title: B_10nM_RA_t_1.5hr

description: 10nM RA for 2hrs; t=1.5hr after wash

data_processing:
Single cell scale RNA-seq libraries were sequenced using on an Illumina HiSeq 4000
Raw sequencing data (Illumina sequencer’s base call files (BCLs) was converted to fastq files using the Illumina bcl2fastq program
Reads were mapped to the genome using the Xenopus laevis 9.1 genome with STAR alignment and a modified BLAST and FASTQC in the NGS pipeline
Count data is rlog transformed (package DESeq2), batch corrected (COMBAT algorithm), expression filtered, quantile normalisation, filtered for significance and annotated with gene names.
The 0.5% ETOH treatments were not included in the downstream analysis
Genome_build: Xenopus laevis 9.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
For each sample, 5-10 staged embryos were collected and stored at -80°C. RNA purification was performed using the Bio-Rad Aurum Total RNA Mini Kit (according to the manufacturer's instructions). RNA samples were used for cDNA synthesis using the Bio-Rad iScriptTM Reverse Transcription Supermix for RT-qPCR kit (according to the manufacturer's instructions).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: female B

value: whole embryo

value: 10nM RA t=1.5hr


title: B_control_t_1.5hr

status: Public on Sep 29 2021

type: SRA

city: Albuquerque

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1 University of New Mexico

country: USA

institute: University of New Mexico

description: control for 2hrs; t=1.5hr after wash

library_source: transcriptomic

molecule: total RNA

organism: Xenopus laevis

source_name: whole embryo

tag: strain

value: wildtype

tag: isolate

tag: Sex

value: not determined

tag: tissue

tag: treatment

value: control t=1.5hr


title: B_0.5_ETOH_t_0hr

description:
0.5% ETOH for 2hrs; t=0hr after wash
The 0.5% ETOH treatment group was not included in downstream analysis

value: 0.5% ETOH t=0hr


title: B_10nM_RA_t_3hr

description: 10nM RA for 2hrs; t=3hr after wash

value: 10nM RA t=3hr


title: L_control_t_0hr

type: RNA

data_processing: Relative gene expression was determined by the ΔΔCt method. Gapdh was used as a housekeeping gene for normalization of the data.

label: Eva Green

label_protocol: not provided

growth_protocol: Embryos were obtained by in vitro fertilization, incubated in 0.1% MBSH and staged according to Nieuwkoop and Faber(Nieuwkoop and Faber, 1967).

extract_protocol: For each sample, 5-10 staged embryos were collected and stored at -80°C. RNA purification was performed using the Bio-Rad Aurum Total RNA Mini Kit (according to the manufacturer's instructions). RNA samples were used for cDNA synthesis using the Bio-Rad iScriptTM Reverse Transcription Supermix for RT-qPCR kit (according to the manufacturer's instructions).

treatment_protocol: The experimental design involves treating embryos for 2 hours from late blastula (st. 9.5) to early gastrula (st. 10.25) and collecting samples every 1.5 hours after terminating and washing the treatment. Embryos were treated with RA (10 nM) or DEAB (50 µM). For each biological repeat, all treatments, controls, and time points were collected from a single fertilization, from the eggs (clutch) of a single female.

tag: genotype

tag: treatment group

value: control for 2hrs , t=0hr after wash


title: RNA-seq_dTAG-24h_SPT5-fkbp-DLD1_rep1

city: Shanghai

first: Linna

last: Peng

address: Dong'an Road

country: China

institute: Fudan University

data_processing:
Raw reads were processed with Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adaptors and low-quality reads with the parameter "-q 25" .
The remaining reads were aligned to human hg19 and mouse mm10 assemblies using STAR v2.7.5c with parameter "--outSAMtype BAM SortedByCoordinate --twopassMode Basic --outFilterMismatchNmax 2 --outSJfilterReads Unique"
PCR duplicates were removed using Picard v2.23.3 (https://broadinstitute.github.io/picard/).
The number of spike-in mm10 reads was counted with SAMtools v1.9 and normalization factor alpha = 1e6/mm10_count was calculated (Li et al., 2009).
Strand-specific RNA-seq signal normalized by spike-in reads was generated by deeptools v3.5.0 (Ramirez et al., 2016).
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files

organism: Homo sapiens

source_name: SPT5-dTAG DLD1

growth_protocol: Colorectal adenocarcinoma cell line DLD1 cells were cultured in DMEM (Dulbecco’s Modified Eagle’s medium, Hyclone) supplemented with 10% fetal bovine serum (FBS, Biowest), nonessential amino acids (Gibco) at 37 °C and 5% CO2.

extract_protocol:
RNA was isolated with TRIzol.
Libraries were prepared according to Vazyme's instructions accompanying the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme NR603-02). Libraries were sequenced on the Illumina HiSeq X Ten following the manufacturer's protocols.

treatment_protocol: Cells were treated with DMSO or dTAG-13 for 12h, or 24h.

tag: cell type

value: colorectal adenocarcinoma cell lines

value: treated with dTAG13 for 24 hours


title: PRO_DMSO-3h_INTS8-dTAG_DLD1_rep1

data_processing:
Library strategy: PRO-Seq
Raw reads were processed with Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adaptors and low-quality reads with the parameter “-q 25 --length 15” .
Ribosomal RNA reads were removed using Bowtie v2.3.5.1 with “--un-conc-gz” (Langmead and Salzberg, 2012)
The remaining reads were aligned to hg19 or mm10 genome using Bowtie v2.3.5.1 with “--local --sensitive-local” (Langmead and Salzberg, 2012).
Removal of low mapping quality reads and duplicated reads and calculation of normalization factor were performed with SAMtools v1.9 (Li et al., 2009) and Picard v2.23.3 (https://broadinstitute.github.io/picard/).
Strand-specific PRO-seq signal normalized by spike-in reads was generated by deeptools v3.5.0 (Ramirez et al., 2016) with "--Offset 1" for single-base files and "--Offset None" for full-length files.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: INTS8-dTAG DLD1

extract_protocol:
RNA was isolated with TRIzol.
Enriched RNA was ligated with RNA adapters. Reverse transcription (RT) was performed using the Superscript III enzyme (Invitrogen). The reverse transcription products were proceeded to library amplification by using the Q5 enzyme mix.  Libraries were sequenced on the Illumina HiSeq X Ten following the manufacturer's protocols.

treatment_protocol: Cells were treated with DMSO or dTAG 13 for 3h.

tag: cell line

value: colorectal adenocarcinoma cells

value: untreated

value: INTS8 knock-in of a dTAG tag


title: PRO_DMSO-3h_INTS8-SPT5-dTAG-SPT5-WT_DLD1

source_name: INTS8-SPT5-dTAG-SPT5-WT DLD1

value: INTS8 and SPT5 double knock-in of a dTAG tag, then ectopic SPT5-WT expression


title: KDM6B1-1 KO

city: Wuhan

first: Wei

last: Jiang

address: Donghu Road 116, District Wuchang

department: Medical Research Institute

institute: Wuhan University

data_processing:
Raw data were mapped to hg38 genome using Hisat2
The raw counts were generated by FeatureCounts
The raw counts were normlized to TPM
Genome_build: hg38

source_name: neuroectoderm differentiation Day0

extract_protocol:
RNA extraction and purification were performed using HiPure Total RNA Mini Kit (Magen, R4111-03). RNA concentration was measured using NanoDrop (Thermo Fisher Scientific). RNA was reverse-transcribed into cDNA using the All-in-One cDNA Synthesis SuperMix (Bimake, B24408). Real-time qPCR was performed with the 2x SYBR Green qPCR Master Mix (Biomake, B21203) on the CFX384 Touch Real-Time PCR Detection System. All the mRNA reaction data were analyzed by 2^-dd(Ct) method. All experiments were repeated at least in triplicate.
Illumina Hiseq X ten

value: ES


title: ATAC_Spt5_Control_rep2_DLD1

library_source: genomic

data_processing:
Raw reads were processed with Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adaptors and low-quality reads with the parameter “-q 25” .
The remaining reads were aligned to human (hg19) genome assembly using Bowtie 2 v2.3.5.1 with parameters “-N 1 -L 25 -X 2000 --no-mixed --no-discordant” (Langmead and Salzberg, 2012).
All unmapped reads, low mapping quality reads (MAPQ < 30) and PCR duplicates were removed using SAMtools v1.9(Li et al., 2009) and Picard v2.23.3 (https://broadinstitute.github.io/picard/).
Reads counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM) with deeptools v3.5.0 and peaks were called using macs2 v2.2.6 (Ramirez et al., 2016; Zhang et al., 2008).
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files include FPKM values for each Sample

molecule: genomic DNA

extract_protocol:
DNA was isolated with PCR clear-up.
Libraries were prepared according to Vazyme's instructions accompanying the TruePrep DNA Library Prep Kit V2 (Vazyme TD501-02). Libraries were sequenced on the Illumina HiSeq X Ten following the manufacturer's protocols.

treatment_protocol: One replicate was DMSO or dTAG-13 treated for 3 hours.


title: L_control_t_1.5hr

value: control for 2hrs , t=1.5hr after wash


title: L_control_t_4.5hr

value: control for 2hrs , t=4.5hr after wash


title: L_control_t_3hr

value: control for 2hrs , t=3hr after wash


title: KDM6A-1 KO


title: ATAC_Spt5_dTAG_3h_rep1_DLD1

value: treated with dTAG13 for 3 hours


title: RNA-seq_DMSO_SPT5-fkbp-DLD1_rep2

source_name: SPT5-DMSO DLD1


title: RNA-seq_DMSO_SPT5-fkbp-DLD1_rep1


title: B_0.5_ETOH_t_1.5hr

description:
0.5% ETOH for 2hrs; t=1.5hr after wash
The 0.5% ETOH treatment group was not included in downstream analysis

value: wildtype

value: female B

value: whole embryo


title: KDM6A-2 KO


title: B_control_t_0hr

description: control for 2hrs; t=0hr after wash

value: not determined

value: control t=0hr


title: KDM6B2-1 KO


title: KO2_D7_rep2

description: neuroectoderm differentiation Day7

source_name: neuroectoderm

value: ES-derived neuroectoderm


title: B_50uM_DEAB_t_1.5hr

description: 50µM DEAB for 2hrs; t=1.5hr after wash

value: 50µM DEAB t=1.5hr


title: ATAC_Spt5_dTAG_3h_rep2_DLD1

value: colorectal adenocarcinoma cell lines


title: B_10nM_RA_t_0hr

description: 10nM RA for 2hrs; t=0hr after wash

value: 10nM RA t=0hr


title: KO2_D7_rep1

description: neuroectoderm differentiation Day7


title: B_50uM_DEAB_t_0hr

description: 50µM DEAB for 2hrs; t=0hr after wash

value: 50µM DEAB t=0hr


title: K_10nM_RA_t_4.5hr

value: 10nM RA for 2hrs , t=4.5hr after wash


title: KO2_D3_rep2

description: neuroectoderm differentiation Day3


title: KDM6B1-2 KO


title: K_10nM_RA_t_3hr

value: 10nM RA for 2hrs , t=3hr after wash


title: KDM6B2-2 KO

value: ES


title: RNA-seq_dTAG-12h_SPT5-fkbp-DLD1_rep1

value: treated with dTAG13 for 12 hours


title: KO2_D3_rep1

description: neuroectoderm differentiation Day3


title: K_50uM_DEAB_t_3hr

value: 50µM DEAB for 2hrs , t=3hr after wash


title: K_10nM_RA_t_0hr

value: 10nM RA for 2hrs , t=0hr after wash


title: KO2_D0_rep1

description: neuroectoderm differentiation Day0

source_name: ES


title: K_50uM_DEAB_t_1.5hr

value: 50µM DEAB for 2hrs , t=1.5hr after wash


title: A_50uM_DEAB_t_4.5hr

description: 50µM DEAB for 2hrs; t=4.5hr after wash

value: wildtype

value: female  A

value: 50µM DEAB t=4.5hr


title: K_10nM_RA_t_1.5hr

value: 10nM RA for 2hrs , t=1.5hr after wash


title: K_50uM_DEAB_t_4.5hr

value: 50µM DEAB for 2hrs , t=4.5hr after wash


title: A_0.5_ETOH_t_4.5hr

description:
0.5% ETOH for 2hrs; t=4.5hr after wash
The 0.5% ETOH treatment group was not included in downstream analysis

value: not determined

value: whole embryo


title: KO2_D0_rep2

description: neuroectoderm differentiation Day0


title: A_10nM_RA_t_4.5hr

description: 10nM RA for 2hrs; t=4.5hr after wash

value: 10nM RA t=4.5hr


title: KO1_D7_rep1

description: neuroectoderm differentiation Day7

value: ES-derived neuroectoderm


title: KO1_D0_rep2

description: neuroectoderm differentiation Day0


title: K_50uM_DEAB_t_0hr

value: 50µM DEAB for 2hrs , t=0hr after wash


title: KO1_D3_rep2

description: neuroectoderm differentiation Day3


title: A_control_t_4.5hr

description: control for 2hrs; t=4.5hr after wash

value: control t=4.5hr


title: A_0.5_ETOH_t_3hr

description:
0.5% ETOH for 2hrs; t=3hr after wash
The 0.5% ETOH treatment group was not included in downstream analysis

