title: F_P7_hyperoxia_CD45_2_DC35_F4

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype

value: neutrophil

tag: mousename

tag: coverage

tag: number of genes


title: HCT116 control CDT1 Replicate 2 (ChIPSeq)

status: Public on Jun 01 2021

type: SRA

city: Bethesda

first: Christophe

middle: E

last: Redon

state: MD

address: 37 Convent Drive

country: USA

institute: NIH

description:
HCT116 no treatment CDT1 ChipSeq
HCT116 control CDT1-2

library_source: genomic

data_processing:
For ChIP-Seq, peaks were called using the  MACS algorithms againt input. Default parameters were used for sample calling.
For nascent strand peak calling the MACS was used. Nascent strand reads were called by comparison to genomic DNA.  Peaks were filtered using the “peak-score” MACS2 metric in R (version 3.5.1) by accepting regions above the inflection-point threshold of “peak-scores” from the raw output.
Single read  75bp (NextSeq for ChipSeq) or Pair End 101, 125 and 150 bp (HiSeq or NovaSeq) for NGS sequencing
Genome_build: hg19
Supplementary_files_format_and_content: Bed file format of replication initiation peaks and ChipSeq

molecule: genomic DNA

organism: Homo sapiens

source_name: Colon carcinoma

growth_protocol: Cancer cells were grown in DMEM medium, 10% FBS

extract_protocol:
DNA from cell cultures was isolated, size fractionated and subject to exunuclease digestion as described in Aladjem et al., Science 281, 1005, 1998. and Wang et al., Molecular and Cellular Biology 24:3373-86, 2004. For ChipSeq, DNA molecules were enriched using antibodies against proteins of interest. Re-replicated DNA was isolated by by Brdu-cesium chloride gradient
Enriched ChIPed DNA molecules were sequenced by Illumina NextSeq 75 cycle High Output kit with single ennd of 75bp. For nascent  DNA, re-replicated DNA, paired-end libraries of genomic DNA (gDNA) were prepared using Illumina TruSeq Nano DNA Library Prep kits. Control genomic DNA was fragmented to ~ 400 bp insert size on the Covaris which generates dsDNA fragments with 3' or 5' overhangs. The sheared DNA was blunt-ended and library size selection was done using sample purification beads. A single 'A' nucleotide was added to the 3' ends of the blunt fragments to prevent them from ligating to each other during the adapter ligation reaction. A corresponding single 'T' nucleotide on the 3' end of the adapter provided a complementary overhang for ligating the adapter to the fragment. The indexed adapters were ligated to the ends of the DNA fragments and then PCR-amplified to enrich for fragments that have adapters on both ends. The final purified product was then quantitated by qPCR before cluster generation and sequencing.

treatment_protocol: Cells were treated with MLN4924 or doxyclcline to induce re-replication.

tag: strain

value: Cultured cancer cell line

tag: chip antibody

value: CDT1 antibody (Cell Signaling, 8064)

tag: molecule subtype

value: ChipSeq DNA


title: M_P7_hyperoxia_CD45_1_DC35_L11

city: Kensington

first: Fabio

last: Zanini

state: NSW

address: High and Botany St

country: Australia

institute: University of New South Wales

library_source: transcriptomic

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.

molecule: total RNA

organism: Mus musculus

source_name: distal lung

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

value: M

tag: treatment

value: Mac III


title: minus_toxIN_30min_T7_rep2

city: Cambridge

first: Chantal

middle: K

last: Guegler

state: MA

address: 31 Ames Street

department: Biology

institute: MIT

data_processing:
Paired-end reads mapped to MG1655 and T7 genomes using bowtie2 with default settings. Any adapter sequences were removed prior to mapping.
For each uniquely mapped fragment, at all aligned positions a count was added (fragment density mapping).
For each uniquely mapped fragment, a count was added to the middle of each fragment (middle fragment mapping).
Counts were depth normalized to a pseudo-reference sample calculated from all samples (fragment density mapping) or by rpkm in each individual sample (middle fragment mapping).
Counts at all positions were log2 transformed and a cleavage ratio was calculated (+ toxIN: - toxIN) for assessing ToxN cleavage in transcripts; this analysis was conducted separately for the E. coli and T7 transcriptomes.
Genome_build: NCBI reference sequence: NC_000913.2 (E. coli); V01146.1 (T4)
Supplementary_files_format_and_content: t7_phage_cleavageratio.csv.gz is a log-transformed list of sequencing depth-normalized counts for the T7 genome for every genomic position at both strands for each sample as well as the average cleavage ratio for each timepoint calculated from both replicates.
Supplementary_files_format_and_content: t7_host_cleavageratio.csv.gz is a log-transformed list of sequencing depth-normalized counts for the E. coli genome for every genomic position at both strands for each sample as well as the average cleavage ratio for each timepoint calculated from both replicates.
Supplementary_files_format_and_content: t7_ERCCspikein_sum.csv.gz is the list of the sum of raw counts for the ERCC spike-in controls for each sample.
Supplementary_files_format_and_content: t7_phage_rpkm.csv.gz is the list of the rpkm per T7 mRNA for every sample at every timepoint calculated from both replicates.
Supplementary_files_format_and_content: t7_host_rpkm.csv.gz is the list of the rpkm per E. coli CDS for every sample at every timepoint calculated from both replicates.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Bacterial liquid culture

growth_protocol: Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM.

extract_protocol:
RNA was extracted using two rounds of hot acid-phenol extraction at 67°C, followed by one round of hot acid-phenol-chloroform extraction at 67°C, followed by isopropanol precipitation.
See publication for complete protocol. Briefly, samples were treated with a custom rRNA depletion kit. Next, RNA was fragmented with RNA fragmentation reagents (Ambion). First strand cDNA synthesis was conducted using random primers and Superscript III (Invitrogen). To enable strand specificity, second strand synthesis was conducted using dUTP instead of dTTP with RNase H, E. coli DNA ligase, and E. coli DNA polymerase. Ends were repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. 3’ ends were adenylated with the Klenow fragment (3’>5’ exo-). Y-shaped adapters were ligated and 9-12 cycles of PCR were conducted with standard Illumina primers with multiplexing indexes. Libraries were extracted from an acrylamide gel and submitted for sequencing at the MIT BioMicro Center using standard Illumina protocols.

treatment_protocol: Cultures were back-diluted to OD600 = 0.2 and grown at 30 °C for 30 min before being infected with T7 at MOI = 5. At each timepoint post-infection, 500 μL infected cells was mixed with 500 μL lysis buffer (SDS 2%, 4 mM EDTA pH = 8) and boiled at 100 °C for 5 min before being flash-frozen.

tag: phage

tag: plasmid

value: pBR322 empty vector

tag: time post-infection

tag: ercc standard

value: Prior to extraction


title: s4A.TL1H3.Cy5

type: RNA

city: Urbana

first: Eunsoo

last: Choe

state: Illinois

address: s-306 Turner hall 1102 S. Goodwin Ave.

institute: USDA-ARS

description:
biological replication 1 of 4
raw data in Cy5 channel of 10004_A.gpr

hyb_protocol: Samples were hybridized to custom designed Agilent maize 4x44k array.

scan_protocol: Axon 4000B microarray scanner (Molecular Devices, Sunnyvale, CA) at 5 μm resolution. Spotfinding was carried out using GenePix 6.1 image analysis software (Molecular Devices, Sunnyvale, CA).

data_processing: R (R Development Core Team, 2014) (v 3.1.0) using the Limma package (v 3.20.1) were used for data processing. Median foreground values from the 16 arrays were read into R, and any spots that had been manually flagged (-100 values) were given a weight of zero (Smyth and Speed, 2003). The individual Cy5 and Cy3 values were all normalized together using the quantile method and then log2-transformed. The mixed effects statistical model were used and accounted for dye as fixed, array as random and labeling efficiency as a covariate. The expression values from the probes were compared with the positive and negative controls and selected based on expression values > 6.25 on the log2 scale in at least 4 samples out of 32 samples.

organism: Zea mays

source_name: DMC21-84 planted in Vegetable Farm at High plant density

label_protocol: Seventy-five ng of total RNA was labeled using the Agilent 2-color Low Input Quickamp Whole Transcriptome Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's protocols.

growth_protocol: Two shrunken2 (sh2) sweet corn hybrids, GSS2259P and DMC21-84, were planted in two environments, Vegetable Farm and Fruit Farm, at the University of Illinois Crop Sciences Research and Education Center, Urbana, IL.

extract_protocol: Total RNA was extracted using RNeasy mini kit (Qiagen, Hilden, North Rhine-Westphalia, Germany).

treatment_protocol: Each environment received two plant density treatments with 4 replications, which were targeted at low (51,500 plants ha-1) and high (96,100 plants ha-1) densities

tag: environment

value: Vegetable Farm

tag: hybrid

tag: density

value: High

tag: tissue

value: leaf at R1


title: genomic DNA from cultured airway epithelial cells (basal cells) [4d6c_4f66-1B]

type: genomic

city: Chicago

first: Carole

last: Ober

state: IL

address: 920 E 58TH ST

department: Human Genetics

institute: The University of Chicago

description:
200517480051_R02C01
4d6c_4f66-1B

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using standard Illumina scanner settings

data_processing:
Probes located on the sex chromosomes and those with detection P values > 0.01 in 90% of samples were removed. Probes mapping to more than one genomic location or overlapping with known SNPs (MAF>5% in either African Americans or European Americans) were also excluded. Data were processed using Minfi; Infinium type I and type II probe bias were corrected using SWAN. Raw probe values were corrected for color imbalance and background by control normalization.
normalized data: Average Beta

label: cy3, cy5

source_name: Cultred airway epithelial cells

label_protocol: Standard Illumina protocol.

value: RV

tag: crs

value: nonCRS

tag: asthma

tag: steroid

tag: smoking

value: Current

tag: gender

value: Female

tag: ethnicity

value: White

tag: age

tag: array


title: genomic DNA from cultured airway epithelial cells (basal cells) [dbb7_449f-2A]

description:
200526210023_R02C01
dbb7_449f-2A

tag: treatment

value: vehicle

value: CRS

value: Prior

value: Male


title: minus_toxIN_5min_T7_rep2

tag: strain

tag: phage


title: minus_toxIN_2.5min_T7_rep2

tag: plasmid

tag: time post-infection


title: M_P7_hyperoxia_CD45_2_DC35_I21

tag: sequencing run

tag: plate

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype

value: T cell

tag: mousename

tag: coverage

tag: number of genes


title: minus_toxIN_0min_T7_rep2

value: pBR322 empty vector

tag: ercc standard


title: HCT116 control CDT1 Replicate 1 (ChIPSeq)

description:
HCT116 no treatment CDT1 ChipSeq
HCT116 control CDT1-1

value: Cultured cancer cell line

tag: chip antibody

value: CDT1 antibody (Cell Signaling, 8064)

tag: molecule subtype

value: ChipSeq DNA


title: genomic DNA from cultured airway epithelial cells (basal cells) [0367_4a9f-2A]

description:
200526210060_R03C01
0367_4a9f-2A

tag: treatment

tag: crs

tag: asthma

value: No

tag: steroid

tag: smoking

tag: gender

tag: ethnicity

tag: age

tag: array


title: genomic DNA from cultured airway epithelial cells (basal cells) [dbb7_449f-1A]

description:
200526210024_R08C01
dbb7_449f-1A

value: RV


title: HCT116 input for HCT116 re-replication CDT1 and p139-MCM2-1&2 (input DNA)

description:
HCT116 36h MLN4924-treated CDT1 ChipSeq input
HCT116 re-replication input

tag: strain

tag: cell type

value: input DNA


title: HCT116 input for HCT116 control CDT1 and p139-MCM2-1&2 (input DNA)

description:
HCT116 no treatment  CDT1 ChipSeq input
HCT116 control input


title: genomic DNA from cultured airway epithelial cells (basal cells) [0367_4a9f-1A]

description:
200526210023_R05C01
0367_4a9f-1A

value: nonCRS


title: genomic DNA from cultured airway epithelial cells (basal cells) [46b9_452a-2A]

description:
200514040052_R04C01
46b9_452a-2A


title: M_P7_hyperoxia_CD45_2_DC35_D15

tag: sequencing run

value: M

tag: plate

tag: well

tag: timepoint

tag: cell subtype

value: DC II

tag: mousename


title: minus_toxIN_30min_T7_rep1

tag: phage

tag: plasmid

tag: time post-infection

tag: ercc standard

value: Prior to extraction


title: HCT116 MS CDT1 Replicate 1 (ChIPSeq)

description:
HCT116 MS (mid S phase) cells CDT1 ChipSeq
HCT116 MS CDT1-1

tag: chip antibody

tag: molecule subtype


title: minus_toxIN_10min_T7_rep2


title: M_P7_hyperoxia_CD45_2_DC35_N4

tag: gender

tag: treatment

value: neutrophil

tag: coverage

tag: number of genes


title: minus_toxIN_10min_T7_rep1

tag: strain


title: genomic DNA from cultured airway epithelial cells (basal cells) [48c7_4117-1A]

description:
200514030130_R02C01
48c7_4117-1A

tag: crs

tag: asthma

tag: steroid

tag: smoking

value: Current

tag: ethnicity

value: White

tag: age

tag: array


title: genomic DNA from cultured airway epithelial cells (basal cells) [46b9_452a-1A]

