%Rha Rep2

value: rhamnose


title: 28 Biofilm M9 0.5%Glu Rep2


title: sample7, oral flora, 16s rRNA, hypertension

value: salivary


title: SUDHL5, Pol II, ChIP-seq, 30 nM CDK-TCIP1 treated, 4hr, rep2

value: DLBCL


title: 28 Biofilm M9 0.5%Rha Rep3

value: 28 °C


title: sample8, oral flora, 16s rRNA, hypertension

value: oral flora


title: sample6, oral flora, 16s rRNA, hypertension


title: p24174-s003-S3_S3

description: VDJ TCR


title: 28 Biofilm M9 0.5%Rha Rep1


title: SUDHL5, Pol II, ChIP-seq, 30 nM CDK-TCIP1 treated, 4hr, rep1


title: p24174-s002-S2_S2

description: VDJ TCR


title: sample5, oral flora, 16s rRNA, hypertension


title: sample10, oral flora, 16s rRNA, hypertension


title: p24174-s001-S1_S1

description: VDJ TCR


title: SUDHL5, Pol II, ChIP-seq, 30 nM CDK-TCIP1 treated, 2hr, rep3

value: 30 nM CDK-TCIP1 2hr


title: 37 Planktonic LB 0.5%Rha Rep3

value: planktonic

value: LB


title: sample4, oral flora, 16s rRNA, hypertension

value: hypertension


title: 37 Biofilm M9 0.5%Rha Rep1


title: 37 Planktonic LB 0% Rep3

value: control


title: sample3, oral flora, 16s rRNA, hypertension


title: 28 Planktonic LB 0.5%Rha Rep3


title: p23121-s004_Mouse-4

description: VDJ TCR

value: Female

value: H2-Kd peptides+CTLA4-Ig


title: SUDHL5, Pol II, ChIP-seq, DMSO treated, 4hr, rep3

value: 0.1% DMSO 4hr


title: sample2, oral flora, 16s rRNA, hypertension


title: sample1, oral flora, 16s rRNA, hypertension


title: SUDHL5, Pol II, ChIP-seq, DMSO treated, 4hr, rep2


title: 28 Planktonic LB 0% Rep3


title: 37 Planktonic LB 0.5%Rha Rep2


title: At_EV_Infected 3

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 B.cinerea infected A.thaliana leaves, biological repeat 3

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
Genome_build: TAIR10/ASM83294v1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism:
Arabidopsis thaliana
Botrytis cinerea

source_name: plant leaves, fungal hyphae

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: host ecotype

value: infected with B.cinerea B05

value: plant leaves, fungal hyphae

tag: sample type

value: extracellular vesicles


title: p23121-s002_Mouse-2

description: VDJ TCR

value: Lymph node

value: CD4 T cells


title: SUDHL5, Pol II, ChIP-seq, 30 nM CDK-TCIP1 treated, 2hr, rep1


title: p23121-s003_Mouse-3

description: VDJ TCR


title: At_EV_Infected 2

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


title: SUDHL5, Pol II, ChIP-seq, DMSO treated, 4hr, rep1


title: 37 Planktonic LB 0% Rep2

value: 37 °C


title: 28 Biofilm M9 0.5%Glu Rep1

value: biofilm


title: SUDHL5, Pol II ser 5 phos, ChIP-seq, 30 nM CDK-TCIP1 treated, 4hr, rep2

value: DLBCL

value: 30 nM CDK-TCIP1 4hr


title: p23121-s001_Mouse-1

description: VDJ TCR


title: p23098-s010_Mouse-10

description: VDJ TCR

value: Skin-graft rejection


title: At_EV_Infected 1

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


title: 28 Planktonic LB 0.5%Rha Rep2

value: planktonic

value: 28 °C

value: rhamnose


title: SUDHL5, Pol II, ChIP-seq, 30 nM CDK-TCIP1 treated, 2hr, rep2

value: 30 nM CDK-TCIP1 2hr


title: SUDHL5, Pol II ser 5 phos, ChIP-seq, 30 nM CDK-TCIP1 treated, 4hr, rep1


title: 28 Planktonic LB 0% Rep2

value: LB

value: control


title: p23121-s005_Mouse-5

description: VDJ TCR

value: Female

value: H2-Kd peptides+CTLA4-Ig


title: H3k4me3_TaDRIM-Seq-Arabidopsis-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

organism: Arabidopsis thaliana

source_name: young leaves

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.