value: 0.5% ETOH t=3hr


title: KO1_D3_rep1

description: neuroectoderm differentiation Day3


title: K_control_t_3hr

value: control for 2hrs , t=3hr after wash


title: KO1_D0_rep1

description: neuroectoderm differentiation Day0

value: ES


title: KO1_D7_rep2

description: neuroectoderm differentiation Day7


title: K_control_t_4.5hr

value: control for 2hrs , t=4.5hr after wash


title: A_10nM_RA_t_3hr

description: 10nM RA for 2hrs; t=3hr after wash

value: 10nM RA t=3hr


title: WT_D7_rep2

description: neuroectoderm differentiation Day7


title: A_50uM_DEAB_t_3hr

description: 50µM DEAB for 2hrs; t=3hr after wash

value: 50µM DEAB t=3hr


title: WT_D7_rep3

description: neuroectoderm differentiation Day7


title: WT_D7_rep1

description: neuroectoderm differentiation Day7


title: WT_D3_rep3

description: neuroectoderm differentiation Day3


title: A_control_t_3hr

description: control for 2hrs; t=3hr after wash

value: wildtype

value: control t=3hr


title: WT_D0_rep1

description: neuroectoderm differentiation Day0


title: WT_D3_rep2

description: neuroectoderm differentiation Day3


title: J_10nM_RA_t_3hr

value: 10nM RA for 2hrs , t=3hr after wash


title: A_50uM_DEAB_t_1.5hr

description: 50µM DEAB for 2hrs; t=1.5hr after wash

value: female  A

value: 50µM DEAB t=1.5hr


title: A_10nM_RA_t_1.5hr

description: 10nM RA for 2hrs; t=1.5hr after wash

value: not determined

value: 10nM RA t=1.5hr


title: K_control_t_1.5hr

value: control for 2hrs , t=1.5hr after wash


title: A_control_t_1.5hr

description: control for 2hrs; t=1.5hr after wash

value: whole embryo

value: control t=1.5hr


title: K_control_t_0hr

value: control for 2hrs , t=0hr after wash


title: J_50uM_DEAB_t_4.5hr

value: 50µM DEAB for 2hrs , t=4.5hr after wash


title: J_10nM_RA_t_1.5hr

value: 10nM RA for 2hrs , t=1.5hr after wash


title: J_10nM_RA_t_0hr

value: 10nM RA for 2hrs , t=0hr after wash


title: J_10nM_RA_t_4.5hr

value: 10nM RA for 2hrs , t=4.5hr after wash


title: A_0.5_ETOH_t_0hr

value: 0.5% ETOH t=0hr


title: A_50uM_DEAB_t_0hr

description: 50µM DEAB for 2hrs; t=0hr after wash

value: 50µM DEAB t=0hr


title: WT_D0_rep2

description: neuroectoderm differentiation Day0

value: ES


title: A_0.5_ETOH_t_1.5hr

value: wildtype


title: Lung_Cap-F_01

city: Nagano

first: Takeshi

last: Shimosato

address: 8304, Minami-minowa, Kami-ina

department: Institute for Biomedical Sciences

country: Japan

institute: Shinshu University

hyb_protocol: 600ng of each labeled cRNA was fragmented by adding 5 μl 10 x blocking agent and 1 μl of 25 x fragmentation buffer, and then heated at 60°C for 30 min. Finally 25 μl 2 x GE hybridization buffer was added to dilute the labeled cRNA. 40μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint G3 Mouse GE 8X60K, Microarrays (Agilent Technology). The slides were incubated for 17 h at 65°C in an Agilent hybridization oven, then washed at room temperature by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010).

scan_protocol: The hybridized array was immediately scanned with an Agilent Microarray Scanner D (Agilent Technologies)

data_processing: Microarray results were extracted using Agilent Feature Extraction software v11.0 (Agilent Technologies) Array probes that have Flag A in samples were filtered out. Selected gProcessedSignal value was transformed by logarithm and normalized by quantile method.

organism: Mus musculus

source_name: Lung, Cap-F

label_protocol: RNA labeling and hybridization were performed by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010). Briefly, 100ng of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA were isolated from lungs. RNA purity and integrity were evaluated by ND-1000 Spectrophotometer and Agilent 2100 Bioanalyzer (Agilent Technologies).

value: lung

tag: diet

value: control particle-containing feed

tag: ova treatment

value: inhalation-challenged with ovalbumin (OVA)

tag: gender

value: female

value: BALB/c


title: A_control_t_0hr

description: control for 2hrs; t=0hr after wash

value: female  A

value: not determined

value: control t=0hr


title: Lung_Ctrl-F_01

source_name: Lung, Ctrl-F

value: standard feed


title: Lung_ODNcap-F_02

source_name: Lung, ODNcap-F

value: ODNcap-containing feed


title: Lung_Cap-F_02


title: Lung_Ctrl-F_02


title: Lung_NT_01

source_name: Lung, NT

value: not treated


title: WT_D3_rep1

description: neuroectoderm differentiation Day3

value: ES-derived neuroectoderm


title: J_50uM_DEAB_t_1.5hr

value: 50µM DEAB for 2hrs , t=1.5hr after wash


title: WT3-NI-3

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

country: France

institute: INRA

data_processing:
Demultiplexing was performed (bcl2fastq2 V2.2.18.12) and adapters were trimmed with Cutadapt (v1.15); only reads longer than 10 bp were kept.
TopHat (version 2.1.1) was used for alignment on the reference genome
Data were evaluated through principal component analysis and hierarchical clustering after transformation of the count data using RLOG function.
Normalization and differential analysis were carried out using the DESeq2 package, with a pre-filter step to remove genes with low counts (sum of all replicates counts<10, in all conditions compared)
Genome_build: Ensembl-100 GRCm38 mouse genome
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Hepatocytes

growth_protocol: Listeria monocytogenes was grown in brain-heart infusion (BHI) at 37°C. PMH were seeded in 6-well collagen-coated plates for 6 h at 37°C in a 5% CO2 atmosphere. After complete adhesion of the hepatocytes and washes to remove the dead cells, PMH were cultured at 37°C in a 5% CO2 atmosphere for 4-6 days before infection in serum-free hepatocyte culture medium (William's E medium and GlutaMAX™ Supplement (Gibco); 100 U/ml penicillin/streptomycin, 0.5 ug/ml fungizone antimycotic B, 4 ug/ml insulin, 0.1% bovine serum albumin and 25 nM dexamethasone) that was renewed daily.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen) and genomic DNA was removed using TURBO DNA-freeTM kit (Ambion), according to the manufacturer’s instructions. The integrity, purity and concentration of RNA samples was assessed on an RNA 6000 pico chip using the Agilent 2100 electrophoresis Bioanalyzer.  RNA was quality checked an then store at -80°C.
RNA-seq libraries of infected and non-infected cell RNA were assembled using 500-1300 ng total RNA using the TruSeq® mRNA Stranded Library Prep kit (Illumina) which includes polyA-selection. The RNA-seq libraries were monitored for quality on the Bioanalyzer 2100 using an Agilent High Sensitivity DNA Kit. Libraries were pooled in equimolar proportions

treatment_protocol: PMH were non-infected or infected with Listeria at multiplicity of infection of 10. After 1h infection, extracellular bacteria were killed by adding gentamicin and cells were incubated for 3 days with 25 μg/ml gentamicin containing media.

value: primary mouse hepatocytes (PMH)

value: control (non-infected)

tag: time


title: WT1-NI-1


title: Lung_ODNcap-F_01


title: WT1-NI-3


title: WT1-NI-2


title: WT3-NI-1


title: J_50uM_DEAB_t_0hr

value: 50µM DEAB for 2hrs , t=0hr after wash


title: WT3-NI-2


title: J_control_t_4.5hr

value: wildtype

value: control for 2hrs , t=4.5hr after wash


title: J_50uM_DEAB_t_3hr

value: 50µM DEAB for 2hrs , t=3hr after wash


title: WT3-Inf-3

value: Listeria monocytogenes 10403S


title: J_control_t_3hr

value: control for 2hrs , t=3hr after wash


title: A_10nM_RA_t_0hr

description: 10nM RA for 2hrs; t=0hr after wash

value: whole embryo

value: 10nM RA t=0hr


title: Westar_D7M_3

city: Winnipeg

first: Nick

last: Wytinck

state: MB

address: 50 Sifton Road

department: Department of Biological Sciences

country: Canada

institute: University of Manitoba

data_processing:
FastQ files were trimmed using Trimmomatic 0.33
adapter sequences, initial 12 bases of raw reads, low quality reads with a quality score under 20 over a sliding window of 4 bases and reads with an average quality score under 30 removed during the trimming process
Remaining reads shorter than 40 nucleotides were also removed. The high sensitivity mapping program HISAT2 was then used to align trimmed reads to the B. napus and S. sclerotiorum genomes
The mapped reads were sorted with Samtools and assigned to genes with featureCounts
EdgeR was used to perform differential gene expression analysis on raw counts using a log2 fold change and FDR cutoff of |2| and <0.01, respectively
Genome_build: B. napus genome from: Song, J. M., Guan, Z., Hu, J., Guo, C., Yang, Z., Wang, S., … Guo, L. (2020). Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus. Nature Plants, 6(1), 34–45. S. sclerotiorum genome from: Derbyshire, M., Denton-Giles, M., Hegedus, D., Seifbarghi, S., Rollins, J., Kan, J. Van, … Oliver, R. (2017). The complete genome sequence of the phytopathogenic fungus Sclerotinia sclerotiorum reveals insights into the genome architecture of broad host range pathogens. Genome Biology and Evolution, 9(3), 593–618. https://doi.org/10.1093/gbe/evx030 https://doi.org/10.1038/s41477-019-0577-7
Supplementary_files_format_and_content: Excel file with trimming and alignment statistics, counts for B. napus and S. sclerotiorum reads as well as enriched GO terms for B. napus

organism: Brassica napus

source_name: stem cross-section

growth_protocol: Seeds of B. napus cv. Westar and the resultant transgenic lines were germinated in germination pouches (Phyto AB Inc.,  San Jose, CA, USA) and transplanted at the cotyledon stage into Sunshine Mix No. 1 (SunGro Horticulture, Agawam, MA, USA) at 22 °C and 50–70% humidity within greenhouse conditions. The plants were grown until the 30% flowering stage for use in infection experiments.

extract_protocol:
RNA was extracted from infected and uninfected plant tissue. For infected stems, cross-section disks (10 mm wide) were taken from the site of infection. The tissue was ground in an RNase-free mortar and RNA extracted using the Qiagen RNeasy Plant Mini kit (Toronto, ON, Canada). RNA was treated with Qiagen RNAse free DNAse (Toronto, ON, Canada), then cDNA synthesized using Quantabio qScript cDNA (Beverly, MA, USA). Quantity and purity were assessed spectrophotometrically and the quality of RNA samples verified using electropherogram profiles and RNA Integrity Numbers (RIN) (All samples had a RIN greater than 8.5) with an Agilent 2100 Bioanalyzer and RNA Pico Chips (Agilent, Santa Clara, CA, USA).
cDNA libraries were constructed by Genome Québec according to their mRNA stranded library protocol. The Illumina HISeq4000 was used to generate 100 bp PE reads.

treatment_protocol: A 3 x 3 mm cube of actively growing S. sclerotiorum from the leading edge of hyphae on a potato dextrose agar plate was collected using a syringe tip and placed onto the stem of a mature B. napus plant 30-50 mm above the soil. The fungus was sealed to the stem using a 30 x 20 mm strip of parafilm and lesion length was measured seven days post inoculation.