description:
200514030034_R02C01
46b9_452a-1A

value: Prior

value: Male


title: M_P7_hyperoxia_CD45_1_DC35_I20

tag: sequencing run

tag: plate

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

value: immune

tag: cell subtype

tag: mousename


title: genomic DNA from cultured airway epithelial cells (basal cells) [9523_4465-2A]

description:
200514030156_R01C01
9523_4465-2A

tag: treatment

value: vehicle

value: Never

tag: gender

value: Female

value: Black


title: M_P7_hyperoxia_CD45_2_DC35_K17

tag: coverage

tag: number of genes


title: M_P7_hyperoxia_CD45_2_DC35_I13

value: T cell


title: minus_toxIN_5min_T7_rep1

tag: strain

tag: phage

tag: plasmid

value: pBR322 empty vector

tag: time post-infection

tag: ercc standard


title: HCT116 G1 CDT1 Replicate 2 (ChIPSeq)

description:
HCT116 G1 phase cells CDT1 ChipSeq
HCT116 G1 CDT1-2

value: Cultured cancer cell line

tag: chip antibody

value: CDT1 antibody (Cell Signaling, 8064)

tag: molecule subtype

value: ChipSeq DNA


title: minus_toxIN_2.5min_T7_rep1

value: Prior to extraction


title: HCT116 G1 CDT1 Replicate 1 (ChIPSeq)

description:
HCT116 G1 phase cells CDT1 ChipSeq
HCT116 G1 CDT1-1


title: HCT116 MS input for HCT116 MS CDT1 (input DNA)

description:
HCT116 MS (mid S phase) cells ChipSeq input
HCT116 MS input

value: input DNA


title: minus_toxIN_0min_T7_rep1


title: M_P7_hyperoxia_CD45_1_DC35_L3

tag: sequencing run

value: M

tag: plate

value: Mac V


title: F_P7_hyperoxia_CD45_2_DC35_L17

value: F

tag: well

tag: timepoint

value: Mac III


title: genomic DNA from cultured airway epithelial cells (basal cells) [9523_4465-1A]

description:
200512330148_R07C01
9523_4465-1A

value: RV

tag: crs

value: nonCRS

tag: asthma

value: No

tag: steroid

tag: smoking

tag: ethnicity

tag: age

tag: array


title: genomic DNA from cultured airway epithelial cells (basal cells) [715b_499f-2A]

description:
200514030130_R05C01
715b_499f-2A

tag: treatment

value: vehicle

value: CRS

value: Inhaled

value: Prior

tag: gender

value: Male

value: White


title: HCT116 G1 input for HCT116 G1 CDT1 (input DNA)

description:
HCT116 G1 phase cells ChipSeq input
HCT116 G1 input

tag: strain

tag: cell type

value: Cultured cancer cell line


title: HCT116 MS CDT1 Replicate 2 (ChIPSeq)

description:
HCT116 MS (mid S phase) cells CDT1 ChipSeq
HCT116 MS CDT1-2

tag: chip antibody

value: CDT1 antibody (Cell Signaling, 8064)

value: ChipSeq DNA


title: M_P7_hyperoxia_CD45_2_DC35_H19

value: hyperoxia

value: immune

tag: cell subtype

value: T cell

tag: mousename

tag: coverage

tag: number of genes


title: minus_toxIN_20min_T7_rep1

tag: phage

tag: plasmid

value: pBR322 empty vector

tag: time post-infection

tag: ercc standard

value: Prior to extraction


title: M_P7_hyperoxia_CD45_1_DC35_H11

tag: sequencing run

value: M

tag: plate

tag: well

tag: timepoint

value: neutrophil


title: M_P7_hyperoxia_CD45_1_DC35_L6

tag: treatment

value: Mac III


title: genomic DNA from cultured airway epithelial cells (basal cells) [c99c_403c-2B]

description:
200517480194_R08C01
c99c_403c-2B

value: vehicle

tag: crs

value: nonCRS

tag: asthma

value: No

tag: steroid

tag: smoking

value: Never

tag: gender

value: Female

tag: ethnicity

tag: age

tag: array


title: plus_toxIN_30min_T7_rep2

tag: strain

tag: phage


title: plus_toxIN_10min_T7_rep2

tag: plasmid

tag: time post-infection


title: Ileum2_1

city: Heidelberg

first: Sergio

last: Triana

address: Meyerhofstr. 1

department: Structural and Computational biology

country: Germany

institute: EMBL

description: 10x V2

data_processing:
Raw sequencing data was processed using the CellRanger software (version 3.1.0). Reads were aligned to a custom reference genome created with the reference human genome (GRCh38) and SARS-CoV-2 reference genome (NC_045512.2).
Genome_build: Homo Sapiens hg38 + Astrovirus reference genome (NC_001943.1)+C45
Supplementary_files_format_and_content: raw count matrix generated by Cell Ranger count (.H5)

molecule: polyA RNA

source_name: Ileum Biopsie

growth_protocol: Stem cells containing crypts were isolated following 2 mM EDTA dissociation of tissue sample for 1 h at 4C. Crypts were spun and washed in ice cold PBS. Fractions enriched in crypts were filtered with 70 uM filters and the fractions were observed under a light microscope. Fractions containing the highest number of crypts were pooled and spun again. The supernatant was removed, and crypts were re-suspended in Matrigel. Crypts were passaged and maintained in basal and differentiation culture media

extract_protocol:
Organoids were harvested after 0 (mock), 4 and 16 hours post-infection were washed in cold PBS and incubated in TrypLE Express for 25 min at 37°C. When microscopic examination revealed that cells had reached a single cell state, they were resuspended in DMEM/F12 and spun at 500 xg for 5 mins. Supernatant was removed and the cell pellet was resuspended in PBS supplemented with 0.04% BSA and passed through a 40-μm cell strainer.
For scRNAseq - Single-cell suspensions were loaded onto the 10x Chromium controller using the 10x Genomics Single Cell 3’ Library Kit NextGem (10x Genomics) according to the manufacturer’s instructions.

treatment_protocol: Media was removed from cells and 106 pfu of SARS-CoV-2 (as determined in Vero cells) was added to cells for 1 hour at 37°C. Virus was removed, cells were washed 1x with PBS and media was added back to the cells.

value: Mock

tag: Sex


title: Ileum2_2

description: 10x V2


title: genomic DNA from cultured airway epithelial cells (basal cells) [c99c_403c-1B]

description:
200517480052_R07C01
c99c_403c-1B

value: RV

value: White


title: M_P7_hyperoxia_CD45_2_DC35_M13

tag: sequencing run

tag: plate

tag: cell type

tag: cell subtype

tag: mousename

tag: coverage

tag: number of genes


title: genomic DNA from cultured airway epithelial cells (basal cells) [5870_4405-2A]

description:
200514040156_R07C01
5870_4405-2A

tag: treatment

tag: crs

value: CRS

tag: asthma

tag: steroid

tag: smoking


title: plus_toxIN_5min_T7_rep2

tag: strain

tag: ercc standard


title: Ileum1_1

description: 10x V2

tag: age


title: genomic DNA from cultured airway epithelial cells (basal cells) [5870_4405-1A]

description:
200526210023_R08C01
5870_4405-1A

tag: gender

tag: ethnicity

tag: array


title: M_P7_hyperoxia_CD45_1_DC35_I15

tag: sequencing run

tag: plate

tag: well

tag: timepoint

value: hyperoxia

value: Mac IV


title: Rev_16h

description: 10x V3.1

source_name: Ileum Organoids

tag: Sex


title: plus_toxIN_2.5min_T7_rep2

tag: phage

tag: plasmid

tag: time post-infection


title: genomic DNA from cultured airway epithelial cells (basal cells) [ea4f_40cf-2A]

description:
200517480189_R02C01
ea4f_40cf-2A

tag: treatment

tag: crs

tag: asthma

value: Current


title: M_P7_hyperoxia_CD45_2_DC35_C1

tag: cell type

value: immune

tag: cell subtype

tag: mousename

tag: coverage

tag: number of genes


title: plus_toxIN_0min_T7_rep2

tag: strain

tag: ercc standard

value: Prior to extraction


title: Rev_M

description: 10x V3.1


title: genomic DNA from cultured airway epithelial cells (basal cells) [715b_499f-1A]

description:
200526210086_R06C01
715b_499f-1A

tag: steroid

value: Inhaled

tag: smoking

value: Prior

tag: gender

value: Male

tag: ethnicity

tag: age

tag: array


title: M_P7_hyperoxia_CD45_1_DC35_O21

tag: sequencing run

value: M

tag: plate

tag: well

tag: timepoint

value: DC I


title: genomic DNA from cultured airway epithelial cells (basal cells) [ea4f_40cf-1A]

description:
200526210092_R01C01
ea4f_40cf-1A

tag: treatment

tag: crs

value: nonCRS

tag: asthma

value: No


title: plus_toxIN_30min_T7_rep1

tag: phage

tag: plasmid

tag: time post-infection


title: Rev_4h

description: 10x V3.1

tag: Sex

value: Female


title: M_P7_hyperoxia_CD45_1_DC35_O9

tag: cell type

tag: cell subtype

value: basophil

tag: mousename

tag: coverage

tag: number of genes


title: plus_toxIN_20min_T7_rep2

tag: strain

tag: ercc standard


title: plus_toxIN_20min_T7_rep1


title: H4_Live2

description: 10x V2

value: Mock


title: Ileum1_2

description: 10x V2

tag: age


title: genomic DNA from cultured airway epithelial cells (basal cells) [90d6_4bfa-2A]

description:
200516380117_R05C01
90d6_4bfa-2A

value: vehicle

tag: steroid

tag: smoking

tag: gender

tag: ethnicity

value: White

tag: array


title: genomic DNA from cultured airway epithelial cells (basal cells) [90d6_4bfa-1A]

description:
200517480083_R07C01
90d6_4bfa-1A

tag: treatment

value: RV

tag: crs

value: CRS

tag: asthma


title: M_P7_hyperoxia_CD45_2_DC35_F2

tag: sequencing run

tag: plate

tag: well

tag: timepoint

value: hyperoxia

value: mast cell


title: Ns_NMock_2

description: 10x V2

tag: Sex


title: genomic DNA from cultured airway epithelial cells (basal cells) [4386_480f-2B]

description:
200514030130_R08C01
4386_480f-2B

value: Current


title: plus_toxIN_10min_T7_rep1

tag: phage

tag: plasmid

tag: time post-infection

value: Prior to extraction


title: plus_toxIN_5min_T7_rep1

tag: strain

tag: ercc standard


title: Ns_NMock_1

description: 10x V2


title: F_P7_hyperoxia_CD45_2_DC35_A15

value: F

tag: cell type

value: immune

tag: cell subtype

value: T cell

tag: mousename

tag: coverage

tag: number of genes


title: genomic DNA from cultured airway epithelial cells (basal cells) [4386_480f-1B]

description:
200514030156_R04C01
4386_480f-1B

tag: treatment

tag: crs

tag: steroid

tag: smoking

tag: gender

value: Male

tag: ethnicity

tag: age

tag: array


title: plus_toxIN_2.5min_T7_rep1

tag: phage

tag: plasmid


title: plus_toxIN_0min_T7_rep1

tag: strain

tag: time post-infection


title: genomic DNA from cultured airway epithelial cells (basal cells) [0c5c_49aa-2B]

description:
200526210023_R07C01
0c5c_49aa-2B

value: nonCRS

tag: asthma

value: Inhaled

value: Never


title: Ns_4h

description: 10x V2

value: 4h post infection

tag: Sex

value: Female


title: M_P7_hyperoxia_CD45_2_DC35_I22

tag: sequencing run

value: M

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

value: B cell

tag: mousename


title: genomic DNA from cultured airway epithelial cells (basal cells) [0c5c_49aa-1B]

description:
200517480108_R03C01
0c5c_49aa-1B

tag: treatment

value: RV

tag: crs

tag: steroid

tag: smoking

tag: gender

value: White


title: Ns_16h

description: 10x V2


title: genomic DNA from cultured airway epithelial cells (basal cells) [7d25_4c19-2A]

description:
200514030067_R03C01
7d25_4c19-2A

value: vehicle

value: CRS

value: No

value: Prior

tag: ethnicity

tag: age

tag: array


title: Sort_16h

description: 10x V2

value: 16h post infection


title: F_P7_hyperoxia_CD45_2_DC35_H16

value: F

value: hyperoxia

value: immune

value: neutrophil

tag: coverage

tag: number of genes


title: F_P7_hyperoxia_CD45_2_DC35_M16

tag: sequencing run

value: mast cell II


title: genomic DNA from cultured airway epithelial cells (basal cells) [7d25_4c19-1A]

description:
200516380119_R02C01
7d25_4c19-1A

tag: asthma

value: Male


title: Sort_Mock

description: 10x V2

value: Mock

tag: Sex


title: M_P7_hyperoxia_CD45_1_DC35_G16

tag: plate

tag: well

tag: timepoint

value: Mac IV


title: F_P7_hyperoxia_CD45_2_DC35_E11

tag: cell type

tag: cell subtype

value: Mac III

tag: mousename


title: minus_toxIN_10min_T4_rep2

data_processing:
Paired-end reads mapped to MG1655 and T4 genomes using bowtie2 with default settings. Any adapter sequences were removed prior to mapping.
For each uniquely mapped fragment, at all aligned positions a count was added (fragment density mapping).
For each uniquely mapped fragment, a count was added to the middle of each fragment (middle fragment mapping).
Counts were depth normalized to a pseudo-reference sample calculated from all samples (fragment density mapping) or by rpkm in each individual sample (middle fragment mapping).
Counts at all positions were log2 transformed and a cleavage ratio was calculated (+ toxIN: - toxIN) for assessing ToxN cleavage in transcripts; this analysis was conducted separately for the E. coli and T4 transcriptomes.
Genome_build: NCBI reference sequence: NC_000913.2 (E. coli); NC_000866.4 (T4)
Supplementary_files_format_and_content: t4_phage_cleavageratio.csv.gz is a log-transformed list of sequencing depth-normalized counts for the T4 genome for every genomic position at both strands for each sample as well as the average cleavage ratio for each timepoint calculated from both replicates.
Supplementary_files_format_and_content: t4_host_cleavageratio.csv.gz is a log-transformed list of sequencing depth-normalized counts for the E. coli genome for every genomic position at both strands for each sample as well as the average cleavage ratio for each timepoint calculated from both replicates.
Supplementary_files_format_and_content: t4_ERCCspikein_sum.csv.gz is the list of the sum of raw counts for the ERCC spike-in controls for each sample. Note that we only included spike-in standards in one replicate each of + toxIN and - toxIN sequencing samples.
Supplementary_files_format_and_content: t4_phage_rpkm.csv.gz is the list of the rpkm per T4 CDS for every sample at every timepoint calculated from both replicates.
Supplementary_files_format_and_content: t4_host_rpkm.csv.gz is the list of the rpkm per E. coli CDS for every sample at every timepoint calculated from both replicates.

