title: 3-4-KO1

value: TAM from APC-KO MC38 tumor 1 replicate 4


title: 3-2-KO1

status: Public on Jul 13 2022

type: SRA

city: Houston

first: Chang-Jiun

last: Wu

state: TX

address: 1515 Holcombe Blvd

department: Genomic Medicine

country: USA

institute: University of Texas, MD Anderson Cancer Center

library_source: transcriptomic

data_processing:
The NextSeq RTA (version 2.4.11.0) was used for base calling and bcl2fastq (version 2.20.0) was used to convert the .bcl files into .fastq files.
Fastq files were aligned to the mouse reference genome (mm9) using HISAT2 software and assembled using StringTie.
Comparisons between groups were hampered by low input of total RNA isolated from tumor macrophages manifesting as inconsistent raw/normalized read counts for housekeeping genes in the different groups.
To enable comparisons between APC-WT and APC-KO tumors, we re-normalized the read counts of multiple M2 macrophage markers with housekeeping gene read counts (GAPDH and ACTB)
Assembly: mm9
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: Tumor infiltrated macrophage from MC38 orthotopic tumors implanted in C57BL/6J mice.

growth_protocol: APC-WT and APC-KO MC38 orthotopic tumors implanted in C57BL/6J mice were digested with Liberase DL (Roche #5401160001) and Liberase TL (Roche #05401020001).

extract_protocol:
Stained cells were sorted as CD45+, CD11b+, and F4/80+.
Total RNA was isolated from sorted cells and were sequenced by Ultra low Input RAN sequencing (Illumina NexteraXT) with six replicates of each sample.

treatment_protocol: After RBC lysis, cells were blocked with CD16/CD32 blocking antibody (BD Biosciences Cat# 553142, RRID:AB_394657) for 30 min and stained with antibodies: CD45 APC 30-F11 (BioLegend Cat# 103111, RRID:AB_312976), CD11b eFluor 605 M1/70 (Thermo Fisher Scientific Cat# 69-0112-82, RRID:AB_2637406), F4/80 PerCp-Cy5.5 BM8 (BioLegend Cat# 123127, RRID:AB_893496), and SYTOX green (ThermoFisher Cat# R37168).

tag: genotype

value: TAM from APC-KO MC38 tumor 1

tag: sample type

value: TAM from APC-KO MC38 tumor 1 replicate 2


title: 4-3-KO2

value: TAM from APC-KO MC38 tumor 2

value: TAM from APC-KO MC38 tumor 2 replicate 3


title: 4-1-KO2

value: TAM from APC-KO MC38 tumor 2 replicate 1


title: 3-5-KO1

value: TAM from APC-KO MC38 tumor 1 replicate 5


title: 4-2-KO2

value: TAM from APC-KO MC38 tumor 2 replicate 2


title: 4-6-KO2

value: TAM from APC-KO MC38 tumor 2 replicate 6


title: 3-1-KO1

value: TAM from APC-KO MC38 tumor 1 replicate 1


title: 2-6-WT2

value: TAM from APC-WT MC38 tumor 2

value: TAM from APC-WT MC38 tumor 2 replicate 6


title: 2-5-WT2

value: TAM from APC-WT MC38 tumor 2 replicate 5


title: 2-2-WT2

value: TAM from APC-WT MC38 tumor 2 replicate 2


title: 2-3-WT2

value: TAM from APC-WT MC38 tumor 2 replicate 3


title: 2-4-WT2

value: TAM from APC-WT MC38 tumor 2 replicate 4


title: 1-6-WT1

value: TAM from APC-WT MC38 tumor 1

value: TAM from APC-WT MC38 tumor 1 replicate 6


title: 2-1-WT2

value: TAM from APC-WT MC38 tumor 2 replicate 1


title: 1-5-WT1

value: TAM from APC-WT MC38 tumor 1 replicate 5


title: 1-4-WT1

value: TAM from APC-WT MC38 tumor 1 replicate 4


title: 1-3-WT1

value: TAM from APC-WT MC38 tumor 1 replicate 3


title: 1-2-WT1

value: TAM from APC-WT MC38 tumor 1 replicate 2


title: MC38ishTDO2-48h-3

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 using STAR software.
The HTSeq-count program was used to generate raw read counts for each gene
Assembly: mm10
Supplementary files format and content: Raw gene counts and RPKM

source_name: MC38 cell line

growth_protocol: The CRC cell lines MC38 (RRID:CVCL_B288) and its isogenic cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) containing 10% Tet System Approved FBS (Clontech) and 100 U/ml ampicillin/penicillin. All cells were confirmed to be mycoplasma-free and maintained at 37 °C and 5% CO2.

extract_protocol:
Cells were pelleted and RNA was isolated with RNeasy Mini Kit (Qiagen, Cat# 74104). RNA was reverse-transcribed into cDNA following SuperScriptTM III First-Strand Synthesis SuperMix (Invitrogen, Cat# 18080400). qRT-PCR was performed using SYBR Green PCR Master Mix (Thermo Fisher Scientific) in a 7500 Fast Real-Time PCR instrument (Applied Biosystems).
For RNA sequencing, RNAs were isolated from ishTDO2 APC-WT and APC-KO MC38 cells with and without Dox treatment (biological triplicates per group) using the RNeasy Mini Kit.

treatment_protocol: Inducible shTDO2 MC38 cell lines were treated with 1 μM of Doxycycline (Sigma-Aldrich, Cat# D9891) for indicated periods to induce TDO2 knockdown.

tag: derivation

value: MC-38 Cell Line derived from C57BL6 murine colon adenocarcinoma cells

tag: tissue

value: colon adenocarcinoma cell line


title: 1-1-WT1

value: TAM from APC-WT MC38 tumor 1 replicate 1


title: MC38APCishTDO2-48h-2


title: MC38APCishTDO2-48h-1


title: MC38ishTDO2-48h-2


title: 4-4-KO2

value: TAM from APC-KO MC38 tumor 2

value: TAM from APC-KO MC38 tumor 2 replicate 4


title: MC38APCishTDO2-24h-3


title: MC38APCishTDO2-24h-2


title: MC38APCishTDO2-48h-3


title: MC38ishTDO2-24h-2


title: MC38ishTDO2-24h-3


title: MC38APC-3


title: MC38-3


title: WBM_3a

status: Public on Jul 12 2022

city: New York

first: Anna

last: Yeaton

state: New York

address: 550 1st ave

department: Pathology

institute: NYU Langone

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Genomics Cell Ranger software.
ADTs and HTOs for each cell were normalized using a centered log ratio (CLR) transformation across cells.
Samples were demultiplexed based on HTOs using the HTODemux function in Seurat.
Genome_build: mm10
Supplementary_files_format_and_content: Indexed BAM files containing position-sorted reads aligned to the genome.

molecule: polyA RNA

source_name: bone marrow

extract_protocol:
Bone marrow cells were isolated from the spine, hips, femur and tibia of mice. A single-cell suspension was generated after red blood cell lysis ACK buffer. Cells were tagged with cell hashing (Stoeckius et al, 2018) oligo-tagged antibodies (BioLegend) according to manufacturer’s instructions and pooled on a 10x Chromium instrument (10x Genomics) to generate barcoded single-cell beads-in emulsion (GEM) according to the manufacturer’s protocol. scRNA-seq libraries were prepared using the Chromium Single-Cell’ v3 Reagent Kit (10x Genomics) following the direction of the manufacturer. The libraries were quantified using Qubit fluorometric quantification (Thermo Fisher Scientific). The quality was assessed on an Agilent Bioanalyzer 2000, obtaining an average library size of 455 bp. Libraries were pooled and normalized to 2 nmol/L and clustered on a HiSeq4000 high output mode on a paired-end read flow cell and sequenced for 28 cycles on R1 (10x barcode and the UMIs). Followed by 8 cycles of i7 index (sample index), and 98 bases on R2 (transcript), with a coverage around 130M reads per sample.
Single Cell 3’ Reagent Kits: Chromium™ Single Cell 3’ Library & Gel Bead Kit v3, PN-1000157; Single Cell 3’ Chip Kit v3 PN-1000123 and i7 Multiplex Kit PN-220103(10x Genomics). Samples were tagged with cell hashing oligo-tagged antibodies (BioLegend) according to manufacturer’s instructions.

tag: cell type

value: bone marrow cells


title: MC38ishTDO2-24h-1


title: MC38ishTDO2-48h-1


title: MC38APC-2


title: MC38-2


title: KOD1-WT-sample-experiment-1

status: Public on Jul 09 2022

city: Tsukuba

first: Yancheng

last: Liu

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

description: whole transcriptosome RNA

data_processing:
fastQC was used to verify the presence of adaptor sequence, adaptor was trimed where necessary using cutadapt
Aligning Reads to T.Kodakarensis genome reference using bowtie2. The reads per kilo-base per million mapped reads (RPKM) was calculated using FeatureCount
A custom perl script was used to identify RNA-Seq reads containing circular junction sequences.
Assembly: NC_006624.1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample.

organism: Thermococcus kodakarensis

source_name: Thermococcus kodakarensis KOD1

growth_protocol: Cells were grown in MA-YT-P medium until the absorbance at 600 nm reached ~0.7 as descibred in Liu, Y. et al.  Frontiers Mol Biosci 9, 811548 (2022).

extract_protocol:
Total RNA was isolated from T. kodakarensisand and from tk1545 knock-out strain using TRIZOL reagent (Invitrogen).
Small RNA libraries NEBNext® Small RNA Library Prep Set for SOLiD™
Collected RNAs were subject to adaptor ligation, revere transcribed, and PCR amplified. The amplified cDNA library was size selected (100 - 150 nts) by gel purification.

value: WT

tag: rna resouce

value: small RNA

tag: strain


title: KOD1-KO-sample-experiment-1

description: whole transcriptosome RNA

value: tk1545 Knockout


title: MC38-1


title: MC38APCishTDO2-24h-1


title: KOD1-KO-sample-experiment-2

description: whole transcriptosome RNA


title: MC38APC-1


title: KOD1-WT-sample-experiment-2

description: whole transcriptosome RNA


title: SU-DHL-4 Ento+AZD N3

status: Public on Jul 08 2022

city: Rostock

first: Sina

last: Sender

state: Mecklenburg Vorpommern

address: Schillingallee 70

department: Department of Medicine, Clinic III

country: Germany

institute: Rostock University Medical Center

data_processing:
Base calling with Illumina Software bcl2fastq v2.19; parameters: bcl2fastq --minimum-trimmed-read-length 25 --input-dir {path} --output-dir {path}; all others: default
The RNAseq data were processed as follows. The raw reads from different lanes were concatenated before being trimmed and quality controlled using CutAdapt via TrimGalore!
Trimmed reads were aligned to the human genome (GRCh38.p13) and feature counts were performed using Rsubread
The technical replicates were then averaged, and edgeR was used to filter low read counts using the filterByExpr() function, normalize using the TMM method, and perform a differential expression analysis using the GLM method to fit a generalized linear model, specifying no intercept and with treatment group as the only covariate
All contrasts were tested using the glmQLFTest() function of edgeR, which performs an empirical Bayes quasi-likelihood F-test for each gene, and the results were corrected for multiplicity using the Benjamini-Hochberg correction
A gene was deemed significantly differentially expressed if it had a corrected p-value of < 0.05 and a fold-change > 2
Gene Ontology (GO) enrichment analysis was performed using the “weight01” algorithm of topGO with GO terms with a p-value of < 0.05 being taken as significant.
Assembly: hg19
Supplementary files format and content: TMM_values.txt File containg the normalized read counts
Supplementary files format and content: count_table.txt file containing the read counts

organism: Homo sapiens

source_name: Peritoneal effusion

growth_protocol: SU-DHL-4 cell line were maintained in RPMI 1640  supplemented with 10% heat-inactivated fetal bovine serum (FBS) and and 100 µg/ml penicillin and streptomycin in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cell pellets were resuspended in QIAzol Lysis Reagent (QIAGEN, Venlo, Netherlands) and RNA Isolation was performed with miRNeasy Mini Kit (QIAGEN, Venlo, Netherlands) according to the manufacturer’s instructions
Poly-A RNA was enriched from 1 µg total RNA using the NEBNext Poly (A) mRNA Magnetic Isolation Module (New England Bioabs, Ipswich, USA) and sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (New England Bioabs, Ipswich, USA). Sequencing was conducted on an Illumina NextSeq500 (Illumina, San Diego, USA) as single reads with 75 bp length with a total of 480 million reads.

treatment_protocol: SU-DHL-4 cells were exposed to 1µM Entospletinib  (Absource Diagnostics GmbH, München, Germany), 0.01µM AZD5153  (Absource Diagnostics GmbH, München, Germany), the combination (1µM Ento+ 0.01µM AZD) or DMSO as control for 72h.