tag: developmental stage

value: mature:30percent flowering

value: stem, 30 mm above soil

tag: agent

value: control

tag: time point


title: Westar_D7M_2


title: WT3-Inf-2


title: WT3-Inf-1


title: Lung_NT_02

value: lung

value: standard feed

value: female

value: BALB/c


title: WT1-Inf-1

value: primary mouse hepatocytes (PMH)


title: J_control_t_1.5hr

value: control for 2hrs , t=1.5hr after wash


title: Westar_D1_3


title: I_10nM_RA_t_4.5hr

value: 10nM RA for 2hrs , t=4.5hr after wash


title: WT1-Inf-3


title: S11

city: Boston

first: Nicole

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

data_processing:
Basecalls were performed using bcl2fastq/2.20.0.422
Fastqc (0.11.5) and fastqScreen (0.11.2) were used to performe quality control
RNA-seq reads were psuedo-aligned to the GRCm38  genome assembly using Salmon 1.5.2
Transcripts per million (TPM) were calculated using Salmon, and output quant.sf files were generated for each sample and appended into one matrix in R using  the package txiimport (1.18.0)
Normalization of gene counts using size factors calculated by DESeq2 v 1.30.1 to yield 'norm_count.csv' matrix
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: counts.csv' file include TPM values for each gene (rows) for each sample (columns)
Supplementary_files_format_and_content: norm_count.csv' is matrix  with genes (rows) and sample (columns). Normalization using estimated size factors was peformed using DESeq2 v 1.30.1

source_name: DRG + PBS

extract_protocol:
DRGs were removed and RNA was harvested using Trizol reagent. RNA extraction was performed using the RNeasy mini kit (Qiagen)
RNA libraries were prepared with the poly A selection method followed by multiplexing and sequencing on the Illumina NextSeq500® platform in a 1 × 75bp single-read and 350 million reads per lane (Biopolymer Sequencing Facility)
bulk RNA-seq

treatment_protocol: PBS or ET (2ug protective antigen and 2ug edema factor) was injected intrathecally into mice, and DRGs were dissected 2h later

value: In vivo DRG neurons

value: PBS


title: S10

source_name: DRG + ET

value: male

value: ET


title: I_10nM_RA_t_3hr

value: wildtype

value: 10nM RA for 2hrs , t=3hr after wash


title: S6


title: S7


title: Westar_D7M_1


title: I_10nM_RA_t_1.5hr

value: 10nM RA for 2hrs , t=1.5hr after wash


title: S12


title: Westar_D0_2

value: mature:30percent flowering


title: J_control_t_0hr

value: control for 2hrs , t=0hr after wash


title: Westar_D1_2

value: stem, 30 mm above soil

value: control


title: Westar_D0_3


title: S1


title: S8


title: I_50uM_DEAB_t_1.5hr

value: 50µM DEAB for 2hrs , t=1.5hr after wash


title: S5


title: 1703_D7M_1

value: Sclerotinia sclerotiorum


title: WT1-Inf-2

value: Listeria monocytogenes 10403S


title: S2


title: 1703_D1_2


title: CR19018: Treg_2nd_sgAcsbg1_RNA

city: Kisarazu

first: Toshio

last: Kanno

state: Chiba

address: 2-6-7 Kazusa-kamatari

institute: KAZUSA DNA Research Institute

description: Splenic Naïve CD4_T cells were stimulated under Treg culture conditions (15 ng/ml IL-2, 10ng/ml hTGFb) for 5 days in vitro.

data_processing:
For RNA-sequence, read sequences (75 bp) were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011) using STAR (version 2.7.9a).
Fragments per kilobase of transcripts for each gene were calculated using Subread (version 2.0.1, 13 ).
ATAC-seq reads were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011)  using Bowtie2.
Normalization was performed using RPGC method with Bamcoverage of Deeptools.
Genome_build: mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011)
Supplementary_files_format_and_content: Text files include TPM values for each Sample
Supplementary_files_format_and_content: wig files were generated using "Deep tools".

source_name: Five-day cultured Treg cells generated from primary splenic Naïve CD4_T cells

extract_protocol:
Total cellular RNA was extracted with TRIzol reagent (Invitrogen). Genomic DNA used for ATAC seq was obtained according to the protocol of ATAC-Seq (ACTIVE MOTIF).
QuantSeq 3' mRNA-Seq Library Prep Kit FWD (LEXOGEN) and ATAC-Seq (ACTIVE MOTIF) was used for library constraction according to the manufacturer's protocol.

treatment_protocol: Pharmacolgical drug was not treated in this assay

value: Treg

tag: growth

value: Splenic Naive CD4_T cells were stimulated under Treg culture conditions (15 ng/ml IL-2, 10ng/ml hTGFb) for 5 days in vitro.


title: Treg_1st_ATAC

tag: strain


title: S4

value: female


title: Treg_1st_sgSmad2_ATAC


title: CR19018: Treg_1st_sgAcsbg1_RNA


title: Westar_D1_1


title: Treg_2nd_sgSmad2and3_ATAC


title: S9

value: In vivo DRG neurons


title: I_50uM_DEAB_t_3hr

source_name: whole embryo

value: 50µM DEAB for 2hrs , t=3hr after wash


title: Th0_1st_ATAC

description: Splenic Naïve CD4_T cells were stimulated under Th0 culture conditions (15 ng/ml IL-2) for 5 days in vitro.

source_name: Five-day cultured Th0 cells generated from primary splenic Naïve CD4_T cells

value: Splenic Naive CD4_T cells were stimulated under Th0 culture conditions (15 ng/ml IL-2) for 5 days in vitro.


title: I_50uM_DEAB_t_4.5hr

value: 50µM DEAB for 2hrs , t=4.5hr after wash


title: 1703_D0_3


title: I_10nM_RA_t_0hr

value: wildtype

value: 10nM RA for 2hrs , t=0hr after wash


title: I_control_t_4.5hr

value: control for 2hrs , t=4.5hr after wash


title: CR19012: Treg_2nd_sgSmad2/3_RNA


title: 1703_D7M_2

value: mature:30percent flowering


title: S3

value: PBS


title: H_10nM_RA_t_4.5hr

value: 10nM RA for 2hrs , t=4.5hr after wash


title: Treg_2nd_ATAC


title: 1703_D7M_3

value: stem, 30 mm above soil


title: I_control_t_3hr

value: control for 2hrs , t=3hr after wash


title: Treg_2nd_sgSmad2_ATAC


title: I_50uM_DEAB_t_0hr

value: 50µM DEAB for 2hrs , t=0hr after wash


title: 1703_D1_3

value: Sclerotinia sclerotiorum


title: Westar_D0_1

value: control


title: H_10nM_RA_t_1.5hr

value: 10nM RA for 2hrs , t=1.5hr after wash


title: Treg_1st_sgSmad2and3_ATAC

value: Treg

value: Splenic Naive CD4_T cells were stimulated under Treg culture conditions (15 ng/ml IL-2, 10ng/ml hTGFb) for 5 days in vitro.


title: Th0_2nd_ATAC


title: CR19012: Treg_1st_sgSmad2/3_RNA


title: 1703_D0_2


title: CR19018: Treg_1st_RNA


title: 1703_D1_1


title: I_control_t_0hr

value: control for 2hrs , t=0hr after wash


title: CR19005: Treg_3rd_RNA


title: CR19012: Treg_1st_sgSmad3_RNA


title: Lung, IWC 7d + infection 24 hpi rep2

city: Chengdu

first: Yun

last: Shi

address: No 37, Guoxuexiang

institute: West China Hospital, Sichuan University

data_processing:
Raw data of sequencing were cleaned using Trimmomatic software.
Raw data were cleaned using Trimmomatic.
The clean reads after quality control were mapped to the mouse genome GRCm38 with STAR software (version 2.5.3a). The reads counts for each gene were calculated using FeatureCounts (version1.5.1) and expressed as RPKM (reads per kilobase per million reads). EdgeR package were used to identify the differentially expressed genes by statistics with an adjusted P value < 0.05 and log2(fold change) >1. Gene Ontology (GO) and (Kyoto Encyclopedia of Genes and Genomes) KEGG enrichment was done with Kobas (Version 2.1.1) . Hierarchical clustering and heatmaps were drawing using pheatmap R package and MA-plot was drawn using EdgeR package.
Genome_build: GRCm38
Supplementary_files_format_and_content: ALL samples rpKm .txt

source_name: lung

extract_protocol:
Total RNAs were extracted from lung samples using TRIzol (Invitrogen) and DNA was digested by DNaseI after RNA extraction. A260/A280 was examined with NanodropTM One spectrophotometer (Thermo Fisher Scientific Inc) to determine RNA quality. RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies).
Total RNAs (2 μg) were used for to prepare sequencing library using KC-Total RNA-seq Library Prep Kit for Illumina® (Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Hiseq X 10 sequencer (Illumina).

value: Rag1-/- mice

tag: protocol

value: IWC 7d + infection 24 hpi

value: lung


title: CR19005: Treg_2nd_RNA


title: CR19012: Treg_2nd_sgSmad2_RNA


title: CR19012: Treg_2nd_sgSmad3_RNA


title: CR19005: Th0_2nd_RNA

value: Splenic Naive CD4_T cells were stimulated under Th0 culture conditions (15 ng/ml IL-2) for 5 days in vitro.


title: 1703_D0_1


title: CR19018: Treg_2nd_RNA


title: I_control_t_1.5hr

value: wildtype

value: control for 2hrs , t=1.5hr after wash


title: Lung, IWC 7d + infection 24 hpi rep3


title: Lung, infection 24 hpi rep2

value: infection 24 hpi


title: Lung, IWC 7d + infection 24 hpi rep1


title: CR19005: Naive_3rd_RNA

description: Splenic Naïve CD4_T cells

source_name: Splenic Naïve CD4_T cells

value: Naive CD4 T cells

value: Splenic Naive CD4_T cells


title: H_10nM_RA_t_0hr

value: 10nM RA for 2hrs , t=0hr after wash


title: H_10nM_RA_t_3hr

value: 10nM RA for 2hrs , t=3hr after wash


title: CR19012: Treg_1st_RNA


title: Lung, infection 24 hpi rep1


title: H_50uM_DEAB_t_0hr

value: 50µM DEAB for 2hrs , t=0hr after wash


title: CR19012: Treg_1st_sgSmad2_RNA


title: Lung,  infection 24 hpi rep3


title: CR19005: Th0_3rd_RNA


title: CR19012: Treg_2nd_RNA


title: mESC_IgG

city: Philadelphia

first: Yemin

last: Lan

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Library strategy: Cleavage Under Target and Release (CUT&RUN)
Paired-end reads were aligned against reference genome (mm10) using Bowtie2 version 2.2.5 (36) with default parameters “-X 2000 -N 1 --local --dovetail”. Only properly paired, primary alignments were kept for downstream analysis, as filtered using SAMtools version 1.9.
Duplicated reads, and reads mapping to mitochondria, unassembled contigs and the ENCODE blacklist regions were removed using SAMtools. Visualization tracks for each library were generated using Deeptools version 2.5.7 function bamCoverage with bin size of 50bp and normalized using RPKM.
Using RPKM normalized tracks, IgG was subtracted from the corresponding antibody tracks using Deeptools function bigwigCompare.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: embryonic stem cells

growth_protocol: Murine embryonic multipotent stem cell (ATCC, cat#CRL-1934) were tested negative for mycoplasma contamination and maintained at 37oC cultured in DMEM plus 15% fetal bovine serum, 1mM sodium pyruvate, MEM non-essential amino acids, 50 mM b-mercaptoethanol, 10,000 U/mL Penicillin-Streptomycin, 1,000 U/mL ESGRO LIF, and supplemented with 1 μM MEK inhibitor PD0325901 and 3μM GSK3 inhibtor CH99021. Primary retina cells were isolated from C57BL/J6 mice obtained from Charles River.

extract_protocol:
Retinal cells were isolated using papain isolation kit (Worthington Biochemical Corp, cat#LK003150). Isolation protocol was adopted from the manufacturer recommendations. Retina tissue was isolated and incubated with papain solution for 24-30 min at 37oC in with 600 rpm in a thermal shaker, then papain was blocked with a blocking solution. For CUT&RUN assay, live retina cells isolated from post-natal animals at day 7, 14, 21 and adult animals were flow sorted using Forward Scatter and Side Scatter.
The CUT&RUN protocol was performed as previously described with modifications. Briefly, 1x106 cells (mESCs or rod cells isolated as described above) were harvested and washed twice with ice-cold PBS. Nuclei were isolated with Nuclear Extraction Buffer (20 mM HEPES-KOH, pH 7.9, 10 mM KCl, 0.5 mM Spermidine, 0.1% Triton X-100, 20% Glycerol and 1x protease and phosphatase inhibitor). To aid in nuclear capture, isolated nuclei were incubated with activated Concanavalin A beads for 15 minutes at room temperature followed by incubation with the primary antibody or IgG control (1:100 dilution) overnight. Unbound antibody was removed with Wash Buffer (20 mM HEPES-NaOH pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x protease phosphatase inhibitor) for a total of two washes. Supernatant was removed following bead-liquid separation using a magnetic stand and the fusion of proteinA-micrococcal nuclease (pA-MNase; Batch 6: Stock concentration: 143 μg/ml) was added at a final concentration of 700 ng/ml. The complex was incubated for 1 hour at 4°C. Following incubation, the bound complexes were washed twice with Wash Buffer and placed in a 0°C metal block for 5 minutes to pre-chill the tubes. To activate pA-MNase, CaCl2 was added to the pre-chilled bound complexes at a final concentration of 2 mM and incubated in the 0°C metal block for 30 minutes. The digestion reaction was neutralized by the addition of an equal volume of 2x STOP buffer (200 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 μg/mL RNase A, 40 μg/mL glycogen) followed by incubation at 37°C for 10 minutes to release cleaved DNA fragments. The targeted protein-DNA complex was released via centrifugation at 16,000 x g for 5 minutes and supernatant was collected and transferred to freshly labelled 1.7 mL lo-bind tubes. Digested DNA was purified via spin column (Macherey-Nagel, cat#740609.250) according to the manufacturer’s instructions to recover large DNA-protein complexes. DNA concentration was estimated using the Qubit fluorometer. Protein A-MNase (Batch 6) was kindly provided by Dr. Steve Henikoff. The antibodies used were: Rabbit polyclonal anti-H3K9me2 (Active Motif, cat#39239); Rabbit Polyclonal Anti-H3K9me3 (Abcam, cat#ab8898); Rabbit polyclonal anti-H3K9ac (Active Motif, #39137), normal rabbit IgG (Cell Signaling, cat#2729s).

