title: cCMT3 methylC-seq bent cotyledon (Line #1; biorep #2)

description:
Sample 4
Single-end 75 base read methylC-seq data from second biological replicate of bent cotyledon embryos with miR823 cleavable version of CMT3 transgene (line #1).
allC_gCMT3_L1_BentCotyledon.tsv

tag: accession

value: cCMT3 (cmt3-11)

tag: genotype

value: miR823 cleavable version of CMT3 transgene in cmt3 mutant background (line #1)

tag: tissue


title: PND13- Rep1

status: Public on Jun 01 2021

type: SRA

city: Chicago,

first: Francesca

middle: E.

last: Duncan

state: IL

address: 303 E. Superior Street, Lurie 10-109

department: Department of Obstetrics and Gynecology

country: USA

institute: Northwestern University

library_source: transcriptomic

data_processing:
Data was analyzed by Rosalind (https://rosalind.onramp.bio/), with a HyperScale architecture developed by OnRamp BioInformatics, Inc. (San Diego, CA). Reads were trimmed using cutadapt1. Quality scores were assessed using FastQC. Reads were aligned to the Mus musculus genome build mm10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression (RLE) using DESeq2 R library. Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step using RSeQC. DEseq was also used to calculate fold changes and p-values. Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (Partitioning Around Medoids) method using the fpc R library. Functional enrichment analysis of pathways, gene ontology, domain structure and other ontologies was performed using HOMER. Several database sources were referenced for enrichment analysis, including Interpro, NCBI, MSigDB, REACTOME, WikiPathways. Enrichment was calculated relative to a set of background genes relevant for the experiment. Additional gene enrichment is available from the following partner institutions: Advaita (http://www.advaitabio.com/ipathwayguide).
Genome_build: mm10
Supplementary_files_format_and_content: Oocytes_normalizedCountsWithAnnotations.txt
Supplementary_files_format_and_content: Oocytes_rawCountsWithAnnotations.txt

molecule: total RNA

organism: Mus musculus

source_name: Ovary

extract_protocol:
RNA was isolated using RNeasy Plus mini kit (Qiagen, Germany, 74134)
cDNA synthesis was performed using NEB Next Ultra II directional RNA library prep kit (New England Biolabs, Ipswich, MA, E7760S) after rRNA depletion (NEB Next rRNA depletion kit, E6310S).

tag: age

value: postnatal day; PND 13

tag: strain

tag: cohort


title: cCMT3 methylC-seq bent cotyledon (Line #3; biorep #1)

city: Wageningen

first: Michael

middle: D

last: Nodine

state: Gelderland

address: Radix West

department: Plant Sciences

country: Netherlands

institute: Wageningen University & Research

description:
Sample 5
Single-end 75 base read methylC-seq data from first biological replicate of bent cotyledon embryos with miR823 cleavable version of CMT3 transgene (line #3).
allC_gCMT3_L3_BentCotyledon.tsv

library_source: genomic

data_processing:
MethylC-seq (samples 1 to 26): Adapters and the first six bases corresponding to random hexamers used during the pre-amplification step were trimmed from MethylC-seq reads using Trim Galore. Bisulfite-converted reads were aligned against the TAIR10 genome (Lamesch et al., 2012) using Bismark (bismark --non_directional -q --score-min L,0,-0.4) (Krueger and Andrews, 2011). Methylpy software was used to extract weighted methylation rate at each available cytosine from BAM files containing only deduplicated and uniquely mapped reads (Schultz et al., 2015).
mRNA-seq (samples 27 to 35): Raw FASTQ files were quality filtered and trimmed for adapter sequences with Trim Galore using default parameters. Trimmed reads were aligned using STAR (Dobin et al., 2013) against a genome index generated using the TAIR10 genome fasta file and all transcripts in the GTF of Ensembl build TAIR10 annotation set (release version 44). Aligned transcriptome bam files were used to quantify read counts per gene and transcript abundance using RSEM (Li and Dewey, 2011).
Genome_build: TAIR10
Supplementary_files_format_and_content: MethylC-seq (samples 1-26): TSV files for methylC-seq processed data files (allC_GENOTYPE_TISSUE.tsv.gz) were output from MethylPy (Schultz et al., 2015) and have following seven columns: 1) chromosome, 2) coordinate position, 3) strand, 4) trinucleotide context, 5) number of reads supporting methylation, 6) number of total reads, 7) whether (1) or not (0) binomial test was performed.
Supplementary_files_format_and_content: mRNA-seq (samples 27-35): TSV files for mRNA-seq processed data files (GENOTYPE_TISSUE_BIOREP.genes.results) were output from RSEM (Li and Dewey, 2011) and have following seven columns: 1) gene_id, 2) transcript(s), 3) transcript length, 4) effective_length, 5) expected_count, 6) TPM, 7) FPKM.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Bent cotyledon embryos (8 days after pollination)

growth_protocol: Arabidopsis thaliana accession Columbia-0 (Col-0) were grown in controlled growth chambers at 20-22˚C under a 16-h light/8-h dark cycle with incandescent lights (130 to 150 µmol/m2/s).

extract_protocol:
Samples 1 to 26 : Genomic DNA was extracted with Quick-DNATM Micro prep Kit (Zymo D3020). MethylC-seq libraries were generated as previously described (Papareddy et al. 2020).
Samples 27 to 35: Total RNA was isolated with TRIzol reagent (Thermo Fisher Scientific). Smart-seq2 mRNA libraries were generated from 1 µl of the 7 µl bent cotyledon embryo total RNA as previously described (Picelli 2013; Hoffman 2019).

value: miR823 cleavable version of CMT3 transgene in cmt3 mutant background (line #3)

value: Bent cotyledon embryos


title: F_P7_hyperoxia_CD45_1_DC28_N13

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

value: F

tag: plate

tag: well

tag: timepoint

tag: treatment

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype

value: Mac V

tag: mousename

tag: coverage

tag: number of genes


title: cCMT3 methylC-seq bent cotyledon (Line #1; biorep #1)

description:
Sample 3
Single-end 75 base read methylC-seq data from first biological replicate of bent cotyledon embryos with miR823 cleavable version of CMT3 transgene (line #1).
allC_gCMT3_L1_BentCotyledon.tsv

tag: accession


title: Pfn3-KO3

city: Madrid

first: Lena

last: Arévalo

state: Madrid

address: Avda. Puerta de Hierro, 18

department: Animal Reproduction

country: Spain

institute: INIA-CSIC

data_processing:
All reads were trimmed with Trim Galore! 0.4.5 (Brabraham Bioinformatics) and mapped to the mouse genome (GRCm38.89) using HISAT2 2.1 (Kim et al.2015).
Transcripts were quantified and annotated using StringTie 1.3.3 (Pertea et al.2015).
Gene annotation information for the mouse genome was retrieved from the Ensembl FTP server (ftp://ftp.ensembl.org) (GRCm38.89).
The python script (preDE.py) included in the StringTie package was used to prepare gene-level count matrices for analysis of differential gene expression (DE).
Genome_build: GRCm38.89
Supplementary_files_format_and_content: tab separated text file includes DESeq2 normalized counts for each sample

source_name: testis

extract_protocol:
Total RNA was extracted from testicular tissue after removal of the tunica albuginea using TRIzol™ reagent according to the manufacturer’s protocol (Thermo Fisher Scientific).
RNA sample quality control and library preparation were performed by the University of Bonn Core facility for Next Generation Sequencing (NGS), using the QuantSeq 3´-mRNA Library Prep (Lexogen, Greenland, NH, USA).

tag: genotype

value: KO

tag: Sex

value: male


title: Airway epithelial cells (basal cells) - RNAseq [dbb7_449f-1A]

city: Chicago

first: Carole

last: Ober

address: 920 E 58TH ST

department: Human Genetics

institute: The University of Chicago

description:
gene.counts.txt
gene.counts.normalized.txt

data_processing:
RNAseq reads were mapped to the human reference genome (hg19) using STAR
Gene counts were generated from STAR (--quantMode GeneCounts)
removed X, Y, and mitochondrial genes
Gene counts were voom transformed (TMM normalized)
Genome_build: hg19
Supplementary_files_format_and_content: gene count files were processed using R; files contain gene counts (or normalized gene counts) for each sample; rows are gene Ensembl IDs and the columns are sample names
Supplementary_files_format_and_content: .txt; gene counts for each sample
Supplementary_files_format_and_content: .txt; normalized gene counts (TMM normalized) for each sample

organism: Homo sapiens

source_name: Cultured airway epithelial cells (basal cells)

growth_protocol: Nasal airway epithelial cells (basal cells) were cultured in collagen-coated (PureCol, INAMED BioMaterials, catalog number 5,409, 3 mg/mL, 1:15 dilution) tissue culture plates (6 wells of 2x 12 well plates) using BEGM overnight at 37°C and 5% CO2.

extract_protocol:
QIAGEN AllPrep DNA/RNA Kit
Illumina TruSeq RNA Library Prep Kit v2

treatment_protocol: In preparation for rhinovirus (HRV-16; RV) infection/stimulation, plates at 50-60% confluency were incubated overnight in BEGM without hydrocortisone (HC) followed by a two-hour RV infection at a multiplicity of infection (MOI) of 2 and vehicle treatment (Bronchial epithelial cell basal medium (BEBM) + Gentamicin/Amphotericin) at 33°C (low speed rocking, ~15 RPM). RV- and vehicle-treated cells were washed and then were cultured at 33°C for 46 hours (48 hours total) in BEGM without HC. Cell viability was determined based on trypan blue staining or a LDH assay

value: RV

value: Male

tag: atopy

value: No

tag: asthma

tag: steroids

tag: smoking

value: Prior

tag: crs

value: CRS

tag: tech

value: RN

tag: rin

tag: age

tag: surgeon


title: Pfn3-KO2

tag: strain


title: F_P7_hyperoxia_CD45_1_DC28_D9

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: treatment

tag: cell type

tag: cell subtype

value: B cell


title: Col-0 methylC-seq bent cotyledon (biorep #2)

description:
Sample 2
Single-end 75 base read methylC-seq data from second biological replicate of bent cotyledon Col-0 embryos.
allC_WT_BentCotyledon2020.tsv

tag: accession

tag: genotype

value: wild type

tag: tissue


title: Pfn3-KO1

tag: Sex


title: cCMT3 methylC-seq bent cotyledon (Line #3; biorep #2)

description:
Sample 6
Single-end 75 base read methylC-seq data from second biological replicate of bent cotyledon embryos with miR823 cleavable version of CMT3 transgene (line #3)
allC_gCMT3_L3_BentCotyledon.tsv

value: cCMT3 (cmt3-11)


title: Airway epithelial cells (basal cells) - RNAseq [0367_4a9f-2A]

value: vehicle

tag: atopy

value: Yes

tag: asthma

tag: steroids

tag: smoking

tag: crs

value: Control

tag: tech

value: CB


title: PND16 Large- Rep1

tag: age

value: postnatal day; PND 16

tag: strain

tag: cohort

value: PND16 Large


title: F_P7_hyperoxia_CD45_1_DC28_C23

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

value: hyperoxia

value: immune

value: Mac III

tag: mousename

tag: coverage

tag: number of genes


title: Col-0 methylC-seq bent cotyledon (biorep #1)

description:
Sample 1
Single-end 75 base read methylC-seq data from first biological replicate of bent cotyledon Col-0 embryos.
allC_WT_BentCotyledon2020.tsv

tag: accession

tag: genotype

tag: tissue

value: Bent cotyledon embryos


title: Pfn3-Het3

value: Het

tag: Sex

value: male


title: Airway epithelial cells (basal cells) - RNAseq [0367_4a9f-1A]

tag: treatment

value: RV

value: Male

tag: atopy

tag: asthma

value: No

tag: steroids

tag: smoking

value: Prior

tag: crs

tag: rin

tag: surgeon


title: F_P7_hyperoxia_CD45_1_DC28_F13

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: cell type

tag: cell subtype

value: mast cell


title: Pfn3-Het2

tag: strain

tag: genotype


title: Nkd1-delEAR.24h.rep3

city: Vienna

first: Fernando

last: Navarrete

state: Vienna

address: Dr. Bohr Gasse 3

country: Austria

institute: Gregor Mendel Institute

data_processing:
NextSeq Control Software 2.2.0.4 was used to control the sequencer
RTA v2.4.11 software was used for basecalling
raw RNA-seq reads were aligned to TAIR10 genome using STAR v2.5.1 (Dubin et al doi: 10.1093/bioinformatics/bts635) (non-default parameters: --alignIntronMax 6000 --alignMatesGapMax 6000 --outFilterIntronMotifs RemoveNoncanonical --outFilterMultimapNmax 1). Each sample has two fastq files (sequenced on 2 lanes) that were pooled for the alignment.
RNA-seq read counts for all TAIR10 protein-coding genes were calculated using featureCounts tool from Subread (version 1.4.6) package (Liao et al, Bioinformatics, 2014)
Genome_build: TAIR10
Supplementary_files_format_and_content: process data file is a tab separated text file which contains raw read counts for Arabidopsis thaliana TAIR10 protein-coding genes in all 24 sequenced samples

molecule: polyA RNA

source_name: whole seedlings

growth_protocol: Arabidopsis seedlings grown in ½ MS plates for 7 days. Then transferred to a new ½ MS plate supplemented with Estradiol (5uM)

extract_protocol:
RNA extractions were performed with RNAeasy Plant kit (QIAGEN) and mRNA was isolated by Poly(A) RNA Selection kit (Lexogen) from 1µg of total RNA.
RNA libraries were prepared for sequencing using Lexogen SENSE mRNA-Seq Library Prep Kit V2 following manufacturer's protocol

treatment_protocol: Transgene expression was induced by incubation in estradiol plates for 5h or 24h.