value: Peritoneal effusion

tag: cell line

value: B cell lymphoma

value: wt

tag: treatment

value: Ento+AZD


title: SU-DHL-4 AZD N3

value: AZD


title: SU-DHL-4 Ento N3

value: Ento


title: SU-DHL-4 DMSO N3

value: DMSO


title: SU-DHL-4 Ento+AZD N2


title: SU-DHL-4 AZD N2


title: SU-DHL-4 Ento+AZD N3

type: RNA

description: Gene expression data  of treated SU-DHL-4 cell line

hyb_protocol: Hybridization was performed for 16 hours at 45 degrees celsius using the GeneChip Hybridization Oven 645 (Affymetrix, St. Clara, USA).

scan_protocol: Scanning was done using the GeneChip Scanner 3000/7G (Affymetrix, St. Clara, USA) with 0.7 micron resolution.

data_processing:
Microarray data were RMA normalized using limma and probes were mapped to genes using affycoretools with probe mappings drawn from clariomhumantranscriptcluster.db. and a linear model was fitted of the form:
Where Yij is the intensity for gene j in sample i, Treatmenti is the treatment which sample i was subjected to, Linei is the cell line from which sample i was drawn and Batchi is the batch which sample i belongs to, while ij is the error term, with the coefficients Î²0, Î²1 and Î²2 estimated by least squares.
All contrasts were tested using the eBayes method of limma to perform a moderated t-test for each gene and the results were corrected for multiplicity using the Benjamini-Hochberg correction.

label: biotin

source_name: DLBCL cell line SU-DHL-4

label_protocol: 200 ng total RNA was labeled using WT-labeling protocol (Affymetrix/Thermofisher).

growth_protocol: SU-DHL-4 und DG-75 cell lines were maintained in RPMI 1640  supplemented with 10% heat-inactivated fetal bovine serum (FBS) and and 100 µg/ml penicillin and streptomycin in a humidified atmosphere with 5% CO2 at 37C

extract_protocol: Cell pellets were resuspended in QIAzol Lysis Reagent (QIAGEN, Venlo, Netherlands) and RNA Isolation was performed with miRNeasy Mini Kit (QIAGEN, Venlo, Netherlands) according to the manufacturer’s instructions

treatment_protocol: SU-DHL-4 and DG-75 cells were exposed to 1µM Entospletinib  (Absource Diagnostics GmbH, München, Germany), 0.01µM AZD5153  (Absource Diagnostics GmbH, München, Germany), the combination (1µM Ento+ 0.01µM AZD) or DMSO as control for 72h.

value: Pleural effusion


title: SU-DHL-4 Ento N2


title: SU-DHL-4 Ento+AZD N1


title: SU-DHL-4 AZD N1


title: SU-DHL-4 DMSO N1


title: SU-DHL-4 Ento+AZD N2


title: SU-DHL-4 DMSO N2


title: SU-DHL-4 Ento N2


title: SU-DHL-4 DMSO N3


title: U937-EG_Input_48h

status: Public on Jul 05 2022

city: Shanghai, China

first: Yifan

last: Zhang

address: Ruijin Hospital

country: China

institute: Shanghai Institute of Hematology

library_source: genomic

data_processing:
Clean sequenced reads were alignmented to hg19 by bowtie2(2.2.9) with parameters: -N 1
Alignmented SAM files were handled using samtools(1.7)
Peaks were called by macs2(2.1.1.20160309) callpeaks algorithm with default set
BigWig files were generated by deeptols(3.1.2) bamCoverage algorithm with paprameter --normalizeUsing BPM
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

molecule: genomic DNA

growth_protocol: U937 cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
U937-AE and U937-EG were cross-linked with 1% formaldehyde for 10min and stopped by 125mM glycine. After lysis and sonication, 30μL of anti-HA magnetic beads (MCE, HY-K0201) was incubated with chromatin samples overnight at 4℃ for immunoprecipitation. The DNA were purified with the MinElute PCR Purification Kit (QIAGEN) and subjected to library construction and next-generation sequencing with Illumina systems.
ChIP-seq libraries were used the VAHTS Universal DNA Library Prep Kit for Illumina V3 Kit (ND607).

treatment_protocol: AML1-ETO or ETO2-GLIS2 was induced by treatment with 5ug/ml doxycycline (Sigma) for 48h.

value: monocytic cell line

value: EG over-expressed

value: doxycycline 48h


title: SU-DHL-4 Ento N1


title: DG-75 Ento N1

description: Gene expression data  of treated DG-75 cell line

source_name: Burkitt Lymphoma cell line DG-75


title: U937-AE_AE_48h

value: AE over-expressed


title: DG-75 AZD N3


title: U937-AE_Input_48h


title: SU-DHL-4 DMSO N2


title: DG-75 Ento+AZD N2


title: DG-75 Ento N2


title: DG-75 AZD N1


title: SU-DHL-4 Ento N1


title: SU-DHL-4 DMSO N1


title: SU-DHL-4 AZD N2


title: CO2 -cold stored 3

status: Public on Jul 03 2022

city: Fuencarral-El Pardo,  Madrid

first: Crisanto

last: Gutierrez

state: Madrid

address: C. Nicolás Cabrera, 1

department: Replicación del DNA, división celular y cromatina

country: Spain

institute: CBMSO-CSIC

data_processing:
Image analysis, base calling, and base quality scoring of the run were processed by Sequencer Software HiSeq Control Software 2.2.58—Real-Time Analysis (RTA 1.13.48), followed by the generation of FASTQ sequence files by CASAVA 1.8. The base quality of the sequences obtained was also checked with the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and SeqMonk Mapped Sequence Data Analyser (version: 1.46.0; Babraham Bioinformatics, UK). Likewise, FASTQ Groomer (Version 1.1.5) and Cutadapt (Version 1.16.6) were used to optimise the reads, converting FASTQ quality formats and removing adapter sequences.
Fragaria vesca Whole Genome v4.0.a2 (Li et al., 2019).
Aligned files generated with the HISAT 2.1.0 program (Langmead et al.,2009) that was employed for aligning the sequences against Fragaria vesca Whole Genome

organism: Fragaria vesca

source_name: Ripe strawberries

extract_protocol:
The ripe Mara des Bois strawberries (Fragaria vesca) immediately after harvest (2 hours) were used as the control (AH). Those placed directly in a chamber at 20 ºC and 80 % RH for two days were the non-cold stored (NCS), while the strawberries transferred at 20ºC for 1 day following the 7-day storage at 1ºC (conditions employed to simulate a time in transit) were used to analyse the air-cold stored fruit (ACS) or CO2 -cold stored fruit (CCS). CCS were pretreated for two days with a gas mixture containing 18 % CO2 + 18 % O2 + 64 % N2 and then air-ventilated for another five days (CCS).
The total RNA of three biological replicate samples was extracted from 0.5 g of fruit powder in accordance with Yu et al., (2012). Each biological replicate sample contained a fruit mixture of at least 50 strawberries. A TURBO DNase™ enzyme (Ambion, Austin, Tex.) treatment was used to degrade the contaminant DNA. RNA quantity and purity were measured with the NanoDrop ND-1000 spectrophotometer (Thermo Scientific). RNA integrity was determined by the RNA integrity number (RIN), using a 2100 Bioanalyzer (Agilent).
The mRNA from each biological replica was employed to prepare the RNA-Seq libraries with the reagents provided in the Illumina®TruSeq ™ Stranded Total RNA kit protocol (Illumina Inc., San Diego, CA). The size and quality of the libraries were quality controlled in Agilent DNA 2100 Bioanalyzer assay (Agilent).
RNA-seq: Each library was sequenced using Illumina HiSeq™ 2500 (Illumina Inc.), in paired-end mode with a read length of 2x50 bp, generating minimally 39 million paired-end reads per replica and passing filter for each RNA-Seq library in a fraction of a sequencing lane of the sequencer following the manufacturer’s protocol (max. 200 M/lane).

value: Ripe strawberries

value: Mara des Bois

value: CO2 -cold stored fruit


title: Non-cold stored 1

value: Non-cold stored fruit


title: Non-cold stored 3


title: SU-DHL-4 AZD N1


title: SU-DHL-4 AZD N3


title: Non-cold stored 2


title: CO2 -cold stored 1


title: Air-cold stored biol rep 3

value: Air-cold stored fruit


title: CO2 -cold stored 2


title: DG-75 DMSO N3

value: Peritoneal effusion


title: Air-cold stored biol rep 2


title: After harvest biol rep 2

value: After harvest fruit


title: Air-cold stored biol rep 1


title: DG-75 Ento+AZD N3


title: DG-75 DMSO N1


title: After harvest biol rep 3


title: DG-75 DMSO N2


title: SU-DHL-4 Ento+AZD N1


title: DG-75 AZD N2


title: After harvest biol rep 1


title: DG-75 Ento+AZD N1


title: DG-75 Ento N3


title: Liver-TCP-994.6-mg/kg-1

status: Public on Jul 01 2022

city: Durham

first: Scott

last: Auerbach

state: North Carolina

address: 111 TW Alexander Drive

institute: Division of the National Toxicology Program at NIEHS

hyb_protocol: Labeled aRNA was fragmented and subsequently hybridized to the Affymetrix Rat Genome 230 2.0 Array (Cat #: 900505; 31,099 probe sets) using an Affymetrix GeneChip® Hybridization Oven 645.

scan_protocol: After washing and staining, arrays were scanned using an Affymetrix GeneChip® Scanner 3000 7G, and the raw microarray data (.CEL files) were acquired using Affymetrix GeneChip® Command Console® Software.

data_processing: Probe set intensities from raw microarray data (CEL files from Affymetrix Rat Genome 230 2.0 Arrays) were normalized by applying the Robust Multi-array Average (RMA) algorithm from the genomics analysis tool, GeneSpring GX 12.6 (Agilent Technology, Foster City, CA).

label: Biotin

organism: Rattus norvegicus

label_protocol: Total RNA (100 ng), isolated from each liver sample, was used to synthesize single-stranded DNA, which was subsequently converted into a double-stranded complementary DNA (cDNA) template for transcription. An in vitro transcription (IVT) reaction, which incorporates biotinylated ribonucleotide analogs, then was used to create labeled amplified RNA (aRNA).

extract_protocol: Three pieces (3-mm cubes) of left liver lobe were dissected and flash frozen. The frozen liver tissues were submerged in 10 volumes of prechilled RNAlater®-ICE (Life Technologies, Carlsbad, CA) and stored at −20°C ± 10°C for a minimum of 16 hours. The tissues were removed from the RNAlater®-ICE and weighed. Each liver tissue sample, weighing between 21 and 30 mg, was added to lysis buffer and homogenized using plastic disposable pestles (Fisher Scientific, Pittsburgh, PA). Following homogenization, samples were stored at −70°C ± 10°C until RNA was isolated. Samples were thawed and centrifuged. RNA was extracted from the supernatant, subjected to DNase digestion, and isolated using the Qiagen RNeasy Mini Kit (Cat #: 74104; Qiagen, Valencia, CA).

treatment_protocol: Sprague Dawley SD rats were assigned to one of six dose groups, each containing three rats, with the exception of the vehicle control which contained 5 rats. The rats in each dose group then were administered TCP by gavage in corn oil at a dose level of 0, 62, 125, 249,  497, or 995 mg/kg body weight. These doses correspond to molar equivalencies of 0, 0.169, 0.338, 0.675, 1.35, and 2.7 mmol/kg. Dosing of the test article occurred on 4 consecutive days.

value: Harlan Sprague-Dawley

tag: Sex

value: Male

tag: chemical

value: Tricresyl Phosphate (TCP)

tag: vehicle

value: Corn oil

tag: dose

tag: route

value: Oral Gavage

tag: number of doses

value: Liver


title: Liver-TCP-994.6-mg/kg-2


title: Liver-TCP-62.3-mg/kg-3


title: Liver-TCP-994.6-mg/kg-3


title: Liver-TCP-248.6-mg/kg-3


title: Liver-TCP-124.5-mg/kg-1


title: Liver-TCP-497.3-mg/kg-1


title: Liver-TCP-248.6-mg/kg-2


title: Liver-TCP-497.3-mg/kg-3


title: Liver-TCP-0-mg/kg-5


title: Liver-TCP-124.5-mg/kg-3


title: Liver-TCP-248.6-mg/kg-1


title: Liver-TCP-62.3-mg/kg-2


title: Liver-TCP-62.3-mg/kg-1


title: Liver-TCP-0-mg/kg-3


title: Liver-TCP-497.3-mg/kg-2


title: SU-DHL-4 Ento N3

value: Pleural effusion


title: Liver-TCP-0-mg/kg-2


title: Liver-IPP-611-mg/kg-2

treatment_protocol: Sprague Dawley SD rats were assigned to one of five dose groups, each containing three rats, with the exception of the vehicle control which contained 5 rats. The rats in each dose group then were administered IPP by gavage in corn oil at a dose level of 0, 77, 153, 306,  or 611 mg/kg body weight. These doses correspond to molar equivalencies of 0, 0.169, 0.338, 0.675, and 1.35 mmol/kg. Dosing of the test article occurred on 4 consecutive days.