extract_protocol:
RNA was extracted using two rounds of hot acid-phenol extraction at 67°C, followed by one round of hot acid-phenol-chloroform extraction at 67°C, followed by isopropanol precipitation.
See publication for complete protocol. Briefly, samples were treated with bacterial Ribo-Zero kit (Illumina) or MicrobEXPRESS (ThermoFisher). Next, RNA was fragmented with RNA fragmentation reagents (Ambion). First strand cDNA synthesis was conducted using random primers and Superscript III (Invitrogen). To enable strand specificity, second strand synthesis was conducted using dUTP instead of dTTP with RNase H, E. coli DNA ligase, and E. coli DNA polymerase. Ends were repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. 3’ ends were adenylated with the Klenow fragment (3’>5’ exo-). Y-shaped adapters were ligated and 9-12 cycles of PCR were conducted with standard Illumina primers with multiplexing indexes. Libraries were extracted from an acrylamide gel and submitted for sequencing at the MIT BioMicro Center using standard Illumina protocols.

treatment_protocol: Cultures were back-diluted to OD600 = 0.2 and grown at 30 °C for 30 min before being infected with T4 at MOI = 5. At each timepoint post-infection, 500 μL infected cells was mixed with 500 μL lysis buffer (SDS 2%, 4 mM EDTA pH = 8) and boiled at 100 °C for 5 min before being flash-frozen.

tag: strain

tag: phage

tag: plasmid

value: pBR322 empty vector

tag: time post-infection

tag: ercc standard

value: Prior to extraction


title: minus_toxIN_20min_T4_rep2


title: Ns_Mock

description: 10x V2

tag: treatment

value: Female


title: genomic DNA from cultured airway epithelial cells (basal cells) [5d59_4148-2B]

description:
200516380203_R05C01
5d59_4148-2B

value: vehicle

tag: crs

value: nonCRS

tag: steroid

tag: smoking

tag: gender

tag: ethnicity

value: White

tag: age

tag: array


title: N_16h_2

description: 10x V2

tag: Sex


title: minus_toxIN_5min_T4_rep2


title: M_P7_hyperoxia_CD45_1_DC35_J22

tag: sequencing run

value: M

tag: plate

tag: well

tag: timepoint

tag: cell type

value: DC II

tag: coverage

tag: number of genes


title: minus_toxIN_2.5min_T4_rep2

tag: strain

tag: phage

tag: plasmid

tag: time post-infection

tag: ercc standard


title: genomic DNA from cultured airway epithelial cells (basal cells) [5d59_4148-1B]

description:
200516380203_R04C01
5d59_4148-1B

tag: treatment

value: RV

tag: crs

tag: asthma

value: No

tag: steroid

tag: smoking

value: Prior

tag: gender


title: N_16h_1

description: 10x V2

value: 16h post infection

tag: Sex


title: M_P7_hyperoxia_CD45_1_DC35_E23

tag: sequencing run

tag: plate

tag: well

value: hyperoxia

value: immune

tag: cell subtype

value: neutrophil

tag: mousename


title: minus_toxIN_0min_T4_rep2

tag: strain


title: F_P7_hyperoxia_CD45_2_DC35_H22

value: F

tag: timepoint

tag: cell type

value: Mac IV

tag: coverage

tag: number of genes


title: genomic DNA from cultured airway epithelial cells (basal cells) [7e0a_42d5-2B]

description:
200517480189_R01C01
7e0a_42d5-2B

tag: treatment

value: Never

tag: ethnicity

tag: age

tag: array


title: N_4h

description: 10x V2

value: 4h post infection


title: minus_toxIN_30min_T4_rep2

tag: phage

tag: plasmid

value: pBR322 empty vector

tag: time post-infection

tag: ercc standard

value: Prior to extraction


title: M_P7_hyperoxia_CD45_2_DC35_P10

tag: sequencing run

tag: gender

tag: plate


title: genomic DNA from cultured airway epithelial cells (basal cells) [7e0a_42d5-1B]

description:
200517480011_R01C01
7e0a_42d5-1B

tag: crs

value: nonCRS

tag: asthma

tag: steroid

tag: smoking

value: Female


title: plus_toxIN_30min_T4_rep2

tag: strain


title: N_Mock

description: 10x V2

value: Mock

tag: Sex


title: M_P7_hyperoxia_CD45_1_DC35_K5

value: M

tag: well

tag: timepoint

tag: treatment

tag: cell type

tag: cell subtype

value: Mac III

tag: mousename

tag: coverage

tag: number of genes


title: genomic DNA from cultured airway epithelial cells (basal cells) [4f45_4710-2A]

description:
200517480189_R08C01
4f45_4710-2A

value: vehicle

value: No

value: Male

tag: ethnicity

tag: age

tag: array


title: plus_toxIN_20min_T4_rep2

tag: phage

tag: plasmid

tag: time post-infection

tag: ercc standard


title: F_P7_hyperoxia_CD45_2_DC35_L16

tag: sequencing run

tag: gender

tag: plate

value: hyperoxia

value: T cell


title: Subject 25

city: Philadelphia

first: Ryan

last: Tomlinson

state: PA

address: 1015 Walnut Street

department: Orthopaedic Surgery

institute: Thomas Jefferson University

data_processing:
Raw FASTQ sequencing reads were mapped against the reference genome of Homo sapiens Ensembl version GRCh38 utilizing further information from the gene transfer format (.gtf) annotation from GENCODE version GRCh38.p12 using STAR aligner utilized through RSEM.
Total read counts were obtained using RSEM’s calculate-expression function.
Genome_build: GRCh38
Supplementary_files_format_and_content: Comma-delimited text files for each sample include raw counts for each gene

source_name: Palmar Fascia Tissue

extract_protocol:
Tissue was harvested, placed in RNAlater, and RNA was harvested using Qiagen RNeasy (74104).
Takara Bio SMARTer Stranded Total RNA-Seq Kit (#634837)  was used to prepare libraries using 4 ng of total RNA, following the manufacturer’s protocol.

tag: disease status

value: Control

tag: tissue

value: Palmar Fascia


title: plus_toxIN_10min_T4_rep2

tag: strain


title: Subject 23


title: genomic DNA from cultured airway epithelial cells (basal cells) [4f45_4710-1A]

description:
200517480083_R02C01
4f45_4710-1A

tag: treatment

value: RV

tag: crs

tag: asthma

tag: steroid

tag: smoking


title: Subject 22


title: M_P7_hyperoxia_CD45_1_DC35_D19

tag: well

tag: timepoint

tag: cell type

value: immune

tag: cell subtype

value: Mac II

tag: mousename

tag: coverage

tag: number of genes


title: plus_toxIN_5min_T4_rep2

tag: phage

tag: plasmid

tag: time post-infection

tag: ercc standard


title: plus_toxIN_0min_T4_rep2

tag: strain


title: plus_toxIN_2.5min_T4_rep2


title: Subject 16

tag: disease status

value: Dupuytren's

tag: tissue


title: Subject 13


title: M_P7_hyperoxia_CD45_1_DC35_E19

tag: sequencing run

tag: gender

tag: plate

tag: treatment

value: B cell


title: genomic DNA from cultured airway epithelial cells (basal cells) [668e_48d6-2B]

description:
200514030130_R04C01
668e_48d6-2B

tag: crs

value: CRS

tag: asthma

tag: steroid

value: Inhaled

tag: smoking

value: Current

tag: ethnicity

value: White

tag: age

tag: array


title: genomic DNA from cultured airway epithelial cells (basal cells) [668e_48d6-1B]

description:
200514040156_R03C01
668e_48d6-1B

value: Female


title: M_P7_hyperoxia_CD45_1_DC35_F6

value: M

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

value: mast cell

tag: mousename

tag: coverage

tag: number of genes


title: Subject 12

tag: disease status

tag: tissue


title: genomic DNA from cultured airway epithelial cells (basal cells) [5795_46b9-2A]

description:
200514040156_R08C01
5795_46b9-2A

tag: treatment

value: vehicle

value: Never

tag: gender

value: Asian


title: minus_toxIN_20min_T4_rep1

tag: strain

tag: phage

tag: plasmid

value: pBR322 empty vector

tag: time post-infection

tag: ercc standard

value: No


title: Subject 05

value: Palmar Fascia


title: M_P7_hyperoxia_CD45_1_DC35_P15

tag: sequencing run

tag: plate

value: hyperoxia

value: immune

value: Mac III


title: genomic DNA from cultured airway epithelial cells (basal cells) [5795_46b9-1A]

description:
200516380096_R02C01
5795_46b9-1A

value: RV

tag: crs

tag: asthma

tag: steroid

tag: smoking

tag: ethnicity

tag: age

tag: array


title: minus_toxIN_10min_T4_rep1


title: Valproic_acid_IC5-8

city: Bilthoven

first: Victoria

middle: C

last: de Leeuw

address: PO box 1

country: Netherlands

institute: National Institute for Public Health and the Environment

description:
Valproic_acid_IC5-8_S14
counttable.txt

data_processing:
Sequencing was performed on the NextSeq 500 sequencer (Illumina) using the NextSeq 500/550 High Output Kit version 2.5 (75 cycles).
Raw bcl files were base called and demultiplexed into FASTQ files with Bcl2fastq (Illumina, version 2.20.0.422).
Quality control reports (FastQC, version 0.11.8) were generated using MultiQC (version 1.0).
Transcripts were quantified using Salmon (version 1.3.0).
Transcript level information was summarized into genes using tximport (version 1.16.1).
Normalized gene counts were generated using DESeq2 (version 1.30.0).
Genome_build: Human transcriptome (GRCh38, version 30, Ensembl 96).
Supplementary_files_format_and_content: counttable.txt: Count matrix containing normalized gene counts.

source_name: Neuronal-astrocyte co-culture

growth_protocol: For each experiment, NPCs were thawed and maintained according to the neuronal induction protocol from Stemcell (Document #28782, Stemcell Technologies). Briefly, cells were kept in a humidified chamber (37 °C, 5% CO2, 3% O2) in STEMdiff™ Neural Progenitor (NP) medium (Stemcell) on Poly-L-Ornithine (PLO, 15 µg/mL, Sigma-Aldrich, Saint Louis, MO, USA) - laminin (10 µg/mL, Sigma-Aldrich) coated 6-well plates (Corning, New York, NY, USA). Culture medium was refreshed daily for a week until the NPCs were confluent. For neuron-astrocyte generation, NPCs were dissociated and seeded at 2.56 × 10^5 cells/cm2 on PLO-laminin-coated 8-well micro-slides (Ibidi), 12 or 24-well plates (Corning). Cells were kept for one day in NP medium, after which they were switched to differentiation medium consisting of neurobasal medium, 10 µl/mL N2 supplement, 20 µl/mL B-27-retinoic acid supplement, 10 µl/mL 5000 IU/mL Penicillin / 5000 µg/mL Streptomycin, 10 µl/mL nonessential amino acids, 20 ng/mL glial cell line-derived neurotrophic factor and 20 ng/mL brain-derived neurotrophic factor (all from Gibco), 1 μM dibutyryl cyclic adenosine monophosphate (Sigma-Aldrich), 200 μM ascorbic acid (Sigma-Aldrich) and 2 μg/mL laminin (Sigma-Aldrich). Ciliary neurotrophic factor (Gibco) was added during the first week of neuron-astrocyte generation at a final concentration of 10 ng/mL. Half of the medium was refreshed every two to three days.

extract_protocol:
Eight samples per condition (all technical replicates from one experiment) were fixated in QIAzol (Qiagen) and stored at -80 °C until further processing. Whole RNA extraction was performed following the manufacturer’s protocol using the RNeasy® mini kit (Qiagen) with a DNase digestion step (Qiagen). RNA concentration was determined using the Qubit3 (Invitrogen) and RNA quality was analyzed using the 2100 Bioanalyzer (Agilent Technologies).
Samples were processed according to the TruSeq Stranded mRNA protocol (Illumina, San Diego, CA, USA). Enrichment of mRNA was done using polyA-affinity purification converting it into a multiplex library of 16 samples.