tag: background line

tag: construct

tag: developmental stage

value: 7-day old seedling


title: F_P7_hyperoxia_CD45_1_DC28_J5

tag: timepoint

tag: treatment

value: Mac IV

tag: mousename

tag: coverage

tag: number of genes


title: F_P7_hyperoxia_CD45_1_DC28_F10


title: Nkd1-delEAR.24h.rep2


title: Pfn3-Het1

tag: Sex


title: Airway epithelial cells (basal cells) - RNAseq [46b9_452a-2A]

value: vehicle

tag: atopy

value: Yes

tag: asthma

tag: steroids

tag: smoking

tag: crs

value: Control

tag: tech

value: CB

tag: rin

tag: age

tag: surgeon


title: Airway epithelial cells (basal cells) - RNAseq [46b9_452a-1A]

tag: gender


title: F_P7_hyperoxia_CD45_1_DC28_B13

tag: sequencing run

value: F

tag: plate

tag: well

value: hyperoxia

tag: cell type

tag: cell subtype


title: Pfn3-WT3

tag: strain

tag: genotype

value: WT


title: Airway epithelial cells (basal cells) - RNAseq [9523_4465-2A]

tag: treatment

value: Female

tag: atopy

value: Never


title: Airway epithelial cells (basal cells) - RNAseq [dbb7_449f-2A]

tag: asthma

tag: steroids

value: CRS

value: RN


title: Pfn3-WT2

tag: Sex

value: male


title: Nkd1-delEAR.5h.rep3

tag: background line

tag: construct

tag: developmental stage


title: Airway epithelial cells (basal cells) - RNAseq [9523_4465-1A]

value: RV

value: No

tag: smoking

tag: crs

tag: tech

tag: rin

tag: age

tag: surgeon


title: F_P7_hyperoxia_CD45_1_DC28_J10

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: cell type

value: immune

tag: cell subtype

value: Mac III

tag: mousename

tag: coverage

tag: number of genes


title: Nkd1-delEAR.5h.rep2

tag: background line

tag: construct

tag: developmental stage

value: 7-day old seedling


title: Pfn3-WT1

tag: strain

tag: genotype

tag: Sex


title: F_P7_hyperoxia_CD45_1_DC28_P15

tag: treatment


title: Airway epithelial cells (basal cells) - RNAseq [715b_499f-2A]

value: vehicle

value: Male

tag: atopy

tag: asthma

tag: steroids

value: Inhaled

value: yes

tag: smoking

value: Prior

tag: crs

tag: tech

tag: rin

tag: age

tag: surgeon


title: Nkd1-delEAR.5h.rep1


title: F_P7_hyperoxia_CD45_1_DC28_H7

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

tag: cell subtype

value: neutrophil

tag: mousename

tag: coverage

tag: number of genes


title: Airway epithelial cells (basal cells) - RNAseq [715b_499f-1A]

tag: treatment

tag: atopy

value: Yes

tag: asthma

tag: steroids


title: F_P7_hyperoxia_CD45_1_DC28_P10

value: B cell


title: Nkd1-SRDX.24h.rep3

tag: background line

tag: construct

tag: developmental stage


title: Airway epithelial cells (basal cells) - RNAseq [c99c_403c-2B]

value: Female

tag: smoking

value: Never

tag: crs

value: Control

tag: tech

value: RN

tag: rin

tag: age

tag: surgeon


title: F_P7_hyperoxia_CD45_1_DC28_I13

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: cell type

value: immune

tag: cell subtype

value: DC III


title: Airway epithelial cells (basal cells) - RNAseq [c99c_403c-1B]

tag: treatment

value: RV

tag: atopy

value: No

tag: asthma

tag: steroids


title: Nkd1-SRDX.24h.rep2

tag: background line

tag: construct

tag: developmental stage

value: 7-day old seedling


title: F_P7_hyperoxia_CD45_1_DC28_A16

value: Mac III

tag: mousename

tag: coverage

tag: number of genes


title: Nkd1-SRDX.5h.rep3


title: Nkd1-SRDX.24h.rep1


title: F_P7_hyperoxia_CD45_1_DC28_D12

tag: sequencing run


title: Nkd1-SRDX.5h.rep2


title: F_P7_hyperoxia_CD45_1_DC28_L19

tag: gender

value: mast cell II


title: Airway epithelial cells (basal cells) - RNAseq [ea4f_40cf-2A]

value: vehicle

tag: smoking

value: Current

tag: crs

tag: tech

tag: rin

tag: age

tag: surgeon


title: F_P7_hyperoxia_CD45_1_DC28_L2

value: F

tag: plate

tag: well

tag: timepoint

tag: treatment

value: hyperoxia

tag: cell type

tag: cell subtype

value: Mac IV


title: Nkd1-SRDX.5h.rep1

tag: background line

tag: construct

tag: developmental stage


title: Airway epithelial cells (basal cells) - RNAseq [5870_4405-1A]

tag: atopy

value: Yes

tag: asthma

tag: steroids

value: yes

value: CRS


title: mCherry.24h.rep3

value: mCherry


title: mCherry.24h.rep2


title: F_P7_hyperoxia_CD45_1_DC28_D19

tag: sequencing run

tag: gender

tag: mousename

tag: coverage

tag: number of genes


title: Airway epithelial cells (basal cells) - RNAseq [90d6_4bfa-2A]

value: Male

tag: smoking

value: Prior

tag: crs

tag: tech

value: RN

tag: rin

tag: age

tag: surgeon


title: Airway epithelial cells (basal cells) - RNAseq [5870_4405-2A]

tag: treatment

value: Female

value: Never


title: Airway epithelial cells (basal cells) - RNAseq [90d6_4bfa-1A]

value: RV


title: F_P7_hyperoxia_CD45_1_DC28_F23

tag: plate

tag: well

tag: timepoint

tag: cell type

value: immune

tag: cell subtype

value: Mac III


title: Airway epithelial cells (basal cells) - RNAseq [4386_480f-2B]

value: vehicle

tag: atopy

value: No

tag: asthma

tag: steroids

value: Control


title: Airway epithelial cells (basal cells) - RNAseq [ea4f_40cf-1A]

tag: gender

value: Current


title: F_P7_hyperoxia_CD45_1_DC28_J11

tag: sequencing run

value: F

value: hyperoxia

value: DC I

tag: mousename

tag: coverage

tag: number of genes


title: mCherry.24h.rep1

tag: background line

tag: construct

tag: developmental stage

value: 7-day old seedling


title: mCherry.5h.rep3

value: mCherry


title: F_P7_hyperoxia_CD45_1_DC28_A21

tag: treatment

value: mast cell II


title: mCherry.5h.rep2


title: Nkd1-delEAR.24h.rep1


title: F_P7_hyperoxia_CD45_1_DC28_O11

tag: plate

value: Mac V


title: Airway epithelial cells (basal cells) - RNAseq [4386_480f-1B]

value: Male

tag: smoking

tag: crs

tag: tech

value: RN

tag: rin

tag: age

tag: surgeon


title: mCherry.5h.rep1


title: F_P7_hyperoxia_CD45_1_DC28_D22

tag: well

tag: timepoint

tag: cell type

tag: cell subtype


title: Airway epithelial cells (basal cells) - RNAseq [0c5c_49aa-1B]

tag: gender

value: Female

tag: atopy

value: Yes

tag: asthma

tag: steroids

value: Inhaled

value: yes

value: Never


title: Airway epithelial cells (basal cells) - RNAseq [7d25_4c19-2A]

value: vehicle

value: No

value: Prior

value: CRS


title: Airway epithelial cells (basal cells) - RNAseq [0c5c_49aa-2B]

value: Control


title: F_P7_hyperoxia_CD45_1_DC28_P8

tag: sequencing run

value: F

value: hyperoxia

value: immune

value: Mac IV

tag: mousename

tag: coverage

tag: number of genes


title: Nkd1.24h.rep2

tag: background line

tag: construct

tag: developmental stage

value: 7-day old seedling


title: Nkd1.24h.rep1


title: F_P7_hyperoxia_CD45_1_DC28_L18

tag: plate

tag: treatment

value: Mac V


title: F_P7_hyperoxia_CD45_1_DC28_O9

tag: well

value: Mac III


title: Airway epithelial cells (basal cells) - RNAseq [7e0a_42d5-2B]

value: Female

tag: smoking

tag: crs

tag: tech

value: RN

tag: rin

tag: age

tag: surgeon


title: F_P7_hyperoxia_CD45_1_DC28_C5

tag: gender

tag: timepoint

tag: cell type

tag: cell subtype

value: mast cell


title: Nkd1.5h.rep2


title: Nkd1.5h.rep3


title: Airway epithelial cells (basal cells) - RNAseq [1c59_4ce6-2A]

tag: atopy

tag: asthma

tag: steroids

value: CB


title: F_P7_hyperoxia_CD45_1_DC28_B10

tag: sequencing run

value: neutrophil

tag: mousename

tag: coverage

tag: number of genes


title: Airway epithelial cells (basal cells) - RNAseq [7e0a_42d5-1B]

tag: treatment

value: RV

tag: smoking

value: Never


title: Airway epithelial cells (basal cells) - RNAseq [1c59_4ce6-1A]

value: No

tag: crs

tag: tech


title: F_P7_hyperoxia_CD45_1_DC28_H15

tag: plate

tag: well


title: Nkd1.5h.rep1

tag: background line

tag: construct

tag: developmental stage


title: Airway epithelial cells (basal cells) - RNAseq [4626_44a4-2B]

value: vehicle

tag: gender

value: Male

value: Yes

tag: rin

tag: age

tag: surgeon


title: F_P7_hyperoxia_CD45_1_DC28_F21

tag: sequencing run

value: F

tag: timepoint

value: hyperoxia

tag: cell type

tag: cell subtype

value: DC III


title: WT kidney from mouse 4009 (rep2)

city: Bar Harbor

first: Samuel

last: Beck

state: Maine

address: 159 Old Bar Harbor Rd

department: Davis Center for Regenerative Biology and Medicine

institute: MDI Biological Laboratory

data_processing:
The raw LBR-null kidney RNA-seq data (FASTQ) were aligned to the mouse genome (mm9, NCBI Build 37) using STAR 2.6.0.
The read count data were normalized using DESeq2 1.25.1.
Genome_build: mm9
Supplementary_files_format_and_content: DESeq2-normalized read counts (text file)

source_name: kidney

growth_protocol: All mice were maintained on a standard rodent chow (5K52, LabDiet) in a pathogen-free animal room that had a set temperature ranging from 20-22 °C, and a 12-hour light/dark cycle.

extract_protocol:
The LBR-null kidneys were lysed and homogenized in TRI Reagent (R2050, Zymo Research). Trizol RNA miniprep plus kit (R2070, Zymo Research) was used to isolate total RNA.
Library preparation with poly(A) selection and 150 bp paired-end sequencing on an Illumina HiSeq were performed by Genewiz (South Plainfield, NJ).

