title: Disn-/-_(-/- x -/-)_rep1

description:
from crosses between homozygote parents
KO1(-/- x -/-)


title: H_G16_FAP-Patient_11

status: Public on Jun 01 2021

type: SRA

city: Houston

first: Eduardo

last: Vilar-Sanchez

state: Texas

address: 1515 Holcombe Blvd, Unit 1360

country: USA

institute: UT MD Anderson Cancer Center

description: colon mucosa from patient with Familial Adenomatous Polyposis  (FAP)

library_source: transcriptomic

data_processing:
Sequencing reads quality check - FastQC
Alignment: patient samples - STAR
Expression quantification - rsem-calculate-expression
Genome_build: patient samples - UCSC hg19;  mouse model samples - NCBI mm10
Supplementary_files_format_and_content: tab-delimited output with raw read counts

molecule: total RNA

organism: Homo sapiens

source_name: NORMAL

extract_protocol:
Intestinal (small) crypts from mice were isolated and prepared as single cells. Stem and non stem cells were FACS sorted. Total RNA and total cell extracts (proteins) were generated from a pool of cells.
Total RNA was sequenced on Illumina Hi-seq instrument using 78 base pairs paired end reads. For TCE, tryptic peptides were individually analyzed by nano-LC coupled Synapt G2-si ion-mobility mass spectrometry in HDMSE mode using Waters Masslynx (version 4.1, SCN 851).

tag: tissue

value: NORMAL

tag: localization

value: COLON

tag: pathology

value: UM

tag: batch

tag: mmr status

value: WT


title: Disn-/-_(+/- x +/-)_rep3

city: Kunming

first: Ping

last: Zheng

address: Qingsong Road 21

country: China

institute: Kunming Institute of Zoology, Chinease Academy of Sciences

description:
from crosses between heterzygote parents
KO3(+/- x +/-)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using tophat v2.1.1 with parameters -p 8 -r 50
Fragments Per Kilobase of exon model per Million mapped fragments were calculated using Cufflinks software (version 2.1.1)
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

organism: Mus musculus

source_name: mouse brain

extract_protocol:
RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: brain

tag: genotype

tag: treatment

value: untreated


title: pbs_pc#1

city: Shanghai

first: Junhao

last: Hu

state: Shanghai

address: No.26, Qiuyue Rd., Pudong District

department: Interdisciplinary Research Center of Biology and Chemistry

institute: Chinese Academy of Sciences

data_processing:
Reads cleaning: raw FASTQ files were quality checked using FASTQC . Then fastp was used to quality trim FASTQ files by both read quality and length (Q30 > 20, length > 36).
Alignment: clean reads were processed to pseudo-align to mouse transcriptome GRCm38 using salmon.
Quantification: transcriptional level expression was aggregated to gene level expression using tximport. Ensembl release 95 was used to annotate genes.
Quality check: sample clustering was performed with principle component analysis analysis and sample to sample distance correlation analysis.
DEGs analysis: differential expressed genes were defined by DESeq2 with foldchange > 1.5 and adjusted p-value < 0.05. DEGs based hypergeometric test and gene set enrichment analysis were produced by clusterProfiler.
Genome_build: GRCm38

source_name: Lung pericytes

extract_protocol: standard smartSeq2 protocol

treatment_protocol: Mice were given PBS or LPS trachea instillation and sacrificed after 24 hours

tag: cell type

value: PC

value: PBS


title: Disn-/-_(+/- x +/-)_rep2

description:
from crosses between heterzygote parents
KO2(+/- x +/-)


title: H_G4_FAP-Patient_10


title: H_G54_FAP-Patient_9


title: WT_rep2


title: lps_ec#5

source_name: Lung endothelial cells

value: EC

value: LPS


title: WT_rep1


title: lps_ec#6


title: H_G1_FAP-Patient_8


title: WT_rep3


title: mSCLC_Chemotherapy

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

data_processing:
ScRNA-Seq data were demultiplexed, aligned to the mouse genome, version mm10, and UMI-collapsed with the Cellranger toolkit (version 2.0.2 10X Genomics).  We excluded cells with fewer than 1000 detected genes (where each gene had to have at least one UMI aligned). Gene expression was represented as the fraction of its UMI count with respect to total UMI in the cell and then multiplied by 10,000.
Genome_build: mm10
Supplementary_files_format_and_content: gene-barcode matrices

source_name: tumors were harvested from CGRPCreER/+;Rbf/f;P53f/f;Ptenf/f;Rosa26mTmG mice treated with Cisplatin

extract_protocol:
tumors were harvested from TKO mice treated with vehicle or cisplatin directly into cold RPMI. Tumors were processed by enzymatic dissociation with Collagenase IV (600 U ml−1) and DNAse (2 μg ml−1) for a maximum of 45 min and neutralized in collection buffer (10% fetal bovine serum and 2 mM EDTA in RPMI). Dissociated live cells were sorted by fluoresence-activated cell sorting with GFP fluorescent protein
A total of 5000 cells from vehicle and 5000 cells from cisplatin/etoposide treated tumors were loaded per lane on the 10×GENOMICS platform and processed for complementary DNA synthesis and library preparation, per the manufacturer’s protocol.

treatment_protocol: CGRPCreER/+;Rbf/f;P53f/f;Ptenf/f;Rosa26mTmG mice were treated every four days for 2 weeks with saline or 5 mg per kg (body weight) cisplatin

value: Mixed

value: lung tumor

value: small cell lung cancer


title: lps_ec#4


title: H_G119_FAP-Patient_7

source_name: POLYP

value: POLYP

value: AD


title: mSCLC_Vehicle

source_name: tumors were harvested from CGRPCreER/+;Rbf/f;P53f/f;Ptenf/f;Rosa26mTmG mice treated with vehicle


title: Tet2 KO primary myoblasts-ATAC rep1

city: ShangHai

first: Hongye

last: Wang

address: Yue Yang Road,Shanghai 200031,China

institute: Shanghai Institute of Biochemistry and Cell Biology

library_source: genomic

data_processing:
Base-calling performed by CASAVA
The 150 bp paired-end ATAC-Seq reads were trimmed to 36bp paired-end reads and aligned to the mouse reference genome (mm9) using Bowtie2 with parameters -X 2000 -no-mixed -no-discordant -local.
Peak regions of each sample were called by software MACS2 with options -f BAMPE -g mm -q 0.01
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were generated using …
Supplementary_files_format_and_content: peak text files

molecule: genomic DNA

source_name: Tet2 KO primary myoblasts

growth_protocol: Satellite cells (PI-CD45-CD11b-CD31-Sca1- CD34+ Integrin a7+) were sorted using fluorescent-activated cell sorting from mouse hindlimb skeletal muscle. Then these satellite cells were cultured in conditional proliferating medium (T cell medium ) on 0.5mg/ml Type I collagen coated plates for at least 3 days.

extract_protocol:
Myoblasts were washed with PBS for one time and digested with typsine. ATAC-seq library was constructed from 5000 cells using TruePre DNA Library Pre Kit V2 for Illumina (Vazyme, TD501-01) and big peaks were filtered out using VAHTS DNA Clean Beads (Vazyme, N411-02) acording to the manufacturer’s instructions.
These libraries were sequenced on Illumina HiSeq X Ten instrument with 150-bp reads and paired-end parameter by WuXi NextCODE company.

treatment_protocol: After continuous culture for 3 days, satellite cells became MyoD+ myoblasts and haversted.

value: hindlimb skeletal muscle

value: Tet2 KO

value: mouse satellite cells derived myoblasts


title: Tet2 KO primary myoblasts-ATAC rep2


title: WT primary myoblasts-ATAC rep2

source_name: WT primary myoblasts


title: H_G121_FAP-Patient_7

value: NORMAL

value: COLON


title: lps_ec#3


title: WT primary myoblasts-ATAC repl

value: WT


title: H_G95_FAP-Patient_6

value: UM


title: Tet2 KO primary myoblasts-methyl

data_processing:
Base-calling performed by CASAVA
Reads were aligned to the mm9 genome assembly using BSAligner module in pipeline Methy-Pipe
The methylation density (MD) calculation and the DMRs identification were performed by BSAnalyzer module in pipeline Methy-Pipe
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files with methylation rate

growth_protocol: Satellite cells (PI-CD45-CD11b-CD31-Sca1- CD34+ Integrin a7+) were sorted using fluorescent-activated cell sorting  from mouse hindlimb skeletal muscle. Then these satellite cells were cultured in conditional proliferating medium (T cell medium ) on 0.5mg/ml Type I collagen coated plates for at least 3 days.

extract_protocol:
Genomic DNA was extracted and 1μg genomic DNA was treated with EZ DNA Methylation-Gold Kit (Zymo Research, D5005) according to the manufacturer’s instructions.
The methylation-seq library was constructed using TruSeq Nano DNA High Throughput Library Prep Kit (Illumina, 20015965).
Methylation-seq


title: lps_ec#2


title: Disn-/-_(+/- x +/-)_rep1

description:
from crosses between heterzygote parents
KO1(+/- x +/-)

value: brain

value: untreated


title: lps_ec#1


title: WT primary myoblasts-methyl


title: Tet2 KO primary myoblasts-RNA rep2

data_processing:
Base-calling performed by CASAVA
The raw RNA-seq reads were evaluated by FastQC and preprocessed by Illumina universal adapter trimming and low-quality reads filtering with our in-house scripts
All clean paired-end reads were mapped to the mouse genome (mm9) using Tophat version 2.0.13
Differentially expressed genes (DEGs) between every pairs of KO and WT samples were analyzed with Cuffdiff version 2.2.1 and genes with an adjusted p-value (q-value) < 0.05 were identified as DEGs
Genome_build: mm9

extract_protocol:
Myoblasts were washed with PBS for one time and RNA was harvested using Trizol reagent. TruSeq RNA Library Preparation Kit v2 (Illumina, RS-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries. .
RNA libraries were prepared for sequencing using standard Illumina protocols


title: H_G94_FAP-Patient_6


title: H_G106_FAP-Patient_5


title: WT primary myoblasts-RNA rep2


title: pbs_ec#6

value: PBS


title: pbs_ec#5

value: EC


title: WT primary myoblasts-RNA repl


title: H_G102_FAP-Patient_5


title: pbs_ec#4


title: K5

city: Beijing

first: Qingyuan

last: Sun

state: Beijing

address: Beichen West Rd., Chaoyang

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
We checked the quality of raw sequencing data by FastQC software.  After filtering low quality reads, the clean data were aligned to the mouse reference genome through Hisat2. And the differentially expressed genes were caculated by DESeq2.
The off-machine data is converted into Raw Data using CASAVA software, and Trim Galore! software is used to filter the low-quality sequence and the connector sequence. The filtered sequence is Clean Data. The data at this time is converted at the same time as the mouse genome data (version number: GRCm38/mm10), the C base in the positive strand sequence is converted to T base, and the G base in the reverse strand sequence is converted to A base. Then, the converted sequencing sequence is aligned to the converted reference genome. The software used for comparison is Bismark [94] (V0.18.1). The methylation level of all detected CpG sites was statistically calculated using the R package methylKit. In order to explore the consistency of sequencing and the correlation between cells, based on the methylation level of each CpG site (the number of reads covered by each site is not less than 5), the methylKit package was used to calculate the Correlation coefficients of methylation levels (Pairwise Pearson Correlations), and cluster analysis and PCA analysis. Look for C sites that contain at least 5 differential methylations at the same location in multiple cell genomes, with a coverage depth of not less than 5×, and the average methylation level difference of these sites is >20%, which is a hot spot difference region (DMR). Look for genes that contain at least 5 differentially methylated C sites at the same position in multiple cell genomes, with a coverage depth of not less than 5×, and the average methylation level of these sites differs by >20%. Locus related genes. The genes related to the differential sites were analyzed with GO using the R package clusterProfiler, and plotted with R.
Genome_build: GRCm38
Supplementary_files_format_and_content: DNA methylation levels and counts

molecule: polyA RNA

source_name: MII oocytes

extract_protocol:
RNA and DNA methylation were prepared for sequencing
RNA was isolated from mII and amplified using Smart-Seq v4 Ultra Low Input RNA Kit (Clontech Laboratories,Mountain View, CA, USA) and sequenced by Novogene Corporation (Haidian, Beijing, China). DNA was extracted using the oral swab gene extraction kit TIANamp Genomic DNA Kit (TianGen); the egg cell sample had fewer cells and was directly lysed with proteinase K (Qiagen). The genome DNA or oocytes’ lysate is digested with MspI / XmaI (Fermentas) double digestion. At the same time, Unmethylated λDNA of about 1% of the sample DNA mass should be added to the digestion system as an internal reference to investigate the conversion rate. Digestion products are used for terminal repair, addition of dA, and methylated linker connection (NEB, all cytosines in the linker sequence are methylated); the ligation product is converted to bisulfite and the conversion product is purified and recovered, referring to EZ DNA Methlyation -Direct Kit (ZYMO) instructions; the transformation products are amplified by 2X Kapa HiFi U + master Mix (Kapa), Universal primer (NEB), Index primer (NEB); the products are screened by XP magnetic beads (Beckman Coulter) 200- The 450bp fragment was finally sequenced with HiSeq X10 analyzer (Illumina) 150 bp-read pair-end (PE).