treatment_protocol: Compounds were freshly prepared for each exposure. Acrylamide (CAS# 79-06-1) and valproic acid sodium (CAS# 1069-66-5) were dissolved in medium, and chlorpyrifos (CAS# 2921-88-2), fluoxetine hydrochloride (CAS# 59333-67-4) and methyl mercury chloride (CAS# 115-09-3) were dissolved in dimethyl sulfoxide (DMSO, CAS# 67-68-5). Final concentrations of DMSO in the medium was 0.25% (v/v).

tag: originating cell line

tag: cell type

value: Neuronal-astrocyte co-culture

tag: time point

value: Day 10

tag: exposure

value: Valproic acid IC5

tag: batch


title: M_P7_hyperoxia_CD45_1_DC35_H17

tag: gender

tag: well

tag: timepoint

tag: treatment

tag: cell subtype

value: Mac IV

tag: mousename

tag: coverage

tag: number of genes


title: genomic DNA from cultured airway epithelial cells (basal cells) [4626_44a4-2B]

description:
200526210060_R01C01
4626_44a4-2B

tag: crs

value: nonCRS

tag: asthma

tag: steroid

tag: smoking

value: Male

value: White


title: M_P7_hyperoxia_CD45_1_DC35_A19

tag: sequencing run

value: M

tag: plate

value: neutrophil


title: genomic DNA from cultured airway epithelial cells (basal cells) [61d3_4bc9-2A]

description:
200517480108_R08C01
61d3_4bc9-2A

value: vehicle

value: CRS

value: Never

tag: ethnicity

value: Hispanic

tag: age

tag: array


title: Valproic_acid_IC5-7

description:
Valproic_acid_IC5-7_S14
counttable.txt

tag: originating cell line

tag: cell type

tag: time point

tag: exposure

tag: batch


title: genomic DNA from cultured airway epithelial cells (basal cells) [4626_44a4-1B]

description:
200512330148_R02C01
4626_44a4-1B

tag: treatment

tag: gender


title: M_P7_hyperoxia_CD45_1_DC35_O3

tag: well

tag: timepoint

value: hyperoxia

tag: cell subtype

value: basophil

tag: mousename

tag: coverage

tag: number of genes


title: minus_toxIN_5min_T4_rep1

tag: strain

tag: phage

tag: plasmid

value: pBR322 empty vector

tag: time post-infection

tag: ercc standard

value: No


title: minus_toxIN_2.5min_T4_rep1


title: M_P7_hyperoxia_CD45_1_DC35_H16

tag: sequencing run

tag: plate

tag: cell type

value: immune

value: Mac II


title: Valproic_acid_IC5-6

description:
Valproic_acid_IC5-6_S13
counttable.txt

tag: originating cell line

value: Neuronal-astrocyte co-culture

tag: time point

value: Day 10

tag: exposure

value: Valproic acid IC5

tag: batch


title: M_P7_hyperoxia_CD45_2_DC35_C2

tag: gender

tag: well

tag: timepoint

tag: treatment


title: minus_toxIN_0min_T4_rep1


title: genomic DNA from cultured airway epithelial cells (basal cells) [0d99_4bd9-2A]

description:
200514030130_R01C01
0d99_4bd9-2A

tag: crs

value: nonCRS

tag: asthma

tag: steroid

tag: smoking

value: Current

value: Female

tag: ethnicity

tag: age

tag: array


title: Valproic_acid_IC5-5

description:
Valproic_acid_IC5-5_S13
counttable.txt


title: minus_toxIN_30min_T4_rep1

tag: strain

tag: phage

tag: plasmid

tag: time post-infection

tag: ercc standard


title: plus_toxIN_30min_T4_rep1


title: F_P7_hyperoxia_CD45_2_DC35_F1

tag: sequencing run

value: F

tag: plate

tag: cell type

tag: cell subtype

value: Mac III

tag: mousename

tag: coverage

tag: number of genes


title: plus_toxIN_20min_T4_rep1


title: genomic DNA from cultured airway epithelial cells (basal cells) [f38e_49f0-2A]

description:
200514030034_R05C01
f38e_49f0-2A

tag: treatment

value: vehicle

tag: crs

tag: asthma

tag: steroid

value: Unknown

value: Prior

tag: gender

value: Male

value: White


title: Valproic_acid_IC5-4

description:
Valproic_acid_IC5-4_S13
counttable.txt

tag: originating cell line

tag: time point

tag: exposure

tag: batch


title: Valproic_acid_IC5-3

description:
Valproic_acid_IC5-3_S13
counttable.txt


title: genomic DNA from cultured airway epithelial cells (basal cells) [f38e_49f0-1A]

description:
200517480052_R02C01
f38e_49f0-1A

value: RV

tag: smoking

tag: ethnicity

tag: age

tag: array


title: F_P7_hyperoxia_CD45_2_DC35_E15

tag: sequencing run

tag: plate

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

tag: cell subtype

value: neutrophil


title: M_P7_hyperoxia_CD45_1_DC35_P2

value: M

tag: treatment

value: immune

value: basophil

tag: mousename

tag: coverage

tag: number of genes


title: plus_toxIN_10min_T4_rep1

tag: strain

tag: phage

tag: plasmid

tag: time post-infection

tag: ercc standard

value: No


title: M_P7_hyperoxia_CD45_2_DC35_C11

tag: gender

value: DC III


title: genomic DNA from cultured airway epithelial cells (basal cells) [0f12_4072-2A]

description:
200514030130_R07C01
0f12_4072-2A

tag: crs

value: CRS

tag: asthma

tag: steroid

tag: smoking

tag: ethnicity

tag: age

tag: array


title: Valproic_acid_IC5-2

description:
Valproic_acid_IC5-2_S13
counttable.txt

tag: originating cell line

tag: cell type

value: Neuronal-astrocyte co-culture

tag: time point

value: Day 10

tag: exposure

value: Valproic acid IC5

tag: batch


title: plus_toxIN_5min_T4_rep1

tag: strain

tag: phage


title: genomic DNA from cultured airway epithelial cells (basal cells) [61d3_4bc9-1A]

description:
200526210086_R07C01
61d3_4bc9-1A

tag: treatment

value: Never

value: Hispanic


title: genomic DNA from cultured airway epithelial cells (basal cells) [0f12_4072-1A]

description:
200516380203_R02C01
0f12_4072-1A

value: Prior


title: plus_toxIN_2.5min_T4_rep1

tag: plasmid

tag: time post-infection

tag: ercc standard


title: Valproic_acid_IC20_100-8

description:
Valproic_acid_IC20_100-8_S15
counttable.txt

value: Valproic acid IC20/100


title: plus_toxIN_0min_T4_rep1


title: M_P7_hyperoxia_CD45_2_DC35_N5

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: cell subtype

value: Mac IV

tag: mousename

tag: coverage

tag: number of genes


title: M_P7_hyperoxia_CD45_2_DC35_C17

tag: cell type

value: Mac III


title: genomic DNA from cultured airway epithelial cells (basal cells) [4451_4efc-2A]

description:
200514030073_R03C01
4451_4efc-2A

value: vehicle

tag: crs

value: nonCRS

tag: asthma

tag: steroid

tag: smoking

value: Female

tag: ethnicity

tag: age

tag: array


title: genomic DNA from cultured airway epithelial cells (basal cells) [4451_4efc-1A]

description:
200517480108_R07C01
4451_4efc-1A

tag: treatment

value: RV


title: genomic DNA from cultured airway epithelial cells (basal cells) [0d99_4bd9-1A]

description:
200517480194_R05C01
0d99_4bd9-1A

value: Current

tag: gender


title: F_P7_hyperoxia_CD45_2_DC35_K9

tag: sequencing run

value: F

tag: plate

value: hyperoxia

value: immune

value: Mac V


title: Valproic_acid_IC20_100-7

description:
Valproic_acid_IC20_100-7_S15
counttable.txt

tag: originating cell line

value: Neuronal-astrocyte co-culture

tag: time point

value: Day 10

tag: exposure

tag: batch


title: Valproic_acid_IC20_100-6

description:
Valproic_acid_IC20_100-6_S15
counttable.txt


title: M_P7_hyperoxia_CD45_1_DC35_M9

value: M

tag: well

tag: timepoint

tag: cell subtype

value: neutrophil

tag: mousename

tag: coverage

tag: number of genes


title: ToxN_10m

data_processing:
Paired-end reads mapped to MG1655 genome using bowtie2 with default settings. Any adapter sequences were removed prior to mapping.
For each uniquely mapped fragment, at all aligned positions a count was added.
Counts were depth normalized to a pseudo-reference sample calculated from all samples.
Counts at all positions were log2 transformed and a cleavage ratio was calculated (+ ToxN - empty vector) for assessing ToxN cleavage in transcripts.
Genome_build: NCBI reference sequence: NC_000913.2
Supplementary_files_format_and_content: toxN_OE_cleavageratio.csv.gz is a log-transformed list of sequencing depth-normalized counts for every genomic position at both strands for each sample as well as the average cleavage ratio calculated from all samples.

growth_protocol: Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM. Cultures were centrifuged, washed, and back diluted into media lacking glucose. After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2%. Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge. Pellets were immediately flash frozen in lN2.

extract_protocol:
RNA was extracted using Trizol (Invitrogen) and Direct-zol RNA MiniPrep kit (Zymo).
See publication for complete protocol. Briefly, samples with rRNA subtraction with treated with bacterial Ribo-Zero kit (Illumina). Next, RNA was fragmented with RNA fragmentation reagents (Ambion). First strand cDNA synthesis was conducted using random primers and Superscript III (Invitrogen). To enable strand specificity, second strand synthesis was conducted using dUTP instead of dTTP with RNase H, E. coli DNA ligase, and E. coli DNA polymerase. Ends were repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. 3’ ends were adenylated with the Klenow fragment (3’>5’ exo-). Y-shaped adapters were ligated and 9-12 cycles of PCR were conducted with standard Illumina primers with multiplexing indexes. Libraries were extracted from an acrylamide gel and submitted for sequencing at the MIT BioMicro Center using standard Illumina protocols.

tag: strain

tag: plasmid

tag: ribozero

value: Yes

tag: ercc spike-in

value: No

tag: time induction

value: 10 minutes


title: Valproic_acid_IC20_100-5

description:
Valproic_acid_IC20_100-5_S15
counttable.txt

tag: cell type

value: Valproic acid IC20/100


title: F_P7_hyperoxia_CD45_2_DC35_K20

tag: sequencing run

tag: gender

tag: plate

tag: treatment

value: Mac II


title: ToxN_5m_withpEXT20-toxI

value: pBAD33-ToxN and pEXT20-toxI

value: 5 minutes


title: emptyvec_10m


title: Valproic_acid_IC20_100-4

description:
Valproic_acid_IC20_100-4_S14
counttable.txt

tag: originating cell line

tag: time point

tag: exposure

tag: batch


title: Valproic_acid_IC5-1

description:
Valproic_acid_IC5-1_S13
counttable.txt

value: Valproic acid IC5


title: F_P7_hyperoxia_CD45_2_DC35_L19

tag: well

tag: timepoint

tag: cell subtype

value: basophil

tag: mousename


title: M_P7_hyperoxia_CD45_2_DC35_B1

value: DC I

tag: coverage

tag: number of genes


title: genomic DNA from cultured airway epithelial cells (basal cells) [32d2_46e9-2A]

description:
200526210092_R05C01
32d2_46e9-2A

value: vehicle

tag: crs

value: CRS

tag: asthma

tag: steroid

tag: smoking

value: Current

value: Male

tag: ethnicity

value: Hispanic

tag: age

tag: array


title: Valproic_acid_IC20_100-3

description:
Valproic_acid_IC20_100-3_S14
counttable.txt

tag: originating cell line

tag: cell type

value: Neuronal-astrocyte co-culture

value: Day 10


title: minus_toxIN_30min_rif_rep2

data_processing:
Paired-end reads mapped to MG1655 genome using bowtie2 with default settings. Any adapter sequences were removed prior to mapping.
For each uniquely mapped fragment, at all aligned positions a count was added (fragment density mapping).
Counts were depth normalized to a pseudo-reference sample calculated from all samples (fragment density mapping).
Counts at all positions were log2 transformed and a cleavage ratio was calculated (+ toxIN: - toxIN) for assessing ToxN cleavage in E. coli transcripts
Genome_build: NCBI reference sequence: NC_000913.2 (E. coli)
Supplementary_files_format_and_content: rif_cleavageratio.csv.gz is a log-transformed list of sequencing depth-normalized counts for every genomic position at both strands for each sample as well as the average cleavage ratio for each timepoint calculated from both replicates.

treatment_protocol: Cultures were back-diluted to OD600 = 0.2 and grown at 30 °C for 30 min before being treated with rifampicin at 300 μg/mL. At each timepoint post-treatment, 500 μL cells was mixed with 500 μL lysis buffer (SDS 2%, 4 mM EDTA pH = 8) and boiled at 100 °C for 5 min before being flash-frozen.

