title: HC9N

city: Kyoto

first: Makoto

middle: Mark

last: Taketo

state: Kyoto

address: Yoshida-Honmachi, Sakyo

department: Kyoto University Hospital

country: Japan

institute: Kyoto University

description: Large intestine

data_processing:
RNA-seq analysis was performed by Macrogen.
Prepared libraries were paired-end sequencing (2 × 100 bases) to a depth of ~40 million reads/sample using the Illumina HighSeq 2000 sequencer.
The sequence reads were mapped to the hg19 reference genome with HISAT2 program and the transcripts were assembled using StringTie program.
The read counts were scored using featureCounts program.
Genome_build: hg19
Supplementary_files_format_and_content: A tab-delimited text file include TPM  for each sample

source_name: Normal colorectal epithelial stem cell spheroids

growth_protocol: Collected tumor samples were transferred from the operation room to the laboratory in ice-cold washing medium (DMEM/F12 containing 10% bovine calf serum, 100 U/ml penicillin, and 0.1 mg/ml streptomycin). Fragments of excised tumor were minced and digested by collagenase type I (Thermo Fisher Scientific). Then, epithelial cells were collected and suspended in Matrigel (Corning Inc.) and cultured in the cancer medium (Advanced DMEM/F-12 (Thermo Fisher), 100 units/ml penicillin, 0.1 mg/ml streptomycin, 2 mM L-glutamine, 10 μM Y27632, 10 or 1 μM SB431542, 5 μg/ml Plasmocin (Invivogen, San Diego, CA), and 5% FBS (Thermo Fisher]) with or without 50 ng/mL EGF (PeproTech) and 100 ng/mL basic FGF (PeproTech).

extract_protocol:
After aspiration of the medium, the lysis buffer (Takara Bio Inc., Kusatsu, Japan) was directly added to each well of spheroid culture. RNA was purified using NucleoSpin RNA II kit (Takara).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Untreated

tag: tissue

value: CRC patient-derived spheroids

value: Untreated


title: HC20N

status: Public on Nov 22 2021

type: SRA

description: Large intestine

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: treatment


title: HC6N

description: Large intestine


title: UPN17 posttreatment_geneexpression

city: Bethesda

first: Shouguo

last: Gao

state: MD

address: 9000 Rockville Pike

department: NHLBI

country: USA

institute: National Institutes of Health

data_processing:
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting,and csv files of TCR clonality were performed using the cellranger analysis pipeline.
Paired-end reads were mapped to the hg19 genome with cellranger for gene-level read counts
Data normalization, dimension reduction, and differential expression analysis were performed using R and the Seurat R package. Cells were clustered with PhenoGraph.
T cell receptor VDJ analysis: Cellranger
VDJ of Tcells were infered with cellranger vdj pipeline to get TCR contig annotations.
Genome_build: hg19

source_name: Human peripheral blood

extract_protocol: Cells from T-LGLL patients and healthy donors were loaded into the 10XChromium Controller using the Single Cell 5' Library and Gel BeadKit (10X Genomics). The Chromium Single Cell V(D)J protocol was used to profile  gene expression and T cell receptor.

tag: cell type

value: CD3+ T cells

tag: Sex

value: M

tag: age

tag: diagnosis

value: T-LGLL

tag: subject


title: UPN1 posttreatment_geneexpression

value: F


title: Healthydonor4_geneexpression

value: healthy


title: HC20TT

description: Large intestine

source_name: Colorectal cancer whole tissues

value: CRC whole tissues


title: Akita_2

city: La Jolla

first: Max

last: Chang

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
Sequencing reads were aligned to the human genome using STAR 2.7.3a.
Gene-level read counts were generated using STAR 2.7.3a.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited file containing raw gene counts

source_name: bronchial epithelial cells

extract_protocol:
1 ml Trizol was added to 5-10 x 10^6 cells and the homogenate was incubated at room temperature for 5 minutes. 200 μl chloroform were added per ml of Trizol, shaken vigorously for 15-30 seconds and incubated at room temperature for 15 minutes. Samples were centrifuged for 15 minutes at 4˚C and 12,000 rcf. The aqueous phase was carefully collected in a separate tube. 500 μl isopropanol was added per 1 ml Trizol, inverted to mix and incubated at room temperature for 5-10 minutes. Samples were transferred to Qiagen RNeasy Spin Columns and RNA was isolated according to the manufacturer’s instructions.
RNA-seq libraries were constructed using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

value: bronchial epithelial cells

tag: infection

value: Influenza

tag: viral geographic origin

value: Akita

tag: viral type

value: A

tag: viral hemagglutinin

tag: viral neuraminidase


title: Akita_1


title: UPN17 pretreatment_geneexpression


title: UPN4 posttreatment_geneexpression


title: HC9TT

description: Large intestine


title: UPN1 pretreatment_geneexpression


title: HC6TT

description: Large intestine


title: inflamed gut sample S40 from patient M

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

description:
16S V3-V4 sequencing of a FFPE specimen from an inflamed gut portion of patient 10 affected by Crohn's disease
S40

library_source: genomic

data_processing:
Library strategy: 16S rDNA Metagenomic Sequencing
demultiplexing: from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
pair merging: micca mergepairs -i pair1.fastq -r pair2.fastq -o out.joined.fastq -l 30 -d 3
primer check and trimming: micca trim -i out.joined.fastq -o out.trimmed.fastq -w CCTACGGGNBGCWSCAG -r GACTACHVGGGTATCTAATCC -W -R -c
quality check: micca filter -i out.trimmed.fastq -o out.hiqual.fastq -e 0.5 -m 350 -f fastq
read mergingmicca merge -i *.hiqual.fastq -o merged.fastq -f fastq
OTU table creation by clusteringmicca otu -m denovo_greedy -i merged.fasta -o otudata -d 0.97 -c -t 20
taxonomic assignment (RDP)micca classify -m rdp -i otudata/otus.fasta -o otudata/taxa.txt
further analyses: R phyloseq package (see https://github.com/matteoramazzotti/papers/tree/main/2020crohn)
otu.fasta includes the longest sequence for each OTU that is the source for taxonomy assignment.

molecule: genomic DNA

organism: human gut metagenome

source_name: 16S rDNA amplicons

extract_protocol:
deparaffinatin with xylene followed by DNA extration with QIAamp DNA FFPE tissue kit (QIAGEN)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)

treatment_protocol: isolation of 8 slices of 10 um from paraffin embedded gut tissue for each sample

tag: tissue source

value: ileal mucosa

tag: patient diagnosis

value: Crohn's disease

tag: disease state

value: Inflamed

tag: surgery

value: first

tag: patient


title: UPN4 pretreatment_geneexpression


title: NP2_SDI_12w_naive_1

data_processing:
Sequencing reads were aligned to the mouse genome using STAR 2.6.1a.
Gene-level read counts were generated using STAR 2.6.1a.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited file containing raw gene counts

organism: Mus musculus

source_name: Bronchoalveolar lavage fluid

growth_protocol: mice were housed in SPF conditions

extract_protocol:
bronchioalveolar lavage fluid was collected (2x1ml PBS + 2mM EDTA) 4h after SDI/NanoPart administration and cells were spun down, resuspended in 100 µl Trizol. RNA was extracted using the DirectZol kit (Zymo Research)
RNA-seq libraries were constructed using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

treatment_protocol: Mice were given 1 µg Sendai virus Defective Interfering RNA intranasally in different nanoparticle formulations, suspended in 50 µl PBS under mild sedation.

tag: immunity

value: naive

tag: agonist

value: SDI

tag: delivery

value: Nanoparticle 2

tag: age (weeks)

tag: strain

value: BALB/c


title: HC146T

description: Large intestine

source_name: Colorectal cancer stem cell spheroids

tag: tissue

value: CRC patient-derived spheroids

tag: treatment

value: Untreated


title: inflamed gut sample S39 from patient F

description:
16S V3-V4 sequencing of a FFPE specimen from an inflamed gut portion of patient 9 affected by Crohn's disease
S39

tag: Sex

value: F


title: NP1_SDI_12w_naive_2

value: Nanoparticle 1


title: UPN18 posttreatment_geneexpression

tag: cell type

value: CD3+ T cells

tag: age

tag: diagnosis

value: T-LGLL

tag: subject


title: inflamed gut sample S38 from patient F

description:
16S V3-V4 sequencing of a FFPE specimen from an inflamed gut portion of patient 8 affected by Crohn's disease
S38

tag: tissue source

value: relapse


title: HC129T

description: Large intestine


title: Healthydonor2_geneexpression

value: healthy


title: Dnmt1c/chip MDP rep4

type: RNA

city: Bad Nauheim

first: Sweta

last: Talyan

address: Ludwigstraße 43

country: Germany

institute: MPI

hyb_protocol: 6 µg of fragmented and labeled aRNA were hybridized to Affymetrix Mouse Genome 430 PM peg plate arrays. For hybridization, washing and staining an Affymetrix GeneTitan system was used.

scan_protocol: GeneChip arrays were scanned using an Affymetrix GeneTitan system controlled by the Affymetrix GeneChip Command Console software (AGCC).

data_processing: Data was analyzed with the Bioconductor package version v.3.5.1. The CEL files containing the raw expression intensity values for each probe on the array were opened using the affy package and normalized using the function called Robust Multi-Array Average (RMA). The linear models for microarray data (LIMMA) package was used to find differentially expressed genes. A cutoff of more than 0.58 logFC and p-value of less than 0.05 was used to call genes as differentially expressed between two conditions.

label: biotin

source_name: MDPs flow-sorted from the bone marrow of Dnmt1c/chip mice

label_protocol: The Affymetrix GeneChip 3’ IVT Express Protocol was used for the preparation of biotinylated amplified RNA (aRNA) from 300ng of total RNA.

extract_protocol: BM cells were obtained from adult mice by thoroughly flushing femurs and tibiae with PBS (PAA) supplemented with 1 % FSC (Biochrom). Single cell suspensions were generated by mashing the organ through a cell strainer of 40 µm diameter. Suspension of cells were incubated for 5 min with ice-cold ACK buffer (0.15 M NH4Cl, 10 M KHCO3, 0.1 mM EDTA, pH 7.3) to remove erythrocytes. Cells were first incubated for 10 min in PBS supplemented with 1% FCS and purified CD16/32 antibody to block Fc binding. Antibody labeling was conducted for 10 min on ice in the dark. Discrimination of dead cells was performed by propidium iodide (PI, 0.1 mg/ml, Sigma Aldrich) shortly before measurement. MDPs (Lin-cKithiCD115+CD11b-Ly-6C-) and cMoPs (Lin-cKithiCD115+CD11b-Ly-6C+) were flow-sorted from 8-12 weeks old Dnmt1+/+ and Dnmt1c/chip mice with an FACS Aria III (BD) cytometer equipped with FACSDiva software. The RNAeasy Kit (Qiagen) was used for extraction of RNA according to the supplier’s instructions. DNAse I digestion was performed as part of the protocol to remove residual DNA from the RNA preparation. RNA was stored at -80 °C.

