title: Genomic DNA of the mother

city: Sapporo

first: Yoshikazu

last: Furuta

state: Hokkaido

address: North 20 West 10, Kita-ku

department: International Institute for Zoonosis Control

institute: Hokkaido University

data_processing:
library strategy: Cas9-targeted sequencing (nCATS)
Basecalls were performed using Guppy 5.0.11 using dna_r9.4.1_450bps_sup.cfg as a DNA model
Mapping to the genomic sequence of COL7A1 (RefSeq Accession # NC_000003.12:c48595302-48564073) using minimap2 2.16-r922
Information of reads mapped to the loci of the mutations was extracted using samtools.
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: Haplotype counts of each nCATS experiment.

source_name: Human peripheral blood

extract_protocol:
gDNA was extracted from peripheral blood using QIAamp DNA mini Kit (Qiagen, Valencia, CA, USA).
Libraries were constructed using Ligation Sequencing Kit SQK-LSK109 (Oxford Nanopore Technologies). gDNA was treated with Quick Calf Intestinal Phosphatase and Cas9 before library construction for nanopore Cas9-targeted sequencing (nCATS).

tag: subject

value: proband’s mother

value: Human peripheral blood


title: wtCol rep A

status: Public on May 02 2022

type: SRA

city: St. Louis

first: R. Keith

last: Slotkin

state: Missouri

address: 975 North Warson Road

country: USA

institute: Donald Danforth Plant Science Center

library_source: transcriptomic

data_processing:
Small RNA sequencing reads were processed as in McCue et al., PMID: 25388951 to remove adapters, tRNAs, rRNAs and filtered for size 18-28 nt.
Shortstack (Johnson et al., PMID: 27175019) was used to map the reads to the Arabidopsis genome (TAIR10) with a fractional seeded guide used for multi-mapping reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: Reads per million sequenced (RPM) is provided for each filtered small-RNA read.

molecule: total RNA

organism: Arabidopsis thaliana

growth_protocol: Plants were grown under 16-hour day conditions at 22°C in a growth chamber. All tissue was leaf harvested at the time of the plant's first flower opening.

extract_protocol:
Total RNA was isolated with Trizol reagent (Invitrogen) and enriched for small RNAs using the mirVana microRNA Isolation Kit (Ambion).
Size-enriched small RNAs were used in the Illumina TruSeq Small RNA Library Preparation Kit.
Multiplexed libraries were sequenced on Illumina HiSeq 3000 or HiSeq X Ten or NextSeq 550 or NovaSeq 6000

tag: ecotype

value: Columbia

tag: genotype/variation

value: wtCol


title: CASPTRAWATOSROOT2

city: Riverside

first: Mauricio

middle: A

last: Reynoso

state: CA

address: 4126 Genomics Bldg

department: Botany and Plant Sciences

institute: University of California Riverside

description:
TRAP RNA
Random primed libraries

data_processing:
Genome_build: Genome_build:  RICE: IRGSP-1.0-30 (https://rapdb.dna.affrc.go.jp/download/irgsp1.html)
Rice RNA-seq raw reads were aligned to the IGRSP-1.0-30, with the splice junction aware short read alignment suite Bowtie2/Tophat2, allowing unique alignments with 2 or less mismatches
Rice read count data for RNA-seq was generated for features of exons-by-genes using the summarize Overlaps function of the GenomicRanges package in R.
ATAC-seq raw reads were aligned to the genome using Bowtie2 with default parameters
ATAC-seq mapped reads were filtered to remove 1) reads that mapped to organelle genomes and 2) reads with a mapping quality score of q<10.
Transposase Hypersensitive Sites were identified using the Findpeaks function of the HOMER package, with the parameters "-minDist 150" "-region" and "-regionRes 1"
Filtered ATAC-seq bam files for each sample were converted to the bigwig format using a bin size resolution of 1 base pair and the proccessed with limma-voom to quantile normalize samples
For accurate visualization, all filtered ATAC-seq bigwig files were scaled with quantile normalization and combined per condition to create a single merged bigwig  file for a condition using a bin size resolution of 1 base pair.
Supplementary_files_format_and_content: Transcripts per per million reads (TPM) values for polyA RNA or TRAP RNA datasets were calculated from count data after quantile normalization
Supplementary_files_format_and_content: Read counts values for ATAC datasets were calculated for regions 2kb upstream of ATG

organism: Oryza sativa Japonica Group

source_name: 26 days-old plant roots

growth_protocol: For plate experiments, seeds were dehulled and surface sterilized in 50% (v/v) bleach solution for 30 min, rinsed ten times with sterile distilled water and grown on plates (100 cm2) containing 0.5x Murashige and Skoog medium (MS), 1% (w/v) agar 1% (w/v) sucrose for 7 days (16h day / 8h night; at 28°C/25°C day/night; 110 μEm-2s-1). For greenhouse experiments, seeds were imbibed for 2 d in 5% (v/v) Liquid SmokeTM (Colgin) at 28°C in darkness to promote consistent germination. The seeds were then rinsed with distilled water and returned to 28° C in darkness for 24 h. Germinated seeds (21) were transferred to pots (15 cm diameter and 18 cm height), filled with Profile® Greens GradeTM and placed in a greenhouse at the University of California, Riverside California during June and July 2016. Temperature was controlled at 28° C for 16 h per day and at 25° C for 8 h per night. Pots were placed in trays and watered everyday with fresh water (depth of 1 cm water tray). After 10 d of growth, irrigation was with fertilizer water (Peters® Excel: 21-5-20 at 100 ppm N). Each pot contained 21 plants (combined as a single replicate). The location of each pot was randomized in multiple trays/tanks used. After 21 d of development (from imbibition), when plants were at the V4 to V5 growth stage, four water regimes were applied. For water-sufficiency (control), pots were maintained by daily irrigation with fertilizer water. For water deficit (drought), pots were removed from the tray and watering was stopped. For waterlogging, pots were placed in tanks (56-qt clear storage box; Sterilite® 1659) and flooded with water to 2-3 cm above the root/shoot junction. For submergence, at solar midday, pots were transferred to tanks (grey plastic Rubbermaid® FG265500 containers) and fully submerged with water, with the flood line 70 cm above the root/shoot junction. The containers were covered with two layers of shade cloth (SHANS 90% UV Block). For the field experiments, seedlings were germinated in Magenta boxes on selective medium after sterilization, transferred to Profile®, and grown for 14 d in the greenhouse before before transplantation into a pre-fertilized paddy at the Agricultural Operations field at the University of California Riverside Agricultural Experiment Station. The paddy was maintained at 8-10 cm depth for 35 d. Planting of genotypes was based on a randomized design with ten plants per biological replicate.

extract_protocol:
TRAP was performed as previously described (Mustroph et al 2009, Reynoso et al 2015) with the following modifications: tissue samples were increased to isolate polysomes from low abundant cell populations; ɑ-FLAG conjugated IgG Dynabeads were used for binding; after magnetic collection and washing the polysomes were removed from the magnetic beads by addition of Lysis and Binding Buffer (LBB) buffer for polyA mRNA isolation using biotinylated oligo-dT primers and streptavidin magnetic beads (NEB) (Townsley et al 2014).
Random primer primed RNA-seq libraries were prepared from poly(A)+ selected mRNA as described. (Townsley et al 2014, Reynoso et al. 2019)
Nuclei were purified from frozen and pulverized tissue as previously described for O. sativa (Reynoso et al., 2018) with minor modifications including the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract and extend centrifugation times. Tissue was resuspended in an ice-cold mortar containing 10 mL of freshly prepared nuclei purification buffer (NPB: 20 mM MOPS, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM spermidine, 0.2 mM spermine, pH, 7.0) containing 200 uL Protease Inhibitor Cocktail (0.4X, Sigma, P9599) per 50 mL of buffer. The homogenized extracts were filtered through a 30 µM nylon mesh to remove cell debris and centrifuged at 1000 x g for 15 min at 4° C to pellet nuclei. Nuclei were resuspended in 1 mL of NPB and 25 µL of M-280 streptavidin-coated Dynabeads (Life Technologies, catalog # 11205D) were added to the nuclei. This mixture was slowly rotated in a cold room at 4° C for 30 min. The nuclei/beads suspension was diluted to 14 mL with NPB supplemented with 0.1% (v/v) Triton X-100 (NPB-T), in a 15 mL Falcon tube, mixed thoroughly and placed in a 15 ml magnet (adapted NEB 50 mL tube magnet) to capture bead-bound nuclei for 1 min at 4° C. The supernatant was carefully removed using a plastic Pasteur pipette, taking care to remove bubbles to avoid disturbing the beads. Beads were resuspended in 14 ml of cold NPB-T, placed on a rotating mixer for 30 sec, and then placed back in the 15 ml magnet to capture the beads-nuclei at 4° C for 1 min. This wash step was repeated and bead-bound nuclei were resuspended in 1 mL of NPB-T and transferred to a new tube
Tagmentation using Tn5 insertion and ATAC-seq libraries were prepared using 20,000-50,000 nuclei as previously described (Maher et al 2017, Reynoso et al., 2019), with slight modifications. Minor modifications in nuclei purification include: 1) the use of a 30 µm filter to exclude 30 to 70 µm cellular debris from the crude extract, 2) extended centrifugation times (Reynoso et al 2018b, Reynoso et al 2018), and 3) using AMPureXP beads instead of columns to purify amplified libraries
TRAP was performed as previously described  (Mustroph et al., 2009, Reynoso et al., 2015) with the following modifications: ɑ-FLAG conjugated IgG Dynabeads were used for binding; after magnetic collection and washing the polysomes were removed from the magnetic beads by addition of Lysis and Binding Buffer (LBB) buffer for polyA mRNA isolation using biotinylated oligo-dT primers and streptavidin magnetic beads (NEB) (5). Total RNA was extracted from frozen tissue using polysome extraction buffer (Mustroph et al 2009) followed by LBB polyA mRNA isolation using biotinylated oligodT and streptavidin magnetic beads (Townsley et al 2014)
Random primer-primed RNA-seq library construction for polyadenylated total RNA and polyadenylated TRAP RNA was performed according the BrAD-seq method (Townsley et al 2014) in at least three biological replicates for each condition.

treatment_protocol:
For plate experiments, Oryza sativa cv. Nipponbare seeds from transgenic lines were dehulled and surface sterilized in 50% (v/v) bleach solution for 30 min, rinsed ten times with sterile distilled water and grown on plates (100 cm2) containing 0.5x Murashige and Skoog medium (MS), 1% (w/v) agar 1% (w/v) sucrose for 7 days (16h day / 8h night; at 28°C/25°C day/night; 110 μEm-2s-1). For greenhouse experiments, seeds were imbibed for 2 d in 5% (v/v) Liquid SmokeTM (Colgin) at 28°C in darkness to promote consistent germination. The seeds were then rinsed with distilled water and returned to 28° C in darkness for 24 h. Germinated seeds (21) were transferred to pots (15 cm diameter and 18 cm height), filled with Profile® Greens GradeTM and placed in a greenhouse at the University of California, Riverside California. Temperature was controlled at 28° C for 16 h per day and at 25° C for 8 h per night. Pots were placed in trays and watered everyday with fresh water (depth of 1 cm water tray). After 10 d of growth, irrigation was with fertilizer water (Peters® Excel: 21-5-20 at 100 ppm N). Each pot contained 21 plants (combined as a single replicate). The location of each pot was randomized in multiple trays/tanks used. After 21 d of development (from imbibition), when plants were at the V4 to V5 growth stage, four water regimes were applied. For water-sufficiency (control), pots were maintained by daily irrigation with fertilizer water. For water deficit (drought), pots were removed from the tray and watering was stopped. For waterlogging, pots were placed in tanks (56-qt clear storage box; Sterilite® 1659) and flooded with water to 2-3 cm above the root/shoot junction. For submergence, at midday, pots were transferred to tanks (grey plastic Rubbermaid® FG265500 containers) and fully submerged with water, with the flood line 70 cm above the root/shoot junction. The containers were covered with two layers of shade cloth (SHANS 90% UV Block). For the field experiments, seedlings were germinated in Magenta boxes on selective medium after sterilization, transferred to Profile®, and grown for 14 d in the greenhouse before before transplantation into a pre-fertilized paddy at the Agricultural Operations field at the University of California Riverside Agricultural Experiment Station. The paddy was maintained at 8-10 cm depth for 35 d. Planting of genotypes was based on a randomized design with ten plants per biological replicate.
Five independent biological replicates were grown for each treatment. Pots were placed in trays and watered everyday with fresh water (depth of 1 cm water tray). After 10 d of growth, irrigation was with fertilizer water (Peters® Excel: 21-5-20 at 100 ppm N). Each pot contained 21 plants (combined as a single replicate). The location of each pot was randomized in multiple trays/tanks used. After 21 d of development (from imbibition), when plants were at the V4 to V5 growth stage, four water regimes were applied. For water-sufficiency (control), pots were maintained by daily irrigation with fertilizer water. For water deficit (drought), pots were removed from the tray and watering was stopped. For waterlogging, pots were placed in tanks (56-qt clear storage box; Sterilite® 1659) and flooded with water to 2-3 cm above the root/shoot junction. For submergence, at solar midday, pots were transferred to tanks (grey plastic Rubbermaid® FG265500 containers) and fully submerged with water, with the flood line 70 cm above the root/shoot junction. The containers were covered with two layers of shade cloth (SHANS 90% UV Block). A fiber optic oxygen meter (Neofox Sport, Ocean Optics, Dunedin, USA), in five replicates was used to determine the percentage of dissolved oxygen in the submergence tanks was measured at the start and end of the experiment. Oxygen content was stable a 18.90 ± 0.03% at the start (0 d) and end of the experiment.