tag: strain

tag: tissue

value: kidney

tag: disease

value: 4 weeks old

tag: genotype

value: Lbr+/+


title: Nkd1.24h.rep3

value: 7-day old seedling


title: Airway epithelial cells (basal cells) - RNAseq [4626_44a4-1B]

tag: treatment

tag: atopy

tag: asthma

tag: steroids

tag: smoking

tag: crs

value: Control

tag: tech

value: RN


title: F_P7_hyperoxia_CD45_1_DC28_E15

tag: gender

tag: plate

tag: well

value: immune

value: Mac III

tag: mousename

tag: coverage

tag: number of genes


title: WT kidney from mouse 4009 (rep1)

tag: strain

tag: age


title: Airway epithelial cells (basal cells) - RNAseq [7d25_4c19-1A]

value: RV

value: Prior

value: CRS

tag: rin

tag: surgeon


title: F_P7_hyperoxia_CD45_1_DC28_K9

tag: sequencing run

tag: timepoint

tag: treatment

tag: cell type

tag: cell subtype


title: Airway epithelial cells (basal cells) - RNAseq [668e_48d6-2B]

value: vehicle

value: Female

tag: atopy

tag: asthma

tag: steroids

value: Inhaled

value: yes

tag: smoking

value: Current

tag: crs


title: F_P7_hyperoxia_CD45_1_DC28_N12

tag: gender

value: F

tag: plate

tag: well

value: hyperoxia

tag: mousename


title: LBR-null kidney from mouse 4007 (rep1)

tag: strain

tag: tissue

value: kidney

tag: disease

tag: age

value: 4 weeks old

tag: genotype

value: Lbric-J/ic-J


title: Airway epithelial cells (basal cells) - RNAseq [668e_48d6-1B]

tag: treatment

value: Yes

tag: tech

tag: rin

tag: surgeon


title: F_P7_hyperoxia_CD45_1_DC28_M23

tag: sequencing run

tag: timepoint

tag: cell type

tag: cell subtype

value: Mac IV

tag: coverage

tag: number of genes


title: Airway epithelial cells (basal cells) - RNAseq [5795_46b9-2A]

tag: gender

tag: atopy

tag: asthma

tag: steroids

tag: smoking

value: Never

tag: crs

value: RN


title: LBR-null kidney from mouse 4002

tag: strain

tag: tissue

tag: disease

tag: age

tag: genotype


title: Airway epithelial cells (basal cells) - RNAseq [5795_46b9-1A]

tag: treatment

value: RV

tag: tech

tag: rin

tag: surgeon


title: F_P7_hyperoxia_CD45_1_DC28_I21

tag: sequencing run

tag: plate

tag: well

tag: timepoint

tag: cell type

value: immune

tag: cell subtype

value: neutrophil

tag: mousename

tag: coverage


title: Airway epithelial cells (basal cells) - RNAseq [61d3_4bc9-2A]

value: vehicle

tag: gender

value: Male

tag: atopy

tag: asthma

tag: steroids

tag: smoking

tag: crs

value: CRS

value: CB


title: F_P7_hyperoxia_CD45_1_DC28_I16

tag: treatment

value: Mac V

tag: number of genes


title: LBR-null kidney from mouse 4001 (rep2)

tag: strain

tag: tissue

tag: disease

tag: age

tag: genotype


title: LBR-null kidney from mouse 4001 (rep1)


title: F_P7_hyperoxia_CD45_1_DC28_B14

tag: sequencing run

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

value: Mac III


title: 901_repro

city: New Orleans

first: Victoria

last: Belancio

state: LA

address: 1430 Tulane Avenue

department: Structural and Cellular Biology

institute: Tulane University School of Medicine

data_processing:
We used Bowtie1 to concordantly map read pairs (-X 600) with a single preferred mapping location (-m 1) with the tryhard switch (-y) that forces it to exhaustively search each read pair against the reference genome. The same alignment parameters were used in this study with either mm10 or rn6 genomes.
The generated bam file was strand separated and then intersected with the same-oriented annotation for full-length L1s. Manual curation of resulting L1 loci with greater than 10 mapped reads was performed using IGV
After aligning the .fastq sequences to the appropriate reference genome (mm10 or rn6), we used a list of LINE-1 element genomic coordinates downloaded from L1 base (http://l1base.charite.de/) to quantify how many reads from the aligned files overlapped with annotated LINE-1 element coordinates. This was performed using 'bedtools coverage'. L1 loci are annotated at 'UID-' and their corresponding number of reads are in the 10th column from the left side of the .txt file.
L1Base - L1Resources<http://l1base.charite.de/>
L1Resources. This web portal is dedicated to putatively active LINE-1 elements. What are LINE-1s? LINE-1 (Long Interspersed Nucleotide Element 1, L1) are the only autonomous retrotransposons in the group of non-LTR retrotransposons.
All scripts and protocols used in this analysis are available in our previous publication RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level (doi: 10.3791/59771).
Genome_build: mm10 or rn6
Supplementary_files_format_and_content: L1 loci are annotated at 'UID-' and their corresponding number of reads are in the 10th column from the left side of the .txt file.

molecule: cytoplasmic RNA

source_name: repro

extract_protocol:
Organ samples of approximately 10 mm3 were bluntly dissected and then homogenized in 0.5-1mL of lysis buffer (150 mM NaCl, 50 mM HEPES pH 7.4, 25 ug/mL digitonin with 1000 U/mL SUPERase-In Rnase inhibitor added just prior to application) to lyse the cytoplasmic membrane. The mixture was lightly homogenized in a dounce homogenizer with an autoclaved B pestle, incubated on ice for 5 minutes and then centrifuged for 2 min at 1000 rpm at 4oC. Supernatant, containing the cytoplasmic fraction, was mixed with pre-chilled 7.5 mL of Trizol and 1.5 mL of chloroform and then centrifuged for 35 min at 4000 rpm at 4oC. The aqueous portion was transferred to 4.5 mL of chilled chloroform, mixed and centrifuged for 10 min at 4000 rpm at 4oC. The resulting aqueous portion was precipitated with 4.5 mL of isopropanol overnight in 80oC, centrifuged for 45 min at 4oC at 4000 rpms, washed with 10 mL of ethanol and re-suspended in RNAse-free water.
Cytoplasmic RNA samples were submitted to BGI Genomics for selection of polyadenylated RNAs, and strand-specific, paired-end library preparation. During this study, we used two methods of RNA sequencing with the same read depth: BGI DNA nanoball sequencing (DNBseq), which produces 150 bp read lengths, and Illumina sequencing, which produces 100 bp read lengths. For samples sequenced using Illumina sequencing, samples were pooled in groups of 5-7 and applied to a single lane of an Illumina HiSeq 2500/4000 instrument.

tag: organ

value: repro

tag: Sex


title: Airway epithelial cells (basal cells) - RNAseq [61d3_4bc9-1A]

tag: gender

tag: atopy

tag: asthma

tag: steroids

tag: tech

tag: rin

tag: surgeon


title: LBR-null kidney from mouse 4007 (rep2)

tag: strain

tag: tissue

value: kidney

tag: disease

value: 4 weeks old


title: Airway epithelial cells (basal cells) - RNAseq [0d99_4bd9-2A]

tag: treatment

value: Female

value: No

tag: smoking

value: Current

tag: crs

value: Control

tag: age


title: F_P7_hyperoxia_CD45_1_DC28_L5

tag: sequencing run

tag: plate

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

tag: cell subtype

tag: mousename

tag: coverage

tag: number of genes


title: Airway epithelial cells (basal cells) - RNAseq [0d99_4bd9-1A]

value: RV

tag: gender

tag: atopy

tag: asthma

tag: steroids

tag: tech

value: RN

tag: rin

tag: surgeon


title: 901_lung

source_name: lung

tag: strain

tag: organ

value: lung

tag: age

tag: Sex


title: nlp2_KNO3_rep2

type: RNA

city: Bunkoy-ku

first: Shuichi

last: Yanagisawa

state: Tokyo

address: Yayoi 1-1-1

department: Biotechnology Research Center

country: Japan

institute: The University of Tokyo

description:
Gene expression 1 hour after the treatement with 10 mM KNO3
nlp2_011

hyb_protocol: Cy3-labelled cRNA (1.65 ug, specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction mixture (55 ul) that contained 1x Agilent Fragmentation Buffer and 2x Agilent Blocking Agent, following the manufacturer’s instructions. On completion of the fragmentation reaction, the fragmentation mixture was mixed with 55 ul of 2x Agilent Hybridization Buffer HI-RPM and used for hybridization with Agilent Arabidopsis (v4) Gene Expression Microarray (G2519F-21169) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute at 37°C with GE Wash Buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one-color scan setting for 4x44k array slides with eXtended Dynamic range setting (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green, and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) using default parameters (Protocol: GE1-v5_95_Feb07 and Grid: 021169_D_F_20080807) to obtain background subtracted and spatially detrended Processed Signal intensities. Values are normalized with the 75 percentile values of Control type=0 probes. The values of Features flagged by Feature Extraction as gIsPosAndSignif=0 were set to 0.

source_name: 10 mM KNO3, 1hr, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the Ultrospec 6300 pro Spectrophotometer (Amersham Biosciences).

growth_protocol: Seeds were germinated on 1/2MS agar plates, and seedlings were grown for 4 days under continuous light. Seedlings were then transferred to the nitrate-free plates containing 2.5 mM ammonium succinate and 0.5 mM glutamine as nitrogen sources, and grown under long day (16h light/8h dark) conditions for 10 days.

extract_protocol: RNA was prepared using ISOGEN (NIPPON GENE, Tokyo, Japan), following the manufacturer’s recommendations and treated with DNase I.

treatment_protocol: One hour after the onset of the light period, plants were removed from the agar plates and immersed in a nitrate-free solution [nitrogen-free 1/10MS salts, 0.1 g/L MES-KOH (pH 5.7), 0.5 mM ammonium succinate, 0.5% sucrose]. After 1 hour of incubation, KNO3 or KCl was added to the solution at the final concentration of 10 mM. Plants were then incubated for another 1 hour and collected.

tag: genotype

tag: tissue

value: Whole plants

tag: agent


title: F_P7_hyperoxia_CD45_1_DC28_O19

tag: sequencing run

tag: plate

tag: well

tag: timepoint

tag: treatment

tag: cell type

value: immune

tag: cell subtype

tag: mousename


title: nlp2_KNO3_rep3

description:
Gene expression 1 hour after the treatement with 10 mM KNO3
nlp2_012

source_name: 10 mM KNO3, 1hr, replicate 3


title: F_P7_hyperoxia_CD45_1_DC28_J14

tag: gender

value: NK cell

tag: coverage

tag: number of genes


title: nlp2_KNO3_rep1

description:
Gene expression 1 hour after the treatement with 10 mM KNO3
nlp2_010

source_name: 10 mM KNO3, 1hr, replicate 1


title: nlp2_KCl_rep3

description:
Gene expression 1 hour after the treatement with 10 mM KCl
nlp2_009

source_name: 10 mM KCl, 1hr, replicate 3

value: KCl


title: Col_KNO3_rep3

description:
Gene expression 1 hour after the treatement with 10 mM KNO3
nlp2_006

value: wild type


title: nlp2_KCl_rep1

description:
Gene expression 1 hour after the treatement with 10 mM KCl
nlp2_007

source_name: 10 mM KCl, 1hr, replicate 1


title: Airway epithelial cells (basal cells) - RNAseq [0f12_4072-2A]

value: vehicle

value: Male

tag: atopy

value: Yes

tag: asthma

tag: steroids

tag: smoking

value: Prior

tag: crs

value: CRS

tag: tech

tag: rin

tag: surgeon


title: Col_KCl_rep3

description:
Gene expression 1 hour after the treatement with 10 mM KCl
nlp2_003

tag: genotype

tag: tissue

tag: agent


title: F_P7_hyperoxia_CD45_1_DC28_I17

tag: sequencing run

value: F

tag: plate

tag: well

tag: timepoint

tag: treatment

tag: cell type

value: Mac III


title: nlp2_KCl_rep2

description:
Gene expression 1 hour after the treatement with 10 mM KCl
nlp2_008

source_name: 10 mM KCl, 1hr, replicate 2


title: Col_KNO3_rep2

description:
Gene expression 1 hour after the treatement with 10 mM KNO3
nlp2_005


title: 901_liver

source_name: liver

tag: strain

tag: organ

value: liver

tag: age

tag: Sex


title: 901_brain

source_name: brain

value: brain


title: Col_KNO3_rep1

description:
Gene expression 1 hour after the treatement with 10 mM KNO3
nlp2_004


title: Airway epithelial cells (basal cells) - RNAseq [0f12_4072-1A]

value: RV

tag: gender

tag: atopy

tag: asthma

value: No

tag: steroids

tag: smoking

tag: crs


title: F_P7_hyperoxia_CD45_1_DC28_F18

value: hyperoxia

tag: cell subtype

value: neutrophil

tag: mousename

tag: coverage

tag: number of genes


title: 900_repro

value: repro


title: Col_KCl_rep2

description:
Gene expression 1 hour after the treatement with 10 mM KCl
nlp2_002

tag: genotype

tag: tissue

value: Whole plants

tag: agent


title: Col_KCl_rep1

description:
Gene expression 1 hour after the treatement with 10 mM KCl
nlp2_001

value: KCl


title: 900_lung

tag: strain

value: lung


title: F_P7_hyperoxia_CD45_1_DC28_P1

tag: sequencing run

tag: plate

tag: well

tag: timepoint

tag: treatment

tag: cell type

value: immune


title: Airway epithelial cells (basal cells) - RNAseq [4451_4efc-2A]

value: vehicle

tag: gender

value: Female

tag: atopy

tag: asthma

tag: steroids

value: Never

value: Control

tag: tech

value: CB

tag: rin

tag: age

tag: surgeon


title: Airway epithelial cells (basal cells) - RNAseq [3299_4cc7-2A]

tag: smoking

tag: crs


title: Patient C Primary

city: Jerusalem

first: Rotem

last: Karni

address: Hadassah Ein-Kerem

country: Israel

institute: Hebrew University of Jerusalem

data_processing:
alignment - reads were mapped to human genome using TopHat (version 1.2) which also identifies splicing junctions.
gene expression measure and normalization - The normalized expression of each gene was measured by Fragments Per Kilobase of exon per Million fragments mapped (FPKM), calculated with the program Cuffdiff from the Cufflinks package (version 2.0.2)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file with columns for Ensembl accession number, official gene symbol, FPKM values in each sample, where "P" stands for Primary, "E" for Effusion and "O" for Omentum.