tag: genotype

value: MDPs


title: HC142T

description: Large intestine


title: UPN18 pretreatment_geneexpression


title: NP1_SDI_12w_naive_1


title: inflamed gut sample S37 from patient M

description:
16S V3-V4 sequencing of a FFPE specimen from an inflamed gut portion of patient 7 affected by Crohn's disease
S37

value: ileal mucosa

tag: patient diagnosis

tag: disease state

value: M


title: Manitoba_2

value: bronchial epithelial cells

tag: infection

value: Influenza

tag: viral geographic origin

value: Manitoba

tag: viral type

value: A

tag: viral hemagglutinin

tag: viral neuraminidase


title: Healthydonor1_geneexpression


title: Dnmt1c/chip MDP rep3


title: Dnmt1c/chip MDP rep2


title: HC117T

description: Large intestine


title: HC120T

description: Large intestine


title: UPN19 posttreatment_geneexpression


title: inflamed gut sample S36 from patient F

description:
16S V3-V4 sequencing of a FFPE specimen from an inflamed gut portion of patient 6 affected by Crohn's disease
S36

value: Crohn's disease

value: Inflamed

tag: surgery

tag: patient


title: inflamed gut sample S34 from patient M

description:
16S V3-V4 sequencing of a FFPE specimen from an inflamed gut portion of patient 4 affected by Crohn's disease
S34

value: first


title: HC108T

description: Large intestine

tag: tissue

value: CRC patient-derived spheroids

tag: treatment

value: Untreated


title: UPN19 pretreatment_geneexpression

tag: cell type

tag: Sex

value: F


title: HC106T

description: Large intestine


title: Dnmt1+/+ MDP rep4

source_name: MDPs flow-sorted from the bone marrow of Dnmt1+/+ mice


title: Dnmt1+/+ MDP rep3


title: inflamed gut sample S33 from patient F

description:
16S V3-V4 sequencing of a FFPE specimen from an inflamed gut portion of patient 3 affected by Crohn's disease
S33


title: Dnmt1c/chip MDP rep1


title: UPN10 posttreatment_geneexpression

value: CD3+ T cells

tag: age

tag: diagnosis


title: inflamed gut sample S30 from patient M

description:
16S V3-V4 sequencing of a FFPE specimen from an inflamed gut portion of patient 2 affected by Crohn's disease
S30

tag: tissue source


title: HC80T

description: Large intestine


title: HC93T

description: Large intestine


title: inflamed gut sample S28 from patient M

description:
16S V3-V4 sequencing of a FFPE specimen from an inflamed gut portion of patient 1 affected by Crohn's disease
S28


title: UPN24 posttreatment_geneexpression

value: T-LGLL

tag: subject


title: inflamed gut sample S35 from patient M

description:
16S V3-V4 sequencing of a FFPE specimen from an inflamed gut portion of patient 5 affected by Crohn's disease
S35

tag: patient diagnosis


title: Dnmt1+/+ MDP rep2

tag: genotype


title: UPN10 pretreatment_geneexpression


title: Dnmt1+/+ MDP rep1


title: HC74T

description: Large intestine


title: UPN24 pretreatment_geneexpression


title: non inflamed sample S17 from patient M

description:
16S V3-V4 sequencing of a FFPE specimen from a healthy gut portion of patient 10 affected by Crohn's disease
S17

tag: disease state

value: notInflamed


title: HC67T

description: Large intestine


title: HC73T

description: Large intestine


title: PT9

data_processing:
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting,and csv files of TCR clonality were performed using the Cell Ranger analysis pipeline.
Paired-end reads were mapped to the hg19 genome with cellranger for gene-level read counts
T cell receptor VDJ analysis: CellRanger
VDJ of Tcells were analyzed with cellranger vdj pipeline to get TCR contig annotations
Genome_build: hg19

extract_protocol: Cells were loaded into the 10XChromium Controller using the 10X Chromium Single Cell V(D)J kits (5' gene expression with paired T cellreceptor sequencing)

tag: markers

value: Male

value: 24 years


title: PT10

value: 8 years


title: Dnmt1c/chip cMoP rep4

label: Biotin

source_name: cMoPs flow-sorted from the bone marrow of Dnmt1c/chip mice

value: cMoPs


title: non inflamed sample S15 from patient F

description:
16S V3-V4 sequencing of a FFPE specimen from a healthy gut portion of patient 8 affected by Crohn's disease
S15

value: ileal mucosa

value: relapse


title: Dnmt1c/chip cMoP rep3


title: Dnmt1c/chip cMoP rep2


title: HC40T

description: Large intestine


title: Dnmt1c/chip cMoP rep1


title: non inflamed sample S13 from patient F

description:
16S V3-V4 sequencing of a FFPE specimen from a healthy gut portion of patient 6 affected by Crohn's disease
S13


title: PT7

value: 55 years


title: PT8

value: 57 years


title: Dnmt1+/+ c/chip cMoP rep3

source_name: cMoPs flow-sorted from the bone marrow of Dnmt1+/+ mice


title: HC28T

description: Large intestine


title: Dnmt1+/+ c/chip cMoP rep4


title: non inflamed sample S16 from patient F

description:
16S V3-V4 sequencing of a FFPE specimen from a healthy gut portion of patient 9 affected by Crohn's disease
S16

value: Crohn's disease


title: non inflamed sample S12 from patient M

description:
16S V3-V4 sequencing of a FFPE specimen from a healthy gut portion of patient 5 affected by Crohn's disease
S12

value: M


title: non inflamed sample S10 from patient F

description:
16S V3-V4 sequencing of a FFPE specimen from a healthy gut portion of patient 3 affected by Crohn's disease
S10

value: first


title: non inflamed sample S11 from patient M

description:
16S V3-V4 sequencing of a FFPE specimen from a healthy gut portion of patient 4 affected by Crohn's disease
S11


title: RBM24-/--CMs rep2

city: Miaoli County

first: Paul

middle: Wei-Che

last: Hsu

state: Taiwan

address: Zhunan: 35, Keyan Road, Zhunan Town

department: National Health Research Institutes

country: Taiwan

institute: National Health Research Institutes

data_processing:
On-instrument base-calling with Illumina HiSeq 2500 BclToFastq v2.18.
Adaptor sequences were removed from raw sequences, and the quality of reads was examined by FastQC software. Low-quality regions were trimmed (Phred quality score of <20).
Using STAR to map sequenced reads to whole genome, with additional parameters: --chimSegmentMin 2 --outFilterMismatchNmax 3 --alignEndsType EndToEnd  --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --alignSJDBoverhangMin 6 --alignIntronMax 300000
Splicing event classification was performed using rMATS v4.0.2
Gene expression level of read counts and TPM were calculated using CLC Genomics Workbench 21.
Genome_build: GRCh38/hg38, GRCm39/mm39
Supplementary_files_format_and_content: Excel xlsx files of rMATs alternative splicing results
Supplementary_files_format_and_content: tab-delimited text files include  read counts and TPM for each Sample

source_name: hESCs-CM

extract_protocol:
Total RNA was extracted using a RNeasy Mini Kit (Qiagen, 74106). RNA quality and quantifications were inspected using an Agilent 2100 Bioanalyzer.
The mRNA sequencing libraries were prepared using a Truseq Stranded mRNA kit (Illumina), and 2x150 bp paired-read sequencing was performed using an Illumina HiSeq instrument

tag: cell line

value: MYH6:mCherry hESCs

value: hESCs-CM


title: PT6

value: Female

value: 25 years


title: PT5

value: 21 years


title: RBM24-/--CMs rep1


title: HC21T

description: Large intestine

value: CRC patient-derived spheroids

value: Untreated


title: non inflamed sample S07 from patient M

description:
16S V3-V4 sequencing of a FFPE specimen from a healthy gut portion of patient 2 affected by Crohn's disease
S07

value: notInflamed


title: HC20T

description: Large intestine


title: HC22T

description: Large intestine


title: non inflamed sample S14 from patient M

description:
16S V3-V4 sequencing of a FFPE specimen from a healthy gut portion of patient 7 affected by Crohn's disease
S14


title: WT-CMs rep1

value: wild type


title: Dnmt1+/+ c/chip cMoP rep1

value: cMoPs


title: Dnmt1+/+ c/chip cMoP rep2


title: WT-CMs rep2


title: PT3

value: 16 years


title: HC16T

description: Large intestine


title: HC11T

description: Large intestine


title: PT2

value: 30 years


title: PT4

value: 36 years


title: non inflamed sample S05 from patient M

description:
16S V3-V4 sequencing of a FFPE specimen from a healthy gut portion of patient 1 affected by Crohn's disease
S05

value: ileal mucosa

value: relapse


title: A6WD4

city: Beijing

first: Hui

last: Wang

address: No. 17 Tsing Hua East Road, HaiDian District

country: China

institute: China Agricultural University

data_processing:
Illumina Casava 1.8 for base-calling and Phred score calculation
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning  clean reads to reference genome were used Bowtie2-2.2.3.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing  reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content sequence of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Genome_build: Bowtie2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Bifidobacterium animalis

source_name: probiotics isolated from human feces

extract_protocol:
For RNA extraction, total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA) and purified using the TURBO DNA-free Kit (Ambion, Austin, TX, USA) according to the manufacturer’s instructions.
Sequencing libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

tag: growth

value: growth in MRSc medium at the stationary phase

tag: source

value: feces

tag: strain

value: Bifidobacterium animalis subsp. lactis A6


title: odo1i-4

city: West Lafayette

first: Ryan

last: Patrick

state: Indiana

address: 625 Agriculture Mall Dr

institute: Purdue University

description: Petunia ODO1 ChIP-seq and RNA-seq

data_processing:
RNA-Seq reads were trimmed with cutadapt, aligned using TopHat2, counts within genes were determined using HTSeq, and differentially expressed genes were determined using DESeq2.
ChIP-Seq reads were trimmed with cutadapt, aligned using Bowtie2, and peaks were called using MACS2.
Genome_build: Petunia axillaris draft genome sequence v1.6.2

molecule: polyA RNA

organism: Petunia x hybrida

source_name: corrola

extract_protocol: Extracted total RNA from corolla was used for oligoDT library construction. (RNA-Seq)

value: corolla


title: A6WD3


title: HC10T

description: Large intestine


title: PT1

value: Male

value: 22 years


title: HD5

value: Female

value: 38 years


title: A6WD2


title: odo1i-2

description: Petunia ODO1 ChIP-seq and RNA-seq


title: A6log4

value: growth in MRSc medium at the log phase


title: phwt4

description: Petunia ODO1 ChIP-seq and RNA-seq


title: HC7T

description: Large intestine

value: CRC patient-derived spheroids

value: Untreated


title: odo1i-1

description: Petunia ODO1 ChIP-seq and RNA-seq


title: HC8T

description: Large intestine


title: A6log3


title: HD3


title: HD4

value: 37 years


title: HC6T

description: Large intestine


title: HD2

value: 26 years


title: HD1

value: 23 years


title: phwt2

description: Petunia ODO1 ChIP-seq and RNA-seq


title: A6log2


title: HC1T

description: Large intestine


title: A6log1


title: hdp1-Ty1-anti-GFP_rep2

status: Public on Nov 21 2021

city: New York

first: Bjorn

middle: FC

last: Kafsack

state: NY

address: 1300 York Avenue

department: Microbiology & Immunology

institute: Weill Cornell Medicine

data_processing:
Reads in sequenced libraries were checked for quality with FASTQC v0.11.9, adapter and quality-trimmed with trimmomatic v0.39
Properly paired reads were aligned against P.falciparum 3D7 genome v51 with bwa v.0.7.17 and sorted by name using samtools v1.13
Differential genome-wide enrichment between HDP1-GFP and HDP1-TY1 samples was calculated using macs2 v2.2.7.1 to generate poisson-based FDR and fold-enrichment tracks and significant peaks
Peak annotation and visualization were carried out in R using GenomicRanges v1.44.0, Gviz v1.36.1, and ChIPpeakAnno v3.26.2 packages from Bioconductor using P.falciparum 3D7 genome annotation v51 from PlasmoDB
Motif enrichment for 100bp centered on HDP1-GFP ChIP-Seq summits was carried out using the HOMER2 v4.11 findMotifsGenome function
Genome_build: Plasmodium falciparum 3D7 v51 from PlasmoDB
Supplementary_files_format_and_content: called peaks based on enrichement fdr of <0.001 and 2x FC
Supplementary_files_format_and_content: bedgraph of fold change
Supplementary_files_format_and_content: bedgraph graph of enrichment fdr

organism: Plasmodium falciparum

source_name: day 5 gametocytes

growth_protocol: Gametocytes were induced synchronously, and on first day of gametocyte development (D+1), ring stage parasites were treated with 50mM N-acetyl-D-glucosamine for three consecutive days to kill asexuals. Gametocytes were harvested on day 5 of development.

extract_protocol:
Nuclei were isolated from crosslinked parasite lysates, and later clarified after sonication. HDP1-GFP/DNA complexes were pulled down with specific anti-GFP antibodies
Libraries were prepared according to Illumina's instructions accompanying the KAPA library preparation kit (KK8230) and sequenced on a NovaSeq 6000 machine

tag: chip antibody

value: anti-GFP (abcam ab920)

value: day 5 gametocytes


title: hdp1-gfp-anti-GFP_rep2

tag: tissue


title: phwt1

description: Petunia ODO1 ChIP-seq and RNA-seq


title: hdp1-gfp-anti-GFP_rep1


title: HC9T

description: Large intestine

tag: treatment


title: hdp1-Ty1-anti-GFP_rep1


title: POLRMT_IgG_rep4

city: Nagoya

first: Kenji

last: Ichiyanagi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

data_processing:
Adaptor sequences and low qaulity sequences were remove by Trim Galore with options (-a AGATCGGAAGAGCACA -a2 AGATCGGAAGAGCG).
Sequences were mapped on the human genome (GRCh38) by bowtie2.
After de-duplication, the read coverage was calculated using sam outputs.
Genome_build: GRCh38 (to efficiently map the reads to NCR, the first 10,000 nucleotides in the original chrM sequence was moved (cut-and-pasete) to the end of the original sequence. In the read coverage files, the obtained results have been re-converted to the coordinates of the original chrM sequence.)

