title: P21_ctrl_inf_07 [Single cone cell RNA-seq]


title: T cells, 10mM lactic acid for 24 hours, replicate 1

status: Public on Dec 05 2022

type: SRA

city: Chengdu

first: chen

last: li

address: Renmin South Road

country: China

institute: Sichuan Univercity

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (v0.38) (default parameters)
Trimmed sequence reads were mapped to GRCh38/hg38 using STAR (v2.7.1a) with default parameters
Read count extraction and normalization were performed using DESeq2 (v1.28.1).
Assembly: hg38
Supplementary files format and content: tab-delimited tsv file include FPKM values for all samples

molecule: polyA RNA

organism: Homo sapiens

source_name: PBMC

growth_protocol: Human peripheral blood mononuclear cells (PBMC) from healthy donors were cultured in RMPI-1640 medium supplemented with 5% Human Serum AB (Gemini), 1% penicillin-streptomycin, 1% non-essential amino acids, 1% GlutaMAX, 1mM sodium pyruvate, 0.1M HEPES, 50μM β-mercaptoethanol in the presence of human IL-2 (100U/ml, Peprotech).

extract_protocol:
Total RNA was extracted by homogenizing in Trizol (Takara) and freezing in RNase-free tubes with liquid nitrogen
RNA libraries for RNA-seq were prepared using TruSeq RNA sample prep kit (FC-122-1001, Illumina) following manufacturer's protocols.

treatment_protocol: 1. PBMCs were activated individually in 24-well plates by human anti-CD3/CD28 and expanded in completed medium for 11 days, and then cultured in control or lactic acid (10mM) conditions for 24 h. 2. PBMCs were activated individually in 24-well plates by human anti-CD3/CD28 and expanded for 12 days under control or sodium lactate (10mM or 40mM) conditions.

tag: tissue

value: PBMC

tag: cell type

value: T cells

tag: treatment

value: 10mM lactic acid for 24h


title: CLL_RS6 (RNA-seq)

city: Boston

first: Catherine

last: Wu

state: MA

address: 450 Brookline Avenue

country: USA

institute: Dana-Farber Cancer Institute

description: Counts file.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to the mouse reference genome using STAR (v2.4.0.1).
Count value was used to measure gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Counts file.txt for RNA-seq samples; tsv files (scATAC-seq fragments) for scATAC-seq samples

molecule: total RNA

organism: Mus musculus

extract_protocol:
Harvested spleens were mechanically dissociated to form a single cell suspension. Erythrocyte lysis was carried out using ACK buffer and B cells were immunomagnetically selected from the resulting cell suspension using the MACS B cell Isolation Kit. Cells were washed in cold PBS and total RNA was extracted using Qiagen RNAeasy kit.
RNA-seq libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina).  Droplet-based scATAC-seq optimized for capture of mitochondrial DNA (mtscATAC-seq) described in Lareau et al. (PMID 32788668)

tag: condition

value: CLL

value: Malignant B cells

tag: strain

tag: genotype

value: Multi-plex LOF


title: P21_ctrl_inf_09 [Single cone cell RNA-seq]

city: Bethesda

first: Hong

last: Liu

state: MD

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

library_source: transcriptomic single cell

data_processing:
Libraries were multiplex sequenced in one lane using Illumina HiSeq3000 Sequencer at NIDDK Genomics Facility
single-end, 50 base reads were collected and converted by bcl2fastq (version 2) into fastq files and aligned on (GRCm38/mm10) using STAR (version 2.7.3a)
Output RNA-seq bam files were analyzed with Genomatix programs with transcripts levels calculated as counts/reads per million mapped reads (CPM). ChAP-seq and ATAC-seq data were analyzed by MACS2 (v2.2.7.1)  for peak calling.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include CPM values for each gene of all samples

organism: Mus

source_name: P21 single cone

extract_protocol:
Pieces from superior or inferior zones of retina were dissected from Trb2Cre:Ai6 mice, then dissassociated into suspension cells after brief papain treatment. Fluorescent cells were identified on a Zeiss Axiovert 200M microscope and collected individually using an Eppendorf micromanipulator and suction pipette. Collected single cone cells were transfer into individual PRC tubes for RNA-seq library construction. For ChAP-seq, retinas from ThrbHAB/HAB;Rosa26BirA/BirA and control Rosa26BirA/BirA E18 embryos were cross-linked and affinity-purified with streptavidin to collect the TRb-bound-DNA. For ATAC-seq, cone nuclei were immunopurified from retinas from control (TRb2Cre-het) and TRb2Cre-KO mice on a Rosa26Sun1Gfp/Sun1Gfp background, these purified cone nuclei were treated with Tagment enzyme (using Tagment DNA kit) before DNA purification.
Single-cell RNA-seq libraries were constructed by using SMART-Seq v4 Ultra Low Input RNA Kit and ThruPLEX DNA-Seq Kit. For ChAP-seq, the enriched-DNA samples were constructed into sequencing library by using ThruPLEX DNA-Seq Kit. For ATAC-seq,  Tagment-enzyme processed DNA samples were constructed into ATAC-seq library by using Tagment DNA kit.

value: inferior-cone

tag: age

value: post natal day 21


title: T cells, 10mM sodium lactate, replicate 3

value: 10mM sodium lactate


title: CLL_RS4 (RNA-seq)

description: Counts file.txt


title: RS18 (RNA-seq)

description: Counts file.txt

source_name: RS

value: RS


title: P21_ctrl_inf_11 [Single cone cell RNA-seq]


title: RS11 (RNA-seq)

description: Counts file.txt


title: T cells, 10mM lactic acid for 24 hours, replicate 3


title: CLL_RS7 (RNA-seq)

description: Counts file.txt


title: P21_ctrl_inf_02 [Single cone cell RNA-seq]


title: P21_ctrl_inf_05 [Single cone cell RNA-seq]


title: P21_ctrl_inf_06 [Single cone cell RNA-seq]


title: P21_ctrl_inf_01 [Single cone cell RNA-seq]


title: T cells, 10mM lactic acid for 24 hours, replicate 2


title: P21_ctrl_inf_04 [Single cone cell RNA-seq]


title: CLL_RS2 (RNA-seq)

description: Counts file.txt


title: P8_ctrl_sup_23 [Single cone cell RNA-seq]

source_name: P8 single cone

value: superior-cone

value: post natal day 8


title: P8_ctrl_sup_21 [Single cone cell RNA-seq]


title: P21_ctrl_inf_03 [Single cone cell RNA-seq]


title: P8_ctrl_sup_20 [Single cone cell RNA-seq]


title: P8_ctrl_sup_24 [Single cone cell RNA-seq]


title: SEP036,cultured neural progenitor cells derived from olfactory neuroepithelium, scRNAseq [SEP036]

city: Brooklyn

first: Oleg

middle: V

last: Evgrafov

state: New York

address: 450 Clarkson Ave

institute: SUNY Downstate Health Sciences University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing and mapping  were made using bcl2fastq and STAR (Spliced Transcripts Alignment to a Reference)
Gene counting was done using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: neural progenitor/mesenchymal

growth_protocol: To grow cells we cover Petri dish with 10% Matrigel Basement Membrane (Corning) in F12 Coon’s medium (Sigma) and grow cells in medium 4506 (Ghanbari et al., 2004). We use 0.25% Trypsin-EDTA (VWR) to dislodge cells.

extract_protocol:
Cells at ~80% monolayer on 6 cm Petri dish were dislodged by 1 ml of 0.25% Trypsin-EDTA solution, 3 ml 4506 culture medium was added to stop digestion, cells were gently and thoroughly mixed to break up clumps of cells washed in culture medium and  filtered using 40 µm FLOWMI cell strainer.  Cells were washed with 1x DPBS with 0.04% BSA, then 1X PBS with 0.04% BSA, re-suspended in 500 ul of PBS and filtered using Flowmi™ Tip Strainer. After counting, cell concentration was adjusted to 700 cells/ul.
The concentration and viability of cells were determined using a hemocytometer and Trypan blue. After counting, single-cell libraries were prepared according to the 10x Genomics protocol CG000183 on Chromium controller (10x Genomics) and sequenced on NovaSeq6000 as paired end 28 + 90 bp reads plus two indexing reads.
Tissue samples were obtained from the superior-medial region of the head of the middle turbinate; laterality was determined by ease of access. The mucosa was anesthetized and decongested with topical 1% lidocaine and 0.05% oxymetazoline. After 5 minutes, 0.3 ml of 1% lidocaine and 1:100,000 epinephrine was injected into the targeted mucosal site under visualization. 2mm cupped forceps were used to obtain biopsy specimens. These samples were immediately transported to the lab in Leibovitz's L-15 Medium (ThermoFisher) supplemented with Antibiotic-Antimycotic solution (ThermoFisher) and processed to prepare single-cell suspension. Biopsy pieces were minced with two scalpels in a Petri dish with a small amount of cold Hank’s buffer without magnesium or calcium to prevent drying and then transferred to a 1.5 ml Eppendorf tube and washed twice with 1 ml cold Hank’s buffer. Cells were dissociated in 250 µl of 0.25% Trypsin-EDTA at 37ºC while shaking at 500 rpm. After 10 minutes, the suspension was mixed by pipetting and returned to thermomixer for another 10 minutes. After another mixing, the cells were sedimented by centrifugation at 300 relative centrifugal force for 5 minutes, resuspended in 500 µl of cold Hank’s solution with BSA, filtered using 40 µm FLOWMI cell strainer cell suspension into a 1.5 ml Eppendorf
The concentration and viability of cells were determined using a hemocytometer and Trypan blue. After counting, single-cell libraries were prepared according to the 10x Genomics protocol CG000183 on Chromium controller (10x Genomics) and sequenced on NovaSeq6000 as paired end 28 + 90 bp reads plus two indexing reads.

value: neural progenitor/mesenchymal


title: del(13q)-CLL5 (RNA-seq)

description: Counts file.txt

source_name: CLL

value: MDR


title: SEP181,cultured neural progenitor cells derived from olfactory neuroepithelium, scRNAseq [SEP181]

description: 10x Genomics


title: SEP313,middle turbinate-schizophrenia,scRNAseq [SEPL313_MT1]

description: 10x Genomics

source_name: Middle Turbinate

extract_protocol:
Tissue samples were obtained from the superior-medial region of the head of the middle turbinate; laterality was determined by ease of access. The mucosa was anesthetized and decongested with topical 1% lidocaine and 0.05% oxymetazoline. After 5 minutes, 0.3 ml of 1% lidocaine and 1:100,000 epinephrine was injected into the targeted mucosal site under visualization. 2mm cupped forceps were used to obtain biopsy specimens. These samples were immediately transported to the lab in Leibovitz's L-15 Medium (ThermoFisher) supplemented with Antibiotic-Antimycotic solution (ThermoFisher) and processed to prepare single-cell suspension. Biopsy pieces were minced with two scalpels in a Petri dish with a small amount of cold Hank’s buffer without magnesium or calcium to prevent drying and then transferred to a 1.5 ml Eppendorf tube and washed twice with 1 ml cold Hank’s buffer. Cells were dissociated in 250 µl of 0.25% Trypsin-EDTA at 37ºC while shaking at 500 rpm. After 10 minutes, the suspension was mixed by pipetting and returned to thermomixer for another 10 minutes. After another mixing, the cells were sedimented by centrifugation at 300 relative centrifugal force for 5 minutes, resuspended in 500 µl of cold Hank’s solution with BSA, filtered using 40 µm FLOWMI cell strainer cell suspension into a 1.5 ml Eppendorf
The concentration and viability of cells were determined using a hemocytometer and Trypan blue. After counting, single-cell libraries were prepared according to the 10x Genomics protocol CG000183 on Chromium controller (10x Genomics) and sequenced on NovaSeq6000 as paired end 28 + 90 bp reads plus two indexing reads.
Tissue samples were obtained from the superior-medial region of the head of the middle turbinate; laterality was determined by ease of access. The mucosa was anesthetized and decongested with topical 1% lidocaine and 0.05% oxymetazoline. After 5 minutes, 0.3 ml of 1% lidocaine and 1:100,000 epinephrine was injected into the targeted mucosal site under visualization. 2mm cupped forceps were used to obtain biopsy specimens. These samples were immediately transported to the lab in Leibovitz's L-15 Medium (ThermoFisher) supplemented with Antibiotic-Antimycotic solution (ThermoFisher) and processed to prepare single-cell suspension. Biopsy pieces were minced with two scalpels in a Petri dish with a small amount of cold Hank’s buffer without magnesium or calcium to prevent drying and then transferred to a 1.5 ml Eppendorf tube and washed twice with 1 ml cold Hank’s buffer. Cells were dissociated in 250 µl of 0.25% Trypsin-EDTA at 37ºC while shaking at 500 rpm. After 10 minutes, the suspension was mixed by pipetting and returned to thermomixer for another 10 minutes. After another mixing, the cells were sedimented by centrifugation at 300 relative centrifugal force for 5 minutes, resuspended in 500 µl of cold Hank’s solution with BSA, filtered using 40 µm FLOWMI cell strainer cell suspension into a 1.5 ml Eppendorf
The concentration and viability of cells were determined using a hemocytometer and Trypan blue. After counting, single-cell libraries were prepared according to the 10x Genomics protocol CG000183 on Chromium controller (10x Genomics) and sequenced on NovaSeq6000 as paired end 28 + 90 bp reads plus two indexing reads.