tag: tissue

value: 26 days-old plant roots

tag: cultivar

value: Nipponbarre

tag: line

tag: condition

value: Waterlogged in greenhouse


title: CASPTRACONOSROOT2

description:
TRAP RNA
Random primed libraries

value: Control in greenhouse I


title: 8428N.L_H2O_cortex

city: Irvine

first: Ali

last: Mortazavi

address: 2300E Biological Sciences III

institute: UC Irvine

library_source: transcriptomic single cell

data_processing:
Raw data converted to fastq using bcl2fastq v2.18.0.12 from Illumina.
scRNA-seq reads were aligned to mm10 reference genome and annotated to Gencode v21 transcriptome using KB_python
Data quality control, clustering and downstream analysis were perform using Seurat
Assembly: mm10
Supplementary files format and content: KB_python output counts

molecule: polyA RNA

organism: Mus musculus

source_name: cortex

extract_protocol:
Microglia and astrocytes were respectively isolated using Anti-CD11b and Anti-ACSA-2 MicroBeads (Miltenyi Biotec). Cells were counted and resuspended in 10-15 µL and 20-30 µL of buffer (0.05% BSA in DPBS) for half hippocampus and half cortex respectively, to reach a minimum of 1,000 cells/µL up to around 7,000 cells/µL. Isolated single cells were loaded into the Bio-Rad microfluidic device. Cells were lysed, barcoded, and reverse transcribed inside nanodroplets.
Single-cell RNA-seq: SureCell WTA 3_ Library Prep Kit for the ddSEQ System (20014279, Illumina)

treatment_protocol: PMX205 treatment was administer for 12 weeks (equivalent to ~ 2-8 mg/kg/day). Mice were singly housed and had free access to the drinking water during the whole treatment. Mouse weight and volume of PMX205/vehicle consumed by each mouse. were measured weekly.

tag: Sex

value: female

tag: age

value: 15 months

tag: genotype

value: APP

tag: strain

value: Arctic mouse model of ADtic mice overexpressing C5a under the GFAP promoter


title: CASPTRAWATRECOSROOT2

description:
TRAP RNA
Random primed libraries

source_name: 27 days-old plant roots

value: 27 days-old plant roots

value: Waterlogged recovery in greenhouse


title: 8428N.L_H2O_hippocampus

source_name: hippocampus


title: CASPTRADRORECOSROOT2

description:
TRAP RNA
Random primed libraries

value: Water deficit recovery in greenhouse


title: Genomic DNA of the proband

country: Japan

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

value: proband


title: CASPTRADRORECOSROOT3

description:
TRAP RNA
Random primed libraries


title: 8429N.R_H2O_hippocampus

value: WT

value: WT mice overexpressing C5a under the GFAP promoter


title: CASPTRACONOSROOT4

description:
TRAP RNA
Random primed libraries


title: 10x Genomics Multiome RNA data

city: Houston

first: Katy

last: Rezvani

address: Zayed Building, 5th floor 6565 MD Anderson Blvd. Unit 1061 Houston, TX 77030

department: Stem Cell Transplantation & Cellular Therapy department

institute: MD Anderson Cancer Center

data_processing:
Single cell ATACseq library and 3’RNAseq library were subsequently generated following recommended protocol from 10x Genomics. Libraries were quantified and loaded on Novaseq 6000 and run with the following parameter: 151, 8, 8, 151bp. Data was analyzed using bcl2fastq (to generate fastq files) and CellRanger pipeline (10x Genomics). Among 9,383 detected high-quality nuclei, 1,276 are gated as BCs by known markers for further analysis.
Further processing was done with Seurat v3.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis, peak clustering, gene activity calculation)
Assembly: mm10
Supplementary files format and content: 10x multiomics matrix format: multiomics_mouse_wt_GeneExpression_Peaks_lists.RDS
Supplementary files format and content: Seurat object: retina_10x.atac.RDS
Supplementary files format and content: Seurat object: retina_10x.rna.RDS

source_name: retina

extract_protocol:
One mouse retina was dissociated by papain-based enzymatic digestion as described previously with slight modifications. Briefly, 45 U of activated papain solution (with 1.2 mg L-cysteine (Sigma) and 1200U of DNase I (Affymetrix) in 5ml of HBSS buffer) was added to the tissue and incubated at 37 °C for 20 minutes to release live cells. Post-incubation, papain solution was replaced and deactivated with ovomucoid solution (15 mg ovomucoid (Worthington biochemical) and 15 mg BSA (Thermo Fisher Scientific) in 10 ml of MEM (Thermo Fisher Scientific)). The remaining tissue clumps were further triturated in the ovomucoid solution and filtered through a 20nm nylon mesh. After centrifugation at 300g 10min at 4C, the singe cells were resuspended PBS with 0.04% BSA and checked for viability and cell count.
About 1 million cells were pelleted and resuspend in chilled lysis buffer (10x Genomics), incubate for 2 minutes on ice while monitored under microscope. 1ml of chilled wash buffer (10x Genomics) was added and sample was spun down at 500g 5min at 4C and washed before resuspended in Diluted Nuclei Buffer (10x Genomics). Nuclei concentration was determined using countess and proceed with transposition according to manufacturer’s recommendation (10x Genomics). After incubation for one hour at 37C, the transposed nuclei were combined with barcoded gel beads, RT mix and partition oil on Chromium to generate gel beads in Emulsion (GEMs).

value: retina

tag: library type

value: 10x Genomics  Multiome RNA data


title: wtCol rep B

source_name: leaf harvested at the time of the plant's first flower opening

value: Columbia

value: wtCol


title: 8429N.R_H2O_cortex


title: CASPTRADRORECOSROOT1

description:
TRAP RNA
Random primed libraries

value: Nipponbarre


title: 35S_FLAG-BD rep B


title: 10x Genomics Multiome ATAC

value: 10x Genomics  Multiome ATAC

tag: antibodies/tags


title: CASPTRAWATOSROOT4

description:
TRAP RNA
Random primed libraries

value: 26 days-old plant roots

value: Waterlogged in greenhouse


title: CASPTRACONOSROOT3

description:
TRAP RNA
Random primed libraries

value: Control in greenhouse I


title: 8427N.N_H2O_hippocampus

value: female

value: 15 months

value: APP


title: 8428N.N_H2O_hippocampus

value: Arctic mouse model of ADtic mice with C5ar1 knocked out (constitutive KO)


title: 8427N.N_H2O_cortex


title: 8430N.L_205_cortex


title: 8430N.L_205_hippocampus


title: 8428N.N_H2O_cortex


title: 8429N.L_205_hippocampus

value: WT mice with C5ar1 knocked out (constitutive KO)


title: 8429N.N_205_hippocampus

value: Arctic mouse model of AD


title: 8428N.LR_205_cortex


title: 8428N.LR_205_hippocampus


title: 8427N.R_205_hippocampus

value: WT

value: Wild type


title: 8427N.R_205_cortex


title: 8429N.N_205_cortex


title: 8428N.R_205_hippocampus


title: Root, Roma-salt2_IP

city: Jinan

last: Sui

state: Shandong

address: Wenhua East Road

department: College of Life Sciences

country: China

institute: Shandong normal university

description:
R_S_IPVSR_S_peak.txt
R_S2

data_processing:
First, Cutadapt 26 and in-house Perl scripts were used to remove reads with contaminating adapters, low-quality bases, and undetermined bases. The sequence quality was verified with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used the default parameters of HISAT2 27 to map the reads to the Sorghum bicolor genome (Version: sorghum bicolor Ensembl release58).
The reads for the IP and input libraries were mapped with the R package exomePeak 28, which identifies m6A peaks with a bed or bam format that can be adapted for the visualization with the UCSC genome browser or IGV software (http://www.igv.org/).
Called peaks were annotated according to gene architecture with ChIPseeker 31. Moreover, StringTie 32 was used to determine the mRNA levels for the input libraries by calculating the FPKM [total number of exon fragments/mapped reads (millions) × exon length (kb)]. The differentially expressed mRNAs were identified with the R package edgeR 33 based on the following criteria: log2 (fold-change) > 1 or < −1 and p < 0.05.
Genome_build: sorghum bicolor Ensembl release58
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Sorghum bicolor

source_name: Root

extract_protocol:
Total RNA from roots was extracted with TRIzol reagent (Invitrogen, CA, USA) following the manufacturer’s recommended procedure. The total RNA quality and quantity were analyzed with the 2100 Bioanalyzer and the RNA 6000 Nano LabChip Kit (Agilent, CA, USA), with a RIN number > 7.0.
Poly-A mRNA was isolated from more than 200 µg total RNA with oligo-dT magnetic beads (Invitrogen). The isolated poly-A mRNA was fragmented with divalent cations at elevated temperatures to produce approximately 100-nt-long oligonucleotides. The cleaved RNA fragments were incubated for 2 h at 4 °C in a solution comprising the m6A-specific antibody (Synaptic Systems, Germany), IP buffer (50 mM Tris-HCl, 750 mM NaCl, and 0.5% Igepal CA-630), and BSA (0.5 μg μl−1). The mixture was then incubated with protein-A beads and eluted with elution buffer (1× IP buffer and 6.7 mM m6A). The eluted RNA was precipitated with 75% ethanol. The eluted m6A-containing fragments (IP) and untreated input control fragments were used to construct cDNA libraries according to a strand-specific library preparation method involving dUTP. The average insert size for the paired-end libraries was approximately 100 ± 50 bp
We then completed a paired-end (2 × 150 bp) sequencing analysis with the Illumina HiSeq 4000 following the manufacturer’s recomm ended protocol. Two biological replicates were set for each group.

value: Roma

tag: phenotype

value: salt-sensitive

value: three-leaf phase

value: root

tag: stress

value: salt

tag: rip antibody


title: Root, Roma-salt1_IP

description:
R_S_IPVSR_S_peak.txt
R_S1


title: J46-b_H2O_hippocampus

value: WT mice overexpressing C5a under the GFAP promoter


title: 8430N.R_205_hippocampus

value: Arctic mouse model of ADtic mice overexpressing C5a under the GFAP promoter


title: Root, Roma-CK2_IP

description:
R_CK_IPVSR_CK_peak.txt
R_CK2

value: control


title: Root, Roma-CK1_input


title: 8425N.L_H2O_hippocampus


title: Root, Roma-salt1_input


title: 8425N.N_H2O_cortex


title: 8429N.L_205_cortex


title: 8425N.L_H2O_cortex


title: Root, M-81E-salt2_input

value: salt-tolerant


title: 8426N.N wht_H2O_hippocampus

value: female


title: J46-b_H2O_cortex

value: 15 months


title: 8426N.N wht_H2O_cortex

value: APP


title: Root, M-81E-salt2_IP

description:
M_S_IPVSM_S_peak.txt
M_S2


title: Root, M-81E-salt1_input


title: 8428N.R_205_cortex


title: Root, Roma-salt2_input


title: 8425N.N_H2O_hippocampus

value: Arctic mouse model of ADtic mice with C5ar1 knocked out (constitutive KO)


title: Root, Roma-CK2_input


title: Root, M-81E-salt1_IP

description:
M_S_IPVSM_S_peak.txt
M_S1


title: Root, M-81E-CK2_input


title: 8427N.L_H2O_hippocampus


title: Root, Roma-CK1_IP

description:
R_CK_IPVSR_CK_peak.txt
R_CK1


title: Root, M-81E-CK2_IP

description:
M_CK_IPVSM_CK_peak.txt
M_CK2


title: Root, M-81E-CK1_IP

description:
M_CK_IPVSM_CK_peak.txt
M_CK1


title: Retinal_ECs_P6_4

city: Almada

first: Ana

middle: Rita

last: Grosso

address: Campus de Caparica

department: Departamento Ciências da Vida

country: Portugal

institute: Unidade de Ciências Biomoleculares Aplicadas (UCIBIO)/Faculdade de Ciências e Tecnologia - Universidade Nova de Lisboa

description: RNAseq retinal Ecs P6 (replicate 4)

data_processing:
Data quality was assessed with the FastQC quality-control tool for high throughput sequence data.
RNA-seq reads were mapped to the human reference genome with Star software. Reads counts were estimated for human Ensembl genes annotation.
Supplementary files format and content: xls

source_name: Endothelial cells isolated from P6 mouse retinas

growth_protocol: Retina pairs from P6 C57BL/6J mice were freshly dissected and digested in 1mL DMEM with 2.5mg/mL type II collagenase (Sigma C6885) with orbital shaking at 300rpm, 37°C for 30 min. Homogenates were strained through a 70µm filter and centrifuged at 300g, 10min at 4°C. Cell pellets were resuspended in 100uL of PEB buffer (PBS + 2mM EDTA + 0.5% BSA) and incubated with CD31-FITC (BD Biosciences, #553372) and CD45-PECy7 (Invitrogen, #25-0451-82) for 30min at 4°C. Viable ECs (CD31+/CD45-) were sorted on a BD FACSAria III (BD Bioscience) and collected into RNA Lysis buffer.