source_name: HeLa cybrid

growth_protocol: Cells were cultured in medium that consists of DMEM containing 25 mM glucose and 1 mM sodium pyruvate, 37 µg/mL uridine, 18.5 mM HEPES buffer, 23% (v/v) FBS, and penicillin-streptomycin.

extract_protocol:
Samples were homogenized using a Teflon homogenizer in H buffer [225 mM mannitol, 75 mM sucrose, 10 mM Hepes-NaOH (pH 7.8), 2 mM EDTA (pH 8); pH was adjusted to 7.6 with HCl; 2-mercaptoethanol was added prior to use]. Homogenates were centrifuged two times at 900 g for 10 min to remove nuclei and undisrupted cells. The supernatants were then centrifuged at 12,000 g for 10 min and pellets were resuspended in H buffer and centrifuged again. The obtained pellets were resuspended in H buffer, and formaldehyde was added to the suspension to a final concentration of 1%, and the solution was incubated for 15 min at r.t. The cross-linking reaction was quenched by adding glycine solution at a final concentration of 125 mM to the reaction mixture, followed by incubation for 5 min. Mitochondria were then collected by centrifugation at 12,000 g for 5 min. The pellets were resuspended in ice-cold H buffer and centrifuged at 12,000 g for 5 min.  mitochondria were lysed with IP buffer [150 mM KCl, 25 mM Hepes-KOH (pH 7.8), 5 mM MgCl2, 0.5 mM EDTA, 10% glycerol, 0.5% Tween-20, and a proteinase inhibitor cocktail] and were sonicated using Bioruptor UCW-310. The resulting solution was centrifuged at 14,000 g for 5 min.  Supernatants were incubated with polyclonal rabbit antibodies against either TFB2M or POLRMT, and control normal rabbit IgG for overnight.  Subsequently, Protein G-magnetic beads were added to the mixtures and they were incubated for 1.5 h. After washing the beads with IP buffer three times, elution was performed by adding elution buffer [0.1M glycine-HCl (pH 2.5)] to the beads.
Immunoprecipitation samples were reverse-crosslinked by incubating at 65 degree for 16 h, followed by proteinase K treatment. DNA was prepared by phenol-chloroform extraction and ethanol precipitation, and used for library construction using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs).
Sequncing was run on MiSeq in the 150-bp paired-end mode.

tag: genotype/variation

value: HeLa cells lacking mtDNA fused with cytoplasm containing mitochondria with wild-type mtDNA

value: control IgG


title: POLRMT_input_rep4


title: bone marrow-derived MSC transfected with GFP control vector 3

city: Lund

first: Hongzhe

last: Li

address: Klinikgatan 26

department: Lund Stem Cell Center

country: Sweden

institute: Lund University

scan_protocol: Standard Illumina iScan N240 scanning protocol Direct Hyb

data_processing: The data were normalised using quantile normalisation with BASE

source_name: human bone marrow

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevD, (Modification of Amplification kit v 2.2)

extract_protocol: Illumina protocol

tag: transfection

value: GFP control vector

value: bone marrow


title: bone marrow-derived MSC transfected with short hairpin RNA against EGR1 4

value: short hairpin RNA against EGR1


title: POLRMT_input_rep2


title: POLRMT_rep4

value: anti-POLRMT (GTX105137)


title: bone marrow-derived MSC transfected with short hairpin RNA against EGR1 1


title: POLRMT_IgG_rep2


title: POLRMT_rep3


title: bone marrow-derived MSC transfected with scramble control vector 2

value: scramble control vector


title: POLRMT_IgG_rep3


title: bone marrow-derived MSC transfected with lentiviral vector carrying EGR1-GFP 1

value: lentiviral vector carrying EGR1-GFP


title: POLRMT_input_rep3


title: POLRMT_input_rep1


title: bone marrow-derived MSC transfected with lentiviral vector carrying EGR1-GFP 3


title: POLRMT_rep2


title: bone marrow-derived MSC transfected with GFP control vector 4


title: bone marrow-derived MSC transfected with lentiviral vector carrying EGR1-GFP 4


title: non-transfected bone marrow-derived MSC 3

value: non-transfected


title: bone marrow-derived MSC transfected with scramble control vector 3


title: bone marrow-derived MSC transfected with GFP control vector 1


title: non-transfected bone marrow-derived MSC 4


title: POLRMT_IgG_rep1


title: bone marrow-derived MSC transfected with lentiviral vector carrying EGR1-GFP 2


title: bone marrow-derived MSC transfected with GFP control vector 2


title: bone marrow-derived MSC transfected with scramble control vector 4


title: POLRMT_rep1


title: bone marrow-derived MSC transfected with scramble control vector 1


title: bone marrow-derived MSC transfected with short hairpin RNA against EGR1 2


title: non-transfected bone marrow-derived MSC 1


title: non-transfected bone marrow-derived MSC 2


title: bone marrow-derived MSC transfected with short hairpin RNA against EGR1 3


title: FTB2M_input_rep2


title: FTB2M_rep2

value: anti-TFB2M (AP10145b)


title: FTB2M_IgG_rep3


title: FTB2M_rep3


title: FTB2M_IgG_rep2


title: FTB2M_input_rep3


title: 304L-spleen-03

city: Hefei

first: Cheng

last: Sun

state: Anhui

address: 17, Lujiang Road

department: the First Affiliated Hospital of USTC

institute: University of Science and Technology of China

description:
Pt16-03-spleen
raw data file: Pt16-spleen.txt

scan_protocol: After staining, the tissues were scanned using a GeoMx DSP instrument to generate digital fluorescent images and to select for individual ROIs inside a geometric section. To carry out high-resolution multiplex profiling, each ROI was assigned to CD3+ T-cell-rich or CD68+ macrophage-rich regions.

data_processing: Q3 Normalization – Individual counts were normalized against the 75th percentile of the signal from their own ROI.

label: CD3E mouse monoclonal antibody

source_name: spleen

label_protocol: Following deparaffinization and antigen retrieval procedures, sections were simultaneously incubated overnight with fluorescent-labelled antibodies against CD3 (Origene), CD68 (Santa Cruz) and Pan-Cytokeratin (Novus Biologicals), smooth muscle actin (Invitrogen), or cytokeratin 8/18 (Novus Biologicals) to visualize morphological features in the regions of interest (ROI).

growth_protocol: NanoString spatial profiling was used for DSP analysis of three protein-level and 1,800 transcriptomic-level immune-markers simultaneously on FFPE tissue slides.Autopsy FFPE slides were baked in oven at 60 °C for at least 1 h, and then rehydrated and blocked by Nanostring block buffer for 1 h.

extract_protocol: UV light was directed through a programmable digital micro mirror device (DMD) or dual DMD (DDMD) to accurately illumine the ROI and cleave PC oligos from the selected region, which were collected by microcapillary tube inspiration and dispensed into a 96-well plate. Inside the microplate, the single-molecule counting nCounter System enabled the digital counting of released oligos

tag: individual

value: Patient 16

tag: infection

tag: Sex

value: Female

tag: age

value: 66 years

tag: status

value: Death

value: spleen

tag: section

value: CD3 Rich


title: 304L-spleen-06

description:
Pt16-06-spleen
raw data file: Pt16-spleen.txt

hyb_protocol: Autopsy FFPE slides were baked in oven at 60 °C for at least 1 h, and then rehydrated and blocked by Nanostring block buffer for 1 h.

label: CD68 Antibody (KP1)

value: CD68 Rich


title: 304L-spleen-04

description:
Pt16-04-spleen
raw data file: Pt16-spleen.txt


title: 304L-spleen-05

description:
Pt16-05-spleen
raw data file: Pt16-spleen.txt


title: 304L-spleen-08

description:
Pt16-08-spleen
raw data file: Pt16-spleen.txt


title: 304L-spleen-07

description:
Pt16-07-spleen
raw data file: Pt16-spleen.txt


title: 304L-spleen-01

description:
Pt16-01-spleen
raw data file: Pt16-spleen.txt


title: 229D-spleen-12

description:
Pt6-12-spleen
raw data file: Pt6-spleen.txt

value: Patient 6

value: Male

value: 88 years


title: 304L-spleen-02

description:
Pt16-02-spleen
raw data file: Pt16-spleen.txt


title: 229D-spleen-10

description:
Pt6-10-spleen
raw data file: Pt6-spleen.txt


title: 229D-spleen-09

description:
Pt6-09-spleen
raw data file: Pt6-spleen.txt


title: FTB2M_input_rep1

value: HeLa cells lacking mtDNA fused with cytoplasm containing mitochondria with wild-type mtDNA