value: young leaves

value: no


title: 37 Planktonic LB 0.5%Rha Rep1


title: p23098-s009_Mouse-9

description: VDJ TCR

value: Lymph node


title: p23098-s006_Mouse-6

description: VDJ TCR

value: CD4 T cells


title: SUDHL5, Pol II ser 5 phos, ChIP-seq, 30 nM CDK-TCIP1 treated, 2hr, rep2


title: SUDHL5, Pol II ser 5 phos, ChIP-seq, DMSO treated, 4hr, rep2

value: 0.1% DMSO 4hr


title: 37 Planktonic LB 0% Rep1

value: 37 °C


title: p23098-s007_Mouse-7

description: VDJ TCR


title: SUDHL5, Pol II ser 5 phos, ChIP-seq, DMSO treated, 4hr, rep1

value: DLBCL


title: 28 Planktonic LB 0.5%Rha Rep1


title: H3k4me3_TaDRIM-Seq-Arabidopsis-rep1


title: DP_Na_Col_2

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

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

department: CSRS

country: Japan

institute: RIKEN

data_processing:
base-calling:RTA and bcl2fastq
adapter trim: trimmomatic
alignment: HISAT2
aligned reads count: featureCounts
normalize: DESeq2
Assembly: TAIR10
Supplementary files format and content: text

source_name: Seedlings

growth_protocol: Arabidopsis thaliana (Col-0 ecotype) were grown on liquid MS medium at 22°C under 16-h-light/8-h-dark.

extract_protocol:
Seedlings were flash-frozen on liquid nitrogen, and RNA was extracted using RNeasy Plant Mini Kit (QIAGEN).
Lasy-Seq v1.1 (Kamitani et al., 2019, Sci. Rep. see also　https://sites.google.com/view/lasy-seq/ )

treatment_protocol: DPAM-1 or Coronatine treatment was performed at 4 days after germination. At 16h after these chemical compounds had been applied and absorbed, 100 mM NaCl was added to the growth medium. Young seedlings were harvested at 2h after the onset of NaCl treatment.