tag: disease

value: schizophrenia

value: Middle Turbinate


title: P8_ctrl_sup_22 [Single cone cell RNA-seq]


title: del(13q)-CLL4 (RNA-seq)

description: Counts file.txt


title: P8_ctrl_sup_19 [Single cone cell RNA-seq]


title: SEP310,middle turbinate-control, scRNAseq [SEPL310_MT1]

description: 10x Genomics

value: control


title: del(13q)-CLL2 (RNA-seq)

description: Counts file.txt


title: P8_ctrl_sup_17 [Single cone cell RNA-seq]


title: del(13q)-CLL3 (RNA-seq)

description: Counts file.txt


title: del(13q)-CLL1 (RNA-seq)

description: Counts file.txt


title: P8_ctrl_sup_14 [Single cone cell RNA-seq]


title: P8_ctrl_sup_18 [Single cone cell RNA-seq]


title: P8_ctrl_sup_16 [Single cone cell RNA-seq]


title: P8_ctrl_sup_11 [Single cone cell RNA-seq]


title: P8_ctrl_sup_15 [Single cone cell RNA-seq]


title: P8_ctrl_sup_13 [Single cone cell RNA-seq]


title: P8_ctrl_sup_09 [Single cone cell RNA-seq]


title: Normal_B4 (RNA-seq)

description: Counts file.txt

source_name: B cell

value: normal

value: Splenic B cell

value: wild type


title: P8_ctrl_sup_12 [Single cone cell RNA-seq]


title: Normal_B2 (RNA-seq)

description: Counts file.txt


title: P8_ctrl_sup_08 [Single cone cell RNA-seq]


title: P8_ctrl_sup_07 [Single cone cell RNA-seq]


title: P8_ctrl_sup_06 [Single cone cell RNA-seq]


title: P8_ctrl_sup_05 [Single cone cell RNA-seq]


title: d49MNplusGlia_D8

city: Cambridge

first: Francesco

last: Limone

state: Massachusetts

address: 7 divinity avenue, Bauer Laboratory 008

institute: harvard university

description:
10x Genomics
raw data are located at DUOS:
gs://fc-5126c21e-7f7f-47a5-9329-f8fcc00aec7a/limone_cellreports_2022/scRNAseq/bams/d49MNplusGlia_D8.bam

data_processing:
Raw sequence data was demultiplexed and aligned following the standard Drop-Seq protocol (Macosko et al., 2015)
Human experiments were aligned to the GRCh37 reference. Cultures contain mouse glia, so competitive alignment against mouse reference GRCm38 were made to remove mouse reads. Sequencing reads were then filtered to reads that mapped at high quality (MQ>=10) to the human genome
Matrices were built from 10X Chromium Single Cell 3’ Reagents V2 as described above.
Assembly: GRCh37 with concatenated GRCm38, fasta included
Assembly: gs://fc-5126c21e-7f7f-47a5-9329-f8fcc00aec7a/limone_cellreports_2022/scRNAseq/reference_fasta/h37_m38.fasta.gz
Supplementary files format and content: raw_counts: Raw DGE counts. Tab-delimited text compressed using gzip. First column name is "GENE", ther column names are cell barcodes.Values of column 1 are gene names from GRCh38. Remaining values are integer counts of transcripts.
donor_cell_map: 2-column tab-delimited text file without header. Column 1 contains cell barcodes. Column 2 contains the name of the sample the cell barcode was assigned to.
counts: Filtered counts to only include cells assignable to donors. Also filtered to remove cells identified as doublets using Drop-Seq tools methods. Same format as raw_counts.
donor_pseudobulk_counts: Sum of reads across all cells for each donor for use in place of bulk RNA-seq counts matrix. Same format as raw_counts.
scRNAseq/analysis/seurat_features.csv
Comma-separated text file with quote='"'. Row names are cell barcodes
Any barcode with less than 400 genes and combined UMI matrices were used for downstream analysis using Seurat (v3.0.2) (Stuart et al., 2019).  The matrix was then processed via the Seurat pipeline as described in publication methods. This file is the matrix used for analysis as described in the text.
orig.ident: timepoint  nCount_RNA: number of transcripts associated with cell barcode  nFeature_RNA: number of genes detected in cell  percent.mito: percentage of transcripts from cell aligned to mitochondrial genome  seurat_clusters: Cluster assignment for cell

source_name: Pooled liMNs villages, day 49, replicate4, scRNAseq

growth_protocol: liMNs differentiated using the protocol described in Limone et. al,  Cell Reports 2022 were plated on murine glial co-cultures and cultured as described in publication

extract_protocol:
Cells were washed once with PBS1X, incubated with Accutase 20 minutes. Cells were detached, colleced in faclon tube, spun down for 5 minutes at 300xg  and resuspended in PBS
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics)

treatment_protocol: No treatment

value: stem cell derived MNs


title: d49MNplusGlia_D9

description:
10x Genomics
raw data are located at DUOS:
gs://fc-5126c21e-7f7f-47a5-9329-f8fcc00aec7a/limone_cellreports_2022/scRNAseq/bams/d49MNplusGlia_D9.bam

source_name: Pooled liMNs villages, day 49, replicate2, scRNAseq


title: d49MNplusGlia_D10

description:
10x Genomics
raw data are located at DUOS:
gs://fc-5126c21e-7f7f-47a5-9329-f8fcc00aec7a/limone_cellreports_2022/scRNAseq/bams/d49MNplusGlia_D10.bam

source_name: Pooled liMNs villages, day 49, replicate3, scRNAseq


title: d49MNplusGlia_D7

description:
10x Genomics
raw data are located at DUOS:
gs://fc-5126c21e-7f7f-47a5-9329-f8fcc00aec7a/limone_cellreports_2022/scRNAseq/bams/d49MNplusGlia_D7.bam

source_name: Pooled liMNs villages, day 49, replicate1, scRNAseq


title: Normal_B3 (RNA-seq)

description: Counts file.txt


title: P8_ctrl_sup_10 [Single cone cell RNA-seq]


title: Normal_B1 (RNA-seq)

description: Counts file.txt


title: d35MNplusGlia_E12

description:
10x Genomics
raw data are located at DUOS:
gs://fc-5126c21e-7f7f-47a5-9329-f8fcc00aec7a/limone_cellreports_2022/scRNAseq/bams/d35MNplusGlia_E12.bam

source_name: Pooled liMNs villages, day 35, replicate4, scRNAseq


title: P8_ctrl_inf_24 [Single cone cell RNA-seq]


title: 34931: Liver, WSD/CD

city: Oklahoma city

first: Philip

last: ONeill

state: OK

address: 945 9th st

institute: OUHSC

data_processing:
Quality trim to a minimum of Q15
Map using GSNAP version 2012-07-20 using the commandline: gsnap -d mmul10_104 -v mmul10_104.snp138 --use-splicing=mmul10_104.splicesites --max-mismatches=0.06 -i2 -n2 -Q --gunzip --force-xs-dir --nofails -B5 -t${num_processors} --read-group-id=$j --read-group-name=$j --read-group-library=$j --read-group-platform=illumina -A sam $outfile_R1 $outfile_R2 | samtools view -bS -@ ${num_processors} - | samtools sort -@ ${num_processors} -o ./Illumina_data/${j}.sorted.bam -; samtools index ./Illumina_data/${j}.sorted.bam
sort and index using SAMTOOLS
call FPKM using CUFFLINKS
Assembly: mmul10_104
Supplementary files format and content: Excel file containing FPKM values

organism: Macaca mulatta

source_name: Liver

extract_protocol:
Total RNA was extracted with Qiagen Rneasy Mini Kit
Swift directional mRNA prep
NovaSeq 6000 using 2x150bp format

value: Liver

value: 3 years

value: WSD/CD


title: T cells, PH control, replicate 2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (v0.38) (default parameters)
Trimmed sequence reads were mapped to GRCh38/hg38 using STAR (v2.7.1a) with default parameters
Read count extraction and normalization were performed using DESeq2 (v1.28.1).
Assembly: hg38
Supplementary files format and content: tab-delimited tsv files include RPKM values for each Sample

source_name: T cells

growth_protocol: Human peripheral blood mononuclear cells (PBMC) from healthy donors were cultured in RMPI-1640 medium supplemented with 5% Human Serum AB (Gemini), 1% penicillin-streptomycin, 1% non-essential amino acids, 1% GlutaMAX, 1mM sodium pyruvate, 0.1M HEPES, 50μM β-mercaptoethanol in the presence of human IL-2 (100U/ml, Peprotech). Anti-human CD3 (1μg/ml, BioLegend) and anti-human CD28 (1μg/ml, BioLegend) monoclonal antibodies were used to activate PBMCs for three days.

treatment_protocol: Purified human T cells were activated and expanded in the indicated culture conditions: pH7.4, pH6.6, lactic acid (Sangon) or sodium lactate (Sangon). The following metabolites were used to supplement pH6.6 or 10mM lactic acid medium: Met 800μM (MCE), SAM 100μΜ (MCE) or SAH 100μM (Sigma).

value: T cells

value: PH Control


title: d35MNplusGlia_E9

description:
10x Genomics
raw data are located at DUOS:
gs://fc-5126c21e-7f7f-47a5-9329-f8fcc00aec7a/limone_cellreports_2022/scRNAseq/bams/d35MNplusGlia_E9.bam

source_name: Pooled liMNs villages, day 35, replicate2, scRNAseq


title: P8_ctrl_sup_04 [Single cone cell RNA-seq]


title: d35MNplusGlia_E11

description:
10x Genomics
raw data are located at DUOS:
gs://fc-5126c21e-7f7f-47a5-9329-f8fcc00aec7a/limone_cellreports_2022/scRNAseq/bams/d35MNplusGlia_E11.bam

source_name: Pooled liMNs villages, day 35, replicate3, scRNAseq


title: P8_ctrl_inf_22 [Single cone cell RNA-seq]

value: inferior-cone


title: P8_ctrl_sup_03 [Single cone cell RNA-seq]

value: superior-cone


title: d35MNplusGlia_F1

description:
10x Genomics
raw data are located at DUOS:
gs://fc-5126c21e-7f7f-47a5-9329-f8fcc00aec7a/limone_cellreports_2022/scRNAseq/bams/d35MNplusGlia_F1.bam

source_name: Pooled liMNs villages, day 35, replicate1, scRNAseq


title: P8_ctrl_inf_19 [Single cone cell RNA-seq]

value: post natal day 8


title: P8_ctrl_sup_01 [Single cone cell RNA-seq]


title: P8_ctrl_inf_18 [Single cone cell RNA-seq]


title: 34850: Liver, WSD/CD


title: T cells, control, replicate 4

value: Control


title: T cells, pH6.6, replicate 1


title: P8_ctrl_inf_16 [Single cone cell RNA-seq]


title: P8_ctrl_inf_17 [Single cone cell RNA-seq]


title: P8_ctrl_inf_23 [Single cone cell RNA-seq]


title: T cells, PH control, replicate 1


title: P8_ctrl_inf_14 [Single cone cell RNA-seq]


title: 33499: Liver, WSD/CD


title: T cells, control, replicate 2


title: 34471: Liver, WSD/CD


title: 34551: Liver, WSD/CD


title: T cells, 10mM lactic acid, replicate 4

value: 10mM lactic acid


title: P8_ctrl_inf_11 [Single cone cell RNA-seq]


title: P8_ctrl_inf_12 [Single cone cell RNA-seq]


title: T cells, pH6.6, replicate 2


title: P8_ctrl_inf_09 [Single cone cell RNA-seq]


title: 33335: Liver, CD/CD

value: CD/CD


title: P8_ctrl_inf_21 [Single cone cell RNA-seq]


title: P8_ctrl_inf_20 [Single cone cell RNA-seq]


title: T cells, 10mM lactic acid, replicate 3


title: 34886: Liver, WSD/CD


title: T cells, 10mM lactic acid, replicate 2


title: P8_ctrl_sup_02 [Single cone cell RNA-seq]


title: P8_ctrl_inf_05 [Single cone cell RNA-seq]


title: 33573: Liver, CD/CD


title: P8_ctrl_inf_15 [Single cone cell RNA-seq]


title: P8_ctrl_inf_03 [Single cone cell RNA-seq]


title: T cells, H3K4me3, control, replicate 1

library_source: genomic

data_processing:
Sequence reads were quality trimmed to a minimum phred score of 20 using Trimmomatic (v0.38).
All reads were aligned to the hg38 human genome using Bowtie2 (v 2.2.8) (--local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700)
The samples without spike-in DNA were normalized using ChIPseqSpikeInFree method.
For H3K27me3, peaks were called using MACS2 (v 2.2.6) with options ‘-g hs -f BAMPE --keep-dup all --broad --broad-cutoff 0.1’. While for H3K4me3, peak calling used MACS2 with parameters ‘-g hs -q 0.01 -f BAMPE --keep-dup all’.
bigWig files were generated using the BEDtools (v2.25.0). Score represents the normalized coverage of DNA fragments at a given genomic coordinate. BroadPeak and narrowPeak files were generated using MACS v2.
Assembly: hg38
Supplementary files format and content: bigWig, broadPeak, narrowPeak
Library strategy: CUT&Tag

molecule: genomic DNA

extract_protocol:
1×10^5 T cells were lysed to extract nucleic materials and incubated with ConA beads at room temperature for 10 min. Resuspend cells in 50 µL antibody buffer pre-mixed with primary antibody (Anti-H3K27me3 or H3K4me3), incubated for overnight at 4℃. The samples were incubated with mixing secondary antibody at room temperature for 30 minutes, and then co-incubated with the proteinA/G-Tn5 transposase at room temperature for 1 h to disturb DNA fragmentation.
ChIP-seq libraries were prepared using Hyperactive Universal CUT&Tag Assay Kit for Illumina (TD903, Vazyme, China)

tag: chip antibody


title: 33500: Liver, WSD/CD


title: P8_ctrl_inf_13 [Single cone cell RNA-seq]


title: T cells, control, replicate 1


title: 31508: Liver, CD/WSD

value: CD/WSD


title: 33657: Liver, CD/CD


title: 33337: Liver, WSD/CD


title: T cells, control, replicate 3


title: P8_ctrl_inf_08 [Single cone cell RNA-seq]


title: T cells, H3K4me3, lactic acid with 800μM methionine, replicate 1

value: lactic acid with 800μM methionine


title: P2_ctrl_sup_21 [Single cone cell RNA-seq]

source_name: P2 single cone

value: post natal day 2


title: P8_ctrl_inf_07 [Single cone cell RNA-seq]


title: 33316: Liver, CD/CD


title: 31347: Liver, CD/WSD


title: P2_ctrl_sup_20 [Single cone cell RNA-seq]


title: 31266: Liver, CD/CD


title: P2_ctrl_sup_18 [Single cone cell RNA-seq]