title: FTB2M_rep1


title: FTB2M_IgG_rep1

value: control IgG


title: 229D-spleen-08

description:
Pt6-08-spleen
raw data file: Pt6-spleen.txt


title: 229D-spleen-06

description:
Pt6-06-spleen
raw data file: Pt6-spleen.txt


title: 229D-spleen-04

description:
Pt6-04-spleen
raw data file: Pt6-spleen.txt


title: 229D-spleen-05

description:
Pt6-05-spleen
raw data file: Pt6-spleen.txt


title: 229D-spleen-07

description:
Pt6-07-spleen
raw data file: Pt6-spleen.txt


title: 229D-spleen-03

description:
Pt6-03-spleen
raw data file: Pt6-spleen.txt


title: 229D-spleen-02

description:
Pt6-02-spleen
raw data file: Pt6-spleen.txt


title: 229D-spleen-11

description:
Pt6-11-spleen
raw data file: Pt6-spleen.txt


title: 229D-spleen-01

description:
Pt6-01-spleen
raw data file: Pt6-spleen.txt


title: 306Z-spleen-12

description:
Pt2-12-spleen
raw data file: Pt2-spleen.txt

value: Patient 2

value: 87 years


title: 306Z-spleen-09

description:
Pt2-09-spleen
raw data file: Pt2-spleen.txt


title: 306Z-spleen-10

description:
Pt2-10-spleen
raw data file: Pt2-spleen.txt


title: 306Z-spleen-06

description:
Pt2-06-spleen
raw data file: Pt2-spleen.txt


title: 306Z-spleen-04

description:
Pt2-04-spleen
raw data file: Pt2-spleen.txt


title: 306Z-spleen-11

description:
Pt2-11-spleen
raw data file: Pt2-spleen.txt


title: 306L-spleen-04

description:
Pt1-04-spleen
raw data file: Pt1-spleen.txt

value: Patient 1

value: 64 years


title: 306L-spleen-03

description:
Pt1-03-spleen
raw data file: Pt1-spleen.txt


title: 306L-spleen-06

description:
Pt1-06-spleen
raw data file: Pt1-spleen.txt


title: 306L-spleen-05

description:
Pt1-05-spleen
raw data file: Pt1-spleen.txt


title: 306L-spleen-01

description:
Pt1-01-spleen
raw data file: Pt1-spleen.txt


title: 226F-heart-07

description:
Pt5-07-heart
raw data file: Pt5-heart.txt

source_name: heart

value: Patient 5

value: 73 years

value: heart


title: 306Z-spleen-08

description:
Pt2-08-spleen
raw data file: Pt2-spleen.txt


title: 226F-heart-04

description:
Pt5-04-heart
raw data file: Pt5-heart.txt

value: Female


title: 226F-heart-08

description:
Pt5-08-heart
raw data file: Pt5-heart.txt

value: Death


title: 226F-heart-02

description:
Pt5-02-heart
raw data file: Pt5-heart.txt


title: 226F-heart-03

description:
Pt5-03-heart
raw data file: Pt5-heart.txt


title: 226F-heart-05

description:
Pt5-05-heart
raw data file: Pt5-heart.txt


title: 306Z-spleen-07

description:
Pt2-07-spleen
raw data file: Pt2-spleen.txt

value: spleen


title: 306Z-spleen-01

description:
Pt2-01-spleen
raw data file: Pt2-spleen.txt

value: CD3 Rich


title: 306Z-spleen-05

description:
Pt2-05-spleen
raw data file: Pt2-spleen.txt


title: 306Z-spleen-02

description:
Pt2-02-spleen
raw data file: Pt2-spleen.txt


title: 219X-heart-07

description:
Pt4-07-heart
raw data file: Pt4-heart.txt

value: Patient 4

value: 62 years

value: CD68 Rich


title: 219X-heart-05

description:
Pt4-05-heart
raw data file: Pt4-heart.txt

value: Male


title: 306L-spleen-02

description:
Pt1-02-spleen
raw data file: Pt1-spleen.txt


title: 219X-heart-06

description:
Pt4-06-heart
raw data file: Pt4-heart.txt


title: 219X-heart-03

description:
Pt4-03-heart
raw data file: Pt4-heart.txt


title: 306Z-spleen-03

description:
Pt2-03-spleen
raw data file: Pt2-spleen.txt


title: 306L-spleen-07

description:
Pt1-07-spleen
raw data file: Pt1-spleen.txt


title: 219X-heart-01

description:
Pt4-01-heart
raw data file: Pt4-heart.txt


title: 219X-heart-02

description:
Pt4-02-heart
raw data file: Pt4-heart.txt


title: 226F-heart-06

description:
Pt5-06-heart
raw data file: Pt5-heart.txt


title: 304L-kidney-12

description:
Pt16-12-kidney
raw data file: Pt16-kidney.txt

source_name: kidney

value: Patient 16

value: 66 years

value: kidney


title: 304L-kidney-11

description:
Pt16-11-kidney
raw data file: Pt16-kidney.txt


title: 304L-kidney-08

description:
Pt16-08-kidney
raw data file: Pt16-kidney.txt


title: 304L-kidney-10

description:
Pt16-10-kidney
raw data file: Pt16-kidney.txt


title: 304L-kidney-07

description:
Pt16-07-kidney
raw data file: Pt16-kidney.txt


title: 304L-kidney-06

description:
Pt16-06-kidney
raw data file: Pt16-kidney.txt


title: 304L-kidney-05

description:
Pt16-05-kidney
raw data file: Pt16-kidney.txt


title: 219X-heart-04

description:
Pt4-04-heart
raw data file: Pt4-heart.txt


title: 304L-kidney-01

description:
Pt16-01-kidney
raw data file: Pt16-kidney.txt


title: 304L-kidney-03

description:
Pt16-03-kidney
raw data file: Pt16-kidney.txt


title: 229D-kidney-08

description:
Pt6-08-kidney
raw data file: Pt6-kidney.txt

value: Patient 6

value: 88 years


title: 229D-kidney-05

description:
Pt6-05-kidney
raw data file: Pt6-kidney.txt


title: 229D-kidney-06

description:
Pt6-06-kidney
raw data file: Pt6-kidney.txt


title: 229D-kidney-07

description:
Pt6-07-kidney
raw data file: Pt6-kidney.txt


title: 229D-kidney-03

description:
Pt6-03-kidney
raw data file: Pt6-kidney.txt


title: 226F-kidney-08

description:
Pt5-08-kidney
raw data file: Pt5-kidney.txt


title: 229D-kidney-02

description:
Pt6-02-kidney
raw data file: Pt6-kidney.txt


title: 226F-kidney-07

description:
Pt5-07-kidney
raw data file: Pt5-kidney.txt


title: 229D-kidney-01

description:
Pt6-01-kidney
raw data file: Pt6-kidney.txt


title: 229D-kidney-04

description:
Pt6-04-kidney
raw data file: Pt6-kidney.txt


title: 304L-kidney-09

description:
Pt16-09-kidney
raw data file: Pt16-kidney.txt


title: 226F-kidney-06

description:
Pt5-06-kidney
raw data file: Pt5-kidney.txt


title: 226F-kidney-05

description:
Pt5-05-kidney
raw data file: Pt5-kidney.txt


title: 226F-kidney-04

description:
Pt5-04-kidney
raw data file: Pt5-kidney.txt


title: 226F-kidney-03

description:
Pt5-03-kidney
raw data file: Pt5-kidney.txt


title: 304L-kidney-04

description:
Pt16-04-kidney
raw data file: Pt16-kidney.txt


title: 226F-kidney-02

description:
Pt5-02-kidney
raw data file: Pt5-kidney.txt


title: 304L-kidney-02

description:
Pt16-02-kidney
raw data file: Pt16-kidney.txt


title: 226F-kidney-01

description:
Pt5-01-kidney
raw data file: Pt5-kidney.txt


title: 306Z-kidney-12

description:
Pt2-12-kidney
raw data file: Pt2-kidney.txt

value: Patient 2

value: 87 years


title: 306Z-kidney-09

description:
Pt2-09-kidney
raw data file: Pt2-kidney.txt


title: 306Z-kidney-10

description:
Pt2-10-kidney
raw data file: Pt2-kidney.txt


title: 306Z-kidney-11

description:
Pt2-11-kidney
raw data file: Pt2-kidney.txt


title: 306Z-kidney-08

description:
Pt2-08-kidney
raw data file: Pt2-kidney.txt


title: 226F-heart-01

description:
Pt5-01-heart
raw data file: Pt5-heart.txt

value: Patient 5

value: 73 years


title: 306Z-kidney-07

description:
Pt2-07-kidney
raw data file: Pt2-kidney.txt


title: 306Z-kidney-06

description:
Pt2-06-kidney
raw data file: Pt2-kidney.txt


title: 306L-spleen-08

description:
Pt1-08-spleen
raw data file: Pt1-spleen.txt

value: Patient 1

value: 64 years


title: 306Z-kidney-05

description:
Pt2-05-kidney
raw data file: Pt2-kidney.txt

value: Death


title: 306Z-kidney-03

description:
Pt2-03-kidney
raw data file: Pt2-kidney.txt

value: CD3 Rich


title: 306Z-kidney-02

description:
Pt2-02-kidney
raw data file: Pt2-kidney.txt


title: 306Z-kidney-04

description:
Pt2-04-kidney
raw data file: Pt2-kidney.txt


title: 306Z-kidney-01

description:
Pt2-01-kidney
raw data file: Pt2-kidney.txt


title: 229D-liver-08

description:
Pt6-08-liver
raw data file: Pt6-liver.txt

source_name: liver

value: liver


title: 229D-liver-07

description:
Pt6-07-liver
raw data file: Pt6-liver.txt


title: 229D-liver-05

description:
Pt6-05-liver
raw data file: Pt6-liver.txt


title: 229D-liver-04

description:
Pt6-04-liver
raw data file: Pt6-liver.txt


title: 229D-liver-06

description:
Pt6-06-liver
raw data file: Pt6-liver.txt


title: 229D-liver-03

description:
Pt6-03-liver
raw data file: Pt6-liver.txt


title: 229D-liver-02

description:
Pt6-02-liver
raw data file: Pt6-liver.txt


title: 229D-liver-01

description:
Pt6-01-liver
raw data file: Pt6-liver.txt


title: 226F-liver-08

description:
Pt5-08-liver
raw data file: Pt5-liver.txt

value: Female


title: 226F-liver-04

description:
Pt5-04-liver
raw data file: Pt5-liver.txt


title: 226F-liver-07

description:
Pt5-07-liver
raw data file: Pt5-liver.txt


title: 226F-liver-05

description:
Pt5-05-liver
raw data file: Pt5-liver.txt

value: CD68 Rich


title: 226F-liver-06

description:
Pt5-06-liver
raw data file: Pt5-liver.txt


title: 219X-liver-12

description:
Pt4-12-liver
raw data file: Pt4-liver.txt

value: Patient 4

value: Male

value: 62 years


title: 226F-liver-03

description:
Pt5-03-liver
raw data file: Pt5-liver.txt


title: 226F-liver-02

description:
Pt5-02-liver
raw data file: Pt5-liver.txt


title: 226F-liver-01

description:
Pt5-01-liver
raw data file: Pt5-liver.txt


title: 219X-liver-11

description:
Pt4-11-liver
raw data file: Pt4-liver.txt


title: 219X-liver-08

description:
Pt4-08-liver
raw data file: Pt4-liver.txt


title: 219X-liver-09

description:
Pt4-09-liver
raw data file: Pt4-liver.txt


title: 219X-liver-07

description:
Pt4-07-liver
raw data file: Pt4-liver.txt


title: 219X-liver-06

description:
Pt4-06-liver
raw data file: Pt4-liver.txt


title: 219X-liver-04

description:
Pt4-04-liver
raw data file: Pt4-liver.txt


title: 219X-liver-05

description:
Pt4-05-liver
raw data file: Pt4-liver.txt


title: 306L-liver-12

description:
Pt1-12-liver
raw data file: Pt1-liver.txt


title: 219X-liver-03

description:
Pt4-03-liver
raw data file: Pt4-liver.txt


title: 219X-liver-02

description:
Pt4-02-liver
raw data file: Pt4-liver.txt


title: 306L-liver-10

description:
Pt1-10-liver
raw data file: Pt1-liver.txt


title: 306L-liver-09

description:
Pt1-09-liver
raw data file: Pt1-liver.txt


title: 219X-liver-01

description:
Pt4-01-liver
raw data file: Pt4-liver.txt


title: 219X-liver-10

description:
Pt4-10-liver
raw data file: Pt4-liver.txt


title: 306L-liver-03

description:
Pt1-03-liver
raw data file: Pt1-liver.txt


title: 306L-liver-08

description:
Pt1-08-liver
raw data file: Pt1-liver.txt


title: 306L-liver-05

description:
Pt1-05-liver
raw data file: Pt1-liver.txt


title: 306L-liver-06

description:
Pt1-06-liver
raw data file: Pt1-liver.txt


title: 306L-liver-02

description:
Pt1-02-liver
raw data file: Pt1-liver.txt


title: 312G-lung-08

description:
Pt7-08-lung
raw data file: Pt7-lung.txt

source_name: lung

value: Patient 7

value: 76 years

value: lung


title: 312G-lung-05

description:
Pt7-05-lung
raw data file: Pt7-lung.txt


title: 312G-lung-09

description:
Pt7-09-lung
raw data file: Pt7-lung.txt


title: 312G-lung-06

description:
Pt7-06-lung
raw data file: Pt7-lung.txt


title: 312G-lung-04

description:
Pt7-04-lung
raw data file: Pt7-lung.txt


title: 312G-lung-07

description:
Pt7-07-lung
raw data file: Pt7-lung.txt


title: 306L-liver-11

description:
Pt1-11-liver
raw data file: Pt1-liver.txt


title: 306L-liver-07

description:
Pt1-07-liver
raw data file: Pt1-liver.txt


title: 229D-lung-07

description:
Pt6-07-lung
raw data file: Pt6-lung.txt

value: Patient 6

value: 88 years


title: 229D-lung-06

description:
Pt6-06-lung
raw data file: Pt6-lung.txt


title: 229D-lung-08

description:
Pt6-08-lung
raw data file: Pt6-lung.txt


title: 229D-lung-01

description:
Pt6-01-lung
raw data file: Pt6-lung.txt


title: 229D-lung-05

description:
Pt6-05-lung
raw data file: Pt6-lung.txt


title: 312G-lung-02

description:
Pt7-02-lung
raw data file: Pt7-lung.txt


title: 312G-lung-01

description:
Pt7-01-lung
raw data file: Pt7-lung.txt


title: 229D-lung-02

description:
Pt6-02-lung
raw data file: Pt6-lung.txt


title: 229D-lung-04

description:
Pt6-04-lung
raw data file: Pt6-lung.txt


title: 229D-lung-03

description:
Pt6-03-lung
raw data file: Pt6-lung.txt


title: 226F-lung-05

description:
Pt5-05-lung
raw data file: Pt5-lung.txt

value: Patient 5


title: 226F-lung-02

description:
Pt5-02-lung
raw data file: Pt5-lung.txt

value: 73 years


title: 219X-lung-11

description:
Pt4-11-lung
raw data file: Pt4-lung.txt


title: 226F-lung-01

description:
Pt5-01-lung
raw data file: Pt5-lung.txt


title: 226F-lung-03

description:
Pt5-03-lung
raw data file: Pt5-lung.txt


title: 306L-liver-04

description:
Pt1-04-liver
raw data file: Pt1-liver.txt

value: Patient 1


title: 312G-lung-10

description:
Pt7-10-lung
raw data file: Pt7-lung.txt


title: 219X-lung-10

description:
Pt4-10-lung
raw data file: Pt4-lung.txt


title: 219X-lung-05

description:
Pt4-05-lung
raw data file: Pt4-lung.txt


title: 219X-lung-07

description:
Pt4-07-lung
raw data file: Pt4-lung.txt


title: 219X-lung-06

description:
Pt4-06-lung
raw data file: Pt4-lung.txt


title: 219X-lung-02

description:
Pt4-02-lung
raw data file: Pt4-lung.txt


title: 219X-lung-09

description:
Pt4-09-lung
raw data file: Pt4-lung.txt


title: 219X-lung-03

description:
Pt4-03-lung
raw data file: Pt4-lung.txt


title: DIPG13_siRNA_DNMT3A_3B_RNAseq_rep4

city: Washington

first: Jia-Ray

last: Yu

state: DC

address: 7144 13th Pl Nw

institute: FBRI at Virginia Tech Carilion

description: siRNA targeting DNMT3A and DNMT3B

data_processing:
Sequnecing files are mapped to genome hg38 downloaded from ucsc genome database, using Bowtie2/STAR for ChIP-seq and RNA-seq samples respectively. Bedtools was used for creating big wiggle tracks of ChIP-seq data. RSEM and DESeq2 were used for gene expression quantification and differential expression analysis on RNA-seq data.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig, gene expression quantification

source_name: Pediatric glioma cells

extract_protocol: RNA was isolated using RNeasy mini spin columns (Qiagen) according to the manufacturer’s instruction. Total RNA (1 to 5 μg) was then processed by oligo(dT) selection and library preparation using the Automated KAPA Library Prep Kit.