tag: strain

tag: plasmid

value: pBR322 empty vector

tag: time post-addition of rifampicin


title: F_P7_hyperoxia_CD45_2_DC35_A2

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: treatment

value: hyperoxia

value: immune

value: neutrophil


title: Valproic_acid_IC20_100-2

description:
Valproic_acid_IC20_100-2_S14
counttable.txt

tag: time point

tag: exposure

value: Valproic acid IC20/100

tag: batch


title: M_P7_hyperoxia_CD45_2_DC35_E4

value: M

tag: cell subtype

value: Mac III

tag: mousename

tag: coverage

tag: number of genes


title: genomic DNA from cultured airway epithelial cells (basal cells) [32d2_46e9-1A]

description:
200526210086_R03C01
32d2_46e9-1A

value: RV

tag: crs

tag: asthma

value: No

tag: steroid

tag: smoking

tag: ethnicity

tag: age

tag: array


title: Valproic_acid_IC20_100-1

description:
Valproic_acid_IC20_100-1_S14
counttable.txt

tag: originating cell line

tag: cell type


title: M_P7_hyperoxia_CD45_1_DC35_K1

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: treatment


title: genomic DNA from cultured airway epithelial cells (basal cells) [be18_4d66-1A]

description:
200517480202_R01C01
be18_4d66-1A

value: Nasal

value: Prior

value: Female

value: White


title: minus_toxIN_10min_rif_rep2

tag: strain

tag: plasmid

tag: time post-addition of rifampicin


title: genomic DNA from cultured airway epithelial cells (basal cells) [3299_4cc7-2A]

description:
200517480051_R06C01
3299_4cc7-2A

value: vehicle

tag: crs

value: nonCRS

tag: asthma

value: Never


title: MeHg_IC5-8

description:
MeHg_IC5-8_S11
counttable.txt

value: Neuronal-astrocyte co-culture

tag: time point

value: Day 10

tag: exposure

value: Methyl mercury IC5

tag: batch


title: genomic DNA from cultured airway epithelial cells (basal cells) [4f20_48f8-2A]

description:
200516380185_R01C01
4f20_48f8-2A

value: CRS

tag: steroid

tag: smoking

value: Current

tag: ethnicity

value: Hispanic

tag: age

tag: array


title: MeHg_IC5-7

description:
MeHg_IC5-7_S11
counttable.txt

tag: originating cell line

tag: cell type


title: minus_toxIN_20min_rif_rep2

value: pBR322 empty vector


title: genomic DNA from cultured airway epithelial cells (basal cells) [be18_4d66-2A]

description:
200514030067_R08C01
be18_4d66-2A

tag: gender


title: F_P7_hyperoxia_CD45_2_DC35_A12

tag: sequencing run

value: F

tag: plate

tag: well

tag: timepoint

tag: treatment

value: hyperoxia

value: immune

tag: cell subtype

value: Mac III

tag: mousename

tag: coverage

tag: number of genes


title: F_P7_hyperoxia_CD45_2_DC35_P1

value: Mac V


title: genomic DNA from cultured airway epithelial cells (basal cells) [4f20_48f8-1A]

description:
200514030104_R03C01
4f20_48f8-1A

value: RV

tag: crs

tag: asthma

tag: steroid

value: Female


title: genomic DNA from cultured airway epithelial cells (basal cells) [3299_4cc7-1A]

description:
200517480202_R02C01
3299_4cc7-1A

tag: smoking

tag: ethnicity

value: White

tag: age


title: emptyvec_5m_withpEXT20

tag: strain

tag: plasmid

value: pBAD33-empty and pEXT20-empty

tag: ribozero

value: Yes

tag: ercc spike-in

value: No

tag: time induction

value: 5 minutes


title: minus_toxIN_5min_rif_rep2

tag: time post-addition of rifampicin


title: minus_toxIN_2.5min_rif_rep2


title: MeHg_IC5-6

description:
MeHg_IC5-6_S11
counttable.txt

tag: originating cell line

tag: cell type

value: Neuronal-astrocyte co-culture

tag: time point

value: Day 10

tag: exposure

value: Methyl mercury IC5

tag: batch


title: genomic DNA from cultured airway epithelial cells (basal cells) [92af_4cba-2A]

description:
200514040156_R01C01
92af_4cba-2A

tag: treatment

value: vehicle

tag: crs

value: CRS

value: Never

tag: gender

value: Hispanic

tag: array


title: minus_toxIN_0min_rif_rep2

value: pBR322 empty vector


title: minus_toxIN_30min_rif_rep1


title: MeHg_IC5-5

description:
MeHg_IC5-5_S11
counttable.txt


title: genomic DNA from cultured airway epithelial cells (basal cells) [92af_4cba-1A]

description:
200526210092_R08C01
92af_4cba-1A

tag: asthma

tag: steroid

tag: smoking

tag: ethnicity


title: M_P7_hyperoxia_CD45_1_DC35_G21

tag: sequencing run

value: M

tag: plate

tag: well

tag: timepoint

value: hyperoxia

value: immune

tag: cell subtype

value: DC I

tag: mousename

tag: coverage

tag: number of genes


title: F_P7_hyperoxia_CD45_2_DC35_P12

value: F

tag: cell type

value: Mac IV


title: MeHg_IC5-4

description:
MeHg_IC5-4_S10
counttable.txt

tag: originating cell line

tag: time point

tag: exposure

tag: batch


title: minus_toxIN_20min_rif_rep1

tag: strain

tag: plasmid

tag: time post-addition of rifampicin


title: MeHg_IC5-3

description:
MeHg_IC5-3_S10
counttable.txt


title: minus_toxIN_10min_rif_rep1


title: M_P7_hyperoxia_CD45_2_DC35_G15

tag: gender

tag: treatment


title: M_P7_hyperoxia_CD45_1_DC35_K6

tag: sequencing run

tag: plate

value: Mac III


title: genomic DNA from cultured airway epithelial cells (basal cells) [38cc_4577-1A]

description:
200516380096_R01C01
38cc_4577-1A

value: RV

tag: crs

value: nonCRS

tag: asthma

value: No

tag: steroid

tag: smoking

value: Prior

value: Female

tag: ethnicity

tag: age

tag: array


title: genomic DNA from cultured airway epithelial cells (basal cells) [38cc_4577-2A]

description:
200516380117_R01C01
38cc_4577-2A

value: vehicle


title: genomic DNA from cultured airway epithelial cells (basal cells) [77ea_427f-2A]

description:
200526210060_R08C01
77ea_427f-2A

value: CRS

value: Current

value: Male

value: White


title: genomic DNA from cultured airway epithelial cells (basal cells) [77ea_427f-1A]

description:
200516380117_R02C01
77ea_427f-1A


title: minus_toxIN_5min_rif_rep1

value: pBR322 empty vector


title: M_P7_hyperoxia_CD45_2_DC35_N3

value: M

tag: well

tag: timepoint

value: hyperoxia

tag: cell type

tag: cell subtype

tag: mousename

tag: coverage

tag: number of genes


title: minus_toxIN_2.5min_rif_rep1

tag: strain

tag: plasmid

tag: time post-addition of rifampicin


title: M_P7_hyperoxia_CD45_1_DC35_L17

tag: sequencing run

tag: gender

tag: plate

tag: treatment

value: immune

value: neutrophil


title: minus_toxIN_0min_rif_rep1


title: genomic DNA from cultured airway epithelial cells (basal cells) [e82f_4d16-2A]

description:
200514030034_R04C01
e82f_4d16-2A

tag: crs

tag: asthma

tag: steroid

value: Inhaled

tag: smoking

tag: ethnicity

value: Black


title: MeHg_IC5-1

description:
MeHg_IC5-1_S10
counttable.txt

tag: originating cell line

tag: cell type

value: Neuronal-astrocyte co-culture

tag: time point

value: Day 10

tag: exposure

value: Methyl mercury IC5

tag: batch


title: F_P7_hyperoxia_CD45_2_DC35_I1

value: F

tag: well

tag: timepoint

tag: cell subtype

value: Mac V

tag: mousename

tag: coverage

tag: number of genes


title: MeHg_IC5-2

description:
MeHg_IC5-2_S10
counttable.txt


title: F_P7_hyperoxia_CD45_2_DC35_A7

tag: sequencing run

tag: gender

tag: plate

tag: treatment

value: Mac IV


title: genomic DNA from cultured airway epithelial cells (basal cells) [e82f_4d16-1A]

description:
200514040052_R07C01
e82f_4d16-1A

value: RV

tag: crs

value: CRS

tag: asthma

tag: steroid

tag: smoking

value: Prior

tag: age

tag: array


title: genomic DNA from cultured airway epithelial cells (basal cells) [c5cf_4251-2A]

description:
200526210024_R03C01
c5cf_4251-2A

value: vehicle

value: nonCRS

value: No

value: Current

value: Female

tag: ethnicity


title: M_P7_hyperoxia_CD45_1_DC35_E16

value: M

tag: well

value: hyperoxia

tag: cell type

value: immune

value: neutrophil


title: MeHg_IC20_100-7

description:
MeHg_IC20_100-7_S12
counttable.txt

tag: originating cell line

value: Neuronal-astrocyte co-culture

tag: time point

value: Day 10

tag: exposure

value: Methyl mercury IC20/100

tag: batch


title: plus_toxIN_30min_rif_rep2

tag: strain

tag: plasmid

tag: time post-addition of rifampicin


title: plus_toxIN_20min_rif_rep2


title: MeHg_IC20_100-5

description:
MeHg_IC20_100-5_S12
counttable.txt


title: plus_toxIN_10min_rif_rep2


title: F_P7_hyperoxia_CD45_2_DC35_C18

tag: sequencing run

tag: gender

value: F

tag: plate

tag: timepoint

tag: treatment

tag: cell subtype

value: IL cell

tag: mousename

tag: coverage

tag: number of genes


title: MeHg_IC20_100-6

description:
MeHg_IC20_100-6_S12
counttable.txt

tag: cell type


title: genomic DNA from cultured airway epithelial cells (basal cells) [c5cf_4251-1A]

description:
200514030130_R03C01
c5cf_4251-1A

value: RV

tag: crs

tag: asthma

tag: steroid

tag: smoking

tag: ethnicity

value: Black

tag: age

tag: array


title: M_P7_hyperoxia_CD45_1_DC35_A22

tag: sequencing run

tag: well

value: Mac IV


title: genomic DNA from cultured airway epithelial cells (basal cells) [f513_4469-2A]

description:
200517480108_R04C01
f513_4469-2A

value: vehicle

value: CRS

value: Never

tag: gender

value: Male


title: plus_toxIN_2.5min_rif_rep2

tag: strain

tag: plasmid

tag: time post-addition of rifampicin


title: genomic DNA from cultured airway epithelial cells (basal cells) [f513_4469-1A]

description:
200514030104_R07C01
f513_4469-1A

tag: treatment


title: MeHg_IC20_100-8

description:
MeHg_IC20_100-8_S12
counttable.txt

tag: originating cell line

tag: time point

tag: exposure

tag: batch


title: F_P7_hyperoxia_CD45_2_DC35_I11

tag: plate

tag: timepoint

tag: cell type

tag: cell subtype

value: Mac III

tag: mousename

tag: coverage

tag: number of genes


title: MeHg_IC20_100-4

description:
MeHg_IC20_100-4_S12
counttable.txt


title: MeHg_IC20_100-3

description:
MeHg_IC20_100-3_S12
counttable.txt


title: M_P7_hyperoxia_CD45_2_DC35_H3

tag: sequencing run

value: M

tag: well


title: MeHg_IC20_100-2

description:
MeHg_IC20_100-2_S11
counttable.txt


title: plus_toxIN_0min_rif_rep2

tag: strain


title: M_P7_hyperoxia_CD45_1_DC35_N10

tag: gender

value: hyperoxia


title: plus_toxIN_30min_rif_rep1

tag: plasmid

tag: time post-addition of rifampicin


title: genomic DNA from cultured airway epithelial cells (basal cells) [fa59_4849-1A]

description:
200517480189_R04C01
fa59_4849-1A

tag: treatment

tag: crs

tag: asthma

value: No

tag: steroid

tag: smoking

value: Female

tag: ethnicity

tag: age

tag: array


title: M_P7_hyperoxia_CD45_1_DC35_C12

tag: plate

tag: timepoint

tag: cell type

value: immune

tag: cell subtype

value: Mac V

tag: mousename


title: genomic DNA from cultured airway epithelial cells (basal cells) [fa59_4849-2A]

description:
200514030034_R07C01
fa59_4849-2A


title: MeHg_IC20_100-1

description:
MeHg_IC20_100-1_S11
counttable.txt

tag: originating cell line

value: Neuronal-astrocyte co-culture

tag: time point

value: Day 10

tag: exposure

value: Methyl mercury IC20/100

tag: batch


title: plus_toxIN_20min_rif_rep1

tag: strain

tag: plasmid

tag: time post-addition of rifampicin


title: genomic DNA from cultured airway epithelial cells (basal cells) [f584_41bb-2B]

description:
200517480083_R08C01
f584_41bb-2B

tag: treatment

tag: crs

value: nonCRS

tag: asthma

tag: steroid

tag: gender


title: Fluoxetine_IC5-8

description:
Fluoxetine_IC5-8_S8
counttable.txt

value: Fluoxetine IC5


title: genomic DNA from cultured airway epithelial cells (basal cells) [f584_41bb-1B]