title: P8_ctrl_inf_06 [Single cone cell RNA-seq]


title: 33215: Liver, CD/CD


title: T cells, H3K4me3, 10mM lactic acid, replicate 1


title: P8_ctrl_inf_04 [Single cone cell RNA-seq]


title: T cells, 10mM lactic acid, replicate 1


title: P8_ctrl_inf_10 [Single cone cell RNA-seq]


title: 30734: Liver, WSD/CD


title: P2_ctrl_sup_17 [Single cone cell RNA-seq]


title: 31701: Liver, CD/WSD


title: P8_ctrl_inf_02 [Single cone cell RNA-seq]


title: T cells, H3K4me3, control, replicate 2

value: control


title: 31700: Liver, WSD/WSD

value: WSD/WSD


title: P2_ctrl_sup_26 [Single cone cell RNA-seq]


title: P2_ctrl_sup_25 [Single cone cell RNA-seq]


title: P2_ctrl_sup_13 [Single cone cell RNA-seq]


title: P2_ctrl_sup_24 [Single cone cell RNA-seq]


title: T cells, H3K4me3, lactic acid with 800μM methionine, replicate 2


title: P2_ctrl_sup_23 [Single cone cell RNA-seq]


title: T cells, H3K27me3, lactic acid with 800μM methionine, replicate 2


title: 31479: Liver, WSD/WSD


title: 30638: Liver, WSD/CD


title: P2_ctrl_sup_22 [Single cone cell RNA-seq]


title: P8_ctrl_inf_01 [Single cone cell RNA-seq]


title: P2_ctrl_sup_09 [Single cone cell RNA-seq]


title: P2_ctrl_sup_08 [Single cone cell RNA-seq]


title: 30726: Liver, CD/CD


title: P2_ctrl_sup_19 [Single cone cell RNA-seq]


title: T cells, H3K4me3, 10mM lactic acid, replicate 2


title: P2_ctrl_sup_16 [Single cone cell RNA-seq]


title: T cells, H3K27me3, control, replicate 2


title: P2_ctrl_sup_06 [Single cone cell RNA-seq]


title: 30639: Liver, CD/CD


title: T cells, H3K27me3, control, replicate 1


title: T cells, H3K27me3, 10mM lactic acid, replicate 1


title: 30398: Liver, WSD/WSD


title: P2_ctrl_sup_04 [Single cone cell RNA-seq]


title: P2_ctrl_sup_02 [Single cone cell RNA-seq]


title: P2_ctrl_sup_12 [Single cone cell RNA-seq]


title: P2_ctrl_sup_10 [Single cone cell RNA-seq]


title: P2_ctrl_sup_01 [Single cone cell RNA-seq]


title: 30397: Liver, WSD/WSD


title: T cells, H3K27me3, lactic acid with 800μM methionine, replicate 1


title: WM_Lesion, CD8, 06

city: Amsterdam

first: Jeen

last: Engelenburg

address: Meibergdreef 47

country: Netherlands

institute: Netherlands Institute for Neuroscience

data_processing:
Adapter sequences were trimmed using Trimmomatic (version 0.39).
Trimmed reads were mapped to the human GRCh38 genome using HISAT2 (version 2.2.1) on default settings
Feature counts of reads mapped to genes were determined using HTSeq (version 1.99.2) with the ‘Homo_sapiens.CRCh38.105.gtf’ file (options: -m union -f bam -r name -s no -a 10 -t exon -i gene_id)
Resulting counts of both datasets were analyzed separately using R (version 4.2.0) and Bioconductor (version 3.15)
Assembly: GRCh38
Supplementary files format and content: tab-delimited .txt file containing raw, unnormalised counts for each sample

extract_protocol:
Sorted cells were lysed in buffer RLT (QIAGEN) plus 1% β-mercaptoethanol and stored at -80°C until further processing. Total RNA was isolated with the RNeasy micro kit (QIAGEN) according to the manufacturers’ instructions.
PolyA-enrichment and NebNEXT low input library prep kit

treatment_protocol: Brain T cells were isolated from post-mortem brain tissue using enzymatic dissociation, followed by density gradient centrifugation and fluorescence-activated cell sorting using live/dead, CD3, CD4, CD8, CD69, and CD103 staining.

tag: cell number

tag: tcell

tag: lesion type

tag: patient

tag: Sex

value: F


title: 30637: Liver, CD/CD

value: Liver


title: P2_ctrl_sup_15 [Single cone cell RNA-seq]


title: P2_ctrl_inf_29 [Single cone cell RNA-seq]


title: T cells, H3K27me3, 10mM lactic acid, replicate 2


title: 30339: Liver, CD/WSD

value: 3 years


title: P2_ctrl_sup_14 [Single cone cell RNA-seq]


title: P2_ctrl_sup_07 [Single cone cell RNA-seq]


title: 30586: Liver, CD/CD


title: NAWM, CD8, 06

source_name: NAWM

value: NAWM


title: P2_ctrl_sup_05 [Single cone cell RNA-seq]


title: P2_ctrl_sup_11 [Single cone cell RNA-seq]


title: 30399: Liver, WSD/WSD


title: GM_Lesion, CD4, 06


title: GM_Lesion, CD8, 06


title: P2_ctrl_sup_03 [Single cone cell RNA-seq]


title: 30224: Liver, CD/WSD


title: P2_ctrl_inf_24 [Single cone cell RNA-seq]


title: WM_Lesion, CD4, 06


title: 30181: Liver, WSD/WSD


title: P2_ctrl_inf_22 [Single cone cell RNA-seq]


title: P2_ctrl_inf_23 [Single cone cell RNA-seq]


title: P2_ctrl_inf_30 [Single cone cell RNA-seq]


title: 30155: Liver, WSD/WSD


title: NAGM, CD8, 06

source_name: NAGM

value: NAGM


title: P2_ctrl_inf_21 [Single cone cell RNA-seq]


title: P2_ctrl_inf_27 [Single cone cell RNA-seq]


title: 30292: Liver, CD/WSD


title: P2_ctrl_inf_26 [Single cone cell RNA-seq]


title: NAGM, CD4, 06


title: P2_ctrl_inf_28 [Single cone cell RNA-seq]


title: P2_ctrl_inf_17 [Single cone cell RNA-seq]


title: NAWM, CD4, 06


title: P2_ctrl_inf_20 [Single cone cell RNA-seq]


title: P2_ctrl_inf_19 [Single cone cell RNA-seq]


title: WM_Lesion, CD8, 05


title: NAGM, CD8, 05


title: P2_ctrl_inf_13 [Single cone cell RNA-seq]


title: P2_ctrl_inf_18 [Single cone cell RNA-seq]


title: P2_ctrl_inf_12 [Single cone cell RNA-seq]


title: GM_Lesion, CD8, 05


title: P2_ctrl_inf_14 [Single cone cell RNA-seq]


title: P2_ctrl_inf_25 [Single cone cell RNA-seq]


title: P2_ctrl_inf_15 [Single cone cell RNA-seq]


title: NAWM, CD8, 05


title: P2_ctrl_inf_11 [Single cone cell RNA-seq]


title: P2_ctrl_inf_07 [Single cone cell RNA-seq]


title: GM_Lesion, CD4, 05


title: P2_ctrl_inf_10 [Single cone cell RNA-seq]


title: P2_ctrl_inf_09 [Single cone cell RNA-seq]


title: P2_ctrl_inf_04 [Single cone cell RNA-seq]


title: P2_ctrl_inf_03 [Single cone cell RNA-seq]


title: NAWM, CD4, 05


title: wt 9we rep1

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
Reads were aligned to the mouse mm10 genome using the aligner STAR (version 2.7.3a) with extra options "--outFilterMultimapNmax 10 --outSAMmultNmax 1" for handling multimapping reads.
Aligned reads were assigned to ensembl genes (version 101) using the tool featureCounts from the subread package (version 2.0.1) with extra options "-O -M --read2pos 5 --primary -s 2".
All further analysis steps were performed with R/Bioconductor (R version 4.0.3, Bioconductor version 2.50.0). Gene counts were loaded in to R and differential gene expression analysis followed the edgeR workflow.
Specifically, genes were filter for expression using the function filterByExpr which retained 19504 genes.
Samples were classified into 4 groups according to genotype (wt and mut) and time point (5 days and 9 weeks) and differential gene expression was performed between all 4 groups using the functions glmQLFit and glmQLFTest.
Genome_build: mm10
Supplementary_files_format_and_content: tab seperated text file with columns: 1. ENSEMBL ID; 2. ENTREZ ID; 3. Symbol; 4. Description; 5. Length (exon union); 6. - 18. counts

source_name: Left and right cardiac ventricle

growth_protocol: No growth

extract_protocol:
Tissue was lysed in TRI reagent (Molecular Research Center, Inc., Cincinnati, OH, USA) and RNA extracted with Direct-zol RNA MiniPrep kit including Zymo-Spin II and DNAse restriction step (R2050, Zymo research, Irvine, CA, USA).
Library preparation was performed, starting from 200ng total RNA, using the TruSeq Stranded mRNA Library Kit (#20020595, Illumina, San Diego, CA, USA) and the TruSeq RNA UD Indexes (#20022371, Illumina). 15 cycles of PCR were performed.

value: wild type

tag: time point

value: m


title: WM_Lesion, CD8, 04

value: M


title: P2_ctrl_inf_08 [Single cone cell RNA-seq]

value: inferior-cone


title: P2_ctrl_inf_06 [Single cone cell RNA-seq]


title: WM_Lesion, CD4, 05


title: NAGM, CD4, 05


title: wt 9we rep3

value: f


title: NAGM, CD8, 04


title: wt 9we rep2


title: P2_ctrl_inf_02 [Single cone cell RNA-seq]


title: NAWM, CD8, 04


title: wt 5d rep3


title: P2_ctrl_inf_01 [Single cone cell RNA-seq]


title: P2_ctrl_inf_16 [Single cone cell RNA-seq]


title: NAWM, CD4, 04


title: P2_ctrl_inf_05 [Single cone cell RNA-seq]


title: wt 5d rep1


title: mut 9we rep3

value: Dsg2-W2A homozygouse mutant


title: NAWM, CD8, 03


title: NAWM, CD4, 03


title: mut 5d rep3


title: wt 5d rep2


title: mut 5d rep4


title: WM_Lesion, CD8, 02


title: mut 5d rep2


title: NAGM, CD8, 02


title: mut 5d rep1


title: TrtdD12

city: Richland

first: James

middle: Michael

last: Fulcher

state: Washington

address: 902 Battelle Blvd

department: Environmental Molecular Sciences Laboratory

institute: Pacific Northwest National Laboratory

data_processing:
Data quality was assessed with fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Read-trimming was conducted using bbduk (http://jgi.doe.gov/data-and-tools/bb-tools/).
Reads were aligned to the mouse genome using STAR (https://github.com/alexdobin/STAR).
BAM file outputs were mapped to genes using featureCounts (Liao, Smyth and Shi, 2013) using default settings.
Assembly: Genome Reference Consortium Mouse Build 39 (https://www.ncbi.nlm.nih.gov/genome/?term=txid10090)
Supplementary files format and content: .txt files represent number of raw read counts mapping to each gene

source_name: C10 alveolar type II epithelial cells

growth_protocol: C10 alveolar type II epithelial cells were cultured in RPMI containing 10% (vol/vol) FBS, 2 mM L-glutamine.

extract_protocol:
Single cell was sorted using CellenONE into NanoPOTS wells containing 0.1% DDP in 10 mM Tris pH8
For RNA‐Seq, TheSMART-seq V4 (cat#R400753) was used to generate cDNA library for illumina NextSeq 550 platform according to the manufacture protocol. Single-read sequencing of the cDNA libraries with a read length of 150 was performed with NextSeq 500 Sequencing System using NextSeq 500/550 High Output v2 kit 150 cycles (cat#20024907).

treatment_protocol: C10 cells were seeded at 200,000 cells per 10mM dish and incubate overnight. The cells were treated with 10nM R03306 for 36 hours before harvesting for single cell sorting using CellenONE.

value: alveolar type II epithelial cells


title: NAWM, CD8, 02


title: TrtdD9


title: WM_Lesion, CD4, 02


title: NAGM, CD4, 02


title: TrtdD8


title: mut 9we rep1


title: mut 9we rep2


title: TrtdD7


title: WM_Lesion, CD8, 01


title: NAGM, CD8, 01


title: TrtdD6


title: NAWM, CD4, 02


title: TrtdD4


title: NAWM, CD8, 01


title: TrtdD5


title: differentiated hiPSCs_dMet_H3K27me3_rep2

city: Yokohama

first: Hiroki

last: Ozawa

state: Kanagawa

address: 4259-B-25 Nagatsuta-cho, Midori-ku

department: School of Life Science and Technology

country: Japan

institute: Tokyo Institute of Technology

data_processing:
The Reads were then mapped on hg38 using bowtie.
For normalization and peak calling of ChIP-seq data, we used DROMPA2 (Nakato et al., 2013).
Data visualization, genomic location analysis, and differential analysis were performed using Subio platform (Subio, Inc.) and Integrative Genomics Viewer (Broad Institute).
Assembly: hg38
Supplementary files format and content: peak text files

source_name: undifferentiated hiPSCs

growth_protocol: Ff-I01s01 was maintained in StemFit AK03N (Ajinomoto, Tokyo). StemFit media were supplemented with Penicillin and Streptomycin. Human iPSCs were freeze-thawed and cultured on a 100 mm CellBIND dish (Corning) pre-coated overnight with Synthemax II (Corning Cat No.3535) in maintenance media supplemented with 10 µM Y27632 (Wako Cat No.251-00514). Initiation of differentiation was done by replacing the culture with StemFit Basic03 media with 3 µM CHIR99021 (Stemgent), 100 ng/mL recombinant human Activin-A (Cell Guidance Systems).