source_name: human tumor samples

extract_protocol:
Total RNA was extracted with TRI Reagent (Sigma)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Surgical specimens were snap-frozen at -70°C without any treatment. Effusions were centrifuged immediately after tapping, and cell pellets were frozen at -70°C in equal amounts of RPMI 1640 medium (GIBCO-Invitrogen, Carlsbad, CA) containing 50% fetal calf serum (PAA Laboratories GmbH, Pasching, Austria) and 20% dimethylsulfoxide (Merck KGaA, Darmstadt, Germany).

tag: tumor stage

value: Primary

tag: tissue

value: high grade serous ovarian cancer


title: Patient C Omentum

value: Omentum


title: Airway epithelial cells (basal cells) - RNAseq [32d2_46e9-2A]

value: Male

value: Yes

value: Current

value: CRS

value: RN


title: F_P7_hyperoxia_CD45_1_DC28_M20

tag: sequencing run

value: F

tag: plate

value: hyperoxia

tag: cell subtype

value: Mac III

tag: mousename

tag: coverage

tag: number of genes


title: F_P7_hyperoxia_CD45_1_DC28_H23

tag: gender

tag: well

tag: timepoint

tag: treatment

tag: cell type

value: immune

value: DC III


title: Patient C Effusion

value: Effusion


title: Patient B Omentum


title: F_P7_hyperoxia_CD45_1_DC28_J1


title: 900_liver

tag: strain

tag: organ

value: liver

tag: age

tag: Sex


title: Genome-wide mapping of CTNNB1 binding sites in HepG2

city: Meguro-ku

first: Genta

last: Nagae

address: 4-6-1, Komaba

department: Genome Science Division

institute: RCAST, University of Tokyo

data_processing:
Reads are mapped using bowtie-1.2.1.1 and samtools-0.1.16.
Local coverage is calculated by deepTools package (bamCoverage 2.5.4) with a smoothing length of 300 bp (smoothLength = 300).
The coverage of an alignment of reads or fragments (BAM file) is calculated as the number of reads per bin, where bins are short consecutive counting windows of a defined size. A coverage track was generated as a bigwig file. *bamCoverage* offers normalization by scaling factor, Reads Per Kilobase per Million mapped reads (RPKM).
Genome_build: hg19

source_name: HepG2 cells

growth_protocol: The cells were cultured in Dulbecco’s modified Eagle medium (DMEM) (Life Technologies) supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin.

extract_protocol:
TF-DNA complexes were isolated by anti-ASCL2 or anti-CTNNB1. Briefly, the cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and cross-linked cell lysates underwent ultrasonic fragmentation and incubated with antibodies bound to Dynabeads (Thermo Fisher, #10001D and #10003D) at 4°C overnight. The beads were washed and eluted with elution buffer (0.5% SDS, 25 mM Tris-HCl, 5 mM EDTA). The eluates were treated with 1.5 μg of pronase at 42°C for 2 h, then incubated at 65°C overnight to reverse the cross-links. The immunoprecipitated DNA was purified by QIAquick PCR Purification Kit (QIAGEN, #28106).
Sequencing libraries were generated using the TruSeq ChIP Sample Prep Kit (Illumina), according to the manufacturer’s instructions.

value: hepatoblastoma cells

tag: antibody

value: CTNNB1 (Santa Cruz, sc-7963)

value: untreated


title: Patient B Effusion

tag: tumor stage

tag: tissue

value: high grade serous ovarian cancer


title: 899_repro

value: repro


title: F_P7_hyperoxia_CD45_1_DC28_N4

source_name: distal lung

tag: sequencing run

tag: plate

value: Mac II


title: F_P7_hyperoxia_CD45_1_DC28_J15

tag: cell subtype

tag: mousename


title: Patient B Primary

value: Primary


title: 899_lung

value: lung

value: Male


title: 900_brain

value: brain


title: Airway epithelial cells (basal cells) - RNAseq [32d2_46e9-1A]

value: RV

tag: atopy

value: Yes

tag: asthma

value: No

tag: steroids

tag: smoking

value: Current

tag: crs

value: CRS

tag: tech

value: RN

tag: rin

tag: surgeon


title: Patient A Effusion

value: Effusion


title: 1325_ovary

source_name: ovary

tag: strain

tag: organ

value: ovary

tag: age

value: Female


title: F_P7_hyperoxia_CD45_1_DC28_P7

tag: gender

value: F

tag: well

tag: timepoint

tag: treatment

value: hyperoxia

tag: cell type

value: immune

value: Mac III

tag: coverage

tag: number of genes


title: 1325_uterus

source_name: uterus

value: uterus

tag: Sex


title: Airway epithelial cells (basal cells) - RNAseq [4451_4efc-1A]

source_name: Cultured airway epithelial cells (basal cells)

tag: atopy

tag: asthma

tag: steroids

value: Never

value: Control

value: CB


title: Airway epithelial cells (basal cells) - RNAseq [be18_4d66-1A]

value: RV

value: Nasal

value: yes

tag: smoking

value: Prior

tag: crs

tag: tech


title: Patient A Omentum

tag: tumor stage

value: Omentum

tag: tissue

value: high grade serous ovarian cancer


title: F_P7_hyperoxia_CD45_1_DC28_H3

tag: sequencing run

tag: plate

tag: cell subtype

value: neutrophil

tag: mousename


title: 1325_lung

tag: strain

tag: organ

value: lung

tag: age


title: Airway epithelial cells (basal cells) - RNAseq [4f20_48f8-2A]

tag: treatment

value: vehicle

tag: gender

value: Female

value: Yes

value: Current

value: CRS

tag: rin

tag: surgeon


title: Airway epithelial cells (basal cells) - RNAseq [3299_4cc7-1A]

tag: atopy

value: No

tag: asthma

tag: steroids


title: Patient A Primary

value: Primary


title: 1325_brain

value: brain

tag: Sex


title: Airway epithelial cells (basal cells) - RNAseq [be18_4d66-2A]

tag: smoking

tag: crs

tag: tech

value: RN


title: F_P7_hyperoxia_CD45_1_DC28_G20

tag: sequencing run

value: F

tag: plate

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

value: immune

value: B cell

tag: coverage

tag: number of genes


title: F_P7_hyperoxia_CD45_1_DC28_D20

tag: gender

tag: treatment

tag: cell subtype

value: mast cell

tag: mousename


title: F_P7_hyperoxia_CD45_1_DC28_B5

value: Mac III


title: F_P7_hyperoxia_CD45_1_DC28_P12

value: mast cell II


title: F_P7_hyperoxia_CD45_1_DC28_F19

value: DC II


title: 1324_lung

tag: strain

tag: organ

value: lung

tag: age


title: Airway epithelial cells (basal cells) - RNAseq [92af_4cba-2A]

value: vehicle

value: Female

tag: atopy

tag: asthma

tag: steroids

tag: smoking

value: Never

tag: rin

tag: surgeon


title: 1324_ovary

value: ovary

tag: Sex


title: Airway epithelial cells (basal cells) - RNAseq [92af_4cba-1A]

value: RV

value: Yes

tag: crs

value: CRS

tag: tech


title: Airway epithelial cells (basal cells) - RNAseq [38cc_4577-2A]

value: No

value: Prior

value: Control

value: RN


title: 1324_brain

value: brain


title: Airway epithelial cells (basal cells) - RNAseq [38cc_4577-1A]


title: F_P7_hyperoxia_CD45_1_DC28_O13

tag: sequencing run

value: F

tag: plate

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

value: immune

tag: coverage

tag: number of genes


title: WT 3

city: St. Louis

first: Marco

last: Colonna

state: MO

address: 660 S. Euclid Ave.

institute: Washington University in St. Louis

description: Sort-purified CCR6+ ILC3 from small intestine lamina propria

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5.
Genome_build: mm10
Supplementary_files_format_and_content: Aligned gene count tables (.tsv) for all samples

source_name: CCR6+ ILC3

extract_protocol: Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq.

tag: strain

tag: genotype

value: WT

tag: tissue

value: small intestine lamina propria


title: 1305_repro

source_name: repro

tag: organ

value: repro

tag: age

value: Male


title: WT 2


title: CXCR5 KO 1

value: KO


title: Airway epithelial cells (basal cells) - RNAseq [77ea_427f-2A]

description:
gene.counts.txt
gene.counts.normalized.txt

tag: treatment

value: vehicle

tag: gender

tag: atopy

tag: asthma

tag: steroids

tag: smoking

value: Current

tag: rin


title: WT 1


title: 1305_liver

value: liver

tag: Sex


title: F_P7_hyperoxia_CD45_1_DC28_C1

tag: sequencing run

tag: plate

tag: well

tag: timepoint

tag: cell subtype

value: neutrophil

tag: mousename


title: Airway epithelial cells (basal cells) - RNAseq [4f20_48f8-1A]

value: RV

value: Female

value: Yes

tag: crs

value: CRS

tag: tech

value: CB

tag: surgeon


title: 1324_uterus

tag: strain

tag: organ

value: uterus

tag: age


title: CXCR5 KO 3

tag: genotype

tag: tissue


title: shCdGAP rep 3

city: Boston

first: Marie-Anne

last: Goyette

address: 450 Brookline avenue

institute: DFCI

data_processing:
Illumina CASAVA 1.8 pipeline
Data were trimmed with Trimmomatic (v. 0.30)
Reads were aligned to the GRCm38 reference genome with TopHat (v. 2.0.14)
Differential gene expression was then quantified with Cuffdiff (v 2.2.1)
Illumina HiSeq 2000
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file with raw alignment counts of each sample
Supplementary_files_format_and_content: excel file of Deseq analysis including raw counts normalized relative to the total number of reads

source_name: NMuMG-derived ErbB2-expressing mammary tumor explant cells

extract_protocol:
Total RNA was extracted using TRIZOL and cleaned up with RNeasy columns (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treament

value: shCdGAP

value: CdGAP KD


title: CXCR5 KO 2


title: 1305_brain

value: brain


title: F_P7_hyperoxia_CD45_1_DC28_K4

tag: gender

value: F

tag: treatment

value: hyperoxia

tag: cell type

value: immune

value: Mac V

tag: coverage

tag: number of genes


title: Airway epithelial cells (basal cells) - RNAseq [e82f_4d16-2A]

value: vehicle

value: Male

tag: atopy

tag: asthma

tag: steroids

value: Inhaled

value: yes

tag: smoking

value: Prior

value: RN

tag: rin


title: 1303_repro

value: repro

tag: Sex


title: shCdGAP rep 2


title: F_P7_hyperoxia_CD45_1_DC28_H9

tag: sequencing run

tag: plate

tag: well

tag: timepoint

tag: cell subtype

value: mast cell II

tag: mousename


title: Airway epithelial cells (basal cells) - RNAseq [e82f_4d16-1A]

value: RV

tag: gender

value: Yes

tag: crs

value: CRS

tag: tech

tag: age

tag: surgeon


title: Airway epithelial cells (basal cells) - RNAseq [c5cf_4251-2A]

tag: treatment

value: Female

tag: atopy

value: No

value: Current

value: Control

value: CB


title: shCTL rep 3

tag: treament

value: shCTL

tag: genotype

value: WT


title: 1303_lung

source_name: lung

tag: strain

tag: organ

value: lung

value: Male


title: 1303_brain

value: brain

tag: Sex


title: F_P7_hyperoxia_CD45_1_DC28_N6

tag: sequencing run

value: F

tag: plate

value: hyperoxia

tag: cell type

value: immune

value: Mac III

tag: coverage

tag: number of genes


title: shCTL rep 2


title: 1303_liver

value: liver


title: 1209_repro

value: repro


title: F_P7_hyperoxia_CD45_1_DC28_E8

tag: gender

tag: well

tag: timepoint

tag: cell subtype

value: T cell

tag: mousename


title: Airway epithelial cells (basal cells) - RNAseq [f513_4469-2A]

tag: treatment

value: vehicle

value: Yes

tag: asthma

tag: steroids

tag: smoking

value: Never

tag: crs

value: CRS

tag: tech

value: RN

tag: rin

tag: age

tag: surgeon


title: shCTL rep 1

tag: treament

value: shCTL

tag: genotype


title: Airway epithelial cells (basal cells) - RNAseq [77ea_427f-1A]

value: RV

tag: atopy

value: No

value: Current


title: Airway epithelial cells (basal cells) - RNAseq [f513_4469-1A]

tag: gender

value: Male


title: KITKO3 (Vav1R63W-Themis1-T-/-)

city: Toulouse Cedex 3

first: Mehdi

last: Benamar

address: CHU Purpan – BP 3028

country: France

institute: Inserm-CPTP

data_processing:
The quality of the RNA-Seq data was assessed with FastQC. Then the reads were poly-A and adaptor-trimmed with Trim Galore. The reads were aligned to the transcriptome with STAR
MultiQC was used to assess the performance of the preprocessing steps
The genome assembly and annotation for the RNA-Seq data analysis was downloaded from ENSEMBL (version 90)
The counts were normalized by the size factor method of DESeq2
Next, the differential gene expression analysis was done with DESeq2 using SARTools R package with FDR<0.05. All analyses were performed within the R environment and most plots were produced with the ggplot2 package  and pheatmap package
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: KITKO_Treg cel

extract_protocol:
Treg cell RNA was isolated using using Rneasy Micro Kit (Qiagen). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: genotype/variation