value: Isopropylated Phenol Phosphate (IPP)


title: Liver-TCP-0-mg/kg-1


title: Liver-TCP-0-mg/kg-4


title: Liver-IPP-611-mg/kg-3


title: Liver-IPP-611-mg/kg-1


title: Liver-IPP-305.5-mg/kg-3


title: Liver-IPP-305.5-mg/kg-1


title: Liver-IPP-305.5-mg/kg-2


title: Liver-TCP-124.5-mg/kg-2


title: Liver-IPP-153-mg/kg-2


title: Liver-IPP-153-mg/kg-1


title: Liver-IPP-76.5-mg/kg-3


title: Liver-IPP-76.5-mg/kg-2


title: Liver-IPP-0-mg/kg-4


title: U937-EG_EG_48h

value: monocytic cell line

value: EG over-expressed

value: doxycycline 48h


title: Liver-IDDP-527.1-mg/kg-1

treatment_protocol: Sprague Dawley SD rats were assigned to one of six dose groups, each containing three rats, with the exception of the vehicle control which contained 5 rats. The rats in each dose group then were administered IDDP by gavage in corn oil at a dose level of 0, 66, 132, 264, 527, or 1054 mg/kg body weight. These doses correspond to molar equivalencies of 0, 0.169, 0.338, 0.675, 1.35, and 2.7 mmol/kg. Dosing of the test article occurred on 4 consecutive days.

value: Isodecyl Diphenyl Phosphate (IDDP)


title: Liver-IPP-0-mg/kg-2


title: Liver-IPP-76.5-mg/kg-1


title: Liver-IDDP-263.6-mg/kg-1


title: Liver-IPP-0-mg/kg-3


title: Liver-IDDP-527.1-mg/kg-2


title: Liver-IPP-0-mg/kg-1


title: Liver-IDDP-263.6-mg/kg-2


title: Liver-IPP-0-mg/kg-5


title: Liver-IDDP-1054.2-mg/kg-3


title: Liver-IDDP-132-mg/kg-2


title: Liver-IDDP-263.6-mg/kg-3


title: Liver-IDDP-527.1-mg/kg-3


title: Liver-IDDP-1054.2-mg/kg-2


title: Liver-IDDP-1054.2-mg/kg-1


title: Liver-IDDP-132-mg/kg-3


title: Liver-IDDP-66-mg/kg-1


title: Liver-IDDP-132-mg/kg-1


title: Liver-IDDP-0-mg/kg-5


title: Liver-IDDP-66-mg/kg-2


title: Liver-IDDP-0-mg/kg-2


title: Liver-EDHP-978.5-mg/kg-3

treatment_protocol: Sprague Dawley SD rats were assigned to one of six dose groups, each containing three rats, with the exception of the vehicle control which contained 5 rats. The rats in each dose group then were administered EDHP by gavage in corn oil at a dose level of 0, 61, 123, 245, 489, or 979 mg/kg body weight. These doses correspond to molar equivalencies of 0, 0.169, 0.338, 0.675, 1.35, and 2.7 mmol/kg. Dosing of the test article occurred on 4 consecutive days.

value: 2-Ethylhexyl Diphenyl Phosphate (EDHP)


title: Liver-EDHP-489.2-mg/kg-3


title: Liver-IDDP-0-mg/kg-4


title: Liver-IDDP-0-mg/kg-1


title: Liver-IDDP-0-mg/kg-3


title: Liver-EDHP-978.5-mg/kg-2


title: Liver-EDHP-978.5-mg/kg-1


title: Liver-EDHP-489.2-mg/kg-1


title: Liver-EDHP-489.2-mg/kg-2


title: Liver-EDHP-244.6-mg/kg-3


title: Liver-EDHP-244.6-mg/kg-1


title: Liver-EDHP-122.5-mg/kg-1


title: Liver-EDHP-0-mg/kg-5


title: Liver-EDHP-61.2-mg/kg-3


title: Liver-EDHP-122.5-mg/kg-3


title: Liver-EDHP-0-mg/kg-6


title: Liver-EDHP-0-mg/kg-3


title: Liver-EDHP-61.2-mg/kg-2


title: Liver-EDHP-122.5-mg/kg-2


title: Liver-BPDP-1032.5-mg/kg-3

treatment_protocol: Sprague Dawley SD rats were assigned to one of six dose groups, each containing three rats, with the exception of the vehicle control which contained 5 rats. The rats in each dose group then were administered BPDP by gavage in corn oil at a dose level of 0, 65, 129, 258, 516, or 1033 mg/kg body weight. These doses correspond to molar equivalencies of 0, 0.169, 0.338, 0.675, 1.35, and 2.7 mmol/kg. Dosing of the test article occurred on 4 consecutive days.

value: tert-Butylphenyl Diphenyl Phosphate (BPDP)


title: Liver-EDHP-244.6-mg/kg-2


title: Liver-EDHP-0-mg/kg-4


title: Liver-EDHP-0-mg/kg-1


title: Liver-EDHP-61.2-mg/kg-1


title: Liver-EDHP-0-mg/kg-2


title: Liver-IDDP-66-mg/kg-3


title: Liver-BPDP-1032.5-mg/kg-2


title: Liver-BPDP-1032.5-mg/kg-1


title: THP-1 cells, shDNMT3B, DMSO, replicate2

status: Public on Jun 25 2022

city: Seoul

first: Junyoung

last: Park

address: 84, Heukseok-ro

department: Department of Life Science

country: South Korea

institute: Chung-Ang University

data_processing:
Low-quality reads were filtered based on the following criteria: reads containing more than 10% of skipped bases (marked as ‘N’s), reads containing more than 40% of bases with quality scores of less than 20, and reads with average quality scores for each read of less than 20.
The filtering process was performed using in-house scripts. Filtered reads were mapped to the reference genome related to the species using the aligner STAR v.2.4.0b.
Gene expression levels were measured using Cufflinks v2.1.1 and the gene annotation database of the species. For differentially expressed gene (DEG) analysis, gene-level count data were generated using HTSeq-count v0.6.1p1. Based on the calculated read count data, DEGs were identified using the R package ‘TCC’.
The normalization factors were calculated using the iterative DEGES/edgeR method. The Q-value was calculated based on the P-value using the p.adjust function of the R package, with default parameter settings. The DEGs were identified based on a Q-value threshold of less than 0.05 for correcting errors caused by multiple testing.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts for each sample

source_name: Blood

extract_protocol:
RNA was extracted using TruSeq Stranded mRNA Sample Prep Kit (Illumina)
mRNA molecules were purified and fragmented from 0.1-1 ug of total RNA using oligo (dT) magnetic beads. Fragmented mRNAs were synthesized as single-stranded cDNAs through random hexamer priming. Double-stranded cDNA was prepared by using this cDNA as a template for second strand synthesis. After a sequential process of end repair, A-tailing, and adpter ligation, cDNA libraries were amplifed using PCR.

value: Blood

value: acute myeloid leukemia cell line

value: DNMT3B knockdown

value: DMSO


title: Liver-BPDP-258.1-mg/kg-3

value: Harlan Sprague-Dawley

value: Male


title: Liver-BPDP-516.2-mg/kg-1

value: Corn oil


title: THP-1 cells, shDNMT3B, DMSO, replicate1


title: THP-1 cells, shDNMT3B, PMA, replicate2

value: PMA


title: Liver-BPDP-129.2-mg/kg-2

value: Oral Gavage

value: Liver


title: Liver-BPDP-258.1-mg/kg-2


title: Liver-BPDP-129.2-mg/kg-1


title: Liver-BPDP-0-mg/kg-6


title: THP-1 cells, shDNMT1, PMA, replicate2

value: DNMT1 knockdown


title: Liver-BPDP-516.2-mg/kg-2


title: Liver-BPDP-516.2-mg/kg-3


title: Liver-BPDP-258.1-mg/kg-1


title: THP-1 cells, shDNMT1, PMA, replicate1


title: Liver-BPDP-64.6-mg/kg-2


title: Liver-BPDP-64.6-mg/kg-3


title: Liver-BPDP-0-mg/kg-5


title: THP-1 cells, shUHRF1, PMA, replicate2

value: UHRF1 knockdown


title: Liver-BPDP-0-mg/kg-4


title: THP-1 cells, shDNMT1, DMSO, replicate2


title: Liver-BPDP-0-mg/kg-3


title: Liver-BPDP-64.6-mg/kg-1


title: Liver-BPDP-129.2-mg/kg-3


title: Liver-IPP-153-mg/kg-3

value: Isopropylated Phenol Phosphate (IPP)


title: Liver-BPDP-0-mg/kg-1


title: Liver-BPDP-0-mg/kg-2


title: THP-1 cells, shUHRF1, DMSO, replicate1


title: THP-1 cells, shDNMT1, DMSO, replicate1


title: THP-1 cells, shUHRF1, DMSO, replicate2


title: THP-1 cells, shNC, PMA, replicate2

value: Control


title: THP-1 cells, shNC, DMSO, replicate1


title: THP-1 cells, shNC, DMSO, replicate2


title: THP-1 cells, shNC, PMA, replicate1


title: THP-1 cells, shUHRF1, PMA, replicate1


title: THP-1 cells, shDNMT3B, PMA, replicate1


title: spe44.r3_86A3

status: Public on Jun 22 2022

city: Santa Cruz

first: Jordan

middle: David

last: Ward

state: California

address: 1156 HIGH ST, UCSC THIMANN RECEIVING, SINSHEIMER 327

department: Molecular, Cell, and Developmental Biology

institute: University of California, Santa Cruz

data_processing:
The first 10 bases were trimmed with fastx_trimmer using option -f 11
Reads were mapped to transcriptome version WS220 using Tophat2 (Kim et al., 2013). Reads with one unique mapping were retained, otherwise default options for paired-end mapping were used.
HTSeq (Anders et al., 2015) was used to obtain read counts per transcript. All libraries were sequenced twice and for each transcript read counts from both sequencing runs were added together.
DESeq2 (Love et al., 2014) was used for read count normalization and differential expression analysis.
Assembly: WS220
Supplementary files format and content: txt file, DESeq2 results for coding genes with fold changes and adjusted p-values for all comparisons with control

organism: Caenorhabditis elegans

source_name: Whole male animals

growth_protocol: All worms were grown at 20ºC for 3 days according to Brenner 1974 except replacing NGM with MYOB.

extract_protocol:
500 L4/young adult males were hand-picked into M9 + 0.05% gelatin, washed 1X and pelleted.  Liquid was removed down to 25ul and 500ul TRIzol (Invitrogen) was added.  The mixture incubated at room temperature for 5 minutes with periodic vortexing.  Carcasses were pelleted by centrifugation and supernatant was removed to a clean tube.  100 ul chloroform was added to the supernatant, vortexed for 30 seconds and phases separated by centrifugation at 15,000 RPM for 5 minutes.  250 ul of the upper aqueous phase was removed to a new tube and 350 ul chloroform was added, vortexed and separated as in the previous steps.  250 ul of isopropanol was added to the aqueous phase along with 1ul Glycoblue (Invitrogen) and vortexed.  The solution was centrifuged for 20 minutes at 15,000 RPM and the supernatant was decanted.  The pellet was washed with 1 ml 75% ethanol twice and dried at room temperature for 10 minutes.  The dried pellet was resuspended in 16 ul nuclease-free water. Concentration was determined with the NanoDrop.
Using the NEXTFLEX® Rapid Directional RNA-Seq Kit 2.0 (BioO/PerkinElmer), polyA-selected RNA was isolated from 300 ng of total RNA according to manufacturer's instructions.  Sequencing libraries were prepared using the same kit according to manufacturer's instructions.

treatment_protocol: Samples 4-12 were grown on MYOB supplemented with 0.25% ethanol and 4mM indole-3-acetic acid (auxin) while samples 1-3 were grown on MYOB with 0.25% ethanol, but lacking auxin.

value: Whole male animals

value: 4 mM auxin


title: spe44.r2_86A2


title: PSLR-2_rep3

city: Philadelphia

first: Ramkrishna

last: Mitra

state: Pennsylvania

address: 233 S 10th street

institute: Thomas Jefferson University

data_processing:
Adapter sequences were trimmed using Cutadapt version 2.4.
For sequence mapping, Human reference genome (Ensembl version GRCh38)  was used.
Sequence mapping and transcript assembling were performed using Hisat2 and StringTie (version 1.3.6). A python script prepDE.py from StringTie was used to extract read count information.
The read counts were imported into edgeR for differential expression analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include Ensembl gene ids and read counts for each sample.

source_name: lung adenocarcinoma cell line

growth_protocol: Lung adenocarcinoma cell line A549 was cultured in RPMI-1640 media supplemented with 10% FBS, 100U/mL penicillin, and 100µg/mL streptomycin. A549 media was also supplemented with additional L-glutamine. Cells were confirmed to be negative for mycoplasma.

extract_protocol:
RNA was isolated using TRIzol.
Libraries were made and RNA-seq profiles were generated by GeneWiz (www.GENEWIZ.com). The NEBNext Ultra II RNA Library Prep kit was used and the libraries were sequenced on HiSeq 4000.