extract_protocol:
HiPSCs were suspended in 1x Lysis buffer [15 mM NaCl, 60mM KCl, 5 mM MgCl2, 15 mM Tris-HCl (pH 7.5), 0.1 mM EGTA (pH 8.0), 0.3M Sucrose, 0.5mM DTT, 1% Nonidet P-40 (NP40), 1 mM PMSF, 1x Protease Inhibitor Cocktail (Nacalai Tesque)] and harvested with 1.2M Sucrose supplemented 1x Lysis buffer. Pellets were resuspended in micrococcal nuclease (MNase) buffer [0.3M Sucrose, 4mM MgCl2, 1mM CaCl2, 50mM Tris-HCl (pH 7.5)] and applied for chromatin fragmentation with 1.5U MNase for 15 min at 37°C. The reaction was stopped by adding 0.5M EDTA. The supernatant was added with Incubation buffer [50mM NaCl, 20mM Tris-HCl (pH 7.5), 0.1% NP40, 1mM PMSF] then incubated with Dynabeads M-280 Sheep anti-Mouse IgG (Invitrogen) and the following antibodies at 4°C overnight: mouse control IgG (#ab37355, Abcam), anti-H3K4me3 (#307-34813, Wako), anti-H3K27me3 (#301-95253, Wako). The ChIP samples were washed with the wash buffer [20mM Tris-HCl (pH 7.5), 10mM EDTA, 0.01% NP40, gradient salt concentration (75 - 100 - 175 mM NaCl)] 3 times. After 30 min RNase reaction at 37°C, DNA was eluted with Proteinase K (Nacalai Tesque) for 4 h at 56°C. To check the yield of chromatin shearing, 50% of input material was added with SDS (final concentration 5%) followed by RNase and Proteinase K reactions. DNA samples were purified using QIAquick PCR Purification Kit (Qiagen).
ChIP samples were prepared as sequencing libraries using NEBNext Ultra II DNA Library Prep Kit for Illumina and sequenced using Illumina HiSeq 2000, and single-end reads were generated.

treatment_protocol: Met deprival pretreatment was done by culturing the cells for 5 h in Met-deprived StemFit AK03N (= KA01 medium) or control complete media (StemFit KA01+100 µM Met) (Ajinomoto, Tokyo), before initiation of differentiation.

value: undifferentiated hiPSCs

value: Met deprived medium


title: differentiated hiPSCs_complete_H3K27me3_rep2

value: Complete medium


title: TrtdD3


title: TrtdD2


title: differentiated hiPSCs_dMet_H3K27me3_rep1


title: medulla, CD8_TRM, 06

data_processing:
Adapter sequences were trimmed using Trimmomatic (version 0.39), fastp (version 0.23.2).
Trimmed reads were mapped to the human GRCh38 genome using HISAT2 (version 2.2.1) on default settings
Feature counts of reads mapped to genes were determined using HTSeq (version 2.0.2) with the ‘Homo_sapiens.CRCh38.105.gtf’ file (options: -m union -f bam -r name -s no -a 10 -t exon -i gene_id)
Resulting counts of both datasets were analyzed separately using R (version 4.2.0) and Bioconductor (version 3.15)
Assembly: GRCh38
Supplementary files format and content: tab-delimited .txt file containing raw, unnormalised counts for each sample

source_name: medulla

value: medulla

value: PIFTD


title: TrtdD10


title: TrtdD1


title: TrtdD11


title: undifferentiated hiPSCs_dMet_H3K27me3_rep2


title: TrtdC12


title: undifferentiated hiPSCs_dMet_H3K27me3_rep1


title: sub_WM, CD8_TRM, 06


title: CC_WM, CD8_TRM, 06


title: TrtdC11


title: TrtdC10


title: medulla, CD8_TRM, 05

value: VD


title: undifferentiated hiPSCs_complete_H3K27me3_rep1


title: NAGM, CD4, 01


title: differentiated hiPSCs_dMet_H3K4me3_rep2


title: TrtdC9


title: TrtdC8


title: NAWM, CD4, 01


title: differentiated hiPSCs_complete_H3K27me3_rep1


title: medulla, CD8_TRM, 04


title: differentiated hiPSCs_dMet_H3K4me3_rep1


title: TrtdC7


title: differentiated hiPSCs_complete_H3K4me3_rep2


title: WM_Lesion, CD4, 01


title: sub_WM, CD8_TRM, 04


title: differentiated hiPSCs_complete_H3K4me3_rep1


title: sub_WM, CD8_TRM, 03

value: NARCO


title: CC_WM, CD8_TRM, 03


title: undifferentiated hiPSCs_dMet_H3K4me3_rep2


title: undifferentiated hiPSCs_complete_H3K27me3_rep2


title: TrtdC4


title: TrtdC3


title: Blood, CD8_TEMRA, 03

source_name: Blood

value: Blood


title: TrtdC6


title: TrtdC2


title: undifferentiated hiPSCs_dMet_H3K4me3_rep1


title: undifferentiated hiPSCs_complete_H3K4me3_rep2


title: Blood, CD8_TEM, 03


title: sub_WM, CD8_TRM, 05


title: TrtdB12


title: medulla, CD8_TRM, 02


title: TrtdB11


title: undifferentiated hiPSCs_complete_H3K4me3_rep1


title: TrtdC1


title: GM, CD8_TRM, 02

source_name: GM

value: GM


title: medulla, CD8_TRM, 03


title: CC_WM, CD8_TRM, 02


title: TrtdC5


title: TrtdB9


title: TrtdB8


title: TrtdB7


title: TrtdB10


title: sub_WM, CD8_TRM, 02


title: blood_ROBE_S9_T1

type: RNA

city: Oklahoma City

first: Susan

middle: Kasko

last: Munster

address: 6500 S. MacArthur Blvd.

department: Office of Aerospace Medicine

institute: Federal Aviation Admininistration

hyb_protocol: Thermo Fisher Scientific GeneChip Hybridization, Wash, and Stain Kit

scan_protocol: Washed on GeneChip fluidics station 450 using protocol FS450-0001, then scanned using a 7G GeneChip Scanner 3000

data_processing: Data was normalized in R using the oligo package and assessed for differential expression using the limma package. R package Timecourse was also used to rank probesets for significant gene expression changes over the four timepoints.

label: biotin

source_name: blood, ROBE, pre-hypoxia exposure

label_protocol: labeling protocol not provided

extract_protocol:
collection protocol: samples collected in PAXgene blood RNA tubes, inverted 10X, then frozen at -20°C overnight, then frozen at -80°C until thawed for extraction
QIAGEN PAXgene Blood miRNA kit performed on a QIAcube
QA/QC protocol: concentration measured using a Nanodrop 2000, quality assessed using an Agilent Bioanalyzer 2100 & Agilent RNA6000 Nano assay

treatment_protocol: Blood was collected prior to exposure to hypoxic environment (T1), exposure to hypoxic environment (AC, ROBE, or ROBD) occurred for up to 45 minutes, subjects breathed 100% O2 for 5 minutes before and after exposure to hypoxic environment, blood collection occurred immediately thereafter (T2), blood collection conducted at 15 minutes after (T3) and 2 hours after (T4) cessation of hypoxic environment exposure.

value: blood

tag: gender

value: male

tag: treatment group

value: ROBE

tag: time

value: pre-hypoxia exposure


title: Blood, CD8_TEMRA, 01

tag: tissue

value: COVID

value: F


title: blood_ROBE_S9_T2

source_name: blood, ROBE, 0 minutes post hypoxia exposure

value: 0 minutes post hypoxia exposure


title: blood_ROBE_S9_T4

source_name: blood, ROBE, 2 hours post hypoxia exposure

value: 2 hours post hypoxia exposure


title: blood_ROBE_S9_T3

source_name: blood, ROBE, 15 minutes post hypoxial exposure

value: 15 minutes post hypoxial exposure


title: TrtdB4

tag: cell type

value: alveolar type II epithelial cells

tag: treatment


title: blood_ROBD_S9_T4

source_name: blood, ROBD, 2 hours post hypoxia exposure

value: ROBD


title: GM, CD8, TRM, 11

treatment_protocol: Brain T cells were isolated from post-mortem brain tissue using enzymatic dissociation, followed by density gradient centrifugation and fluorescence-activated cell sorting using live/dead, CD3, CD4, CD8, CD69, and CD103 staining. Blood T cells were isolated from paired peripheral blood using density gradient centrifugation, followed by fluorescence-activated cell sorting using live/dead, CD3, CD4, CD8, CD45, and CCR7 staining.

value: AD

tag: marker

value: TRM


title: blood_ROBD_S9_T3

source_name: blood, ROBD, 15 minutes post hypoxia exposure

value: 15 minutes post hypoxia exposure


title: Blood, CD8_TEM, 01


title: GM, CD8, TRM, 07

value: PD

value: M


title: blood_ROBD_S9_T2

source_name: blood, ROBD, 0 minutes post hypoxia exposure


title: GM, CD8, TRM, 10

value: GM

value: HC


title: GM, CD8, TRM, 09


title: TrtdB6


title: TrtdB3


title: TrtdB2


title: TrtdB1


title: GM, CD8, TRM, 03


title: GM, CD8, TRM, pooled

value: pooled

value: ed

value: not determined


title: blood_AC_S9_T2

source_name: blood, AC, 0 minutes post hypoxia exposure

value: blood

value: male

value: AC


title: blood_ROBE_S7_T4

value: ROBE

value: 2 hours post hypoxia exposure


title: blood_AC_S9_T3

source_name: blood, AC, 15 minutes post hypoxia exposure


title: WM, CD4, TRM, 11

source_name: WM

value: WM

value: F


title: TrtdB5

value: alveolar type II epithelial cells


title: blood_AC_S9_T4

source_name: blood, AC, 2 hours post hypoxia exposure


title: blood_AC_S9_T1

source_name: blood, AC, pre-hypoxia exposure

value: pre-hypoxia exposure


title: GM, CD4, TRM, pooled

value: TRM


title: TrtdA12

source_name: C10 alveolar type II epithelial cells


title: blood_ROBD_S9_T1

source_name: blood, ROBD, pre-hypoxia exposure

value: ROBD


title: blood_ROBE_S7_T3

value: 15 minutes post hypoxial exposure


title: WM, CD8, TRM, 11

value: AD


title: Blood, CD4, TEMRA, 11

value: Blood

value: TEMRA


title: TrtdA11


title: blood_ROBE_S7_T2

value: 0 minutes post hypoxia exposure


title: TrtdA5


title: GM, CD8, TRM, 06

value: GM

value: PD

value: M


title: TrtdA10


title: blood_ROBD_S7_T4

value: blood

value: male


title: TrtdA9


title: TrtdA8


title: Blood, CD8, TEMRA, 11


title: Blood, CD8, TEM, 11

value: TEM


title: blood_ROBE_S7_T1

value: ROBE


title: WM, CD4, TRM, 10

value: WM

value: HC

value: F


title: TrtdA7

value: alveolar type II epithelial cells


title: Blood, CD8, TEM, 10


title: blood_AC_S7_T2

value: AC


title: Blood, CD4, TEMRA, 10


title: Blood, CD4, TEM, 11


title: Blood, CD4, TEM, 10


title: TrtdA6


title: WM, CD8, TRM, 10

value: TRM


title: TrtdA4


title: CtrlD11


title: blood_ROBD_S7_T3

value: ROBD

value: 15 minutes post hypoxia exposure


title: blood_ROBD_S7_T2


title: CtrlD10


title: blood_ROBE_S6_T4

value: 2 hours post hypoxia exposure


title: WM, CD4, TRM, 09

value: AD


title: blood_AC_S7_T4


title: Blood, CD8, TEMRA, 09

value: Blood

value: TEMRA


title: TrtdA3


title: Blood, CD8, TEMRA, 10


title: TrtdA2


title: CtrlD8


title: blood_ROBD_S7_T1

value: pre-hypoxia exposure


title: blood_AC_S7_T3

value: blood


title: TrtdA1


title: CtrlD7


title: CtrlD12


title: blood_AC_S7_T1

value: male


title: CtrlD5


title: CtrlD6


title: WM, CD8, TRM, 09


title: blood_ROBE_S6_T1


title: CtrlD9


title: Blood, CD4, TEMRA, 09


title: blood_ROBE_S6_T3

value: 15 minutes post hypoxial exposure


title: blood_ROBE_S6_T2

value: ROBE

value: 0 minutes post hypoxia exposure


title: Blood, CD8, TEMRA, 08

value: FTD

value: M


title: blood_ROBD_S6_T4


title: Blood, CD4, TEM, 09

value: TEM

value: F


title: Blood, CD4, TEMRA, 08


title: blood_AC_S6_T2

value: AC


title: WM, CD8, TRM, 08

value: WM

value: TRM


title: blood_AC_S6_T1


title: WM, CD4, TRM, 08


title: blood_ROBD_S6_T2

value: ROBD


title: CtrlD4

value: alveolar type II epithelial cells


title: CtrlC12


title: CtrlC11


title: blood_ROBD_S6_T3

value: 15 minutes post hypoxia exposure


title: blood_ROBD_S6_T1


title: Blood, CD8, TEM, 09

value: Blood

value: AD


title: Blood, CD8, TEM, 08


title: blood_AC_S6_T4

value: blood

value: 2 hours post hypoxia exposure


title: CtrlD1


title: blood_AC_S6_T3

value: male


title: WM, CD4, TRM, 07

value: PD


title: Blood, CD4, TEM, 08


title: WM, CD8, TRM, 07


title: CtrlD2


title: Blood, CD8, TEMRA, 07

value: TEMRA


title: CtrlC8


title: CtrlD3


title: Blood, CD8, TEM, 07


title: blood_ROBE_S21_T1

value: ROBE

value: pre-hypoxia exposure


title: blood_ROBE_S21_T2

value: 0 minutes post hypoxia exposure


title: blood_ROBD_S21_T4


title: CtrlC6


title: CtrlC7


title: CtrlC10


title: Blood, CD4, TEM, 07

value: TEM

value: M


title: CtrlC5


title: Blood, CD4, TEMRA, 07


title: blood_ROBE_S21_T4


title: blood_ROBE_S21_T3

value: 15 minutes post hypoxial exposure


title: WM, CD4, TRM, 06

value: WM

value: TRM


title: blood_ROBD_S21_T3

value: ROBD


title: CtrlC4

value: alveolar type II epithelial cells


title: CtrlC9


title: Blood, CD8, TEMRA, 06

value: Blood


title: Blood, CD8, TEM, 06


title: CtrlC1


title: CONTROL, RECOVERY, REP3

city: Princeton

first: Juechun

last: Tang

state: NJ

address: 25 william streeet

department: Chemical and Biological Engineering

institute: Princeton University

data_processing:
Reads qualities were assessed and mapped to Mu_origin 1 as reference genome using STAR.
Gene expression was quantified using featureCounts (Galaxy version 1.6.4+galaxy1).
DESeq2 v1.34.0 (code available at: https://github.com/CathyTJC/GCS-seq/blob/main/DEseq.R ) was performed to identify differential gene expression in both the drug treatment period and the recovery period.
Assembly: E.coli MG1655 U00096.3 modified to incorporate the Mu sequence. FASTA file and annotation file inlucded in the records
Supplementary files format and content: fasta file and *.gtf annoation file
Supplementary files format and content: text files containing the raw read counts mapped to each feature (gene)
Supplementary files format and content: tab-delimited text files containing  the log2FoldChange and p-values from differntial gene analysis

organism: Escherichia coli

growth_protocol: Cells were culutred in 25ml M9 glucose media for 20 h O/N shaking at 37 ˚C to reach stationary phase.