value: glioma


title: 219X-lung-01

description:
Pt4-01-lung
raw data file: Pt4-lung.txt

value: Death


title: DIPG13_siRNA_DNMT3A_3B_RNAseq_rep3

description: siRNA targeting DNMT3A and DNMT3B


title: DIPG13_siRNA_control_RNAseq_rep3

description: siRNA controls


title: DIPG13_siRNA_control_RNAseq_rep4

description: siRNA controls


title: 306S-lung-05

description:
Pt3-05-lung
raw data file: Pt3-lung.txt

value: Patient 3

value: 57 years

value: CD3 Rich


title: 306S-lung-07

description:
Pt3-07-lung
raw data file: Pt3-lung.txt

value: Female


title: 306S-lung-08

description:
Pt3-08-lung
raw data file: Pt3-lung.txt

value: CD68 Rich


title: DIPG13_siRNA_DNMT3A_3B_RNAseq_rep2

description: siRNA targeting DNMT3A and DNMT3B


title: 306S-lung-06

description:
Pt3-06-lung
raw data file: Pt3-lung.txt


title: 306S-lung-04

description:
Pt3-04-lung
raw data file: Pt3-lung.txt


title: 219X-lung-08

description:
Pt4-08-lung
raw data file: Pt4-lung.txt

value: Patient 4

value: Male


title: DIPG13_siRNA_control_RNAseq_rep2

description: siRNA controls


title: 306S-lung-03

description:
Pt3-03-lung
raw data file: Pt3-lung.txt


title: DIPG13_siRNA_control_RNAseq_rep1

description: siRNA controls


title: 306S-lung-02

description:
Pt3-02-lung
raw data file: Pt3-lung.txt


title: 306S-lung-01

description:
Pt3-01-lung
raw data file: Pt3-lung.txt


title: 219X-lung-04

description:
Pt4-04-lung
raw data file: Pt4-lung.txt

value: 62 years


title: DIPG13_siRNA_DNMT3A_3B_RNAseq_rep1

description: siRNA targeting DNMT3A and DNMT3B


title: DIPG13_N2KO7_HDGF2_ChIP

description: NSD2 knockout clone #7

extract_protocol: Cells were lysed in ChIP buffer (50 mM Tris-HCl pH 7.9, 150 mM NaCl, 1% Triron X-100, 0.5% NP-40, 5 mM EDTA pH 8.0, 1 mM PMSF and protease inhibitor) and chromatin was sonicated to ~200 bp with a Diagenode Bioruptor  Libraries were prepared according to manufacturer’s instructions (Illumina). Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters. Fragments of 300±100 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Q5 polymerase (NEB M0530).

value: HDGF2 (Proteintech) Rabbit Polyclonal, catalog number 15134-1-AP


title: 306Z-lung-08

description:
Pt2-08-lung
raw data file: Pt2-lung.txt

value: Patient 2

value: 87 years

value: lung


title: 306Z-lung-05

description:
Pt2-05-lung
raw data file: Pt2-lung.txt


title: 306Z-lung-07

description:
Pt2-07-lung
raw data file: Pt2-lung.txt


title: 306Z-lung-06

description:
Pt2-06-lung
raw data file: Pt2-lung.txt


title: DIPG13_parental_HDGF2_ChIP

description: Parental


title: DIPG13_N2KO7_LEDGF_ChIP

description: NSD2 knockout clone #7

value: LEDGF (Proteintech) Rabbit Polyclonal, catalog number 25504-1-AP


title: DIPG13_N2KO10_LEDGF_ChIP

description: NSD2 knockout clone #10


title: 306Z-lung-03

description:
Pt2-03-lung
raw data file: Pt2-lung.txt


title: 306Z-lung-02

description:
Pt2-02-lung
raw data file: Pt2-lung.txt


title: DIPG13_parental_LEDGF_ChIP

description: Parental


title: DIPG13_LEDGF_HDGF2_dKD_RNAseq_rep2

description: shRNA targeting LEDGF and HDGF2


title: DIPG13_LEDGF_HDGF2_dKD_RNAseq_rep1

description: shRNA targeting LEDGF and HDGF2


title: DIPG13_shRNA_control_RNAseq_rep2

description: shRNA control


title: 306L-lung-10

description:
Pt1-10-lung
raw data file: Pt1-lung.txt

value: 64 years


title: DIPG13_N2KO10_siN1_RNAseq_rep2

description: NSD2 knockout clone #10, siRNA targeting NSD1


title: DIPG13_shRNA_control_RNAseq_rep1

description: shRNA control


title: 306L-lung-09

description:
Pt1-09-lung
raw data file: Pt1-lung.txt

value: Patient 1


title: 306L-lung-07

description:
Pt1-07-lung
raw data file: Pt1-lung.txt


title: 306L-lung-08

description:
Pt1-08-lung
raw data file: Pt1-lung.txt


title: 306Z-lung-04

description:
Pt2-04-lung
raw data file: Pt2-lung.txt


title: DIPG13_N2KO10_siN1_RNAseq_rep1

value: glioma


title: DIPG13_N2KO7_siN1_RNAseq_rep1

description: NSD2 knockout clone #7, siRNA targeting NSD1


title: DIPG13_N2KO7_siN1_RNAseq_rep2


title: 306L-lung-06

description:
Pt1-06-lung
raw data file: Pt1-lung.txt

value: Death


title: DIPG13_parental_RNAseq_rep2

description: Parental


title: 306L-lung-05

description:
Pt1-05-lung
raw data file: Pt1-lung.txt


title: DIPG13_parental_RNAseq_rep1

description: Parental


title: 306L-lung-02

description:
Pt1-02-lung
raw data file: Pt1-lung.txt


title: 306L-lung-03

description:
Pt1-03-lung
raw data file: Pt1-lung.txt


title: 306L-lung-04

description:
Pt1-04-lung
raw data file: Pt1-lung.txt


title: 306L-lung-01

description:
Pt1-01-lung
raw data file: Pt1-lung.txt


title: HKDC1-knockout; KO rep3

city: Chicago

first: Md. Wasim

last: Khan

state: IL

address: 835 S Wolcott Ave

department: Medicine

institute: University of Illinois at Chicago

data_processing:
RNA integrity was assessed with Agilent Bioanalyzer 2100 to select RNA samples with RIN >7.3 to 9.3. Two hundred fifty to 300 base pair insert cDNA libraries, non–strand-specific, were prepared with New England Biolabs (Ipswich, MA) Next Ultra RNA Library Prep and sequenced with Illumina (San Diego, CA) HiSeq PE150 Platform ∼6G/sample Q30 >90%.
The reads were mapped to the human reference genome sequence using STAR v2.5 and v2.6.1, with a total mapping rate >90%/sample.
For gene expression level analysis and to calculate the fragments per kilobase of transcript per million mapped reads, HTSeq v0.6.1 was used.
The differential expression analysis between 2 different groups was done with DESeq2 R package v2_1.6.3.
The P values were adjusted using the Benjamini-Hochberg approach for controlling the false discovery rate, adjusted P <.05. TFCat and Cosmic databases were used to annotate the differential expressed gene.

source_name: HepG2 cells

growth_protocol: Cells were grown in 5.5mM DMEM with 10%FBS in a 5%CO2 humidified incubator.

extract_protocol:
RNA was extracted using RNAeasy kit (Bio-Rad)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Knockout


title: HKDC1-knockout; KO rep2


title: Pt15_Lung

data_processing:
The clean  data were compared using Hisat2 (Pertea et al., 2016)
The sequence reads were aligned to the human genome hg19 (GRCh38), and the aligned reads were counted within exons using FeatureCounts with default parameters to generate the expression matrices of the raw read counts
For the raw data, the rowSums () function in the base package was used that filters out data with read counts <2.
Genome_build: hg19 (GRCh38)
Supplementary_files_format_and_content: counts

source_name: Lung

extract_protocol:
RNA electrophoresis was extracted from FFPE samples, 200-500bp fragments were recovered, PCR amplified and recovered fragments were constructed to construct a sequencing library.
The sequencing library construction and sequencing reaction used Illumina's standard procedures (Illumina, USA), and the library size 300bp, the sequencing strategy is PE150.
Bulk RNA-Seq

treatment_protocol: All samples are taken from autopsy specimens, and then bulk RNA is directly extracted for sequencing

tag: disease state

value: Pulmonary bronchiectasis

value: Lung


title: Pt14_Lung

value: Pneumonia


title: Pt13_Lung

value: Lung squamous cell carcinoma


title: Pt12_Lung

value: Female


title: Empty Vector; EV rep3

value: Control


title: 306Z-lung-01

description:
Pt2-01-lung
raw data file: Pt2-lung.txt

value: Male

value: CD3 Rich


title: Empty Vector; EV rep2


title: Empty Vector; EV rep1


title: Pt10_Lung


title: Drug_1

first: Jie

address: Shuaifuyuan No.1,Dongcheng District

department: Department of Endocrinology

institute: Peking Union Medical College Hospital, Chinese Academy of Medical Science

data_processing:
The qualified total RNA was digested with DNase I, enriched using Oligo (dT) magnetic beads, then fragmented. Fragmented mRNA was added to random primers for cDNA synthesis, PCR reaction to obtain a single-stranded DNA library. Qualified library was formed into DNA nanospheres (DNB) by rolling circle replication, and finally sequenced on the computer.
Clean reads were obtained and aligned to reference genome of the mice. Based on the alignment results, the expression level of each gene was calculated, and the samples were analyzed further in terms of difference, enrichment and cluster analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Tibia

extract_protocol:
Immediately after euthanasia, bone samples were cleaned of all muscle and connective tissue, snap frozen in liquid nitrogen and stored at -80℃ until RNA extraction.In brief, total RNA was extracted using TRIzol reagent (Invitrogen Co., USA) according to the manufacture’s protocol. The RNA was then checked for purity and stability by gel electrophoresis and the concentration was determined using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).
RNA libraries were prepared for sequencing using standard protocols

tag: disease

value: Type 1 diabetes

value: Liraglutide for 8 weeks


title: Drug_2


title: Drug_3

value: Liraglutide for 9 weeks


title: 312G-lung-03

description:
Pt7-03-lung
raw data file: Pt7-lung.txt

value: Patient 7

value: 76 years

value: lung

value: CD68 Rich


title: ACD + RRSP inoculated cells Replicate1

first: Karla

middle: Jean Fullner

last: Satchell

address: 303 East Chicago Ave

department: Microbiology-Immunology

institute: Northwestern University

data_processing:
The quality of DNA reads, in fastq format, was evaluated using FastQC. Adapters were trimmed and reads of poor quality or aligning to rRNA sequences were filtered. The cleaned reads were aligned to the human reference genome using STAR. Read counts for each gene were calculated using htseq-count (39). Normalization and differential expression were determined using R Studio packages tidyverse (40) and DESeq2 (41). Bayesian shrinkage estimator for effect sizes was conducted using apeglm (42). The cutoff for determining significantly differentially expressed genes was an FDR-adjusted p-value less than 0.05 and fold change of greater than 1.8 or less than -1.8.
Genome_build: hg19
Supplementary_files_format_and_content: fold change

source_name: Cultured T84 colorectal carcinoma cells

growth_protocol: T84 cells were cultured in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F-12 (DMEM F12) with GlutaMAX supplement (ThermoFisher Gibco, #10565018) with 10% (w/v) fetal bovine serum (FBS, Gemini Bio-products, #900-108) and 0.1% penicillin/streptomycin (ThermoFisher Gibco). Cells were maintained at 37°C in the presence of 5% CO2.

extract_protocol:
Following 60 minute bacterial treatment, T84 cells were washed once with cold 1x PBS and mRNA was extracted using the Qiagen RNeasy Kit (Qiagen, #74014) following manufacturers instructions.
The Illumina TruSeq Stranded mRNA Library Preparation Kit was used to prepare sequencing libraries from 750 ng of high-quality RNA samples (RIN=10). The Kit procedure was performed without modifications. This procedure includes mRNA purification and fragmentation, cDNA synthesis, 3’ end adenylation, Illumina adapter ligation, library PCR amplification and validation. lllumina NextSeq 500 Sequencer was used to sequence the libraries with the production of single-end, 75 bp reads.