value: embryonic stem cells

value: mouse embryonic stem cells (mESCs)

value: undifferentiated

tag: cut&run antibody

value: IgG

tag: sorting

value: unsorted


title: CR19005: Naive_2nd_RNA

description: Splenic Naïve CD4_T cells


title: mESC_H3K9me3

tag: tissue


title: CR19005: Th0_1st_RNA


title: CR19005: Naive_1st_RNA

description: Splenic Naïve CD4_T cells


title: CR19005: Treg_1st_RNA

value: Treg

value: Splenic Naive CD4_T cells were stimulated under Treg culture conditions (15 ng/ml IL-2, 10ng/ml hTGFb) for 5 days in vitro.


title: Lung, IWC 7d rep2

value: Rag1-/- mice

value: IWC 7d

value: lung


title: Lung, IWC 7d rep1


title: H_50uM_DEAB_t_3hr

tag: genotype

value: wildtype

value: 50µM DEAB for 2hrs , t=3hr after wash


title: H_50uM_DEAB_t_1.5hr

tag: treatment group

value: 50µM DEAB for 2hrs , t=1.5hr after wash


title: H_50uM_DEAB_t_4.5hr

value: 50µM DEAB for 2hrs , t=4.5hr after wash


title: H_control_t_3hr

value: control for 2hrs , t=3hr after wash


title: H_control_t_1.5hr

value: control for 2hrs , t=1.5hr after wash


title: Adult_RodCells_H3K27me3

source_name: retina

value: retina

tag: cell type

value: rod cells

value: Adult

value: flow sorted


title: Adult_RodCells_H3K9ac


title: mESC_H3K9me2

value: embryonic stem cells

value: mouse embryonic stem cells (mESCs)

value: undifferentiated


title: H_control_t_4.5hr

value: control for 2hrs , t=4.5hr after wash


title: H_control_t_0hr

value: control for 2hrs , t=0hr after wash


title: Lung, control rep3

value: Rag1-/- mice

value: control


title: RodCells_IgG

value: postnatal day 7 (P7)

value: IgG


title: P14_RodCells_H3K9me3

value: postnatal day 14 (P14)


title: P14_RodCells_H3K9me2


title: P21_RodCells_H3K9me2

value: postnatal day 21 (P21)


title: P21_RodCells_H3K9me3


title: G_10nM_RA_t_4.5hr

value: wildtype

value: 10nM RA for 2hrs , t=4.5hr after wash


title: Adult_RodCells_H3K9me2

value: retina


title: G_10nM_RA_t_1.5hr

value: 10nM RA for 2hrs , t=1.5hr after wash


title: G_10nM_RA_t_3hr

value: 10nM RA for 2hrs , t=3hr after wash


title: Lung, control rep1

value: lung


title: Lung, control rep2


title: P9_RodCells_H3K9me3

value: rod cells

value: postnatal day 9 (P9)

value: flow sorted


title: Adult_RodCells_H3K9me3

value: Adult


title: Lung, IWC 2d rep2

value: IWC 2d


title: P7_RodCells_H3K9me3


title: P1_RodCells_H3K9me2

value: postnatal day 1 (P1)

value: unsorted


title: P9_RodCells_H3K9me2


title: P1_RodCells_H3K9me3


title: P7_RodCells_H3K9me2

value: postnatal day 7 (P7)


title: G_50uM_DEAB_t_4.5hr

value: 50µM DEAB for 2hrs , t=4.5hr after wash


title: HuDko3

first: Nora

last: Perrone-Bizzozero

state: NM

address: 1 University of New Mexico MSC08 4740

department: Neurosciences

description: small RNA/miRNA-sequencing

data_processing:
See data processing flowchart on the right
Raw sequencing data was filtered using QC scores of over 90% by FASTQC, then pre-processed with cutadapt, and processed using miRDeep2
After mapping aligned reads and determining CPMs, differentially expressed miRNAs in Elavl4 KO vs WT were determined using edgeR software.
Genome_build: miRbase22
Supplementary_files_format_and_content: All_Differentially_Expressed_miRNAs HuD STR

source_name: striatum

extract_protocol:
Brains were removed and the straita were dissected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Total RNA was pretreated using NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, NEB, Ipswich, MA, USA) and RiboZero Magnetic Gold Kit (Human/Mouse/Rat) (Epicentre) b
The treated RNA was used to prepare miRNA sequencing libraries with NEB Multiplex Small RNA Library Prep Set for Illumina. The DNA fragments in well mixed libraries were denatured with 0.1 M NaOH to generate single-stranded DNA molecules. These were then captured on Illumina flow cells, amplified in situ and sequenced for 51 cycles on an Illumina NextSeq 500 platorm (Illumina, Inc. San Diego, CA, USA).

value: striatum

value: Elavl4 -/- (HuD KO)

tag: age and gender

value: adult male (2-4 month)


title: Sth1-K501R_G1+IAA_rep2

city: Daejeon

first: Hyelim

last: Jo

address: 335 Gwahangno, Yuseong-Gu

department: Biological science

country: South Korea

institute: KAIST

data_processing:
HiCPro pipeline (PMID26619908)
Convert .cool format using HiCExplorer (PMID29335486)
Genome_build: SaCcer3
Supplementary_files_format_and_content: 5kb resolution cool matrix

organism: Saccharomyces cerevisiae

source_name: yeast culture

growth_protocol: After 3hr of pre-incubation step, the yeast culture was diluted to 0.2 O.D. and treat auxin (+IAA) or ethanol and incubate for 3hr at 30℃.

extract_protocol:
Total 50 O.D.600 of final 3% formaldehyde fixed yeast cells was cultured and pre-incubated with β-ME buffer (20mM EDTA, 0.7M β-ME) for 10min at 30℃. The yeast cell pellet permeabilized with 2mg of zymolyase (USbiological, Z1004) with 2ml lyticase buffer (1M sorbitiol, 50mM Tris-Cl (pH 8.0), 5mM β-ME) for 20min at 30℃. The obtained spheroplast was re-suspended into 2ml of ice-cold PBS.
in situ Hi-C library preparation was performed as previously reported (PMID:25497547), with some modifications in yeast nucleus isolation steps. The generated libraries sequenced using 150bp paired-end reads on Novaseq6000 and/or HiSeqX.

treatment_protocol: Final conc. 0.5mM of auxin (+IAA) or same volume of 100% ethanol(Con.) was treated.

tag: treatment

value: 0.5mM IAA,alpha factor (50ng/ml)

value: bar1[delta] STH1-AID STH1-K501R


title: Sth1-K501R_G1_control_rep2

value: control, alpha factor (50ng/ml)


title: HuDko2

description: small RNA/miRNA-sequencing


title: G_50uM_DEAB_t_1.5hr

value: wildtype

value: 50µM DEAB for 2hrs , t=1.5hr after wash


title: G_50uM_DEAB_t_3hr

value: 50µM DEAB for 2hrs , t=3hr after wash


title: WT3

description: small RNA/miRNA-sequencing


title: WT1

description: small RNA/miRNA-sequencing


title: Spt6_G1+IAA_rep2

value: bar1[delta] SPT6-AID


title: G_50uM_DEAB_t_0hr

value: 50µM DEAB for 2hrs , t=0hr after wash


title: Mandibular FcgRIIB-KO_rep3

city: Bangkok

first: Nithidol

last: Sakunrangsit

address: Rama IV

country: Thailand

institute: Chulalongkorn University

data_processing:
Base calling and quality scoring were performed using RTA software version 2.0 on the NextSeq instrument
Adaptor and low-quality sequences were removed using Trim Galore software and mapped to mm10 whole genome reference using HISAT v02.1.0 with default parameters
Feature Counts software was implemented to obtain raw counts for all mouse genes. Subsequently, the gene counts were used for differential expression analysis with the DESeq2 package
Genome_build: mm10
Supplementary_files_format_and_content: Raw gene counts for every gene and every sample

source_name: Mandibular

extract_protocol:
Mandibular bones were removed, flash frozen on liquid nitrogen, and RNA was isolated using Trizol reagent. All mRNA libraries were constructed using 200 ng of input total RNA according to NEBNext Ultra Directional RNA Library Preparation Kit (New England Biolabs, USA). Briefly, poly-A containing mRNA molecules were captured using magnetic oligo (dT) beads, purified and directed to cDNA synthesis
Library quality assurance was prepared for sequencing by the Bioanalyzer and fluorometer (DeNovix, USA)

value: mandibular

tag: age

value: FcgRIIB-/-


title: Spt6_G1_control_rep2


title: Mandibular FcgRIIB-KO_rep1


title: Mandibular FcgRIIB-KO_rep2


title: HuDko1

description: small RNA/miRNA-sequencing


title: Mandibular FcgRIIB-KO_rep4


title: Mandibular WT_rep4

value: wild type


title: Sth1-K501R_G1_control_rep1


title: Chd1Isw1_G1+IAA_rep1

value: bar1[delta] CHD1ISW1-AID


title: WT2

description: small RNA/miRNA-sequencing


title: ILL10759-12SA001

city: Melbourne

first: Gurpreet Kaur

last: Suri

state: Victoria

address: 5Ring Road, Bundoora

country: Australia

institute: AgriBio

data_processing:
Read trimming performed using custom perl script (Braich et al., 2020).  Reads were filtered by removing adaptor sequences along with reads and bases of low quality (Q≤ 30). Reads with three consecutive unassigned nucleotides (N) were also trimmed and finally any reads shorter than 50 bp in length were removed from the final set.
The remaining high-quality trimmed sequence reads were aligned to the lentil reference transcriptome (Sudheesh et al., 2016) using BWA-MEM (Li et al., 2013). The number of properly paired reads were obtained using the SAMtools flagstat option and the mapping reads were obtained (Li et al., 2009). Variant calling was performed using SAMtools (version-1.5) (Li et al.., 2016).
Variant calling performed through SAMtools mpileup, and filtered using vcftools (v0.1.16)
Genome_build: Cassab reference transcriptome (Sudheesh et al., 2016), PRJNA352096
Supplementary_files_format_and_content: vcf file -Filtered SNPs

organism: Lens culinaris

source_name: Leaf

extract_protocol:
Total RNA was extracted from leaves of 4 week old lentil genotypes using the RNeasy® 96 kit (Qiagen Inc., Hilden, Germany) following the manufacturer’s instructions.
RNA-Seq libraries with an approximate insert size of 350 bp were prepared using Sure Select Strand Specific RNA library prep kit (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s protocols.

value: Leaf tissue

value: 4 weeks old


title: G_control_t_4.5hr

value: control for 2hrs , t=4.5hr after wash


title: G_control_t_3hr

value: control for 2hrs , t=3hr after wash


title: Chd1Isw1_G1+IAA_rep2


title: G_control_t_0hr

value: control for 2hrs , t=0hr after wash


title: HFD + Aroclor + PCB 126 Treatment, Replicate 4 [CK-38-HFDAroPCB4-mRNA_S19]

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Quality control (QC) of the raw sequence data was performed using FastQC (version 0.10.1)
The fastq sequences were directly aligned to the mm10 reference genome assembly (GRCm38.p6.fa) using STAR (version 2.6).
Raw counts were obtained from the STAR aligned bam format files using HTSeq version 0.10.0 and the ENSEMBL 93 mouse gene gtf file.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: HTSeq raw counts

molecule: polyA RNA

source_name: HFD + Aroclor + PCB 126 Treatment_liver

extract_protocol:
Livers were harvested and snap frozen. RNA was isolated using the RNeasy (Qiagen) kit.
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Cat#  20020594) along with TruSeq RNA CD Index Plate (Cat# 20019792).

treatment_protocol: Male C57Bl/6J mice were fed a HFD (42% kCal from fat) and treated with Aroclor 1260, PCB 126, and the combination of Aroclor 1260 + PCB 126 for 12 weeks.

tag: tag

tag: Sex

value: male

value: high fat diet + Aroclor 1260 + PCB 126

value: liver


title: G_10nM_RA_t_0hr

data_processing: Relative gene expression was determined by the ΔΔCt method. Gapdh was used as a housekeeping gene for normalization of the data.