extract_protocol:
RNA was stablized using RNAprotect bacteria reagent (Qiagen, Germantown, MD). Total RNA was extracted using RNeasy Mini Kit with on-column DNA digestion with DNase I (Qiagen, Germantown, MD) following manufacturer’s instruction. rRNA depletion was performed using RiboCop rRNA Depletion Kit (Lexogen, Greenland, NH).
RNA libraryies was prepared using PrepX RNA-seq library preparation kit (Takara Bio, San Jose, CA).

treatment_protocol: Cells were treated with 5 µg/ml LEVO or 5 µg/ml MOXI or 5 µg/ml MMC for 1) 30 mins at 37˚C with shaking before RNA extraction, or 2) 5 h at 37˚C with shaking, followed by removal of drug, and 30 mins recovery in LB media.

tag: strain

tag: genotype

value: MG1655 pstS-glmS::cat-Mu gyrA-FLAG-kan

tag: media

value: LB

value: 30 mins recovery


title: WM, CD8, TRM, 06

tag: disease

tag: age


title: CtrlC3


title: CONTROL, RECOVERY, REP1


title: CtrlC2


title: Blood, CD4, TEMRA, 06

tag: cell number

tag: tcell


title: blood_ROBD_S21_T2

value: blood

value: male


title: Blood, CD4, TEM, 06

value: PD

tag: patient


title: WM, CD8, TRM, 05

value: HC

tag: Sex

value: F


title: CtrlB11


title: CtrlB12


title: blood_AC_S21_T4

value: AC

value: 2 hours post hypoxia exposure


title: blood_AC_S21_T2

value: 0 minutes post hypoxia exposure


title: blood_AC_S21_T1

value: pre-hypoxia exposure


title: MMC, RECOVERY, REP1

value: MMC


title: MMC, RECOVERY, REP3


title: CONTROL, RECOVERY, REP2


title: MMC, RECOVERY, REP2


title: blood_AC_S21_T3

value: 15 minutes post hypoxia exposure


title: WM, CD4, TRM, 05

value: WM

value: TRM


title: CtrlB10

value: alveolar type II epithelial cells


title: MOXI, RECOVERY, REP3

value: MG1655 pstS-glmS::cat-Mu gyrA-FLAG-kan

value: MOXI


title: CtrlB9


title: Blood, CD8, TEMRA, 05

value: Blood

value: TEMRA


title: blood_ROBD_S21_T1

value: blood

value: male

value: ROBD


title: blood_ROBE_S17_T4

value: ROBE


title: blood_ROBE_S17_T3

value: 15 minutes post hypoxial exposure


title: MOXI, RECOVERY, REP2

value: LB

value: 30 mins recovery


title: CtrlB8


title: blood_ROBE_S17_T2

value: 0 minutes post hypoxia exposure


title: Blood, CD8, TEM, 05

value: HC

value: TEM

value: F


title: CtrlB7


title: MOXI, RECOVERY, REP1


title: blood_ROBE_S17_T1

value: pre-hypoxia exposure


title: Blood, CD4, TEMRA, 05


title: LEVO, RECOVERY, REP3

value: LEVO


title: CtrlB6

value: alveolar type II epithelial cells


title: WM, CD8, TRM, 04

value: WM

value: MSA

value: TRM

value: M


title: Blood, CD4, TEM, 05

value: Blood


title: blood_ROBD_S17_T4

value: blood

value: male

value: ROBD

value: 2 hours post hypoxia exposure


title: CtrlB5


title: LEVO, RECOVERY, REP2

value: MG1655 pstS-glmS::cat-Mu gyrA-FLAG-kan

value: LB

value: 30 mins recovery


title: blood_ROBD_S17_T3

value: 15 minutes post hypoxia exposure


title: Blood, CD8, TEMRA, 04

value: TEMRA


title: LEVO, RECOVERY, REP1


title: CtrlB3


title: CONTROL, TREATMENT, REP2

value: M9 glucose

value: 30 mins treatment


title: CONTROL, TREATMENT, REP3


title: blood_ROBD_S17_T2

value: 0 minutes post hypoxia exposure


title: Blood, CD8, TEM, 04

value: TEM


title: CONTROL, TREATMENT, REP1


title: blood_AC_S17_T4

value: AC


title: blood_AC_S17_T3


title: blood_AC_S17_T2


title: Blood, CD4, TEMRA, 04

value: MSA


title: blood_ROBD_S17_T1

value: pre-hypoxia exposure


title: MMC, TREATMENT, REP3

value: MMC


title: CtrlB1

value: alveolar type II epithelial cells


title: CtrlA12


title: Blood, CD4, TEM, 04

value: Blood

value: M


title: CtrlB4


title: CtrlA11


title: WM, CD4, TRM, 04

value: WM

value: TRM


title: WM, CD8, TRM, 03

value: HC

value: F


title: CtrlA10


title: blood_AC_S17_T1

value: blood

value: male


title: MMC, TREATMENT, REP1

value: MG1655 pstS-glmS::cat-Mu gyrA-FLAG-kan

value: M9 glucose


title: CtrlB2


title: WM, CD4, TRM, 03


title: MMC, TREATMENT, REP2

value: 30 mins treatment


title: blood_ROBE_S14_T4

value: ROBE

value: 2 hours post hypoxia exposure


title: MOXI, TREATMENT, REP3

value: MOXI


title: blood_ROBE_S14_T3

value: 15 minutes post hypoxial exposure


title: CtrlA9


title: Blood, CD8, TEMRA, 03

value: TEMRA


title: blood_ROBE_S14_T2

value: 0 minutes post hypoxia exposure


title: CtrlA8

value: alveolar type II epithelial cells


title: CtrlA7


title: MOXI, TREATMENT, REP1


title: MOXI, TREATMENT, REP2


title: LEVO, TREATMENT, REP3

value: LEVO


title: Blood, CD4, TEMRA, 03

value: Blood


title: blood_ROBD_S14_T4

value: ROBD


title: LEVO, TREATMENT, REP2


title: CtrlA6


title: Blood, CD4, TEM, 03

value: HC

value: TEM


title: blood_ROBD_S14_T3

value: blood

value: 15 minutes post hypoxia exposure


title: WM, CD8, TRM, 02

value: WM

value: MDD

value: TRM

value: F


title: CtrlA5


title: blood_ROBD_S14_T2

value: male


title: CtrlA4


title: WM, CD4, TRM, 02


title: Blood, CD8, TEMRA, 02


title: Mu-ori-ter, FLAGless, LEVO, rep3, Input Control

description:
4MU 12
Mu_ori_ter_MG_genomic.fasta
4Mu-LEVO-strength.txt

data_processing:
Sequencing reads were trimmed using Trim Galore! (Galaxy Version 0.6.3) and mapped to Mu_origin 1 genome using BWA-MEM (version 0.7.17.1).
The resulting BAM files was filtered to retain reads that have a mapping quality >=20.
Read depth at each position was calculated using SAMtools depth taking the filtered BAM file as input. The maximum number of considered alignments was set to 100000 to prevent depth saturation with default upper boundary.
For further processing, we used GCS-seq pipeline avaialbe at (https://github.com/CathyTJC/GCS-seq/blob/main/GCS_calling.py). Briefly, we built an algorithm that searches for the 4-bp gap pattern using the sequencing coverage depth as the sole input to identify genome-wide gyrase cleavage sites
Assembly: E.coli MG1655 U00096.3 modified to incorporate the Mu sequence at designated locations. FASTA files are inlucded in the records
Supplementary files format and content: *.fasta/.fa files: file used for mapping of raw sequencing data
Supplementary files format and content: *.txt files (e.g., LEVO_Flag1.txt) contain the coverage depth at each position
Supplementary files format and content: *sh.txt/*strength.txt files contain the identified GCS genomic coordinates and assocaited cleavage strengths for each replicate

extract_protocol:
All steps ares performed at 4˚C. The cultures were centrifuged at 4000 rpm for 10 mins at 4˚C, washed twice with 10 ml ice-cold PBS, and the cell pellet was store at -80 ˚C for at least 24 h. Cell pellet was thawed and resuspended in 2ml ChIP lysis buffer followed by incubation for ~1 h. After incubation, the samples were then sonicated for ~9-13 mins (10 sec on/10 sec off, 30% amplitude) to yield DNA fragments of ~300-500 bps using Q500 sonicator (500W, 110V with four probe horn assembly, QSONICA, Newtown, CT). Lysate was then centrifuged at 4000 rpm for 10 minutes and the cleared supernatant was kept for further processing. 20 µL supernatant was used as input controls and stored at -20˚C in low-bind tubes (Eppendorf, Enfield, CT). For each sample, 50μL Agarose Anti-FLAG M2 gel pack (Sigma-Aldrich, St. Louis, MO) was prepared by three successive washes with 1 ml TBS buffer and equilibration with 1 ml ChIP Lysis Buffer. Each wash was achieved by centrifugation at 8000xg for 30sec and removal of supernatant. 900µl supernatant was transferred to the prepared resin and incubated at 4 ˚C for 18 h on a tube rotator (Thermo Fisher Scientific, Waltham, MA). After 18 h of incubation, the samples were washed twice with 1 ml ChIP buffer and once in 1ml TE buffer at room temperature. Each wash was achieved by centrifugation at 8000 xg for 30sec and the removal of supernatant. TE buffer was added to both the ChIPped samples and thawed input controls to reach a total volume of 200 µl. 5µL of 20mg/ml proteinase K solution was added to the 200 µl sample and the sample was incubated for 3 h at 55˚C with occasional vortexing for mixing purpose. After 3 h of incubation, the samples were treated with 5 µl RNase (10 mg/ml) and further incubated for another 30 mins at 37˚C. Following the incubation, the samples were purified using Qiagen’s PCR Purification kit (Germantown, MD).
Library preparation was carried out using Accel-NGS 1S plus DNA library kit (Integrated DNA Technologies, formerly Swift Biosciences, Ann Arbor, MI) following manufacturer’s instruction. We used ~20 ng per sample for library preparation. For the clean-up steps, we used SPRI select purchased from Beckman Coulter (Indianapolis, IN). Swift Unique Dual Indexing Primers (X9096, Swift Biosciences, Ann Arbor, MI) were used for PCR indexing. The samples were mixed at equal amount (~50 ng) for a pooled library.

treatment_protocol: After 20 h incubation, the cells were treated with selected FQ (5 µg/ml LEVO or 5 µg/ml MOXI or 1 µg/ml CIP or 5 µg/ml GEMI or 5 µg/ml NOR) for 30 mins at 37˚C with shaking.

value: MG1655 pstS-glmS::cat-Mu yddY-yddW::Mu ydiY-pfkB::Mu aptI-rsmG::Mu gyrA-kan

tag: chip antibody

value: M9 glucose


title: CtrlA3


title: blood_ROBD_S14_T1

tag: gender

value: pre-hypoxia exposure


title: Blood, CD8, TEM, 03


title: blood_ROBE_S14_T1

tag: treatment group

value: ROBE


title: Blood, CD8, TEM, 02


title: CtrlA2

value: alveolar type II epithelial cells


title: blood_AC_S14_T4

value: AC

tag: time

value: 2 hours post hypoxia exposure


title: CtrlA1


title: Blood, CD4, TEMRA, 02

tag: tissue

value: Blood

value: TEMRA


title: blood_AC_S14_T3


title: O2D60

city: Providence

first: Nathalie

last: Oulhen

state: RI

address: 185 meeting street

institute: Brown university

description: single cell mRNA

data_processing:
The Cell Ranger Single Cell Software Suite 3.0.2 was used to perform single cells demultiplexing and UMI counting. Cell Ranger pre-build mouse transcriptome reference (mm10) was used for this analysis. Clustering analysis was performed using Seurat v 3.2.1. The data were filtered using a mitochondrial cut off at 5%. Cells with at least 700 and at most 8000 expressed genes (features) were included in the downstream analysis. Using SCTransform, the three datasets were normalized and integrated to identify conserved cell populations across the samples. The integration step was performed using 3000 features, the shared nearest neighbor graph was constructed using 50 dimensions, and clusters were identified using a resolution of 2. The rds attached here represents the integrated data before the filtration steps. Here is the link to the github: https://github.com/compbiocore/Dennery_scRNA/tree/senescence
Assembly: mm10

source_name: Hyperoxia at pnd60

extract_protocol: The single‐cell RNA‐seq protocol was performed using the ChromiumTM Single Cell 3′ reagent kit v3.1 chemistry and cells were loaded on a 10x Chromium Controller (10× Genomics, Pleasanton, CA). Libraries were sequenced on Illumina HiSeq with the  configuration of 2x150 bp paired-end runs.