treatment_protocol: V. vulnificus strains were grown at 30°C in LB medium supplemented with 50 μg mL-1 rifampicin. Overnight cultures were diluted 1:100 and grown at 30°C with shaking until exponential phase (OD60 range 0.45-0.60). Bacteria from 1 mL were pelleted by centrifugation and resuspended in phosphate buffered saline (PBS) to a final concentration of 5 x 108 bacterial cells mL-1. T84 cells (seeded the day before into cell culture-treated plates) were twice washed with PBS and then media changed to antibiotic- and FBS-free DMEM/F12. Resuspended V. cholerae was added to media over cells (multiplicity of infection = 5). Inoculations were synchronized by centrifugation at 500 xg for 3 min. T84 cells were subsequently incubated for 60 minutes at 37°C in the presence of 5% CO2.

tag: atcc catalog #

value: ATCC CCL-248

value: 98-783-DP-A1 V. vulnificus ACD + RRSP MARTX toxin

value: male


title: ACD + RRSP inoculated cells Replicate2


title: Pt9_Lung

value: Lung


title: Pt8_Lung


title: Model_3

value: Saline


title: HKDC1-knockout; KO rep1

value: Knockout


title: No active effector inoculated cells Replicate1

value: 98-783-DP-A1 V. vulnificus Triple inactive effector MARTX toxin


title: S11-EL

first: Mehdi

last: Pirooznia

address: 12 SOUTH DR

description: EKLF-GATA1 long - replicate3

data_processing:
After sequencing on a Hiseq 2500 per manufacturer instructions, ChiLin pipeline (v2.0.0) was used for quality control and pre-processing of the fastq files .
The pipeline includes Burrows-Wheeler Aligner (BWA) for read alignment to hg38 and Model-based Analysis of ChIP-Seq (MACS) as a peak caller
Genome_build: hg38

source_name: EKLF-GATA1 long - replicate3

growth_protocol: Bone marrow CD34+ cells were purchased from Poietic Technologies and grown in StemSpan serum-free expansion medium supplemented with 1× CC100 cytokine mix for 6 days.  Lentiviral gene transduction was performed on day 4. On day 6, gene-transduced CD34+ cells were reseeded into Eagle minimum essential medium containing 30% fetal bovine serum, 4 U/mL erythropoietin (EPO), 1% deionized bovine serum albumin, 40mM glutamine, 100μM β-mercaptoethanol, 1μM dexamethasone, 0.3 mg/mL holotransferrin, and 3 μg/mL blasticidin (Invitrogen).

extract_protocol:
Samples were prepared using Magna ChIP™ G ChIP Kit (millipore)
Nextera XT DNA Library Preparation Kit (Illumina)

value: Bone marrow

tag: cell type

value: CD34 cells

tag: transduction

value: EKLF-GATA1 long


title: ACD + MCF-ABH inoculated cells Replicate2

value: 98-783-DP-A1 V. vulnificus ACD + MCF-ABH MARTX toxin


title: Model_2

tag: strain

value: Type 1 diabetes


title: S10-EM

description: EKLF-GATA1 medium  - replicate3

source_name: EKLF-GATA1 medium  - replicate3

value: EKLF-GATA1 medium


title: Pt6_Lung

value: Male


title: Model_1


title: ACD + MCF-ABH inoculated cells Replicate1


title: Pt11_Lung

value: Female


title: Pt5_Lung


title: S9-GATA1

description: GATA1 - replicate3

source_name: GATA1 - replicate3


title: Control_3

value: Normal glucose tolerance


title: S8-Input

description: Input - replicate2

source_name: Input - replicate2

value: Input


title: S12-Input

description: Input - replicate3

source_name: Input - replicate3


title: ACD inoculated cells Replicate2

value: ATCC CCL-248

value: 98-783-DP-A1 V. vulnificus ACD Active only MARTX toxin


title: Pt4_Lung


title: S7-EL

description: EKLF-GATA1 long - replicate2

source_name: EKLF-GATA1 long - replicate2


title: ACD inoculated cells Replicate1

value: male


title: Control_2


title: Pt2_Lung

value: Lung


title: Pt3_Lung


title: S6-EM

description: EKLF-GATA1 medium  - replicate2

source_name: EKLF-GATA1 medium  - replicate2


title: Control_1

value: Saline


title: NF54

data_processing:
Read files were checked for quality by using FASTQC v0.11.5. Reads were trimmed to remove low-quality positions and adapter sequences using cutadapt (version 1.16)
Reads were mapped against the P. falciparum 3D7 reference genome v40 using STAR aligner (version 2.61) and nuclear-encoded genes were analyzed for differential gene expression using cufflinks (version 2.2.1)
Genes with a false discovery rate of <=0.05 with a mean FPKM >5 in at least one strain were called significant. For genes with FPKM > 5 in one strain and no detectable expression in the other, FKPM values were set to 0.1 for purposes of fold-change calculation.
Gene Set Enrichment Analysis was carried out with the FGSEA v1.16.0 Bioconductor v3.12 package with an FDR cutoff of <=0.05
Genome_build: Plasmodium falciparum 3D7 v40 from PlasmoDB
Supplementary_files_format_and_content: Annotated cuffdiff output comparing gene expression of the combined  HDP1 knockout clones C1a and C8 versus their  NF54 parent line with FPKM values shown in columns 7/8

source_name: day 2 gametocytes

growth_protocol: Gametocytes were induced synchronously, and on first day of gametocyte development (D+1), ring stage parasites were treated with 50mM N-acetyl-D-glucosamine to block the development of hemozoin-containing aexual trophozoites. On day 2 of gametocyte development, stage I gametocytes were purified magnetically and total RNA was extracted

extract_protocol:
Total RNA from saponin-lysed parasites was extracted using Trizol (Invitrogen) and Direct-Zol RNA MiniPrep Plus Kit (Zymo Research)
rRNA was removed from Total RNA using Illumina Ribo Zero Gold for human/mouse/rat kit. Using Illumina TruSeq RNA Sample Library Preparation v2 kit (Illumina, San Diego, CA), Messenger RNA was fragmented into small pieces using divalent cations under elevated temperature.The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers.
Second strand cDNA synthesis followed, using DNA Polymerase I and RNase H. The cDNA fragments then went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products were then purified and enriched with PCR to create the final cDNA library. Libraries were pooled and sequenced on Illumina HiSeq4000 sequencer with single-end 50 cycles.
rRNA was removed from Total RNA using Illumina Ribo Zero Gold for human/mouse/rat kit. Using Illumina TruSeq RNA Sample Library Preparation v2 kit (Illumina, San Diego, CA), Messenger RNA was fragmented into small pieces using divalent cations RNA-seq


title: WT inoculated cells Replicate1

value: 98-783-DP-A1 V. vulnificus WT MARTX toxin


title: S5-GATA1

description: GATA1 - replicate2

source_name: GATA1 - replicate2


title: PBS treated cells Replicate2

value: PBS


title: S4-Input

description: Input - replicate1

source_name: Input - replicate1

value: Bone marrow


title: Pt6_Spleen

description: other organs_data.csv

source_name: Spleen

value: Spleen


title: Pt1_Lung


title: Δhdp1 clone C8


title: PBS treated cells Replicate1


title: Brain control 4

city: Bonn

first: Silvia

last: Cases

address: Venusberg-Campus 1

institute: Uniklinikum Bonn

description:
Control
DE37NGSUKBR101745

data_processing:
HiSeq 2500 sequencer (Illumina)
All bioinformatics analyses were performed on a linux system and R/Bioconductor packages Rsubread, edgeR and limma. After quality control and trimming (low quality tails, adapter and poly(A)-contamination) the raw sequencing data were mapped to the GRCm38/mm10 mouse and GrCh38/hg38 genome assemblies using the STAR aligner v.2.4.0.1. The read count matrix per gene was generated from the aligned sequencing data using the corresponding ENSEMBL transcript annotation files and featureCounts v.1.5.3.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Control

extract_protocol:
RNA was isolated using the RNeasy Micro Kit (Qiagen)
Library preparation was performed using QuantSeq 3´ mRNA-Seq Library Prep kit (Lexogen). Samples were subjected to sequencing on a HiSeq 2500 sequencer (Illumina) with 1x50 bp single-end reads and a coverage of 10.000 reads per sample

value: brain

tag: genotype

value: WT


title: Sample_pSCI-90d

city: nanjing

first: Jinxing

last: Hou

state: china

address: Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, 321 Zhongshan Road

department: Department of Orthopedic Surgery

data_processing:
ScRNA-sequence tissues were processed, normalized, and filtered by using the Cell Ranger 2.1.0 pipeline with default and recommended parameters.
FASTQs generated from Illumina sequencing output were aligned to the GRCm38.p6 (mm10, NCBI: GCA_000001635.8) mouse reference genome, using the STAR algorithm
For each tissue, counting UMIs and filtering non-cell associated barcodes were used to generate a Gene-Barcode digital matrix of gene expression. The quality control and downstream analysis of our single-cell transcriptome data using the Seurat (v3.0.2) R toolkit
In each tissue, based on median genes per cell, we calculated and removed the outliers cells using boxplot.stats to remove double cells
For each cell, we excluded cells that were detected fewer than 400. For each gene, we excluded gene that was detected in fewer than ten cells. The mitochondria genes were calculated using Percentage Feature Set function of the Seurat package (Satija et al., 2015). And the cells with more than 20 percent expression of mitochondria genes were excluded to remove low activity cells. These single-cell transcriptome data were normalized by using Normalize Data function in Seurat package. In normalized data, we extracted a subset of variable genes which were identified while controlling for the strong relationship between variability and average expression. Finally, we integrated data from different tissues after identifying anchors between datasets using Find Integration Anchors and Integrate Data in Seurat package
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: injured spinal cord tissue

extract_protocol:
SCI mice are anesthetized by intraperitoneal injection of ketamine (100 mg/kg) and xylazine (10 mg/kg) and put into the ice immediately for 5 minutes. Subsequent of the protocols were kept on the ice except for digestion. 1-cm segment centered on the lesion site from SCI mice and an equivalent segment from uninjured mice were performed to isolate single cells. Spinal cord tissue was moved membrane and transferred into ice-cold RNase-free DPBS (14190144, Thermo Fisher) with 2% FBS (SV30087.02, Thermo Fisher), washed three times by DPBS to remove residual free cells and blood. Carefully dissected and minced tissue was digested in 0.25% (W/V) trypsin (25200-072, Thermo Fisher) with 10 mg/ml DNase I (11284932001, Sigma) for 10 minutes at 37℃. Termination of digestion by adding FBS to 5% (V/V), the cell suspension was gently triturated through pipettes for ten times and filtered by 40 μm sieve to remove large pieces of undigested tissue. The filtrate was centrifuged for 20 minutes at 300 g to remove the debris and myelin sheath. The cell pellet was gently re-suspended in appropriate DPBS (+2% FBS) into 700 cells/ul. Cells were stained with 0.4% Trypan blue (Thermo Fisher, Cat. No.14190144) to check the viability on Countess II Automated Cell Counter (Thermo Fisher). The quality of single-cell suspension is controlled by the ratio of live cells versus death cells (>80%) and single cells versus cell clumps (>95%).
Single-cell libraries were prepared and connected by Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation, to ensure that each cell was paired with a Bead in a Gel Beads-in emulsion. After cell lysis, polyadenylated mRNA molecules hybridized to the Beads. Followed by barcoded reverse transcription of RNA (cDNA), cDNA amplification, enzymatic fragmentation, 5’ adaptor attachment, and tissue indexing. All the remaining procedures were performed according to the standard manufacturer’s protocol. Approximately 5,180-15,144 single cells were recovered and the libraries were purified, quantified, and then sequenced on NovaSeq6000 (Illumina) using 2x150 chemistry (average depth of ~30,000-50,000 reads).