treatment_protocol: The oocyte-specific mutant mice Ehmt2flox/flox; Gdf9-Cre+ (Ehmt2mNull) with the deletion of Ehmt2 exons 4-20 were generated by crossing Ehmt2flox/flox mice with transgenic mice expressing Gdf9 promoter mediated Cre recombinase.

value: Ovary

value: Ehmt2(flox/flox); Gdf9-Cre

tag: age

value: 8 week


title: K4


title: H_G93_FAP-Patient_4


title: K3


title: pbs_ec#3


title: C6


title: C2


title: H_G87_FAP-Patient_4


title: C1


title: MII-KO-1112


title: pbs_ec#2


title: EC_S34

extract_protocol:
standard smartSeq2 protocol
standard smartSeq2 protocol

treatment_protocol: Mice were given PBS or LPS trachea instillation. Vehicle or Riociguat was given at 9 hours interval. Mice were sacrificed after 24 hours.

value: LPS

tag: drug

value: Riociguat


title: pbs_ec#1


title: H_G86_FAP-Patient_3


title: Tet2 KO primary myoblasts-RNA rep1


title: H_G85_FAP-Patient_3

value: POLYP

value: AD


title: H_G79_FAP-Patient_2


title: EC_S30


title: H_G110_FAP-Patient_1


title: KO_E6_5_epi-E4

source_name: E6.5 embryo

value: Embryo

value: Embryonic day 6.5


title: MII-con-1112


title: MII-C4


title: KO_E6_5_epi-E1


title: E6-5


title: 1C-6-5


title: 1C_E6_5-E3


title: EC_S28


title: 1C_6_5-E2


title: EC_S26


title: MII-G-KO-3


title: IPSC-derived neurons-24h MCI-186 10μM rep2

city: Baltimore

first: Mingyao

last: Ying

state: MD

address: 733 N Broadway

department: Department of Neurology

institute: Johns Hopkins School of Medicine

description: Biological replicate 2

data_processing:
The raw reads were aligned to reference human genome build hg19 using HISAT2 with default parameters. For each gene, the number of reads aligned to its exons were counted and summarized into gene level counts by StringTie the R Bioconductor package GenomicFeatures based on the GENCODE hg19 annotation.
Genome_build: hg19
Supplementary_files_format_and_content: Read count matrix of genes for all samples in csv

source_name: iPSC-derived neurons

growth_protocol: IPSC-derived motor neurons were routinely generated by replating in neuronal medium (BDNF/GDNF/AA/cAMP/DAPT) on day4 after delivery of NSA and OSA mRNAs for 3 days in N2 medium (SHH/DAPT)

extract_protocol: Total RNA was extrated from cells

treatment_protocol: MCI-186 was treated at 10μM for 24h

value: IPSC-derived motor neurons


title: MII-G-KO-2


title: H_G84_FAP-Patient_2

value: NORMAL

value: COLON


title: 4T1_tumor_KDM1AKO_2

city: Boston

first: Yujiang

last: Shi

state: MA

address: 221 longwood Ave, EBRC (LMRC) 222A

department: Division of Endocrinology, Diabetes and Hypertension

institute: Brigham and Women's Hospital

description:
RNA-seq KDM1A KO 4T1 tumor rep2
Expression_FPKM_Count_4T1_tumor_WT_KDM1BKO_KDM1AKO.txt

data_processing:
Raw sequencing data were trimmed using Trim Galore (v0.4.5) to remove low quality bases and adaptor sequences.
The trimmed reads were mapped onto the hg38 genome for human origin and mm9 genome for mouse origin, using STAR (v2.5.4)  with parameter --twopassMode Basic.
Quantification of gene expression was performed using featureCounts in Rsubread package (v1.32.4). RPKM of genes was calculated using ‘rpkm’ function in edgeR package (v3.24.3) and gene annotations were determined through featureCounts built-in hg38/mm9 annotation.
Genome_build: mm9, hg38

source_name: tumor in immune competent mice

growth_protocol: MDA-MB-231 cells (WT and KDM1B KO) were cultured in DEME supplemented with 10% FBS and 1% penicillin/streptomycin in a 5% CO2 incubator at 37C. For tumor growth, 1x10E5 4T1 cells were injected subcutaneously at the right flank of BalB/cJ; 3 × 10E6 MDA-MB-231 cells were injected subcutaneously at the right flank of athymic BALB/c nude mice.

extract_protocol:
Total RNA was first extract by Trizol, and further purified from genomic DNA by on-column DNaseI digestion and Qiagen RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue type

value: tumor

tag: mouse

value: Balb/cJ

value: KDM1A KO


title: EC_S24

value: Vehicle


title: 4T1_tumor_KDM1AKO_3

description:
RNA-seq KDM1A KO 4T1 tumor rep3
Expression_FPKM_Count_4T1_tumor_WT_KDM1BKO_KDM1AKO.txt


title: IPSC-derived neurons-24h MCI-186 10μM rep1

description: Biological replicate 1


title: 4T1_tumor_KDM1AKO_1

description:
RNA-seq KDM1A KO 4T1 tumor rep1
Expression_FPKM_Count_4T1_tumor_WT_KDM1BKO_KDM1AKO.txt


title: EC_S22

value: EC


title: 4T1_tumor_KDM1BKO_2

description:
RNA-seq KDM1B KO 4T1 tumor rep2
Expression_FPKM_Count_4T1_tumor_WT_KDM1BKO_KDM1AKO.txt

value: KDM1B KO


title: EC_S32


title: IPSC-derived neurons-24h Ctrl (motor neuron control) rep2

description: Biological replicate 2


title: EC_S20


title: 4T1_tumor_KDM1BKO_1

description:
RNA-seq KDM1B KO 4T1 tumor rep1
Expression_FPKM_Count_4T1_tumor_WT_KDM1BKO_KDM1AKO.txt


title: 4T1_tumor_KDM1BKO_3

description:
RNA-seq KDM1B KO 4T1 tumor rep3
Expression_FPKM_Count_4T1_tumor_WT_KDM1BKO_KDM1AKO.txt


title: 4T1_tumor_WT_3

description:
RNA-seq wild type 4T1 tumor rep3
Expression_FPKM_Count_4T1_tumor_WT_KDM1BKO_KDM1AKO.txt

value: WT


title: IPSC-derived neurons-24h Ctrl (motor neuron control) rep1

description: Biological replicate 1


title: EC_S16


title: 4T1_tumor_WT_1

description:
RNA-seq wild type 4T1 tumor rep1
Expression_FPKM_Count_4T1_tumor_WT_KDM1BKO_KDM1AKO.txt


title: IPSC-derived neurons-24h styrene oxide 100μM rep2

description: Biological replicate 2

source_name: IPSC-derived neurons

growth_protocol: IPSC-derived neurons were routinely generated by replating in neuronal medium (BDNF/GDNF/AA/cAMP/DAPT) on day4 after incubating with doxycycline for 4 days in N2 medium (DAPT)

extract_protocol: Total RNA was extrated from cells.

treatment_protocol: Styrene oxide was treated at 100μM for 24h

value: IPSC-derived neurons

value: styrene oxide 100μM 24h


title: H_G108_FAP-Patient_1


title: EC_S14

value: LPS


title: Genotyping data for sample 3559G

type: genomic

city: Toronto

first: Stephen

middle: W

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

country: Canada

institute: The Hospital for Sick Children

description: Genomic DNA extracted was analyzed using Illumina's BeadStudio software

hyb_protocol: Standard Illumina protocol for Infinium 2.5M  Beadchip

data_processing:
Intra-chip normalization was performed using the Illumina's GenomeStudio software v.1.0.1 with a GenCall cutoff of 0.1 and call rate cutoff of 98%. For CNV calling on the Illumina 2.5M platform we used QuantiSNP, iPattern, PennCNV.
For CNV detection using different algorithms, various measurements were exported directly from GenomeStudio: the intra-chip normalized X and Y intensity values from the A and B allele-specific probes respectively, and two other measurements derived from X and Y after normalization with respect to reference population, i.e. the Log R ratios (LRR) and B allele frequency (BAF) values. For the algorithms that used LRR, representing the total signal intensity, and BAF, representing the allelic balance, the Illumina’s cluster file made of >120 HapMap was used to generate intensities and genotypes using GenomeStudio.

source_name: genomic DNA from whole blood

extract_protocol: Genomic DNA extracted using the Qiagen DNA micro kit (QIAgen, Hilden, Germany)

tag: gender

value: Male

tag: ethnicity

value: Roma ancestry

tag: celltype

value: DNA extracted from whole blood


title: Genotyping data for sample 3478G

scan_protocol: Standard Illumina protocol for Infinium 2.5M  Beadchip

value: North-Central European ancestry


title: Genotyping data for sample 3557G

label_protocol: Standard Illumina protocol for Infinium 2.5M  Beadchip


title: Genotyping data for sample 3555G


title: EC_S10

value: PBS


title: Genotyping data for sample 3553G


title: IPSC-derived neurons-24h Ctrl rep2

description: Biological replicate 2

value: vehicle


title: Genotyping data for sample 3550G


title: EC_S8


title: IPSC-derived neurons-24h Ctrl rep1

description: Biological replicate 1


title: EC_S6


title: Genotyping data for sample 3495G


title: Genotyping data for sample 3547G


title: Genotyping data for sample 3548G


title: EC_S4


title: Compound_D_in_H2O_Rep_3

city: Paris cedex 15

first: Christian

last: MUCHARDT

address: 25 rue du Dr-Roux

department: Developmental and Stem Cell Biology

country: France

institute: Institut Pasteur Paris

data_processing:
Reads were aligned with STAR on unmasked human genome version Hg19 without patches, allowing only single alignments. Bigwigs were generated with RPKM normalization.
Genome_build: Hg19
Supplementary_files_format_and_content: bigwig file after alignment on unmasked Hg19 and RPKM normalization
Supplementary_files_format_and_content: The bigWig format is for display of dense, continuous data that will be displayed as a graph.

source_name: Jurkat cells + H2O2 30 min.

growth_protocol: Jurkat cells were cultured in RPMI-1640, all with 10% decomplemented fetal bovine serum (FBS) and 100 U.ml−1 penicillin-streptomycin at 37°C in a 5% CO2 incubator.

extract_protocol:
Total RNA from Jurkat cells was extracted with Phenol-chloroform methods and quantified with an ND-1000 (Nanodrop).
Samples were enriched in mRNA (with poly(A) tails) using oligo(dT) beads. After enrichment, the RNAs were fragmented into 250-400 bp fragments and the cDNA was synthesized with random hexamer primers and amplified

treatment_protocol: Jurkat cells were treated with hydrogen peroxide (H2O2) or water (H2O) at 2mM for 30 min.

tag: cell line

value: Jurkat, Clone E6-1 (ATCC TIB-152)

tag: library type

value: poly(A) enriched


title: Genotyping data for sample 3549G


title: Compound_D_in_H2O_Rep_2


title: Genotyping data for sample 3494G


title: 4T1_tumor_WT_2

description:
RNA-seq wild type 4T1 tumor rep2
Expression_FPKM_Count_4T1_tumor_WT_KDM1BKO_KDM1AKO.txt

value: tumor

value: Balb/cJ


title: Genotyping data for sample 3496G


title: Genotyping data for sample 3493G


title: EC_S2

value: Vehicle


title: Genotyping data for sample 3492G


title: H2O_Rep_3

source_name: Jurkat cells + H2O 30 min.