value: Seedlings

value: 5 µM DPAM-1 and 100 mM NaCl


title: DP_Na_Col_1


title: SUDHL5, Pol II ser 2 phos, ChIP-seq, 30 nM CDK-TCIP1 treated, 4hr, rep2

city: Stanford

value: 30 nM CDK-TCIP1 4hr


title: DP_Na_Col_3


title: p23098-s004_Mouse-4

description: VDJ TCR

value: Skin-graft rejection


title: 37 Biofilm LB 0.5%Rha Rep3

value: biofilm

value: rhamnose


title: DP_Col_3

value: 5 µM DPAM-1


title: p23098-s008_Mouse-8

description: VDJ TCR


title: SUDHL5, Pol II ser 2 phos, ChIP-seq, 30 nM CDK-TCIP1 treated, 4hr, rep1


title: DP_Col_1


title: 37 Biofilm LB 0% Rep3

value: LB

value: control


title: SUDHL5, Pol II ser 5 phos, ChIP-seq, 30 nM CDK-TCIP1 treated, 2hr, rep1

value: 30 nM CDK-TCIP1 2hr


title: SUDHL5, Pol II ser 2 phos, ChIP-seq, 30 nM CDK-TCIP1 treated, 2hr, rep2


title: p23098-s001_Mouse-1

description: VDJ TCR

value: Female


title: 28 Biofilm LB 0% Rep3

value: 28 °C


title: Cor_Na_Col_3

value: 5 µM Coronatine and 100 mM NaCl


title: 28 Biofilm LB 0.5%Rha Rep3


title: 28 Planktonic LB 0% Rep1

value: planktonic


title: p23098-s005_Mouse-5

description: VDJ TCR

value: Lymph node

value: CD4 T cells


title: p22306-s005-Mouse5

description: VDJ TCR


title: SUDHL5, Pol II ser 2 phos, ChIP-seq, DMSO treated, 4hr, rep2

value: DLBCL

value: 0.1% DMSO 4hr


title: Cor_Na_Col_2

value: Seedlings


title: 37 Biofilm LB 0% Rep2

value: 37 °C


title: Cor_Na_Col_1


title: HiC in ZNF274KO ov  ZNF274dSCAN 3

city: Lausanne

first: Julien

last: Duc

address: Station 19 CH-1015 Lausanne

institute: EPFL

description: HiC in ZNF274KO overexpressing ZNF274 delta SCAN rep3

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

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.

value: ZNF274dSCAN overexpression


title: 28 Biofilm LB 0.5%Rha Rep2

value: biofilm


title: p22306-s003-Mouse3

description: VDJ TCR

value: Skin-graft rejection


title: SUDHL5, Pol II ser 2 phos, ChIP-seq, 30 nM CDK-TCIP1 treated, 2hr, rep1


title: p23098-s002_Mouse-2

description: VDJ TCR


title: 28 Biofilm LB 0% Rep2


title: Cor_Col_3

value: 5 µM Coronatine


title: p22306-s002-Mouse2

description: VDJ TCR


title: Cor_Col_2


title: HiC in ZNF274KO ov ZNF274 3

description: HiC in ZNF274KO overexpressing ZNF274 rep3

value: ZNF274 overexpression


title: p22306-s004-Mouse4

description: VDJ TCR


title: HiC in ZNF274KO 3

description: HiC in ZNF274KO rep3


title: 37 Biofilm LB 0.5%Rha Rep2

value: LB

value: rhamnose


title: SUDHL5, Pol II ser 2 phos, ChIP-seq, DMSO treated, 4hr, rep1


title: Cor_Col_1


title: 37 Biofilm LB 0.5%Rha Rep1


title: 37 Biofilm LB 0% Rep1

value: control


title: 28 Biofilm LB 0.5%Rha Rep1

value: 28 °C


title: KO-2

city: GRANADA

last: Toro

state: Spain

address: Avenida de la Ilustracion

department: Bioinformatics

institute: GENYO

description: 10x genomics chromium system

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1
Assembly: mm10
Supplementary files format and content: h5 files

source_name: Spleen

extract_protocol:
Spleens from 3 animals per group (TLR7.tg6, TLR7.tg6.Bank1-/- and control C57Bl/6J 32 week-old male mice) were individually homogenized, and red cells were lysed with ACK buffer.
Library was performed according to the manufacter's instructions (10x genomics chromium system at the Institute of Parasitology and Biomedicine López Neyra (CSIC), in Granada, Spain)

value: Spleen

value: splenocytes

value: 32 weeks


title: KO-3

description: 10x genomics chromium system


title: DMSO_Na_Col_2

value: 1% (v/v) DMSO and 100 mM NaCl


title: DMSO_Na_Col_3


title: DMSO_Na_Col_1


title: KO-1

description: 10x genomics chromium system


title: TLR7-3

description: 10x genomics chromium system


title: HiC in ZNF274KO ov  ZNF274dSCAN 2

description: HiC in ZNF274KO overexpressing ZNF274 delta SCAN rep2


title: 28 Biofilm LB 0% Rep1


title: DMSO_Col_3

value: 1% (v/v) DMSO


title: HiC in WT 2

description: HiC in WT rep2

value: WT


title: HiC in ZNF274KO 1

description: HiC in ZNF274KO rep1


title: TLR7-1

description: 10x genomics chromium system


title: TLR7-2

description: 10x genomics chromium system


title: p22306-s001-Mouse1

description: VDJ TCR

value: Female

value: Lymph node

value: CD4 T cells


title: HiC in ZNF274KO 2

description: HiC in ZNF274KO rep2


title: HiC in WT 3

description: HiC in WT rep3


title: DMSO_Col_2

value: Seedlings


title: HiC in WT 1

description: HiC in WT rep1


title: DMSO_Col_1


title: HiC in ZNF274KO ov ZNF274 2

description: HiC in ZNF274KO overexpressing ZNF274 rep2


title: Treatment time 3

city: Indianapolis

first: Caleb

last: Class

state: IN

address: 4600 Sunset Ave

department: Pharmaceutical Sciences

institute: Butler University

description: Sequenced by Novogene (Instrument K00124)