treatment_protocol: Two-month-old C57Bl/6 mice were anesthetized with 100 mg/kg ketamine and 10 mg/kg xylazine, we performed a laminectomy and lateral paraplegia as previously described (Hilton et al., 2019). Briefly, the thoracic 10 (T10) of the spinal cord was exposed, we carefully used a micro knife and under a microscope to over-hemisection only at the right side of the spinal cord midline. Sugi tips were used to stop the bleeding as well as possible. Secure the skin with clips. The spinal cord injury (SCI) mouse was put in the wake-up cage at 35℃ until awaking. The study included scRNA-seq profiles from uninjured and seven-time points groups: post-SCI 0.5 days (pSCI-0.5d) (4 female and 3 male mice), pSCI-1d (3 female and 3 male mice), pSCI-3d (3 female and 3 male mice), pSCI-7d (3 female and 3 male mice), pSCI-14d (3 female and 3 male mice), pSCI-60d (2 female and 2 male mice) pSCI-90d (3 female and 3 male mice) and uninjured (3 female and 3 male mice). For pSCI-3d, pSCI-7d, pSCI-14d, pSCI-60d, and pSCI-90d group mice, we manually emptied bladders twice daily until sacrifice or recovery of full sphincter control. All SCI mice were checked for body weight, clinical signs of pain, or infection. We euthanized mice that were too painful, infected, or more than 15% decrease in body weight.

value: post natal day 151

tag: tissue

value: T10 injured spinal cord

tag: time


title: Pt6_Kidney

description: other organs_data.csv

source_name: Kidney

value: Male

value: Kidney


title: Brain control 3

description:
Control
DE69NGSUKBR101751


title: S2-EM

description: EKLF-GATA1 medium  - replicate1

source_name: EKLF-GATA1 medium  - replicate1

value: CD34 cells

value: EKLF-GATA1 medium


title: DIPG13_N2KO10_HDGF2_ChIP

description: NSD2 knockout clone #10

source_name: Pediatric glioma cells

value: glioma

tag: chip antibody

value: HDGF2 (Proteintech) Rabbit Polyclonal, catalog number 15134-1-AP


title: WT incoulated cells Replicate2

source_name: Cultured T84 colorectal carcinoma cells

value: ATCC CCL-248

tag: treatment

value: male


title: S3-EL

description: EKLF-GATA1 long - replicate1

source_name: EKLF-GATA1 long - replicate1

value: EKLF-GATA1 long


title: S1-GATA1

description: GATA1 - replicate1

source_name: GATA1 - replicate1


title: Pt3_Kidney

description: other organs_data.csv

value: Female


title: Brain control 2

description:
Control
DE91NGSUKBR101743


title: Sample_pSCI-60d

institute: The Affiliated Hospital of Nanjing University Medical School

value: post natal day 121


title: Tumor 2, ALDH +

city: Cincinnati

first: Michael

last: Haas

state: OH

address: 3125 Eden Ave Vontz 3442

institute: University of Cincinnati

data_processing:
Sequence reads were aligned to the genome using standard Illumina sequence analysis pipeline, which was analyzed by The Laboratory for Statistical Genomics and Systems Biology in the University of Cincinnati.
Supplementary_files_format_and_content: Excel spreadsheet with differential gene expression

source_name: spontaneous breast tumor

extract_protocol:
Two tumors were dissected, subjected to enzymatic digestion, and cell suspensions obtained. The cells were incubated with ALDH, CD29, and CD61 fluorophore-conjugated antibodies, then FACS sorted for ALDH +, CD29 hi & CD61 +, and remaining (non-CSC) populations. The Genomics, Epigenomics, and Sequencing Core at the University of Cincinnati extracted RNA, and targeted RNA enrichment was achieved using the NEB-Next Poly(A) mRNA Magnetic Isolation Module.
PrepX mRNA Library Kit (WaferGen) combined with Apollo 324 NGS automated library prep system was used for library preparation.
Cluster generation was carried out using the cBot system.

value: FVBN

tag: oncogene

value: MMTV-Polyoma Virus Middle-T Antigen


title: Brain control 1

description:
Control
DE80NGSUKBR101747

value: brain


title: Tumor 2, CD29 hi, CD61 +


title: Sample_pSCI-7d

value: post natal day 68


title: Brain tumor 4

description:
BRAFV600E/ pAkt/ Trp53KO
DE10NGSUKBR101746

source_name: Tumor

value: brain tumor

value: Trp53-/- induced by IUE


title: Sample_pSCI-14d

value: post natal day 75

value: T10 injured spinal cord


title: Tumor 2, non-CSC


title: Pt7_Liver

description: other organs_data.csv

source_name: Liver

value: Male

value: Liver


title: Pt5_Spleen

description: other organs_data.csv

value: COVID-19 (Severe pneumonia)

value: Spleen


title: Brain tumor 3

description:
BRAFV600E/ pAkt/ Trp53KO
DE96NGSUKBR101750


title: Pt6_Heart

description: other organs_data.csv

source_name: Heart

value: Heart


title: Tumor 1, ALDH +


title: Tumor 1, CD29 hi, CD61 +


title: Brain tumor 2

description:
BRAFV600E/ pAkt/ Trp53KO
DE42NGSUKBR101752


title: Pt5_Liver

description: other organs_data.csv


title: Pt3_Liver

description: other organs_data.csv


title: Tumor 1, non-CSC


title: Pt2_Liver

description: other organs_data.csv

value: COVID-19 (Critical)


title: Brain tumor 1

description:
BRAFV600E/ pAkt/ Trp53KO
DE53NGSUKBR101748


title: 306L-liver-01

description:
Pt1-01-liver
raw data file: Pt1-liver.txt

source_name: liver

tag: individual

value: Patient 1

tag: infection

value: 64 years

value: Death

value: liver

value: CD3 Rich


title: Green needles Indv 6

status: Public on Nov 20 2021

city: Malaga

first: Rafael

middle: A

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

country: Spain

institute: Universidad de Málaga

data_processing:
Base calling was made with the NovaSeq 6000 RTA3 software (Illumina). Conversion of cbcl files to fastq files were made with bcl2fastq2 Conversion Software (Illumina)
The raw reads were trimmed (quality and contamination) using SeqTrimBB software (https://github.com/rafnunser/seqtrimbb). Only the pairs in which both reads passed the quality test were further analysed (Q>20).
The reads were assembled using Trinity 2.11.0 (Haas et al., 2013, Nature Protocols 8:1494-512). Contigs lower than 400 pb were eliminated, for the rest of contigs the redundancy was reduced using CD-HIT-EST software (Fu et al., 2012, Bioinformatics 28: 3150-3152).
The final transcriptome was used as the reference for the read mapping that was performed with BWA using the MEM option (Li and Durbin, 2009, Bioinformatics 25: 1754-1760). The read count was obtained with the phyton script sam2counts (https://github.com/vsbuffalo/sam2counts).
The transcript expression was normalised by cpm. Finally the transcripts were filtered; 2 cpm in at least 2 samples (Robinson et al., 2010, Bioinformatics 26: 139-140).
Genome_build: Assembled reference transcriptome
Supplementary_files_format_and_content: Tab-delimited text files include CPM values for each sample.The column ID is the sequence identifier.

organism: Abies pinsapo

source_name: Samples from adult trees with green needles

growth_protocol: Field-grown adult trees from Sierra de las Nieves (Yunquera, Spain).

extract_protocol:
Total root RNA from maritime pine seedlings was isolated following the protocol described by Liao et al. (2004, Preparative Biochemistry & Biotechnology 34: 209–214) and modified by Canales et al. (2012, Frontiers in Plant Science 3: 100). The RNA concentration and purity were determined via spectrophotometry on a Nanodrop ND-1000 (Thermo Scientific, Waltham, MA, USA). Purity was determined through the 260/280 and 260/230 ratios. RNA quality was also determined in a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA). The concentration was verified with a Qubit 4 Fluorometer (Invitrogen, Paisley, UK) and Qubit RNA BR, Broad-Range, Assay Kit (Invitrogen, Paisley, UK). Samples with a RIN value > 7 were selected to mRNA isolation. The polyA-RNA isolation was performed using Dynabeads™ mRNA Purification Kit (Invitrogen, Paisley, UK) following the manufacturer’s instructions. This process was carried out twice per sample to avoid rRNA contamination. polyA-RNA quality was determined in a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA). The concentration was verified with a Qubit 4 Fluorometer (Invitrogen, Paisley, UK) and Qubit RNA HS, High Sensitivity, Assay Kit (Invitrogen, Paisley, UK).
RNA-seq was carried out by Novogen (UK). mRNA was enriched using oligo(dT) beads. First, the mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment. RNA sequencing was made in a NovaSeq 6000 sequencer according to the manufacturer’s instructions for paired-end reads (Illumina, San Diego, CA, USA). The samples were sequenced producing paired-end reads of 150 bp length.

treatment_protocol: The samples were harvested from adult trees. The trees were selected depending on the color of their needles, blue or green. Developing needles were avoided because their pigment composition.

value: Needles

value: Spain:Sierra de las Nieves

tag: phenotype

value: green


title: Green needles Indv 5


title: Pt5_Heart

description: other organs_data.csv

tag: age

tag: Sex

value: Female


title: Δhdp1 clone C1a

source_name: day 2 gametocytes


title: Sample_uninjured

source_name: uninjured spinal cord  tissue

value: post natal day 61

value: T10 uninjured spinal cord

value: control


title: Green needles Indv 4


title: Sample_pSCI-3d

value: post natal day 64

value: T10 injured spinal cord


title: Green needles Indv 1


title: Green needles Indv 2


title: No active effector inoculated cells Replicate2

value: ATCC CCL-248

value: 98-783-DP-A1 V. vulnificus Triple inactive effector MARTX toxin

value: male


title: 226F-lung-04

description:
Pt5-04-lung
raw data file: Pt5-lung.txt

source_name: lung

value: Patient 5

value: 73 years

tag: status

value: lung

tag: section


title: Blue needles Indv 5

source_name: Samples from adult trees with blue needles

value: blue


title: Blue needles Indv 4


title: Sample_pSCI-1d

source_name: injured spinal cord tissue

value: post natal day 62


title: Sample_pSCI-0.5d


title: Blue needles Indv 1

value: Needles


title: Blue needles Indv 2

value: Spain:Sierra de las Nieves


title: Blue needles Indv 3


title: stem_rep3

city: fuzhou

first: Lianfeng

last: Gu

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

description: Dendrocalamus latiflorus Munro (D. latiflorus)

data_processing:
RNA-seq reads were mapped to the assembled genome using Tophat (v2.0.11) with options : --read-mismatches 5 --read-gap-length 5 --read-edit-dist 5 -p 10 -r 50 -a 8 (Trapnell et al., 2009) with anchor length more than 8-nt. BigWig files are created initially from wiggle (wig) type files, using the program wigToBigWig.
Genome_build: D. latiflorus 1.0 deposited at NCBI under accession ID JACBGG000000000. Raw data for genome sequencing has been deposited in NCBI Sequence Read Archive (SRA) under BioProject PRJNA600661.
Supplementary_files_format_and_content: bigWig

organism: Dendrocalamus latiflorus

growth_protocol: In total, tissues including shoot, abortive shoot, and shoot shell, leaf, root, were collected from the botanical garden of bamboo at Fujian Agriculture and Forestry University (E119°140 ; N26°050)

extract_protocol:
The total RNA was extracted using TRIZOL reagent.
RNA-Seq libraries generated from samples above were constructed using dUTP method (Parkhomchuk et al., 2009) and sequenced on Illumina NovaSeq.

treatment_protocol: without treatment

value: stem

value: seedling


title: shoot_shell_rep2

institute: Fujian Agriculture and Forestry University

value: from ten year old bamboo


title: shoot_shell_rep3


title: shoot_shell_rep1


title: shoot_rep3

value: shoot


title: shoot_rep2


title: root_rep2

value: root


title: root_rep1


title: shoot_rep1


title: Blue needles Indv 6


title: Green needles Indv 3

value: green


title: root_rep3


title: leaf_rep2

value: leaf


title: lateral_bud_rep3


title: leaf_rep1


title: lateral_bud_rep2


title: internode_rep3

value: internode


title: internode_rep2


title: abortive_shoot_rep2


title: internode_rep1


title: lateral_bud_rep1


title: stem_rep2


title: abortive_shoot_rep1


title: stem_rep1


title: N1014M-4

city: Shanghai

first: Xiang

last: Liping

address: 180 Fenglin Road, Xuhui, Shanghai

institute: Fudan university

data_processing:
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
Library quality was assessed on the Agilent Bioanalyzer 2100 system. The sequencing libraries were sequenced on an Illumina Hiseq2500/X platform. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
Cuffquant and cuffnorm (v2.2.1) was used to calculate FPKMs of genes in each sample.
Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group.
Genome_build: mm9
Supplementary_files_format_and_content: Raw gene counts and fpkm for every gene and every sample

extract_protocol:
Total RNAs were extracted using TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: disease state

value: Normal


title: N1014C-3

value: NASH


title: N1014C-4


title: Sample 38: CB2 KO 2

city: Los Angeles

first: Benjamin

middle: Pierre

last: Hurrell

address: 1450 Biggy Street

department: MMI

institute: University of Southern California

data_processing:
Image analysis and base calling was carried out using RTA 1.13.48.0.  Final file formatting, demultiplexing and fastq generation were carried out using CASAVA v 1.8.2.
Raw sequencing reads were first trimmed from both ends with Quality Score method (bases with quality score Phred less than 20 were trimmed from both ends, and trimmed reads shorter than 25 nt were excluded from downstream analyses)
Trimmed reads were then mapped to the mouse genome mm10 using STAR (v3.5.3) with default parameter settings
Gencode M20 annotation was used to quantify the aligned reads to genes/transcripts using Partek E/M method.
read counts per gene/transcript in all samples were normalized using Upper Quartile normalization and analyzed for differential expression using Partek Gene Specific Analysis method (genes/transcripts with less than 10 reads in any sample among a data set were excluded).
Genome_build: mm10
Supplementary_files_format_and_content: .txt file with normalized gene counts

source_name: sorted ILC2s

extract_protocol:
Total RNA was isolated using MicroRNAeasy (Qiagen, Valencia, California). 10ng of input RNA was used to produce cDNA for downstream library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Freshly isolated ILC2s after 3 i.n. injections of 1µg rm-IL33 were stimulated with rm-IL-2 (10ng/mL) and rm-IL-7 (10ng/mL) at 37°C  for 24 hours.