title: PC_S35

value: PC

value: Riociguat


title: Compound_D_in_H2O_Rep_1


title: PC_S33


title: IPSC-derived neurons-24h styrene oxide 100μM rep1

description: Biological replicate 1


title: Genotyping data for sample 3491G


title: Genotyping data for sample 3490G


title: Genotyping data for sample 3489G


title: Genotyping data for sample 3488G


title: PC_S31


title: H2O_Rep_2


title: Genotyping data for sample 3486G


title: Genotyping data for sample 3487G


title: PC_S29


title: Genotyping data for sample 3482G


title: Genotyping data for sample 3481G


title: Genotyping data for sample 3480G


title: Genotyping data for sample 3477G


title: PC_S23


title: Genotyping data for sample 3479G


title: RNA-seq from FL patient B7316

city: London

first: James

last: Heward

state: England

address: Haemato Oncology, Barts Cancer Institute, Charterhouse Square

country: United Kingdom

institute: Barts Cancer Institute

description:
RNA
FL_patient_rpkm

data_processing:
For ChIP seq analysis - Input FASTQ files were mapped to hg19 using Bowtie, whilst H3K4me3 FASTQ files were mapped to hg19 and dm3. The number of reads mapping to the dm3 genome were used to calculate a scaling factor and sequencing reads were randomly removed from samples requiring normalization using SAMtools (samtools view -b -s <scaling.factor> <filename.bam>  > <scaled.bam>). Peaks were identified using the broad source option in MACS2 (macs2 callpeak -t <filename.bam> -c <input.bam> --broad -n <filename> -g hs --broad-cutoff 0.1 -q 0.05) and regions known to result in poor quality sequencing (https://www.encodeproject.org/annotations/ENCSR636HFF/) removed using BEDtools
For KDM5i RNA-seq analysis - mRNA isolation and strand-specific cDNA libraries were prepared using the Illumina TruSeq stranded mRNA Prep kit according to the manufactures instructions. For SU-DHL-6 and OCI-LY-18, two hundred cycles of sequencing on the Illumina HiSeq 2500 instrument were performed to generate 2x100bp paired-end sequencing reads. HT libraries were sequenced by 300 cycles of sequencing on the HiSeq 4000 to generate 2x150bp paired-end sequencing reads. Raw data was aligned to hg19 using STAMPY and BWA. The number of uniquely aligned reads (quality score q > 10) aligned to the exonic region of each gene were counted using HTSeq based on the Ensembl annotation (version 75). Only genes that achieved at least one read per million reads (CPM) in at least 3 samples were kept. Aligned reads numbers were further normalised using the ‘cqn’ method, accounting for gene length and GC content. Differential expression (DE) analysis was then performed using the edgeR R package, employing the generalised linear model (GLM) approach, for the treated versus control pairwise matched comparisons.
For FL patient RNA-seq analysis - 14 FL RNA samples  with a RIN value > 6 were isolated from fresh frozen biopsies and sequenced on the HiSeq 2000. 100bp reads were aligned to the reference genome hg19 using Tophat2 and analysed as above using the ‘cqn’ method to obtain RPKM values for all filtered genes.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files of ChIP seq data and data matrix of analysed RNA-seq data.

source_name: Primary FL sample

growth_protocol: Cells were cultured in RPMI-1640 media at 37°C 5% CO2

extract_protocol:
mRNA was extracted using QIAGEN Rneasy kits. ChIP was performed using a modied version of the Active Motif ChIP-IT High Sensitivity Kit protocol.
RNA-seq libraries were prepared using the TruSeq stranded mRNA Prep kit and ChIP-seq libraries prepared using the NEBNext Ultra II kit .

treatment_protocol: Cells were treated with DMSO or 1μM GS-701644 for 24 or 72 hours

tag: sample type

value: Sorted germinal centre cells


title: Genotyping data for sample 3485G


title: RNA-seq from FL patient B6242

description:
RNA
FL_patient_rpkm


title: PC_S19


title: RNA-seq from FL patient B6312

description:
RNA
FL_patient_rpkm


title: Genotyping data for sample 3475G


title: Genotyping data for sample 3476G


title: RNA-seq from FL patient B5581

description:
RNA
FL_patient_rpkm


title: PC_S17


title: RNA-seq from FL patient B6091

description:
RNA
FL_patient_rpkm


title: Genotyping data for sample 3474G


title: PC_S15


title: RNA-seq from FL patient B3097

description:
RNA
FL_patient_rpkm


title: Genotyping data for sample 3473G


title: H2O_Rep_1


title: Genotyping data for sample 3472G


title: PC_S13


title: Genotyping data for sample 2703G


title: Genotyping data for sample 2702G


title: Genotyping data for sample 3483G


title: RNA-seq from FL patient B3019

description:
RNA
FL_patient_rpkm


title: PC_S11


title: PC_S25


title: Genotyping data for sample 2700G


title: RNA-seq from FL patient B1851

description:
RNA
FL_patient_rpkm


title: SA_Pancreas

city: Shenzhen

first: Fan

middle: ding

last: ding

address: yantian shashen Road

institute: EasyATCG

description: RNAseq from tissue:Pancreas

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to referenced genome using histat2 (version 2.1.0)
StringTie 1.3.4d were used to calculate FPKM
bam_to_bigwig(https://github.com/hotdogee/bam_to_bigwig) were used to product bigWig
Genome_build: under Bioproject : PRJNA427250; See also SA.tbl.txt for transcriptome annotation.
Supplementary_files_format_and_content: bigwig files and text file with FPKM.

organism: Silurus asotus

source_name: Pancreas

growth_protocol: Use adult sample from benthic environment

extract_protocol:
Total RNA was extracted from each sample using Trizol Reagent (Invitrogen, Carlsbad, CA, U.S.A) according to the manufacturer’s instructions. The extracted RNA was further treated with DNaseⅠ (RNase-free 5 U/mL) to eliminate genomic DNA contamination. Poly (A) + mRNA was purified using the DynaBeads mRNA Purification kit (Life Technologies).
Paired-end cDNA libraries were constructed using the RNA Seq NGS Library Preparation Kit for Whole-Transcriptome Discovery (Gnomegen).

tag: tissue

value: Pancreas

tag: developmental stage

value: adult


title: PC_S9

source_name: Lung pericytes


title: PC_S7


title: RNA-seq from FL patient B350

description:
RNA
FL_patient_rpkm


title: SA_Muscle

description: RNAseq from tissue:Muscle

source_name: Muscle

value: Muscle


title: SA_Skin

description: RNAseq from tissue:Skin

source_name: Skin

value: Skin


title: PC_S3


title: SA_Maxillary_barbel

description: RNAseq from tissue:Maxillary_barbel


title: SA_Testis

description: RNAseq from tissue:Testis

source_name: Testis

value: Testis


title: LPS+Riociguat-3

source_name: Lung lysate

extract_protocol:
Sangon RNA extraction kit (Order NO. B511321)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: LPS


title: RNA-seq from FL patient B173

description:
RNA
FL_patient_rpkm


title: RNA-seq from FL patient B161

description:
RNA
FL_patient_rpkm


title: PC_S5


title: SA_Pituitary

description: RNAseq from tissue:Pituitary

source_name: Pituitary

value: Pituitary


title: RNA-seq from FL patient B3058

description:
RNA
FL_patient_rpkm


title: LPS+Riociguat-2


title: RNA-seq from FL patient B120

description:
RNA
FL_patient_rpkm


title: SA_Ovary

description: RNAseq from tissue:Ovary

source_name: Ovary

value: Ovary


title: SA_Spleen

description: RNAseq from tissue:Spleen

source_name: Spleen

value: Spleen


title: Genotyping data for sample 2698G

value: Male

value: Roma ancestry

value: DNA extracted from whole blood


title: SA_Kidney

description: RNAseq from tissue:Kidney

source_name: Kidney

value: Kidney


title: SA_Liver

description: RNAseq from tissue:Liver

source_name: Liver

value: Liver


title: SA_Heart

description: RNAseq from tissue:Heart

source_name: Heart

value: Heart


title: LPS+Riociguat-1

value: Riociguat


title: LPS+Vehicle-4

value: Vehicle


title: Genotyping data for sample 2697G


title: SA_Head_kidney

description: RNAseq from tissue:Head_kidney


title: LPS+Vehicle-3


title: RNA-seq from FL patient B205

description:
RNA
FL_patient_rpkm

value: Sorted germinal centre cells


title: SA_Mandibular_barbel

description: RNAseq from tissue:Mandibular_barbel

value: adult


title: SA_Brain

description: RNAseq from tissue:Brain

source_name: Brain

value: Brain


title: SA_Gill

description: RNAseq from tissue:Gill

source_name: Gill

value: Gill


title: SM_Skin

description: RNAseq from tissue:Skin

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to referenced genome using histat2 (version 2.1.0)
StringTie 1.3.4d were used to calculate FPKM
bam_to_bigwig(https://github.com/hotdogee/bam_to_bigwig) were used to produce bigWig
Genome_build: under Bioproject : PRJNA427243; See also SM.tbl.txt for transcriptome annotation.
Supplementary_files_format_and_content: bigwig and text file with FPKM.

organism: Silurus meridionalis

value: Skin


title: LPS+Vehicle-2

value: LPS


title: SM_Muscle

description: RNAseq from tissue:Muscle

value: Muscle


title: SM_Telecephlon

description: RNAseq from tissue:Telecephlon

source_name: Telecephlon

value: Telecephlon


title: PBS+Vehicle-4

value: PBS


title: PBS+Vehicle-3


title: SM_Olfactory_bulb

description: RNAseq from tissue:Olfactory_bulb


title: SM_Retina

description: RNAseq from tissue:Retina

source_name: Retina

value: Retina


title: PBS+Vehicle-1


title: SM_Maxillary_barbel

description: RNAseq from tissue:Maxillary_barbel


title: SM_Mandibular_barbel

description: RNAseq from tissue:Mandibular_barbel


title: SM_Intestine

description: RNAseq from tissue:Intestine

source_name: Intestine

value: Intestine


title: SM_Testis

description: RNAseq from tissue:Testis

value: Testis


title: SM_Spleen

description: RNAseq from tissue:Spleen

value: Spleen


title: M_P24_WT-3

description: Colon epithelial cell from MSH2+/+ mice

source_name: Epithelial cell

extract_protocol:
Intestinal (small) crypts from mice were isolated and prepared as single cells. Stem and non stem cells were FACS sorted. Total RNA and total cell extracts (proteins) were generated from a pool of cells.
Total RNA was sequenced on Illumina Hi-seq instrument using 78 base pairs paired end reads. For TCE, tryptic peptides were individually analyzed by nano-LC coupled Synapt G2-si ion-mobility mass spectrometry in HDMSE mode using Waters Masslynx (version 4.1, SCN 851).

value: Epithelial cell

tag: localization

value: COLON

tag: pathology

tag: gfp

tag: batch

value: Mice

tag: mmr status

value: WT


title: SM_Pancreas

description: RNAseq from tissue:Pancreas

source_name: Pancreas

value: Pancreas


title: SM_Ovary

description: RNAseq from tissue:Ovary

value: Ovary

value: adult


title: SM_Liver

description: RNAseq from tissue:Liver

value: Liver


title: SM_Heart

description: RNAseq from tissue:Heart

value: Heart


title: SM_Head_kidney

description: RNAseq from tissue:Head_kidney


title: M_P21_WT-2

description: Colon stem cell from MSH2+/+ mice

source_name: Stem cell

value: Stem cell


title: M_P23_WT-3

description: Colon stem cell from MSH2+/+ mice


title: SM_Gill

description: RNAseq from tissue:Gill

value: Gill


title: M_P20_WT-1

description: Colon epithelial cell from MSH2+/+ mice


title: M_P19_WT-1

description: Colon stem cell from MSH2+/+ mice


title: SM_Brain

description: RNAseq from tissue:Brain

value: Brain


title: M_P18_HET-3

description: Colon epithelial cell from MSH2+/- mice

value: HET


title: M_P22_WT-2

description: Colon epithelial cell from MSH2+/+ mice


title: SM_Kidney

description: RNAseq from tissue:Kidney

value: Kidney


title: VCaP Input

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

data_processing:
Raw fastq files were aligned against human genome hg38 assembly using Burrows-Wheeler Alignment tool and then processed using methylQA to generate bed and bigwig files.
The MACS2 peak caller was used to compare the ChIP-Seq signal to a corresponding input control to identify narrow regions of enrichment (peaks) using default parameters.
ChIP-Seq signals and peak locations were further visualized using UCSC Genome Browser.
The top 500-1000 ChIP-Seq peaks were assigned to the nearest genes using the annotatePeaks function from HOMER2, motif binding sites were determined using HOMer2, and GO and pathway enrichment analyses were performed by EnrichR.
Genome_build: hg38
Supplementary_files_format_and_content: fastq and peak files

source_name: Prostate Cancer

growth_protocol: VCaP cells were grown in DMEM media with charcoal stripped fetal bovine serum.

extract_protocol:
The lysates were immunoprecipitation with acK609-AR antibodies (2 ug) for overnight.
Ten nanograms of immunoprecipitated DNA was fragmented to 300 base pairs using a Covaris M220 Focused-ultrasonicator (Covaris, Inc., Woburn, MA) and then used to generate sequencing libraries using the Kapa Hyper Prep Kit (Roche Sequencing Solutions Inc., Pleasanton, CA). The size and quality of the library was evaluated using the Agilent BioAnalyzer (Agilent Technologies, Inc., Santa Clara, CA), and the library was quantitated with the Kapa Library Quantification Kit.  Each enriched DNA library was then sequenced on an Illumina NextSeq 500 sequencer to generate 40-50 million 75-base paired-end reads (Illumina, Inc., San Diego, CA).  The raw sequence data were aligned using BowTie 2 [1], and the binding sites were identified using the MACS peak-finding software

treatment_protocol: 5x10^7 cells were treated with R-9b inhibitor overnight (5 uM) and lysates were prepared by sonication in RLB bufffer.