value: 7 weeks old

tag: cell type

value: CD4+CD62L+CD25bright Tregs


title: 1209_lung

tag: organ

value: lung

tag: Sex


title: Airway epithelial cells (basal cells) - RNAseq [fa59_4849-1A]

tag: treatment

value: Female

tag: asthma

value: CB


title: KITKO2 (Vav1R63W-Themis1-T-/-)


title: Airway epithelial cells (basal cells) - RNAseq [fa59_4849-2A]

tag: steroids

tag: smoking


title: F_P7_hyperoxia_CD45_1_DC28_G21

tag: sequencing run

value: F

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_1_DC28_F9

tag: gender

value: Mac II


title: F_P7_hyperoxia_CD45_1_DC28_E9


title: shCdGAP rep 1

tag: treament

value: shCdGAP

tag: genotype

value: CdGAP KD


title: Airway epithelial cells (basal cells) - RNAseq [c5cf_4251-1A]

tag: atopy

value: Yes

tag: crs

value: Control

tag: tech

tag: rin

tag: age

tag: surgeon


title: Airway epithelial cells (basal cells) - RNAseq [f584_41bb-2B]

tag: treatment

value: vehicle

value: No

tag: asthma

tag: steroids

value: yes

tag: smoking

value: Never

value: RN


title: F_P7_hyperoxia_CD45_1_DC28_J20

tag: sequencing run

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

value: B cell


title: KI2 (Vav1R63W)

source_name: KI_Treg cel

tag: strain

tag: genotype/variation

value: 7 weeks old

value: CD4+CD62L+CD25bright Tregs


title: F_P7_hyperoxia_CD45_1_DC28_L8

tag: gender

value: F

value: IL cell

tag: mousename

tag: coverage

tag: number of genes


title: Airway epithelial cells (basal cells) - RNAseq [a38e_4452-2A]

value: Male

tag: atopy

value: Current

tag: crs

tag: tech

tag: rin

tag: age

tag: surgeon


title: HF.KO.prog.rep4

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

data_processing:
HiSeq2000 using v3 chemistry. Software: Control v2.2.58, RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
RNAseq reads were aligned to the mouse transcriptome prepared with the mm10 primary assembly and the Ensembl version 89 annotation using STAR version 2.5.3a (Dobin et al., 2013). Gene expression was summarized with RSEM version 1.3.0 (Li and Dewey, 2011) and samtools version 1.3 (Li et al., 2009).
Genome_build: mm10 with ensembl v89 annotation
Supplementary_files_format_and_content: mmana_2018_IntCt.txt.gz is a text file of integer count data
Supplementary_files_format_and_content: mmana_2018_l2tpm.txt.gz is a text file of log2 tpm data with a plus 1 offset

source_name: Intestinal Stem Cell Progenitors

growth_protocol: Following crypt isolation, the crypt suspensions were pelleted (100 g, 5 min, 4°C) and supernatant was discarded. Crypts were resuspended in TrypLE (Gibco, no phenol red, 12604039) and dissociated into individual cells by warming crypts in water bath at 32ºC for 60 seconds. Dissociated single cells were treated with the following antibody cocktail for flow cytometry analysis: CD45-PE (eBioscience, 12-0451-83), CD31-PE (Biolegend, 102514), Ter-119PE (Biolegend, 116208), CD24-Pacific Blue (Biolegend, 101820), CD117-APC/Cy7 (Biolegend, 105826), and EpCAM-APC (eBioscience, 17-5791-82). 7AAD (Invitrogen, A1310) was used a viability dye to exclude dead cells from the analysis. ISCs were isolated as Lrg5-eGFPhiEpCAM+CD24low/-CD31-Ter119-CD45-7AAD-. eGFPlow progenitors were isolated as Lrg5-eGFPlowEpCAM+CD24low/-CD31-Ter119-CD45-7AAD-. Cells were sorted using a BD FACS II SORP cell sorter.

extract_protocol:
Sigma Aldrich TRI reagent
Standard clonetech RNAseq preparation

value: M

tag: genotype

tag: diet

value: High Fat


title: F_P7_hyperoxia_CD45_1_DC28_D1

tag: sequencing run

tag: plate

tag: well

tag: timepoint

tag: treatment

value: hyperoxia

value: immune

value: neutrophil


title: F_P7_hyperoxia_CD45_1_DC28_A7

tag: gender

tag: cell type

tag: cell subtype

value: Mac III


title: Airway epithelial cells (basal cells) - RNAseq [a38e_4452-1A]

value: RV

value: No

tag: asthma

tag: steroids

tag: smoking

value: Control


title: Airway epithelial cells (basal cells) - RNAseq [f584_41bb-1B]

value: Female

tag: atopy

value: yes

value: Never

tag: crs

tag: tech

value: RN


title: F_P7_hyperoxia_CD45_1_DC28_L13

value: F

tag: mousename

tag: coverage

tag: number of genes


title: HF.WT.prog.rep4

tag: strain

tag: genotype

value: Villin-CreER; Lgr5-GFP-IRES-CreER

tag: diet


title: Airway epithelial cells (basal cells) - RNAseq [a4a0_4b9c-2A]

value: vehicle

value: Male

value: CRS

value: CB

tag: rin

tag: age

tag: surgeon


title: F_P7_hyperoxia_CD45_1_DC28_K17

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: treatment

value: hyperoxia

tag: cell type


title: Msc80_Sox10ko cells, biological replicate 3

city: Erlangen

last: Wegner

state: Bavaria

address: Fahrstr. 17

department: Institut of Biochemistry

country: Germany

description: RNAseq data from Msc80 Sox10-deficient cells (Sox10ko)

data_processing:
Sequencing data were pooled using the Illumina HiSeq 2500 platform and converted into fastq files.
Reads from rRNA, tRNA, mt-rRNA and mt-tRNA were purged from demultiplexed reads.
Reads were aligned to mm10 reference genome (GRCm38, Ensembl Annotation Version 93) using STAR (v2.6.0c).
Unique maps were generated using HTSeq count relating to Ensembl genes version 85.
Statistical analysis of raw data was done with DESeq2 by R version 1.22.2.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file

source_name: Msc80 cell clone with CRISPR/Cas9-mediated Sox10 inactivation

growth_protocol: Msc80 cells were kept in DMEM with PenStrep and 10% FCS. Cells were split every 4th day.

extract_protocol:
Total RNA was extracted from Msc80 cells using the RNeasy Mini Kit according to the manufacturer's (QIAGEN) protocol.
RNA libraries were prepared for sequencing using TrueSeq Stranded mRNA Kit (Illumina).

treatment_protocol: Msc80 cells underwent CRISPR/Cas9-dependent genome editing to prevent Sox10 expression.

tag: cell line

value: Msc80 Schwann cell line


title: F_P7_hyperoxia_CD45_1_DC28_B23

value: immune

tag: cell subtype

value: Mac V

tag: mousename


title: KI3 (Vav1R63W)

tag: genotype/variation

value: 7 weeks old

value: CD4+CD62L+CD25bright Tregs


title: Msc80_Sox10ko cells, biological replicate 2


title: Airway epithelial cells (basal cells) - RNAseq [9be6_4904-2A]

tag: atopy

value: No

tag: asthma

tag: steroids

tag: smoking

tag: crs

value: Control

tag: tech


title: F_P7_hyperoxia_CD45_1_DC28_J8

tag: sequencing run

value: Mac III

tag: coverage

tag: number of genes


title: HFC.KO.prog.rep4

tag: strain

tag: gender

value: M

tag: genotype

tag: diet

value: High Fat Control


title: F_P7_hyperoxia_CD45_1_DC28_A18

value: F

tag: plate

tag: well

tag: timepoint

tag: treatment

tag: cell type

value: Mac IV


title: Msc80_Sox10ko cells, biological replicate 1

tag: cell line


title: Msc80_ctrl cells, biological replicate 3

description: RNAseq data from Msc80 cells (ctrl)

source_name: Msc80 cell line

value: Sox10 wt


title: Airway epithelial cells (basal cells) - RNAseq [9be6_4904-1A]

value: RV

value: Female

tag: atopy

tag: asthma

tag: steroids

value: Never

value: RN

tag: rin

tag: age

tag: surgeon


title: HF.KO.isc.rep4

source_name: Intestinal Stem Cells

value: High Fat


title: HFC.WT.prog.rep4

value: Villin-CreER; Lgr5-GFP-IRES-CreER


title: F_P7_hyperoxia_CD45_1_DC28_J7

tag: sequencing run

value: hyperoxia

value: immune

tag: cell subtype

value: Mac V

tag: mousename

tag: coverage

tag: number of genes


title: HFC.KO.isc.rep4

tag: strain

tag: gender

tag: genotype

tag: diet


title: Airway epithelial cells (basal cells) - RNAseq [9eb4_4cec-1A]

tag: treatment

value: No

tag: smoking

tag: crs

tag: tech

value: CB


title: Msc80_ctrl cells, biological replicate 2

description: RNAseq data from Msc80 cells (ctrl)

tag: cell line

value: Msc80 Schwann cell line


title: F_P7_hyperoxia_CD45_1_DC28_N2

tag: plate

tag: well

tag: timepoint

tag: cell type

value: neutrophil


title: Airway epithelial cells (basal cells) - RNAseq [9eb4_4cec-2A]

value: vehicle

tag: atopy

tag: asthma

tag: steroids

value: Control

tag: rin

tag: age

tag: surgeon


title: HF.KO.isc.rep3

tag: strain

tag: gender

value: M

tag: genotype


title: F_P7_hyperoxia_CD45_1_DC28_F2

tag: sequencing run

value: F

tag: treatment

tag: cell subtype

value: basophil

tag: mousename

tag: coverage

tag: number of genes


title: HF.KO.prog.rep3

tag: diet


title: Airway epithelial cells (basal cells) - RNAseq [a4a0_4b9c-1A]

value: RV

value: Male

tag: smoking

tag: crs

value: CRS

tag: tech


title: HF.WT.isc.rep4

value: High Fat


title: Airway epithelial cells (basal cells) - RNAseq [8b40_4142-2A]

tag: atopy

tag: asthma

tag: steroids

value: Never

value: RN


title: Dicer KO mouse testis (18 days), dsRNA immunopurification with J2 (160718_FR07934961)

city: Newcastle

first: Andreas

last: Werner

address: Framlington Place

department: Biosciences Institute

country: United Kingdom

institute: Newcastle University

description: double-stranded RNA

data_processing:
Quality assessment with FastQC and adaptors trimmed using Trimmomatic.
Transcript abundance was determined using Salmon (Patro R et al. (2017) Nat Methods 14:417-419) and different expression using DESeq2 (Love MI et al. (2014) Genome Biology, 15, 550.)
Genome_build: mm10
Supplementary_files_format_and_content: Normalized count table

source_name: Dicer KO mouse testis (18 days)

extract_protocol:
Double-stranded dsRNA immunopurification with J2 antibody (Scicons) according to the protocol published by Dhir (Nature 2018, 560:238-242)
Strand-specific RNA-Seq libraries were prepared using the NuGEN Ovation SoLo kit (Ovation SoLo RNA-Seq System, Tecan)
Total RNA Deep Depth (HiSeq 2500) v4.0

value: C57BL/6 x 129S4/SvJae

tag: tissue

value: testis

tag: age

value: post natal day 18

value: Dcr-/-

tag: rip antibody

value: J2 monoclonal antibody (mAb),mouse, IgG2a, kappa chain

tag: fraction

value: dsRNA immunopurification with J2


title: Adult mouse testis, dsRNA immunopurification with J2 (160718_FR07934960)

description: double-stranded RNA

source_name: Adult mouse testis

tag: strain

value: unknown

value: adult

tag: genotype

value: wild type


title: F_P7_hyperoxia_CD45_1_DC28_O17

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: treatment

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype

value: neutrophil


title: F_P7_hyperoxia_CD45_1_DC28_I15

value: mast cell

tag: mousename

tag: coverage

tag: number of genes


title: HF.WT.prog.rep3

value: M

value: Villin-CreER; Lgr5-GFP-IRES-CreER

tag: diet

value: High Fat


title: Airway epithelial cells (basal cells) - RNAseq [4ce3_4f19-2A]

value: vehicle

value: Male

tag: atopy

value: Yes

tag: asthma

value: No

tag: steroids

tag: smoking

value: Prior

tag: crs

value: CRS

tag: tech

value: CB

tag: rin

tag: age

tag: surgeon


title: HF.WT.isc.rep3

tag: strain

tag: gender

tag: genotype


title: WT mouse testis (18 days), dsRNA immunopurification with J2 (160718_FR07934959)

description: double-stranded RNA

source_name: WT mouse testis (18 days)

value: C57BL/6 x 129S4/SvJae

tag: tissue

value: testis

value: post natal day 18

tag: rip antibody

value: J2 monoclonal antibody (mAb),mouse, IgG2a, kappa chain

tag: fraction

value: dsRNA immunopurification with J2


title: HFC.KO.prog.rep3

value: High Fat Control


title: Airway epithelial cells (basal cells) - RNAseq [4ce3_4f19-1A]