value: BALB/c

value: 6 weeks

tag: cell type

value: sorted ILC2s


title: abortive_shoot_rep3


title: Sample 35: WT 2

value: lung


title: PECs IFNγ + eNAMPT [Sample 4d]

city: Novara

first: Giorgia

last: Colombo

state: NO

address: Via Bovio 6, Presso Fondazione Novara Sviluppo

department: Department of Pharmaceutical Sciences

institute: UNIUPO

description: Sample 4d       4_4

data_processing:
Quality check of RNA-seq reads was performed using fastQC
RNA-seq reads were mapped against the murine genome (mm9) using ContextMap version 2.7.9
Number of read counts per gene and exon were determined from the mapped RNA-seq reads in a strand-specific manner using featureCounts gene annotations from GENCODE version 27.
Differential gene expression analysis was performed using DESeq2
Genome_build: mm9
Supplementary_files_format_and_content: base mean and log2 fold change
Supplementary_files_format_and_content: Raw_counts

source_name: peritoneal macrophages

growth_protocol: PECs were isolated from mice peritoneum and seeded in complete RPMI medium for 24h.

extract_protocol:
RNA was extracted using SPLIT RNA Extraction Kit (Lexogen, Vienna, Austria).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PECs were treated with eNAMPT (500ng/ml), IFNγ (200 U/ml) and both for 4h

tag: agent

value: IFNgamma + eNAMPT

value: peritoneal exudate cells

value: wild-type


title: PECs IFNγ + eNAMPT [Sample 4c]

description: Sample 4c       4_3

tag: strain


title: PECs eNAMPT [Sample 3e]

description: Sample 3e       3_5

value: eNAMPT

tag: genotype


title: Sample 39: CB2 KO 3

tag: tissue


title: PECs eNAMPT [Sample 3d]

description: Sample 3d       3_4


title: Sample 37: CB2 KO 1


title: PECs IFNγ + eNAMPT [Sample 4b]

description: Sample 4b       4_2


title: PECs IFNγ + eNAMPT [Sample 4e]

description: Sample 4e       4_5


title: PECs IFNγ + eNAMPT [Sample 4a]

description: Sample 4a       4_1


title: N1014M-3


title: PECs IFNγ [Sample 2b]

description: Sample 2b       2_2

value: IFNgamma


title: PECs IFNγ [Sample 2c]

description: Sample 2c       3_2


title: PECs IFNγ [Sample 2d]

description: Sample 2d       4_2


title: N1014M-2


title: PECs eNAMPT [Sample 3a]

description: Sample 3a       1_3


title: PECs IFNγ [Sample 2e]

description: Sample 2e       5_2


title: PECs eNAMPT [Sample 3c]

description: Sample 3c       3_3


title: Sample 36: WT 3


title: PECs CTRL [Sample 1e]

description: Sample 1e       5_1

value: CTRL


title: N1014C-1


title: PECs CTRL [Sample 1d]

description: Sample 1d       4_1


title: PECs CTRL [Sample 1c]

description: Sample 1c       3_1


title: PECs IFNγ [Sample 2a]

description: Sample 2a       1_2


title: Sample 34: WT 1


title: PECs eNAMPT [Sample 3b]

description: Sample 3b       2_3


title: PECs CTRL [Sample 1b]

description: Sample 1b       2_1


title: L3_WTvsSPTLungs_G06

first: Simone

last: Caielli

address: 413 E 69th Street

department: Department of Pediatrics

data_processing:
Sequencing reads were aligned with STAR_2.4.0f1  against the mm10 mouse genome
SAMTOOLS v0.1.19 was used for sorting and indexing reads
Gene counts were generated using htseq-count
Genome_build: mm10
Supplementary_files_format_and_content: csv file with raw gene counts for every gene and every sample

source_name: Lung tissue

growth_protocol: All experiments included sex- and age-matched SPT and WT-littermates between 8 and 12 weeks of age

extract_protocol:
RNA was extracted using Promega Maxwell 16 MDx instrument, (Maxwell 16 LEV simplyRNA Tissue Kit). RNA integrity was verified using the Agilent Bioanalyzer 2100 (Agilent Technologies). cDNA was synthesized from total RNA using Superscript III (Invitrogen)
Specimens were prepared for RNA sequencing using TruSeq RNA Library Preparation Kit v2 or riboZero

treatment_protocol: Mice were intransally inoculated with 5x10E6 TCID50 Human rhinovirus strain A-1B or equal volumes of PBS

value: SPT

value: Lung

value: HRV


title: K3_WTvsSPTLungs_C06

value: WT


title: L2_WTvsSPTLungs_F06


title: L4_WTvsSPTLungs_H06


title: L1_WTvsSPTLungs_E06


title: K2_WTvsSPTLungs_B06


title: J4_WTvsSPTLungs_H05

value: No infection


title: J2_WTvsSPTLungs_F05


title: J1_WTvsSPTLungs_E05


title: J3_WTvsSPTLungs_G05


title: K1_WTvsSPTLungs_A06


title: I3_WTvsSPTLungs_C05


title: I1_WTvsSPTLungs_A05


title: H1_WTvsSPTLungs_E04

source_name: Immune cells (CD45)

value: Immune cells (CD45)


title: G3_WTvsSPTLungs_C04


title: H4_WTvsSPTLungs_H04


title: G4_WTvsSPTLungs_D04


title: G1_WTvsSPTLungs_A04


title: I2_WTvsSPTLungs_B05


title: H3_WTvsSPTLungs_G04


title: G2_WTvsSPTLungs_B04


title: F4_WTvsSPTLungs_H03


title: F3_WTvsSPTLungs_G03


title: K4_WTvsSPTLungs_D06


title: F2_WTvsSPTLungs_F03


title: E3_WTvsSPTLungs_C03


title: E2_WTvsSPTLungs_B03


title: D4_WTvsSPTLungs_H02

source_name: Epithelial cells (EpCAM)

value: Epithelial cells (EpCAM)


title: E1_WTvsSPTLungs_A03


title: iPAM cells- H3K27_rep1

city: Minhang District

first: Min

last: Zhang

state: Shanghai

address: 518 Ziyue RD

department: The viruses and Swine diseases of reproductive failures

institute: Shanghai Veterinary Research Institute, CAAS

data_processing:
Quality of FASTQ file were evaluated by FastQC software
Raw reads were filtered with Cutadapt sofware with parameters of 10 bp overlap, 20% base mismatch
Reas were mapped to sus scrofa genome Sus_scrofa.Sscrofa11.1.dna.toplevel.fa with Bowtie2 with default parameter
Raw counts were generated using Htseq with Sus_scrofa.Sscrofa11.1.dna.toplevel.fa annotation file
Peaks were called using HOMER and annotated with ChIPseeker.
Supplementary_files_format_and_content: bigwig files were generated using Megadepth with R

organism: Sus scrofa

source_name: iPAM cells

growth_protocol: Immortalized PAM (PAM) 3D4/21 (ATCC CRL-2843) were obtained from American Type Culture Collection and cultured in RPMI 1640 (Gibco) supplemented with penicillin (100 units/mL), streptomycin (100 μg/mL) and 10% fetal bovine serum (Gibco).

extract_protocol:
Lysates were clarified from sonicated nuclei and EGR1-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: untreated

value: iPAM cells

value: untreated


title: iPAM cells- IgG_rep1


title: E4_WTvsSPTLungs_D03

institute: Weill Cornell Medicine


title: iPAM cells- Input_rep1


title: iPAM cells- EGR1_rep1


title: C4_WTvsSPTLungs_D02


title: D1_WTvsSPTLungs_E02


title: PECs CTRL [Sample 1a]

description: Sample 1a       1_1


title: C3_WTvsSPTLungs_C02


title: N1701= 6w TAC in NRON WT

city: Hannover

first: Julia

last: Leonardy

address: Carl-Neuberg-Straße 1

department: IMTTS

institute: Medical School Hannover

description: 6w TAC in NRON WT

data_processing:
BCL files were converted to FASTQ files using bcl2fastq Conversion Software version v2.20.0.422
nfcore/rnaseq (v1.3), pipeline: Nextflow (v18.10.1), FastQC (v0.11.8), TrimGalore (v0.5.0), STAR (vSTAR_2.6.1d), RSeQC (v3.0.0), dupRadar, Preseq (v2.0.3), featureCounts (v1.6.4), StringTie (v1.3.5), Sample_correlation, MultiQC (v1.7)
Normalization and differential expression analysis was performed with DESeq2 (Galaxy Tool Version 2.11.40.2) with default settings except for “Output normalized counts table” which was set to “Yes”.
Genome_build: GRCm38; release M18
Supplementary_files_format_and_content: tab-delimited text files of raw read counts from each sample.

source_name: murine cardiac RNA sample

extract_protocol:
Total RNA was isolated from mouse hearts after 6 weeks of TAC or Sham surgery with miRNeasy mini kit (Qiagen). 250ng of total RNA was used for mRNA enrichment procedure with NEBNext PolyA mRNA magnetic Isolation Module.
Stranded cDNA library was generated using using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina with an additional purification step using Agencourt® AMPure® XP Beads. cDNA libraries were barcoded by dual indexing approach with NEBNext Multiplex Oligos for Illumina – 96 Unique Dual Index Primer Pairs.

value: 6w TAC in NRON WT


title: H2_WTvsSPTLungs_F04


title: N1702= 6w TAC in NRON WT

description: 6w TAC in NRON WT


title: N1700= 6w TAC in NRON WT

description: 6w TAC in NRON WT


title: N1697= 6w Sham in NRON WT

description: 6w Sham in NRON WT

value: 6w Sham in NRON WT


title: C1_WTvsSPTLungs_A02


title: N1699= 6w TAC in NRON WT

description: 6w TAC in NRON WT


title: C2_WTvsSPTLungs_B02


title: I4_WTvsSPTLungs_D05


title: F1_WTvsSPTLungs_E03


title: B4_WTvsSPTLungs_H01


title: B3_WTvsSPTLungs_G01


title: N1696= 6w Sham in NRON WT

description: 6w Sham in NRON WT


title: N1695= 6w Sham in NRON WT

description: 6w Sham in NRON WT


title: D2_WTvsSPTLungs_F02


title: B2_WTvsSPTLungs_F01


title: leaf_rep3

value: leaf

value: seedling


title: N1694= 6w TAC in NRON KO

description: 6w TAC in NRON KO

value: 6w TAC in NRON KO


title: B1_WTvsSPTLungs_E01


title: N1698= 6w Sham in NRON WT

description: 6w Sham in NRON WT


title: N1693= 6w TAC in NRON KO

description: 6w TAC in NRON KO


title: A3_WTvsSPTLungs_C01


title: A1_WTvsSPTLungs_A01


title: N1691= 6w TAC in NRON KO

description: 6w TAC in NRON KO


title: A2_WTvsSPTLungs_B01


title: siECHS1-2#

city: Chengdu

first: Xiaoqiang

last: Tang

address: Renminnan Road

institute: Sichuan 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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
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: Rnor_6.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Rattus norvegicus

extract_protocol:
RNA was harvested from cardiomyocytes using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cardiomyocytes

value: SD

value: Heart

tag: genotype/variation


title: A4_WTvsSPTLungs_D01

city: New York


title: siECHS1-3#