treatment_protocol: A459 cells were infected with lentiviral vectors expressing lncRNA PSLR-1, -2 or empty vector and were harvested 48 hrs later (four replicates of each).

tag: transfection

value: PSLR-2 transfected

value: A459 cells


title: PSLR-2_rep2


title: ctrl.r2_181A2


title: double.r1_146A1


title: double.r3_146A3


title: double.r2_146A2


title: spe44.r1_86A4


title: ctrl.r3_181A3


title: PSLR-2_rep4


title: ctrl.r1_181A1


title: nhr23.r3_92A4

value: wrdSi19[mex-5p::TIR1:F2A:mTagBFP2:tbb-2 3'UTR, I:-5.32], nhr-23(kry61(nhr-23::AID*-TEV-3xFLAG)) I; him-5(e1490) V.


title: nhr23.r2_92A3


title: PSLR-2_rep1


title: nhr23.r1_92A2


title: PSLR-1_rep4

value: PSLR-1 transfected


title: PSLR-1_rep2


title: PSLR-1_rep3


title: PSLR-1_rep1


title: AMI day 3 [N2677]

status: Public on Jun 20 2022

city: Hannover

first: Marc

middle: R.

last: Reboll

state: NDS

address: Carl-Neuberg-Str. 1

department: Molecular and Translational Cardiology, Department of Cardiology and Angiology

institute: Hannover Medical School

description: Endothelial cells from infarcted left ventricle

data_processing:
The 10x Genomics Cell Ranger analysis pipeline (v4.0.0) was used with default parameters and expected cell numbers set to 10,000. The mkfastq command was used to demultiplex the data from raw BCL sequencer images (10x Genomics sample sheet with the utilized 10x barcodes) yielding standard FASTQ files and 10x specific metadata. Next, CellRanger was used to align read data to the reference genome provided by 10X Genomics (Mus musculus reference data set, refdata-gex-mm10-2020-A) via the RNA-seq aligner STAR. Aligned reads were counted per gene and clustering and summary statistics were calculated accordingly.
Assembly: 10x Genomics (Mus musculus reference data set, refdata-gex-mm10-2020-A)
Supplementary files format and content: Filtered feature-barcode matrix, containing only detected cell-associated barcodes. Stored in the Market Exchange Format (MEX) including gzipped TSV files with feature and barcode sequences corresponding to row and column indices.

source_name: Day 3 infarcted left ventricle

extract_protocol:
Loading of Chromium 10x controller, library generation, and quality control: Libraries were generated according to the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 user guide (10x Genomics; manual number, CG000204 Rev B). A twofold excess of cells was loaded into the 10x Genomics Chromium Controller to reach a target number of 10,000 cells per sample. Fragment length distribution of generated cDNAs and libraries was monitored using the Bioanalyzer High Sensitivity DNA kit (Agilent Technologies; catalog number, 5067-4626). Library quantification was performed using the Qubit dsDNA HS-assay kit (Thermo Fisher Scientific; catalog number, Q32854).
Sequencing run: Equal molar proportions of generated mRNA expression libraries were pooled, denatured with NaOH, and diluted to 2 pmol/L as outlined in the Denature and Dilute Libraries Guide (Illumina; document number, 15048776 v02). 1.3 mL of denatured pool was sequenced on an Illumina NextSeq 550 sequencer using one High Output Flowcell for 75 cycles and 400 million clusters (NextSeq 500/550 High Output Kit v2.5; catalog number, 20024906). RNA sequencing was performed with the following settings: 28 bp as sequence read 1; 56 bp as sequence read 2; 8 bp as index read 1; no index read 2.

treatment_protocol: CD45low CD31high endothelial cells were isolated from the infarct region (anteroapical wall distal to the coronary artery ligation site representing the infarct core and border zone) 3 days after sham or AMI surgery in C57BL/6N wild-type mice.

value: Endothelial cells

value: acute myocardial infarction (AMI) surgery

tag: time point


title: 10326_BI00894999_10nM_CCS1477_300nM_24h_rep3

city: Vienna

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer Ingelheim RCV GmbH & Co KG

data_processing:
Multiplexed samples were sequenced on an Illumina NextSeq 500 system. Base-calling was performed using the Real-Time Analysis (RTA) software version 2.4.11. Conversion of the raw bcl2 output files to gzipped FASTQ files was performed using the bcl2fastq2 software version 2.20.0 provided by Illumina.
Data was processed with a pipeline building upon the implementation of the ENCODE "Long RNA-seq" pipeline: In brief, single-end sequencing reads were mapped against the Homo sapiens (human) genome hg38/GRCh38 (source 1000 Genomes Project - GRCh38_full_analysis_set_plus_decoy_hla.fa,  excluding alternate contigs, chromosome mapping via grch38_ucsc2ensembl.txt) using the STAR (v2.5.2b) aligner allowing for soft clipping of adapter sequences. For quantification, transcript annotation files from Ensembl version 86 were used. Samples were quantified with the above annotations using featureCount (v1.5.1). Quality controls were implemented using FastQC (v0.11.5), picardmetrics (v0.2.4), and dupRadar (v1.0.0) at the respective steps. Finally, differential expression analysis was performed on the counts derived from featureCount using limma/voom.
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data files contain sample-wise results produced by FeaturesCounts and include raw count values for each gene.

source_name: 10326 cancer cell line

growth_protocol: The NUT carcinoma cell line Ty-82 was purchased from JCRB Japan No. 1330 and cultivated in RPMI 1640 supplemented with 10% fetal calf serum (FCS). The NC cell lines 10-15, 14169, and 10326 were in-licensed from Christopher French, Brigham & Womens Hospital, Boston, and were cultivated in DMEM supplemented with glutamax and 10% FCS.

extract_protocol:
Cells were lysed in TRI lysis reagent (Qiagen, #79306) according to the manufacturer's instructions. Total RNA was isolated with RNAeasy Mini Kit (Qiagen, #73404).
Quant-seq libraries were prepares using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina from Lexogene (#015.96) according to manufacturer's instructions.

treatment_protocol: See samples section.

tag: cellline

tag: disease

value: NUT midline carcinoma

tag: replicate

tag: ID


title: 10326_BI00894999_10nM_CCS1477_300nM_24h_rep1


title: 10326_CCS1477_300nM_24h_rep1


title: 10326_CCS1477_300nM_24h_rep2


title: 10326_CCS1477_300nM_24h_rep3


title: Sham day 3 [N2676]

description: Endothelial cells from non-infarcted (sham-operated) left ventricle

source_name: Day 3 non-infarcted (sham-operated) left ventricle

tag: cell type

value: non-infarcted (sham-operated)


title: 10326_BI00894999_10nM_CCS1477_300nM_24h_rep2


title: 10326_BI00894999_10nM_24h_rep3


title: 10326_BI00894999_10nM_24h_rep2


title: 10326_BI00894999_10nM_CCS1477_300nM_4h_rep2


title: 10326_BI00894999_10nM_24h_rep1


title: 10326_BI00894999_10nM_4h_rep3


title: 10326_CCS1477_300nM_4h_rep1


title: 10326_BI00894999_10nM_CCS1477_300nM_4h_rep3


title: 10326_BI00894999_10nM_CCS1477_300nM_4h_rep1


title: 10326_CCS1477_300nM_4h_rep3


title: 10326_BI00894999_10nM_4h_rep2


title: 10326_DMSO_4h_rep3


title: 10326_CCS1477_300nM_4h_rep2


title: 14169_BI00894999_10nM_CCS1477_300nM_24h_rep3

source_name: 14169 cancer cell line


title: 14169_BI00894999_10nM_CCS1477_300nM_24h_rep1


title: 10326_BI00894999_10nM_4h_rep1


title: 10326_DMSO_4h_rep2


title: 14169_CCS1477_300nM_24h_rep1


title: 14169_BI00894999_10nM_24h_rep2


title: 14169_CCS1477_300nM_24h_rep3


title: 14169_BI00894999_10nM_CCS1477_300nM_24h_rep2


title: 14169_BI00894999_10nM_24h_rep3


title: 14169_CCS1477_300nM_24h_rep2


title: ATAC_HH35_FB_rep2

city: Geneva

first: Aurelie

last: Hintermann

address: 30 quai Ernest-Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

description:
ATAC HH35 forebrain
ATAC

data_processing:
All scripts are available on https://gitlab.unige.ch/Aurelie.Hintermann/hintermannetal2022
Sequenced DNA fragments were processed as previously reported in (Amândio et al., 2020) with a minor modification on a local Galaxy server: the BAM file was converted to BED prior to peak calling with bedtools version 2.30.0
Peak calling was done using MACS2 (v2.1.1.20160309) callpeak (--no-model --shift -100 --extsize 200 --call-summits --keep-dup all).
Peak regions for each condition were obtained from the union of the peak region of both replicates with bedtools merge (v2.30.0) and extended by 660 bp each side with bedtools slop.
Each replicate was normalized per million reads mapped in their own peaks, subsetted in the HoxD region (mm10,chr2:73000000-77000000 ; galGal6, chr7:13000000-17000000) and the neq2 coverage is the mean of normalized replicates
Assembly: mm10
Assembly: galGal6
Supplementary files format and content: bigwig: coverage from MACS2
Supplementary files format and content: narrowPeak: narrowPeak from MACS2
Supplementary files format and content: bedgraph: replicates were  normalized to the number of million reads falling in their own peaks, subsetted in the HoxD region (mm10,chr2:73000000-77000000 ; galGal6, chr7:13000000-17000000) and averaged.
Supplementary files format and content: bed: narrowPeaks of both replicates were pooled, extended by 660 bp each side and then merged to obtain non-overlapping intervals.

organism: Gallus gallus

source_name: White Leghorn

extract_protocol:
ATAC-seq experiments were performed as described in (Bolt et al., 2022)
ATAC-seq librairies were prepared as described in (Bolt et al., 2022)

tag: developmental stage

value: White Leghorn

tag: genotype

value: WT

tag: dissection

value: One telencephalon was micro-dissected from one HH35 embryo.


title: 14169_DMSO_4h_rep3

tag: treatment


title: 14169_BI00894999_10nM_4h_rep2


title: 10-15_BI00894999_10nM_24h_rep3

source_name: 10-15 cancer cell line


title: 14169_BI00894999_10nM_4h_rep1


title: 10-15_BI00894999_10nM_CCS1477_300nM_24h_rep2


title: 10-15_CCS1477_300nM_24h_rep1


title: 14169_DMSO_4h_rep1


title: 14169_BI00894999_10nM_24h_rep1


title: 14169_CCS1477_300nM_4h_rep3


title: 10-15_BI00894999_10nM_24h_rep2


title: 14169_BI00894999_10nM_CCS1477_300nM_4h_rep2


title: 10-15_BI00894999_10nM_CCS1477_300nM_4h_rep3


title: 14169_BI00894999_10nM_4h_rep3


title: 14169_BI00894999_10nM_CCS1477_300nM_4h_rep3


title: 14169_CCS1477_300nM_4h_rep2


title: 14169_BI00894999_10nM_CCS1477_300nM_4h_rep1


title: 10-15_BI00894999_10nM_CCS1477_300nM_24h_rep1


title: 10-15_BI00894999_10nM_CCS1477_300nM_4h_rep2


title: 10-15_BI00894999_10nM_24h_rep1


title: 14169_CCS1477_300nM_4h_rep1


title: ATAC_HH35_DS_rep2

description:
ATAC HH35 dorsal skin
ATAC

tag: strain

value: A portion of dorsal skin tissue micro-was dissected from the neck to the shoulder from one HH35 embryo.