tag: treatment

value: RV


title: F_P7_hyperoxia_CD45_1_DC28_B16

source_name: distal lung

tag: sequencing run

value: F

tag: plate

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype

value: Mac III

tag: mousename

tag: coverage

tag: number of genes


title: WT mouse testis (18 days), dsRNA immunopurification with J2 (160718_FR07934958)

description: double-stranded RNA

tag: age

value: wild type


title: Airway epithelial cells (basal cells) - RNAseq [830f_4683-2A]

value: vehicle

value: Male

tag: atopy

value: Yes

tag: asthma

tag: steroids

value: yes

tag: smoking

value: Never

tag: crs

value: Control

tag: tech

value: RN

tag: rin

tag: surgeon


title: HFC.KO.isc.rep3

tag: strain

tag: gender

value: M

tag: genotype

tag: diet


title: F_P7_hyperoxia_CD45_1_DC28_D7

tag: sequencing run

tag: plate

tag: well

tag: timepoint

tag: treatment

tag: cell type

tag: cell subtype

value: mast cell


title: Dicer KO mouse testis (18 days), dsRNA immunopurification with J2 (160718_FR07934957)

description: double-stranded RNA

value: C57BL/6 x 129S4/SvJae

tag: tissue

value: testis

tag: age

value: post natal day 18

value: Dcr-/-

tag: rip antibody

value: J2 monoclonal antibody (mAb),mouse, IgG2a, kappa chain

tag: fraction

value: dsRNA immunopurification with J2


title: Msc80_ctrl cells, biological replicate 1

description: RNAseq data from Msc80 cells (ctrl)

tag: cell line

value: Msc80 Schwann cell line

value: Sox10 wt


title: HFC.WT.prog.rep3

value: Villin-CreER; Lgr5-GFP-IRES-CreER

value: High Fat Control


title: F_P7_hyperoxia_CD45_1_DC28_B9

value: F

value: hyperoxia

value: immune

value: Mac IV

tag: mousename

tag: coverage

tag: number of genes


title: Airway epithelial cells (basal cells) - RNAseq [8b40_4142-1A]

value: RV

tag: gender

value: Male

tag: atopy

value: No

tag: asthma

tag: steroids

tag: smoking

value: Never

tag: crs

value: Control

tag: tech

value: RN

tag: rin

tag: surgeon


title: Airway epithelial cells (basal cells) - RNAseq [5bf2_4e77-1A]

tag: treatment

value: Female

value: Yes

value: Prior


title: Airway epithelial cells (basal cells) - RNAseq [5bf2_4e77-2A]

value: vehicle

tag: age


title: F_P7_hyperoxia_CD45_1_DC28_P6

tag: sequencing run

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

value: Mac III


title: WT mouse testis (18 days), dsRNA immunopurification with J2 (160718_FR07934954)

description: double-stranded RNA

tag: strain

value: C57BL/6 x 129S4/SvJae

tag: tissue

value: testis

value: post natal day 18

tag: genotype

value: wild type

tag: rip antibody

value: J2 monoclonal antibody (mAb),mouse, IgG2a, kappa chain

tag: fraction

value: dsRNA immunopurification with J2


title: Airway epithelial cells (basal cells) - RNAseq [830f_4683-1A]

value: RV

tag: gender

tag: atopy

tag: asthma

tag: steroids

value: yes

tag: smoking

tag: crs


title: F_P7_hyperoxia_CD45_1_DC28_K10

tag: sequencing run

value: F

tag: treatment

value: hyperoxia

value: immune

tag: mousename

tag: coverage

tag: number of genes


title: HFC.WT.isc.rep3

value: M

value: Villin-CreER; Lgr5-GFP-IRES-CreER

tag: diet

value: High Fat Control


title: Adult mouse testis, dsRNA immunopurification with J2 (160718_FR07934955)

description: double-stranded RNA

tag: strain

value: unknown

tag: age

value: adult


title: Airway epithelial cells (basal cells) - RNAseq [df18_40fb-2A]

value: vehicle

value: Male

value: Yes

value: No

value: Oral

value: Prior

value: Control

tag: tech

value: RN

tag: rin

tag: surgeon


title: Dicer KO mouse testis (18 days), Flow-through (160718_FR07934953)

description: rRNA and dsRNA depleted RNA

value: C57BL/6 x 129S4/SvJae

tag: tissue

value: testis

value: post natal day 18

tag: genotype

value: Dcr-/-

tag: rip antibody

value: J2 monoclonal antibody (mAb),mouse, IgG2a, kappa chain

tag: fraction

value: Flow-through


title: F_P7_hyperoxia_CD45_1_DC28_M10

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype

value: Mac III


title: Airway epithelial cells (basal cells) - RNAseq [df18_40fb-1A]

tag: treatment

value: RV

value: Male

tag: atopy

tag: asthma

tag: steroids

value: yes

tag: smoking

tag: crs


title: HF.WT.prog.rep2

tag: strain

value: Villin-CreER; Lgr5-GFP-IRES-CreER

tag: diet

value: High Fat


title: Adult mouse testis, Flow-through (160718_FR07934952)

description: rRNA and dsRNA depleted RNA

value: unknown

tag: tissue

tag: age

value: adult

tag: genotype

value: wild type


title: F_P7_hyperoxia_CD45_1_DC28_C3

tag: sequencing run

tag: gender

value: mast cell

tag: mousename

tag: coverage

tag: number of genes


title: WT mouse testis (18 days), Flow-through (160718_FR07934951)

description: rRNA and dsRNA depleted RNA

value: C57BL/6 x 129S4/SvJae

value: testis

value: post natal day 18

tag: rip antibody

tag: fraction


title: Dicer KO mouse testis (18 days), dsRNA immunopurification with J2 (160718_FR07934956)

description: double-stranded RNA

value: Dcr-/-

value: J2 monoclonal antibody (mAb),mouse, IgG2a, kappa chain

value: dsRNA immunopurification with J2


title: F_P7_hyperoxia_CD45_1_DC28_L10

value: F

tag: plate

tag: well

tag: timepoint

tag: treatment

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype

value: neutrophil


title: HF.WT.isc.rep2

tag: strain

tag: diet


title: Airway epithelial cells (basal cells) - RNAseq [a042_4b4d-1A]

value: RV

value: Male

tag: atopy

value: Yes

tag: asthma

tag: steroids

value: Unknown

tag: smoking

value: Never

tag: crs

value: CRS

tag: tech

value: RN

tag: rin

tag: age

tag: surgeon


title: Airway epithelial cells (basal cells) - RNAseq [a042_4b4d-2A]

value: vehicle

tag: gender


title: F_P7_hyperoxia_CD45_1_DC28_C13

tag: sequencing run

tag: plate

tag: well

value: T cell

tag: mousename

tag: coverage

tag: number of genes


title: HFC.KO.prog.rep2

tag: strain

tag: genotype

tag: diet

value: High Fat Control


title: F_P7_hyperoxia_CD45_1_DC28_I14

tag: timepoint

tag: treatment

tag: cell type

tag: cell subtype


title: HF.KO.prog.rep2

value: High Fat


title: WT mouse testis (18 days), Flow-through (160718_FR07934950)

description: rRNA and dsRNA depleted RNA

value: C57BL/6 x 129S4/SvJae

tag: tissue

value: testis

value: post natal day 18

value: wild type

tag: rip antibody

value: J2 monoclonal antibody (mAb),mouse, IgG2a, kappa chain

tag: fraction

value: Flow-through


title: Airway epithelial cells (basal cells) - RNAseq [9b6e_45d9-2A]

tag: gender

tag: atopy

value: No

tag: asthma

tag: steroids

tag: smoking

tag: crs

tag: tech

tag: rin

tag: age

tag: surgeon


title: Airway epithelial cells (basal cells) - RNAseq [9b6e_45d9-1A]

value: RV

value: Male


title: F_P7_hyperoxia_CD45_1_DC28_O6

tag: sequencing run

value: F

tag: plate

tag: well

tag: timepoint

value: hyperoxia

value: immune

value: Mac III

tag: mousename

tag: coverage

tag: number of genes


title: Dicer KO mouse testis (18 days), Flow-through (160718_FR07934949)

description: rRNA and dsRNA depleted RNA

tag: strain

tag: tissue

tag: genotype

value: Dcr-/-

tag: rip antibody

tag: fraction


title: HFC.KO.isc.rep2

tag: gender

tag: diet


title: HF.KO.isc.rep2


title: F_P7_hyperoxia_CD45_1_DC28_M18

tag: treatment

tag: cell type

tag: cell subtype

value: basophil


title: HFC.WT.isc.rep2

value: Villin-CreER; Lgr5-GFP-IRES-CreER

value: High Fat Control


title: Adult mouse testis, Flow-through (160718_FR07934947)

description: rRNA and dsRNA depleted RNA

value: unknown

tag: age

value: adult


title: Airway epithelial cells (basal cells) - RNAseq [94af_490f-1A]

tag: atopy

tag: asthma

tag: steroids

tag: smoking

value: Never

tag: crs

value: Control

tag: tech

value: RN

tag: rin

tag: surgeon


title: F_P7_hyperoxia_CD45_1_DC28_N21

tag: sequencing run

tag: plate

tag: well

tag: timepoint

tag: mousename

tag: coverage

tag: number of genes


title: Dicer KO mouse testis (18 days), Flow-through (160718_FR07934948)

description: rRNA and dsRNA depleted RNA

tag: strain

value: C57BL/6 x 129S4/SvJae

tag: tissue

value: testis

value: post natal day 18

tag: genotype

tag: rip antibody

value: J2 monoclonal antibody (mAb),mouse, IgG2a, kappa chain

tag: fraction

value: Flow-through


title: HF.KO.prog.rep1

tag: gender

value: F

tag: diet

value: High Fat


title: Airway epithelial cells (basal cells) - RNAseq [8838_40c3-2A]

tag: treatment

value: vehicle

value: Male

tag: atopy

value: Yes

tag: asthma

value: No

tag: steroids

value: Oral

value: yes

tag: smoking

value: Prior

tag: crs

value: CRS

tag: tech

tag: age


title: F_P7_hyperoxia_CD45_1_DC28_J21

tag: sequencing run

tag: plate

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype

value: Mac IV

tag: mousename

tag: coverage


title: WT mouse testis (18 days), Flow-through (160718_FR07934946)

description: rRNA and dsRNA depleted RNA

tag: strain

value: C57BL/6 x 129S4/SvJae

tag: tissue

value: testis

tag: genotype

value: wild type

tag: rip antibody

tag: fraction


title: HF.WT.prog.rep1

tag: gender

value: Villin-CreER; Lgr5-GFP-IRES-CreER

tag: diet


title: F_P7_hyperoxia_CD45_1_DC28_O10

value: F

tag: treatment

value: Mac III

tag: number of genes


title: F_P7_hyperoxia_CD45_1_DC28_G22

tag: sequencing run

value: neutrophil


title: HF.KO.isc.rep1

value: High Fat


title: Airway epithelial cells (basal cells) - RNAseq [538f_43e4-2B]

value: vehicle

value: Male

tag: atopy

tag: asthma

tag: steroids

tag: smoking

value: Never

tag: crs

value: Control

tag: tech

value: RN

tag: rin

tag: age

tag: surgeon


title: Airway epithelial cells (basal cells) - RNAseq [8838_40c3-1A]

value: RV

value: Yes

value: No

value: Oral

value: yes

value: Prior

value: CRS


title: WT.Neu_RNA-seq_rep1

city: Stuttgart

first: Haiyang

last: Yun

address: Auerbachstraße 112

institute: Robert Bosch Center for Tumor Diseases

description: RNA-seq

data_processing:
Paired-end reads were trimmed for adaptor sequence and masked for low-quality sequences, then were aligned to mouse genome (mm10) using STAR version 2.4.0.
Uniquely mapped reads were quantified with HTSeq.
Protein-coding (PC) genes with more than 1 read count in at least two samples of all wildtype or mutant HSPC replicates (n = 16,771) were included for downstream analysis.
Reads Per Kilobase Million (RPKM) mapped reads for each PC genes were calculated using Bioconductor package DiffBind.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values of PC genes

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:
Total RNA was extracted from freshly isolated cell population, using RNeasy Plus Mini kit (Qiagen) according to the manufacturer's instructions. RNA quantity and quality was measured using a NanoDrop 1000 Spectrophotometer (Thermo Scientific) and RNA 6000 Nano Kit (Agilent Technologies) on an Agilent 2100 bioanalyzer, respectively.
2-5 µg total RNA was processed for ribosomal RNA depletion and then for library preparation using a Rapid Directional RNA-Seq Kit (NEXTflex).

tag: genotype

value: Wild-type (WT)

tag: cell type

value: Bone marrow neutrophis

tag: strain


title: WT.Neu_RNA-seq_rep2

description: RNA-seq


title: DM.HSPC_RNA-seq_rep2

description: RNA-seq

source_name: Hematopoietic stem and progenitor cells (HSPC)