extract_protocol:
RNA was isolated from HUVECs using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
RNA and library preparation integrity were verified with a LabChip Gx Touch 24 (Perkin Elmer).  Total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol (Illumina).
Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry, resulting in minimum of 32M reads per library with 1x75bp single end setup.

tag: cell type

value: retinal endothelial cells

value: Postnatal day 6 (P6)

tag: treatment


title: Root, M-81E-CK1_input


title: Retinal_ECs_P6_2

description: RNAseq retinal Ecs P6 (replicate 2)


title: 8427N.L_H2O_cortex

value: WT


title: Retinal_ECs_P6_1

description: RNAseq retinal Ecs P6 (replicate 1)


title: Neuronal Progenitor Cell, deletion, 2

city: San Francisco

first: Arun

middle: P

last: Wiita

state: CALIFORNIA

address: 185 Berry St, Ste 290/Rm 2410

institute: University of California San Francisco

data_processing:
For genome mapping, clean reads were mapped to reference genome using HISAT. The average mapping ratio to the genome is 95.24% across samples.
For gene expression analysis, clean reads were mapped to reference transcripts using Bowtie2 (ver 2.2.5) and expression levels calculated using RSEM (v1.2.8)
For DESeq2-neuron-deletion-vs-control.xls, the differential expression analysis was performed on counts data using DESeq2 (version 1.34.0) in R (version 4.1.2)
For Paranjape et al_processed_read_counts_NPC_neuron_BGI_RNAseq file, HISAT was used to map clean reads to the reference genome. Bowtie2 was used to map the clean reads to the reference gene sequence (transcriptome)
and DESeq2-NPC-deletion-vs-control.xls files, the differential expression analysis was performed on counts data using DESeq2 (version 1.34.0) in R (version 4.1.2)
Assembly: hg38
Supplementary files format and content: read counts, DESeq2 results

source_name: NPC derived from iPSC (22q AB del)

growth_protocol: Control and deletion NPCs were grown in STEMdiff™ Neural Progenitor Medium on PDL/laminin coated plates prior to harvesting.

extract_protocol:
After treatment, cell lines (1 - 2e6 cells) were washed with PBS twice, pelleted and flash frozen and frozen cell pellets were sent to BGI Genomics for further processing for RNA Seq
RNA extraction, library preparation, and sequencing were performed at BGI (Shenzhen, China).   RNA QC done with Agilent 2100 Bio analyzer and Agilent RNA 6000 Nano kit
Samples were sequenced using the DNB Seq platform from BGI

treatment_protocol: Control and deletion NPCs were differentiated in neurons using Neuronal Differentiation Medium supplemented with growth factors for 3 weeks in in-vitro culture

value: iPS line differentiated to NPC

value: 22qAB deletion


title: mcervix_D18_HAKO

city: Dallas

first: Anne

last: Cooley

state: TX

address: 5323 Harry Hines Blvd

institute: UTSW

description: LW16; scRNA-seq

data_processing:
scRNA-seq libraries were demultiplexed and mapped to the mouse reference genome (mm10) by using the Cellranger software (ver 3.0.2, 10X Genomics).
Assembly: mm10
Supplementary files format and content: The top level of the file contains a single HDF5 group, called matrix, and metadata stored as HDF5 attributes. Within the matrix group are datasets containing the dimensions of the matrix, the matrix entries, as well as the features and cell-barcodes associated with the matrix rows and columns, respectively. The contents include: filtered gene counts, genes, and cell-barcodes.

source_name: cervical tissue

extract_protocol:
Cervices were collected by dissection below the transition zone and all vaginal tissue was removed. Tissues were minced with a sterile razor. Minced cervices were dissociated with 10mg/ml cold protease (Sigma-Aldrich) with 1mg/ml DNase I (Roche) and 0.5 M EDTA (Fisher Scientific). After a 60 min incubation at 4ºC, cells were filters through a 40 µm cell strainer (BD Biosciences) and washed twice with fresh ice cold 1x PBS and then resuspended in 1x PBS +0.005% BSA.
Library prepared following 10x v3 gene expression protocol.

value: cervix

tag: timepoint

value: Gestation day 18

value: (Has1-/- and Has3-/-) (Has2fl/fl; PRCre+/-)


title: Neuronal Progenitor Cell, deletion, 3

description: NPC_control_3 and NPC deletion_3 were not used in the analysis due to poor correlation with other replicates


title: mcervix_D15_HAKO

description: LW15; scRNA-seq

value: Gestation day 15


title: 8430N.R_205_cortex


title: Bulk RNA sequencing [449-12]

city: Utrecht

first: Jens

last: Puschhof

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
RNA was extracted from mouse intestinal tissue and subjected to bulk RNAseq
mouse_invivo_RNAseq_counts.csv

data_processing:
Sequencing data were demultiplexed, paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the human genome release hg19. For MUC2-Neon reporter organoids, the sequence of mNeon green was added to the human reference genome and neon and MUC2 read counts were merged. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: The data are in csv format. The table contains UMI deduplicated counts (for scSeq data poisson corrected).

source_name: mouse intestine

growth_protocol: Organoids were differentiated in enterocyte or goblet cell differentiation medium for 5 days in the absence or presence of BMP2 and 4, respectivelys

extract_protocol: RNA was processed using the previously described SORT-seq tecnique, which is an implemented version of the CEL-seq2 technique. Libraries were sequenced on an Illumina NextSeq500 using 60bp and 26bp paired end sequencing.

treatment_protocol: For scSeq, live cells  were sorted in 384-  well hard shell plates (Biorad) with 5 μl of vapor-lock (QIAGEN) containing 100 nl of RT primers (consisting of a  24 bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific barcode, the 5′ Illumina TruSeq small RNA  kit adaptor and a T7 promoter), dNTPs and mRNA ERCC Spike-Ins (Agilent) and immediately frozen to −80°C. Before starting with SORT-seq, cells were first lysed 5 min at 65°C.

value: wt

value: proximal intestine


title: Neuronal Progenitor Cell, deletion, 1


title: Neuronal Progenitor Cell, control, 2

source_name: NPC derived from iPSC (control)

value: control


title: Bulk RNA sequencing [449-0]

value: distal intestine


title: Neuronal Progenitor Cell, control, 3


title: Retinal_ECs_P6_3

description: RNAseq retinal Ecs P6 (replicate 3)


title: Neuron, deletion, 3

source_name: 3 wk in-vitro differentiated neuron from 22q deletion NPC

value: iPS line differentiated to NPC then neuron


title: Neuronal Progenitor Cell, control, 1


title: Neuron, deletion, 2


title: Bulk RNA sequencing [448-0]

value: Bmpr1a ko


title: Bulk RNA sequencing [446-12]


title: Bulk RNA sequencing [448-12]


title: Bulk RNA sequencing [446-0]


title: Neuron, deletion, 1


title: Bulk RNA sequencing [442-12]


title: Neuron, control, 2

source_name: 3 wk in-vitro differentiated neuron from control NPC


title: Bulk RNA sequencing [440-0]


title: Neuron, control, 3


title: Bulk RNA sequencing [440-12]


title: Bulk RNA sequencing [436-12]


title: Bulk RNA sequencing [436-0]


title: PBMCs+PAT

city: Shanghai

first: Yigang

last: Tang

address: No 197 RUIJIN ER RD

institute: Shanghai Jiaotong University

data_processing:
The CellRanger (10x Genomics, default settings, Version 5.0.1) pipelines were used to process Chromium single-cell data to align reads, generate feature-barcode matrices.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: Peripheral blood

growth_protocol: PBMCs were cultured at 37 ℃ in RPMI 1640 Medium, supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 mg/mL streptomycin.

extract_protocol:
Cellular suspensions were copartitioned with barcoded gel beads to generate single-cell gel bead-in-emulsion (GEM) and poly-adenylated transcripts were reverse-transcribed using Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1
RNA libraries were prepared with Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to  the standard manufacturer’s protocol (PN-1000121, 10x Genomics)

treatment_protocol: PBMCs were treated with or without  5 μM PAT for 24 hr in vivtro.

tag: subject status

value: AML patient

value: PBMCs

tag: pat treatment

value: yes


title: Bulk RNA sequencing [433-0]

tag: tissue


title: Bulk RNA sequencing [433-12]


title: PBMCs+PBS

value: no


title: Bulk RNA sequencing [431-12]


title: microRNA_2101_40_mkd_Placenta

city: Indianapolis

first: Kamin

last: Johnson

state: IN

address: 9330 Zionsville Rd

institute: Corteva Agriscience

data_processing:
Basecalls performed using Illumina CASAVA software version 1.8
The raw mRNA sequencing reads for each sample were processed with the fastq-mcf tool from the ea-utils software package (v1.1.0) for adapter sequence removal and trimming low quality bases (parameters for minimum remaining sequence length option set to 50 and quality threshold set to 30).
Trimmed reads were subsequently mapped to the rat reference genome (version 6.0.80) using the hisat2 mapping software (v2.0.3) run using default parameter settings and in stranded mode
Using HTSeq (v0.7.2), the reads mapped to the antisense strand of each gene were counted and tabulated across samples that was used for downstream data normalization and gene expression analysis.
Similarly, the microRNA raw reads for each sample were processed for adapter sequence removal using the cutadapt bioinformatics tool (v1.16, with the minimum-length parameter (-m) set to 14 bases and minimum-overlap (-O) parameter set to 6 bases).
The trimmed microRNA reads were mapped to the rat reference genome (version 6.0.80) using the bowtie2 mapping software (v2.3.2) using default parameter settings.
the coverageBed function of the bedtools software (v2.17.0) was used to obtain counts of microRNA reads that overlapped microRNA and mRNA features in the rat reference genome annotation (using the -s strandedness option enabled). The resulting mapped read counts were tabulated across samples and used for downstream data normalization and microRNA expression analysis.
Assembly: Rattus norvegicus (version 6.0.80)
Supplementary files format and content: one tab-delimited text matrix file include raw mRNA count values for each Sample and one tab-delimited text matrix file include raw mRNA count values for each Sample

organism: Rattus norvegicus

source_name: Placenta

extract_protocol:
Total RNA was extracted from organs stored in RNAlater using a mirVana RNA isolation kit (catalog number AM1560; ThermoFisher Scientific) according to the manufacturer’s instructions.  RNA quantity was measured using a NanoDrop ND-1000 spectrophotometer.  Total RNA quality was examined using an Agilent Bioanalzyer (Agilent Technologies).  miRNA was purified from the same tissue homogenate as the Total RNA,  using mirvana (catalog number AM1560; ThermoFisher Scientific, Waltham, MA) and quanitified using the Bioanalyzer (Agilent Technologies, Santa Clara, CA).
).  A sequencing library was prepared from 1ug total RNA using the Illumina TruSeq Stranded mRNA Library Prep Kit and protocol (Illumina, San Diego, CA).  Briefly, mRNAs were fragmented using ZnCl2 solution, reverse transcribed into cDNA using random primers, end repaired to create blunt end fragments, 3’ A-tailed, and ligated with Illumina paired-end library adaptors. Ligated cDNA fragments were PCR amplified using Illumina paired-end library primers and purified PCR products were checked for quality and quantity on the Agilent TapeStation (Agilent, Santa Clara, CA).  Average library insert size was 300bp, and final sequencing concentration was determined by quantitation on the Agilent TapeStation (Agilent, Santa Clara, CA). For the microRNA libraries, sequencing libraries from each small RNA sample were prepared using 1 µg input with the TruSeq small RNA kit according to manufacturer’s instructions (Illumina, Inc., San Diego, CA). Briefly, Illumina TruSeq adapters are ligated onto purified smRNA ends, reverse transcribed, and the cDNA are PCR-amplified using Illumina indexed TruSeq primers. PCR-amplified libraries were checked for quality and quantified using the Agilent Tapestation 4200 with D1000 screentape.  Equal amounts of library were pooled based on nano-molarity concentration and then size-selected using a PippinHT automated DNA size selector (Sage Science Inc., Beverly, MA).  The size-selected samples were ethanol precipitated to concentrate and then checked for quality and quantity using an Agilent TapeStation 4200 with D1000 screentape.