title: 14169_DMSO_4h_rep2


title: ATAC_HH35_FB_rep1

description:
ATAC HH35 forebrain
ATAC


title: 10-15_CCS1477_300nM_4h_rep3


title: 10-15_BI00894999_10nM_CCS1477_300nM_24h_rep3


title: 10-15_BI00894999_10nM_CCS1477_300nM_4h_rep1


title: 10-15_CCS1477_300nM_4h_rep2


title: 10-15_CCS1477_300nM_24h_rep2


title: ATAC_HH35_DS_rep1

description:
ATAC HH35 dorsal skin
ATAC


title: Ty-82_BI00894999_10nM_CCS1477_300nM_24h_rep2

source_name: Ty-82 cancer cell line


title: 10-15_DMSO_4h_rep2


title: 10-15_BI00894999_10nM_4h_rep3


title: Ty-82_BI00894999_10nM_CCS1477_300nM_24h_rep3


title: 10-15_BI00894999_10nM_4h_rep2


title: 10-15_DMSO_4h_rep3


title: Ty-82_CCS1477_300nM_24h_rep2


title: Ty-82_BI00894999_10nM_CCS1477_300nM_4h_rep3


title: 10-15_DMSO_4h_rep1


title: Ty-82_CCS1477_300nM_4h_rep2


title: Ty-82_CCS1477_300nM_24h_rep1


title: Ty-82_BI00894999_10nM_CCS1477_300nM_4h_rep1


title: Ty-82_CCS1477_300nM_4h_rep3


title: Ty-82_BI00894999_10nM_24h_rep2


title: Ty-82_BI00894999_10nM_4h_rep3


title: Ty-82_BI00894999_10nM_CCS1477_300nM_24h_rep1


title: Ty-82_BI00894999_10nM_4h_rep2


title: Ty-82_BI00894999_10nM_24h_rep3


title: Ty-82_DMSO_4h_rep3


title: Ty-82_DMSO_4h_rep2


title: Ty-82_BI00894999_10nM_4h_rep1


title: Ty-82_DMSO_4h_rep1


title: 10-15_BI00894999_10nM_4h_rep1


title: Ty-82_BI00894999_10nM_CCS1477_300nM_4h_rep2


title: Ty-82_BI00894999_10nM_24h_rep1


title: Tumour replicate 2

status: Public on Jun 14 2022

city: Toronto

first: Akram

last: Hamed

department: Molecular Genetics

country: Canada

institute: University of Toronto

library_source: transcriptomic single cell

data_processing:
The raw single-cell RNA sequencing fastq files were aligned and quantified using Cell Ranger (v3.1.0, 10x Genomics Inc.) and the mm10 mouse reference (Cell Ranger reference, v3.00). Cells with fewer than 1000 genes detected were considered to be empty droplets or nuclei and removed from the data-set. For doublet detection, the over-clustering approach by Pijuan-Sala et al. in combination with Scrublet (v0.2.1) was adapted. In addition, a mitochondrial threshold to exclude cells with high mitochondrial content which might indicate stressed or lysing cells was determined at a per sample basis. To remove any sex specific effects, the genes Xist, Tsix, Eif2s3y, Ddx3y, Uty, and Kdm5d were excluded from the analysis. For the regular single cell analysis the default scanpy (v1.5.1) pipeline in python (v3.6.9) was used for highly variable gene selection, regression (counts), dimensionality reduction, clustering, etc
Assembly: mm10
Supplementary files format and content: Raw count matrix of the mouse forebrain atlas including counts for all cells and genes before quality control.
Supplementary files format and content: File containing the metadata information such as sampleID, timepoint, cell annotation and UMAP coordinates for the various subsets. This file can be used to subset the count matrix.
Supplementary files format and content: AnnData object containing the mouse forebrain atlas with log-normalised data in adata.raw slot and metadata for the subsets in adata.obs.

source_name: Brain

extract_protocol:
Fresh brain tissues from embryo/postnatal Sox2eGFP mice were collected following intracardial perfusion of mice (pregnant females in case of embryo samples) with PBS. The tissue was transferred to a petri dish placed on ice and the cerebrum was isolated under a Leica stereoscope, rinsed in PBS, dissociated into single cells as previously reported then passed through a 40-µm mesh cell strainer. Debris was removed using a debris-removal kit (Miltenyi) and the cells were stained with DAPI followed by sorting the live GFP+ve/-ve cells. For the mouse tumour samples, the mouse harboring the tumour was imaged by MRI 30 minutes before sample collection through intracardial perfusion with PBS and dissection of the hemisphere encompassing the tumour followed by tissue dissociation as described above. Finally, the cells were stained with DAPI before sorting the live tdTomato+ cells.
Single-cell suspensions with an average cell viability of 80% were loaded onto the 10x Genomics Chromium Platform (10X Genomics, Pleasanton, CA, USA) to recover 6,000 single-cell-containing gel beads in emulsion (GEMs). Single Cell RNA-seq libraries were prepared according to 10x Genomics manufacturing protocols (Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3, 16 rxns PN-1000075. User Guide CG000183 Rev A) using a Veriti thermal cycler (ThermoFisher Scientific, Waltham, MA, USA). cDNA and Library quality were assessed using an Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA). Quantification of Library was performed using StepOne Real-Time PCR System (ThermoFisher Scientific, Waltham, MA, USA). Sequencing was done on the Illumina Hiseq 2500 paired-end sequencing 29+8+101bp.

value: Tumour sample

value: Nestin-Cre; P53 f/f; Pten f/+; R26 tdTomato/+

tag: tissue

value: brain


title: Tumour replicate 1


title: Ty-82_CCS1477_300nM_4h_rep1


title: P365_GFP-ve

value: Postnatal day 365


title: P111_GFP+ve

value: Postnatal day 111


title: P365_GFP+ve


title: P111_GFP-ve


title: Ty-82_CCS1477_300nM_24h_rep3


title: P39_GFP+ve

value: Postnatal day 39


title: P39_GFP-ve


title: P19_GFP-ve

value: Postnatal day 19


title: P13_GFP-ve

value: Postnatal day 13


title: P2_GFP+ve

value: Postnatal day 2


title: P7_GFP-ve

value: Postnatal day 7


title: P7_GFP+ve


title: P13_GFP+ve


title: P0_GFP-ve

value: Postnatal day 0


title: E14.5_GFP-ve

value: Prenatal day E14.5


title: E16.5_GFP+ve

value: Prenatal day E16.5


title: P0_GFP+ve


title: E14.5_GFP+ve


title: P2_GFP-ve


title: P19_GFP+ve


title: E12.5_GFP+ve

value: Prenatal day E12.5


title: Donor3_MPA+PGE2

status: Public on Jun 06 2022

city: columbia

first: Hongyu

state: mo

address: 920 east campus drive.

institute: university of missouri

data_processing:
Pair-end sequencing was performed on hormone treated EEO derived from three donors. FastQC (v 0.11.9) and MultiQC (v 1.10.1) were used to evaluate the quality of the sequence. Trimmomatic (v 1.10.1) was used to remove adapters and low-quality bases from the reads. Trimmed reads were aligned to the human genome (GRCh38) with STAR aligner (v 2.7.9a) (average unique mapping rate of 89.21% and read length of 200 bp). Gene quantification was calculated by using featureCounts from Subread package (v 2.0.3).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: endometrial epithelial organoid (

extract_protocol:
Total RNA was extracted from EEO and stromal cells using a standard TRIzol-based protocol and Direct-zol RNA MiniPrep Plus isolation kit (Zymo Research, R2070). To eliminate genomic DNA contamination, isolated RNA was treated with DNase I (RNase-Free DNase Set, Qiagen, 79256).
Total RNA (500ng) from each sample was reverse transcribed using iScript RT Supermix (Bio-Rad, 1708841). Real-time PCR was performed using SsoAdvanced Universal SYBR Green Supermix

value: endometrial epithelial organoid (

tag: age


title: Donor3_MPA

value: MPA


title: Donor3_E2+MPA


title: E16.5_GFP-ve


title: Donor2_MPA+PGE2


title: Donor1_MPA+PGE2


title: Donor3_E2


title: Donor2_E2+MPA


title: Donor3_control

value: WT


title: Donor2_MPA


title: Donor2_E2


title: Donor2_control


title: Donor1_E2+MPA


title: Donor1_E2


title: 10-15_CCS1477_300nM_4h_rep1

value: NUT midline carcinoma


title: Input_trimmed_sort_dedup_mapped_45M

status: Public on Jun 03 2022

city: Omaha

first: Samikshan

last: Dutta

state: NE

address: 42 and Emile

department: BMB

institute: univ of nebraska medical center

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
Resulting fastq files were aligned to the human genome (hg38) using the sequence aligner Bowtie2 (version 2.2.3).
Picard routine MarkDuplicates (http://broadinstitute.github.io/picard/ [broadinstitute.github.io]) was used to remove sequence duplications.
Peak calling, of ChIP enriched regions the THOR peak caller software of each ChIP to corresponding input DNA sample was used to determine binding regions based on a FDR adjusted p-value (q-value) <0.05.
BigWig files were generated using the resulting bam files and deeptools bamCoverage routine (https://deeptools.readthedocs.io/en/develop/ [deeptools.readthedocs.io]).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

growth_protocol: RPMI, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Disuccinimidyl glutarate (DSG) was used at a final concentration of 2mM and incubated for 45 minutes at room temperature. At the end of fixation, cells were centrifuge at 1500 rpm for 10 minutes. The pellete was washed in PBS for 3 times and the treated with 1% formaldehyde for 10mins at room temperature.  After quenching and cell lysis, chromatin was sonicated using a Bioraptor (Diagenode)
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

tag: cell line

value: Human prostate adenocarcinoma

tag: chip antibody


title: C4-2B_trimmed_sort_dedup_mapped_45M_set 1

value: NRP2 (C9) (Santa Cruz, sc-13117)


title: C4-2B_trimmed_sort_dedup_mapped_45M_set 2


title: Donor1_MPA


title: E12.5_GFP-ve

value: brain


title: Wen_Tle4_P48_final_R3

status: Public on May 31 2022

city: Cambridge

first: Paola

last: Arlotta

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing:
Raw sequencing reads were trimmed 8bp from the 5’ end and 40 to 60bp from the 3’ end, depending on library quality
Reads were aligned to the genome build NCBI37
Aligned data was then filtered for PCR duplicates
CpG methylation calling was performed on the duplicate filtered data
Assembly: mm9
Supplementary files format and content: BED format files with methylation calls

source_name: somatosensory cortex and motor cortex

growth_protocol: Experiments using mice were conducted under protocols approved by the Harvard University Institutional Animal Care and Use Committee and followed the guidelines set forth in the National Institute of Health Guide for the Care and Use of Laboratory Animals.

extract_protocol:
To prepare nuclei, around 50,000 cells at 500g for 5 min, which was followed by a wash using 50 μL of cold 1× PBS and centrifugation at 500g for 5 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min using a refrigerated centrifuge.
Pools of 5,000-10,000 cortical pyramidal neurons were sorted into PBS. The EZ DNA Methylation-Direct Kit (Zymo Research) was used to perform bisulfite conversion and libraries were prepared with the EpiGnome Methyl-Seq Kit (Illumina).

treatment_protocol:
4-Hydroxytamoxifen (4-OHT; Sigma) dissolved in corn oil was administered to pregnant mice at 1 mg 4-OHT/10g body weight.
Cortex was dissected in cold dissociation medium (20 mm glucose, 0.8 mm kynurenic acid, 0.05 mmAPV, 50 U/ml penicillin–0.05 mg/ml streptomycin, 0.09mNa2SO4, 0.03mK2SO4, and 0.014m MgCl2). The cortex was enzymatically digested in dissociation medium containing 0.16 gm/l l-cysteine and 12 U/ml papain at 37°C for 30 min. Papain digestion was then blocked with dissociation medium containing 10 mg/ml ovomucoid (Sigma, St. Louis, MO) and 10 mg/ml bovine serum albumin (BSA) at room temperature. Neurons were mechanically dissociated to create a single cell suspension by gentle trituration in iced OptiMem (Life Technologies, Gaithersburg, MD) containing 20 mm glucose and both 0.4 mmkynurenic acid and 0.025 mm APV to protect against glutamate-induced neurotoxicity. Td-tomato labeled projection neurrons were purified from the cortical cell suspension by fluorescence-activated cell sorting (FACS) using a FACSVantage flow cytometer.

value: somatosensory cortex and motor cortex

value: 4-HydroxyTamoxifen injection


title: Wen_Tle4_P1_final_R3


title: Donor1_control


title: Wen_Tle4_P1_final_R4


title: Wen_Tle4_P21_final_R3


title: Wen_Cux2_P48_R1


title: Wen_Cux2_P48_R2


title: Wen_Cux2_P21_R2


title: Wen_Tle4_P21_final_R4


title: Wen_Cux2_P1_R2


title: Wen_Tle4_P48_final_R4


title: RBC23676 High Dosage HMB

status: Public on Jun 01 2022

hyb_protocol: RNA was hybridized to Affymetrix Rat Genome 230 2.0 Array using Affymetrix GeneChip Hybridization Oven 640 according to Battelle SOP No. BBRC VI-107 Standard Operating Procedure for the Operation and  Maintenance of the Affymetrix GeneChip Hybridization Oven 640

scan_protocol: Each array was scanned using an Affymetrix GeneChip Scanner, model 3000 7G according to Battelle SOP No. BBRC VI-108 Standard Operating Procedure for the Operation and  Maintenance of the Affymetrix GeneChip Scanner 3000

data_processing: The raw microarray data was normalized using the Robust Multi-array Average (RMA) probe set summarization method to produce the file. No other data processing procedures (e.g. statistical analysis) were performed.

source_name: liver

label_protocol: Standard Affymetrix protocol

extract_protocol: Liver samples were placed in RNAlater and treated according to the manufacturer's protocol. The sample placed in RNAlater were minced into 2-3 mm pieces, maintained on wet ice until the end of necropsy, and subsequently refrigerated overnight. The liver samples were then frozen in liquid nitrogen and maintained at  -80 derees centigrade until shipped frozen to an NTP-designated laboratory for RNA extraction and microarray assessment.

treatment_protocol: HMB was administered by dosed feed to rats for 13-weeks. Rats received the test article in the diet at 10000 ppm. All rats remained on the treatment regimen until the day of sacrifice. Rats were housed 5 per cage and maintained on NTP-2000 diet.