data_processing:
Cut adapter sequences and demultiplex to 5 biological replicates per sample, using cutadapt (parameters: --pair-adapters, -e 0.15, --max-ee 2, -a file:biorep_bc.fa, -G file:biorepRev_bc.fa)
Quantify sequence abundance using STAR (parameters: --outFilterMismatchNmax 0, --quantMode GeneCounts)
Assembly: Library4.fasta (supplementary file, containing the designed TAD sequences)
Supplementary files format and content: tab-delimited TXT file, containing a matrix of counts of each sequence in each biorep
Supplementary files format and content: tab-delimited TXT file, containing a matrix of counts of each sequence in each sample
Library strategy: DNA-Seq

organism: Saccharomyces cerevisiae

source_name: Y2H Gold Yeast Cell Strain

growth_protocol: The cell culture was grown in -trp synthetic yeast growth medium containing 200 mig/mL aureobasidin, and grown for four days with daily 1/100 dilution to maintain the culture in mid-log phase.

extract_protocol:
Samples were taken at 0, 1, 2, 3, and 4 days. DNA was isolated with a Thermo Scientific Pierce Yeast DNA Extraction Reagent Kit, and the component from the library was isolated by PCR with the Invitrogen AccuPrime SuperMix I kit.
Designed sequences were provided as an Excel file to GenScript. The sequence pool was synthesized by massive parallel synthesis, stripped from the chip, amplified by PCR appending biorep barcodes, cloned into parental vector with estimation of library complexity by manual colony counting. DNA sequencing was conducted by NovoGene.

value: Y2H Gold Yeast Cell Strain

tag: time

value: 1 day

value: Growth on 200 mM aureobasidin


title: HiC in ZNF274KO ov  ZNF274dSCAN 1

description: HiC in ZNF274KO overexpressing ZNF274 delta SCAN rep1

value: ZNF274dSCAN overexpression


title: Treatment time 4


title: WT-3

description: 10x genomics chromium system


title: Treatment time 2


title: S. Heidelberg 18-9079 in media_2

description:
processed data files:
raw_counts.txt

organism: Salmonella enterica subsp. enterica serovar Heidelberg

value: bacterial cells

value: Heidelberg 18-9079


title: WT-2

description: 10x genomics chromium system


title: HiC in ZNF274KO ov ZNF274 1

description: HiC in ZNF274KO overexpressing ZNF274 rep1

value: ZNF274 overexpression


title: Baseline sample, replicate 1

value: 0 days


title: S. Heidelberg 18-9079 in media_1

description:
processed data files:
raw_counts.txt


title: DP_Col_2

value: 5 µM DPAM-1


title: hy5-2, SIM 8D, High light, replicate 3

status: Public on Sep 16 2024

first: Yu

last: Chen

address: 1-7-22 Suehirocho, Tsurumi-ku

data_processing:
Sequenced reads were mapped to the TAIR10 Arabidopsis genome by STAR 87 using the “--outFilterMultimapNmax 1 --alignIntronMax 10000 --alignMatesGapMax 10000” options.
After indexing by the samtools, mapped reads were further counted by bedtools multicov.
Differentially expressed genes (DEGs) are defined by edgeR package on R by comparing between different timepoints, light conditions and genotypes with the criteria |log2fold change (FC)| > log2(1.5) & false discovery rate (FDR) <= 0.05.
Assembly: TAIR10
Supplementary files format and content: raw_counts.txt is a tab-delimited file containing the read counts of each genes mapped to TAIR10 Arabidopsis genome in each sample.