tag: developmental stage

value: Adult

value: Crl:CD (SD); Sprague-Dawley

tag: rat body weight at gestation day 0 (grams)

tag: sex/pregnancy status

value: Female

tag: pregnancy status at gestation day 21

value: Pregnant

tag: agent

value: Ketoconazole

tag: exposure

value: Daily via oral gavage from gestation days 6 to 20

tag: interval between last dosing and necropsy

value: Approximately 24 hours

tag: gestation day definition

value: The morning of observing a vaginal plug was considered gestation day 0

tag: corn oil vehicle dose level

value: 2 ml/kg body weight

tag: ketoconazole dose level (mg/kg/day)

tag: rna integrity number (rin) of isolated total rna


title: Bulk RNA sequencing [431-0]

tag: genotype

value: wt


title: Bulk RNA sequencing [HUB-JB-b005]

description:
Organoids were lysed in RLT buffer, RNA was extracted and libraries prepared for bulk RNAseq
BMPBULK_mouse_organoids_counts.csv

source_name: mouse intestinal organoids

value: Intestine


title: microRNA_2094_40_mkd_Placenta

tag: strain


title: Bulk RNA sequencing [442-0]

value: distal intestine


title: microRNA_2092_20_mkd_Placenta


title: microRNA_2097_40_mkd_Placenta


title: microRNA_2100_40_mkd_Placenta


title: Neuron, control, 1

tag: cell type

value: iPS line differentiated to NPC then neuron

value: control


title: mcervix_D12

description: scRNA-seq

data_processing:
scRNA-seq libraries were demultiplexed and mapped to the mouse reference genome (mm10) by using the Cellranger software (ver 3.0.2, 10X Genomics).
Genome_build: mm10
Supplementary_files_format_and_content: The top level of the file contains a single HDF5 group, called matrix, and metadata stored as HDF5 attributes. Within the matrix group are datasets containing the dimensions of the matrix, the matrix entries, as well as the features and cell-barcodes associated with the matrix rows and columns, respectively. The contents include: filtered gene counts, genes, and cell-barcodes.

value: cervix

tag: timepoint

value: Gestation day 12


title: microRNA_2091_20_mkd_Placenta


title: mcervix_D6

description: scRNA-seq

value: Gestation day 6


title: microRNA_2086_20_mkd_Placenta

value: Adult


title: Kras/Keap1/Lkb1 - replicate 5 - tumor B

city: Parkville

first: Waruni

last: Abeysekera

state: Victoria

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the mouse genome by Rsubread version 1.32.2
Read counts were summarized by Ensembl gene ID using the Rsubread featureCounts function and GENCODE Release M24 (GRCm38.p6) annotation
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: Tab-delimited text files; columns represent Ensembl gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene

source_name: Lung tumor

extract_protocol:
RNA was extracted using the Qiagen RNeasy RNA extraction kit (Cat 74104)
Libraries were constructed using the TruSeq RNA Library Prep v2 library construction kit
Paired-end 80 bp RNA-sequencing short reads were generated using an Illumina NextSeq system, yielding between 13 and 76 million reads for each sample

value: Lung tumor

tag: growth protocol

value: intranasal Ad5-CMV-Cre

tag: mouse

tag: gender

value: Male

tag: sequencing run

value: run 1


title: microRNA_2081_6.3_mkd_Placenta

tag: developmental stage

value: Crl:CD (SD); Sprague-Dawley

tag: rat body weight at gestation day 0 (grams)

tag: sex/pregnancy status

value: Female

value: Pregnant

value: Ketoconazole

value: Daily via oral gavage from gestation days 6 to 20


title: Kras/Keap1/Lkb1 - replicate 4 - tumor A

tag: tissue

value: run 5


title: microRNA_2079_6.3_mkd_Placenta

tag: pregnancy status at gestation day 21

tag: agent

tag: exposure

tag: interval between last dosing and necropsy

value: Approximately 24 hours

value: The morning of observing a vaginal plug was considered gestation day 0

value: 2 ml/kg body weight


title: microRNA_2084_20_mkd_Placenta

tag: gestation day definition

tag: corn oil vehicle dose level

tag: ketoconazole dose level (mg/kg/day)

tag: rna integrity number (rin) of isolated total rna


title: Kras/Keap1/Lkb1 - replicate 5 - tumor A

tag: strain

tag: genotype


title: Kras/Keap1/Lkb1 - replicate 3 - tumor B

tag: growth protocol

tag: mouse

value: run 3


title: microRNA_2099_40_mkd_Placenta


title: Kras/Keap1/Lkb1 - replicate 3 - tumor A

tag: gender

tag: sequencing run


title: microRNA_2078_6.3_mkd_Placenta

tag: developmental stage

tag: rat body weight at gestation day 0 (grams)


title: microRNA_2074_6.3_mkd_Placenta

tag: sex/pregnancy status


title: Kras/Keap1/Lkb1 - replicate 2 - tumor A

tag: tissue

value: run 2


title: microRNA_2072_2.0_mkd_Placenta

tag: pregnancy status at gestation day 21

tag: agent


title: microRNA_2087_20_mkd_Placenta

tag: exposure

tag: interval between last dosing and necropsy


title: Kras/Keap1/Lkb1 - replicate 2 - tumor B


title: Kras/Lkb1 - replicate 5 - tumor B

value: run 4


title: Kras/Lkb1 - replicate 5 - tumor A


title: microRNA_2069_2.0_mkd_Placenta

value: Adult

tag: gestation day definition

tag: corn oil vehicle dose level


title: microRNA_2063_0.63_mkd_Placenta

tag: ketoconazole dose level (mg/kg/day)

tag: rna integrity number (rin) of isolated total rna


title: Kras/Keap1/Lkb1 - replicate 1 - tumor A

value: Lung tumor

tag: strain

tag: genotype


title: microRNA_2062_0.63_mkd_Placenta


title: microRNA_2068_2.0_mkd_Placenta


title: Kras/Lkb1 - replicate 4 - tumor A

tag: growth protocol

value: intranasal Ad5-CMV-Cre

tag: mouse


title: microRNA_2061_0.63_mkd_Placenta


title: microRNA_2060_0.63_mkd_Placenta


title: Kras/Lkb1 - replicate 3 - tumor B

tag: gender

value: Male

tag: sequencing run


title: microRNA_2053_0.2_mkd_Placenta

tag: developmental stage

tag: rat body weight at gestation day 0 (grams)


title: microRNA_2077_6.3_mkd_Placenta

tag: sex/pregnancy status


title: microRNA_2047_0.2_mkd_Placenta

tag: pregnancy status at gestation day 21


title: Kras/Lkb1 - replicate 2 - tumor B

tag: tissue


title: Kras/Lkb1 - replicate 3 - tumor A

value: run 1


title: microRNA_2046_0.2_mkd_Placenta

value: Crl:CD (SD); Sprague-Dawley

tag: agent

tag: exposure


title: microRNA_2055_0.63_mkd_Placenta

value: Female

tag: interval between last dosing and necropsy

tag: gestation day definition


title: Kras/Lkb1 - replicate 2 - tumor A


title: Kras/Keap1/Lkb1 - replicate 1 - tumor B


title: microRNA_2051_0.2_mkd_Placenta

value: Pregnant

tag: corn oil vehicle dose level

tag: ketoconazole dose level (mg/kg/day)


title: microRNA_2070_2.0_mkd_Placenta

tag: strain

value: Ketoconazole

tag: rna integrity number (rin) of isolated total rna


title: microRNA_2042_0.063_mkd_Placenta

value: Daily via oral gavage from gestation days 6 to 20


title: microRNA_2027_0_mkd_Placenta

value: Corn oil (vehicle)


title: microRNA_2043_0.063_mkd_Placenta

value: Approximately 24 hours


title: Kras/Keap1 - replicate 5 - tumor B

tag: genotype

tag: growth protocol


title: microRNA_2032_0_mkd_Placenta

value: The morning of observing a vaginal plug was considered gestation day 0


title: microRNA_2065_2.0_mkd_Placenta

value: 2 ml/kg body weight


title: Kras/Keap1 - replicate 5 - tumor A

tag: mouse

tag: gender


title: microRNA_2101_40_mkd_Liver

source_name: Liver

tag: developmental stage


title: microRNA_2030_0_mkd_Placenta

tag: rat body weight at gestation day 0 (grams)


title: Kras/Lkb1 - replicate 1 - tumor B

tag: sequencing run


title: microRNA_2026_0_mkd_Placenta

tag: sex/pregnancy status

tag: pregnancy status at gestation day 21


title: microRNA_2041_0.063_mkd_Placenta

tag: agent


title: Kras/Lkb1 - replicate 4 - tumor B

tag: tissue

value: run 3


title: microRNA_2025_0_mkd_Placenta

tag: exposure

tag: interval between last dosing and necropsy


title: Kras/Lkb1 - replicate 1 - tumor A

value: run 2


title: Kras/Keap1 - replicate 4 - tumor B


title: microRNA_2099_40_mkd_Liver

tag: gestation day definition

tag: corn oil vehicle dose level


title: Kras/Keap1 - replicate 4 - tumor A

tag: strain


title: microRNA_2100_40_mkd_Liver

tag: ketoconazole dose level (mg/kg/day)

tag: rna integrity number (rin) of isolated total rna


title: Kras/Keap1 - replicate 3 - tumor B

tag: genotype

tag: growth protocol

value: run 5


title: microRNA_2044_0.2_mkd_Placenta

value: Adult


title: Kras/Keap1 - replicate 3 - tumor A

value: Lung tumor

tag: mouse

tag: gender


title: microRNA_2087_20_mkd_Liver

tag: developmental stage

tag: rat body weight at gestation day 0 (grams)


title: microRNA_2092_20_mkd_Liver

tag: sex/pregnancy status

value: Could not be computed


title: microRNA_2034_0.063_mkd_Placenta

tag: pregnancy status at gestation day 21


title: microRNA_2091_20_mkd_Liver

tag: agent


title: microRNA_2097_40_mkd_Liver


title: microRNA_2094_40_mkd_Liver


title: Kras/Keap1 - replicate 2 - tumor B

tag: tissue

value: intranasal Ad5-CMV-Cre

tag: sequencing run


title: microRNA_2074_6.3_mkd_Liver

tag: exposure

tag: interval between last dosing and necropsy


title: microRNA_2077_6.3_mkd_Liver

tag: gestation day definition

tag: corn oil vehicle dose level


title: Kras/Keap1 - replicate 1 - tumor B

tag: strain


title: microRNA_2069_2.0_mkd_Liver

tag: ketoconazole dose level (mg/kg/day)

tag: rna integrity number (rin) of isolated total rna


title: Kras/Keap1 - replicate 1 - tumor A

tag: genotype

tag: growth protocol


title: Normal lung tissue - replicate 5

source_name: Lung tissue

value: Lung tissue

tag: mouse

tag: gender

value: Male


title: microRNA_2072_2.0_mkd_Liver

tag: developmental stage

value: Crl:CD (SD); Sprague-Dawley

tag: rat body weight at gestation day 0 (grams)