tag: treatment

value: Vehicle(DMSO) treated

tag: cell type

value: Prostate Cancer Cell Line

tag: chip antibody


title: VCaP acK609-AR Vehicle

value: acK609-AR antibody


title: VCaP acK609-AR (R)-9b

value: R-9b inhibitor treatment


title: HCT116 120KO

data_processing:
Raw sequences generated from Illumina/Solexa sequencer were aligned using NCBI Build 36.1 (UCSC hg18) of the human genome. Only sequences that mapped uniquely to the genome with zero or one mismatch were used for further analysis. When multiple sequences mapped to the same genomic position, a maximum of two reads mapping to the same position were used. The sequenced reads represent only the ends of each immunoprecipitated fragments instead of the precise protein-DNA binding sites. To illustrate the entire DNA fragment, the 3’ end of each read was extended 250 bp. The reference genome was partitioned into 25 bp bins and the total reads (including partial reads) in each bin were summed and used to generate the visualization file in wiggle (WIG) format.
Genome_build: hg18
Supplementary_files_format_and_content: fastq and wig

source_name: colorectal carcinoma (ATCC CCL-247)

growth_protocol: Cell lines were cultured and propagated according ATCC recommendations. HCT16: https://www.atcc.org/products/all/CCL-247.aspx#culturemethod

extract_protocol: Lysates were clarified from sonicated nuclei and TFAP2A-DNA complexes were isolated with AP-2α 3B5 antibody (Santa Cruz, catalog no. sc-12726X) .

tag: modification

value: clone 120 with CRISPR/Cas9 KO of AP-2a

tag: pasages

tag: antibody


title: Liver_PH3_6H_Rat789

type: RNA

city: Aberdeen Proving Ground

first: Heidi

last: Hoard-Fruchey

address: 2900 Ricketts Point Rd

institute: USAMRICD

description: 660 ppm  x 32.2 min (21,252 ppm x min)

hyb_protocol: The complimentary RNA (cRNA) produced from the isolated total RNA was then fragmented and hybridized to GeneChip HT RG-230PM array plates (Affymetrix) according to the manufacturer’s instructions.

scan_protocol: The HT RG-230PM array plates were scanned using an Affymetrix GeneTitan system.

data_processing: Raw data (CEL files) were imported into Partek Genomic suite v6.6 (Partek Incorporated, St. Louis, MO) and normalized using robust multiarray averaging (RMA)

label: Biotin

organism: Rattus norvegicus

label_protocol: The isolated RNA was amplified and biotinylated using the GeneChip 3’ in vitro transcription (IVT) Plus reagent kit (Affymetrix; Santa Clara, CA) according to the manufacturer’s instructions.

growth_protocol: Male Sprague-Dawley rats (300-400 g, Charles-River Laboratories, Wilmington, MA) were individually housed under standard conditions (12 hour light/dark cycle) with standard rodent chow and water provided ad libitum.

extract_protocol: Following eutanasia (ketamine (90 mg/kg) and xylazine (10 mg/kg)  by im followed by exsanguination), tissues were flash frozen in liquid nitrogen and stored at -80 until processing. Tissues were cryopulverized and total RNA isolated using RNeasy Plus mini kits (Qiagen; Germantown, MD) according to manufacturer's instructions with a DNase digestion step. Blood samples were collected via heart stick. RNA was isolated from collected blood samples and processed using the RNeasy Protect Animal Blood System (Qiagen) according to manufacturer’s instructions.

treatment_protocol: Whole-body PH3 inhalation exposures were conducted as described in Wong et al., 2017. PH3 concentration was 21,252 ppm x minute (660 ppm x 32.2 minutes), representing a “high” concentration Ct.

tag: time point

tag: exposure


title: Blood_PH3_6H_Rat790

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Blood


title: Lung_PH3_6H_Rat789

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Lung


title: HCT116 24KO

value: clone 24 with CRISPR/Cas9 KO of AP-2a

value: AP-2α 3B5 antibody (Santa Cruz, catalog no. sc-12726X)


title: Brain_PH3_6H_Rat789

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: M_P17_HET-3

description: Colon stem cell from MSH2+/- mice

data_processing:
Sequencing reads quality check - FastQC
Alignment: patient samples - STAR
Expression quantification - rsem-calculate-expression
Genome_build: patient samples - UCSC hg19;  mouse model samples - NCBI mm10
Supplementary_files_format_and_content: tab-delimited output with raw read counts

value: COLON

value: Mice


title: Kidney_PH3_6H_Rat789

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: Blood_PH3_6H_Rat789

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: Heart_PH3_6H_Rat789

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Heart


title: Kidney_Air_6H_Rat763

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Air


title: Lung_Air_6H_Rat763

description: 0 ppm  x 32.2 min (0 ppm x min)


title: M_P16_HET-2

description: Colon epithelial cell from MSH2+/- mice

value: Epithelial cell


title: Liver_Air_6H_Rat763

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Liver


title: M_P15_HET-2

description: Colon stem cell from MSH2+/- mice

value: Stem cell

value: HET


title: Lung_Air_6H_Rat762

description: 0 ppm  x 32.2 min (0 ppm x min)


title: HCT116 WT

value: parental cell line


title: Liver_Air_6H_Rat762

description: 0 ppm  x 32.2 min (0 ppm x min)


title: Brain_Air_6H_Rat763

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Brain


title: Heart_Air_6H_Rat763

description: 0 ppm  x 32.2 min (0 ppm x min)


title: Unknown outside region collected from sample 2

city: Bronx

first: Anita

middle: E

last: Autry

state: NY

address: 1410 Pelham Parkway S

department: Neuroscience and Psychiatry

institute: Albert Einstein College of Medicine

description: total RNA pooled from 6 laser captured samples=Sample2

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials according to manufacturer's specifications

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
The CEL files were read in and analyzed by oligo Bioconductor package. The data are RMA normalized and differential expression was carried out by limma.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm8.mps

label: biotin

source_name: Unknown outside region

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: All samples contained 5Î¼g of carrier glycogen and were prepared using Trizol. Samples were then treated with the RiobMinus rRNA reduction kit (Invitrogen), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

tag: strain

tag: Sex

value: male

tag: age

value: adult (10-15 weeks)

tag: genotype

value: wild-type

tag: region

value: control outside region (unk)

value: laser captured hypothalamic cells


title: M_P13_HET-1

description: Colon stem cell from MSH2+/- mice

tag: tissue

tag: localization

tag: pathology


title: Unknown outside region collected from sample 3

description: total RNA pooled from 6 laser captured samples=Sample3


title: M_P14_HET-1

description: Colon epithelial cell from MSH2+/- mice

tag: gfp

tag: batch

tag: mmr status


title: Heart_Air_6H_Rat762

description: 0 ppm  x 32.2 min (0 ppm x min)


title: Unknown outside region collected from sample 1

description: total RNA pooled from 6 laser captured samples= Sample1

tag: cell type


title: Kidney_Air_6H_Rat762

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Kidney


title: Y20-LV

city: Aurora

first: Edward

last: Lau

state: CO

address: 12700 E19th Av RCII Rm 8004

department: Medicine/Cardiology

institute: University of Colorado

description:
Ribosome-depleted RNA
EL23

data_processing:
Read alignment using STAR v.2.7.6a (--sjdgOverhang 150 --readFilesCommand gunzip -c --outSAMtype  BAM SortedByCoordinate)
Transcript assembly using StringTie v.2.1.1 (--rf -e -G gencode.vM25.annotation.gff3)
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Stringtie gene counts

source_name: Left Ventricle

extract_protocol:
Zymo Direct-zol RNA Miniprep Plus
Zymo Zymo-seq ribofree total RNA library kit

value: Left Ventricle

tag: age group

value: M


title: O12-LV

description:
Ribosome-depleted RNA
EL24

value: 86 wk

value: F


title: Y14-LV

description:
Ribosome-depleted RNA
EL22


title: M_P10_KO-2

description: Colon epithelial cell from MSH2-/- mice

value: COLON

value: Mice

value: KO


title: Oxt positive region collected from sample 3

source_name: Oxt positive region

value: oxytocin positive region (oxt)


title: Brain_Air_6H_Rat762

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Air


title: C-fos positive region collected from sample 3

source_name: C-fos positive region

value: c-fos positive region (c-fos)


title: Oxt positive region collected from sample 1


title: Oxt positive region collected from sample 2


title: Liver_PH3_6H_Rat761

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Liver


title: Blood_Air_6H_Rat762

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Blood


title: Lung_PH3_6H_Rat761

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Lung


title: Kidney_PH3_6H_Rat761

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: M_P12_KO-3

description: Colon epithelial cell from MSH2-/- mice

value: Epithelial cell


title: Y19-SM

description:
Ribosome-depleted RNA
EL20

source_name: Skeletal Muscle

value: Skeletal Muscle


title: Y20-Kid

description:
Ribosome-depleted RNA
EL18

source_name: Kidney


title: M_P09_KO-2

description: Colon stem cell from MSH2-/- mice

value: Stem cell


title: O11-SM

description:
Ribosome-depleted RNA
EL19


title: Y15-LV

description:
Ribosome-depleted RNA
EL16


title: O17-Kid

description:
Ribosome-depleted RNA
EL17

value: Kidney


title: M_P11_KO-3

description: Colon stem cell from MSH2-/- mice


title: O12-SM

description:
Ribosome-depleted RNA
EL13


title: O11-Kid

description:
Ribosome-depleted RNA
EL21


title: M_P08_KO-1

description: Colon epithelial cell from MSH2-/- mice


title: Y15-SM

description:
Ribosome-depleted RNA
EL14


title: M_P07_KO-1

description: Colon stem cell from MSH2-/- mice


title: O14-LV

description:
Ribosome-depleted RNA
EL12

value: Left Ventricle


title: Y19-LV

description:
Ribosome-depleted RNA
EL11

value: M


title: VICs with Cre for 72h_2 [GR_plus_Cre_2]

city: New York

first: Maiko

last: Matsui

address: 413 E69th Street

institute: Weill Cornell Medicine

data_processing:
The samples were sequenced using HiSeq4000 sequencer with single-end 50 bps reads. The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
The RNA reads were aligned and mapped to the GRCm38 mouse reference genome by STAR (Version2.5.2).
The transcriptome reconstruction was performed by Cufflinks (Version 2.1.1). The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM).
Gene expression profiles were constructed using the DESeq2 package.
The resulting corrected p-values were calculated based on the Benjamin-Hochberg’s method to adjust multiple testing and control the false discovery rate.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include raw read counts at gene level for each samples

source_name: VICs with Cre for 72h

growth_protocol: Mouse vavular interstitial cells (mVICs) were isolated from aortic valves using enzymatic digestion method with collagenase and cultured on uncoated plastic in DMEM. Passage between 3 and 8 were used.

extract_protocol:
RNA was isolated from cultured mVICs using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
Library was constructed on the purified RNAs using Illumina TruSeq Strandard mRNA library preparation kit.

treatment_protocol: Cultured cells were treated with adenovirus expressing GFP or Cre recombinase and incuvated for 48h or 72h.

value: valvular interstitial cells (VICs)

tag: genotype/variation

value: VICs with floxed GOF mutation in exon8 of Cacna1c

tag: treatment

value: treated with adenovirus expressing Cre recombinase


title: VICs with Cre for 72h_4 [GR_plus_Cre_4]


title: C-fos positive region collected from sample 2

value: male

value: adult (10-15 weeks)

value: wild-type

value: laser captured hypothalamic cells


title: VICs with Cre for 72h_1 [GR_plus_Cre_1]


title: Brain_PH3_6H_Rat761

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Brain

tag: time point


title: O14-Kid

description:
Ribosome-depleted RNA
EL9

value: 86 wk


title: O17-SM

description:
Ribosome-depleted RNA
EL15


title: Heart_PH3_6H_Rat761

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Heart

tag: exposure


title: C-fos positive region collected from sample 1

tag: strain

value: c-fos positive region (c-fos)


title: O11-LV

description:
Ribosome-depleted RNA
EL7

tag: Sex

value: F


title: VICs with GFP for 72h_3 [GR_plus_GFP_3]

source_name: VICs with GFP for 72h

value: treated with adenovirus expressing GFP


title: Y15-Kid

description:
Ribosome-depleted RNA
EL8


title: Liver_PH3_6H_Rat760

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Liver


title: O17-LV

description:
Ribosome-depleted RNA
EL6


title: Y14-Kid

description:
Ribosome-depleted RNA
EL5

value: Kidney


title: Y19-Kid

description:
Ribosome-depleted RNA
EL4


title: VICs with GFP for 72h_2 [GR_plus_GFP_2]


title: Y20-SM

description:
Ribosome-depleted RNA
EL3

value: Skeletal Muscle


title: Blood_PH3_6H_Rat761

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Blood


title: Brain_PH3_6H_Rat760

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: O14-SM

description:
Ribosome-depleted RNA
EL2

value: M


title: Heart_PH3_6H_Rat760

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: VICs with GFP for 72h_1 [GR_plus_GFP_1]

value: valvular interstitial cells (VICs)

value: VICs with floxed GOF mutation in exon8 of Cacna1c


title: Kidney_PH3_6H_Rat760

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: Lung_PH3_6H_Rat760

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Lung


title: Y14-SM

description:
Ribosome-depleted RNA
EL1


title: O12-Kid

description:
Ribosome-depleted RNA
EL10


title: VICs with Cre for 48h_4 [C4]

source_name: VICs with Cre for 48h

value: treated with adenovirus expressing Cre recombinase


title: VICs with Cre for 48h_2 [C2]


title: VICs with Cre for 48h_3 [C3]


title: M_P7_hyperoxia_CD45_2_DC35_C21

city: Kensington

first: Fabio

last: Zanini

state: NSW

address: High and Botany St

country: Australia

institute: University of New South Wales

data_processing:
Mapping against human genome with VEEV-TC83-GFP added as an additional chromosome (using STAR 2.5.2b)
Counting gene expression using htseq-count 0.10
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts table: raw read counts, not notmalized, rows are gene names, columns are cell names. Metadata file: rows are cell names, columns are metadata.