value: lung


title: Mu-ori-ter, FLAGless, LEVO, rep3

description:
4MU 9
Mu_ori_ter_MG_genomic.fasta
4Mu-LEVO-strength.txt

value: Anti-FLAG M2 gel pack (Sigma-Aldrich, St. Louis, MO)

value: LEVO


title: blood_AC_S14_T2

value: blood

value: 0 minutes post hypoxia exposure


title: Blood, CD4, TEM, 02

source_name: Blood

value: MDD

value: TEM


title: Mu-ori-ter, FLAGless, LEVO, rep2

description:
4MU 8
Mu_ori_ter_MG_genomic.fasta
4Mu-LEVO-strength.txt


title: Mu-ori-ter, FLAGless, LEVO, rep1, Input Control

description:
4MU 10
Mu_ori_ter_MG_genomic.fasta
4Mu-LEVO-strength.txt


title: AirD60

description: single cell mRNA

source_name: Normoxia at pnd60


title: WM, CD8, TRM, 01

value: WM

value: MS

value: TRM

value: F


title: LEVO, TREATMENT, REP1

value: MG1655 pstS-glmS::cat-Mu gyrA-FLAG-kan

value: M9 glucose

value: 30 mins treatment


title: blood_ROBE_S13_T4

value: male

value: ROBE

value: 2 hours post hypoxia exposure


title: Mu-ori-ter, FLAGless, LEVO, rep1

description:
4MU 7
Mu_ori_ter_MG_genomic.fasta
4Mu-LEVO-strength.txt

value: MG1655 pstS-glmS::cat-Mu yddY-yddW::Mu ydiY-pfkB::Mu aptI-rsmG::Mu gyrA-kan


title: Mu-ori-ter, FLAGless, LEVO, rep2, Input Control

description:
4MU 11
Mu_ori_ter_MG_genomic.fasta
4Mu-LEVO-strength.txt

value: Anti-FLAG M2 gel pack (Sigma-Aldrich, St. Louis, MO)


title: WM, CD4, TRM, 01


title: O2D7

description: single cell mRNA

source_name: Hyperoxia at pnd7

value: lung


title: Mu-ori-ter, FLAG, LEVO, rep3, Input Control

description:
4MU 6
Mu_ori_ter_MG_genomic.fasta
4Mu-LEVO-strength.txt

value: LEVO


title: AirD7

description: single cell mRNA

source_name: Normoxia at pnd7


title: blood_ROBE_S13_T2

source_name: blood, ROBE, 0 minutes post hypoxia exposure

value: blood

value: 0 minutes post hypoxia exposure


title: blood_ROBE_S13_T3

source_name: blood, ROBE, 15 minutes post hypoxial exposure

value: 15 minutes post hypoxial exposure


title: SD7

description: single cell mRNA

source_name: Senescent cells at pnd7


title: Mu-ori-ter, FLAG, LEVO, rep1, Input Control

description:
4MU 4
Mu_ori_ter_MG_genomic.fasta
4Mu-LEVO-strength.txt


title: Blood, CD8, TEM, 01

value: Blood

value: TEM


title: Blood, CD4, TEMRA, 01

value: MS

value: TEMRA


title: blood_AC_S14_T1

value: AC

value: pre-hypoxia exposure


title: blood_ROBE_S13_T1

source_name: blood, ROBE, pre-hypoxia exposure


title: Mu-ori-ter, FLAG, LEVO, rep2, Input Control

description:
4MU 5
Mu_ori_ter_MG_genomic.fasta
4Mu-LEVO-strength.txt

value: M9 glucose


title: blood_ROBD_S13_T4

source_name: blood, ROBD, 2 hours post hypoxia exposure

value: male

value: ROBD


title: Blood, CD4, TEM, 01

value: F


title: Mu-ori-ter, FLAG, LEVO, rep2

description:
4MU 2
Mu_ori_ter_MG_genomic.fasta
4Mu-LEVO-strength.txt

value: MG1655 pstS-glmS::cat-Mu yddY-yddW::Mu ydiY-pfkB::Mu aptI-rsmG::Mu gyrA-kan


title: mouse 40 sepsis 3 d ST-HSC

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

data_processing:
Illumina HD.3.4.0/RTA 2.7.7 software used for sequencing and basecalling.
10x Genomics Cell Ranger v2.0.2/3.0.2 used for sequencing read alignment and UMI counting.
Genome_build: mm10
Supplementary_files_format_and_content: tar ball of mtx, tsv: UMI counts of individual genes in single cells

source_name: Bone marrow

extract_protocol:
Single cells were captured using the 10x Chromium system and further processed following the Chromium Single Cell 3’ Reagent Kit protocol.
cDNA library were fragmented and the sequencing library was generated according to the Single Cell 3’ Reagent Kit protocol.

tag: mouseid

value: Bone marrow

tag: cell type

value: ST-HSC

tag: condition

value: sepsis 3 d

tag: strain/genotype

value: Tie2-bG-Micm x RosaYFP

tag: age at experiment

value: 13-14 weeks


title: mouse 40 sepsis 3 d MPP

value: MPP


title: Mu-ori-ter, FLAG, LEVO, rep1

description:
4MU 1
Mu_ori_ter_MG_genomic.fasta
4Mu-LEVO-strength.txt

tag: strain

tag: genotype

value: Anti-FLAG M2 gel pack (Sigma-Aldrich, St. Louis, MO)

tag: media

tag: treatment

value: LEVO


title: mouse 40 sepsis 3 d CMP

value: CMP


title: Blood, CD8, TEMRA, 01

value: Blood

tag: disease

value: MS

tag: cell number

tag: tcell

tag: marker

value: TEMRA

tag: age


title: HCT116, BAP1 KO, RNA, rep2

first: Kai

last: Ge

address: 50 South Dr Rm 4154

description: mRNA

data_processing:
Basecalls performed using Bcl2fastq.
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2.
Peaks were called using SICER2 with following configuration - For ChIP-Seq of MLL4 and BAP1-T7: Windows (50), Gaps (50), FDR (1e-3); for ChIP-Seq of H3K4me1: Windows (200), Gaps (200), FDR (1e-3).
Paired-end reads of RNA-seq are aligned to the hg38 genome assembly using STAR.
SICER v1.1 was used to calculate the fragments per kilo base per million (FPKM) on exonic regions as expression measurements for each gene.
Assembly: hg38
Supplementary files format and content: wig files were generated using in-house script and the scores represent RPKM.
Supplementary files format and content: tab-delimited text files include RPKM values for each gene.

growth_protocol: HCT116 human colon cancer cells were cultured in McCoy’s 5A medium supplemented with 10% FBS.

extract_protocol:
1 μg total RNA was subjected to mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490).
Isolated mRNAs were reverse-transcribed into double stranded cDNA and subjected to sequencing library construction using the NEBNext Ultra™ II RNA Library Prep Kit for Illumina (NEB, E7770) according to the manufacturer’s instructions.

treatment_protocol: Wild type or MLL4 knockout HCT116 cells were infected with Doxycycline-inducible lentiviral pCW57.1 vector (Addgene #41393) expressing triple T7-tagged BAP1. 24 hours later, cells were selected with 1.5 μg/ml puromycin for 4 days and recovered for 2 days in culture media without puromycin. Cells were treated with 1 μg/mL Doxycycline for 24 hours and collected for Western blot and ChIP-Seq analyses.

tag: cell line

value: Human colorectal cancer

value: BAP1 KO


title: HCT116, BAP1 KO, RNA, rep1

description: mRNA


title: blood_ROBD_S13_T3

source_name: blood, ROBD, 15 minutes post hypoxia exposure

value: blood

tag: gender

value: male

tag: treatment group

value: ROBD

tag: time

value: 15 minutes post hypoxia exposure


title: blood_ROBD_S13_T2

source_name: blood, ROBD, 0 minutes post hypoxia exposure

tag: tissue

value: 0 minutes post hypoxia exposure


title: blood_ROBD_S13_T1

value: pre-hypoxia exposure


title: HCT116, control, RNA, rep2

description: mRNA

tag: cell type

value: WT


title: mouse 42 control CMP

tag: mouseid

value: Bone marrow

tag: condition

value: Uninfected control

tag: strain/genotype

value: Tie2-bG-Micm x RosaYFP

value: 13-14 weeks


title: FLAGless, CIP, rep3, Input Control

description:
CIP 12
Mu_ori_MG1655.edit.fa
CIP_sh.txt

tag: strain

tag: genotype

value: MG1655 pstS-glmS::cat-Mu gyrA-FLAG-kan

tag: chip antibody

value: Anti-FLAG M2 gel pack (Sigma-Aldrich, St. Louis, MO)

value: M9 glucose

value: CIP


title: FLAGless, CIP, rep2, Input Control

description:
CIP 11
Mu_ori_MG1655.edit.fa
CIP_sh.txt

tag: media

tag: treatment


title: HCT116, control, RNA, rep1

description: mRNA

value: Human colorectal cancer


title: Mu-ori-ter, FLAG, LEVO, rep3

description:
4MU 3
Mu_ori_ter_MG_genomic.fasta
4Mu-LEVO-strength.txt

value: MG1655 pstS-glmS::cat-Mu yddY-yddW::Mu ydiY-pfkB::Mu aptI-rsmG::Mu gyrA-kan

value: LEVO


title: mouse 42 control MPP

value: MPP

value: male

tag: age at experiment


title: mouse 42 control ST-HSC

value: ST-HSC


title: HCT116, MLL4 KO, RNA, rep2

description: mRNA

value: MLL4 KO


title: FLAGless, CIP, rep1, Input Control

description:
CIP 10
Mu_ori_MG1655.edit.fa
CIP_sh.txt


title: FLAGless, CIP, rep3

description:
CIP 9
Mu_ori_MG1655.edit.fa
CIP_sh.txt


title: blood_AC_S13_T3

source_name: blood, AC, 15 minutes post hypoxia exposure

value: blood

value: AC

value: 15 minutes post hypoxia exposure


title: mouse 40 sepsis 3 d HSC

value: Bone marrow

value: HSC

value: sepsis 3 d


title: mouse 42 control HSC

value: Uninfected control

value: Tie2-bG-Micm x RosaYFP

value: 13-14 weeks


title: HCT116, MLL4 KO, RNA, rep1

description: mRNA


title: blood_AC_S13_T4

source_name: blood, AC, 2 hours post hypoxia exposure

value: 2 hours post hypoxia exposure


title: blood_AC_S13_T1

source_name: blood, AC, pre-hypoxia exposure

value: pre-hypoxia exposure


title: FLAGless, CIP, rep2

description:
CIP 8
Mu_ori_MG1655.edit.fa
CIP_sh.txt

value: MG1655 pstS-glmS::cat-Mu gyrA-FLAG-kan

value: Anti-FLAG M2 gel pack (Sigma-Aldrich, St. Louis, MO)

value: M9 glucose

value: CIP


title: HCT116, WT, RNA, rep2

description: mRNA

value: Human colorectal cancer

value: WT


title: mouse 31 sepsis 1 d CMP

value: CMP

value: sepsis 1 d

value: male


title: FLAGless, CIP, rep1

description:
CIP 7
Mu_ori_MG1655.edit.fa
CIP_sh.txt


title: blood_AC_S13_T2

source_name: blood, AC, 0 minutes post hypoxia exposure

value: blood

value: AC

value: 0 minutes post hypoxia exposure


title: mouse 31 sepsis 1 d ST-HSC

value: Bone marrow

value: ST-HSC


title: mouse 31 sepsis 1 d MPP

value: MPP

value: Tie2-bG-Micm x RosaYFP

value: 13-14 weeks


title: HCT116, BAP1 KO, MLL4

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 min. Crosslinking reaction was stopped by 125 mM glycine for 10 min. 30 – 40 million cross-linked cells were resuspended in 5 mL lysis buffer (5 mM PIPES, pH 7.5, 85 mM KCl, 1% NP-40 and protease inhibitors), incubated on ice for 10 min, and spun down at 1,000 g for 5 min at 4°C. The pellet was washed once with 5 mL lysis buffer. Resulting nuclei were resuspended with 2 mL TE buffer (50 mM Tris-HCl, pH8.0, 10 mM EDTA and protease inhibitors) and sonicated for 10 min (30 sec on and 30 sec off) at 20% amplitude. After adding detergents to a final concentration of 1% Triton-X100, 0.1% SDS, 0.1% sodium deoxycholate (1x RIPA), sonicated chromatin was spun down at 15,000 g for 10 min at 4°C. For each ChIP, 10 µg of target antibodies and 2 μg of spike-in antibody (anti-H2Av, Active Motif, #61686) were mixed with 400 – 600 mg sonicated chromatin and incubated on a rotator at 4°C overnight. Next day, 50 μL prewashed protein A Dynabeads (Thermo Fisher) were added to chromatin-antibody complex and incubated for 2 hours at 4°C. ChIPed samples were washed twice with 1 mL RIPA, twice with 1 mL RIPA + 300mM NaCl, twice with 1 mL LiCl buffer and once with PBS. Samples were eluted in 100 μL buffer containing 0.1M NaHCO3, 1% SDS, and 20μg Proteinase K at 65°C overnight and DNA was purified using QIAquick PCR purification kit (Qiagen).
Libraries were prepared according to NEB (Illumina kit) instructions. DNA were used to construct libraries using NEBNext® Ultra™ II DNA Library Prep kit with AMPure XP magnetic beads (Beckman Coulter).