value: Female


title: microRNA_2040_0.063_mkd_Placenta

tag: sex/pregnancy status

tag: pregnancy status at gestation day 21

value: Pregnant

value: Ketoconazole


title: microRNA_2084_20_mkd_Liver

tag: agent

value: Daily via oral gavage from gestation days 6 to 20


title: microRNA_2081_6.3_mkd_Liver

value: Approximately 24 hours


title: microRNA_2063_0.63_mkd_Liver

value: The morning of observing a vaginal plug was considered gestation day 0


title: microRNA_2065_2.0_mkd_Liver

value: 2 ml/kg body weight


title: microRNA_2062_0.63_mkd_Liver


title: Normal lung tissue - replicate 2

tag: tissue

tag: sequencing run

value: run 3


title: microRNA_2053_0.2_mkd_Liver

tag: exposure

tag: interval between last dosing and necropsy


title: Normal lung tissue - replicate 1

value: run 2


title: microRNA_2078_6.3_mkd_Liver

tag: gestation day definition

tag: corn oil vehicle dose level


title: Kras/Keap1 - replicate 2 - tumor A

tag: strain

value: run 1


title: microRNA_2060_0.63_mkd_Liver

value: Adult

tag: ketoconazole dose level (mg/kg/day)

tag: rna integrity number (rin) of isolated total rna


title: microRNA_2068_2.0_mkd_Liver


title: Normal lung tissue - replicate 3

tag: genotype

tag: growth protocol


title: Normal lung tissue - replicate 6

tag: mouse

tag: gender


title: microRNA_2061_0.63_mkd_Liver

tag: developmental stage

tag: rat body weight at gestation day 0 (grams)


title: microRNA_2086_20_mkd_Liver

tag: sex/pregnancy status

tag: pregnancy status at gestation day 21


title: microRNA_2070_2.0_mkd_Liver

tag: agent


title: Normal lung tissue - replicate 4

tag: tissue

tag: sequencing run

value: run 4


title: microRNA_2079_6.3_mkd_Liver

tag: exposure

tag: interval between last dosing and necropsy


title: microRNA_2040_0.063_mkd_Liver

tag: gestation day definition

tag: corn oil vehicle dose level


title: microRNA_2032_0_mkd_Liver

tag: strain

value: Corn oil (vehicle)

tag: ketoconazole dose level (mg/kg/day)


title: microRNA_2042_0.063_mkd_Liver

tag: rna integrity number (rin) of isolated total rna


title: ex vivo prostate epithelial cells - J_rep3

city: Vienna

first: Tanja

last: Limberger

address: Waehringer Guertel 18-20

country: Austria

institute: Medical University of Vienna

data_processing:
Raw FASTQ files from murine RNA-seq were quality checked with FastQC (v0.11.5) and MultiQC (v1.4)
Adapters and low-quality read ends were trimmed using Trimmomatic (v0.36) and reads shorter than 35 nt were discarded. The pre-processed reads were mapped to the reference mouse genome (Ensembl GRCm38) utilizing gene annotation (Ensembl v91) with STAR
The quality of mapping was evaluated with RSeQC (v2.6.4) and Picard (v2.10.6) and rRNA content was checked with FastQ Screen (v0.13.0)
Gene quantification was performed on uniquely mapped reads only with featureCounts (v1.5.2)
Differential expression analysis was carried out in R (version 3.5.1) with DESeq2 package (v1.20.0)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab delimited file with raw counts from featureCounts for all samples

source_name: prostate

extract_protocol:
Prostates were removed, single cell suspensions were prepared and EpCAM positive epithelial cells were enriched using a magnetic bead based sorting approach. RNA was harvested using ReliaPrep RNA Tissue Miniprep Kit (Promega). For library preparation, the Ultra II Directional RNA Library Prep Kit (E7760, NEB) was used in combination with a poly(A) mRNA magnetic isolation module (E7490). 250ng total RNA were used.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: prostate

tag: age

value: 19 week post natal

tag: genotype

value: Pten-/- Jun-/-


title: ex vivo prostate epithelial cells - J_rep5


title: ex vivo prostate epithelial cells - J_rep2


title: microRNA_2055_0.63_mkd_Liver

value: Crl:CD (SD); Sprague-Dawley


title: microRNA_2043_0.063_mkd_Liver

value: Female


title: microRNA_2051_0.2_mkd_Liver

value: Pregnant


title: microRNA_2027_0_mkd_Liver


title: ex vivo prostate epithelial cells - J_rep1


title: microRNA_2026_0_mkd_Liver


title: microRNA_2047_0.2_mkd_Liver

value: Ketoconazole


title: microRNA_2046_0.2_mkd_Liver

value: Daily via oral gavage from gestation days 6 to 20


title: microRNA_2044_0.2_mkd_Liver

value: Approximately 24 hours


title: ex vivo prostate epithelial cells - D_rep5

value: Pten-/- Kmt2c-SET-/-


title: mRNA_2101_40_mkd_Placenta

value: The morning of observing a vaginal plug was considered gestation day 0

value: 2 ml/kg body weight


title: mRNA_2099_40_mkd_Placenta


title: ex vivo prostate epithelial cells - J_rep4


title: 19 IBET Ova

city: Cambridge

first: John

middle: Robert

last: Ferdinand

address: Department of Medicine

country: United Kingdom

institute: University of Cambridge

data_processing:
Files were demutiplexed using Casava
Reads were checked for quality with FastQC and trimmed using TrimGalore!
Trimmed reads were alligned to the mm10 genome with Hisat2 and counted usign Feature Counts from Rseubread
Assembly: mm10
Supplementary files format and content: csv

source_name: Bone Marrow

growth_protocol: Bone marrow cells were flushed from femurs and tibias of mice and incubated in cRPMI supplemented with 40ng/mL murine GM-CSF, and cultured at 37C for 8 days. Media replaced on day 3 and 6.

extract_protocol:
Cells were sorted into lysis buffer and RNA extracted using Rneasy plus micro kit (Qiagen)
Librarys were prepaired using SMARTer® Universal Pico Input RNA Kit (Takara Bio)

treatment_protocol: Cells were treated simultaneously with I-BET151 (3.3 uM) or 5% DMSO and Ovalbumin / IC for 4 hours.

value: BMDC

tag: treatment

tag: stimulation

value: Ovalbumin

tag: mouse

value: E


title: mRNA_2097_40_mkd_Placenta

tag: developmental stage

value: Adult

tag: rat body weight at gestation day 0 (grams)

tag: sex/pregnancy status


title: 18 DMSO IC

value: DMSO

value: Ovalbumin-IC


title: 20 IBET IC


title: microRNA_2034_0.063_mkd_Liver

tag: pregnancy status at gestation day 21

tag: agent


title: 17 DMSO Ova


title: mRNA_2086_20_mkd_Placenta

tag: exposure


title: microRNA_2041_0.063_mkd_Liver

tag: interval between last dosing and necropsy


title: mRNA_2084_20_mkd_Placenta

tag: gestation day definition


title: microRNA_2025_0_mkd_Liver

value: Corn oil (vehicle)

tag: corn oil vehicle dose level


title: LPS_TNFa_IL1B

city: Nijmegen

first: Kim

middle: de

last: Kleijn

address: Geert Grooteplein Zuid 26-28

institute: Radboud University

data_processing:
Reads mapped to rRNAs were removed. Low quality reads (more than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) were removed with the SOAPnuke software (parameters: -l 20 -q 0.4 -n 0.1 -Q 2 -G).
Reads were mapped to reference genome h38 using Bowtie2 Version: v2.2.5 (Parameters: -q --phred33 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X  1000 --no-mixed --no-discordant -p 1 -k 200) and gene expression levels were calculated with RSEM Version: v1.2.12 (Parameters: default).
Differentially expressed genes (DEGs) were detected with the Poisson distribution method as described in Audic et al. (Audic, S. & Claverie, J. M. (1997) The significance of digital gene expression profiles. Genome Res. 7, 986-995; DOI: 10.1101/gr.7.10.986).  (1997))
Assembly: h38
Supplementary files format and content: FPKM values for all detected genes in each sample

source_name: Human cortical spheroid

growth_protocol: To generate hCSs, intact H9 ESC-colonies were detached with ReLESR (STEMcell technologies, 05872) and low-adherence V-bottom 96-wells (S-Bio, #MS-9096VZ) were seeded with ~ 1.25*104 cells per well. For the first seven days, spheroids were incubated with Spheroid Starter Medium (SSM: DMEM-F12 (Gibco, 31331-028) with 20% knock-out serum (Gibco, 10828-028), 1% non-essential amino acids (Gibco, 11140050), 1% Pen-Strep and 0.1% 2-mercaptoethanol (Thermo Fisher, 31350-010) supplemented with 10 μM of the TGF-β signaling inhibitor SB-431542 (Sigma-Aldrich, S4317) and 1 μM of the BMP4 signaling inhibitor dorsomorphin (Sigma-Aldrich, P5499). Only during cell seeding 2 μM ROCK inhibitor thiazovivin (Sigma-Aldrich, SML1045) was added. Medium was then switched to Neurobasal-A spheroid medium (Thermo Fisher, 10888-022) with 2% B27 supplement minus vitamin A (Gibco; 12587-010), 1% Gluta-MAX (Gibco, 35050-061) and 1% Pen-Strep (NSMnogel) (day 7 (d7) until d25) and subsequently to NSMnogel medium with 15 μg/ml Geltrex (Thermo Fisher, A1413302) (NSM medium) until d150. Between d14 and d25 half of the medium was refreshed daily. At d25, hCSs were transferred to 6-well low-attachment plates with a P1000 cut-open tip (~ 24 spheroids in 6 ml per dish). Between d25 and d150 half of the medium was refreshed every other day. Between d27 and d43 the NSM medium was supplemented with 20 ng/ml NT-3 (Sigma-Aldrich, SRP3128) and 20 ng/ml BDNF (Sigma-Aldrich, SRP3014). Between d43 and d51 the NSM medium was not supplemented with NT-3 and BDNF. Between d51 and d61 the NSM medium was supplemented with 10 ng/ml PDGF-AA (Sigma-Aldrich; H8291) and 10 ng/ml IGF1 (R&D systems; 291-G1-200). From d61 until d73, half of the medium was refreshed with NSM medium containing 4 μM ketoconazole (Sigma-Aldrich, K1003).

extract_protocol:
Human cortical spheroids were snap-frozen in liquid nitrogen. Upon RNA isolation, spheroids were thawed in TriZOL reagent and RNA isolation was performed according to the manufacturer's instructions (Thermo Fisher Scientific).
Libraries were prepared at BGI Genomics (Shenzhen, China) according to their standards for the DNBseq platform DNBSEQ-T7.

treatment_protocol: For cytokine-stimulation experiments, d150 hCSs were transferred to low-attachment 6-well plates (Corning) that were placed on a gentle cell-culture incubator rocker in order to achieve an optimal flow of cytokines during the stimulation period. hCSs were incubated with 5 ng/ml TNFα (Sigma-Aldrich T0157-10UG; in PBS) or 5 ng/ml IL-1β (Sigma-Aldrich SRP3083-10UG; in PBS) for 4h, 12h or 36h, or first with LPS 100 ng/ml (Sigma-Aldrich L4391-1MG; in PBS) and subesequently with TNFα and IL-1β (in PBS) both at 5 ng/ml for 24 hours. The 0h and 0h_2 controls involved the use of unstimulated spheroids.