source_name: distal lung

extract_protocol:
no extraction
plate-based illumina-compatible Tn5 transposase single cell RNA-Seq

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

value: hyperoxia

value: immune

tag: cell subtype

value: Mac III

tag: mousename

tag: coverage

tag: number of genes


title: F_P7_hyperoxia_CD45_2_DC35_N7

tag: cell type

value: neutrophil


title: F_P7_hyperoxia_CD45_2_DC35_G15

value: Mac V


title: Lung_PH3_6H_Rat758

description: 660 ppm  x 32.2 min (21,252 ppm x min)

tag: tissue


title: M_P7_hyperoxia_CD45_1_DC35_I8


title: M_P7_hyperoxia_CD45_1_DC35_N22


title: VICs with Cre for 48h_1 [C1]

tag: genotype/variation


title: M_P7_hyperoxia_CD45_2_DC35_A21

tag: treatment


title: M_P7_hyperoxia_CD45_1_DC35_B23

value: Mac IV


title: Liver_PH3_6H_Rat758

description: 660 ppm  x 32.2 min (21,252 ppm x min)

tag: time point


title: Blood_PH3_6H_Rat760

description: 660 ppm  x 32.2 min (21,252 ppm x min)

tag: exposure


title: M_P7_hyperoxia_CD45_1_DC35_O7

value: B cell


title: Kidney_PH3_6H_Rat758

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: M_P7_hyperoxia_CD45_1_DC35_N13


title: M_P7_hyperoxia_CD45_2_DC35_N12


title: VICs with GFP for 48h_4 [G4]

source_name: VICs with GFP for 48h

tag: strain

value: treated with adenovirus expressing GFP


title: VICs with GFP for 48h_3 [G3]


title: M_P7_hyperoxia_CD45_1_DC35_A11


title: M_P7_hyperoxia_CD45_1_DC35_D10


title: Heart_PH3_6H_Rat758

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Heart


title: VICs with GFP for 48h_2 [G2]


title: M_P7_hyperoxia_CD45_2_DC35_A5


title: Brain_PH3_6H_Rat758

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Brain


title: M_P7_hyperoxia_CD45_1_DC35_P8


title: VICs with GFP for 48h_1 [G1]


title: Liver_Air_24H_Rat751

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Liver

value: Air


title: M_P7_hyperoxia_CD45_2_DC35_D3

value: M


title: Blood_PH3_6H_Rat758

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Blood


title: M_P7_hyperoxia_CD45_2_DC35_I5


title: F_P7_hyperoxia_CD45_2_DC35_O22

value: F


title: M_P7_hyperoxia_CD45_2_DC35_F6


title: M_P7_hyperoxia_CD45_2_DC35_J16


title: M_P7_hyperoxia_CD45_1_DC35_J16


title: Lung_Air_24H_Rat751

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Lung


title: M_P7_hyperoxia_CD45_2_DC35_P16

value: Mac II


title: single-cell_RNAseq_TAF4 KO pancreas 5 weeks

city: Strasbourg

first: Irwin

last: Davidson

address: 1 Rue Laurent Fries

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment to reference genome mm10 and gene quantification for each cell was done using CellRanger v3.1.
Data are imported into R and analyzed using the Seurat package v3.1.4.
Genome_build: mm10
Supplementary_files_format_and_content: TSV files containing raw UMI counts for cells used in Seurat analysis.

source_name: Captured single cell RNA

growth_protocol: Langerhans islets were purified from mice

extract_protocol:
After islet isolation,further digestion was performed with Accutase (A6964, Sigma) at 27 °C for 5 minutes and the cells were suspended in culture medium. Cells were then FACS sorted to select only live cells. 300 islets froma male WT mouse and 300 islets pooled from 2 male mutant mice 1 week or 5 weeks after Taf4 inactivation were used for scRNA-seq. Cell capture was  performed using  10X Genomics Chromium Analyzer.
Single Cell 3ʹ Gene Expression libraries comprise standard Illumina paired-end constructs which begin with P5 and end with P7. 16  bp 10x Barcodes are encoded at the start of TruSeq Read 1, while 8 bp sample index sequences are incorporated as the i7 index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired-end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 12 bp UMI.

value: Isolated Langerhans Islets

tag: genotype

value: TAF4 KO

tag: time

value: 5 weeks


title: Kidney_Air_24H_Rat751

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Kidney


title: M_P7_hyperoxia_CD45_1_DC35_C18

tag: sequencing run

tag: gender

value: hyperoxia

value: immune


title: single-cell_RNAseq_TAF4 KO pancreas 1 week

value: 1 week


title: RNA-seq_TAF-KO pancreas 5 week-3

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were preprocessed in order to remove adapter and low-quality sequences (Phred quality score below 20) using cutadapt version 1.10.
Reads were mapped to rRNA sequences using bowtie version 2.2.8, and reads mapping to rRNA sequences were removed for further analysis. Reads were mapped to spike sequences using bowtie2 version 2.2.8, and reads mapping to spike sequences were removed for further analysis.
Reads were mapped to reference genome mm9 using STAR v2.5.3a. Only uniquely aligned reads were retained for further analyses.
Gene expression quantification was performed from uniquely aligned reads using htseq-count version v0.6.1 with annotations from Ensembl version 67.
Data normalization and fold-change across conditions computation were performed using the DESeq2 Bioconductor package. Significantly deregulated genes were selected using a log2 fold change >1 and <1 and adjusted p-value cutoff of 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: Excel file containing raw read counts and normalized (by sequencing depth and gene length) expression for each sample. Additional tabs contain deregulated genes for each comparison.

source_name: Total RNA: Nucleospin RNA plus XS

extract_protocol:
RNA was extracted from isolated islets with Nucleospin RNA plus XS. Complementary DNA was generated and linearly amplified from 3 ng total RNA using the Ovation RNA-seq V2 system (NuGEN technologies Inc., Leek, The Netherlands), according to the manufacturer's instructions. The amplified cDNA was then purified using Agencourt AMPure XP beads (Beckman-Coulter, Villepinte, France) in a 1.8:1 bead to sample ratio and fragmented by sonication using a Covaris E220 instrument (with duty cycle: 10%, maximum incident power: 175 watts and cycles/burst: 200 for 120 seconds).
Complementary DNA were generated and linearly amplified from 6 ng of total RNA using the Ovation RNA-seq system V2 (NuGEN technologies Inc., Leek, Netherlands), according to manufacturer's instructions. Amplified cDNA was then purified using Agencourt AMPure XP beads (Beckman-Coulter, Villepinte, France) in a 1.8:1 ratio of beads to sample and fragmented by sonication using a Covaris E220 instrument (with duty factor: 10 percent, peak incident power: 175 watts and cycles/burst: 200 for 120 seconds). RNA-Seq libraries were generated from 100 ng of fragmented ds-cDNA using Ovation Ultralow Library System v2 (NuGEN technologies Inc., Leek, Netherlands) according to manufacturer's instructions with only 8 PCR cycles for library amplification. The final libraries were checked for quality and quantified using capillary electrophoresis.


title: M_P7_hyperoxia_CD45_2_DC35_D1

tag: plate

tag: well

value: Mac V


title: M_P7_hyperoxia_CD45_2_DC35_J13

tag: timepoint

tag: cell subtype

value: neutrophil


title: F_P7_hyperoxia_CD45_2_DC35_E5

value: Mac IV

tag: mousename

tag: coverage


title: RNA-seq_TAF-KO pancreas 5 week-1


title: M_P7_hyperoxia_CD45_2_DC35_D7

tag: cell type

value: Mac III

tag: number of genes


title: F_P7_hyperoxia_CD45_2_DC35_F3

value: mast cell


title: RNA-seq_TAF-KO pancreas 3 week-3

tag: tissue

value: 3 weeks


title: F_P7_hyperoxia_CD45_2_DC35_O23

tag: treatment


title: F_P7_hyperoxia_CD45_2_DC35_K3


title: Brain_Air_24H_Rat751

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Brain

tag: time point

value: Air


title: single-cell_RNAseq_WT pancreas

value: Wild type


title: F_P7_hyperoxia_CD45_2_DC35_D7

value: F

value: IL cell


title: M_P7_hyperoxia_CD45_2_DC35_J1

value: M

value: DC I


title: M_P7_hyperoxia_CD45_2_DC35_M20


title: M_P7_hyperoxia_CD45_1_DC35_M13


title: M_P7_hyperoxia_CD45_1_DC35_O5


title: RNA-seq_TAF-KO pancreas 3 week-1

value: Isolated Langerhans Islets

value: TAF4 KO


title: RNA-seq_TAF-KO pancreas 5 week-2

value: 5 weeks


title: F_P7_hyperoxia_CD45_2_DC35_N2

value: hyperoxia

value: immune

value: T cell


title: Heart_Air_24H_Rat751

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Heart

tag: exposure


title: RNA-seq_TAF-KO pancreas 3 week-2

tag: strain


title: Liver_Air_24H_Rat750

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Liver


title: Lung_Air_24H_Rat750

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Lung


title: M_P7_hyperoxia_CD45_1_DC35_D17

value: Mac II


title: Brain_Air_24H_Rat750

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Brain


title: RNA-seq_Wild type pancreas 3

tag: genotype


title: Kidney_Air_24H_Rat750

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Kidney

value: Air


title: Heart_Air_24H_Rat750

description: 0 ppm  x 32.2 min (0 ppm x min)


title: M_P7_hyperoxia_CD45_2_DC35_L9

value: B cell


title: F_P7_hyperoxia_CD45_2_DC35_D11

value: F

value: mast cell


title: Liver_PH3_24H_Rat749

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: RNA-seq_Wild type pancreas 1

value: Wild type

tag: time


title: Lung_PH3_24H_Rat749

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: F_P7_hyperoxia_CD45_2_DC35_H8

tag: sequencing run

value: Mac IV


title: M_P7_hyperoxia_CD45_2_DC35_N11

tag: gender

value: M

value: mast cell II


title: RNA-seq_TAF-KO pancreas 1 week-3

value: Isolated Langerhans Islets

value: TAF4 KO

value: 1 week


title: M_P7_hyperoxia_CD45_2_DC35_E21

tag: plate

value: hyperoxia

value: immune

value: IL cell


title: Kidney_PH3_24H_Rat749

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: Heart_PH3_24H_Rat749

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Heart


title: M_P7_hyperoxia_CD45_2_DC35_H12

tag: well


title: M_P7_hyperoxia_CD45_1_DC35_F17

tag: timepoint

value: Mac V


title: RNA-seq_Wild type pancreas 2


title: RNA-seq_TAF-KO pancreas 1 week-2


title: M_P7_hyperoxia_CD45_2_DC35_P5

tag: cell subtype

value: Mac III


title: ATAC-seq_TAF-KO pancreas 5 week

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm9 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Peaks were called using MACS 2.1.1 with ‘--nomodel --shift -100 --extsize 200 --broad’ parameters
Genome_build: mm9
Supplementary_files_format_and_content: Peaks called by MACS2 in broadPeak format.