extract_protocol: For each sample, 5-10 staged embryos were collected and stored at -80°C. RNA purification was performed using the Bio-Rad Aurum Total RNA Mini Kit (according to the manufacturer's instructions). RNA samples were used for cDNA synthesis using the Bio-Rad iScriptTM Reverse Transcription Supermix for RT-qPCR kit (according to the manufacturer's instructions).

value: wildtype

value: 10nM RA for 2hrs , t=0hr after wash


title: HFD + Aroclor + PCB 126 Treatment, Replicate 3 [CK-36-HFDAroPCB3-mRNA_S18]


title: Mandibular WT_rep5


title: Mandibular WT_rep2


title: G_control_t_1.5hr

value: control for 2hrs , t=1.5hr after wash


title: Chd1Isw1_G1_control_rep1

value: control, alpha factor (50ng/ml)


title: Mandibular WT_rep3


title: ILL10668-12SA001


title: Isw1_G1+IAA_rep2

value: 0.5mM IAA,alpha factor (50ng/ml)

value: bar1[delta] ISW1-AID


title: HFD + PCB 126 Treatment, Replicate 5 [CK-30-HFDPCB5-mRNA_S15]

source_name: HFD + PCB 126 Treatment_liver

value: high fat diet + PCB 126


title: ILL10659-12SA002


title: HFD + Aroclor + PCB 126 Treatment, Replicate 2 [CK-34-HFDAroPCB2-mRNA_S17]


title: Spt6_G1+IAA_rep1

value: bar1[delta] SPT6-AID


title: Chd1Isw1_G1_control_rep2

value: bar1[delta] CHD1ISW1-AID


title: ILL10758-12SA001

value: Leaf tissue


title: Spt6_G1_control_rep1


title: HFD + Aroclor + PCB 126 Treatment, Replicate 1 [CK-32-HFDAroPCB1-mRNA_S16]


title: Isw1_G1+IAA_rep1


title: HFD + PCB 126 Treatment, Replicate 3 [CK-27-HFDPCB3-mRNA_S13]


title: HFD + Aroclor + PCB 126 Treatment, Replicate 5 [CK-40-HFDAroPCB5-mRNA_S20]


title: Mandibular WT_rep1

value: mandibular

value: wild type


title: HFD + PCB 126 Treatment, Replicate 4 [CK-29-HFDPCB4-mRNA_S14]


title: HFD + PCB 126 Treatment, Replicate 2 [CK-24-HFDPCB3-mRNA_S12]


title: FLIP11-62L

value: 4 weeks old


title: Swr1_G2+IAA_rep2

value: 0.5mM IAA, 15ug/ml nocodazole

value: bar1[delta] SWR1-AID


title: HFD + PCB 126 Treatment, Replicate 1 [CK-22-HFDPCB1-mRNA_S11]

value: male


title: Isw1_G1_control_rep2


title: Swr1_G2+IAA_rep1


title: HFD Control, Replicate 4 [CK-06-HFDcontrol4-mRNA_S4]

source_name: HFD Control_liver

value: high fat diet (control)

value: liver


title: HFD + Aroclor Treatment, Replicate 2 [CK-14-HFDAro2-mRNA_S7]

source_name: HFD + Aroclor Treatment_liver

value: high fat diet + Aroclor 1260


title: FLIP2011-51L


title: Isw1_G1_control_rep1


title: FLIP2010-9L


title: HFD + Aroclor Treatment, Replicate 4 [CK-18-HFDAro4-mRNA_S9]


title: HFD + Aroclor Treatment, Replicate 3 [CK-17-HFDAro3-mRNA_S8]


title: Swr1_G2_control_rep2

value: control, 15ug/ml nocodazole


title: FLIP11-57L


title: HFD Control, Replicate 2 [CK-02-HFDcontrol2-mRNA_S2]


title: FLIP09-32L-12SA001


title: HFD Control, Replicate 5 [CK-10-HFDcontrol5-mRNA_S5]


title: HFD + Aroclor Treatment, Replicate 5 [CK-20-HFDAro5-mRNA_S10]


title: FLIP07-22L


title: HFD Control, Replicate 1 [CK-01-HFDcontrol1-mRNA_S1]


title: CIPAL1621


title: HFD + Aroclor Treatment, Replicate 1 [CK-12-HFDAro1-mRNA_S6]


title: NPC_Chow_Animal3_Capture1

city: tarrytown

first: Xiping

last: Cheng

state: new york

address: 777 old saw mill river rd

institute: Regeneron

data_processing:
BCLs converted to Fastq performed using Cell Ranger v2.2
Reads were aligned to the mm10 mouse genome assembly using Cell Ranger v2.2
Genome_build: mm10
Supplementary_files_format_and_content: cell_raw_counts.txt

source_name: Liver

extract_protocol:
Mice were anesthetized using isoflurane and perfused with two-step liver perfusion protocol (Kreamer et al., 1986; Seglen, 1976). After perfusion, hepatocytes were spun and collected at 50g, then processed for 10x Genomics single cell processing. The suspension went through 50% and 20% Percoll gradient centrifuge and NPCs were collected. FACS sorted unstained/DAPI- cells were loaded on a Chromium Single Cell Instrument (10x Genomics)
RNAseq libraries were prepared using Chromium Signle Cell 3' Library, Gel Breads & Muliplex Kit (10X Genomics)
Paired-end, single index

treatment_protocol: Cells were freshly isolated from liver without any other treatment

tag: diet

value: Chow

value: NPC


title: NPC_Chow_Animal3_Capture2


title: Swr1_S+IAA_rep2

value: 0.5mM IAA, 200 mM hydroxyurea


title: Swr1_G2_control_rep1


title: HFD Control, Replicate 3 [CK-04-HFDcontrol3-mRNA_S3]


title: NPC_Chow_Animal2_Capture2


title: CIPAL1602


title: NPC_Chow_Animal2_Capture1


title: NPC_Chow_Animal1_Capture2


title: NPC_Chow_Animal1_Capture1


title: Swr1_S_control_rep2

value: control, 200 mM hydroxyurea


title: Swr1_S+IAA_rep1


title: Lung, IWC 2d rep1

value: Rag1-/- mice

value: IWC 2d

value: lung


title: CIPAL1601

value: Leaf tissue


title: NPC_34weeks_Animal1_Capture1

value: HFHFD diet, 34weeks


title: NPC_30weeks_Animal4_Capture1

value: HFHFD diet, 30weeks


title: NPC_30weeks_Animal4_Capture2


title: NPC_34weeks_Animal1_Capture2


title: Swr1_S_control_rep1


title: NPC_30weeks_Animal3_Capture1


title: CIPAL1302

value: 4 weeks old


title: NPC_30weeks_Animal2_Capture2


title: CIPAL1504


title: Swr1_G1+IAA_rep1

value: 0.5mM IAA,alpha factor (50ng/ml)

value: bar1[delta] SWR1-AID


title: Swr1_G1+IAA_rep2


title: CIPAL1301


title: Swr1_G1_control_rep2

value: control, alpha factor (50ng/ml)


title: NPC_30weeks_Animal1_Capture2


title: NPC_15weeks_Animal3_Capture2

value: HFHFD diet, 15weeks


title: NPC_30weeks_Animal1_Capture1


title: NPC_30weeks_Animal2_Capture1


title: NPC_15weeks_Animal3_Capture1


title: NPC_30weeks_Animal3_Capture2


title: Swr1_G1_control_rep1


title: NPC_15weeks_Animal1_Capture2


title: NPC_15weeks_Animal2_Capture2


title: 11H234L-12HS2006


title: 11H399L-14HHI4005


title: NPC_15weeks_Animal2_Capture1


title: 11H153L-1-13BOHI3003


title: Chd1_G2+IAA_rep2

value: 0.5mM IAA, 15ug/ml nocodazole

value: bar1[delta] CHD1-AID


title: Hepatocyte_Chow_Animal3_Capture1

value: Chow

value: Hepatocyte


title: 11H104L-12HS2004


title: Chd1_G2_control_rep2

value: control, 15ug/ml nocodazole


title: Chd1_S+IAA_rep1

value: 0.5mM IAA, 200 mM hydroxyurea


title: Hepatocyte_Chow_Animal6_Capture1


title: CIPAL1522


title: Hepatocyte_30weeks_Animal2_Capture2


title: Chd1_G2_control_rep1


title: Sth1-K501R_G1+IAA_rep1

value: bar1[delta] STH1-AID STH1-K501R


title: Chd1_S_control_rep2

value: control, 200 mM hydroxyurea


title: Hepatocyte_30weeks_Animal2_Capture1


title: Hepatocyte_Chow_Animal2_Capture1


title: 11H022L-12HS2004


title: Chd1_G2+IAA_rep1


title: Hepatocyte_Chow_Animal5_Capture1


title: Hepatocyte_Chow_Animal4_Capture1


title: 10H444L-11-12HS3002


title: Chd1_S+IAA_rep2


title: Hepatocyte_30weeks_Animal1_Capture1


title: 10H442L-11HS2001


title: Hepatocyte_Chow_Animal1_Capture1


title: Hepatocyte_30weeks_Animal1_Capture2


title: 10H397L-14HHI4001


title: Chd1_S_control_rep1


title: 10H450L-7-12HS3003


title: Hepatocyte_15weeks_Animal3_Capture2


title: Hepatocyte_15weeks_Animal3_Capture1


title: NPC_15weeks_Animal1_Capture1

value: NPC


title: Chd1_G1+IAA_rep2


title: Hepatocyte_15weeks_Animal1_Capture2


title: Hepatocyte_15weeks_Animal2_Capture2


title: Hepatocyte_15weeks_Animal2_Capture1


title: 10H383L-12HS3009

value: Leaf tissue


title: 10H196L-3-12AHM2009


title: 10H202L-10HG1006-11HSHI2001


title: Hepatocyte_15weeks_Animal1_Capture1


title: Fxr-livKO - 141

city: Innsbruck

first: Jose Miguel

last: Ramos Pittol

address: Innrain 80-82

department: Institute of Biochemistry

country: Austria

institute: University of Innsbruck

description:
genes.count_table
Fxr-livKO.diff

data_processing:
Sequencing reads were aligned to the reference genome (mm9 assembly, MGSCv37) using Tophat2.18 with options "--b2-sensitive --microexon-search -p 2 -G Mus_musculus.NCBIM37.67.gtf"
Duplicated reads were removed with Samtools rmdup (v1.9 , using htslib 1.9)
The normalized read numbers per gene were calculated using the cuffnorm feature of Cufflinks (v2.2.1 linked against Boost version 105500) against the Mus_musculus.NCBIM37.67 gene annotation
sequencing reads were aligned to the reference genome (mm9 assembly, MGSCv37) using Tophat2.18 with options "--b2-sensitive --microexon-search -p 2 -G Mus_musculus.NCBIM37.67.gtf"
Differentially expressed genes deffinition and fold-inductions upon selective Fxr ablation were estimated with CuffDiff v2.2.1 comparing each Fxr-KO model against Fxr-fl/fl controls, with options "--library-norm-method quartile -p 2 Mus_musculus.NCBIM37.67.gtf"
Genome_build: mm9
Supplementary_files_format_and_content: diff tab-delimited text file, output from CuffDiff2 with differential gene expression values and statistics (q1=control, q2=KO)
count_table tab-delimited text file, output from CuffNorm containing normalized count values per gene for all samples

source_name: colon tissue

growth_protocol: Homozygous Fxr floxed mice (C57Bl6 Fxr-fl/fl), kindly provided by K. Schoonjans (Ecole Polytechnique Federale de Lausanne, Switzerland), were crossed with mice harboring a cre-recombinase allele under the control of the meox2 promoter (Meox2-cre mice, stock 003755), albumin promoter (Alb-Cre mice, stock 003574) and villin promoter (Villin-Cre mice, stock 004586) to generate Whole body (Fxr-totKO), liver-specific (Fxr-livKO), and intestine-specific (Fxr-intKO) Fxr -null mice, respectively.  Fxr fl/fl mice were used as control. Mice were purchased from The Jackson laboratory, unless otherwise stated.

extract_protocol:
Tissue was lysed using TRIzol reagent, whereafter the RNA was further processed from the aqueous phase using the Qiagen RNEasy kit, including treatment with DNaseI.
mRNA was enriched from total RNA using the Poly(A) Beads (NEXTflex). Sequencing libraries were prepared using the Rapid Directional RNA-Seq Kit (NEXTflex) acording to the providers protocol

treatment_protocol: Male mice of 9-12 weeks old were included. Mice were fed a purified diet (AIN-93M, Research Diets, Wijk bij Duurstede) and drinking water ad libitum. Mice were individually housed in a room with controlled temperature (20-24°C), relative humidity (55%±15%) and a 12h light dark cycle. Mice were acclimatized for 1 week, after that the intervention period of 1 week started in which mice remained on the same diet and body weight was recorded. Mice were starved 4 hours before sacrifice, the colon was excised, mesenteric fat was removed and the colon was opened longitudinally, washed in PBS, and cut into three parts. The middle 1.5 cm colon tissue was formalin-fixed and paraffin embedded for histology. The remaining proximal and distal parts were scraped, pooled per mouse, snap-frozen in liquid nitrogen and stored at -80°C until RNA extraction.