tag: cell line

value: H9 embryonic stem cells

value: LPS 100 ng/ml 24 hours, subesequently TNFα+IL-1β both 5 ng/ml 24 hours

tag: spheroid age

value: ~150 days old


title: 0h_2


title: mRNA_2094_40_mkd_Placenta

tag: strain

value: Crl:CD (SD); Sprague-Dawley

value: Female

value: Pregnant

tag: ketoconazole dose level (mg/kg/day)

tag: rna integrity number (rin) of isolated total rna


title: ex vivo prostate epithelial cells - D_rep1

tag: tissue

value: prostate

tag: age

value: 19 week post natal

tag: genotype


title: microRNA_2030_0_mkd_Liver

tag: developmental stage

value: Daily via oral gavage from gestation days 6 to 20

value: Approximately 24 hours

value: The morning of observing a vaginal plug was considered gestation day 0


title: mRNA_2092_20_mkd_Placenta

tag: rat body weight at gestation day 0 (grams)

value: Ketoconazole

value: 2 ml/kg body weight


title: ex vivo prostate epithelial cells - D_rep2

value: Pten-/- Kmt2c-SET-/-


title: mRNA_2087_20_mkd_Placenta

value: Adult

tag: sex/pregnancy status


title: mRNA_2091_20_mkd_Placenta

tag: pregnancy status at gestation day 21


title: IL1B_12h

tag: treatment

value: IL-1β 5 ng/ml 12 hours


title: ex vivo prostate epithelial cells - P_rep2

value: Pten-/-


title: ex vivo prostate epithelial cells - P_rep4


title: 16 IBET IC

value: BMDC

tag: stimulation

value: Ovalbumin-IC

tag: mouse

value: D


title: 15 IBET Ova

value: Ovalbumin


title: ex vivo prostate epithelial cells - P_rep3


title: IL1B_36h

value: H9 embryonic stem cells

value: IL-1β 5 ng/ml 36 hours

value: ~150 days old


title: mRNA_2081_6.3_mkd_Placenta

value: Crl:CD (SD); Sprague-Dawley

value: Female

value: Pregnant

tag: agent

tag: exposure

tag: interval between last dosing and necropsy

tag: gestation day definition


title: 12 IBET IC

value: C


title: mRNA_2077_6.3_mkd_Placenta

tag: strain

value: Ketoconazole

value: Daily via oral gavage from gestation days 6 to 20

value: Approximately 24 hours

value: The morning of observing a vaginal plug was considered gestation day 0

tag: corn oil vehicle dose level


title: mRNA_2079_6.3_mkd_Placenta

value: Adult

value: 2 ml/kg body weight

tag: ketoconazole dose level (mg/kg/day)

tag: rna integrity number (rin) of isolated total rna


title: 13 DMSO Ova

value: BMDC

value: DMSO


title: mRNA_2078_6.3_mkd_Placenta


title: ex vivo prostate epithelial cells - D_rep4

tag: tissue

value: prostate

tag: age

value: 19 week post natal

value: Pten-/- Kmt2c-SET-/-


title: TNFa_36h

tag: cell line

value: H9 embryonic stem cells

value: TNFα 5 ng/ml 36 hours

tag: spheroid age


title: ex vivo prostate epithelial cells - K_rep5

tag: genotype


title: 11 IBET Ova

value: Ovalbumin


title: TNFa_12h

value: TNFα 5 ng/ml 12 hours

value: ~150 days old


title: ex vivo prostate epithelial cells - D_rep3


title: mRNA_2072_2.0_mkd_Placenta

tag: developmental stage

value: Crl:CD (SD); Sprague-Dawley

tag: rat body weight at gestation day 0 (grams)

tag: sex/pregnancy status

value: Female

tag: pregnancy status at gestation day 21

value: Pregnant


title: ex vivo prostate epithelial cells - P_rep1

value: Pten-/-


title: ex vivo prostate epithelial cells - P_rep5


title: mRNA_2100_40_mkd_Placenta

tag: agent

value: Ketoconazole

value: Daily via oral gavage from gestation days 6 to 20

value: Approximately 24 hours

value: The morning of observing a vaginal plug was considered gestation day 0


title: 14 DMSO IC

value: BMDC

tag: treatment

value: DMSO

tag: stimulation

value: Ovalbumin-IC

tag: mouse

value: D


title: mRNA_2074_6.3_mkd_Placenta

value: Adult

tag: strain

tag: exposure

tag: interval between last dosing and necropsy

tag: gestation day definition

value: 2 ml/kg body weight


title: TNFa_4h

value: H9 embryonic stem cells

value: TNFα 5 ng/ml 4 hours


title: mRNA_2070_2.0_mkd_Placenta

tag: corn oil vehicle dose level

tag: ketoconazole dose level (mg/kg/day)

tag: rna integrity number (rin) of isolated total rna


title: ex vivo prostate epithelial cells - K_rep2

tag: tissue

value: prostate

tag: age

value: 19 week post natal


title: ex vivo prostate epithelial cells - K_rep3

tag: genotype


title: 8 IBET IC

value: B


title: IL1B_4h

tag: cell line

value: IL-1β 5 ng/ml 4 hours

tag: spheroid age

value: ~150 days old


title: ex vivo prostate epithelial cells - K_rep1


title: 7 IBET Ova

value: Ovalbumin


title: HOG_stimulated

data_processing:
Reads mapped to rRNAs were removed. Low quality reads (more than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) were removed with the SOAPnuke software Version v1.5.2 (parameters: -l 20 -q 0.4 -n 0.1 -Q 2 -G).
Reads were mapped to reference genome h38 using Bowtie2 Version: v2.2.5 (Parameters: -q --phred33 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X  1000 --no-mixed --no-discordant -p 1 -k 200) and gene expression levels were calculated with RSEM Version: v1.2.12 (Parameters: default).
Differentially expressed genes (DEGs) were detected with the Poisson distribution method as described in Audic et al. (Audic, S. & Claverie, J. M. The significance of digital gene expression profiles. Genome Res. 7, 986-995, 1997)
Assembly: h38
Supplementary files format and content: Excel files include FPKM values for all detected genes.

source_name: Human oligodendroglioma

growth_protocol: HMC3 cells were purchased from ATCC (CRL-3304). The HOG cell line was a kind gift of Dr. José Antonio López Guerrero (University of Madrid, Spain). The HMC3 and HOG cells were grown in EMEM (Lonza, BE12-662F) with 10% heat-treated FBS (Gibco, 10270106), 1% glutamax and 1% Pen-Strep, and passaged twice per week at a 1:20 splitting ratio (maximum passage number 35).

extract_protocol:
RNA was extracted with the RNAeasy Qiagen RNA extraction kit.
Libraries were prepared at BGI Genomics (Shenzhen, China) according to their standards for the DNBseq platform DNBSEQ-T7.

treatment_protocol: For pro-inflammatory stimulation experiments with HMC3 (30.000 cells/cm2) and HOG cells (30.000 cells/cm2), the cells were incubated with 100 ng/ml LPS (Sigma-Aldrich, L4391-1MG) (dissolved in PBS) for 24 hours (24h) and subsequently with 5 ng/ml TNFα  (in PBS) and 5 ng/ml IL-1β (in PBS) for 24h.

value: HOG cell line

value: Brain

value: stimulated


title: mRNA_2069_2.0_mkd_Placenta

tag: developmental stage

value: Crl:CD (SD); Sprague-Dawley

tag: rat body weight at gestation day 0 (grams)

tag: sex/pregnancy status

value: Female

tag: pregnancy status at gestation day 21

value: Pregnant

value: Ketoconazole

value: Daily via oral gavage from gestation days 6 to 20

value: Approximately 24 hours

value: The morning of observing a vaginal plug was considered gestation day 0


title: 10 DMSO IC

value: BMDC

tag: treatment

value: DMSO

tag: stimulation

value: Ovalbumin-IC

tag: mouse

value: C


title: ex vivo prostate epithelial cells - K_rep4

value: prostate

value: 19 week post natal


title: 6 DMSO IC

value: B


title: ex vivo prostate epithelial cells - W_rep4

value: wild type


title: ex vivo prostate epithelial cells - W_rep5


title: HMC3_unstimulated

source_name: Human fetal microglia

value: HMC3 cell line

value: Brain

value: unstimulated


title: mRNA_2063_0.63_mkd_Placenta

value: Adult

tag: strain

value: Crl:CD (SD); Sprague-Dawley

value: Female

tag: agent

tag: exposure

tag: interval between last dosing and necropsy

value: 2 ml/kg body weight


title: 5 DMSO Ova

value: Ovalbumin


title: ex vivo prostate epithelial cells - W_rep3


title: 4 IBET IC

value: A


title: ex vivo prostate epithelial cells - W_rep2


title: HMC3_stimulated

value: stimulated


title: 3 IBET Ova

value: BMDC


title: HOG_unstimulated

value: HOG cell line


title: mRNA_2065_2.0_mkd_Placenta

value: Pregnant

value: Ketoconazole

value: Daily via oral gavage from gestation days 6 to 20

value: Approximately 24 hours

tag: gestation day definition

value: The morning of observing a vaginal plug was considered gestation day 0

tag: corn oil vehicle dose level

tag: ketoconazole dose level (mg/kg/day)

tag: rna integrity number (rin) of isolated total rna


title: 0h

tag: cell line

value: H9 embryonic stem cells

value: ~150 days old


title: mRNA_2061_0.63_mkd_Placenta


title: ex vivo prostate epithelial cells - W_rep1

tag: tissue

value: prostate

tag: age

value: 19 week post natal

tag: genotype

value: Wild type


title: 1A

city: Birmingham

first: Andrzej

middle: T

last: Slominski

state: AL

address: 1720 2nd Avenue South

department: Dermatology

institute: UAB

description: male samples FPKM-normalized counts values.xlsx

data_processing:
Samples were sequenced on the BGISEQ platform and FASTQ files were generated
FASTQ files were aligned to the mouse genome using STAR version 2.7.0c using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Trancript abundances were calculated using Cufflinks version 2.2.1 using parameters --library-type fr-firststrand -G -L
Cuffdiff (part of Cufflinks) was used to calculate fold change using default parameters
Genome_build: Gencode GRCm38 p4 Release M11
Supplementary_files_format_and_content: tab-delimited Excel file containing the FPKM values and count values (from Cuffnorm) for each gene in each sample

source_name: lymph nodes

extract_protocol: The mice were euthanized 24 hours after the last D3 treatment and the inquinal lymph nodes were collected. RNA was prepared with a standard Trizol RNA Extraction protocol.

treatment_protocol: Female and male C57BL/6j mice were applied topically  with a chemical DNFB on abdominal skin. Three days after the DNFB treatment, the mice were injected intraperitoneally with 20(OH)D3 or 25(OH)D3 at 4 ug/kg per day for 4 consecutive days. The control mice were treated intraperitoneally with the vehicle EtOH.

tag: Sex

value: male

value: Control


title: 3A


title: mRNA_2060_0.63_mkd_Placenta

tag: developmental stage

value: Adult

value: Crl:CD (SD); Sprague-Dawley

tag: rat body weight at gestation day 0 (grams)

tag: sex/pregnancy status

value: Female

tag: pregnancy status at gestation day 21

value: 2 ml/kg body weight


title: 9 DMSO Ova

value: BMDC

tag: treatment

value: DMSO

tag: stimulation

value: Ovalbumin

tag: mouse

value: C


title: mRNA_2062_0.63_mkd_Placenta

tag: strain

value: Pregnant

tag: agent

value: Ketoconazole

tag: exposure

value: Daily via oral gavage from gestation days 6 to 20

tag: interval between last dosing and necropsy

value: Approximately 24 hours


title: Sample 8 (Zbtb46 KO)

city: New York

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

data_processing:
Base calling and demultiplexing with Illumina Casava 1.8.2
Adapter trimming using FLEXBAR (v2.4)
Alignment to mm10 reference genome using STAR version 2.3.0 with default settings
Reads per gene counted using Rsubread R package
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text giving raw number of counts mapped to each gene (identified by Entrez ID) in each sample

source_name: Sorted ILC3s

extract_protocol:
Sorted cells were used to prepare RNAseq libraries using the Clontech SMARTer Ultra Low Input RNA Kit V4 (Clontech Laboratories).
Standard Illumina protocols

tag: cell type

value: Sorted ILC3s

value: Zbtb46 KO


title: 2A


title: 1 DMSO Ova

value: A


title: Sample 7 (Zbtb46 KO)


title: mRNA_2055_0.63_mkd_Placenta

tag: gestation day definition

value: The morning of observing a vaginal plug was considered gestation day 0

tag: corn oil vehicle dose level

tag: ketoconazole dose level (mg/kg/day)

tag: rna integrity number (rin) of isolated total rna


title: 2 DMSO IC

value: Ovalbumin-IC


title: day21-lung

city: Kashiwa

first: BIN

last: WU

state: Chiba

address: #304, 6-6-2, Kashiwanoha

department: Research

institute: ImmunoGeneTeqs

description: BD Rhapsody WTA

data_processing:
R1 = cell barcode and UMI read
R2 = mRNA read (complement)
Adapter trimming of sequencing data was performed by using Cutadapt 3.4.  Filtered reads were chunked to 16 parts for parallel processing by using Seqkit 0.15.0.  Filtered cell barcode reads were annotated by Python script provided by BD with minor modification for compatible to Python3.8.  Associated cDNA reads were mapped to reference RNA (build GRCm38 release-101) by using bowtie2-2.4.2 by the following parameters: -p 2 –very-sensitive-local -N 1 –norc –seed 656565 –reorder.  Then, cell barcode information of each read were added to the bowtie2-mapped BAM files, and read counts of each gene in each cell barcode were counted by using mawk.  Resulted count data was converted to genes x cells matrix file and inflection threshold of the knee-plot was detected by using DropletUtils package in R version 4.1.3 (2022-03-10).
Assembly: GRCm38
Supplementary files format and content: txt

source_name: lung

extract_protocol:
Murine lung cells were isolated at 0, 3, 7,10, 14 and 21 days post-bleomycin administration. Lungs were cut into small pieces with a razor blade and digested enzymatically using 0.25 mg/ml Liberase TM (Roche) and 20 kU/mL DNase I (Sigma-Aldrich, St Louis, MO) for 60 min at 37°C. Erythrocytes and dead cells were removed by 25%/65% Percoll (GE Healthcare, Buckinghamshire, UK) density separation. Resulting cells were stained with Calcein AM for 5 min at 37°C, immediately chilled on ice, and filtered through 30 μm filter (Miltenyi).
15000 cells were loaded onto BD Rhapsody cartrige and captured cell number was asessed by BD Rhapsody scanner. Cell lysis, mRNA trap, cDNA synthesis, and primer digestion were performed according to the manufacture's instruction.
cDNA amplification was performed by TAS-Seq protocol (Shichino et al bioRxiv 2021). Sequencing libraries from amplified cDNAs were produced by using NEB UltraII FS Kit (New England Biolabs) with some modifications. Sequencing was performed by using a Novaseq S2 200 cycle kit and a Novaseq 6000 sequencer (Illumina) according to the manufacture's instructions. 20% PhiX spike-in was used for sequencing.

