title: LS_PRRX1_ChIP_cond2

value: PRRX1 (Sigma, hpa051084)


title: LS_PRRX1_ChIP_Input_cond1

status: Public on Nov 09 2023

type: SRA

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

library_source: genomic

data_processing:
Reads were aligned to hg19 with BWA-mem v0.7.17 (http://bio-bwa.sourceforge.net).
Duplicates were removed using Picard MarkDuplicates v2.18.17 (http://broadinstitute.github.io/picard/), with parameters (REMOVE_DUPLICATES=TRUE, VALIDATION_STRINGENCY=LENIENT).
ChIP-signal was quantified and peaks were called using MACS2 v2.1.2 {Zhang, 2008, PMID:18798982}, with parameters (--SPMR -B --keep-dup=1 --extsize=146 --nomodel, -q 0.05).
Assembly: hg19
Supplementary files format and content: bigwig of signals & bed files of called peaks

molecule: genomic DNA

organism: Homo sapiens

source_name: neuroblastoma cells

growth_protocol: Cells were grown in their respective media prepared per provider's guidelines, at 37 degree C, 5% CO2.

extract_protocol:
Cells (1 × 10^7) were fixed with 1% paraformaldehyde for 10 min at room temperature. DSG was then removed and replaced with fixing buffer (50 mM HEPES-NaOH (pH 7.5), 100 mM NaCl, 1mM EDTA) containing 1% paraformaldehyde (Electron Microscopy Sciences, 15714) and cross-linked for 10 min at 37 °C. Crosslinking was quenched by adding glycine to a final concentration of 0.125 M. The cells were washed with ice-cold PBS, harvested in PBS. The nuclear fraction was extracted by first resuspending the pellet in 1 ml of lysis buffer (50 mM HEPES-NaOH (pH 8.0), 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) for 10 min at 4 °C. Cells were pelleted and washed in 1 ml of wash buffer (10 mM Tris-HCL (pH 8.0), 200 mM NaCl, 1 mM EDTA) for 10 min at 4 °C. Cells were then pelleted and resuspended in 1 ml of shearing buffer (10 mM Tris-HCl (pH 8), 1 mM EDTA, 0.1% SDS) and sonicated in a Covaris sonicator. Lysate was centrifuged for 5 min at 14,000 rpm to purify the debris. Then 100 µl of 10% Triton X-100 and 30 µl of 5M NaCl were added. The sample was then incubated with 20 µl of Dynabeads Protein G (LifeTechnologies,10003D) for 1 h at 4 °C. Primary antibodies were added to each tube, and immunoprecipitation (IP) was conducted overnight at 4 °C. Cross-linked complexes were precipitated with Dynabeads Protein G for 2 hr at 4 °C. The beads were then washed in low salt wash buffer (20 mM Tris-HCl pH 8, 150 mM NaCl, 10 mM EDTA, and 1% SDS) for 5 min at 4 °C, high salt wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) for 5 min at 4 °C and LiCl wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) for 5 min at 4 °C. DNA was eluted in elution buffer (100 mM sodium bicarbonate and 1% SDS). Cross-links were reversed overnight at 65 °C. RNA and protein were digested with 0.2 mg ml−1 RNase A for 30 min at 37 °C followed by 0.2 mg ml−1 Proteinase K for 1 h at 55 °C. DNA was purified with phenol-chloroform extraction and isopropanol precipitation.
ChIP-seq libraries were prepared using the Rubicon ThruPLEX DNA-seq Kit from 1 ng of purified ChIP DNA or input DNA according to the manufacturer’s protocol.

tag: cell line

value: LS

tag: antibody

tag: sonication condition


title: Infant 6 - 2 months after vaccination

city: Farmington

first: Djamel

last: Nehar-Belaid

state: CONNECTICUT

address: 10 discovery drive

institute: THE JACKSON LABORATORY

library_source: transcriptomic single cell

data_processing:
Illumina basecall files (*.bcl) were converted to fastqs using cellranger v3.0.2 which uses bcl2fastq v2.17.1.14. FASTQ files were then aligned to hg19 genome and transcriptome using the cellranger v3.0.2 pipeline, which generates a gene - cell expression matrix.
For all single cell samples, R1 contains a 16bp cell barcode + 12bp UMI barcode.  For all samples, R2 contains a 91bp biological read.
Assembly: hg19
Supplementary files format and content: Transcriptomic counts matrices in Matrix Market CSR format.  Rows correspond to genes in the order provided in features.tsv.gz/features.tsv.gz and columns correspond to cell-barcodes in the order provided in barcodes.tsv.gz.