value: BAP1 KO

value: MLL4 (homemade, #3)


title: blood_ROBE_S12_T3

value: ROBE

value: 15 minutes post hypoxial exposure


title: HCT116, WT, RNA, rep1

description: mRNA

value: Human colorectal cancer


title: mouse 31 sepsis 1 d HSC

value: HSC


title: blood_ROBE_S12_T1

value: pre-hypoxia exposure


title: FLAG, CIP, rep3, Input Control

description:
CIP 6
Mu_ori_MG1655.edit.fa
CIP_sh.txt

value: MG1655 pstS-glmS::cat-Mu gyrA-FLAG-kan

value: Anti-FLAG M2 gel pack (Sigma-Aldrich, St. Louis, MO)

value: M9 glucose

value: CIP


title: FLAG, CIP, rep2, Input Control

description:
CIP 5
Mu_ori_MG1655.edit.fa
CIP_sh.txt


title: FLAG, CIP, rep1, Input Control

description:
CIP 4
Mu_ori_MG1655.edit.fa
CIP_sh.txt


title: HCT116, BAP1 KO, input


title: blood_ROBD_S12_T4

value: blood

value: male

value: ROBD

value: 2 hours post hypoxia exposure


title: blood_ROBE_S12_T4

source_name: blood, ROBE, 2 hours post hypoxia exposure


title: HCT116, MLL4 KO, MLL4

value: MLL4 KO


title: mouse 29 sepsis 1 d MPP

value: Bone marrow

value: MPP

value: sepsis 1 d

value: Tie2-bG-Micm x RosaYFP

value: 13-14 weeks


title: HCT116, MLL4 KO, input

value: Human colorectal cancer


title: FLAG, CIP, rep3

description:
CIP 3
Mu_ori_MG1655.edit.fa
CIP_sh.txt


title: mouse 29 sepsis 1 d ST-HSC

value: ST-HSC


title: blood_ROBD_S12_T3

value: 15 minutes post hypoxia exposure


title: mouse 29 sepsis 1 d HSC

value: HSC


title: FLAG, CIP, rep2

description:
CIP 2
Mu_ori_MG1655.edit.fa
CIP_sh.txt

value: MG1655 pstS-glmS::cat-Mu gyrA-FLAG-kan

value: Anti-FLAG M2 gel pack (Sigma-Aldrich, St. Louis, MO)


title: FLAG, CIP, rep1

description:
CIP 1
Mu_ori_MG1655.edit.fa
CIP_sh.txt

value: M9 glucose

value: CIP


title: HCT116, WT, input, rep2

value: WT


title: blood_ROBD_S12_T2

value: blood

value: male

value: ROBD

value: 0 minutes post hypoxia exposure


title: blood_ROBE_S12_T2

value: ROBE


title: mouse 25 control CMP

value: Bone marrow

value: CMP

value: Uninfected control


title: mouse 25 control MPP

value: MPP

value: Tie2-bG-Micm x RosaYFP

value: 13-14 weeks


title: mouse 29 sepsis 1 d CMP

value: sepsis 1 d


title: HCT116, ASXL2 KO, MLL4

value: Human colorectal cancer

value: ASXL2 KO

value: MLL4 (homemade, #3)


title: FLAGless, GEMI, rep2, Input Control

description:
GEMI 11
Mu_ori_MG1655.edit.fa
GEMI_sh.txt

value: MG1655 pstS-glmS::cat-Mu gyrA-FLAG-kan

value: Anti-FLAG M2 gel pack (Sigma-Aldrich, St. Louis, MO)

value: M9 glucose

value: GEMI


title: mouse 25 control ST-HSC

value: ST-HSC

value: male


title: FLAGless, GEMI, rep1, Input Control

description:
GEMI 10
Mu_ori_MG1655.edit.fa
GEMI_sh.txt


title: HCT116, ASXL2 KO, input


title: blood_AC_S12_T3

value: blood

value: AC

value: 15 minutes post hypoxia exposure


title: blood_AC_S12_T4

value: 2 hours post hypoxia exposure


title: mouse 25 control HSC

value: Bone marrow

value: HSC

value: Uninfected control


title: HCT116, WT, MLL4, rep1

value: WT


title: blood_AC_S12_T2

value: 0 minutes post hypoxia exposure


title: HCT116, WT, MLL4, rep2

value: Human colorectal cancer


title: FLAGless, GEMI, rep3

description:
GEMI 9
Mu_ori_MG1655.edit.fa
GEMI_sh.txt


title: mouse 24 control CMP

value: CMP

value: Tie2-bG-Micm x RosaYFP

value: 13-14 weeks


title: FLAGless, GEMI, rep2

description:
GEMI 8
Mu_ori_MG1655.edit.fa
GEMI_sh.txt

value: MG1655 pstS-glmS::cat-Mu gyrA-FLAG-kan

value: Anti-FLAG M2 gel pack (Sigma-Aldrich, St. Louis, MO)

value: M9 glucose


title: FLAGless, GEMI, rep3, Input Control

description:
GEMI 12
Mu_ori_MG1655.edit.fa
GEMI_sh.txt

value: GEMI


title: HCT116, WT, input, rep1


title: FLAGless, GEMI, rep1

description:
GEMI 7
Mu_ori_MG1655.edit.fa
GEMI_sh.txt


title: mouse 24 control MPP

value: MPP

value: male


title: HCT116, MLL4 KO/BAP1-T7, T7

value: MLL4 KO

value: Doxycycline

value: T7 tag (Cell Signaling Technology, 13246)


title: mouse 24 control ST-HSC

value: Bone marrow

value: ST-HSC


title: FLAG, GEMI, rep3, Input Control

description:
GEMI 6
Mu_ori_MG1655.edit.fa
GEMI_sh.txt


title: blood_ROBD_S12_T1

source_name: blood, ROBD, pre-hypoxia exposure

value: blood

value: ROBD

value: pre-hypoxia exposure


title: blood_AC_S12_T1

value: AC


title: HCT116, WT, H3K4me1

value: Human colorectal cancer

value: WT

value: H3K4me1 (Epicypher, 13-0040)


title: blood_ROBE_S11_T4

value: ROBE

value: 2 hours post hypoxia exposure


title: HCT116, MLL4 KO/BAP1-T7, input


title: blood_ROBE_S11_T3

value: 15 minutes post hypoxial exposure


title: HCT116, WT/BAP1-T7, T7


title: blood_ROBE_S11_T1


title: blood_ROBE_S11_T2

value: 0 minutes post hypoxia exposure


title: HCT116, WT/BAP1-T7, input


title: FLAG, GEMI, rep1, Input Control

description:
GEMI 4
Mu_ori_MG1655.edit.fa
GEMI_sh.txt

value: MG1655 pstS-glmS::cat-Mu gyrA-FLAG-kan

value: Anti-FLAG M2 gel pack (Sigma-Aldrich, St. Louis, MO)

value: M9 glucose

value: GEMI


title: FLAG, GEMI, rep3

description:
GEMI 3
Mu_ori_MG1655.edit.fa
GEMI_sh.txt


title: Pt21 (day1, day29) - CSP

city: Woolloongabba

first: Ranjeny

last: Thomas

address: 37 Kent St

country: Australia

institute: University of Queensland Diamantina Institute, Translational Research Institute

description:
Pt21_D1_D29_filtered_feature_bc_matrix.tar.gz
Pt04_Pt11_Pt19_Pt21_integrated_metadata.csv.gz
Pt04_Pt11_Pt19_Pt21_integrated_NormExpresMatrix.csv.gz

library_source: other

data_processing:
Single cell RNA-seq data was processed using the 10x Genomics Cell Ranger Software (v3.0.2). The command “cellranger mkfastq” was used to demultiplex raw BCL files and generate FASTQ files for individual samples. The command “cellranger count” was used to align RNA-Seq reads to the pre-built human reference genome GRCh38 and to filter out low quality cell barcodes and unique molecular identiﬁers (UMI). The resulting single-cell gene count matrices were further processed using the Seurat R package (v3.0.5)
Assembly: human GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.tar.gz, filtered_TCR_table.csv.gz

molecule: protein

source_name: CD45+ cells

extract_protocol:
PBMC were collected from each participant at baseline day1 and 28 days post-dosing (day29). CD45+ immune cells from all thawed PBMC samples were sorted via flow cytometric activated cell sorting.
The 10x Genomics Chromium instrument was used to partition each single cell with barcoded beads. GEM generation and barcoding, cDNA amplification, T-cell enrichment, cell surface protein and library construction was performed according to the 10X Genomics Chromium User Guide. Sequencing was performed using the Illumina NovaSeq 6000.

tag: individual

tag: disease state

value: RA

tag: duration ra

tag: treatment dose

value: 3mL dose

tag: mtx dose (mg)

value: PBMC

tag: sorted cells

value: CD45+ immune cells

value: day1 baseline and 28 days post-dosing


title: HD010_Healthy

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

data_processing:
FASTQ files were mapped using STAR to GRCh38 genome build
Gene counts were obtained using featureCounts on Gencodev31 annotations
Assembly: Gencodev31
Supplementary files format and content: gene_counts

source_name: PBMC

extract_protocol:
Venous blood was collected from subjects into ethylenediaminetetraacetic acid tubes.  Peripheral blood monocular cells (PBMCs) were isolated using SepMate tubes (STEMCELL Technologies) according to the manufacturer’s instructions.  Briefly, blood was diluted with phosphate buffered saline (PBS; Gibco) after plasma collection.  The diluted blood was then layered on top of Ficoll-Paque PLUS (Merck).  After centrifugation (1200 g, 10 min, brake on), the supernatant was poured into a 50 mL polypropylene tube.  Collected PBMCs were washed twice in PBS.  PBMCs were counted using a hemacytometer with trypan blue (Lonza) to determine cell viability.  Ribonucleic acid (RNA) was prepared using the PureLink RNA Mini kit (Thermo Fisher Scientific).
The total RNA was quantified using Qubit Fluorometer (ThermoFisher Scientific).  The purity was checked using NanoPhotometer spectrophotometer (Implen).  The integrity and quality of the RNA was assessed using Agilent Bioanalyzer 2100 system (Agilent Technologies) and agarose gel electrophoresis (1% agarose gel, 180 V, 16 min).  A total of 2 µg RNA from each sample was subjected to ribosomal RNA (rRNA) removal using Epicentre RiboZeroTM rRNA Removal Kit (Epicentre). The rRNA was cleaned up using ethanol precipitation method.  The Next Generation Sequencing (NGS) library was prepared using NEBNext UltraTM Directional RNA Library Prep Kit for Illumina (NEB).  In brief, the RNA were fragmented using divalent cations at 94°C in the presence of NEBNext First Strand Synthesis Reaction Buffer and Random Primers.  Subsequently, the first strand complementary deoxyribonucleic acid (cDNA) was synthesized using random hexamer and M-MulV reverse transcriptase and the second strand cDNA was synthesized using DNA Polymerase and RNAse H.  The dTTP was replaced by dUTP during the second strand cDNA synthesis. The double stranded cDNA fragment was converted to blunt end via end repair reaction and the NEBNext adapter (hairpin loop structure adapter) was ligated to the adenylated cDNA fragment using ligase.  Next, the second-strand cDNA was degraded with the aids of USER enzyme.  Size selection and sample purification was performed using AMPure XP Beads (Beckman Coulter).  Subsequently, Illumina sequencing adapter and indexes were added onto the cDNA fragment via PCR amplification (hereafter known as sequencing library).  The sequencing library was purified using Ampure XP Beads (Beckman Coulter).  The size distribution of the sequencing library was assessed using Agilent Bioanalyzer 2100 system (Agilent Technologies). The qualified sequencing library was loaded onto NovaSeq 6000 (Illumina) for sequencing using paired-end 150 sequencing strategy.  Raw data generated from the sequencer were demultiplexed and converted to FASTQ file using Illumina bcl2fastq.

tag: treatment/timpoint

value: Healthy

tag: subject status

value: NSAID-tolerant control


title: HD006_Healthy

tag: cell type


title: HD007_Healthy


title: Pt21 (day1, day29) - TCR

data_processing:
Single cell RNA-seq data was processed using the 10x Genomics Cell Ranger Software (v3.0.2). The command “cellranger mkfastq” was used to demultiplex raw BCL files and generate FASTQ files for individual samples. The command “cellranger count” was used to align RNA-Seq reads to the pre-built human reference genome GRCh38 and to filter out low quality cell barcodes and unique molecular identiﬁers (UMI). The resulting single-cell gene count matrices were further processed using the Seurat R package (v3.0.5)
Assembly: human GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.tar.gz, filtered_TCR_table.csv.gz
Library strategy: TCR-seq

tag: time


title: HD005_Healthy


title: FLAGless, NOR, rep3, Input Control

description:
NOR 12
Mu_ori_MG1655.edit.fa
NOR_sh.txt

value: NOR


title: FLAG, GEMI, rep2, Input Control

description:
GEMI 5
Mu_ori_MG1655.edit.fa
GEMI_sh.txt


title: HD009_Healthy


title: HD008_Healthy


title: HD003_Healthy


title: FLAG, GEMI, rep1

description:
GEMI 1
Mu_ori_MG1655.edit.fa
GEMI_sh.txt


title: HD004_Healthy


title: FLAG, GEMI, rep2

description:
GEMI 2
Mu_ori_MG1655.edit.fa
GEMI_sh.txt


title: FLAGless, NOR, rep2, Input Control

description:
NOR 11
Mu_ori_MG1655.edit.fa
NOR_sh.txt


title: Pt19 (day1, day29) - CSP

description:
Pt19_D1_D29_filtered_feature_bc_matrix.tar.gz
Pt04_Pt11_Pt19_Pt21_integrated_metadata.csv.gz
Pt04_Pt11_Pt19_Pt21_integrated_NormExpresMatrix.csv.gz

value: Placebo (0mL)


title: Pt19 (day1, day29) - TCR


title: Pt21 (day1, day29) - GEX


title: HD002_Healthy


title: FLAGless, NOR, rep3

description:
NOR 9
Mu_ori_MG1655.edit.fa
NOR_sh.txt


title: FLAGless, NOR, rep1, Input Control

description:
NOR 10
Mu_ori_MG1655.edit.fa
NOR_sh.txt


title: Pt19 (day1, day29) - GEX


title: FLAGless, NOR, rep2

description:
NOR 8
Mu_ori_MG1655.edit.fa
NOR_sh.txt


title: Pt11 (day1, day29) - CSP

description:
Pt11_D1_D29_filtered_feature_bc_matrix.tar.gz
Pt04_Pt11_Pt19_Pt21_integrated_metadata.csv.gz
Pt04_Pt11_Pt19_Pt21_integrated_NormExpresMatrix.csv.gz