value: Harlan Sprague Dawley

tag: animal number

tag: chemical

value: HMB

tag: dose


title: Wen_Cux2_P1_R1


title: single-cell RNA-seq of tdTomato+ cells from placenta and yolk sac of E13.5 chimera

status: Public on May 25 2022

city: Haidian

first: Pengcheng

last: Tan

address: 30 Shuangqing Rd

institute: Tsinghua University

data_processing:
Cell Ranger (v6.0.2) was used to align and quantify the ciTotiSCs scRNA-seq data
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes cell barcodes
Supplementary_files_format_and_content: tab-delimited text file includes features
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: placenta and yolk sac of E13.5 chimera

growth_protocol: For sc-ciTotiSC sample preparation, ciTotiSCs were cultured in KSR basal medium composed of KO DMEM, 5% KSR (Gibco, 10828010), CDL (CD lipid concentrate, 500X, Gibco, 11905-031), 1% N2 (ThermoFisher, A1370701), 1X L-glutaMAX, 1X penicillin-streptomycin, 1X non-essential amino acids (NEAA), 1X sodium pyruvate, 55 μM 2-mercaptoethanol and 1000 U/mL mouse leukemia inhibitory factor (mLIF), 50 ng/ml Sodium L-ascorbyl-2-phosphate (Selleck, S5115) supplemented with 2.5 μM 1-Azakenpaullone (Selleck, S7193), 0.5 μM WS6 (Selleck, S7442) and 0.2 μM TTNPB (Selleck, S4627). Cells were passaged every 2-3 days using 0.05% Trypsin-EDTA at a ratio of 1:3-1:5 on inactivated MEF feeder layers.

extract_protocol:
RNA was extracted according to the manufacture’s manual for 10X Genomic’s scRNA-seq .
About 10,000 cells were used to generate 10X Genomic’s scRNA-seq library using single cell 3’ library and Gel Bead kit V2 according to the manufacture’s manual.
10X Genomics scRNA-seq

value: placenta and yolk sac of E13.5 chimera


title: RBC23674 High Dosage HMB


title: RBC23677 High Dosage HMB


title: RBC23667 Control

value: Control

value: 0 ppm


title: RBC23675 High Dosage HMB


title: OG2 mESC RNA-seq rep2

data_processing:
TrimGalore software (with Cutadapt v1.18) was used to trim adaptor and first 10-bp of both reads
TopHat2 (v2.1.1) was used for the alignment to the mm10 reference genome with default parameters
The gene expression count matrix and FPKM value were analyzed by Cufflinks (v2.2.1) default pipline
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated-value table with FPKM values for every gene and every sample

source_name: OG2 mESC

growth_protocol: ciTotiSCs were cultured in KSR basal medium composed of KO DMEM, 5% KSR (Gibco, 10828010), CDL (CD lipid concentrate, 500X, Gibco, 11905-031), 1% N2 (ThermoFisher, A1370701), 1X L-glutaMAX, 1X penicillin-streptomycin, 1X non-essential amino acids (NEAA), 1X sodium pyruvate, 55 μM 2-mercaptoethanol and 1000 U/mL mouse leukemia inhibitory factor (mLIF), 50 ng/ml Sodium L-ascorbyl-2-phosphate (Selleck, S5115) supplemented with 2.5 μM 1-Azakenpaullone (Selleck, S7193), 0.5 μM WS6 (Selleck, S7442) and 0.2 μM TTNPB (Selleck, S4627). Cells were passaged every 2-3 days using 0.05% Trypsin-EDTA at a ratio of 1:3-1:5 on inactivated MEF feeder layers.

extract_protocol:
Total RNAs were extracted using TRIzol reagent.
mRNA-seq libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) according to the manufacturer’s protocol.

value: mESC


title: RBC23673 High Dosage HMB


title: OG2 mESC RNA-seq rep1


title: RBC23663 Control


title: P8 ciTotiSC RNA-seq rep1

source_name: ciTotiSC induced from OG2 mESC

value: ciTotiSC

tag: passage


title: RBC23665 Control


title: ciTotiSC single-cell RNA-seq

source_name: ciTotiSC


title: Wen_Cux2_P21_R1


title: P4 ciTotiSC RMA-seq rep2


title: P4 ciTotiSC RNA-seq rep1


title: RBC23666 Control


title: P1 ciTotiSC RNA-seq rep1


title: P2 ciTotiSC RNA-seq rep2


title: P1 ciTotiSC RNA-seq rep2


title: Autoimmune Rheumatic Diseases scRNAseq7_CMO

status: Public on May 19 2022

city: Taichung City

first: thh

last: lab

address: 1650 Taiwan Boulevard Sect. 4, Taichung, Taiwan 40705, ROC

country: Taiwan

institute: TCVGH

description: CMO counts are in processed data files on GEX sample GSM6153523

data_processing:
we used the cell multiplex labeling technic, which could label several samples and pool samples together to build one single-cell RNA-seq library. Through this technic, the library comprised two parts, CMO (or multiplex) and GEX. Therefore, there might have been more than one sample in a single library. In this case, The CMO fastq file should not merge with the fastq file of GEX. The cellranger software will need both of them and produce the *.barcode.tsv, *.feature.tsv and *.matrix.tsv files. We use R package Seurat to read these tsv files and a build-in function could demultiplex the CMO tags for separating each sample in the same library.
sequence reads were mapped to the human reference genome GRCh38 by CellRanger (version 6.0.1)
cells with unique feature counts over 9000 or less 200 will be filtered and cells with mitochondrial counts over than 10% will be eliminate as noise signals.
SCTransform was applied to the cells in each batch for normalization, then the 5 batches were integrated by using SCTransform integration workflow.
Assembly: GRCh38
Supplementary files format and content: tab delimited text file include raw read counts for each sample

source_name: PBMC

extract_protocol: Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index, CG000388, Rev A)

tag: group

value: multiplexed sample:Vaccine_Hgih and Vaccine_Low

tag: library

tag: cmo

value: multiplexed sample:CMO310, CMO311


title: Autoimmune Rheumatic Diseases scRNAseq6

value: multiplexed sample:CMO302, CMO305, CMO0306, CMO0308


title: P2 ciTotiSC RNA-seq rep1

tag: cell type


title: Autoimmune Rheumatic Diseases scRNAseq6_CMO

description: CMO counts are in processed data files on GEX sample GSM6153521


title: mutant 50 uM Hemin biol rep 2

status: Public on May 16 2022

city: Haifa

last: Kornitzer

address: 1, Efron St

department: Faculty of Medicine

country: Israel

institute: Technion - IIT

description: P2 flow cell

data_processing:
Quality control was assessed using Fastqc (v0.11.8)
Reads were trimmed for adapters, low quality 3` and minimum length of 20 using CUTADAPT (v1.10).
100 bp single reads were aligned to a Candida_Albicans reference genome (GCF_000182965.3_ASM18296v3_genomic.fna from NCBI) using Tophat (v2.1.0, uses Bowtie2 version 2.2.6).
The number of reads per gene was counted using HTSeq-count (v2.2.0).
Assembly: GCF_000182965.3_ASM18296v3_genomic.fna from NCBI
Supplementary files format and content: The number of reads per gene was extracted into merged_counts.csv and normalized_counts.csv files for raw counts and normalized counts, respectively.

organism: Candida albicans

growth_protocol: Overnight cultures grown in YPD were diluted to OD600=0.5 and grown another 2.5 hours

extract_protocol:
Total RNA was extracted using hot phenol.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, cat no. E7760, using 800ng total RNA as a starting material. mRNAs pull-down was performed using the Magnetic Isolation Module (NEB, cat no. E7490). After construction, the concentration of each library was measured using Qubit (Invitrogen) and the size was determined using the TapeStation 4200 with the High Sensitivity D1000 kit (cat no. 5067-5584).

treatment_protocol: At time 0, the cultures were split and 50 mM hemin was added to one half each.

value: hap1 mutant

value: ura3-/- his1-/- arg4-/- leu2-/- hap1::NATr/hap1::LEU2 ADE2/ade2::URA3

value: YPD + 50 mM hemin 30'


title: mutant no Hemin biol rep 2

description: P2 flow cell

value: YPD


title: mutant 50 uM Hemin biol rep 3

description: P2 flow cell


title: HAP1 50 uM Hemin biol rep 3

description: P2 flow cell

value: Wild-type reintegrant

value: ura3-/- his1-/- arg4-/- leu2-/- hap1::NATr/hap1::LEU2 ADE2/ade2::HAP1 URA3


title: HAP1 no Hemin biol rep 3

description: P2 flow cell


title: Autoimmune Rheumatic Diseases scRNAseq7


title: HAP1 50 uM Hemin biol rep 2

description: P2 flow cell


title: mutant no Hemin biol rep 1

description: P2 flow cell


title: mutant 50 uM Hemin biol rep 1

description: P2 flow cell


title: HAP1 50 uM Hemin biol rep 1

description: P2 flow cell


title: HAP1 no Hemin biol rep 1

description: P2 flow cell


title: HAP1 no Hemin biol rep 2

description: P2 flow cell


title: AG39_CD4_28_pos_Mem

status: Public on May 05 2022

city: Bethesda

first: Jason

last: Brenchley

state: MD

address: 4 Center Drive

institute: NIAID

data_processing:
ATAC-seq samples were sequenced as 76bp paired-end libraries on a NextSeq or as 151bp paired-end libraries on a Novaseq S2. All samples had over 60 million reads.
Samples were trimmed for adapters using Cutadapt v 1.18 before alignment. The trimmed reads were aligned to the RheMac10 reference using Bowtie2 v2.3.4.1 with flag -k 10.
Genome_build: RheMac10
Supplementary_files_format_and_content: The peaks were called using Genrich v0.6 with the following flags -j -y -r -v -d 150 -m 5 -e chrM,chrY.
Supplementary_files_format_and_content: Genrich-produced bedgraphs were normalized by library size (reads per million sequenced reads, RPM) for visualization.

organism: Chlorocebus pygerythrus

source_name: T cells

extract_protocol:
Cells were isolated from fresh peripheral blood by density gradient centrifugation using lymphocyte separation media (MP Biomedicals, #0850494-CF), washed in PBS, counted, and approximately 5e6 cells resuspended in 100ul PBS. Cells were stained with LIVE/DEAD amine-reactive viability dye (Thermo Fisher Scientific, #L34966) and a panel of antibodies including anti-CD3 alexa fluor 700 (clone SP43-2, BD Biosciences, #557917), anti-CD4 allophycocyanin (clone L200, BD, #551980), anti-CD8α pacific blue (clone RPA-T8, BD, #558207), CD28 energy-coupled dye [ECD] (clone 28.2, Beckman Coulter, Brea, CA, #6607111), CD95 Cy5-PE (clone DX2, BD, #561977), for 20 minutes at 4°C. Cells were washed in PBS and resuspended in complete RPMI with 10% FBS. For each population, 30,000 cells were sorted using a FACSymphony S6 cell sorter (BD).
Tagmentation was performed by pelleting 30,000 sorted cells and resuspending in 2x Tagmentation Buffer (Illumina, #20034198), 0.02% Digitonin, and 0.1% Tween-20, with Tagment DNA TDE1 Enzyme (Illumina) and incubating at 37°C for one hour. The mix was then incubated with proteinase K for 30 minutes at 40°C. High molecular weight DNA was removed with a 0.7x selection ratio of Agencourt AMPureXP beads (Beckman Coulter, #A63881) and low molecular weight DNA was isolated from the remainder with a 1.2x selection ratio. Library amplification was performed with KAPA HiFi HotStart ReadyMix (KAPA, #KK2601) and i5 and i7 indexing primers (Nextera DNA CD Indexes, #20018708) for 11-15 total cycles depending on the sample concentration reached after 5 cycles (KAPA Library Quantification kit, #KK4835). Library DNA was purified with a 1x selection ratio of AMPureXP beads. The final library was verified by High Sensitivity DNA Bioanalyzer (Agilent, #5067-4626) to ensure the presence of appropriately sized DNA fragments.