source_name: ATAC-seq fragmented chromatin

growth_protocol: Langerhans islets were purified from mice and cells dissociated by digestion with Accutase (A6964, Sigma) at 27 °C for 5 minutes

extract_protocol: ATAC-seq was performed by standard procedures

value: Cells from isolated Langerhans Islets

value: Taf4 KO

value: 5 weeks


title: ATAC-seq_TAF-KO pancreas 1 week


title: RNA-seq_TAF-KO pancreas 1 week-1


title: M_P7_hyperoxia_CD45_2_DC35_K23

value: DC I

tag: mousename


title: M_P7_hyperoxia_CD45_1_DC35_A2

value: B cell

tag: coverage


title: F_P7_hyperoxia_CD45_2_DC35_B16

value: F

tag: cell type

value: basophil


title: Brain_PH3_24H_Rat749

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Brain


title: M_P7_hyperoxia_CD45_2_DC35_M1

value: M

value: DC II

tag: number of genes


title: ATAC-seq_Wild type pancreas

tag: tissue

value: wild type


title: Lung_PH3_24H_Rat748

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Lung


title: M_P7_hyperoxia_CD45_2_DC35_L22

tag: treatment

value: hyperoxia

value: immune


title: M_P7_hyperoxia_CD45_2_DC35_I18


title: M_P7_hyperoxia_CD45_2_DC35_B21


title: F_P7_hyperoxia_CD45_2_DC35_G6


title: Liver_PH3_24H_Rat748

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Liver

tag: time point


title: M_P7_hyperoxia_CD45_2_DC35_K3

value: Mac IV


title: M_P7_hyperoxia_CD45_1_DC35_O1

value: Mac II


title: WT.Neu_pCHiC_rep2

city: Stuttgart

first: Haiyang

last: Yun

address: Auerbachstraße 112

country: Germany

institute: Robert Bosch Center for Tumor Diseases

description: promoter capture HiC (pCHiC)

data_processing:
Library strategy: promoter capture HiC (pCHiC)
Paired-end sequences were processed using the HiCUP pipeline with default parameters for the following steps: quality control, identification of reads containing HiC junctions, mapping to reference genome mm10, and filtering duplicated HiC di-tags.
HiCUP output bam files containing valid HiC di-tags were further processed by Bioconductor package CHiCAGO, to call significant promoter-based interactions.
CHiCAGO scores represent -log weighted p-values, the higher the more likelihood of interaction formed. CHiCAGO scores were calculated for each pCHiC sample, and significant interactions were called when CHiCAGO scores > 5.
Significant hign-confidence (HC) interactions were defined by CHiCAGO score > 5 at least in both individual replicates of one cell type, and were combined to form a matrix of total unique interactions.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include CHiCAGO scores for total HC interactions across WT and mutant HSPCs, and significant interactions in WT neutrophils.

source_name: Neutrophils

growth_protocol: Hematopoietic bone marrow (BM) cells were collected by flushing femurs and tibias of WT or mutant mice with sterile PBS and were filtered through 70-µm EASYstrainer (Greiner). Red blood cells were then depleted using RBC lysis buffer (5 PRIME). The isolation of lineage negative (Lin-) HSPCs or neutrophils were performed using Lineage Cell depletion kit or Neutrophil Isolation Kit (Miltenyi Biotec).

extract_protocol:
20-25 million cells were crosslinked by 1% formaldehyde for 10 minutes at room temperature and was then quenched by glycine. Cells were lysed with the help of homogenization. Chromatin digestion was achieved overnight using HindIII. Digested DNA ends were biotinylated by filling with biotin-14-dATP (Invitrogen) and underwent in-nucleus ligation using T4 DNA ligase at 16 °C overnight. Crosslink was then reversed by incubation with Proteinase K at 65  ̊C overnight. RNA was removed by adding RNase A and incubating at 37  ̊C for 1 hour. DNA was purified twice with Phenol:Chloroform:Isoamyl Alcohol. Extra Biotin-14-dATP was first removed using T4 DNA polymerase and incubating at 20  ̊C for 4 hours. 40 μg DDNA was sheared using Covaris S2 to achieve a target peak around 400 bp. Sheared DNA was subject to end repair and purification, followed by addition of dATP as A-tail. DNA fragments were size selected to enrich at 200-650 bp by double-sided SPRI beads (Invitrogen). Biotin-labeled fragments were pulled down using Dynabeads MyOne Streptavidin C1 (Invitrogen) and ligated to pre-annealed paired-end (PE) adapter on beads. Eventually, HiC DNA was amplified using PE PCR primers for 7-9 cycles. HiC library was purified twice using 1.8x SPRI beads.
500 ng of HiC library was used for hybridization with biotinylated RNA bait library (Agilent Technologies), which contained 39684 biotinylated RNA probes covering 22047 promoters. Hybridization was performed as per manufacture’s protocol. Dynabeads MyOne Streptavidin T1 beads were utilized to pull down biotin-labeled DNA-RNA hybrids. Final PCR amplification and DNA purification of promoter capture HiC library were performed similarly as for HiC library, with the difference for 4 cycles of PCR. pCHiC were performed in biological duplicates of each cellular states.

value: Wild-type (WT)

value: Bone marrow neutrophis


title: M_P7_hyperoxia_CD45_2_DC35_D13

value: Mac III


title: M_P7_hyperoxia_CD45_2_DC35_I12


title: M_P7_hyperoxia_CD45_2_DC35_C16


title: F_P7_hyperoxia_CD45_2_DC35_E23

value: mast cell II


title: M_P7_hyperoxia_CD45_2_DC35_O5


title: Kidney_PH3_24H_Rat748

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Kidney

tag: exposure


title: M_P7_hyperoxia_CD45_2_DC35_K5

value: Mac V


title: Brain_PH3_24H_Rat748

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: Heart_PH3_24H_Rat748

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Heart


title: Flt3-ITD.HSPC_pCHiC_rep2

description: promoter capture HiC (pCHiC)

source_name: Hematopoietic stem and progenitor cells (HSPC)

value: Flt3ITD/+ (Flt3-ITD)

value: Bone marrow lineage negative cells

tag: strain


title: Flt3-ITD.HSPC_pCHiC_rep1

description: promoter capture HiC (pCHiC)

tag: genotype


title: Lung_Air_24H_Rat745

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Air


title: M_P7_hyperoxia_CD45_2_DC35_E11

value: M


title: Npm1c.HSPC_pCHiC_rep2

description: promoter capture HiC (pCHiC)

value: Npm1flox-cA/+;Mx1-Cre+ (Npm1c)


title: Npm1c.HSPC_pCHiC_rep1

description: promoter capture HiC (pCHiC)


title: Kidney_Air_24H_Rat745

description: 0 ppm  x 32.2 min (0 ppm x min)


title: DM.HSPC_pCHiC_rep2

description: promoter capture HiC (pCHiC)

value: Npm1flox-cA/+;Flt3ITD/+;Mx1-Cre+ (double mutant, DM)


title: M_P7_hyperoxia_CD45_2_DC35_J15

value: hyperoxia

value: immune

value: basophil


title: M_P7_hyperoxia_CD45_1_DC35_E12

value: DC I


title: Heart_Air_24H_Rat745

description: 0 ppm  x 32.2 min (0 ppm x min)


title: WT.Neu_ATAC-seq_rep2

description: ATAC-seq

data_processing:
Trimmed sequences were mapped against mm10 reference genome using Bowtie2 and only uniquely mapped reads were kept.
Peaks were called using MACS2 with the setting with a P-value cutoff of 1e-9 and “-nomodel -nolambda”.
Genome_build: mm10
Supplementary_files_format_and_content: bed files containing peak coordinates (chr, start, end)
Supplementary_files_format_and_content: Normalised (CPM) bigwig files including genome-wide enrichment features

extract_protocol:
100,000 freshly isolated cells were pelleted and resuspended in 100 µL Lysis buffer, followed by tagmentation using Nextera DNA Sample Preparation Kit (Illumina) for 30 minutes incubation at 37 °C.
Transposed DNA was purified using with MinElute PCR Purification kit (Qiagen). Eluted DNA was amplified via PCR and purified with Qiagen MinElute PCR Purification kit. The quantity  and quality of library DNA was measured using KAPA Library Quantification kit (Kapa Biosystems) and Bioanalyzer 2100 system with a High Sensitivity DNA chip (Agilent Technologies) respectively.

value: Wild-type (WT)


title: M_P7_hyperoxia_CD45_2_DC35_A13

value: neutrophil


title: F_P7_hyperoxia_CD45_2_DC35_P10

value: F


title: Lung_Air_24H_Rat744

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Lung


title: WT.Neu_ATAC-seq_rep1

description: ATAC-seq

value: Bone marrow neutrophis


title: Liver_Air_24H_Rat744

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Liver


title: Liver_Air_24H_Rat745

description: 0 ppm  x 32.2 min (0 ppm x min)


title: Brain_Air_24H_Rat745

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Brain


title: M_P7_hyperoxia_CD45_1_DC35_O13

value: DC III


title: F_P7_hyperoxia_CD45_2_DC35_H11

value: B cell


title: M_P7_hyperoxia_CD45_1_DC35_D11


title: Kidney_Air_24H_Rat744

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Kidney

value: Air


title: DM.HSPC_ATAC-seq_rep1

description: ATAC-seq

value: Bone marrow lineage negative cells


title: M_P7_hyperoxia_CD45_2_DC35_M3

value: M

value: Mac V


title: F_P7_hyperoxia_CD45_2_DC35_B14

value: hyperoxia

value: immune

value: T cell


title: Heart_Air_24H_Rat744

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Heart


title: M_P7_hyperoxia_CD45_2_DC35_D16

value: Mac III


title: Flt3-ITD.HSPC_ATAC-seq_rep2

description: ATAC-seq

value: Flt3ITD/+ (Flt3-ITD)


title: M_P7_hyperoxia_CD45_2_DC35_K2


title: F_P7_hyperoxia_CD45_2_DC35_L20

value: F

value: basophil


title: F_P7_hyperoxia_CD45_2_DC35_G9

value: Mac IV


title: M_P7_hyperoxia_CD45_1_DC35_J15


title: Npm1c.HSPC_ATAC-seq_rep2

description: ATAC-seq

value: Npm1flox-cA/+;Mx1-Cre+ (Npm1c)


title: M_P7_hyperoxia_CD45_1_DC35_G1


title: Brain_Air_24H_Rat744

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Brain


title: M_P7_hyperoxia_CD45_2_DC35_P6

value: DC I


title: M_P7_hyperoxia_CD45_2_DC35_A20

value: DC III


title: Liver_PH3_24H_Rat742

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Liver


title: Lung_PH3_24H_Rat742

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Lung


title: DM.HSPC_ATAC-seq_rep2

description: ATAC-seq

value: Npm1flox-cA/+;Flt3ITD/+;Mx1-Cre+ (double mutant, DM)

value: Bone marrow lineage negative cells


title: M_P7_hyperoxia_CD45_2_DC35_J12

value: M

value: hyperoxia


title: M_P7_hyperoxia_CD45_2_DC35_H21

value: immune


title: Kidney_PH3_24H_Rat742

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Kidney


title: WT.HSPC_ATAC-seq_rep2

description: ATAC-seq

value: Wild-type (WT)


title: Npm1c.HSPC_ATAC-seq_rep1

description: ATAC-seq


title: WT.HSPC_ATAC-seq_rep1

description: ATAC-seq


title: M_P7_hyperoxia_CD45_2_DC35_N6

value: NK cell


title: F_P7_hyperoxia_CD45_2_DC35_C9

value: F

value: Mac III


title: Brain_PH3_24H_Rat742

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: M_P7_hyperoxia_CD45_2_DC35_O11

value: DC II


title: Heart_PH3_24H_Rat742

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Heart


title: M_P7_hyperoxia_CD45_1_DC35_E10

value: Mac V


title: F_P7_hyperoxia_CD45_2_DC35_A8

value: B cell


title: Flt3-ITD.HSPC_ATAC-seq_rep1

description: ATAC-seq

value: Flt3ITD/+ (Flt3-ITD)


title: F_P7_hyperoxia_CD45_2_DC35_D16


title: ctrl_endo4

first: Weijia

last: Zhang

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The reads with good quality were aligned to several reference databases including mm10 mouse genome, exon, splicing-junction segments, and contamination database including ribosome and mitochondrial sequences using BWA alignment algorithm.
After filtering reads mapped to the contamination database, the reads that are uniquely aligned to the exon and splicing-junction segments with a maximal 2 miss-matches for each transcript were then counted as expression level for the corresponding transcripts.
The read counts were log2 transformed and normalized at an equal global median value in order to compare transcription levels across samples.
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: Glomerular endothelial cell

extract_protocol:
Kidney were removed, YFP+ cells were sorted by FACS, and RNA was harvested using Qiagen Rneasy mini kit. Illumina TruSeq RNA Sample Prep Kit  was used with 50ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Glomerular endothelial cell

tag: genotype/variation

value: Nphs2-Cre/iDTR+/+/Flk1 EYFP


title: ctrl_endo2


title: ctrl_endo1


title: Liver_PH3_24H_Rat741

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Liver


title: Blood_PH3_24H_Rat742

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Blood


title: M_P7_hyperoxia_CD45_1_DC35_B11

tag: sequencing run

value: M


title: F_P7_hyperoxia_CD45_2_DC35_L23

tag: gender

value: hyperoxia


title: Dendo3

value: Nphs2-Cre/iDTR-/+/Flk1 EYFP


title: M_P7_hyperoxia_CD45_2_DC35_J8

tag: plate

value: immune


title: M_P7_hyperoxia_CD45_2_DC35_C6

tag: well

value: Mac IV


title: Dendo2

value: Kidney


title: M_P7_hyperoxia_CD45_1_DC35_H20

tag: timepoint


title: F_P7_hyperoxia_CD45_2_DC35_M1

value: F

tag: cell subtype


title: Dendo1


title: Genotyping data for sample 1225G

data_processing:
Intra-chip normalization was performed using the Illumina's GenomeStudio software v.1.0.1 with a GenCall cutoff of 0.1 and call rate cutoff of 98%. For CNV calling on the Illumina 2.5M platform we used QuantiSNP, iPattern, PennCNV.
For CNV detection using different algorithms, various measurements were exported directly from GenomeStudio: the intra-chip normalized X and Y intensity values from the A and B allele-specific probes respectively, and two other measurements derived from X and Y after normalization with respect to reference population, i.e. the Log R ratios (LRR) and B allele frequency (BAF) values. For the algorithms that used LRR, representing the total signal intensity, and BAF, representing the allelic balance, the Illumina’s cluster file made of >120 HapMap was used to generate intensities and genotypes using GenomeStudio.