value: 0.3mL dose


title: Pt11 (day1, day29) - TCR


title: Pt11 (day1, day29) - GEX


title: FLAG, NOR, rep3, Input Control

description:
NOR 6
Mu_ori_MG1655.edit.fa
NOR_sh.txt


title: FLAG, NOR, rep2, Input Control

description:
NOR 5
Mu_ori_MG1655.edit.fa
NOR_sh.txt


title: HD001_Healthy


title: ASP012_Predose

value: Predose

value: NIUA patient


title: Pt04 (day1, day29) - CSP

description:
Pt04_D1_D29_filtered_feature_bc_matrix.tar.gz
Pt04_Pt11_Pt19_Pt21_integrated_metadata.csv.gz
Pt04_Pt11_Pt19_Pt21_integrated_NormExpresMatrix.csv.gz

value: 1mL dose


title: ASP011_Pre_dose


title: ASP012_Postdose

value: Postdose


title: ASP011_Postdose


title: blood_ROBD_S11_T1

tag: tissue

value: blood

tag: gender

value: male

tag: treatment group

value: ROBD

value: pre-hypoxia exposure


title: blood_ROBD_S11_T4

value: 2 hours post hypoxia exposure


title: Pt04 (day1, day29) - TCR

value: RA

value: PBMC


title: FLAG, NOR, rep1, Input Control

description:
NOR 4
Mu_ori_MG1655.edit.fa
NOR_sh.txt

tag: strain

tag: genotype

value: MG1655 pstS-glmS::cat-Mu gyrA-FLAG-kan

tag: chip antibody

value: Anti-FLAG M2 gel pack (Sigma-Aldrich, St. Louis, MO)

value: M9 glucose


title: FLAG, NOR, rep3

description:
NOR 3
Mu_ori_MG1655.edit.fa
NOR_sh.txt

tag: media

tag: treatment

value: NOR


title: FLAGless, NOR, rep1

description:
NOR 7
Mu_ori_MG1655.edit.fa
NOR_sh.txt


title: Pt04 (day1, day29) - GEX

tag: individual

tag: disease state

value: CD45+ immune cells

value: day1 baseline and 28 days post-dosing


title: FLAG, NOR, rep2

description:
NOR 2
Mu_ori_MG1655.edit.fa
NOR_sh.txt


title: ASP010_Post_dose


title: blood_AC_S11_T1

value: AC


title: ASP010_Predose

value: Predose

value: NIUA patient


title: differentiated hiPSCs_dMet_rep3

data_processing:
The Reads were mapped on hg38 using HiSAT2, followed by Steringtie for genome-guided assembly.
Differential gene expression analysis was performed using the Subio platform (Subio, Inc.).
Assembly: hg38
Supplementary files format and content: peak text files

source_name: undifferentiated hiPSCs

extract_protocol:
RNA was extracted using the RNeasy micro-kit (Qiagen, Germany), DNase I (Qiagen) treatment was done according to the manufacturer's instructions.
Library preparation and RNA sequencing were performed by Novagene Co. ltd. Briefly, a total amount of 1 μg RNA per sample was used. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer's instructions, and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer's instructions. After cluster generation, the library preparations were sequenced on an Illumina platform (Novaseq 6000PE150), and paired-end reads were generated.

value: undifferentiated hiPSCs

value: Met deprived medium


title: blood_ROBD_S11_T2

value: blood

value: male

value: 0 minutes post hypoxia exposure


title: blood_AC_S11_T4

value: 2 hours post hypoxia exposure


title: blood_ROBD_S1_T2

value: ROBD


title: FLAG, NOR, rep1

description:
NOR 1
Mu_ori_MG1655.edit.fa
NOR_sh.txt


title: blood_ROBE_S1_T3

value: ROBE

value: 15 minutes post hypoxial exposure


title: blood_ROBE_S1_T2

source_name: blood, ROBE, 0 minutes post hypoxia exposure


title: blood_ROBE_S1_T4


title: differentiated hiPSCs_dMet_rep2


title: blood_ROBD_S11_T3

value: 15 minutes post hypoxia exposure


title: blood_ROBD_S1_T1

value: pre-hypoxia exposure


title: differentiated hiPSCs_dMet_rep1


title: blood_AC_S11_T2


title: blood_ROBD_S1_T3


title: blood_ROBD_S1_T4


title: ASP009_Predose

value: PBMC


title: blood_AC_S11_T3


title: differentiated hiPSCs_complete_rep3

value: Complete medium


title: differentiated hiPSCs_complete_rep2


title: FLAGless, MOXI, rep3, Input Control

description:
MOXI 12
Mu_ori_MG1655.edit.fa
MOXI_sh.txt

value: MG1655 pstS-glmS::cat-Mu gyrA-FLAG-kan

value: Anti-FLAG M2 gel pack (Sigma-Aldrich, St. Louis, MO)

value: M9 glucose

value: MOXI


title: FLAGless, MOXI, rep3

description:
MOXI 9
Mu_ori_MG1655.edit.fa
MOXI_sh.txt


title: FLAGless, MOXI, rep2, Input Control

description:
MOXI 11
Mu_ori_MG1655.edit.fa
MOXI_sh.txt


title: ASP008_Predose

value: Predose

value: NIUA patient


title: ASP009_Postdose

value: Postdose


title: ASP007_Predose


title: blood_AC_S1_T4

value: blood

value: male

value: AC


title: ASP008_Postdose


title: FLAGless, MOXI, rep1, Input Control

description:
MOXI 10
Mu_ori_MG1655.edit.fa
MOXI_sh.txt


title: ASP006_Predose


title: ASP007_Postdose


title: blood_AC_S1_T1


title: undifferentiated hiPSCs_dMet_rep2

value: undifferentiated hiPSCs

value: Met deprived medium


title: blood_AC_S1_T3


title: FLAGless, MOXI, rep2

description:
MOXI 8
Mu_ori_MG1655.edit.fa
MOXI_sh.txt


title: differentiated hiPSCs_complete_rep1


title: WT-kidney-2

city: Seoul

first: Han-Sung

last: Jung

address: 50, Yonsei-ro, Seodaemun-gu

department: Dental School

country: South Korea

institute: Yonsei University

data_processing:
Data processing: Library preparation was by the TruSeq Stranded mRNA LT Sample Prep Kit. Paired-end sequencing reads (101bp) generated from Illumina instruments were verified its sequence quality with FastQC (version 0.11.7). Before starting analysis, Trimmomatic(version 0.38) (Bolger et al., 2014) is used to remove adapter sequences and remove bases with base quality lower than 3 from the ends reads. Also using sliding window trim method, bases that does not qualify for window size=4, and mean quality=15 are removed. Afterwards, reads with minimum length of 36bp are removed to produce cleaned data.
Aligning reads to reference genome:  We preprocessed the raw reads from the sequencer to remove low quality and adapter sequence before analysis and aligned the processed reads to the Mus musculus (mm10) using HISAT v2.1.0(1). HISAT utilizes two types of indexes for alignment (a global, whole-genome index and tens of thousands of small local indexes). These two types’ indexes are constructed using the same BWT (Burrows–Wheeler transform) a graph FM index (GFM) as Bowtie2. Because of its use of these efficient data structures and algorithms, HISAT generates spliced alignments several times faster than Bowtie and BWA widely used. The reference genome sequence of Mus musculus (mm10) and annotation data were downloaded from the NCBI.   Transcript assembly and abundance estimation using StringTie(2, 3). After alignment, StringTie v1.3.4b was used to assemble aligned reads into transcripts and to estimate their abundance. It provides the relative abundance estimates as Read Count of transcript and gene expressed in each sample.
Statistical analysis of gene expression level:  Expression profile quantified by the HISAT-Stringtie pipeline is used to analyze differentially expressed genes between comparable samples. In the data preprocessing step, genes with one more than zeroed read count values in the samples were excluded. Filtered data were log2-transformed and subjected to TMM Normalization. Statistical significance of the differential expression data was determined using edgeR exactTest (Robinson, Mark D. et al. 2010) and fold change in which the null hypothesis was that no difference exists among groups. False discovery rate (FDR) was controlled by adjusting p-value using Benjamini-Hochberg algorithm. For DE genes which are satisfied with |fold change|≥2 and raw p <0.05, hierarchical clustering analysis was performed using complete linkage method and Euclidean distance as a measure of similarity. Gene-enrichment and functional annotation analysis and pathway analysis for significant gene list were performed based on gProfiler (https://biit.cs.ut.ee/gprofiler/orth), and KEGG pathway database (https://www.genome.jp/kegg/) respectively. All data analysis and visualization of differentially expressed genes was conducted using R 3.6.1 (www.r-project.org).
Reference    1. KIM, Daehwan; LANGMEAD, Ben; SALZBERG, Steven L. HISAT: a fast spliced aligner with low memory requirements. Nature methods, 2015, 12.4: 357-360.  2. PERTEA, Mihaela, et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature biotechnology, 2015, 33.3: 290-295.  3. PERTEA, Mihaela, et al. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nature Protocols, 2016, 11.9: 1650-1667.
Total RNA concentration was calculated by Quant-IT RiboGreen (Invitrogen, #R11490). To assess the integrity of the total RNA, samples are run on the TapeStation RNA screentape (Agilent, #5067-5576). Only high-quality RNA preparations, with RIN greater than 7.0, were used for RNA library construction.  A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA, #RS-122-2101). The first step in the workflow involves purifying the poly‐A containing mRNA molecules using poly‐T‐attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using SuperScript II reverse transcriptase (Invitrogen, #18064014) and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I, RNase H and dUTP. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.  The libraries were quantified using KAPA Library Quantificatoin kits for Illumina Sequecing platforms according to the qPCR Quantification Protocol Guide (KAPA BIOSYSTEMS, #KK4854) and qualified using the TapeStation D1000 ScreenTape (Agilent Technologies, # 5067-5582). Indexed libraries were then submitted to an Illumina NovaSeq (Illumina, Inc., San Diego, CA, USA), and the paired-end (2×100 bp) sequencing was performed by the Macrogen Incorporated.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Kidney

extract_protocol: The library was constructed, sequenced using an Illumina HiSeq2500 sequencer, and the data obtained through RNA-seq.

treatment_protocol: Kidney and ureter tissues were washed with cold PBS after gentle scrapping from the extracted premolar. Total RNA was extracted from PDL cells using TRIzol Reagent. The RNA was stored at −70 °C and measured at an optical density of 260 nm. The mixtures of total RNA were incubated with Oligo dT. Real-time PCR was performed for the selected upregulated and downregulated genes to verify RNA-seq results.

tag: cell line

value: Kidney

value: tissue

value: WT


title: FLAGless, MOXI, rep1

description:
MOXI 7
Mu_ori_MG1655.edit.fa
MOXI_sh.txt


title: blood_ROBE_S1_T1

value: ROBE

value: pre-hypoxia exposure


title: KO-kidney-3

source_name: Ureter

value: Ureter

value: Ahnak KO


title: FLAG, MOXI, rep3, Input Control

description:
MOXI 6
Mu_ori_MG1655.edit.fa
MOXI_sh.txt

value: MG1655 pstS-glmS::cat-Mu gyrA-FLAG-kan

value: Anti-FLAG M2 gel pack (Sigma-Aldrich, St. Louis, MO)

value: M9 glucose


title: blood_AC_S1_T2

value: 0 minutes post hypoxia exposure


title: KO-kidney-2


title: WT-kidney-3


title: undifferentiated hiPSCs_dMet_rep3


title: ASP005_Predose

value: Predose

value: PBMC

value: NIUA patient


title: ASP006_Postdose

value: Postdose


title: undifferentiated hiPSCs_dMet_rep1

value: undifferentiated hiPSCs


title: WT-kidney-1


title: KO-kidney-1


title: ASP005_Postdose


title: SG205

city: Bangkok

first: Supreda

middle: Suphanatachat

last: Srithanyarat

address: 34 Henri-Dunant Rd. Pathumwan District

department: Periodontology

country: Thailand

institute: Faculty of Dentistry, Chulalongkorn University

data_processing:
Illumina software used for basecalling.
Reads quality was checked, trimmed and filtered by FastQC and TrimGalore software.
Raw data fastq files were generated on NextSeq using bcl2fastq2 V2.19 software
Reads mapping with Homo sapiens UCSC hg38 using HISAT2
Transcripts quantification using HTSeq
Gene differential expression using DESeq2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: Human supracrestal gingival connective tissue-derived MSCs

growth_protocol: All cell types were cultured in T75 primariaTM culture flasks with  a-MEM plus 10% fetal bovine serum and 1% penicillin/streptomycin at 37 °C in a humidified 5% CO2 atmosphere. Cells from the 3rd – 6th passage were used in this study.

extract_protocol:
After treatment, total RNA was isolated using RNeasy Plus Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols


title: undifferentiated hiPSCs_complete_rep3

value: Complete medium


title: FLAG, MOXI, rep3

description:
MOXI 3
Mu_ori_MG1655.edit.fa
MOXI_sh.txt

value: MOXI


title: FLAG, MOXI, rep2, Input Control

description:
MOXI 5
Mu_ori_MG1655.edit.fa
MOXI_sh.txt


title: ASP004_Predose


title: undifferentiated hiPSCs_complete_rep1


title: ASP001_Predose


title: SG202

value: Human supracrestal gingival connective tissue-derived MSCs


title: FLAG, MOXI, rep1

description:
MOXI 1
Mu_ori_MG1655.edit.fa
MOXI_sh.txt


title: SG204


title: FLAG, MOXI, rep2

description:
MOXI 2
Mu_ori_MG1655.edit.fa
MOXI_sh.txt


title: SG203


title: FLAG, MOXI, rep1, Input Control

description:
MOXI 4
Mu_ori_MG1655.edit.fa
MOXI_sh.txt


title: undifferentiated hiPSCs_complete_rep2


title: ASP001_Postdose


title: SG201


title: FLAGless, LEVO, rep3, Input Control

description:
LEVO 12
Mu_ori_MG1655.edit.fa
LEVO_sh.txt

value: LEVO


title: FLAGless, LEVO, rep2, Input Control

description:
LEVO 11
Mu_ori_MG1655.edit.fa
LEVO_sh.txt