description:
200514030073_R06C01
f584_41bb-1B

value: RV

tag: smoking

tag: ethnicity

value: Black

tag: age

tag: array


title: Fluoxetine_IC5-7

description:
Fluoxetine_IC5-7_S8
counttable.txt

tag: cell type


title: M_P7_hyperoxia_CD45_2_DC35_F10

tag: sequencing run

tag: plate

tag: well

tag: timepoint

tag: cell subtype

tag: mousename

tag: coverage

tag: number of genes


title: M_P7_hyperoxia_CD45_1_DC35_N3

tag: treatment

value: mast cell


title: genomic DNA from cultured airway epithelial cells (basal cells) [a38e_4452-2A]

description:
200516380119_R01C01
a38e_4452-2A

value: vehicle

tag: crs

tag: asthma

value: Current

value: White


title: Fluoxetine_IC5-6

description:
Fluoxetine_IC5-6_S8
counttable.txt

tag: originating cell line

tag: time point

tag: exposure

tag: batch


title: plus_toxIN_5min_rif_rep1

tag: strain

tag: plasmid

tag: time post-addition of rifampicin


title: plus_toxIN_5min_rif_rep2


title: genomic DNA from cultured airway epithelial cells (basal cells) [a38e_4452-1A]

description:
200514030112_R04C01
a38e_4452-1A

tag: steroid

tag: smoking

tag: gender

value: Male

tag: ethnicity

tag: age

tag: array


title: Fluoxetine_IC5-5

description:
Fluoxetine_IC5-5_S8
counttable.txt

tag: cell type


title: plus_toxIN_2.5min_rif_rep1


title: F_P7_hyperoxia_CD45_2_DC35_D23

tag: sequencing run

value: F

tag: plate

tag: well

tag: timepoint

tag: treatment

value: hyperoxia

tag: cell subtype

value: Mac II

tag: mousename

tag: coverage

tag: number of genes


title: F_P7_hyperoxia_CD45_2_DC35_O10

value: immune

value: Mac III


title: genomic DNA from cultured airway epithelial cells (basal cells) [a4a0_4b9c-2A]

description:
200514030104_R02C01
a4a0_4b9c-2A

tag: crs

value: CRS

tag: asthma

value: No

value: Never


title: plus_toxIN_0min_rif_rep1

tag: strain

tag: plasmid

tag: time post-addition of rifampicin


title: M_P7_hyperoxia_CD45_2_DC35_J14

tag: gender

value: M

value: Mac IV


title: genomic DNA from cultured airway epithelial cells (basal cells) [a4a0_4b9c-1A]

description:
200526210092_R03C01
a4a0_4b9c-1A

value: RV

tag: steroid

tag: smoking

tag: ethnicity

tag: age

tag: array


title: 2125_STC1_G

city: Houston

first: Kunal

last: Rai

state: TX

address: 1801 East Rd

department: Genomic Medicine

institute: MD Anderson Cancer Center

description: Input-DNA

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using a snakemake based pipeline https://github.com/crazyhottommy/pyflow-ChIPseq. Briefly, raw reads were first processed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and uniquely mapped reads were aligned to the hg19 reference genome using Bowtie version 1.1.2 (Langmead et al., 2009). Duplicate reads were removed using SAMBLASTER (Faust and Hall, 2014) before compression to bam files. To directly compare ChIP-seq samples uniquely mapped reads for each mark were downsampled per condition to 18 million, sorted and indexed using samtools version 1.5 (Li et al., 2009). To visualize ChIP-seq libraries on the IGV genome browser, we used deepTools version 2.4.0 (Ramirez et al., 2014) to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM). Super ChIP-seq tracks were generated by merging bam files from each cancer type, sorting and indexing using samtools and scaling to RPKM using deepTools.
Genome_build: hg19
Supplementary_files_format_and_content: deepTools version 1.5.11 was used to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM).

source_name: Cell Line

growth_protocol: Melanoma tumors were obtained from the Melcore tumor bank at MD Anderson Cancer Center. Tissue was disassociated (50 mg of tissue; ~8 mg per histone modification antibody) manually in 2 mL of Hanks' Balanced Salt Solution (HBSS) using a sterile razor blade. Mince the tissue into 3 to 4 mm pieces for approximately 5 min in a sterile tissue culture dish. Transfer the tissue and HBSS solution into a dissociator tube and add another 8 mL of HBSS. Further disassociate the tissue using a dissociator until homogenized. For melanoma tumors, place the tubes in a dissociator and run the following cycles each one time in this order: h_tumor_01.01, h_tumor_02.01, h_tumor_03.01 and m_heart_02.01.

extract_protocol:
ChIP assays were performed as described previously in Terranova et al (An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues; JoVE 2018). Briefly, 50mg of tissue or 20million cells were harvested via cross-linking with 1% (wt/ vol) formaldehyde for 10 min at 37 °C with shaking. After quenching with 150 mM glycine for 10 min at 37 °C with shaking, cells were washed twice with ice-cold PBS and frozen at −80 °C for further processing. Cross-linked pellets were thawed and lysed on ice for 30 min in ChIP harvest buffer (12 mM Tris-Cl, 1 × PBS, 6 mM EDTA, 0.5% SDS) with protease inhibitors (Sigma). Lysed cells were sonicated with a Bioruptor (Diagenode) to obtain chromatin fragments (~200–500 bp) and centrifuged at 15,000 × g for 15 min to obtain a soluble chromatin fraction. In parallel with cellular lysis and sonication, antibodies (5 μg/3 × 106 cells) were coupled with 30 μl of magnetic protein G beads in binding/blocking buffer (PBS + 0.1% Tween + 0.2% BSA) for 2 h at 4 °C with rotation. Soluble chromatin was diluted five times using ChIP dilution buffer (10 mM Tris-Cl, 140 mM NaCl, 0.1% DOC, 1% Triton X, 1 mM EDTA) with protease inhibitors and added to the antibody-coupled beads with rotation at 4 °C overnight. After washing, samples were treated with elution buffer (10 mM Tris-Cl, pH 8.0, 5 mM EDTA, 300 mM NaCl, 0.5% SDS), RNase A, and Proteinase K, and cross-links were reversed overnight at 37. Immune complexes were then washed five times with cold RIPA buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 140mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC), twice with cold high-salt RIPA buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 500mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC), and twice with cold LiCl buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 250mM LiCl, 0.5% NP-40, 0.5% DOC). ChIP DNA was purified using AMPure XP beads (Agencourt) and quantified using the Qubit 2000 (Invitrogen) and Bioanalyzer 1000 (Agilent). Libraries for Illumina sequencing were generated following the New England BioLabs (NEB) Next Ultra DNA Library Prep Kit protocol. A total of 10 cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments (~200–500 bp) and quantified using the Qubit 2000 and Bioanalyzer 1000 before multiplexing. Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and TapeStation 2000 before multiplexing.
Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and TapeStation 2000 before multiplexing.

tag: chip-antibody

tag: cell type

value: melanoma short-term patient culture cell line

tag: cell genotype

value: NRAS mutation


title: Fluoxetine_IC5-4

description:
Fluoxetine_IC5-4_S8
counttable.txt

tag: originating cell line

value: Neuronal-astrocyte co-culture

tag: time point

value: Day 10

tag: exposure

value: Fluoxetine IC5

tag: batch


title: F_P7_hyperoxia_CD45_2_DC35_O15

tag: sequencing run

tag: plate

tag: well

tag: timepoint

tag: treatment

tag: cell subtype

value: Mac V

tag: mousename

tag: coverage

tag: number of genes


title: 2125_STC1_F

description: ChIP-DNA


title: Fluoxetine_IC5-3

description:
Fluoxetine_IC5-3_S8
counttable.txt


title: Fluoxetine_IC5-2

description:
Fluoxetine_IC5-2_S7
counttable.txt


title: F_P7_hyperoxia_CD45_2_DC35_J21

tag: gender

value: F


title: genomic DNA from cultured airway epithelial cells (basal cells) [9be6_4904-2A]

description:
200516380203_R07C01
9be6_4904-2A

value: vehicle

tag: crs

value: nonCRS

tag: asthma

tag: steroid

tag: smoking

value: Female

tag: ethnicity

value: Black

tag: age

tag: array


title: 2125_STC1_E

description: ChIP-DNA

tag: chip-antibody

tag: cell type

tag: cell genotype


title: plus_toxIN_10min_rif_rep1

tag: strain

tag: plasmid

tag: time post-addition of rifampicin


title: Fluoxetine_IC5-1

description:
Fluoxetine_IC5-1_S7
counttable.txt

tag: originating cell line

tag: time point

tag: exposure

tag: batch


title: genomic DNA from cultured airway epithelial cells (basal cells) [9be6_4904-1A]

description:
200514040156_R04C01
9be6_4904-1A

tag: treatment

tag: crs

tag: gender


title: M_P7_hyperoxia_CD45_2_DC35_J21

tag: sequencing run

tag: plate

tag: well

tag: timepoint

value: hyperoxia

value: immune

tag: cell subtype

value: neutrophil

tag: mousename

tag: coverage

tag: number of genes


title: 2770_STC1_G

description: Input-DNA

tag: chip-antibody

tag: cell type

tag: cell genotype


title: Fluoxetine_IC20_100-8

description:
Fluoxetine_IC20_100-8_S10
counttable.txt

tag: originating cell line

tag: time point

value: Fluoxetine IC20/100


title: Fluoxetine_IC20_100-7

description:
Fluoxetine_IC20_100-7_S10
counttable.txt

tag: exposure

tag: batch


title: M_P7_hyperoxia_CD45_1_DC35_A21

value: M

tag: treatment

value: Mac III


title: genomic DNA from cultured airway epithelial cells (basal cells) [9eb4_4cec-1A]

description:
200526210023_R06C01
9eb4_4cec-1A

value: RV

tag: crs

tag: asthma

tag: steroid

tag: smoking

value: Never

tag: gender

tag: ethnicity

value: White

tag: age

tag: array


title: Fluoxetine_IC20_100-6

description:
Fluoxetine_IC20_100-6_S9
counttable.txt

value: Neuronal-astrocyte co-culture

value: Day 10


title: genomic DNA from cultured airway epithelial cells (basal cells) [8b40_4142-2A]

description:
200517480189_R05C01
8b40_4142-2A

value: No

value: Male


title: Fluoxetine_IC20_100-5

description:
Fluoxetine_IC20_100-5_S9
counttable.txt


title: 2770_STC1_F

description: ChIP-DNA

value: melanoma short-term patient culture cell line

value: NRAS mutation


title: 2770_STC1_E

description: ChIP-DNA


title: M_P7_hyperoxia_CD45_1_DC35_N14

tag: sequencing run

tag: plate

tag: well

tag: timepoint

tag: cell subtype

tag: mousename

tag: coverage

tag: number of genes


title: M_P7_hyperoxia_CD45_1_DC35_O18

tag: treatment

tag: cell type

value: NK cell


title: Fluoxetine_IC20_100-4

description:
Fluoxetine_IC20_100-4_S9
counttable.txt

tag: originating cell line

tag: time point

tag: exposure

tag: batch


title: genomic DNA from cultured airway epithelial cells (basal cells) [8b40_4142-1A]

description:
200517480083_R04C01
8b40_4142-1A

tag: crs

value: nonCRS

tag: asthma

tag: steroid

tag: smoking

tag: gender

tag: ethnicity


title: HCT116 DNA from normal replicating cells for timing (genomic DNA)

description:
Asynchronous HCT116 cells replication timing
HCT116 normal replication for timing

data_processing:
Library strategy: WGS
For ChIP-Seq, peaks were called using the  MACS algorithms againt input. Default parameters were used for sample calling.
For nascent strand peak calling the MACS was used. Nascent strand reads were called by comparison to genomic DNA.  Peaks were filtered using the “peak-score” MACS2 metric in R (version 3.5.1) by accepting regions above the inflection-point threshold of “peak-scores” from the raw output.
Single read  75bp (NextSeq for ChipSeq) or Pair End 101, 125 and 150 bp (HiSeq or NovaSeq) for NGS sequencing
Genome_build: hg19
Supplementary_files_format_and_content: Bed file format of replication initiation peaks and ChipSeq

tag: strain

value: Cultured cancer cell line

tag: chip antibody

tag: molecule subtype

value: Genomic DNA


title: HCT116 DNA from re-replicating cells for timing (genomic DNA)

description:
HCT116 MLN4924-treated cells re-replication timing
HCT116 re-replication for timing


title: M_P7_hyperoxia_CD45_1_DC35_G8

tag: sequencing run

tag: plate

tag: well

tag: timepoint

value: hyperoxia

value: immune

tag: cell subtype

value: neutrophil

tag: mousename

tag: coverage


title: HCT116 DNA from G1 cells  for timing (genomic DNA)

description:
G1 HCT116 cells DNA for replication timing
HCT116 G1 for timing

tag: cell type


title: Fluoxetine_IC20_100-2

description:
Fluoxetine_IC20_100-2_S9
counttable.txt

tag: originating cell line

tag: time point

tag: exposure

value: Fluoxetine IC20/100

tag: batch


title: genomic DNA from cultured airway epithelial cells (basal cells) [9eb4_4cec-2A]

description:
200526210060_R02C01
9eb4_4cec-2A

tag: treatment

value: vehicle

tag: crs

tag: asthma

tag: steroid

tag: smoking

tag: gender

value: Female

tag: age

tag: array


title: genomic DNA from cultured airway epithelial cells (basal cells) [4ce3_4f19-1A]