treatment_protocol: C57BL/6J female mice were administered with a single dose of bleomycin sulfate (2 mg/kg dissolved in 50 μL of sterile saline solution; Nippon Kayaku) by oropharyngeal aspiration under deep anesthesia.

tag: day

value: lung single cell suspension

tag: Sex

value: female

tag: model

value: bleomycin-induced lung fibrosis

tag: organ

value: lung


title: day14-lung

description: BD Rhapsody WTA


title: mRNA_2053_0.2_mkd_Placenta

tag: developmental stage

value: Adult

value: Crl:CD (SD); Sprague-Dawley

tag: rat body weight at gestation day 0 (grams)

tag: sex/pregnancy status

value: Female

tag: pregnancy status at gestation day 21

value: 2 ml/kg body weight


title: mRNA_2068_2.0_mkd_Placenta

tag: strain

value: Pregnant


title: 12_IBET_IC

growth_protocol: Bone marrow cells were flushed from femurs and tibias of mice and incubated in cRPMI supplemented with 100ng/mL murine M-CSF, and cultured at 37C for 5 days. Media replaced on day 3.

treatment_protocol: Cells were treated simultaneously with I-BET151 (5.0 uM) or 5% DMSO and Ovalbumin / IC for 4 hours.

value: BMDM

tag: treatment

tag: stimulation

tag: mouse

value: C


title: 11_IBET_IC

tag: cell type

value: B


title: day10-lung

description: BD Rhapsody WTA


title: Sample 6 (Zbtb46 KO)

value: Sorted ILC3s

tag: genotype


title: mRNA_2051_0.2_mkd_Placenta

tag: agent

value: Ketoconazole

tag: exposure

value: Daily via oral gavage from gestation days 6 to 20

tag: interval between last dosing and necropsy

value: Approximately 24 hours

tag: gestation day definition

tag: corn oil vehicle dose level


title: Sample 5 (Zbtb46 KO)

value: Zbtb46 KO


title: day07-lung

description: BD Rhapsody WTA

tag: day

value: lung single cell suspension

tag: Sex

tag: model


title: 10_IBET_IC

value: Ovalbumin-IC

value: A


title: mRNA_2047_0.2_mkd_Placenta

tag: developmental stage

tag: rat body weight at gestation day 0 (grams)

value: The morning of observing a vaginal plug was considered gestation day 0

tag: ketoconazole dose level (mg/kg/day)

tag: rna integrity number (rin) of isolated total rna


title: 9_DMSO_IC

tag: treatment

value: DMSO

tag: strain


title: Sample 4 (Wild type)

value: WT


title: day03-lung

description: BD Rhapsody WTA

value: female

value: bleomycin-induced lung fibrosis

tag: organ

value: lung


title: mRNA_2046_0.2_mkd_Placenta

value: Adult

value: Crl:CD (SD); Sprague-Dawley

tag: sex/pregnancy status

value: Female

tag: pregnancy status at gestation day 21

value: Pregnant

value: 2 ml/kg body weight


title: Sample 3 (Wild type)

tag: cell type

value: Sorted ILC3s

tag: genotype


title: day00-lung

description: BD Rhapsody WTA


title: mRNA_2044_0.2_mkd_Placenta

tag: agent

value: Ketoconazole

tag: exposure

value: Daily via oral gavage from gestation days 6 to 20

tag: interval between last dosing and necropsy

value: Approximately 24 hours


title: Sample 2 (Wild type)


title: 7_DMSO_IC

value: BMDM

tag: stimulation

value: Ovalbumin-IC

tag: mouse


title: mRNA_2043_0.063_mkd_Placenta

tag: gestation day definition

value: The morning of observing a vaginal plug was considered gestation day 0

tag: corn oil vehicle dose level


title: Sample 1 (Wild type)


title: 5_IBET_Ova

value: Ovalbumin

value: B


title: 6_IBET_Ova

value: C


title: mRNA_2041_0.063_mkd_Placenta

tag: developmental stage

tag: rat body weight at gestation day 0 (grams)


title: Input 0h

city: Philadelphia

first: Jing

last: Luan

address: 3615 Civic Center Blvd, ARC 315

institute: University of Pennsylvania

data_processing:
Bowtie 1.1.0 was used to align sequences (Langmead and Salzberg, 2012) to the mm9 reference genome. Reads with more than one mismatch or multiple alignments were excluded.
Significantly enriched regions were called using MACS2 version 2.1.0 (Y. Zhang et al., 2008) with the following parameters: P = 10−5, extsize = 300 and local lambda = 100,000 using whole-cell extract input controls.
Reads for the bigwigs were RPM normalized.
Genome_build: mm9

source_name: CTCF-AID-mCherry+TIR

growth_protocol: G1E-ER4 (Weiss et al., 1997) derived cells were grown in IMDM+15% FBS, penicillin/streptomycin, kit ligand, monothioglycerol and Epoetin alpha in a standard tissue culture incubator at 37 degrees with 5% CO2 (as described in Weiss et al., 1997).

extract_protocol:
Lysates were prepared from sonicated nuclei and histone-DNA complexes were isolated with indicated antibodies.
ChIP-seq libraries were prepared using Illumina’s TruSeq ChIP sample preparation kit (Illumina, catalog no. IP-202-1012) according to manufacturer’s specifications, with the addition of size selection (left side at 0.9x, right side at 0.6x) using SPRIselect beads (Beckman Coulter, catalog no. B23318). Library size was determined (average 351 bp, range 333-372 bp) using the Agilent Bioanalyzer 2100, followed by quantitation using real-time PCR using the KAPA Library Quant Kit for Illumina (KAPA Biosystems catalog no. KK4835). Libraries were then pooled and sequenced (1x75bp) on the Illumina NextSeq 500 platform according to manufacturer’s instructions. Bclfastq2 v 2.15.04 (default parameters) was used to convert reads to fastq.

treatment_protocol: Cells were treated with auxin (1mM). See Description column for Samples.

value: ES-derived erythroid progenitor cells

tag: chip antibody

value: Input for No-treatment groups


title: Input 4h

tag: treatment

value: Input for 4h auxin groups


title: mRNA_2042_0.063_mkd_Placenta

value: Adult

tag: strain

value: Crl:CD (SD); Sprague-Dawley

tag: ketoconazole dose level (mg/kg/day)

tag: rna integrity number (rin) of isolated total rna


title: 4_IBET_Ova

value: A


title: 3_DMSO_Ova

value: DMSO


title: POLR2A_4h_ChIPseq_Rep2

value: anti-Rpb1 NTD mAb (Cell Signaling, #14958)

value: 4h auxin


title: mRNA_2034_0.063_mkd_Placenta

tag: sex/pregnancy status

value: Female

tag: pregnancy status at gestation day 21

value: Pregnant

value: Ketoconazole

value: Daily via oral gavage from gestation days 6 to 20

value: 2 ml/kg body weight


title: POLR2A_4h_ChIPseq_Rep1

tag: cell type


title: 2_DMSO_Ova

value: BMDM

value: Ovalbumin


title: 8_DMSO_IC

value: Ovalbumin-IC

value: B


title: mRNA_2040_0.063_mkd_Placenta

tag: agent

value: Approximately 24 hours

value: The morning of observing a vaginal plug was considered gestation day 0


title: P70 WT rep 4

city: Exeter

first: Nicholas

middle: E

last: Clifton

address: RILD Building

institute: University of Exeter

data_processing:
Raw sequencing reads were trimmed of adapters using Trimmomatic and passed through FastQC quality control. Reads were aligned to the mouse genome (GRCm38) with STAR and mapped to genes using featureCounts.
Assembly: GRCm38
Supplementary files format and content: Featurecounts ouput. Tab telimited text file containing raw gene counts for each gene

source_name: Frontal cortex

extract_protocol:
RNA was extracted using an AllPrep DNA/RNA micro kit (QIAGEN)
Library preparation and sequencing were performed by Novogene. cDNA libraries with 250-300 bp inserts were prepared using poly-A capture. A single batch of Illumina high-throughput sequencing was performed at 12Gb read depth per sample with 150bp paired-end reads

tag: genotype

value: WT

tag: tissue

value: Frontal cortex


title: P70 WT rep 3


title: P70 Het rep 5

value: Het


title: P70 Het rep 4


title: mRNA_2032_0_mkd_Placenta

value: Adult

value: Crl:CD (SD); Sprague-Dawley

value: Corn oil (vehicle)

tag: exposure

tag: interval between last dosing and necropsy


title: P70 Het rep 3


title: mRNA_2030_0_mkd_Placenta

value: Female

tag: gestation day definition


title: POLR2A_0h_ChIPseq_Rep2

value: ES-derived erythroid progenitor cells

value: anti-Rpb1 NTD mAb (Cell Signaling, #14958)

value: No treatment


title: P70 WT rep 5


title: POLR2A_0h_ChIPseq_Rep1


title: P70 Het rep 2


title: TIL Flox 3

city: Boston

first: Andrew

last: Wight

state: MA

address: 450 Brookline Ave

department: Cancer Immunology & Virology

institute: Dana-Farber Cancer Institute

data_processing:
BAM files were generated from provided fastq files using Rsubread version 2.6.4 using default settings
Read counts were generated using Rsubread version 2.6.4 using default settings, considering only those reads that were correctly paired
Genome_build: mm10
Supplementary_files_format_and_content: Read counts are presented as a .csv file, with each row corresponding to one gene and each column to one sample. Entrez gene IDs are given

source_name: Tumor-infiltrating FoxP3+ Treg

growth_protocol: Cells isolated ex-vivo and sorted based on FoxP3-YFP expression

extract_protocol:
RNA was extracted using Qiagen RNEasy Plus micro kit, following manufacturer's instructions
Library was constructed by GeneWiz following their ultra-low input RNA pipeline

value: B6.IL23RFlox FoxP3Cre-YFP

value: Endpoint MC38 flank tumor


title: TIL Flox 2


title: mRNA_2026_0_mkd_Placenta

value: Pregnant

value: Daily via oral gavage from gestation days 6 to 20

tag: corn oil vehicle dose level

value: 2 ml/kg body weight


title: P70 WT rep 1

tag: developmental stage


title: P70 WT rep 2


title: P70 Het rep 1


title: 1_DMSO_Ova

value: BMDM

value: DMSO

tag: stimulation

value: Ovalbumin

tag: mouse

value: A


title: scRNA-Seq library of FLT3int cells

city: Lund

first: Göran

last: Karlsson

state: Scania

address: Kilinkgatan 26 BMC B12

department: Division of Molecular Hematology

country: Sweden

institute: Lund University

data_processing:
ScATAC-Seq:Cell identification: The sequencing data were processed using cellranger-atac pipeline (v 1.1.0) from 10x Genomics to obtain the aligned reads. The pipeline annotates each aligned read with a cell barcodes (corrected or uncorrected). Mouse mm10 genomic assembly was used as the reference. The number of fragments associated with each barcode was used as a filter to remove the background barcodes. Barcode multiplets were removed using 10x Genomics recommended scripts for v1.1.0. Additionally, the cells with percentage mitochondrial contamination > 3 or less than -1 (both values in log2 scale) were removed.
ScATAC-Seq: Peak calling: Fragments associated with valid cell barcodes was obtained from cellranger-atac generated BAM files. Only properly aligned read-pairs, each with MAPQ > 20 were retained. Based on the read pairs, both ends of the fragments (accounting for soft clipping of reads during alignment) were identified and these were considered as cut sites and used in downstream analysis. A cell-barcode was allowed only one cut site for a particular genomic location. The cut sites were aggregated from all the cell barcodes, de-duplicated and saved in BED format where each line is 1 nucleotide-long range with start position indicating the cut site. MACS2 was called on the aggregated BED files separately for each chromosome to speed up the peak calling process. Default MACS2 parameters were overridden with  -s=150 --nomodel --shift=-75 --extsize=150 and the genome size parameter was set as the respective chromosome size. The narrow peaks from each chromosome were merged to create a reference peak set for use in the downstream analyses. For each cell, the number of cut sites within the peak set was counted, and the resulting cell-peak matrix was saved in the MTX format.
ScRNA-Seq: The data were processed using Cellranger 3.0.2 to generate counts matrices against the mm10 transcriptome. Seurat v2 R package was used to filter and normalize the data.
Genome_build: mm10
Supplementary_files_format_and_content: ScATAC-Seq: MTX format sparse matrix contain insertion site counts in peak and cells. ScRNA-Seq: MTX format sparse matrix containing UMI counts in genes and ells.