molecule: polyA RNA

source_name: BLOOD

extract_protocol:
10% DMSO + 90% FBS. PBMCs were thawed quickly at 37oC and into DMEM supplemented with 10% FBS. Cells exhibiting a viability rate less than 70% were excluded. Cells were quickly spun down at 400 g, for 10 min. Cells were washed once with 1 x PBS supplemented with 0.04% BSA and finally re-suspended in 1 x PBS with 0.04% BSA. Viability was determined using trypan blue staining and measured on a Countess FLII.
12,000 single cells were loaded into one lane of a 10X Genomics Chromium [Controller, X], targeting 6,000 barcoded single cells. Single cell capture, barcoding and library preparation were performed using the 10X Chromium platform, version [3, 3.1] chemistry. cDNA and libraries were checked for quality on Agilent 4200 Tapestation, quantified by KAPA qPCR, and sequenced on an Illumina NovaSeq 6000  targeting 100,000 raw read pairs per cell.
10x Genomics 3' single cell RNA-seq

tag: cell type

value: PBMCs

tag: time point

tag: age (months)


title: WT_6h_3

city: Chengdu

first: wenzheng

last: Pei

state: Sichuan Province

address: No. 211, Huimin Road, Fair Street, Wenjiang District, Chengdu, Sichuan Province

department: State Key Laboratory of Crop Gene Exploraion and Utilization in Southwest China

country: China

institute: Sichuan Agricultural University

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit. 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost 2 insertion cost 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using Cl _C genomic benchwork
Assembly: B73V4_ctg23
Supplementary files format and content: tab-delimited text file includes fpkm for each Sample
Supplementary files format and content: tab-delimited text file includes raw counts each Sample

molecule: total RNA

organism: Zea mays

source_name: maize seed

growth_protocol: Seeds of KN5585 and ereb92 mutants were sterilized with 10% NaClO solution for 20 min and washed 5 times with sterile water. After that, 30 seeds were evenly placed on the filter paper infiltrated with sterile water in the germination box.

extract_protocol:
RNA was extracted from the seeds of ereb92 knockout mutant lines and KN5585 using standard extraction methods
The starting RNA for library construction is total RNA, which is enriched with polyA tailed mRNA using Oligo (dT) magnetic beads. Subsequently, the resulting mRNA is randomly interrupted with divalent cations in the Fragmentation Buffer. Using fragmented mRNA as a template and random oligonucleotides as primers, the first strand of cDNA was synthesized in the M-MuLV reverse transcriptase system. Subsequently, the RNA strand was degraded using RNaseH, and the second strand of cDNA was synthesized using dNTPs as raw material in the DNA polymerase I system. The purified double stranded cDNA undergoes end repair, A-tailed addition, and sequencing connections. cDNA of approximately 370-420 bp was screened using AMPure XP beans, amplified by PCR, and the PCR product was purified again using AMPure XP beans, ultimately obtaining a library.

treatment_protocol: 28°C with dark condition,Samples were taken after 0 h and 6 h of imbibition.

tag: tissue

value: maize seed

value: maize seed cells

tag: genotype

value: WT

tag: treatment

value: 6h after imbibition


title: CnR_H3K4me3_NPC_rep2

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Library strategy: CUT&RUN
Sequencing reads were trimmed and filtered using version 0.4.5 of TrimGalore
Reads were aligned to human assembly hg19 with version 2.3.4.1 of bowtie2
Read density profiles were made using BEDTools and normalized to a depth of 10 million mapped fragments
Global peak atlas was made using version 1.6.1 of featureCounts
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files containing read densities normalized to a depth of 10 million mapped fragments

source_name: hPSC-derived neural progenitor cells

growth_protocol: WA09 (H9 ) human pluripotent stem cell (hPSC) line was cultured in Essential 8 on Vitronectin coated dishes and expanded by dissociation with 0.5mM EDTA. Neural induction was completed using the dual SMAD inhibition protocol and WNT inhibition on Matrigel coated dishes. hPSC for differentiation and neuronal progenitors were dissociated using Accutase. Neurons were maintained on poly-L-ornithine and Laminin/ Fibronectin coated plates in Neurobasal medium supplemented with B27, L-glutamine, BDNF, GDNF, cAMP, AA. DAPT was added to the neuronal maintenance medium from day20 to day30 of differentiation.