source_name: genomic DNA from whole blood

extract_protocol: Genomic DNA extracted using the Qiagen DNA micro kit (QIAgen, Hilden, Germany)

value: Male

tag: ethnicity

value: Roma ancestry

tag: celltype

value: DNA extracted from whole blood


title: M_P7_hyperoxia_CD45_2_DC35_A2

tag: cell type

value: Mac III

tag: mousename

tag: coverage


title: F_P7_hyperoxia_CD45_2_DC35_C13

tag: treatment

value: B cell

tag: number of genes


title: F_P7_hyperoxia_CD45_2_DC35_D1

value: NK cell


title: Genotyping data for sample 974G

value: North-Central European ancestry


title: F_P7_hyperoxia_CD45_2_DC35_G12

value: mast cell


title: F_P7_hyperoxia_CD45_2_DC35_A16


title: M_P7_hyperoxia_CD45_2_DC35_M11


title: Heart_PH3_24H_Rat741

description: 660 ppm  x 32.2 min (21,252 ppm x min)

tag: tissue

value: Heart

tag: time point

tag: exposure


title: M_P7_hyperoxia_CD45_1_DC35_F7


title: Genotyping data for sample 973G


title: Brain_PH3_24H_Rat741

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Brain


title: Genotyping data for sample 972G


title: M_P7_hyperoxia_CD45_2_DC35_M22

value: M

value: DC I


title: M_P7_hyperoxia_CD45_2_DC35_A17

value: hyperoxia


title: Blood_PH3_24H_Rat741

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Blood


title: F_P7_hyperoxia_CD45_2_DC35_B21

value: immune


title: Genotyping data for sample 969G


title: Kidney_PH3_24H_Rat741

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Kidney


title: F_P7_hyperoxia_CD45_2_DC35_E7

value: F


title: Liver_Air_3H_Rat739

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Liver

value: Air


title: Lung_PH3_24H_Rat741

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Lung


title: Kidney_Air_3H_Rat739

description: 0 ppm  x 32.2 min (0 ppm x min)


title: Heart_Air_3H_Rat739

description: 0 ppm  x 32.2 min (0 ppm x min)


title: M_P7_hyperoxia_CD45_1_DC35_D22

value: DC II


title: Genotyping data for sample 871G

value: Male

value: Roma ancestry

value: DNA extracted from whole blood


title: M_P7_hyperoxia_CD45_1_DC35_J21

value: B cell


title: M_P7_hyperoxia_CD45_1_DC35_N2

value: neutrophil


title: M_P7_hyperoxia_CD45_1_DC35_P16

value: mast cell


title: Lung_Air_3H_Rat739

description: 0 ppm  x 32.2 min (0 ppm x min)


title: Genotyping data for sample 870G


title: Brain_Air_3H_Rat739

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Brain


title: F_P7_hyperoxia_CD45_2_DC35_J18


title: F_P7_hyperoxia_CD45_2_DC35_N20

value: Mac III


title: Genotyping data for sample 864G

value: North-Central European ancestry


title: Liver_Air_3H_Rat738

description: 0 ppm  x 32.2 min (0 ppm x min)


title: Blood_Air_3H_Rat739

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Blood


title: M_P7_hyperoxia_CD45_2_DC35_M16

value: M

value: hyperoxia

value: immune


title: Genotyping data for sample 863G


title: Genotyping data for sample 862G


title: F_P7_hyperoxia_CD45_2_DC35_H18

value: F


title: M_P7_hyperoxia_CD45_1_DC35_N4

value: T cell


title: M_P7_hyperoxia_CD45_1_DC35_P17

value: Mac V


title: M_P7_hyperoxia_CD45_2_DC35_H7

value: Mac IV


title: Genotyping data for sample 861G

value: Male


title: F_P7_hyperoxia_CD45_2_DC35_D14

value: basophil


title: Genotyping data for sample 859G

value: DNA extracted from whole blood


title: F_P7_hyperoxia_CD45_2_DC35_D17


title: M_P7_hyperoxia_CD45_1_DC35_G18

value: DC I


title: F_P7_hyperoxia_CD45_2_DC35_O6


title: F_P7_hyperoxia_CD45_2_DC35_I6


title: M_P7_hyperoxia_CD45_1_DC35_C6


title: M_P7_hyperoxia_CD45_2_DC35_D8

value: neutrophil


title: M_P7_hyperoxia_CD45_1_DC35_P6

value: mast cell


title: Heart_Air_3H_Rat738

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Heart

value: Air


title: Genotyping data for sample 550G

value: Roma ancestry


title: Kidney_Air_3H_Rat738

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Kidney


title: Genotyping data for sample 857G


title: M_P7_hyperoxia_CD45_1_DC35_E7

value: M


title: M_P7_hyperoxia_CD45_1_DC35_E20

value: hyperoxia

value: Mac III


title: Genotyping data for sample 549G


title: F_P7_hyperoxia_CD45_2_DC35_F13

value: F

value: immune


title: Genotyping data for sample 548G


title: M_P7_hyperoxia_CD45_1_DC35_L15


title: F_P7_hyperoxia_CD45_2_DC35_G18


title: M_P7_hyperoxia_CD45_2_DC35_F4


title: Genotyping data for sample 547G


title: Lung_Air_3H_Rat733

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Lung


title: Lung_Air_3H_Rat738

description: 0 ppm  x 32.2 min (0 ppm x min)


title: M_P7_hyperoxia_CD45_2_DC35_H4


title: M_P7_hyperoxia_CD45_1_DC35_B20


title: Genotyping data for sample 545G


title: M_P7_hyperoxia_CD45_1_DC35_I6


title: Genotyping data for sample 546G

value: North-Central European ancestry


title: M_P7_hyperoxia_CD45_2_DC35_A7

value: Mac V


title: M_P7_hyperoxia_CD45_1_DC35_H1


title: Blood_Air_3H_Rat738

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Blood


title: Heart_Air_3H_Rat733

description: 0 ppm  x 32.2 min (0 ppm x min)


title: Brain_Air_3H_Rat738

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Brain


title: M_P7_hyperoxia_CD45_1_DC35_D15


title: F_P7_hyperoxia_CD45_2_DC35_D15


title: Genotyping data for sample 544G

value: Male

value: DNA extracted from whole blood


title: Liver_Air_3H_Rat733

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Liver


title: M_P7_hyperoxia_CD45_1_DC35_K23


title: M_P7_hyperoxia_CD45_1_DC35_J11


title: Kidney_Air_3H_Rat733

description: 0 ppm  x 32.2 min (0 ppm x min)


title: Blood_Air_3H_Rat733

description: 0 ppm  x 32.2 min (0 ppm x min)


title: M_P7_hyperoxia_CD45_1_DC35_K12


title: Liver_Air_3H_Rat732

description: 0 ppm  x 32.2 min (0 ppm x min)


title: Genotyping data for sample 530G


title: Kidney_Air_3H_Rat732

description: 0 ppm  x 32.2 min (0 ppm x min)


title: Brain_Air_3H_Rat733

description: 0 ppm  x 32.2 min (0 ppm x min)


title: F_P7_hyperoxia_CD45_2_DC35_I18

value: Mac II


title: M_P7_hyperoxia_CD45_1_DC35_M14


title: Genotyping data for sample 526G


title: Heart_Air_3H_Rat732

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Heart

value: Air


title: M_P7_hyperoxia_CD45_2_DC35_K12


title: Genotyping data for sample 524G


title: M_P7_hyperoxia_CD45_1_DC35_L19

value: neutrophil


title: M_P7_hyperoxia_CD45_1_DC35_M20

value: M

value: Mac IV


title: Genotyping data for sample 504G

value: Roma ancestry


title: M_P7_hyperoxia_CD45_1_DC35_C11

value: hyperoxia

value: Mac III


title: Genotyping data for sample 502G


title: Genotyping data for sample 531G


title: M_P7_hyperoxia_CD45_1_DC35_I11

value: immune

value: IL cell


title: Brain_Air_3H_Rat732

description: 0 ppm  x 32.2 min (0 ppm x min)


title: F_P7_hyperoxia_CD45_2_DC35_G4

value: F

value: basophil


title: Genotyping data for sample 500G

value: North-Central European ancestry


title: M_P7_hyperoxia_CD45_2_DC35_N22


title: Genotyping data for sample 499G

value: Male


title: F_P7_hyperoxia_CD45_2_DC35_G13


title: M_P7_hyperoxia_CD45_1_DC35_I13


title: Lung_Air_3H_Rat732

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Lung


title: Liver_PH3_3H_Rat731

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Liver


title: Blood_Air_3H_Rat732

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Blood


title: M_P7_hyperoxia_CD45_2_DC35_N10


title: Genotyping data for sample 525G

value: DNA extracted from whole blood


title: Kidney_PH3_3H_Rat731

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Kidney


title: Lung_PH3_3H_Rat731

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: M_P7_hyperoxia_CD45_1_DC35_B4


title: Genotyping data for sample 497G


title: Heart_PH3_3H_Rat731

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Heart


title: M_P7_hyperoxia_CD45_1_DC35_I19

value: M

value: mast cell


title: M_P7_hyperoxia_CD45_1_DC35_F3

value: B cell


title: M_P7_hyperoxia_CD45_1_DC35_C16

value: hyperoxia


title: Blood_PH3_3H_Rat731

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: Genotyping data for sample 485G

value: Roma ancestry


title: M_P7_hyperoxia_CD45_1_DC35_A14

value: immune

value: Mac III


title: Genotyping data for sample 486G


title: F_P7_hyperoxia_CD45_2_DC35_B8

value: F

value: DC III


title: F_P7_hyperoxia_CD45_2_DC35_E18


title: Brain_PH3_3H_Rat731

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Brain


title: F_P7_hyperoxia_CD45_2_DC35_J2

value: Mac IV


title: Genotyping data for sample 484G

value: Male

value: North-Central European ancestry


title: F_P7_hyperoxia_CD45_2_DC35_N9


title: M_P7_hyperoxia_CD45_2_DC35_D19


title: M_P7_hyperoxia_CD45_2_DC35_O10

value: DC I


title: Genotyping data for sample 482G

value: DNA extracted from whole blood


title: Genotyping data for sample 483G


title: M_P7_hyperoxia_CD45_1_DC35_H12

value: neutrophil


title: Liver_PH3_3H_Rat730

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Liver


title: M_P7_hyperoxia_CD45_2_DC35_E16

value: M


title: M_P7_hyperoxia_CD45_2_DC35_O1

value: basophil


title: F_P7_hyperoxia_CD45_2_DC35_N10

value: T cell


title: F_P7_hyperoxia_CD45_2_DC35_G20

value: hyperoxia

value: B cell


title: Kidney_PH3_3H_Rat730

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Kidney


title: Genotyping data for sample 481G

value: Roma ancestry


title: F_P7_hyperoxia_CD45_2_DC35_A13

value: F

value: immune


title: Lung_PH3_3H_Rat730

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Lung


title: Blood_PH3_3H_Rat730

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Blood


title: Genotyping data for sample 478G

value: Male


title: Heart_PH3_3H_Rat730

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Heart


title: M_P7_hyperoxia_CD45_2_DC35_P15

value: Mac IV


title: M_P7_hyperoxia_CD45_2_DC35_A10


title: Genotyping data for sample 477G

value: North-Central European ancestry

value: DNA extracted from whole blood


title: M_P7_hyperoxia_CD45_2_DC35_B20

value: Mac V


title: M_P7_hyperoxia_CD45_2_DC35_G16

value: M

value: Mac III


title: M_P7_hyperoxia_CD45_2_DC35_L8


title: Genotyping data for sample 476G


title: M_P7_hyperoxia_CD45_2_DC35_D14


title: M_P7_hyperoxia_CD45_1_DC35_M4


title: M_P7_hyperoxia_CD45_2_DC35_A18


title: Genotyping data for sample 474G


title: Liver_PH3_3H_Rat729

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Liver


title: M_P7_hyperoxia_CD45_2_DC35_K22

value: hyperoxia


title: F_P7_hyperoxia_CD45_2_DC35_A19


title: Genotyping data for sample 384G


title: Genotyping data for sample 381G


title: Lung_PH3_3H_Rat729

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: Genotyping data for sample 379G