value: male

value: Fxr-livKO

value: colon


title: Chd1_G1_control_rep2


title: Chd1_G1_control_rep1


title: 10H367L-12HSHI2001

value: 4 weeks old


title: Fxr-intKO - 15

description:
genes.count_table
Fxr-intKO.diff

value: Fxr-intKO


title: 10H171L-11HS2010


title: Fxr-intKO - 75

description:
genes.count_table
Fxr-intKO.diff


title: Fxr-totKO - 60

description:
genes.count_table
Fxr-totKO.diff

value: Fxr-totKO


title: Fxr-intKO - 13

description:
genes.count_table
Fxr-intKO.diff


title: 10H178L-11HS2005


title: Fxr-livKO - 151

description:
genes.count_table
Fxr-livKO.diff


title: Chd1_G1+IAA_rep1

value: 0.5mM IAA,alpha factor (50ng/ml)


title: 10H168L-11HS2008


title: Fxr-totKO - 3

description:
genes.count_table
Fxr-totKO.diff


title: Fxr-totKO - 2

description:
genes.count_table
Fxr-totKO.diff


title: Fxr-livKO - 132

description:
genes.count_table
Fxr-livKO.diff


title: 10H061L-12HS3005


title: Fxr-fl/fl - 82

value: Fxr-fl/fl


title: Snf2_control_rep2

description:
Hi-C
all_Min_snf2_no_5000.cool

value: 0.5mM IAA


title: Sth1_S_control_rep2

description:
Hi-C
S_no_5000.cool

value: control

value: bar1[delta] STH1-AID


title: Fxr-fl/fl - 45


title: Snf2_control_rep1

description:
Hi-C
all_Min_snf2_no_5000.cool


title: Sth1_S_control_rep1

description:
Hi-C
S_no_5000.cool


title: Fxr-fl/fl - 44


title: 10H039L-12HS3001


title: Snf2+IAA_rep2

description:
Hi-C
all_Min_snf2_IAA_5000.cool


title: 09H165L-12H3002


title: Sth1_S+IAA_rep1

description:
Hi-C
S_IAA_5000.cool


title: Snf2+IAA_rep1

description:
Hi-C
all_Min_snf2_IAA_5000.cool


title: 09H150L-12HSHI3007


title: Sth1_S+IAA_rep2

description:
Hi-C
S_IAA_5000.cool


title: 09H111L-11HS3006-13BO001


title: 09H111L-11HS3006


title: 07H205L-10H4018


title: 09H155L-13H4012


title: 07H212L-07HG1005-08HS2023


title: 07H190L-07HG1006-08HS2015


title: Sth1_G2_control_rep1

description:
Hi-C
G1_no_5000.cool


title: Sth1_G2+IAA_rep2

description:
Hi-C
G2_IAA_5000.cool


title: Sth1_G1_control_rep2

description:
Hi-C
G1_no_5000.cool


title: G1EINPUT

city: Hershey

first: Bowen

last: Yan

address: HERSHEY MED CTR 500 UNIVERSITY DRIVE 500 UNIVERSITY DRIVE

institute: PENNSYLVANIA STATE UNIV

data_processing:
Data quality was evaluated through Fastqc program
ChIP-seq reads were aligned to the mm10 genome assembly using using Bowtie2
The Bamcoverage tool from Deeptools was used to create the coverage files for visualization
Peaks were identified using the MACS program
wig files were generated using the Bamcoverage tool from Deeptools was used to create the coverage files for visualization
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: G1E cells

growth_protocol: Cells were cultured in Iscove’s modified Dulbecco’s medium with 15% fetal calf serum, 4.5X10e-5M mono-thioglycerol, 2U/ml of Epo, and 50ng/ml of KL

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions

tag: cell line

value: G1E cells

tag: chip antibody


title: Sth1_G1+IAA_rep2

description:
Hi-C
G1_IAA_5000.cool


title: Old_D0_A

city: Ithaca

first: Lauren

middle: D

last: Walter

state: NY

address: 161 Weill Hall

department: Biomedical Engineering

institute: Cornell University

data_processing:
Libraries were sequenced on Illumina NextSeq 500 using paired-end 26 + 8 + 58 (according to 10X Chromium Single Cell 3' protocol)
Sequences were aligned to mm10 using cellranger v3.1.0 pipeline
Ambient RNA content was removed using SoupX v1.4.5
Gene expression data was processed with Seurat v3.1.5
Initial data filtering (minimum cells to express an included gene = 3, minium genes to be expressed in an included cell = 500)
Filtering by percent mitochondiral genes in included cells (maximum 30%), number of UMIs in included cells (minimum 1000)
Log-normalization of expression data
Cell annotations in metadata derived from shared nearest neighbor clustering
Genome_build: mm10
Supplementary_files_format_and_content: zipped, market exchange format (MEF) for raw, filtered, and scrubbed (SoupX) transcript count matrices; .csv files of single-cell metadata information

source_name: Tibialis anterior muscle

extract_protocol:
Single-cell RNA-sequencing libraries were prepared using a Chromium Single Cell 3' Reagent Kit (10X Genomics, v3 kit) following the directions of the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 20 months

value: F

value: Tibialis anterior muscle

tag: injury

value: Uninjured


title: Sth1_G2+IAA_rep1

description:
Hi-C
G2_IAA_5000.cool

tag: strain


title: 06H138L-07HS2012-10SA002

value: Leaf tissue


title: G1E2RA-HDAC1

value: β-estrodiol induction


title: Sth1_G1+IAA_rep1

description:
Hi-C
G1_IAA_5000.cool


title: RNAseq_MCF10A_2D_rep3

city: Milwaukee

first: Victor

last: Jin

state: WI

address: 8701 Watertown Plank Rd

department: IHE

institute: Medical college of Wisconsin

data_processing:
All raw reads were mapped to HG19 reference genome by using hisat2.
Raw bam files were further processed by samtools and picard.
Differential genes were identified by DESeq2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: read_counts_summary_byDESeq2_noDupBams.txt: Tab-delimited text files include read counts.
Supplementary_files_format_and_content: xlsx: Excel files include differential expression genes.

source_name: Breast cancer cells

growth_protocol: MCF7TR cells were derived from Osborne et al. MCF7 cells were grown in RPMI-1640 supplemented with 10% fetal bovine serum and 1% penicillin and streptomycin (pen/strep) until 90% confluent. MCF10A were culture in DMEM/F12 with 10% FBS and 1% pen/strep. All the cells were grown at 37 °C and 5% CO2 until they reach 90% confluence. Spheroids were generated as described in [18,19]. Spheroids formed by MCF10A, MCF7 and MCF7TR were grown on Matrigel (Corning). Briefly, each plate was coated with 300ul of Matrigel and kept at 37 °C incubator for 30 min for gel formation. The Matrigel was overlaid with 2 ml of cell culture medium containing 5 X 104 cells with MCF10A, MCF7 or MCF7TR cells, and incubated at 37 °C, 5% CO2 for 3-4 days to allow spheroid formation.

extract_protocol:
Total RNA was extracted by ZYMO Research Quick-RNA MiniPrep kit from lysed 10 million of cells and spheroids in RNA lysis buffer, then removed most of gDNA with the spin-away filter. After that, the mixture of RNA was transferred with ethanol to Zymo-Spin IIICG column to remove trace DNA by DNase I on the column, then washed twice with RNA wash buffer followed by elution with 50 μl DNase/RNase-free water.
RNA-seq library was prepared with NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB #E7490). The Oligo dT Beads were washed with RNA binding buffer and incubated with a total 1 μg RNA to purify mRNA, followed with more washing by beads washing buffer. Then mRNA was eluted with elution buffer and reverse transcribed. After that, the first and the second strand cDNA were synthesized. After purification of Double-stranded DNA, an adaptor was added. Adaptor-ligated DNA was enriched by PCR followed by purification, then the DNA library was sequenced with Illumina HiSeq3000.

treatment_protocol: MCF7TR cells were cultured in phenol red free RPMI-1640 containing 10% charcoal-stripped FBS, 1% pen/strep and 100 nM Tamoxifen (Sigma-Aldrich). Tamoxifen was replaced every 48 h.

value: breast epithelial cell line

tag: passages

tag: culture type

value: 2D monolayer


title: 09H043L-12H3005

value: 4 weeks old


title: G1E2RA-GATA-1

value: GATA-1(N6, Santa Cruz)


title: Sth1_G2_control_rep2

description:
Hi-C
G1_no_5000.cool


title: Sth1_G1_control_rep1

description:
Hi-C
G1_no_5000.cool


title: siMnt R3

city: Odense M

first: Vijay

last: Tiwari

state: Denmark

address: Campusvej 55

department: Institut for Molekylær Medicin (IMM)

country: Denmark

institute: Queen’s University Belfast

data_processing:
Low quality bases were trimmed from pre-aligned reads, then aligned to mm9 whole genome using TopHat v2.1.0 with default parameters
Raw read counts were filtered to remove counts where maximum <=1. Differential analysis was performed with DESeq2 (R, v3.5) with default parameters, with the median of ratios method of normalisation performed prior to differntial analysis.
After library size normalization using DESeq (v3.5), expression was quantified and differential expression analysis was performed using DESeq2.
Gene set enrichment analysis for biological processes was performed using DAVID with P-value<0.05
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with gene counts from DESeq2, for every gene and every sample

source_name: NMuMG cell line

growth_protocol: Cells were seeded at the same starting density (200K per well) 16 hours before treatment

extract_protocol:
RNA was extracted using Trizol, isolated using chloroform, precipitated using isopropanol and the RNA pellet washed with ethanol before re-suspension in DEPC water
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cells were transfected with siRNA at the same time as TGF? induction (16 hours after plating), with TGF-? and siRNA replenishment and medium changed on day 2

value: siRNA mediated Mnt knockdown in NMuMG cells after TGF-beta induction (d4)


title: siMnt R1


title: RNAseq_MCF10A_2D_rep1


title: siNTC R3

value: Non-targeting control in NMuMG cells after TGF-beta induction (d4)


title: RNAseq_MCF10A_3D_rep2

value: 3D spheroid


title: NT-/- Fast-5

city: Lexington

first: Mark

last: Evers

address: 800 Rose Street

department: College of Medicine

institute: University of Kentucky

data_processing:
Sequencing and base-calling were performed by University of Kentucky Markey Cancer Center Oncogenomics core.
Sequencing reads were trimmed and filtered using Trimmomatic (V0.39) to remove adapters and low quality reads.
Reads were mapped to Ensembl GRCm38 (release 100) transcripts annotation using RSEM.
Genome_build: GRCm38 (release 100)
Supplementary_files_format_and_content: tab-delimited text files including TPM, FPKM and expected_count for each gene

source_name: intestinal crypt

extract_protocol:
RNA was isolated from intestinal crypts using RNeasy Mini Kit according to manufacturer's protocol. RNA was DNAse-treated and quality analyzed on Agilent Bioanalyzer 2100 RNA Nano chip.
RNA-Seq libraries were prepared using KAPA RNA Hyper + RiboErase HMR (Roche). The manufacturer’s protocols were used to sequence ribosomal RNA-depleted libraries at 1x100 single-end read on an Illumina HiSeq 2500 in rapid mode, to an average depth of 32 million single-end reads per sample.

value: intestinal crypt

value: Fasted 48h


title: RNAseq_MCF10A_3D_rep1


title: 07H081L-08HS2015


title: NT-/- Fast-3

value: Male


title: 06H319L-10H4002


title: NT-/- Fast-2

value: Female


title: siMnt R2


title: RNAseq_MCF10A_2D_rep2


title: RA-hBD2, 3

city: Hamilton

first: Nadia

last: Milad

state: Ontario

address: 1280 Main St W

institute: McMaster University

hyb_protocol: 5.5 μg of the fragmented and labeled cDNA was hybridized to Mouse Clariom S array for 16 h at 45°C and 60 rpm in an Affymetrix Hybridization Oven 640. Arrays were washed and stained with Streptavidin Phycoerythrin in an Affymetrix Fluidics Station 450 according to Affymetrix GeneChip Pico Reagent Kit guide (Thermo Fisher).

scan_protocol: The arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G and CEL. intensity files were generated by Affymetrix GeneChip Command Console Software (AGCC, Thermo Fisher).