tag: monkey identifier

tag: siv status

value: negative


title: AG39_CD8ab_Naive


title: AG39_CD8aa_28_pos_Mem


title: AG39_CD4_Naive


title: AG33_CD8ab_28_pos_Mem


title: RBC23664 Control

value: Harlan Sprague Dawley


title: AG33_CD8aa_28_pos_Mem


title: AG33_CD8ab_Naive


title: AG39_CD8ab_28_pos_Mem


title: AG33_CD4_28_pos_Mem


title: mutant no Hemin biol rep 3

description: P2 flow cell

tag: genotype


title: AG33_CD4_Naive


title: AG49_CD8ab_Naive


title: AG49_CD4_28plus_Mem


title: AG49_CD8ab_28plus_Mem


title: AG49_CD8aa_28plus_Mem


title: AG43_CD8ab_Naive


title: AG45_CD4_Naive


title: AG45_CD4_28plus_Mem


title: AG45_CD8aa_28plus_Mem


title: AG38_SIV_CD8ab_28plus_Mem

value: SIV positive


title: AG38_SIV_CD8aa_28plus_Mem


title: AG43_CD8ab_28plus_Mem


title: AG43_CD8aa_28plus_Mem


title: AG43_CD4_28plus_Mem


title: AG43_CD4_Naive


title: AG38_SIV_CD8ab_Naive


title: AG45_CD8ab_Naive


title: AG49_CD4_Naive


title: AG45_CD8ab_28plus_Mem


title: AG32_SIV_CD8ab_Naive


title: AG32_SIV_CD8ab_28plus_Mem


title: AG302_SIV_CD4_Naive


title: AG28_SIV_CD8aa_28plus_Mem


title: AG32_SIV_CD4_Naive


title: AG32_SIV_CD4_28plus_Mem


title: AG302_SIV_CD8ab_Naive


title: AG302_SIV_CD8ab_28plus_Mem


title: AG38_SIV_CD4_28plus_Mem


title: AG302_SIV_CD8aa_28plus_Mem


title: AG302_SIV_CD4_28plus_Mem


title: AG28_SIV_CD8ab_Naive


title: AG28_SIV_CD4_28plus_Mem


title: AG14_SIV_CD8ab_28plus_Mem


title: AG14_SIV_CD8ab_Naive


title: AG28_SIV_CD8ab_28plus_Mem


title: Airway Asthma 142

status: Public on May 04 2022

city: Chicago

first: Carole

last: Ober

state: IL

address: 920 E 58TH ST

department: Human Genetics

institute: The University of Chicago

data_processing:
Quality control checks were performed using FastQC. RNA sequences were then aligned and annotated to known RNA sequences using Spliced Transcripts Alignment to a Reference using STAR.
Genes with low count data (<1 CPM in at least 25% of the sample) and those on the X, Y, and mitochondrial chromosomes were removed.
Raw counts were normalized using the trimmed mean of M-values (TMM) method. Mean-variance trend was adjusted using variance modeling in voom.
Sequencing batch, age, sex, current smoking status, and the first three ancestry principal components were regressed out from the gene expression data using the removeBatchEffect function as implemented in limma.
Assembly: GRCh38.primary_Gencode27
Supplementary files format and content: normalized and covariate-adjusted gene expression data

source_name: primary bronchial epithelial cells

extract_protocol:
Genomic DNA was isolated and purified from primary bronchial epithelial cells using the QIAzol lysis reagent or the AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN).
Standard Illumina protocol.

value: primary bronchial epithelial cells

tag: batch

tag: recruitment source

value: Re-CABFIR

tag: Sex

value: Female

tag: self-reported race/ethnicity

value: African American

tag: asthma

value: Asthma

tag: maternal asthma

value: No

tag: step

tag: ige

tag: bmi

tag: feno

value: N


title: AG28_SIV_CD4_Naive


title: Airway Control 117

tag: tissue

value: CABFIR

tag: age

value: Male

value: Control


title: AG38_SIV_CD4_Naive


title: Airway Control 118


title: AG32_SIV_CD8aa_28plus_Mem


title: AG14_SIV_CD8aa_28plus_Mem


title: AG14_SIV_CD4_Naive


title: AG14_SIV_CD4_28plus_Mem


title: Airway Asthma 126

value: European American


title: Airway Asthma 124


title: Airway Asthma 136

value: ROLD


title: Airway Control 132

value: Other


title: Airway Control 20

value: ABRIDGE


title: Airway Control 38

value: Y


title: Airway Control 39


title: Airway Asthma 119

value: Yes


title: Airway Asthma 114


title: Airway Control 125


title: Airway Asthma 140


title: Airway Asthma 99


title: Airway Control 97


title: Airway Asthma 67


title: Airway Asthma 87


title: Airway Asthma 7


title: Airway Asthma 123


title: Airway Asthma 55


title: Airway Control 35


title: Airway Asthma 131


title: Airway Asthma 107


title: Airway Asthma 72


title: Airway Asthma 58


title: Airway Asthma 129


title: Airway Asthma 11


title: Airway Control 17


title: Airway Asthma 128


title: Airway Asthma 9


title: Airway Asthma 137


title: Airway Asthma 120


title: Airway Asthma 115


title: Airway Asthma 111


title: Airway Asthma 48


title: Airway Asthma 73


title: Airway Control 81


title: Airway Control 18


title: Airway Asthma 79


title: Airway Asthma 91


title: Airway Control 69


title: Airway Asthma 23


title: Airway Asthma 116


title: Airway Control 85


title: Airway Asthma 76


title: Airway Control 95


title: Airway Control 100


title: Airway Control 80


title: Airway Asthma 52


title: Airway Asthma 66


title: Airway Asthma 78


title: Airway Asthma 92


title: Airway Asthma 71


title: Airway Asthma 53


title: Airway Control 62


title: Airway Asthma 110


title: Airway Asthma 112


title: Airway Asthma 75


title: Airway Control 82


title: Airway Control 93


title: Airway Control 64


title: Airway Control 105


title: Airway Control 86


title: Airway Asthma 108


title: Airway Asthma 98


title: Airway Asthma 90


title: Airway Control 89


title: Airway Asthma 106


title: Airway Control 109


title: Airway Control 57


title: Airway Control 50


title: Airway Asthma 43


title: Airway Control 32


title: Airway Asthma 30


title: Airway Control 34


title: Airway Asthma 25


title: Airway Control 28


title: Airway Asthma 37


title: Airway Control 46


title: Airway Control 12


title: Airway Control 33


title: Airway Asthma 27


title: Airway Asthma 26


title: Airway Asthma 1


title: Airway Control 40


title: Airway Asthma 29


title: Airway Asthma 31


title: Airway Control 19


title: Airway Control 21


title: Airway Control 14


title: Airway Asthma 5


title: Airway Control 16


title: Airway Asthma 10


title: Airway Asthma 3


title: Airway Asthma 41


title: Airway Asthma 6


title: Airway Control 15


title: Airway Asthma 8


title: Airway Asthma 4


title: Airway Asthma 70


title: Airway Asthma 102


title: Airway Asthma 36


title: Airway Asthma 101


title: Airway Asthma 68


title: Airway Asthma 88


title: Airway Asthma 56


title: Airway Asthma 60


title: Airway Asthma 96


title: Airway Asthma 59


title: Airway Asthma 51


title: Airway Asthma 63


title: Airway Asthma 83


title: Airway Asthma 49


title: Airway Asthma 104


title: Airway Asthma 94


title: Airway Asthma 61


title: Airway Asthma 44


title: ATACseq_blastula_rep2

city: London

first: Yan

last: Liang

state: London

address: mile end road

department: SBBS

country: United Kingdom

institute: Queen Mary Univerisity of London

data_processing:
RNA-seq: Sequencing adaptors were removed from raw reads by using trimomatic (version 0.39)
RNA-seq:the reads were mapped to the transcriptome by using Kallisto (0.46.2)
RNA-seq: the gene expression profile was normalized from 13 developmental stages by DESeq2 package (1.30.1) in R (version 3.6).
ATAC-seq: The adaptors of raw reads of each library were removed by using cutadaptor (version 2.5).
ATAC-seq: the reads were mapped to the genome by using NextGenMap (version 0.5.5) as paired-end reads (--paired). Duplications were removed by samtools (view -b -F 0x400 -f 0x2) (version 1.9). The mapped reads (bamfiles) were shifted by using deeptools (alignmentSieve ---ATACshift) (version 3.4.3).
ATAC-seq: MACS2 (version 2.2.7.1) were applied to each shifted bam file to call peaks (-f BAMPE; --min-length 100; --max-gap 75; -q 0.01).
genome build: owenia fusiformis
processed data files format and content: RNA-seq:Owenia_annotation_v250920_filtered_mRNA.fasta is the filtered gene model we used for Kallisto mapping; Ofus_gene_expression_matrix.txt is the output results from DESeq2 normalization; ATAC-seq: all the narrowPeak files are the output from MACS2 analysis.

organism: Owenia fusiformis

source_name: Blastula stage

growth_protocol: The Owenia fusiformis embryos, larvae and juvenile were reared in artificial sea water, and the larvae were fed with mix algae.

extract_protocol:
RNA-seq: All the fresh samples were snapped freezed by liquid nitrogen, then extracted using the Monarch total RNA Miniprep Kit; ATAC-seq:50,000 cells (~900 blastula, ~500 gastrula, ~300 elongation, ~150 mature larvae and ~40 competent larvae) were washed in 1 ml cold PBS and resuspended in 100  µl cold ATAC lysis buffer 1 (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) IGEPAL, 0.1% (v/v) Tween-20, 0.01% (v/v) Digitonin) and used the pestle to homogenize the samples, then and incubated on ice for 3 minutes to lyse cells. The lysis reaction was stopped by adding 1 ml of cold ATAC wash buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Tween-20) and inverting the tube for 3 times to mix. The nuclei were pelleted by centrifugation at 500xg for 10 minutes at 4℃ in a fixed angle centrifuge.
RNA-seq: All the libraries were constructed by Oxford genomic center; ATAC-seq:  The supernatant was removed and the nuclei pellet was resuspended in transposition mix containing 5 µl of 10x TMg buffer (100 mM Tris-HCl pH 8.5, 50 mM MgCl2), 5 µl Dimethyl Formamide, 2.5 µl of 100 nM in-house made Tn5 enzyme, 16.5 µl PBS, 0.5 µl of 1% (v/v) digitonin, 0.5 µl of 10% (v/v) Tween-20, and 20 µl H2O. The transposition reaction was incubated at 37°C for 30 minutes in a thermomixer with 1000 rpm mixing. Transposed DNA was cleaned up using the NEB DNA Cleanup kit following manufacturer’s instructions. All 10 µl eluted DNA was subjected to 5 cycles of PCR amplification, and 5 µl of this pre-amplified library was used for qPCR to determine the PCR cycles, finally all the libraries were amplified in 7~12 cycles using the NEBNext High-Fidelity 2X PCR Master Mix.
RNA-seq and ATAC-seq

treatment_protocol: By adding few mud to stimulate the metaphomorphsis of competent larvae to  juvenile.

tag: developmental stage

value: Blastula stage

tag: developmental time points

value: 5h hpf

tag: morphology

value: embryo


title: 11D

status: Public on May 02 2022

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

data_processing:
Illumina Pipeline  Casava 1.9
Data were analyzed using DEseq2
Genome_build: Genome_build: mm10
Supplementary_files_format_and_content: raw counts after read mapping are provided, as well as differential analysis output from DEseq2

source_name: sciatic nerve

growth_protocol: Mice were housed with a normal light/dark cycles and ad libitum access to rat chow and water. Bap1-floxed mice were mated to mP0TOTA-Cre (B6N.FVB-Tg(Mpz-cre)26Mes/J, obtained from Jackson Laboratory, RRID: IMSR_JAX:017927).

extract_protocol:
Total RNA was purified using Zymo RNA purification kit
Illumina, RNA with PolyA selection,
Illumina HiSeq 2x150bp, performed by Genewiz (South Plainfield, NJ)

treatment_protocol: The sciatic nerves of adult mice were harvested at the age of 2 months.

value: ~8 wk

tag: treatment

value: Intact

value: Bap1 fl/fl, Cre


title: Sp24

tag: genotype

value: Bap1 fl/fl


title: Sp4


title: Sp2


title: Sp25


title: ATACseq_blastula_rep1


title: Sp26


title: Sp22


title: 10D


title: Sp21


title: 9C


title: Sp23


title: 6C

data_processing:
Illumina Pipeline  Casava 1.9
Reads were aligned to GRCm38/mm10 genome using the STAR aligner.
Data were analyzed using DEseq2
Genome_build: Genome_build: mm10
Supplementary_files_format_and_content: raw counts after read mapping are provided, as well as differential analysis output from DEseq2


title: Airway_Asthma_141

type: genomic

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to the Illumina Infinium Human Methylation 450K Bead Chip or the Illumina Infinium Human Methylation EPIC Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using standard Illumina scanner settings.

data_processing: Only probes that were present on both arrays were retained usign the combineArrays function in the minfi package. Probes located on the sex chromosomes and those with detection p-values > 0.01 in more than 10% of samples were removed from the analysis. Cross-reactive probes and probes within two nucleoties of a SNP with MAF > 0.05 were removed using the function rmSNPandCH() from the R package DMRcate. Data were processed using Minfi. A preprocessing control normalization function was applied to correct for raw probe values or background and single-sample Noob (ssNoob) was used to correct for technical differences between the Infinium type I and type II probes and across the two generations of Infinium Methylation arrays.

label_protocol: Standard Illumina protocol.

extract_protocol: Genomic DNA was isolated and purified from primary bronchial epithelial cells using the QIAzol lysis reagent or the AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN).