title: F_P7_hyperoxia_CD45_2_DC35_A22


title: M_P7_hyperoxia_CD45_2_DC35_D2


title: Genotyping data for sample 2665G


title: Heart_PH3_3H_Rat729

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: M_P7_hyperoxia_CD45_1_DC35_D13


title: Brain_PH3_3H_Rat730

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Brain


title: M_P7_hyperoxia_CD45_1_DC35_G4


title: Brain_PH3_3H_Rat729

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: M_P7_hyperoxia_CD45_1_DC35_G5

value: basophil


title: Genotyping data for sample 2664G


title: F_P7_hyperoxia_CD45_2_DC35_D5

value: neutrophil


title: Genotyping data for sample 2663G


title: M_P7_hyperoxia_CD45_1_DC35_D6


title: F_P7_hyperoxia_CD45_2_DC35_G19

value: F


title: F_P7_hyperoxia_CD45_2_DC35_B15

value: immune


title: Genotyping data for sample 2662G


title: M_P7_hyperoxia_CD45_1_DC35_K16

value: Mac II


title: Blood_PH3_3H_Rat729

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Blood


title: M_P7_hyperoxia_CD45_1_DC35_D18


title: M_P7_hyperoxia_CD45_1_DC35_B17

value: mast cell II


title: M_P7_hyperoxia_CD45_1_DC35_O22


title: Genotyping data for sample 2564G

value: Male


title: Kidney_PH3_3H_Rat728

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Kidney


title: M_P7_hyperoxia_CD45_2_DC35_B15


title: Heart_PH3_3H_Rat728

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Heart


title: Genotyping data for sample 2661G

value: North-Central European ancestry

value: DNA extracted from whole blood


title: Lung_PH3_3H_Rat728

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Lung


title: Genotyping data for sample 2565G


title: F_P7_hyperoxia_CD45_2_DC35_L14

value: Mac III


title: M_P7_hyperoxia_CD45_2_DC35_C19

value: M


title: M_P7_hyperoxia_CD45_2_DC35_J10

value: hyperoxia


title: Genotyping data for sample 2563G

value: Roma ancestry


title: M_P7_hyperoxia_CD45_1_DC35_L8


title: Brain_PH3_3H_Rat728

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Brain


title: F_P7_hyperoxia_CD45_2_DC35_K18

value: B cell


title: M_P7_hyperoxia_CD45_2_DC35_P18

value: neutrophil


title: Genotyping data for sample 2507G


title: M_P7_hyperoxia_CD45_2_DC35_G5

value: immune


title: Lung_Air_1H_Rat727

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Air


title: F_P7_hyperoxia_CD45_2_DC35_A1

value: F

value: Mac II


title: M_P7_hyperoxia_CD45_1_DC35_I14

value: DC I


title: Blood_PH3_3H_Rat728

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Blood


title: Kidney_PH3_3H_Rat729

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Kidney


title: M_P7_hyperoxia_CD45_2_DC35_E12

value: T cell


title: M_P7_hyperoxia_CD45_1_DC35_G11


title: M_P7_hyperoxia_CD45_1_DC35_G2


title: Liver_PH3_3H_Rat728

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Liver


title: Liver_Air_1H_Rat727

description: 0 ppm  x 32.2 min (0 ppm x min)


title: Kidney_Air_1H_Rat727

description: 0 ppm  x 32.2 min (0 ppm x min)


title: Genotyping data for sample 2506G

value: Male

value: North-Central European ancestry

value: DNA extracted from whole blood


title: Genotyping data for sample 2505G


title: Genotyping data for sample 2504G


title: Brain_Air_1H_Rat727

description: 0 ppm  x 32.2 min (0 ppm x min)


title: F_P7_hyperoxia_CD45_2_DC35_K10

value: hyperoxia

value: Mac III


title: Genotyping data for sample 2562G


title: F_P7_hyperoxia_CD45_2_DC35_C11

value: DC III


title: Lung_Air_1H_Rat726

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Lung


title: Blood_Air_1H_Rat727

description: 0 ppm  x 32.2 min (0 ppm x min)


title: F_P7_hyperoxia_CD45_2_DC35_B20

value: basophil


title: Heart_Air_1H_Rat727

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Heart


title: Genotyping data for sample 2503G


title: F_P7_hyperoxia_CD45_2_DC35_J5

value: immune

value: Mac V


title: F_P7_hyperoxia_CD45_2_DC35_N6

value: F

value: B cell


title: Genotyping data for sample 2337G

value: Roma ancestry


title: M_P7_hyperoxia_CD45_2_DC35_D18

value: M

value: Mac II


title: Kidney_Air_1H_Rat726

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Kidney

value: Air


title: Genotyping data for sample 2336G

value: Male

value: North-Central European ancestry


title: M_P7_hyperoxia_CD45_2_DC35_B3

value: hyperoxia


title: M_P7_hyperoxia_CD45_2_DC35_E23

value: Mac IV


title: Genotyping data for sample 2332G

value: DNA extracted from whole blood


title: M_P7_hyperoxia_CD45_1_DC35_H5

value: T cell


title: F_P7_hyperoxia_CD45_2_DC35_G5

value: Mac III


title: F_P7_hyperoxia_CD45_2_DC35_K2


title: Genotyping data for sample 2331G


title: F_P7_hyperoxia_CD45_2_DC35_L12


title: F_P7_hyperoxia_CD45_2_DC35_O3


title: Heart_Air_1H_Rat726

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Heart


title: Blood_Air_1H_Rat726

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Blood


title: Genotyping data for sample 2330G


title: Liver_Air_1H_Rat726

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Liver


title: Blood_PH3_1H_Rat722

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: M_P7_hyperoxia_CD45_2_DC35_F11

value: immune

value: neutrophil


title: Genotyping data for sample 2328G


title: M_P7_hyperoxia_CD45_2_DC35_F20


title: F_P7_hyperoxia_CD45_2_DC35_E9

value: F


title: F_P7_hyperoxia_CD45_2_DC35_A20

value: DC I


title: M_P7_hyperoxia_CD45_2_DC35_L23

value: M


title: Brain_Air_1H_Rat726

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Brain


title: M_P7_hyperoxia_CD45_2_DC35_F15


title: Kidney_Air_1H_Rat721

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Kidney

value: Air


title: F_P7_hyperoxia_CD45_2_DC35_C23


title: M_P7_hyperoxia_CD45_1_DC35_L20

value: B cell


title: Genotyping data for sample 2326G

value: Male

value: North-Central European ancestry


title: Genotyping data for sample 2327G

value: DNA extracted from whole blood


title: Lung_Air_1H_Rat721

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Lung


title: Liver_Air_1H_Rat721

description: 0 ppm  x 32.2 min (0 ppm x min)


title: M_P7_hyperoxia_CD45_2_DC35_P13

value: hyperoxia

value: Mac III


title: Heart_Air_1H_Rat721

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Heart


title: Genotyping data for sample 2325G


title: F_P7_hyperoxia_CD45_2_DC35_L8


title: F_P7_hyperoxia_CD45_2_DC35_E13

value: IL cell


title: F_P7_hyperoxia_CD45_2_DC35_F10

value: immune

value: Mac V


title: F_P7_hyperoxia_CD45_2_DC35_F20

value: F


title: Genotyping data for sample 2329G

value: Roma ancestry


title: Genotyping data for sample 2324G


title: M_P7_hyperoxia_CD45_2_DC35_O6

value: M


title: M_P7_hyperoxia_CD45_2_DC35_K16


title: M_P7_hyperoxia_CD45_1_DC35_J10


title: F_P7_hyperoxia_CD45_2_DC35_B18

value: Mac IV


title: M_P7_hyperoxia_CD45_2_DC35_N17


title: Genotyping data for sample 2322G


title: M_P7_hyperoxia_CD45_1_DC35_G12

value: neutrophil


title: Genotyping data for sample 2321G


title: M_P7_hyperoxia_CD45_2_DC35_F7

value: DC III


title: M_P7_hyperoxia_CD45_2_DC35_B9

value: B cell


title: M_P7_hyperoxia_CD45_1_DC35_N19

value: mast cell


title: Genotyping data for sample 2296G

value: Male

value: North-Central European ancestry


title: Genotyping data for sample 2295G

value: DNA extracted from whole blood


title: Genotyping data for sample 2323G


title: M_P7_hyperoxia_CD45_2_DC35_O16

value: hyperoxia


title: M_P7_hyperoxia_CD45_2_DC35_L5


title: M_P7_hyperoxia_CD45_2_DC35_N2

value: Mac III


title: M_P7_hyperoxia_CD45_1_DC35_K2

value: basophil


title: Liver_Air_1H_Rat720

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Liver

value: Air


title: Genotyping data for sample 2293G


title: Blood_Air_1H_Rat721

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Blood


title: Brain_Air_1H_Rat721

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Brain


title: Heart_Air_1H_Rat720

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Heart


title: F_P7_hyperoxia_CD45_2_DC35_N5

value: F

value: immune


title: Genotyping data for sample 2298G

value: Roma ancestry


title: Kidney_Air_1H_Rat720

description: 0 ppm  x 32.2 min (0 ppm x min)

value: Kidney


title: F_P7_hyperoxia_CD45_2_DC35_A18


title: M_P7_hyperoxia_CD45_1_DC35_N6

value: M

value: Mac IV


title: Genotyping data for sample 2290G

value: Male


title: Lung_PH3_1H_Rat719

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Lung


title: Blood_Air_1H_Rat720

description: 0 ppm  x 32.2 min (0 ppm x min)


title: Liver_PH3_1H_Rat719

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: Lung_Air_1H_Rat720

description: 0 ppm  x 32.2 min (0 ppm x min)


title: F_P7_hyperoxia_CD45_2_DC35_I12


title: F_P7_hyperoxia_CD45_2_DC35_M17

value: Mac II


title: Heart_PH3_1H_Rat719

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: Genotyping data for sample 1616G

value: North-Central European ancestry

value: DNA extracted from whole blood


title: F_P7_hyperoxia_CD45_2_DC35_J4

value: hyperoxia


title: M_P7_hyperoxia_CD45_2_DC35_O2


title: Genotyping data for sample 1614G


title: M_P7_hyperoxia_CD45_1_DC35_N15

value: Mac III


title: M_P7_hyperoxia_CD45_1_DC35_P13


title: Blood_PH3_1H_Rat719

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: Brain_PH3_1H_Rat719

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: Kidney_PH3_1H_Rat719

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: M_P7_hyperoxia_CD45_2_DC35_G13


title: M_P7_hyperoxia_CD45_2_DC35_G19

value: Mac V


title: M_P7_hyperoxia_CD45_2_DC35_E7


title: Liver_PH3_1H_Rat716

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Liver


title: Genotyping data for sample 1611G


title: F_P7_hyperoxia_CD45_2_DC35_L22


title: Genotyping data for sample 1610G


title: Lung_PH3_1H_Rat716

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: F_P7_hyperoxia_CD45_2_DC35_L9


title: Genotyping data for sample 1608G


title: Kidney_PH3_1H_Rat716

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: M_P7_hyperoxia_CD45_1_DC35_C21


title: M_P7_hyperoxia_CD45_1_DC35_B12


title: Genotyping data for sample 1607G


title: Genotyping data for sample 1603G


title: Genotyping data for sample 1613G


title: Heart_PH3_1H_Rat716

description: 660 ppm  x 32.2 min (21,252 ppm x min)


title: M_P7_hyperoxia_CD45_1_DC35_F20


title: M_P7_hyperoxia_CD45_1_DC35_M8


title: M_P7_hyperoxia_CD45_2_DC35_M17

value: basophil


title: F_P7_hyperoxia_CD45_2_DC35_B23

value: neutrophil


title: F_P7_hyperoxia_CD45_2_DC35_J11

value: F


title: Blood_PH3_1H_Rat716

description: 660 ppm  x 32.2 min (21,252 ppm x min)

value: Blood


title: F_P7_hyperoxia_CD45_2_DC35_J22

value: immune

value: T cell


title: M_P7_hyperoxia_CD45_2_DC35_C14

value: M


title: Genotyping data for sample 1602G


title: F_P7_hyperoxia_CD45_2_DC35_H2

value: B cell


title: F_P7_hyperoxia_CD45_2_DC35_H1