data_processing:
The Affymetric Clariom S microarrays were further analyzed using Affymetrix Expression Console with the SST-RMA procedure.  The gene-level differential expression was performed using the Affymetrix Transcriptome Anaylsis Console (TAC) Software using default parameters. The significant genes were ranked by fold-change with a cutoff of 2 and the ANOVA p-value less than 0.05 according to Affymetrix.  affymetrix-algorithm-name = sst-rma-gene-full  affymetrix-algorithm-version = 1.0  affymetrix-array-type = Clariom_S_Mouse  program-name = Expression Console  program-version = 1.4.1.46
Sample 4 was removed due to poor cDNA quality, did not pass quality control criteria.

label: biotin

source_name: Lung

label_protocol: Microarray was performed at the GenomeQuebec in Montreal. RNA integrity was examined on a bioanalyzer (Agilent). High-quality RNA (RNA integrity number >8.5) was used for expression microarray analysis. 700 pg of total RNA was used to generate double strand cDNA, which was fragmented and biotin labeled according to Affymetrix GeneChip Pico Reagent Kit manual (Thermo Fisher).

growth_protocol: Sacrifice at 5 months of age

extract_protocol: QIAzol Rneasy

treatment_protocol: Exposed to cigarette smoke for 7 weeks (2h/day), treated with hBD-2 via intranasal instillation during final 2 weeks

tag: group


title: siNTC R1


title: NT+/+ Fast-3

tag: tissue


title: NT+/+ Fast-2

tag: genotype


title: RNAseq_MCF7TR_3D_rep1

value: tamoxifen-resistant breast cancer cell line


title: RA-hBD2, 1


title: RA-hBD2, 5


title: RA-PBS, 4

value: RA-PBS


title: RNAseq_MCF7TR_3D_rep3


title: NT-/- AL-4

value: Ad libitum


title: NT-/- Fast-4


title: RNAseq_MCF7TR_3D_rep2


title: G1EWT-GATA-1

value: G1E cells


title: siNTC R2


title: NT-/- AL-3


title: RNAseq_MCF7_3D_rep2

value: breast cancer cell line


title: NT+/+ Fast-4


title: NT-/- Fast-1


title: RNAseq_MCF10A_3D_rep3


title: RNAseq_MCF7_3D_rep1


title: RA-PBS, 2


title: NT+/+ Fast-5


title: NT+/+ AL-3


title: G1EWT-HDAC1

value: β-estrodiol induction


title: NT-/- AL-2


title: NT+/+ Fast-1


title: RNAseq_MCF7_3D_rep3


title: RA-hBD2, 2


title: HiC_MCF10A_3D_rep1

data_processing:
All raw reads were mapped to HG19 reference genome and processed to Hi-C interaction matrices by using HiC-Pro v2.11.1 with default parameters and 20kb as well as 40kb tiling window size.
The significant interactions (SIFs) were identified by HiSIF with parameter t =1 and fdr-cutoff 0.1.
The significant interactions (SIFs) were further mapped to promoter and distal regions based on UCSC RefSeq HG19 where the mapping definition was defined in Methods.
P1D1 looping genes were compared by using an in-house python code to obtain DLGs.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_loops.xlsx: Excel files include differential gene loops.

extract_protocol:
Hi-C was performed as previously described in Zhou. Y et. In brief, spheroids were crosslinked with 1% formaldehyde and lysed with cold lysis buffer to collect nuclei. The pelleted nuclei were digested with 200 units of HindIII (NEB, R3104L) at 37 °C for overnight. The HindIII digested fragment overhangs were filled with biotin-labelled dATP (Life Technologies, 19524-016) in a Klenow end-filling reaction. Four hundred units of T4 DNA Ligase (NEB, M0202) were added for ligation and samples were incubated for 4 h at room temperature with slow rotation.
The ligation products were purified, and the chromatin was sheared to a size of 300-500bp using Covaris sonicator (Covaris Woburn, MA). Dynabeads MyOne Streptavidin T1 beads (Life technologies, 65601) were used to pull down the Biotin-labelled DNA. The end repair, dA tailing was performed and ligated with Illumina TruSeq adapters to form the final Hi-C ligation products. Each Hi-C library was amplified with 12 cycles of PCR using Illumina primers. The Hi-C library was purified and then sequenced with Illumina HiSeq3000.

value: breast epithelial cell line

tag: restriction enzyme

value: HindIII


title: CS-FC3

city: Baltimore

first: S. Amer

last: Riazuddin

address: 600 N. Wolfe street

institute: Johns Hopkins University

description: mRNA library

data_processing:
Illumina Casava1.8 used for basecalling and de-indexing.
The paired-end reads were aligned to the Mus musculus genome (GRCm38/mm10) using the STAR algorithm (Ver. 2.5).
The HTSeq (Ver. 0.6.1) was used for the quantification of gene expression using mapped reads.
The expression data were normalized by calculating the fragment per kilobase per million mapped reads (FPKM) values for each gene (Mortazavi et al., Nat Methods, 2008)
Differential gene expression analysis was performed using the DESeq2 (Ver. 2_1.6.3).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file include FPKM values for each Sample

source_name: Lens fiber cells from cigarette smoke exposed mice

extract_protocol:
The control and cigarette smoke exposed mice were first anesthetized with isoflurane and subsequently euthanized through cervical dislocation, and the lenses were extracted from mouse eyes and fiber cells were separated from the epithelium under a microscope as described previously. The extracted tissue was maintained in four distinct pools, each consisting of fiber cells from four mice eyes to serve as biological replicate for the control (CT-FC) and CS-exposed (CS-FC) mice. Upon extraction, lenses were dissolved immediately in Trizol reagent and total RNA was extracted for RNA-Seq library prepration.
NEB Next Ultra RNA Library Prep Kit was used to prepare RNA-Seq libraries using total RNA isolated from control and cigarette smoke exposed mice.

tag: mouse status

value: cigarette smoke (CS-FC) exposed

value: Ocular lens

tag: cell type

value: Ocular lens fiber cells


title: HiC_MCF7TR_3D_rep1


title: CS-FC1

description: mRNA library


title: RA-hBD2, 4


title: NT+/+ AL-5


title: RA-PBS, 3


title: CS-hBD2, 4


title: RA-PBS, 5


title: CS-hBD2, 2


title: CT-FC3

description: mRNA library

source_name: Lens fiber cells from control mice

value: control (CT-FC)


title: NT+/+ AL-4


title: CS-hBD2, 5


title: HiC_MCF7_3D_rep2

value: 3D spheroid


title: CT-FC4

description: mRNA library


title: CS-hBD2, 1


title: NT-/- AL-1

value: intestinal crypt


title: NT+/+ AL-2


title: RA-PBS, 1


title: CS-FC2

description: mRNA library


title: HiC_MCF7TR_3D_rep2


title: CS-FC4

description: mRNA library


title: CD20- T cells [S22]

city: Groningen

first: Martijn

middle: Ruben

last: Vlaming

state: Groningen

address: Hanzeplein 1

country: Netherlands

institute: UMCG

data_processing:
Aalignment to the human reference genome hg38 using STAR (version 2.5.2).
Genome_build: hg38
Supplementary_files_format_and_content: A matrix table containing raw count processed data for all samples, peak text file

source_name: Buffy coat

growth_protocol: Buffy coat thawed, stained and sorted

extract_protocol:
CD20+ and CD20- CD3+ CD8+ CD45RO+ CCR7- lymphocytes were sorted in 96-wellsplate containing lysis buffer 2 µl lysis buffer (0,2% Triton X-100, 2U RNase inhibitor) supplemented with 1 µl 10 µM oligo-dT primer and 1 µl 10 mM dNTP mix. After sorting, the plate was spun down, incubated at 72°C for 3 minutes and stored on ice.
A modified SMARTseq2 protocol using custom-made primers was used. In brief, SmartScribe reverse transcriptase (Westburg-Clontech) and a template switching oligo (BC-TSO) were used to generate cDNA. Next, a PCR preamplification step was done with KAPA HiFi HotStart Ready Mix (Roche Diagnostics) and a custom-made PCR primer. The cDNA samples were purified using Ampure XP beads (Beckman Coulter) in a ratio of 0,6:1 (Ampure bead : cDNA). Samples were analyzed on a 2100 Bioanalyzer using a PerkinElmer LabChip GX high-sensitivity DNA chip (Agilent) and on a Qubit™ 4 Fluorometer (ThermoFisher Scientific) according to manufacturer’s instructions. Next, 500 pg of each sample was tagmented and N7xx and S5xx index adapters were used for barcoding according to the Illumina Nextera XT DNA sample preparation kit (Illumina). Thereafter, samples were purified using Ampure XP beads (ratio 0,6 Ampure : 1 cDNA) and analyzed on a 2100 Bioanalyzer. Samples were equimolar pooled (4 nM) and subsequently sequened on an Illumina Nextseq500 2500 using 75 bp single-end reads.

treatment_protocol: Buffy coat thawed, stained and sorted

value: CD20- T cells

tag: phenotype

value: CD3+ CD8+ CD45RO+ CCR7-

tag: disease state

value: Healthy


title: CD20- T cells [S20]


title: CD20+ T cells [S21]

value: CD20+ T cells


title: CS-hBD2, 3

tag: age


title: CS-PBS, 4

value: CS-PBS


title: TH946

city: Homburg Saar

first: Masood

last: Abu-Halima

address: Kirrberger St 60

department: Human Genetics

country: Germany

institute: Univeristy of Saarland

description: The expression profile of 2549 human miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturers recommendations

scan_protocol: Array´s were scanned with the Agilent Scanner with default settings.

data_processing: Raw expression values were extracted using the Feature Extraction Software of Agilent.

source_name: Blood/PAXgene

extract_protocol: Total RNA including miRNAs was isolated using the PAXgene™ Blood miRNA Kit on the QIAcube™ robot

tag: desease state

value: Healthy Control

tag: gender

value: Male


title: HiC_MCF10A_3D_rep2

tag: cell line


title: CD20- T cells [S24]


title: Dihydroartemisinin treated protoscoleces of Echinococcus granulosus_3

city: Urumqi

first: Limei

last: Wen

address: No. 137 Liyushan South Road, Pharmaceutical Department

institute: The First Affiliated Hospital of Xinjiang Medical University

description: DHA 3

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent hydatid  4x44k Microarrays for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Echinococcus granulosus

source_name: protoscolece treated with DHA for 3 d

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Nucleospin RNA Clean-up Kit (Macherey-Nagel, Germany) following the manufacturer's recommendations.   RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: protoscolece

tag: treatment

value: 100 uM DHA for 3 d


title: TH939

hyb_protocol: The expression profile of 2549 human miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturers recommendations

value: Female


title: CT-FC2

description: mRNA library


title: NT+/+ AL-1

tag: diet

value: Ad libitum

tag: Sex


title: HiC_MCF7_3D_rep1

value: breast cancer cell line

value: HindIII


title: CD20+ T cells [S19]


title: Dihydroartemisinin treated protoscoleces of Echinococcus granulosus_1

description: DHA 1


title: H295R_for_24_rep2

city: NEW YORK

first: RUI

last: FU

address: 101 6th Ave

department: Computational Biology

institute: New York Genome Center

data_processing:
Reads were mapped using Salmon with custom index containing ERCC spike-ins and precursor transcripts. Settings for salmon quant: -l A --allowDovetail --validateMappings
Genome_build: GRCh38
Supplementary_files_format_and_content: Salmon output quant.sf files, tab-delimited text file of read counts and TPM for each sample

source_name: H295R cells

growth_protocol: H295R cells cultured in DMEM/F12 with 1% ITS and 10% CCS; cadeveric human adrenocortical cells were isolated and cultured as previously (PMC4475723)

extract_protocol:
H295R cells were washed and treated with TRIzol and RNA was extracted using ZYMO DirectZol RNA Miniprep kit. rRNA was depleted using ribozero gold; RNA from human adrenocortical cells was polyA-selected.
All RNA was made into cDNA libraries using Kappa HyperPrep kit an sequenced on Nova-seq.

treatment_protocol: 24 hours prior to stimulation of H295R cells with 10 uM forskolin media was replaced with low sera media (DMEM/F12 with 0.1% CCS, 1% ITS); human adrenocortical cells were treated with 10 nM and 10uM of AngII and ACTH respectively.