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

value: Bone marrow lineage negative cells


title: HF.WT.isc.rep1

tag: gender

value: F

value: Villin-CreER; Lgr5-GFP-IRES-CreER

value: High Fat


title: F_P7_hyperoxia_CD45_1_DC28_K5

tag: plate

tag: well

tag: timepoint

value: hyperoxia

value: immune

tag: cell subtype

value: DC I

tag: mousename

tag: coverage


title: HFC.WT.prog.rep2

tag: diet

value: High Fat Control


title: Airway epithelial cells (basal cells) - RNAseq [538f_43e4-1B]

source_name: Cultured airway epithelial cells (basal cells)

tag: treatment

value: RV

value: Male

tag: atopy

tag: asthma

tag: steroids

tag: smoking

value: Never

value: Control

value: RN


title: HFC.KO.prog.rep1


title: Airway epithelial cells (basal cells) - RNAseq [94af_490f-2A]

value: vehicle

value: No

tag: crs

tag: tech

tag: rin

tag: age

tag: surgeon


title: F_P7_hyperoxia_CD45_1_DC28_O4

tag: sequencing run

tag: gender

tag: plate

tag: cell type

value: T cell

tag: number of genes


title: DM.HSPC_RNA-seq_rep1

description: RNA-seq

tag: genotype

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

tag: strain


title: Airway epithelial cells (basal cells) - RNAseq [4b70_422f-2A]

tag: treatment

value: Yes

value: Oral

value: yes

value: CRS


title: HFC.KO.isc.rep1

value: F

tag: diet


title: Flt3-ITD.HSPC_RNA-seq_rep2

description: RNA-seq

value: Flt3ITD/+ (Flt3-ITD)

value: Bone marrow lineage negative cells


title: Airway epithelial cells (basal cells) - RNAseq [4b70_422f-1A]

tag: atopy

tag: asthma


title: F_P7_hyperoxia_CD45_1_DC28_D15

tag: well

tag: timepoint

value: hyperoxia

value: immune

tag: cell subtype

value: B cell

tag: mousename

tag: coverage


title: HFC.WT.prog.rep1

value: Villin-CreER; Lgr5-GFP-IRES-CreER

value: High Fat Control


title: Flt3-ITD.HSPC_RNA-seq_rep1

description: RNA-seq


title: Airway epithelial cells (basal cells) - RNAseq [483f_4b4e-2A]

value: Female

tag: steroids

tag: smoking

value: Current

tag: crs

value: Control

tag: tech

value: CB

tag: rin

tag: age

tag: surgeon


title: F_P7_hyperoxia_CD45_1_DC28_D8

tag: sequencing run

tag: gender

tag: plate

tag: cell type

value: Mac II

tag: number of genes


title: HFC.WT.isc.rep1

tag: strain

tag: genotype

tag: diet


title: Npm1c.HSPC_RNA-seq_rep2

description: RNA-seq

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


title: F_P7_hyperoxia_CD45_1_DC28_N14

tag: well

tag: timepoint

tag: treatment

tag: cell subtype

value: Mac IV

tag: mousename


title: Airway epithelial cells (basal cells) - RNAseq [483f_4b4e-1A]

value: RV

tag: atopy

value: Yes

tag: asthma

value: No

tag: steroids

tag: smoking

tag: crs

tag: tech


title: F_P7_hyperoxia_CD45_1_DC28_I19

tag: sequencing run

tag: gender

value: F

tag: plate

value: Mac III

tag: coverage


title: Npm1c.HSPC_RNA-seq_rep1

description: RNA-seq

tag: genotype

tag: cell type

value: Bone marrow lineage negative cells

tag: strain


title: NK Cell from RNF2 KO Tumor Replicate #2

city: Winston-Salem

first: Swapan

last: Das

state: NC

address: Bowman Gray Center for Medical Education, 475 Vine St

department: Department of Internal Medicine, Section of Endocrinology and Metabolism

institute: Wake Forest School of Medicine

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Genome_build: GRCm38(mm10)

source_name: Murine Natural killer cell (NK) cell

growth_protocol: 4T1 cells  were cultured in DMEM (Dulbecco’s Modified Eagle’s Medium)/Hams F-12 50/50 Mix (Corning (Corning, NY, USA), Catalogue # 10-090-CV) supplemented with 10% Fetal Bovine Serum (FBS) (MilliporeSigma (St. Louis, MO, USA), Catalogue # 12306C), and 10 units of Penicillin and 10 µg/mL Streptomycin (GE (Pittsburgh, PA, USA), Catalogue # SV30010), and 50 µg/mL Geneticin (Thermo

extract_protocol:
Total RNA from sorted tumor cells and NK cells was extracted using a QIAshredder kit (QIAGEN, Catalogue # 79654) and an RNeasy Plus Micro Kit (QIAGEN, cat# 74034)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Each tumor was cut into small pieces (<3mm) and incubated in 3ml dissociation solution (PBS supplemented with 2% FBS, 1mg/ml collagenase/Dispase and 0.5 mg/ml DNase I) for 1 hour at 37°C with gentle shaking. Cell suspension was then passed through a 70 mm cell strainer and washed with DMEM/2% FBS followed by flow cytometry analysis.

tag: genotype/variation

value: FACS enriched from RNF2 KO tumor

value: BALB/c


title: Airway epithelial cells (basal cells) - RNAseq [b109_4415-2A]

tag: treatment

value: vehicle

value: Male

value: Prior

value: CRS

tag: rin

tag: age

tag: surgeon


title: NK Cell from RNF2 KO Tumor Replicate #1


title: WT.HSPC_RNA-seq_rep2

description: RNA-seq

value: Wild-type (WT)


title: F_P7_hyperoxia_CD45_1_DC28_L4

city: Kensington

last: Zanini

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.

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

tag: well

tag: timepoint

value: hyperoxia

value: immune

tag: cell subtype

tag: mousename

tag: number of genes


title: Airway epithelial cells (basal cells) - RNAseq [b109_4415-1A]

tag: atopy

tag: asthma

tag: steroids

tag: smoking

tag: crs

tag: tech

value: CB


title: NK Cell from Control Tumor (for RNF2 KO Tumor) Replicate #2

value: FACS enriched from control tumor

tag: strain


title: Airway epithelial cells (basal cells) - RNAseq [9f0d_46f8-2A]

tag: gender

value: Current

value: Control


title: F_P7_hyperoxia_CD45_1_DC28_J6

tag: sequencing run

tag: plate

tag: treatment

tag: cell type

value: Mac IV

tag: coverage


title: NK Cell from Control Tumor (for RNF2 KO Tumor) Replicate #1

tag: genotype/variation


title: WT.HSPC_RNA-seq_rep1

description: RNA-seq

tag: genotype


title: WT.Neu_input

description: ChIP-seq

data_processing:
Single-read reads were trimmed for adaptor sequence and masked for low-quality sequence.
Then they were aligned to mm10 genome using Bowtie version 2.1.0 allowing two mismatch.
Duplicates were removed using PICARD tools.
For H3K4me1 or H3K4me3, enriched regions (peaks) were identified using findPeaks program from Homer, with the setting of “-size 1000 -minDist 1000”.
For H3K27ac ChIP-seq, peaks were called using MACS2 against input sample of each cell type with a P-value cutoff of 1e-9 and with setting “nomodel”.
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:
Chromatin immunoprecipitation was performed with iDeal ChIP-seq kit for Histones (Diagenode). Briefly, 1 x 106 Lin- HSPCs or neutrophils were crosslinked with formaldehyde at a final concentration of 1% for 10 minutes and then quenched by addition of Glycine for 5 minutes incubation. Lysis buffers iL1 and iL2 were used to prepare the nuclei pellets. Chromatin was sheared in Shearing buffer iS1 using the Bioruptor Plus (Diagenode) for 20 cycles (each cycle for 30 seconds “ON” and 45 seconds “OFF”) at high power setting. Immunoprecipitation, wash, decrosslinking and elution were carried out as per the manufacturer’s protocol, using 1 µg antibody. 10% of the sheared chromatins were kept aside as input samples.
Immunoprecipitated DNA or input DNA were used library preparation by using TruSeq ChIP Sample Prep Kit (Illumina), following standard procedures from manufacturer. The library DNA was quantified using KAPA Library Quantification Kit (Kapa Biosystems) and library average size was determined by Agilent DNA 1000 Kit (Agilent Technologies).

tag: chip antibody

value: No


title: Airway epithelial cells (basal cells) - RNAseq [9f0d_46f8-1A]

data_processing:
RNAseq reads were mapped to the human reference genome (hg19) using STAR
Gene counts were generated from STAR (--quantMode GeneCounts)
removed X, Y, and mitochondrial genes
Gene counts were voom transformed (TMM normalized)
Genome_build: hg19
Supplementary_files_format_and_content: gene count files were processed using R; files contain gene counts (or normalized gene counts) for each sample; rows are gene Ensembl IDs and the columns are sample names
Supplementary_files_format_and_content: .txt; gene counts for each sample
Supplementary_files_format_and_content: .txt; normalized gene counts (TMM normalized) for each sample

extract_protocol:
QIAGEN AllPrep DNA/RNA Kit
Illumina TruSeq RNA Library Prep Kit v2

value: RV

tag: rin

tag: age

tag: surgeon


title: NK Cell from RSF1 KO Tumor Replicate #2

value: FACS enriched from RSF1 KO tumor


title: F_P7_hyperoxia_CD45_1_DC28_E3

value: F

tag: well

tag: timepoint

tag: cell subtype

value: Mac III

tag: mousename

tag: number of genes


title: F_P7_hyperoxia_CD45_1_DC28_H19

tag: gender

value: basophil


title: Airway epithelial cells (basal cells) - RNAseq [551b_49fb-2A]

value: vehicle

value: Female

tag: atopy

value: Yes

tag: asthma

tag: steroids

tag: smoking

value: Never

tag: crs

tag: tech

value: RN


title: DM.HSPC_input

description: ChIP-seq

tag: strain


title: Flt3-ITD.HSPC_input

description: ChIP-seq

tag: chip antibody


title: F_P7_hyperoxia_CD45_1_DC28_L20

tag: sequencing run

tag: plate

tag: treatment

value: hyperoxia

tag: cell type

value: immune

value: T cell

tag: coverage


title: Airway epithelial cells (basal cells) - RNAseq [551b_49fb-1A]

tag: rin

tag: age

tag: surgeon


title: NK Cell from Control Tumor (for RSF1 KO Tumor) Replicate #2

tag: genotype/variation

value: FACS enriched from control tumor

value: BALB/c


title: Npm1c.HSPC_input

description: ChIP-seq


title: Airway epithelial cells (basal cells) - RNAseq [952a_4dbc-2A]

tag: gender

value: Male

tag: atopy

value: Oral

value: yes

value: CRS

value: CB


title: F_P7_hyperoxia_CD45_1_DC28_P13

value: F

tag: well

tag: timepoint

tag: cell subtype

value: Mac III

tag: mousename

tag: number of genes


title: NK Cell from Control Tumor (for RSF1 KO Tumor) Replicate #1

tag: strain


title: F_P7_hyperoxia_CD45_1_DC28_D13

tag: sequencing run


title: WT.HSPC_input

description: ChIP-seq

tag: chip antibody

value: No


title: Airway epithelial cells (basal cells) - RNAseq [952a_4dbc-1A]

tag: treatment

value: RV

tag: asthma

tag: steroids

tag: smoking

tag: crs

tag: tech


title: F_P7_hyperoxia_CD45_1_DC28_I10

tag: plate

tag: cell type

tag: coverage


title: Airway epithelial cells (basal cells) - RNAseq [b8ff_4982-2A]

value: vehicle

tag: gender

tag: atopy

value: Yes

value: Control

tag: rin

tag: age

tag: surgeon


title: RNF2 KO Tumor Replicate #1

source_name: Murine breast cancer cell

tag: genotype/variation

value: FACS enriched from RNF2 KO tumor

tag: strain


title: F_P7_hyperoxia_CD45_1_DC28_O5

tag: sequencing run

tag: well

tag: timepoint

value: hyperoxia

value: immune

tag: cell subtype

value: Mac V

tag: mousename

tag: number of genes


title: NK Cell from RSF1 KO Tumor Replicate #1

value: FACS enriched from RSF1 KO tumor

value: BALB/c


title: RSF1 KO Tumor Replicate #2


title: WT.Neu_H3K27ac_rep2

description: ChIP-seq

tag: chip antibody

value: anti-H3K27ac, #ab4729, Abcam


title: Airway epithelial cells (basal cells) - RNAseq [b8ff_4982-1A]

tag: treatment

value: Male

tag: asthma

tag: steroids

tag: smoking

value: Never

tag: crs

tag: tech

value: RN


title: F_P7_hyperoxia_CD45_1_DC28_I4

tag: gender

value: F

tag: plate

tag: cell type

value: neutrophil

tag: coverage


title: Airway epithelial cells (basal cells) - RNAseq [323b_40ff-1A]

tag: atopy

value: CRS

tag: rin

tag: age

tag: surgeon


title: Airway epithelial cells (basal cells) - RNAseq [323b_40ff-2A]