description:
200514030034_R01C01
4ce3_4f19-1A

value: RV

value: CRS

value: Prior

tag: ethnicity

value: Black


title: genomic DNA from cultured airway epithelial cells (basal cells) [830f_4683-2A]

description:
200516380173_R02C01
830f_4683-2A

value: Never

value: Male

value: White


title: HCT116 genomic DNA for 30h&45h both control &MLN4924

description:
HCT116 genomic DNA control
HCT116 genomic DNA

data_processing:
Library strategy: NS-seq
For ChIP-Seq, peaks were called using the  MACS algorithms againt input. Default parameters were used for sample calling.
For nascent strand peak calling the MACS was used. Nascent strand reads were called by comparison to genomic DNA.  Peaks were filtered using the “peak-score” MACS2 metric in R (version 3.5.1) by accepting regions above the inflection-point threshold of “peak-scores” from the raw output.
Single read  75bp (NextSeq for ChipSeq) or Pair End 101, 125 and 150 bp (HiSeq or NovaSeq) for NGS sequencing
Genome_build: hg19
Supplementary_files_format_and_content: Bed file format of replication initiation peaks and ChipSeq

tag: strain

tag: chip antibody

tag: molecule subtype


title: F_P7_hyperoxia_CD45_2_DC35_K8

tag: sequencing run

value: F

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype

value: Mac V

tag: mousename

tag: coverage

tag: number of genes


title: Fluoxetine_IC20_100-1

description:
Fluoxetine_IC20_100-1_S9
counttable.txt

tag: originating cell line

value: Neuronal-astrocyte co-culture

tag: time point

value: Day 10

tag: exposure

tag: batch


title: M_P7_hyperoxia_CD45_2_DC35_O23

tag: gender

value: M

tag: treatment

value: hyperoxia

value: Mac III


title: genomic DNA from cultured airway epithelial cells (basal cells) [830f_4683-1A]

description:
200514040052_R08C01
830f_4683-1A

tag: crs

value: nonCRS

tag: asthma

tag: steroid

tag: smoking

tag: ethnicity

tag: age

tag: array


title: HCT116 MLN4924 45h (Nascent strands)

description:
CT116 Nascent strand DNA from re-replicating cells treated with MLN4924 for 45h
HCT116 MLN4924 45h

tag: strain

tag: cell type

value: Cultured cancer cell line

tag: chip antibody

tag: molecule subtype

value: Nascent DNA


title: Chlorpyrifos_IC5-8

description:
Chlorpyrifos_IC5-8_S6
counttable.txt

tag: originating cell line

value: Chlorpyrifos IC5


title: M_P7_hyperoxia_CD45_2_DC35_D5

tag: sequencing run

tag: plate

tag: well

tag: timepoint

value: immune

tag: cell subtype

tag: mousename

tag: coverage

tag: number of genes


title: HCT116 MLN4924 30h (Nascent strands)

description:
HCT116 Nascent strand DNA from re-replicating cells treated with MLN4924 for 30h
HCT116 MLN4924 30h


title: Chlorpyrifos_IC5-7

description:
Chlorpyrifos_IC5-7_S6
counttable.txt

tag: time point

tag: exposure

tag: batch


title: M_P7_hyperoxia_CD45_1_DC35_E1

tag: gender

tag: treatment

value: Mac II


title: HCT116 Control 45h (Nascent strands)

description:
HCT116 Nascent strand DNA from normal replication
HCT116 Control 45h

tag: strain

tag: cell type


title: F_P7_hyperoxia_CD45_2_DC35_D20

value: mast cell II


title: genomic DNA from cultured airway epithelial cells (basal cells) [df18_40fb-2A]

description:
200514030073_R05C01
df18_40fb-2A

value: vehicle

tag: crs

tag: asthma

value: No

tag: steroid

value: Oral

tag: smoking

value: Prior

tag: ethnicity

tag: age

tag: array


title: Chlorpyrifos_IC5-6

description:
Chlorpyrifos_IC5-6_S5
counttable.txt

tag: originating cell line


title: genomic DNA from cultured airway epithelial cells (basal cells) [5bf2_4e77-1A]

description:
200514030067_R06C01
5bf2_4e77-1A

value: RV

value: Female

value: White


title: HCT116 Control 30h (Nascent strands)

description:
HCT116 Nascent strand DNA from normal replication
HCT116 Control 30h

tag: chip antibody

tag: molecule subtype


title: F_P7_hyperoxia_CD45_2_DC35_O12

tag: sequencing run

value: F

tag: plate

tag: well

tag: timepoint

tag: cell subtype

tag: mousename

tag: coverage

tag: number of genes


title: Fluoxetine_IC20_100-3

description:
Fluoxetine_IC20_100-3_S9
counttable.txt

tag: cell type

value: Neuronal-astrocyte co-culture

tag: time point

value: Day 10

tag: exposure

value: Fluoxetine IC20/100

tag: batch


title: M_P7_hyperoxia_CD45_2_DC35_I10

tag: gender

value: M

tag: treatment

value: hyperoxia

value: Mac IV


title: Chlorpyrifos_IC5-5

description:
Chlorpyrifos_IC5-5_S5
counttable.txt

tag: originating cell line

value: Chlorpyrifos IC5


title: genomic DNA from cultured airway epithelial cells (basal cells) [4ce3_4f19-2A]

description:
200514030034_R06C01
4ce3_4f19-2A

tag: crs

value: CRS

tag: asthma

tag: steroid

tag: smoking

value: Male

tag: ethnicity

value: Black

tag: age

tag: array


title: HCT116 MLN4924 HH (Nascent strands)

description:
HCT116 Nascent strand DNA from  re-replication (BrdU-CsCl gradient (HH) from MLNN4924 treated cells)
HCT116 MLN4924 HH

tag: strain

value: Cultured cancer cell line

tag: chip antibody

tag: molecule subtype

value: Nascent DNA


title: M_P7_hyperoxia_CD45_1_DC35_I10

tag: sequencing run

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: Chlorpyrifos_IC5-4

description:
Chlorpyrifos_IC5-4_S5
counttable.txt

tag: originating cell line

tag: time point

tag: exposure

tag: batch


title: genomic DNA from cultured airway epithelial cells (basal cells) [df18_40fb-1A]

description:
200526210024_R07C01
df18_40fb-1A

tag: treatment

value: RV

tag: crs

value: nonCRS

tag: asthma

value: No

tag: steroid

value: Oral

tag: smoking

value: Prior

tag: gender

tag: ethnicity

tag: age

tag: array


title: Chlorpyrifos_IC5-2

description:
Chlorpyrifos_IC5-2_S5
counttable.txt

tag: cell type

value: Neuronal-astrocyte co-culture

value: Day 10


title: genomic DNA from cultured airway epithelial cells (basal cells) [a042_4b4d-2A]

description:
200512330148_R04C01
a042_4b4d-2A

value: vehicle

value: Unknown

value: Never

value: White


title: genomic DNA from cultured airway epithelial cells (basal cells) [5bf2_4e77-2A]

description:
200516380203_R01C01
5bf2_4e77-2A

value: Female


title: HCT116 MLN4924 HL (Nascent strands)

description:
HCT116 Nascent strand DNA from normal replication (BrdU-CsCl gradient (HL) from MLNN4924 treated cells)
HCT116 MLN4924 HL

tag: strain

tag: chip antibody

tag: molecule subtype


title: Chlorpyrifos_IC5-3

description:
Chlorpyrifos_IC5-3_S5
counttable.txt

tag: originating cell line

value: Chlorpyrifos IC5


title: HCT116 MLN4924 genomic DNA for HCT116 MLN4924 HL& HH (Genomic DNA)

description:
Genomic DNA from HCT116 MLN4924-treated cells
HCT116 MLN4924 genomic

value: Cultured cancer cell line

value: Genomic DNA


title: F_P7_hyperoxia_CD45_2_DC35_L11

tag: sequencing run

value: F

tag: plate

tag: well

tag: timepoint

value: hyperoxia

value: immune

tag: cell subtype

value: Mac IV

tag: mousename

tag: coverage

tag: number of genes


title: M_P7_hyperoxia_CD45_2_DC35_C20

tag: gender

value: M

tag: treatment

value: T cell


title: Chlorpyrifos_IC5-1

description:
Chlorpyrifos_IC5-1_S5
counttable.txt

tag: time point

tag: exposure

tag: batch


title: genomic DNA from cultured airway epithelial cells (basal cells) [a042_4b4d-1A]

description:
200517480052_R04C01
a042_4b4d-1A

value: RV

tag: crs

value: CRS

tag: asthma

tag: steroid

tag: smoking

value: Male

tag: ethnicity

tag: age

tag: array


title: genomic DNA from cultured airway epithelial cells (basal cells) [9b6e_45d9-1A]

description:
200516380117_R04C01
9b6e_45d9-1A

value: No


title: HCT116 control genomic DNA for HCT116 control HL (Genomic DNA)

description:
Genomic DNA from control HCT116 cells
HCT116 control genomic

tag: strain

tag: cell type

tag: chip antibody

tag: molecule subtype


title: HCT116 MLN4924 400 nM (Re-replicated DNA)

description:
Re-replicated DNA isolated by BrdU-CsCl gradient from HCT116 cells treated with 400nM of MLN4924
HCT116 MLN4924 400 nM

value: re-replicated DNA


title: Chlorpyrifos_IC20_100-7

description:
Chlorpyrifos_IC20_100-7_S7
counttable.txt

tag: originating cell line

value: Neuronal-astrocyte co-culture

value: Day 10

value: Chlorpyrifos IC20/100


title: Chlorpyrifos_IC20_100-8

description:
Chlorpyrifos_IC20_100-8_S7
counttable.txt


title: M_P7_hyperoxia_CD45_1_DC35_M5

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

tag: cell subtype

tag: mousename

tag: coverage

tag: number of genes


title: genomic DNA from cultured airway epithelial cells (basal cells) [94af_490f-1A]

description:
200514030104_R01C01
94af_490f-1A

tag: treatment

tag: crs

value: nonCRS

tag: asthma

tag: steroid

tag: smoking

value: Never

tag: ethnicity

value: White


title: genomic DNA from cultured airway epithelial cells (basal cells) [8838_40c3-2A]

description:
200526210060_R05C01
8838_40c3-2A

value: vehicle

value: Oral

value: Prior

tag: age

tag: array


title: F_P7_hyperoxia_CD45_2_DC35_O8

tag: sequencing run

value: F

value: hyperoxia

tag: cell type

value: immune


title: M_P7_hyperoxia_CD45_2_DC35_O9

tag: gender

value: M

tag: plate

value: Mac III


title: HCT116 MLN4924 200 nM (Re-replicated DNA)

description:
Re-replicated DNA isolated by BrdU-CsCl gradient from HCT116 cells treated with 200nM of MLN4924
HCT116 MLN4924 200 nM

tag: strain

value: Cultured cancer cell line

tag: chip antibody

tag: molecule subtype


title: Chlorpyrifos_IC20_100-5

description:
Chlorpyrifos_IC20_100-5_S7
counttable.txt

tag: originating cell line

tag: time point

tag: exposure

tag: batch


title: Chlorpyrifos_IC20_100-6

description:
Chlorpyrifos_IC20_100-6_S7
counttable.txt


title: HCT116 HH Control (Genomic DNA with BrdU incoprated)

description:
HCT116 genomic DNA control with BrdU labelled for 48 hours
HCT116 HH Control

value: Genomic DNA


title: M_P7_hyperoxia_CD45_2_DC35_P20

tag: well

tag: timepoint

tag: treatment

tag: cell subtype

tag: mousename

tag: coverage

tag: number of genes


title: HCT116 control HL (Nascent strands)

description:
HCT116 Nascent strand DNA from normal replication (BrdU-CsCl gradient (HL) in control cells)
HCT116 control HL

tag: cell type

value: Nascent DNA


title: genomic DNA from cultured airway epithelial cells (basal cells) [8838_40c3-1A]

description:
200514040156_R06C01
8838_40c3-1A

value: RV

tag: crs

value: CRS

tag: asthma

value: No

tag: steroid

tag: smoking

tag: gender

value: Male

tag: ethnicity

tag: age

tag: array


title: genomic DNA from cultured airway epithelial cells (basal cells) [538f_43e4-2B]

description:
200517480052_R06C01
538f_43e4-2B

value: nonCRS

value: Never


title: Chlorpyrifos_IC20_100-4

description:
Chlorpyrifos_IC20_100-4_S6
counttable.txt

tag: originating cell line

value: Neuronal-astrocyte co-culture

tag: time point

value: Day 10

tag: exposure

value: Chlorpyrifos IC20/100

tag: batch


title: Chlorpyrifos_IC20_100-3

description:
Chlorpyrifos_IC20_100-3_S6
counttable.txt


title: M_P7_hyperoxia_CD45_1_DC35_J20

tag: sequencing run

tag: plate

tag: well

tag: timepoint

tag: treatment

tag: cell subtype

value: Mac V


title: genomic DNA from cultured airway epithelial cells (basal cells) [9b6e_45d9-2A]

description:
200517480052_R03C01
9b6e_45d9-2A

value: vehicle

tag: crs

tag: asthma

value: White


title: M_P7_hyperoxia_CD45_1_DC35_I3

value: M

value: hyperoxia

tag: cell type

value: immune

value: DC II

tag: mousename

tag: coverage

tag: number of genes


title: M_P7_hyperoxia_CD45_2_DC35_H2

tag: gender

value: DC I


title: U2OS_WT_100nMdex

city: Ithaca

first: Erin

middle: Margaret

last: Wissink

state: NY

address: Biotech Bldg Room 417, 529 Campus Rd

department: Molecular Biology & Genetics

institute: Cornell University

description:
Nascent RNA
Cells overexpress human glucocorticoid receptor.