value: EPIC

tag: batch

tag: ChIP

value: Female

value: Asthma

value: No


title: Airway_Asthma_139

tag: recruitment source

tag: Sex

value: Male

value: European American


title: Airway_Asthma_138

value: CABFIR

tag: self-reported race/ethnicity

value: African American

tag: asthma


title: Airway_Control_132

value: Other

value: Control

tag: maternal asthma

tag: step


title: Airway_Asthma_142

tag: ige

tag: bmi


title: Airway_Asthma_140

value: Yes

tag: feno


title: Airway_Asthma_137

value: ROLD

tag: age


title: Airway_Asthma_126


title: Airway_Asthma_135


title: Airway_Control_125


title: Airway_Asthma_130


title: Airway_Asthma_129


title: Airway_Control_134


title: Airway_Asthma_127


title: Airway_Asthma_110


title: Airway_Asthma_108


title: Airway_Asthma_112


title: Airway_Asthma_124


title: Airway_Asthma_119


title: Airway_Asthma_131


title: Airway_Asthma_120


title: Airway_Asthma_128


title: Airway_Control_109


title: Airway_Asthma_122


title: Airway_Asthma_123


title: Airway_Asthma_121


title: Airway_Asthma_111


title: Airway_Asthma_133


title: Airway_Asthma_136


title: Airway_Asthma_107


title: Airway_Asthma_114


title: Airway_Asthma_113


title: Airway_Control_105


title: Airway_Asthma_106


title: Airway_Asthma_116


title: Airway_Control_100


title: Airway_Control_103


title: Airway_Asthma_104


title: Airway_Asthma_115


title: Airway_Asthma_102


title: Airway_Asthma_98


title: Airway_Asthma_94


title: Airway_Control_93


title: Airway_Control_95


title: Airway_Asthma_96


title: Airway_Control_118


title: Airway_Asthma_99


title: Airway_Asthma_101


title: Airway_Asthma_92


title: Airway_Control_97


title: Airway_Control_117


title: Airway_Asthma_88


title: Airway_Asthma_90


title: Airway_Control_89


title: Airway_Asthma_91


title: Airway_Control_85


title: Airway_Asthma_87


title: Airway_Asthma_83


title: Airway_Control_86


title: Airway_Control_81


title: Airway_Control_84


title: Airway_Asthma_79


title: Airway_Control_80


title: Airway_Asthma_72


title: Airway_Asthma_78


title: Airway_Asthma_76


title: Airway_Control_77


title: Airway_Asthma_67


title: Airway_Asthma_75


title: Airway_Control_82


title: Airway_Asthma_74


title: Airway_Control_69


title: Airway_Asthma_56


title: Airway_Asthma_73


title: Airway_Control_57


title: Airway_Asthma_59


title: Airway_Asthma_70


title: Airway_Control_64


title: Airway_Asthma_65


title: Airway_Asthma_66


title: Airway_Asthma_71


title: Airway_Asthma_60


title: Airway_Asthma_61


title: Airway_Asthma_68


title: Airway_Asthma_58


title: Airway_Asthma_63


title: Airway_Asthma_55


title: Airway_Asthma_48


title: Airway_Asthma_49


title: Airway_Control_46

value: ABRIDGE


title: Airway_Asthma_53


title: Airway_Asthma_51


title: Airway_Asthma_52


title: Airway_Asthma_36


title: Airway_Asthma_31


title: Airway_Asthma_27


title: Airway_Control_38


title: Airway_Control_35


title: Airway_Control_39


title: Airway_Control_50


title: Airway_Control_40


title: Airway_Asthma_54


title: Airway_Asthma_30


title: Airway_Control_47


title: Airway_Control_32


title: Airway_Control_34


title: Airway_Asthma_26


title: Airway_Control_33


title: Airway_Control_28


title: Airway_Asthma_44


title: Airway_Asthma_29


title: Airway_Asthma_43


title: Airway_Control_42


title: Airway_Asthma_37


title: Airway_Asthma_45


title: Airway_Asthma_41


title: Airway_Asthma_24


title: Airway_Control_62


title: Airway_Asthma_25


title: Airway_Asthma_22


title: Airway_Asthma_2


title: Airway_Control_12


title: Airway_Control_13


title: Airway_Asthma_10


title: Sm3-WSP2

status: Public on Apr 27 2022

city: Denver

first: Arnav

last: Gupta

state: CO

address: 1400 Jackson St. K720

department: Pulmonary and Critical Care

institute: National Jewish Health

data_processing:
Reads were trimmed for adapters, minimum length, and minimum quality using the bbduk tool from the BBMap Suite (v. 38.73) with arguments ‘ref=adapters.fa ktrim=r qtrim=10 k=23 mink=11 hdist=1 maq=10 minlen=20’
Trimmed reads were mapped to the human genome (hg38; downloaded from the UCSC genome browser on September 16, 2019, with corresponding hisat2 index files) using hisat2 (v. 2.1.0)
Resulting SAM files were converted to BAM format using samtools view (v. 1.9) with arguments ‘-S -b’, duplicates were removed using picard tools MarkDuplicates (v. 2.26.6) and then resulting BAM files were sorted and indexed using samtools sort and index, respectively.
Sorted BAM files were converted to bedGraph coverage format files using genomeCoverageBed from the BEDTools suite (v. 2.29.2) with arguments ‘-bg -ibam -g hg38 -strand +’.
Assembly: hg38
Supplementary files format and content: BedGraph files are non-normalized coverage files.

source_name: Sm3 small airway epithelial cells

growth_protocol: De-identified primary human small airway epithelial cells (< 2 mm diameter) were obtained from the National Jewish Health Biobank from subjects with no history of deployment or chronic lung disease. Cells were first co-cultured with irradiated NIH/3T3 (ATCC) fibroblasts in F-medium containing 1 uM Y-27632 (APEX Bio) and then passaged onto tissue culture dishes double-coated with Type I bovine collagen solution (Advanced Biomatrix) and grown to confluence in BronchiaLife Epithelial Medium with the complete LifeFactors Supplement Kit (Lifeline Cell Technology).

extract_protocol:
Cells were washed twice with 1X PBS and collected by scraping or pelleting prior to counting. Approximately 50K cells were pelleted and processed in duplicate as described in the Omni-ATAC-seq protocol published by Corces et al (Nature Methods, 2017).
Uniquely indexed sequencing adapters from the Nextera DNA CD Indexes Kit were added to both ends of transposed fragment libraries by PCR. Following final purification and size selection for 100-1000 bp fragments, libraries were pooled and sequenced on an Illumina NextSeq instrument using 37 bp paired-end reads.

treatment_protocol: Afghan Desert Particulate Matter (APM) were obtained generously from Drs. Gregory Downey and Hong Wei Chu and exposed to cells by suspension in cell culture medium for 20 hours. Wood Smoke Particles (WSP) were generated as described [Ghio 2012] and generously gifted by Dr. Andrew Ghio at the Environmental Protection Agency Laboratory in North Carolina. Particles were dehydrated for transportation and resuspended in PBS. Particles were disaggregated by sonication and sterilized under UV light for 20 minutes prior to addition directly to cell culture media at a concentration of 1 mg/ml for all experiments.

tag: cell type

value: small airway epithelial cells


title: Airway_Control_18


title: Sm1_PROseq-APM1

data_processing:
Reads were trimmed for adapters, minimum length, and minimum quality using the BBMap Suite (v. 38.05) bbduk.sh tool with arguments ‘literal=AAAAAAAAAAAAAAAAAAAAAAA ktrim=r qtrim=10 k=23 mink=11 hdist=1 maq=10 minlen=25’.
Trimmed reads were mapped to the human genome (hg38) using hisat2 (v. 2.1.0) and hg38 indexes downloaded from UCSC with settings '--very-sensitive and --no-spliced-alignment'.
Resulting SAM files were converted to BAM format using samtools view (v. 1.8) with arguments ‘-S -b’ and then sorted and indexed using samtools sort and index, respectively.
Sorted BAM files were converted to bedGraph coverage format files using genomeCoverageBed from the BEDTools suite (v. 2.25.0) for both positive and negative strands with arguments ‘-bg -ibam -g hg38 -strand [+/-]’. The fourth column (read coverage) of the negative strand file was negated and then concatenated with the positive strand file to generate a strand-differentiated bedGraph file.
FStitch (v. 1.0) was first used to filter regions of inactive transcription in all samples to lessen downstream compute processing requirements. FStitch train was used with arguments ‘-r (sample.positiveStand.bedGraph) -t (trainingFile.bed) -o (outputTrainingParameters.hmminfo)’ using the IGV (v. 2.3.75) Region Navigator tool to produce a BED format training file generated from one of the 10 min dex-treated samples that was determined to be most representative of the data in terms of read coverage, complexity, and total reads mapped.
FStitch segment was then run on all single-strand non-normalized bedGraph files with arguments ‘-r (sample.pos.bedgraph) -w (outputTrainingParameters.hmminfo) -o (sample.bed)’. Positive and negative strand files were then concatenated and sorted using sortBed in the BEDTools suite (v. 2.25.0).
Tfit (v. 1.0) was used to generate the predictions of bidirectionals/eRNAs. BED file annotations of preliminary bidirectional calls were generated using the Tfit bidir old module with arguments ‘-ij (sample.concatenated.bedGraph) -N (bidir old) -k (sample.concatenatedFStitch.bed) -mle 1 -o (output directory) -log out (output directory) -tss (hg38 RefSeq gene transcription start site file).
Using the bidirectional predictions file, the Tfit model module was run to get higher confidence calls with arguments ‘-ij (sample.concatenated.bedGraph) -k (preliminaryBidirectionals.bed) -N (tfit mod) -log out (output directory) -o (output directory) -config (config file)’ to produce a final BED annotation file of predicted bidirectionals.
Using the RefSeq : NCBI Reference Sequences for hg38, including both NM and NR accession types (downloaded from the UCSC track browser on May 18, 2018), counts were calculated for each sorted BAM file using multibBamCov in the BEDTools suite (v. 2.25.0). Genes (NM accession type) and lncRNAs (NR accession type) were then filtered such that only the isoform with the highest number of reads per annotated length was kept in order to minimize duplicate samples being included in differential transcription analysis.
DESeq2 (v. 1.20.0, Bioconductor release v. 3.7) was then used to determine which genes were differentially transcribed between the different cell types. For bidirectional/enhancer comparisons, all bidirectional prediction Tfit calls were first merged using mergeBed (argument -d 60) from the BEDTools suite (v. 2.25.0) to generate an annotation file. Counts were then calculated for each sample using multicov from the BEDTools suite (v. 2.25.0) and DESeq2 was used to calculate differentially transcribed bidirectionals/eRNAs.
Assembly: hg38
Supplementary files format and content: BedGraph files are non-normalized, strand-differentiated coverage files, as described above.

source_name: Sm1 primary small airway epithelial cells

extract_protocol:
Plates were washed in PBS and cells were scraped in Lysis Buffer prior to isolation of nuclei. Nuclear run-on reactions were performed on aliquots of 10 million nuclei in the presence of Biotin-11-CTP, then total RNA was isolated using TRIzol LS Reagent (Invitrogen). RNA was hydrolyzed with NaOH to yield fragments ~100 bp long and nascent RNA was enriched using M-280 Streptavidin Dynabeads (Invitrogen).
Sequencing adapters were ligated onto 3' ends of nascent RNA and then a second enrichment was performed using streptavidin beads. 5' ends were de-capped (RppH) and repaired (PNK) prior to ligation of sequencing adapters and the third and final streptavidin bead enrichment. Reverse transcription was then performed and purified cDNA libraries were amplified for sequencing in PCR reactions containing Illumina TruSeq Small RNA PCR Index Primers to differentially barcode the libraries and enable multiplexing. PCR-amplified libraries were size-selected for a range of ~140–350 bp (average fragment length ~250 bp) using Agencourt AMPure XP beads (Beckman Coulter) at a volume of 1X as instructed by the manufacturer. Libraries were then pooled and sequenced on an Illumina NextSeq instrument using 75 bp single-end reads.

treatment_protocol: Afghan Desert Particulate Matter (APM) were obtained generously from Drs. Gregory Downey and Hong Wei Chu and exposed to cells by suspension in cell culture medium for 20 hours.

value: primary small airway epithelial cells


title: Airway_Control_17


title: Airway_Control_15


title: Sm1_PROseq-APM2


title: Sm1_PROseq-Ctrl1


title: Sm1_PROseq-Ctrl2


title: Airway_Control_21


title: Airway_Control_19


title: Airway_Asthma_9


title: Airway_Control_14


title: Airway_Asthma_5


title: Airway_Asthma_4


title: Airway_Control_16


title: Sm3-WSP1


title: Sm3-veh2


title: Airway_Asthma_8


title: Airway_Asthma_23


title: Airway_Asthma_3


title: Airway_Asthma_6


title: Airway_Asthma_1


title: Airway_Asthma_11


title: Airway_Control_20


title: Airway_Asthma_7


title: Sm3-veh1


title: Sm2-WSP2

source_name: Sm2 small airway epithelial cells


title: Sm2-veh2


title: Sm1-Ctrl1

source_name: Sm1 small airway epithelial cells