title: DM.HSPC_H3K27ac_rep1

description: ChIP-seq

tag: strain


title: WT.Neu_H3K27ac_rep1

description: ChIP-seq


title: RSF1 KO Tumor Replicate #1

tag: genotype/variation


title: F_P7_hyperoxia_CD45_1_DC28_A17

tag: sequencing run

tag: well

tag: timepoint

tag: cell subtype

value: mast cell

tag: mousename

tag: number of genes


title: Control Tumor Replicate #2

value: FACS enriched from control tumor

tag: days after implantaion


title: DM.HSPC_H3K27ac_rep2

description: ChIP-seq

tag: chip antibody


title: Flt3-ITD.HSPC_H3K27ac_rep2

description: ChIP-seq


title: Flt3-ITD.HSPC_H3K27ac_rep1

description: ChIP-seq


title: Airway epithelial cells (basal cells) - RNAseq [d45f_44b0-1A]

tag: treatment

value: RV

tag: gender

value: No

tag: asthma

tag: steroids

tag: smoking

tag: crs

tag: tech


title: Airway epithelial cells (basal cells) - RNAseq [d45f_44b0-2A]

value: vehicle

tag: atopy

value: Control

tag: rin

tag: age

tag: surgeon


title: Airway epithelial cells (basal cells) - RNAseq [7b33_43a0-2A]

value: yes

value: Current

value: CB


title: Control Tumor Replicate #1

tag: genotype/variation

tag: strain

value: BALB/c


title: RNF2 KO Tumor Replicate #2

value: FACS enriched from RNF2 KO tumor


title: Npm1c.HSPC_H3K27ac_rep2

description: ChIP-seq

value: anti-H3K27ac, #ab4729, Abcam


title: F_P7_hyperoxia_CD45_1_DC28_A22

tag: sequencing run

tag: plate

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype

value: Mac IV

tag: mousename

tag: coverage


title: Npm1c.HSPC_H3K27ac_rep1

description: ChIP-seq

tag: chip antibody


title: F_P7_hyperoxia_CD45_1_DC28_B11

tag: gender

value: F

tag: treatment

tag: number of genes


title: F_P7_hyperoxia_CD45_1_DC28_M3


title: F_P7_hyperoxia_CD45_1_DC28_C15


title: Airway epithelial cells (basal cells) - RNAseq [9623_473f-2A]

value: Male

tag: atopy

value: Yes

tag: asthma

tag: steroids

value: Nasal

tag: smoking

value: Prior

tag: crs

value: CRS

tag: tech

value: RN

tag: rin


title: Airway epithelial cells (basal cells) - RNAseq [7b33_43a0-1A]

value: RV

value: No

value: Control

tag: age

tag: surgeon


title: WT.HSPC_H3K27ac_rep2

description: ChIP-seq

tag: strain


title: WT.HSPC_H3K27ac_rep1

description: ChIP-seq


title: Airway epithelial cells (basal cells) - RNAseq [9623_473f-1A]

value: yes


title: LPS+IFNb 2

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: Macrophage from 7 weeks C57BL6 mouse treated with 4hrs IFNb followed by 4 hrs LPS

data_processing:
Following removal of barcodes and adaptors, raw reads were aligned to the mm10 genome (Ensembl transcripts) and quantified using the psuedoaligment of Kallisto.
Data were log2 transformed, normalized using a 75th percentile shift, and baselined to the median of all samples. Transcripts with low expression across all conditions were removed from the analysis.
Genome_build: mm10
Supplementary_files_format_and_content: text file with gene symbol and enseml transcript id.

source_name: Macrophage

extract_protocol:
Illumina TruSeq RNA Sample Prep Kit
Standard Illumina protocols

treatment_protocol: 7 week old male mice were given peritoneal stimulation of 4 hours LPS, 4 hours IFNb, or 4 hours IFNb followed by 4 hours LPS.  Peripheral macrophages were obtained.

value: LPS+IFNb

tag: cell

value: Macrophage

tag: background

value: 7 weeks

tag: trt time

value: 4hrs IFNb followed by 4 hrs LPS


title: IFNb 2

description: Macrophage from 7 weeks C57BL6 mouse treated with 4hrs IFNb

value: IFNb

value: 4hrs IFNb


title: IFNb 1


title: F_P7_hyperoxia_CD45_1_DC28_K12

first: Fabio

address: High and Botany St

institute: University of New South Wales

tag: sequencing run

value: F

tag: plate

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype

value: Mac IV

tag: mousename

tag: coverage


title: LPS 2

description: Macrophage from 7 weeks C57BL6 mouse treated with 4hrs LPS

tag: treatment

value: LPS

value: 4hrs LPS


title: WT.Neu_H3K4me3_rep1

description: ChIP-seq

tag: chip antibody

value: anti-H3K4me3, #c15410003, Diagenode


title: F_P7_hyperoxia_CD45_1_DC28_E6

tag: gender

value: Mac V

tag: number of genes


title: HFC.WT.isc.rep4

value: M

tag: genotype

value: Villin-CreER; Lgr5-GFP-IRES-CreER

tag: diet

value: High Fat Control


title: F_P7_hyperoxia_CD45_1_DC28_M16

value: DC I


title: LPS 1

tag: cell

value: Macrophage

tag: age


title: Airway epithelial cells (basal cells) - RNAseq [db6c_413d-2A]

city: Chicago

last: Ober

value: vehicle

value: Male

tag: atopy

value: Yes

tag: asthma

tag: steroids

tag: smoking

value: Never

tag: crs

value: CRS

tag: tech

value: CB

tag: rin

tag: surgeon


title: WT.Neu_H3K4me3_rep2

description: ChIP-seq

tag: strain


title: Airway epithelial cells (basal cells) - RNAseq [db6c_413d-1A]

tag: treatment

value: RV


title: F_P7_hyperoxia_CD45_1_DC28_A3

tag: sequencing run

value: F

tag: plate

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype

tag: mousename

tag: coverage


title: Saline 2

description: Macrophage from 7 weeks C57BL6 mouse treated with 4 hrs Saline

value: Saline

tag: cell

tag: background

tag: age

value: 7 weeks

tag: trt time

value: 4 hrs Saline


title: LPS+IFNb 1

value: LPS+IFNb

value: 4hrs IFNb followed by 4 hrs LPS


title: DM.HSPC_H3K4me3_rep2

description: ChIP-seq

tag: chip antibody

value: anti-H3K4me3, #c15410003, Diagenode


title: F_P7_hyperoxia_CD45_1_DC28_E10

tag: gender

value: Mac V

tag: number of genes


title: Airway epithelial cells (basal cells) - RNAseq [76b3_439a-2A]

value: vehicle

tag: atopy

value: No

tag: asthma

tag: steroids

tag: smoking

value: Current

tag: crs

tag: tech

value: RN

tag: rin

tag: surgeon


title: Saline 1

tag: treatment

value: Macrophage


title: F_P7_hyperoxia_CD45_1_DC28_O1

tag: sequencing run

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

value: Mac III

tag: mousename

tag: coverage


title: DM.HSPC_H3K4me3_rep1

description: ChIP-seq

tag: strain

tag: chip antibody


title: Airway epithelial cells (basal cells) - RNAseq [76b3_439a-1A]

value: RV

tag: gender

value: Male

tag: atopy

tag: asthma

tag: steroids

value: CRS

tag: age


title: T11.RNA-seq.NBL

city: Shenzhen,Guangdong Province,China

first: Yayan

last: Feng

state: --- Select a state ---

address: No. 7 pengfei road, dapeng new district, shenzhen

country: China

institute: Chinese Academy of Agricultural Sciences

data_processing:
SOAPnuke was used for trimming adapters and filtering on length and quality of the raw sequencing reads, with the following paramaters: -q 0.5 -d -Q 2 --sanger -l 20
Clean reads were mapped to respective reference genome using hisat2 with default settings
The levels of gene expression were quantified using Cufflinks (v2.2.1) with RPKM (reads per kilobase million).
Differentially expressed genes were estimated by Cuffdiff (v2.2.1) with default paramaters
Genes with a threshold false discovery rate (FDR) ≤ 0.05 and the absolute value of log2Ratio ≥ 1 or ≤ -1 were considered significantly differentially expressed
Genome_build: T1 reference genome: ABIR00000000; T4 reference genome: PRJNA451013; Other reference genomes: PRJNA257433
Supplementary_files_format_and_content: rpkm Bed format

organism: Trichinella zimbabwensis

source_name: T. zimbabwensis

extract_protocol:
Total RNA of T. spiralis (Ad, NBL and ML) was purified using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer’s instructions.
To degrade any possible DNA contamination, the total RNA samples were dissolved in diethylpyrocarbonate (DEPC)-treated water and treated with DNaseI. NanoDrop 2000 (Thermo Scientific CA, USA) was then used to assess the quantity and quality of the total mRNA enriched using oligo (dT) magnetic beads. Paired-end sequencing libraries with insert size of 300 bp were conducted on the HiSeq 2,500 platform following the Illumina’s protocols.

tag: passages

value: Newborn larvae


title: F_P7_hyperoxia_CD45_1_DC28_K2

value: F

tag: treatment

value: hyperoxia

value: immune

value: mast cell II

tag: number of genes


title: Flt3-ITD.HSPC_H3K4me3_rep2

description: ChIP-seq


title: Flt3-ITD.HSPC_H3K4me3_rep1

description: ChIP-seq


title: MDA-MD-231, IRE1-alpha KO, Thapsigargin, F12 (RNA-seq)

city: South San Francisco

first: Thomas

middle: D.

last: Wu

state: CA

address: 1 DNA Way

institute: Genentech, Inc.

data_processing:
Sequenced reads were aligned to the genome using GSNAP version 2013-10-10 with parameters -M 2 -n 10 -B 2 -I 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap
Alignments were converted to counts using HTSeqGenie version 4.0.1
Genome_build: GRCh38
Supplementary_files_format_and_content: RNA_counts_matrix.txt  (Matrix table with raw gene counts for every gene and every sample).  RNA_counts_genes.txt (gene annotations)

source_name: MDA-MD-231 cells, IRE1-alpha KO, Thapsigargin

growth_protocol: Cells were cultured in RPMI1640 media supplemented with 10% (v/v) fetal bovine serum (FBS, Sigma), 2 mM glutaMAX (Gibco) and 100 U/ml penicillin plus 100 μg/ml streptomycin (Gibco).

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen #74104) performing on-column DNA digestion for 15 min. The concentration of RNA samples was determined using NanoDrop 8000 (Thermo Scientific) and the integrity of RNA was analyzed by Fragment Analyzer (Advanced Analytical Technologies). Approximately 500 ng of total RNA was used as input for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina).
The size of the libraries was confirmed using 4200 TapeStation and High Sensitivity D1K screen tape (Agilent Technologies) and their concentration was determined by qPCR based method using Library quantification kit (KAPA). The libraries were multiplexed and then sequenced on Illumina HiSeq2500 (Illumina) to generate 30M of single end 50 base pair reads.

treatment_protocol: There were four experimental conditions: WT and IRE1α KO, treated with Tg (100nM) or vehicle control (DMSO) for 8 hr with three biological replicates (n=3) for each condition.

tag: cell line

tag: genotype

value: IRE1-alpha KO

value: Thapsigargin


title: T11.RNA-seq.ML

value: Muscle larvae


title: F_P7_hyperoxia_CD45_1_DC28_J3

tag: sequencing run

tag: plate

tag: well

tag: timepoint


title: T11.RNA-seq.AD

value: Adult


title: T11.WGBS.ML

data_processing:
Raw sequencing reads with more than 30% ‘N’s in over 10% of the sequences or smaller than 30 bp were discarded
Clean reads were aligned to the corresponding reference genome using BSMAP (v2.73) with a of maximal four mismatches and gap size up to 2 nucleotides
Methylation level of each cytosine was calculated as the number of reads ascertained methylated to the total number of reads for each covered CpG sites.
To accurately investigate the methylation levels in each sample, we used CpG sites with a minimal 5× sequencing depth per strand.
Genome_build: T1 reference genome: ABIR00000000; T4 reference genome: PRJNA451013; Other reference genomes: PRJNA257433
Supplementary_files_format_and_content: cout, bed format

extract_protocol:
DNA was extracted using the phenol chloroform extraction method
Genomic DNA extracted from three life stages of all Trichinella species were selected for libraries construction of WGBS. Briefly, approx. two to five micrograms of gDNA were first fragmented by Covaris to an average size of ~200-300 bp. End-repair, A-tailing and ligation were conducted as the Illumina PE genomic DNA sample prep kit protocol, except that ligation was performed using methylated cytosine PE adapters provided by Illumina previously. Ligation products were purified and bisulfited converted using the EZ DNA Methylation-Gold KitTM (ZYMO) according to the manufacturer’s instructions. The libraries were sequenced using Illumina HiSeq 2,500 platform.

tag: tag


title: MDA-MD-231, IRE1-alpha KO, Thapsigargin, F8 (RNA-seq)


title: Npm1c.HSPC_H3K4me3_rep2

description: ChIP-seq

tag: strain

value: anti-H3K4me3, #c15410003, Diagenode


title: MDA-MD-231, IRE1-alpha KO, DMSO, F11 (RNA-seq)

source_name: MDA-MD-231 cells, IRE1-alpha KO, DMSO

value: DMSO


title: T11.WGBS.NBL


title: Npm1c.HSPC_H3K4me3_rep1

description: ChIP-seq

tag: chip antibody