data_processing:
Library strategy: PRO-seq
Sequencing libraries were split based on an in-line barcode, using barcode_splitter v0.18.2.
Reads were deduplicated, using prinseq-lite v0.20.4.
Cutadapt v1.16 was used to trim adapters, remove the inline barcode, discard anything <15 nt long, and trim all reads to 36 nt. The reverse complement reads were generated using fastx_reverse_complement v0.0.14.
Reads were aligned to the full-length human rDNA, and reads that did not align were kept.
A 6mer UMI was trimmed and reads were aligned to the genome using bowtie2 v2.3.4.1 with options --end-to-end and --sensitive. Uniquely mapping reads were retained. BED files were generated using bedtools bamToBed v2.26.0.
Bedgraph files were generated by calculating coverage of reads' 3' ends with bedtools genomeCoverageBed v2.26.0, then converted to bigwigs with bedgraphToBigwig v4.
Bigwigs were normalized by subsampling to the library depth of the sample with the fewest mapped sequencing reads.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Bigwigs of normalized read counts.

source_name: U2OS cells

growth_protocol: Cells were maintained in DMEM supplemented with FBS and pen/strep. 5 million cells were plated per experiment 24 hours prior to treatment.

extract_protocol:
Cells were kept on ice during the extraction protocol. Cells were washed with PBS, then incubated in PBS supplemented with 10 mM PBS for 5 minutes. Cells were scraped and placed in 15 mL Falcon tubes, then washed twice with PBS. Cells were then incubated in permeabilization buffer for 5 minutes, pelleted, and washed twice with permeabilization buffer. Cells were resuspended in freezing buffer and flash frozen.
Run-on reactions with biotin-11-CTP and biotin-11-UTP were performed for 5 minutes. RNA was isolated, fragmented on ice with 0.2 N NaOH, and underwent buffer exchange with a P-30 column. Three biotin enrichments were performed with Dynabead streptavidin beads, and between enrichments, the 3' adapter was ligated, the 5' end was repaired with RppH and PNK enzymatic treatments, and the 5' adapter was ligated. RT was performed with SuperScript III, and 13 cycles of PCR were used to amplify the library, followed by clean-up with Ampure beads (1.6x ratio).

treatment_protocol: Media was supplemented with ethanol or the appropriate concentration of dexamethasone for 45 minutes and kept in a 37° C incubator with 5% CO2 during the incubation.

value: 100 nM dexamethasone


title: genomic DNA from cultured airway epithelial cells (basal cells) [538f_43e4-1B]

description:
200517480202_R05C01
538f_43e4-1B

value: RV

tag: steroid

tag: smoking

tag: ethnicity

tag: age

tag: array


title: genomic DNA from cultured airway epithelial cells (basal cells) [94af_490f-2A]

description:
200514030034_R08C01
94af_490f-2A

value: No


title: U2OS_WT_1nMdex

value: 1 nM dexamethasone


title: U2OS_WT_0nMdex

value: 0 nM dexamethasone (ethanol)


title: Chlorpyrifos_IC20_100-2

description:
Chlorpyrifos_IC20_100-2_S6
counttable.txt

tag: originating cell line

tag: time point

tag: exposure

tag: batch


title: F_P7_hyperoxia_CD45_2_DC35_I22

tag: sequencing run

value: F

tag: plate

tag: well

tag: timepoint

tag: treatment

tag: cell subtype

value: Mac III


title: A549_WT_100nMdex

description: Nascent RNA

source_name: A549 cells

tag: cell type


title: genomic DNA from cultured airway epithelial cells (basal cells) [4b70_422f-2A]

description:
200516380203_R03C01
4b70_422f-2A

tag: crs

value: CRS

tag: asthma

value: Oral

value: Never

tag: gender

value: Male


title: F_P7_hyperoxia_CD45_2_DC35_M19

value: Mac II

tag: mousename

tag: coverage

tag: number of genes


title: A549_WT_1nMdex

description: Nascent RNA


title: Chlorpyrifos_IC20_100-1

description:
Chlorpyrifos_IC20_100-1_S6
counttable.txt

tag: originating cell line

value: Neuronal-astrocyte co-culture

value: Day 10

value: Chlorpyrifos IC20/100


title: genomic DNA from cultured airway epithelial cells (basal cells) [4b70_422f-1A]

description:
200526210092_R07C01
4b70_422f-1A

tag: steroid

tag: smoking

tag: ethnicity

value: White

tag: age

tag: array


title: M_P7_hyperoxia_CD45_2_DC35_L6

tag: sequencing run

value: M

tag: plate

tag: well

value: hyperoxia

value: immune

value: T cell


title: genomic DNA from cultured airway epithelial cells (basal cells) [483f_4b4e-2A]

description:
200526210086_R02C01
483f_4b4e-2A

tag: treatment

value: vehicle

value: nonCRS

value: No

value: Current

value: Female

value: Hispanic


title: Acrylamide_IC5-8

description:
Acrylamide_IC5-8_S3
counttable.txt

tag: cell type

tag: time point

tag: exposure

value: Acrylamide IC5

tag: batch


title: DX-PALF_CC-23

first: Matthew

middle: J.

last: Schipma

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file with read counts per gene

source_name: Liver tissue

extract_protocol:
Total RNA was extracted from archived frozen liver tissue using a TissueLyser LT and the RNeasy® Mini Kit protocol (QIAGEN, Hilden, Germany). RNA purity and concentration were confirmed using the NanoDrop 2000™ Spectrophotometer (Thermo Scientific, DE, USA). RNA quantity was determined with Qubit fluorometer. Total RNA samples were checked for quality based on fragment size using Agilent Bioanalyzer 2100.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: liver

tag: diagnosis

value: pediatric acute liver failure (PALF)


title: M_P7_hyperoxia_CD45_2_DC35_D21

tag: gender

tag: timepoint

tag: cell subtype

value: Mac IV

tag: mousename

tag: coverage

tag: number of genes


title: genomic DNA from cultured airway epithelial cells (basal cells) [b109_4415-2A]

description:
200514030112_R07C01
b109_4415-2A

tag: crs

value: CRS

tag: asthma

tag: steroid

tag: smoking

value: Prior

value: Male

tag: ethnicity

tag: age

tag: array


title: Acrylamide_IC5-6

description:
Acrylamide_IC5-6_S3
counttable.txt

tag: originating cell line

tag: cell type

value: Neuronal-astrocyte co-culture

tag: time point

value: Day 10

tag: exposure


title: Acrylamide_IC5-7

description:
Acrylamide_IC5-7_S3
counttable.txt

tag: batch


title: F_P7_hyperoxia_CD45_2_DC35_O19

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: treatment

value: hyperoxia

value: immune

value: mast cell


title: genomic DNA from cultured airway epithelial cells (basal cells) [b109_4415-1A]

description:
200514030156_R07C01
b109_4415-1A

value: RV

tag: crs

tag: asthma

value: No

value: White


title: DX-PALF_CC-19

tag: tissue

tag: diagnosis


title: Acrylamide_IC5-5

description:
Acrylamide_IC5-5_S3
counttable.txt


title: DX-PALF_CC-18


title: M_P7_hyperoxia_CD45_1_DC35_M19

value: M

tag: cell subtype

value: Mac III

tag: mousename

tag: coverage

tag: number of genes


title: Acrylamide_IC5-4

description:
Acrylamide_IC5-4_S2
counttable.txt

tag: originating cell line

tag: cell type

tag: time point

value: Acrylamide IC5


title: Acrylamide_IC5-3

description:
Acrylamide_IC5-3_S2
counttable.txt

tag: exposure

tag: batch


title: genomic DNA from cultured airway epithelial cells (basal cells) [9f0d_46f8-2A]

description:
200514030073_R01C01
9f0d_46f8-2A

value: vehicle

value: nonCRS

tag: steroid

tag: smoking

value: Current

tag: gender

tag: ethnicity

tag: age

tag: array


title: DX-PALF_CC-20

tag: tissue

value: liver

value: pediatric acute liver failure (PALF)


title: genomic DNA from cultured airway epithelial cells (basal cells) [9f0d_46f8-1A]

description:
200517480108_R05C01
9f0d_46f8-1A

tag: treatment

tag: crs

tag: asthma

value: Male


title: M_P7_hyperoxia_CD45_1_DC35_G14

tag: sequencing run

tag: plate

tag: well

tag: timepoint

tag: cell subtype

value: DC I

tag: mousename

tag: coverage


title: A549_WT_0nMdex

description: Nascent RNA

tag: cell type

value: 0 nM dexamethasone (ethanol)


title: F_P7_hyperoxia_CD45_2_DC35_L2

value: F

value: hyperoxia

value: basophil

tag: number of genes


title: genomic DNA from cultured airway epithelial cells (basal cells) [551b_49fb-2A]

description:
200514040052_R01C01
551b_49fb-2A

tag: steroid

tag: smoking

value: Never

tag: gender

value: Female


title: Acrylamide_IC5-2

description:
Acrylamide_IC5-2_S2
counttable.txt

tag: originating cell line

value: Neuronal-astrocyte co-culture

tag: time point

value: Day 10

tag: exposure

tag: batch


title: DX-PALF_CC-17

tag: tissue

tag: diagnosis


title: DX-PALF_CC-16


title: Acrylamide_IC5-1

description:
Acrylamide_IC5-1_S2
counttable.txt


title: genomic DNA from cultured airway epithelial cells (basal cells) [551b_49fb-1A]

description:
200517480108_R06C01
551b_49fb-1A

tag: treatment

value: RV

tag: crs

tag: asthma

tag: ethnicity

value: White

tag: age

tag: array


title: F_P7_hyperoxia_CD45_2_DC35_O11

tag: sequencing run

tag: plate

tag: well

tag: timepoint

tag: cell type

value: immune

tag: cell subtype

value: Mac III

tag: mousename

tag: coverage


title: Acrylamide_IC20_100-8

description:
Acrylamide_IC20_100-8_S4
counttable.txt

tag: originating cell line

tag: time point

tag: exposure

value: Acrylamide IC20/100

tag: batch


title: M_P7_hyperoxia_CD45_2_DC35_F1

tag: gender

value: M

tag: treatment

value: mast cell

tag: number of genes


title: F_P7_hyperoxia_CD45_2_DC35_G16


title: genomic DNA from cultured airway epithelial cells (basal cells) [483f_4b4e-1A]

description:
200517480194_R01C01
483f_4b4e-1A

tag: crs

value: nonCRS

tag: asthma

value: No

tag: steroid

tag: smoking

value: Current

tag: ethnicity

value: Hispanic

tag: age


title: IND-PALF_CC25

tag: tissue

value: liver

tag: diagnosis

value: pediatric acute liver failure (PALF)


title: Acrylamide_IC20_100-7

description:
Acrylamide_IC20_100-7_S4
counttable.txt

tag: cell type


title: genomic DNA from cultured airway epithelial cells (basal cells) [952a_4dbc-2A]

description:
200514030156_R05C01
952a_4dbc-2A

value: vehicle

value: CRS

value: Oral

value: Never

value: Male

tag: array


title: genomic DNA from cultured airway epithelial cells (basal cells) [952a_4dbc-1A]

description:
200514030073_R07C01
952a_4dbc-1A

value: RV

value: White


title: IND-PALF_CC24


title: IND-PALF_CC-15


title: M_P7_hyperoxia_CD45_1_DC35_H15

tag: sequencing run

tag: plate

tag: well

tag: timepoint

value: hyperoxia

value: immune

tag: cell subtype

value: Mac III

tag: mousename

tag: coverage


title: M_P7_hyperoxia_CD45_1_DC35_P18

tag: gender

value: M

tag: treatment

tag: number of genes


title: genomic DNA from cultured airway epithelial cells (basal cells) [b8ff_4982-1A]

description:
200514030130_R06C01
b8ff_4982-1A

tag: crs

value: nonCRS

tag: asthma

tag: steroid

tag: smoking


title: Acrylamide_IC20_100-6

description:
Acrylamide_IC20_100-6_S4
counttable.txt

tag: originating cell line

value: Neuronal-astrocyte co-culture

tag: time point

value: Day 10

tag: exposure

value: Acrylamide IC20/100

tag: batch


title: genomic DNA from cultured airway epithelial cells (basal cells) [b8ff_4982-2A]

description:
200514030156_R08C01
b8ff_4982-2A

tag: ethnicity

tag: age

tag: array


title: M_P7_hyperoxia_CD45_1_DC35_F18

tag: sequencing run

tag: plate

tag: well

tag: timepoint

tag: cell type

tag: cell subtype


title: genomic DNA from cultured airway epithelial cells (basal cells) [323b_40ff-1A]

description:
200517480108_R02C01
323b_40ff-1A

tag: treatment

tag: crs

tag: gender


title: IND-PALF_CC-13

tag: tissue

value: liver

tag: diagnosis


title: Acrylamide_IC20_100-4

description:
Acrylamide_IC20_100-4_S4
counttable.txt

tag: originating cell line

tag: time point