extract_protocol:
50,000 cells were freshly harvested and bound to concanavalin A-coated magnetic beads after an 8min incubation at RT on a rotator. Cell membranes were permeabilized with digitonin and the different antibodies were incubated overnight at 4°C on a rotator. Beads were washed and incubated with pA-MN. Ca2+-induced digestion occurred on ice for 30min and stopped by chelation. DNA was finally isolated using an extraction method with phenol and chloroform as described in Skene et al., 2018
Libraries were prepared for sequencing using standard Illumina protocols

value: neural progenitor cells

value: wild type

value: rabbit anti-H3K4me3 (ab8580, abcam)


title: LS_PRRX1_ChIP_cond1


title: Sample 4-CD8+CAR T cells

city: Beijing

first: Wang

last: Yao

address: No. 28, fuxing street

institute: Chinese general PLA hospital

data_processing:
The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).
The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
cutadapt-1.9 [1] (cutadapt.readthedocs.io/en/stable/)was used to remove the reads that contained adapter contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC v0.10.1 [2] (www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used hisat2-2.0.4 [3](ccb.jhu.edu/software/hisat2/)to map reads to the genome of Homo sapiens two rounds of purification.
transcripts that overlapped with known mRNAs and transcripts shorter than 200 bp were discarded. Then we utilized CPC0.9-r2 [6] (cpc2.cbi.pku.edu.cn/) with default parameters(cpc2 -i novel.fa -o cpc2.out) and CNCI2.0 [7] (wwww.bioinfo.org/software/cnci) with default parameters (CNCI.py -f novel.fa -o CNCI.result -p 1 -m ve -g novel.gtf -d genome.fa) to predict transcripts with coding potential. All transcripts with CPC score <-1 and CNCI score <0 were removed and remained transcripts were considered as lncRNAs.
Assembly: hisat2-2.0.4
Supplementary files format and content: tab-delimited text file includes fpkm values for each Sample

source_name: CAR T of DLBCL patient

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: patient id

value: CAR T cells

tag: cell subtype

value: CD8+CAR T cells

tag: time

value: Day 10

tag: disease state

value: CR patient


title: Infant 6 - Before vaccination

value: Before (baseline)


title: CnR_H3K4me3_NPC_rep1


title: Infant 6 - 1 week after  vaccination


title: WT_6h_2


title: WT_6h_1


title: GIMEN_PRRX1_ChIP_Input_cond2

value: GIMEN


title: Infant 5 - 2 months after vaccination


title: CnR_H3K4me3_D53_rep2

source_name: hPSC-derived neurons

value: neurons


title: GIMEN_PRRX1_ChIP_Input_cond1


title: Infant 5 - 1 week after  vaccination


title: CnR_H3K4me3_D53_rep1


title: GIMEN_PRRX1_ChIP_cond2

value: PRRX1 (Sigma, hpa051084)


title: WT_0h_2

value: 0h after imbibition


title: WT_0h_1


title: GIMEN_PRRX1_ChIP_cond1


title: CnR_H3K27me3_NPC_rep1

value: rabbit anti-H3K27me3 (9733, Cell Signaling Technologies)


title: Infant 4 - 2 months after vaccination

value: PBMCs


title: TT642_PRRX1_ChIP_Input_cond2

source_name: rhabdoid tumor cells


title: Infant 4 - 1 week after  vaccination


title: CnR_H3K27me3_D53_rep1


title: CnR_H3K27me3_D53_rep2


title: Infant 4 - Before vaccination


title: e92_6h_3

value: maize seed

value: maize seed cells

value: ereb92 Knockout


title: Infant 3 - 2 months after vaccination


title: e92_0h_3


title: TT642_PRRX1_ChIP_cond2


title: TT642_PRRX1_ChIP_cond1


title: Infant 3 - 1 week after  vaccination


title: WT_0h_3

value: WT


title: CnR_H3K27ac_NPC_rep1

value: neural progenitor cells

value: wild type

value: rabbit anti-H3K27ac (39133, Active Motif)


title: e92_0h_2


title: e92_6h_1

value: 6h after imbibition


title: CnR_H3K27ac_D53_rep2


title: CnR_H3K27me3_NPC_rep2


title: Infant 3 - Before vaccination


title: e92_0h_1


title: HDQP1_PRRX1_ChIP_Input_cond1

source_name: breast cancer cells


title: Infant 5 - Before vaccination


title: CnR_H3K27ac_D53_rep1


title: HDQP1_PRRX1_ChIP_cond2


title: Infant 2 - 2 months after vaccination


title: Infant 2 - 1 week after  vaccination


title: HDQP1_PRRX1_ChIP_cond1


title: BY4741, 20h PeAfpA 4 ug/ml, rep3

city: Paterna

first: Moisés

last: Giner Llorca

state: Valencia

address: Catedrático Agustín Escardino, 7

department: Department of Food Biotechnology

country: Spain

institute: Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC)

data_processing:
Library quality was assessed in an Agilent Bioanalyzer® (Agilent, USA) and sequenced single-end 75 base pairs in an Illumina Nextseq® sequencer (Illumina).
Reads were adapted and quality trimmed with Trimmomatic (v0.39).
Filtered reads were mapped to Saccharomyces cerevisiae reference genome with bowtie2 (v2.3.2)
The number of reads mapped to each gene was calculated with htseq-count (v0.9.0)
Genes for which Transcripts Per Millions (TPM) < 1 in at least one sample were removed.
Count data output was used for pairwise differential expression analysis with DESeq2.  Differentially expressed genes (DEGs) were identified using p-adjusted < 0.05.
Assembly: R64-2-1_20150113
Supplementary files format and content: tab-delimited text file include raw counts of sequencing reads in gene_id features (htseq-count output). Each row is a gene and each column is a sample