value: forskolin, 24hr

value: immortalized adrenocortical cells


title: H295R_for_1_rep2

value: forskolin, 1hr


title: H295R_for_4_rep2

value: forskolin, 4hr


title: H295R_for_8_rep2

value: forskolin, 8hr


title: TH933

label_protocol: The expression profile of 2549 human miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturers recommendations


title: CD20+ T cells [S23]

value: CD3+ CD8+ CD45RO+ CCR7-


title: TH940


title: H295R_for_2_rep2

value: forskolin, 2hr


title: H295R_for_0_rep2

value: Unstimulated


title: H295R_for_0.25_rep2

value: forskolin, 0.25hr


title: H295R_for_24_rep1


title: CT-FC1

description: mRNA library

tag: strain

value: control (CT-FC)

value: Ocular lens

value: Ocular lens fiber cells


title: CS-PBS, 3

value: CS-PBS


title: DMSO treated protoscoleces of Echinococcus granulosus_2

description: D 2

source_name: protoscolece treated with DMSO for 3 d

value: protoscolece

value: 1% DMSO for 3 d


title: DMSO treated protoscoleces of Echinococcus granulosus_1

description: D 1


title: H295R_for_4_rep1


title: CS-PBS, 1


title: CS-PBS, 2


title: TH908

value: Healthy Control

value: Male


title: iHEECs/Luc 2mM n-butyrate rep 1

city: Saint Louis

first: Ramakrishna

last: Kommagani

state: MO

address: 425 S. Euclid Ave

department: OB/GYN

institute: Washington university School of Medicine in St. Louis.

data_processing:
Basecalls and demultiplexing were performed with Illumina’s RTA version 1.9 and bcl2fastq2 software with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1b. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5.  The counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust samples for differences in library size
Genes expressed less than one count-per-million in at least three sample were excluded from further analysis and new effective TMM size factors were recalculated. The rescaled matrix of counts were then imported into R/Bioconductor package Limma and weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights function.
Generalized linear models were then created to test for differential expression and the results were then filtered for Benjamini-Hochberg FDR adjusted p-values less than or equal to 0.05 and linear fold change≥ 2.0 fold-change.
Genome_build: Human Ensembl release 76

source_name: iHEECs/Luc

extract_protocol:
iHEECs/Luc were treated with Vehicle or 2 mM n-butyrate for 24 hours and then total RNA was isolated using RNeasy total RNA isolation kit (Qiagen) for RNA-seq.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ishikawa cells

value: SF3B1 siRNA


title: iHEECs/Luc 2mM n-butyrate rep 3


title: TH906


title: H295R_for_0.25_rep1

value: immortalized adrenocortical cells


title: TH839


title: TH942


title: iHEECs/Luc Vehicle rep 3

value: Control siRNA


title: H295R_for_8_rep1

value: forskolin, 8hr


title: Dihydroartemisinin treated protoscoleces of Echinococcus granulosus_2

description: DHA 2

value: 100 uM DHA for 3 d


title: H295R_for_0.5_rep1

value: forskolin, 0.5hr


title: H295R_for_0.5_rep2


title: sample HC42, plate 3

city: Worcester

first: Alan

middle: G

last: Derr

state: Massachusetts

address: 55 Lake Ave North

department: Program in Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

data_processing:
Convert paired-end reads to single-ended, extracting the 12-base cell barcode and 8-base unique molecule identifier (UMI) from R1 read and appending them to the R2 read name as a colon-separated pair. Reads with Ns in either the cell barcode or UMI are discarded. (custom Python script)
Align reads to human hg38 genome, with GENCODE v28 gene annotations. (tophat2 v2.0.12)
Quantify transcript counts using GENCODE v28 gene annotations. (ESAT v1.0, https://github.com/garber-lab/ESAT)
Build t-SNE map of all cells (custom R script, using the dim_reduce() function from the SignallingSingleCell package, https://github.com/garber-lab/SignallingSingleCell)
Density-based clustering (custom R script, using the cluster_sc() function from the SignallingSingleCell package, https://github.com/garber-lab/SignallingSingleCell)
Cell type identification (custom R script based on density-based cluster boundaries and known marker genes to identify major cell types)
Viral transcript counting - NCBI magic-blast (https://ncbi.github.io/magicblast/) of all transcript sequence reads against all Influenza A and SARS-CoV2 genomes in the NCBI virus database as of 1 Agust 2020, followed by a custom Python script to quantify the number of unique viral transcripts in each cell, using UMIs to remove PCR duplicates.
Genome_build: hg38
Supplementary_files_format_and_content: raw transcript counts from ESAT.
Supplementary_files_format_and_content: per-cell phenotype information

source_name: saline nasal wash

extract_protocol: Seq-Well S^3 Master Protocol (June 2019) (http://shaleklab.com/wp-content/uploads/2019/07/SeqWell-S3-Protocol.pdf)

value: healthy


title: H295R_for_1_rep1

value: forskolin, 1hr


title: iHEECs/Luc Vehicle rep 1


title: exvivo_ACTH_48_rep3

source_name: adrenocortical cells

value: ACTH, 48hr

value: isolated adrenocortical cells


title: sample HC03, plate 2


title: H295R_for_0_rep1

value: Unstimulated


title: sample HC03, plate 1


title: DMSO treated protoscoleces of Echinococcus granulosus_3

description: D 3


title: H295R_for_2_rep1

value: forskolin, 2hr


title: TH838


title: sample f84, plate 4

data_processing:
Convert paired-end reads to single-ended, extracting the 12-base cell barcode and 8-base unique molecule identifier (UMI) from R1 read and appending them to the R2 read name as a colon-separated pair. Reads with Ns in either the cell barcode or UMI are discarded. (custom Python script)
Align reads to human hg38 genome, with GENCODE v28 gene annotations. (tophat2 v2.0.12)
Quantify transcript counts using GENCODE v28 gene annotations. (ESAT v1.0, https://github.com/garber-lab/ESAT)
Build t-SNE map of all cells (custom R script, using the dim_reduce() function from the SignallingSingleCell package, https://github.com/garber-lab/SignallingSingleCell)
Density-based clustering (custom R script, using the cluster_sc() function from the SignallingSingleCell package, https://github.com/garber-lab/SignallingSingleCell)
Cell type identification (custom R script based on density-based cluster boundaries and known marker genes to identify major cell types)
Viral transcript counting - NCBI magic-blast (https://ncbi.github.io/magicblast/) of all transcript sequence reads against all Influenza A and SARS-CoV2 genomes in the NCBI virus database as of 1 Agust 2020, followed by a custom Python script to quantify the number of unique viral transcripts in each cell, using UMIs to remove PCR duplicates.
Genome_build: hg38
Supplementary_files_format_and_content: raw transcript counts from ESAT.: 41442 genes x 29406 cell transcript counts matrix
Supplementary_files_format_and_content: per-cell phenotype information: 29406 cell x 13 column cell phenotype information. Columns: sampID (sample ID prefix), plateID (Seq-Well plate ID, 4 or 5 for each sample), status (disease status: COVID-19, fluA, healthy), donorID (unique ID for each donor), cDate (sample collection date), age (donor age), sex (donor sex - M or F), tSNE1, tSNE2 (t-SNE mapping coordinates), group (major cell type group), cellType (assigned cell type), SARS.CoV.2 (SARS-CoV2 virus transcript count), fluA (influenza A virus transcript count)

value: fluA


title: exvivo_ACTH_48_rep1


title: sample HC42, plate 5


title: TH931


title: sample HC42, plate 2


title: iHEECs/Luc 2mM n-butyrate rep 2


title: TH897


title: TH902


title: sample HC03, plate 3


title: sample HC42, plate 1


title: TH827

value: Female


title: iHEECs/Luc Vehicle rep 2


title: sample f83a, plate 4


title: sample HC42, plate 4


title: sample f83a, plate 1


title: sample f84, plate 1


title: TH893

value: Healthy Control


title: sample HC03, plate 4


title: exvivo_AngII_48_rep3

value: AngII, 48hr


title: TH816

value: Male


title: sample f84, plate 3


title: exvivo_ACTH_48_rep2


title: TH915


title: TH842


title: TH812


title: exvivo_basal_48_rep1

value: basal media, 48hr


title: TH817


title: TH811


title: exvivo_basal_48_rep3


title: sample f84, plate 2


title: exvivo_AngII_48_rep1


title: sample f83, plate 2


title: sample f82a, plate 4


title: sample f82a, plate 3


title: sample f82a, plate 2


title: sample f83a, plate 3


title: exvivo_ACTH_12_rep1

value: ACTH, 12hr


title: TH518


title: sample f83a, plate 2


title: sample f82b, plate 3


title: TH822


title: sample f82a, plate 1


title: TH500


title: exvivo_basal_48_rep2


title: TH815


title: sample f83, plate 1


title: sample f82b, plate 2


title: sample f82, plate 1


title: exvivo_ACTH_12_rep2


title: TH452


title: exvivo_AngII_12_rep1

value: AngII, 12hr


title: sample f83, plate 3


title: sample f83, plate 4


title: TH814


title: exvivo_AngII_48_rep2


title: TH810


title: sample f81, plate 1


title: sample f82, plate 4


title: exvivo_ACTH_12_rep3


title: sample f82b, plate 1


title: exvivo_basal_12_rep3

value: basal media, 12hr


title: sample f82b, plate 4


title: exvivo_basal_12_rep2


title: exvivo_AngII_12_rep2


title: sample f80, plate 3


title: exvivo_AngII_12_rep3


title: TH437


title: TH433


title: sample f81, plate 2


title: exvivo_ACTH_6_rep3

value: ACTH, 6hr


title: sample f82, plate 2


title: sample f79, plate 3


title: sample f82, plate 3


title: sample f79, plate 2


title: exvivo_ACTH_6_rep2


title: sample f81, plate 4


title: TH442


title: sample f80, plate 4


title: exvivo_AngII_6_rep3

value: AngII, 6hr


title: sample f78a, plate 1


title: sample f80, plate 2


title: sample f81, plate 3


title: TH455


title: sample f78, plate 4


title: exvivo_basal_12_rep1


title: sample f78a, plate 4


title: sample f79, plate 4


title: TH426


title: exvivo_AngII_6_rep1


title: sample f80, plate 1


title: sample f78a, plate 2


title: exvivo_ACTH_6_rep1


title: sample f72b, plate 4


title: sample f79, plate 1


title: sample f72b, plate 3


title: exvivo_basal_6_rep3

value: basal media, 6hr


title: TH422


title: sample f78a, plate 3


title: TH424


title: sample f78, plate 2


title: exvivo_AngII_6_rep2


title: sample f72a, plate 3


title: TH935


title: sample f78, plate 3


title: TH944


title: sample f72a, plate 1


title: TH929


title: TH432


title: sample f72, plate 4


title: exvivo_basal_6_rep1


title: TH937


title: sample f72b, plate 2


title: sample f78, plate 1


title: TH936


title: TH930


title: sample f72a, plate 2


title: sample f72b, plate 1


title: ChIP-SPT5_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2

city: Shanghai

first: Linna

last: Peng

address: Dong'an Road

institute: Fudan University

data_processing:
Raw reads were processed with Trim Galore v0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adaptors and low-quality reads with the parameter “-q 25” .
The remaining reads were aligned to the human hg19 and mouse mm10 assemblies using Bowtie v2.3.5.1 with default parameters (Langmead and Salzberg, 2012).
All unmapped reads, low mapping quality reads (MAPQ < 30) and PCR duplicates were removed using SAMtools v1.9 (Li et al., 2009) and Picard v2.23.3 (https://broadinstitute.github.io/picard/).
The number of spike-in mm10 reads was counted with SAMtools v1.9 and normalization factor alpha = 1e6/mm10_count was calculated (Li et al., 2009).
Normalized bigwig was generated with deeptools v3.5.0 and reads mapped to the ENCODE blacklist regions were removed using bedtools v2.29.2 (Amemiya et al., 2019; Quinlan and Hall, 2010; Ramirez et al., 2016).
Peaks were called using macs2 v2.2.6 with a q-value threshold of 0.05 and peak annotation was performed with ChIPseeker R package v1.24.0 (Yu et al., 2015; Zhang et al., 2008).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: SPT5-dTAG DLD1

extract_protocol:
Lysates were clarified from sonicated cells and INTAC-DNA complexes were isolated with antibody.
Libraries were prepared according to Vazyme's instructions accompanying the VAHTS Universal DNA Library Prep Kit (Vazyme ND607-02). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq X Ten following the manufacturer's protocols.

treatment_protocol: One replicate was DMSO or dTAG treated for 3 hours.

value: colorectal adenocarcinoma cell lines

tag: chip antibody

value: treated with dTAG13 for 3 hours


title: exvivo_basal_6_rep2

value: isolated adrenocortical cells


title: sample f72a, plate 4


title: ChIP-SPT5_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2

value: untreated


title: ChIP-SPT5_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1


title: TH913


title: TH919


title: sample f72, plate 2


title: TH927


title: sample Cov16N, plate 4


title: ChIP-SPT5_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1


title: sample f72, plate 3


title: sample f72, plate 1


title: sample Cov15, plate 4


title: ChIP-RPB1_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep1


title: sample Cov16N, plate 3


title: sample Cov16N, plate 2


title: TH904


title: ChIP-RPB1_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2


title: sample Cov15, plate 2


title: sample Cov15, plate 3


title: sample Cov16N, plate 1


title: ChIP-RPB1_DMSO-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2


title: sample Cov14, plate 2


title: ChIP-Med1_dTAG-3h_SPT5-N-PURO-Fkbp12_DLD1_rep2


title: sample Cov15, plate 1