source_name: Bone marrow from all bones

extract_protocol:
ScRNA-Seq: LSKCD34+Flt3intCD9high, LSKCD34+Flt3intCD9low, and LSKCD34+Flt3int cells were sorted from the bone marrow of age-matched C57BL/6J mice, and loaded into 10X Chromium lanes, and the libraries were prepared as per the instruction manual of 10X Chromium. The final libraries were paired-end sequenced using 26 cycles for Read 1, 8 cycles for i7 index, and 98 cycles for read 2.  SCATAC-Seq: LSKCD34-Flt3- (LT-HSC), LSKCD34+Flt3- (ST-HSC), LSKCD34+Flt3int (LSKFlt3int), LSKCD34+Flt3high (LMPP), LSKFlt3-CD150+CD48+ (MPP2), Lin-Sca1-Kit+FcgRII/IIIlowCD150+EndoglinlowCD41-/low (Pre-MegE), LSKCD34+Flt3intCD9high (LSKCD9high), and LSKCD34+Flt3intCD9low (LSKCD9low) cells were sorted, and nuclei isolated following 3 minutes of cell lysis as per low input protocol from 10X Genomics, CA, USA. Single-cell chromatin accessibility profiles were generated by tagmentation followed by library preparation according to the Chromium Single Cell ATAC Reagent Kits User Guide (Satpathy A, 2019). The libraries were run on TapeStation (Agilent, CA, USA) and sequenced on Nova-Seq (Illumina Inc, CA, USA) using SP100 flow cell with the following specification: 48 (49 for MPP2 and preMegE) cycles for read 1N, 8 cycles for i7 index, 16 cycles for i5 index and 48 (50 for MPP2 and preMegE)  cycles for read 2N.
ScRNA-Seq: As per 10x genomics instructions for Chromium (v2). ScATAC-Seq. As per 10x genomics instructions for v1 and v1.1 of single cell ATAC protocol

tag: genotype/variation

value: WT

tag: age

value: 8-12 weeks

value: Bone marrow from all bones

value: FLT3int cells


title: mRNA_2025_0_mkd_Placenta

source_name: Placenta

value: Adult

tag: strain

value: Crl:CD (SD); Sprague-Dawley

tag: rat body weight at gestation day 0 (grams)

value: Female

value: Corn oil (vehicle)

value: Approximately 24 hours

value: The morning of observing a vaginal plug was considered gestation day 0

tag: ketoconazole dose level (mg/kg/day)


title: GIST-T1_CUTTAG_MLL1n

city: Worcester

first: Matthew

last: Hemming

address: 364 Plantation Street

institute: UMass Medical School

data_processing:
Library strategy: CUT&Tag
All Chip-Seq and CUT&Tag data were aligned to the human reference genome assembly hg19, GRCh37 (ncbi.nlm.nih.gov/assembly/2758/) using Bowtie2 (version 2.2.1), and gene annotations by gencode annotation release 19 (gencodegenes.org/releases/19.html)
Normalized read density was calculated using Bamliquidator (version 1.0) read density calculator. Aligned reads were extended by 200 bp and the density of reads per base pair was calculated. In each region, the density of reads was normalized to the total number of million mapped reads, generating read density in units of reads per million mapped reads per bp (rpm/bp).
Peak finding was performed using Model-based Analysis for ChIP-Seq (MACS, version 1.4.2). As control, matched input chromatin was used to generate background signal for peak determination.
Genome_build: hg19

source_name: KIT-dependent GIST cell line GIST-T1

growth_protocol: Dulbecco’s modified Eagle’s medium containing 10% FBS, 2 mM L- glutamine, 100 mg/ml penicillin, and 100 mg/ml streptomycin

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries for single-end 75 bp sequencing on an Illumina NextSeq 500 or paired-end 37 bp sequencing on an Illumina NextSeq 550 were prepared with a ThruPLEX DNA-seq Kit (Takara).

tag: cell line

value: Gastrointestinal stromal tumor (GIST)

tag: antibody

value: MLL, Bethyl Cat# A300-086A

tag: technique

value: CUT&Tag

tag: target

value: Endogenous MLL1


title: GIST-T1_CUTTAG_MEN1

tag: cell type

value: Menin, Bethyl Cat# A300-105A

value: Endogenous Menin


title: P7 WT rep 5

tag: genotype

tag: tissue

value: Frontal cortex


title: P7 WT rep 4

value: WT


title: GIST-T1_CUTTAG_IgG


title: scRNA-Seq library of FLT3intCD9hi cells

value: 8-12 weeks

value: FLT3intCD9hi cells


title: P7 WT rep 3


title: mRNA_2099_40_mkd_Liver

tag: sex/pregnancy status

tag: pregnancy status at gestation day 21

value: Pregnant

tag: agent

value: Ketoconazole

tag: exposure

value: Daily via oral gavage from gestation days 6 to 20

tag: interval between last dosing and necropsy

tag: gestation day definition

value: 2 ml/kg body weight

tag: rna integrity number (rin) of isolated total rna


title: TIL WT 3

tag: strain

value: B6.IL23RWT FoxP3Cre-YFP

tag: treatment

value: Endpoint MC38 flank tumor


title: P7 Het rep 5

value: Het

tag: developmental stage


title: mRNA_2101_40_mkd_Liver

value: Adult

value: Crl:CD (SD); Sprague-Dawley

tag: rat body weight at gestation day 0 (grams)

value: Female

value: Approximately 24 hours

value: The morning of observing a vaginal plug was considered gestation day 0

tag: corn oil vehicle dose level

tag: ketoconazole dose level (mg/kg/day)


title: TIL WT 2


title: mRNA_2100_40_mkd_Liver


title: TIL WT 1


title: GIST-T1_MEAF6_WM1119

data_processing:
All Chip-Seq and CUT&Tag data were aligned to the human reference genome assembly hg19, GRCh37 (ncbi.nlm.nih.gov/assembly/2758/) using Bowtie2 (version 2.2.1), and gene annotations by gencode annotation release 19 (gencodegenes.org/releases/19.html)
Normalized read density was calculated using Bamliquidator (version 1.0) read density calculator. Aligned reads were extended by 200 bp and the density of reads per base pair was calculated. In each region, the density of reads was normalized to the total number of million mapped reads, generating read density in units of reads per million mapped reads per bp (rpm/bp).
Peak finding was performed using Model-based Analysis for ChIP-Seq (MACS, version 1.4.2). As control, matched input chromatin was used to generate background signal for peak determination.
Genome_build: hg19

tag: cell line

value: Gastrointestinal stromal tumor (GIST)

tag: antibody

value: HA, Cell Signaling Technology Cat# 3724

tag: technique

value: ChIP-seq

tag: target

value: Overexpressed HA-tagged MEAF6


title: mRNA_2097_40_mkd_Liver

tag: sex/pregnancy status


title: mRNA_2094_40_mkd_Liver

tag: pregnancy status at gestation day 21


title: mRNA_2027_0_mkd_Placenta

tag: agent

value: Corn oil (vehicle)


title: Spleen Flox 3

source_name: Spleen FoxP3+ Treg

value: B6.IL23RFlox FoxP3Cre-YFP


title: P7 Het rep 4

tag: genotype

tag: tissue

value: Frontal cortex


title: GIST-T1_MEAF6_VTP

tag: cell type


title: scRNA-Seq library of FLT3intCD9lo cells

tag: genotype/variation

value: WT

tag: age

value: 8-12 weeks

value: Bone marrow from all bones

value: FLT3intCD9lo cells


title: TIL Flox 1

tag: strain

tag: treatment

value: Endpoint MC38 flank tumor


title: TIL WT 4

value: B6.IL23RWT FoxP3Cre-YFP


title: Spleen Flox 2


title: P7 WT rep 2

tag: developmental stage


title: mRNA_2092_20_mkd_Liver

source_name: Liver

value: Adult

value: Crl:CD (SD); Sprague-Dawley

tag: rat body weight at gestation day 0 (grams)

value: Pregnant

value: Ketoconazole

tag: exposure

value: Daily via oral gavage from gestation days 6 to 20

tag: interval between last dosing and necropsy

tag: gestation day definition

tag: corn oil vehicle dose level

value: 2 ml/kg body weight

tag: rna integrity number (rin) of isolated total rna

value: Could not be computed


title: P7 Het rep 3

value: Het


title: GIST-T1_MEAF6_DMSO

tag: cell line

value: Gastrointestinal stromal tumor (GIST)

tag: antibody

value: HA, Cell Signaling Technology Cat# 3724

tag: technique

value: ChIP-seq

tag: target

value: Overexpressed HA-tagged MEAF6


title: GIST-T1_DOT1L_WM1119

value: DOT1L, Cell Signaling Technology Cat# 77087

value: Endogenous DOT1L


title: mRNA_2091_20_mkd_Liver

tag: sex/pregnancy status

value: Female

tag: pregnancy status at gestation day 21

tag: agent

value: Approximately 24 hours

value: The morning of observing a vaginal plug was considered gestation day 0

tag: ketoconazole dose level (mg/kg/day)


title: P7 WT rep 1

tag: strain

tag: genotype

value: WT

tag: tissue

value: Frontal cortex


title: P7 Het rep 2

tag: developmental stage


title: mRNA_2087_20_mkd_Liver

value: Adult

value: Crl:CD (SD); Sprague-Dawley

tag: rat body weight at gestation day 0 (grams)

value: Pregnant

tag: exposure


title: Spleen WT 4

value: B6.IL23RWT FoxP3Cre-YFP

tag: treatment

value: Endpoint MC38 flank tumor


title: GIST-T1_DOT1L_VTP

tag: cell type


title: Spleen Flox 1

value: B6.IL23RFlox FoxP3Cre-YFP


title: mRNA_2086_20_mkd_Liver

value: Ketoconazole

value: Daily via oral gavage from gestation days 6 to 20

tag: interval between last dosing and necropsy

tag: gestation day definition

tag: corn oil vehicle dose level

value: 2 ml/kg body weight

tag: rna integrity number (rin) of isolated total rna


title: Spleen WT 2


title: P7 Het rep 1

value: Het


title: GIST-T1_KAT6A

tag: cell line

value: Gastrointestinal stromal tumor (GIST)

tag: antibody

value: KAT6A, Cell Signaling Technology Cat# 78462

tag: technique

value: ChIP-seq

tag: target

value: Endogenous KAT6A


title: GIST-T1_DOT1L_DMSO

value: DOT1L, Cell Signaling Technology Cat# 77087

value: Endogenous DOT1L


title: mRNA_2081_6.3_mkd_Liver

tag: sex/pregnancy status

value: Female

tag: pregnancy status at gestation day 21

tag: agent

value: Daily via oral gavage from gestation days 6 to 21

value: Approximately 24 hours

value: The morning of observing a vaginal plug was considered gestation day 0

tag: ketoconazole dose level (mg/kg/day)

value: Could not be computed


title: P35 WT rep 5

tag: strain

tag: genotype

value: WT

tag: developmental stage

tag: tissue

value: Frontal cortex


title: GIST-T1_H3K4me3

tag: cell type

value: H3K4me3, Abcam Cat# ab8580

value: Endogenous H3K4me3


title: Spleen WT 1

value: B6.IL23RWT FoxP3Cre-YFP

tag: treatment

value: Endpoint MC38 flank tumor


title: GIST-T1_BRPF1

value: Gastrointestinal stromal tumor (GIST)

value: BRPF1, Thermo Fisher Scientific Cat# PA5-27783

value: Endogenous BRPF1