source_name: hypocotyls

growth_protocol: Arabidopsis seeds were surface-sterilized with 70 % (v/v) ethanol for 1 min and then 20 % (v/v) bleach for 5 min. Sterilized seeds were rinsed with autoclaved water 3 times before sowing onto the MS media supplied with 1 % sucrose and solidified by 0.6 % Gelzan. After 4 days of stratification at 4ºC under darkness, seeds were stimulated for germination at 22ºC under continuous high light (40 µmol/m2/s) for several hours before growing under continuous low light (2 µmol/m2/s). 7-day-old seedlings grown at 22ºC under continuous low light (2 µmol/m2/s) were used for hormone-induced shoot regeneration.

extract_protocol:
Hypocotyl explants were frozen with liquid nitrogen and ground with beads by a TissueLyser II (QIAGEN). RNA extraction with DNase digestion was performed by the RNeasy Plant Mini Kit (QIAGEN) following the default instructions.
Isolated RNA was then subjected for library preparation using the KAPA Stranded mRNA-Seq Kit (NIPPON Genetics) with NEB adaptors for Illumina (New England Biolabs) and AMPure XP beads (Beckman Coulter).

treatment_protocol: Briefly, the excised hypocotyl explants were initially cultured on CIM (Gamborg’s B5 vitamin medium supplied with 2 % glucose and solidified by 0.25 % Gelzan, together with 0.5 mg/L 2,4-Dichlorophenoxyacetic acid (2,4-D) and 0.1 mg/L kinetin) for 4 days to induce callus formation. These explants were subsequently transferred to SIM (Gamborg’s B5 vitamin medium supplied with 2 % glucose and solidified by 0.25 % Gelzan, together with 0.15 mg/L Indole-3-acetic acid (IAA) and 0.5 mg/L 2-Isopentenyladenine (2-iPA)) for 14 days to induce shoot regeneration.

value: hypocotyls

value: SIM

value: 8 days after SIM incubation


title: hy5-2, SIM 8D, High light, replicate 2


title: hy5-2, SIM 8D, High light, replicate 1


title: hy5-2, SIM 4D, High light, replicate 1

value: 4 days after SIM incubation


title: hy5-2, SIM 4D, High light, replicate 3


title: hy5-2, SIM 4D, High light, replicate 2


title: hy5-2, CIM 4D, High light, replicate 3

value: CIM

value: 4 days after CIM incubation


title: Treatment time 1


title: hy5-2, CIM 4D, High light, replicate 2


title: Baseline sample, replicate 2


title: hy5-2, CIM 4D, High light, replicate 1


title: hy5-2, T0, Low light, replicate 3

value: before culture

value: time 0


title: hy5-2, T0, Low light, replicate 2


title: S. Heidelberg 18-9079 in media_3

description:
processed data files:
raw_counts.txt

value: WT


title: hy5-2, T0, Low light, replicate 1


title: Col-0, SIM 8D, High light, replicate 2


title: Col-0, SIM 8D, High light, replicate 3


title: Col-0, SIM 8D, Low light, replicate 1


title: Col-0, SIM 8D, High light, replicate 1


title: WT-1

description: 10x genomics chromium system

value: Spleen

value: splenocytes

value: 32 weeks


title: Col-0, SIM 4D, Low light, replicate 3


title: Col-0, SIM 8D, Low light, replicate 2


title: Col-0, SIM 8D, Low light, replicate 3


title: Col-0, SIM 4D, High light, replicate 2


title: Col-0, CIM 4D, High light, replicate 2


title: Col-0, SIM 4D, Low light, replicate 1


title: Col-0, SIM 4D, High light, replicate 3


title: Col-0, CIM 4D, High light, replicate 1


title: Col-0, CIM 4D, Low light, replicate 1


title: Col-0, CIM 4D, High light, replicate 3


title: Col-0, T0, Low light, replicate 3


title: Col-0, CIM 4D, Low light, replicate 2


title: Col-0, T0, Low light, replicate 2


title: Col-0, CIM 4D, Low light, replicate 3


title: Col-0, T0, Low light, replicate 1


title: Col-0, SIM 4D, High light, replicate 1