organism: Saccharomyces cerevisiae

source_name: mycelia

growth_protocol: 2x10^4 cfu/ml were inoculated in 100 ml Erlenmeyer flasks containing 10 mL of 5% Yeast, Peptone and Dextrose (YPD) for 20h at 30 ºC and 120 rpm

extract_protocol:
Total RNA was isolated following the protocol described by Garre et al. (2013) (doi: 10.1371/journal.pone.0061240)
Complementary DNA (cDNA) libraries were prepared with the TruSeq RNA Sample Preparation Kit v2 (Illumina)

treatment_protocol: Treatment 1: BY4741 grown without PeAfpA (control) during 20 h, 2: BY4741 grown with 1 μg/ml PeAfpA for 20 h; 3: BY4741 grown with 2 μg/ml PeAfpA for 20 h; 4: BY4741 grown with 4 μg/ml PeAfpA for 20 h

value: mycelia

tag: strain

value: Growth in YPD 5% + 4 ug/ml PeAfpA


title: e92_6h_2


title: UACC3199_PRRX1_ChIP_Input_cond2


title: CnR_H3K27ac_NPC_rep2


title: HDQP1_PRRX1_ChIP_Input_cond2


title: BY4741, 20h PeAfpA 4 ug/ml, rep2


title: Infant 2 - Before vaccination

value: Before (baseline)


title: BY4741, 20h PeAfpA 4 ug/ml, rep1


title: UACC3199_PRRX1_ChIP_Input_cond1


title: Infant 1 - 2 months after vaccination


title: Infant 1 - 1 week after  vaccination


title: UACC3199_PRRX1_ChIP_cond2


title: BY4741, 20h PeAfpA 2 ug/ml, rep3

value: Growth in YPD 5% + 2 ug/ml PeAfpA


title: BY4741, 20h PeAfpA 2 ug/ml, rep2


title: Infant 1 - Before vaccination


title: UACC3199_PRRX1_ChIP_cond1


title: BY4741, 20h PeAfpA 2 ug/ml, rep1


title: BY4741, 20h PeAfpA 1 ug/ml, rep3

value: Growth in YPD 5% + 1 ug/ml PeAfpA


title: MDAMB436_PRRX1_ChIP_Input_cond2


title: MDAMB436_PRRX1_ChIP_Input_cond1


title: BY4741, 20h PeAfpA 1 ug/ml, rep2


title: MDAMB436_PRRX1_ChIP_cond2

value: PRRX1 (Sigma, hpa051084)


title: MDAMB436_PRRX1_ChIP_cond1


title: MDAMB157_PRRX1_ChIP_Input_cond2


title: BY4741, control, rep3

value: Growth in YPD 5%


title: MDAMB157_PRRX1_ChIP_Input_cond1


title: Hs578_B2_scRNA

data_processing:
Single-cell RNA-seq data generated by 10x genomics are preprocessed using the Cell Ranger (https://www.10xgenomics.com/) to obtain the UMI (unique molecular identifier) counts for each gene in each indexed cell type.
To get a reliable single cell transcriptome dataset, we first exclude the cells with log proportion UMIs from mitochondrial genes >4 median absolute deviations (MADs) above the median, and then exclude cells with log detected genes <4 MADs below the median.
For downstream analyses, the filtered data were normalized by using Seurat v3 {Stuart, 2019, PMID: 31178118}, after removing genes expressed in fewer than 10 cells.
Batch 1 samples: Read 1 (R1) has a length of 26 bases corresponding to the 10x cell barcode's 16 bases, followed by the UMI's 10 bases. Read 2 (R2) has a length of 96 bases corresponding to biological RNA. Index 1 (I1) contains the sample index sequence information that is incorporated into the i7 index read (8-bp).
Batch 2 samples: Read 1 (R1) has a length of 28 bases corresponding to the 10x cell barcode's 16 bases, followed by the UMI's 12 bases. Read 2 (R2) has a length of 91 bases corresponding to biological RNA. Index 1 (I1) contains the sample index sequence information that is incorporated into the i7 index read (8-bp).
Assembly: hg19
Supplementary files format and content: Rdata file contains the raw UMI counts at the gene level.

growth_protocol: Cells were grown in their respective medias and plated in 15cm plates and collected during exponential growth by trypsinization.

extract_protocol:
Cells were collected by trypsinization and processed according to the 10xGenomics sample preparation protocol (Chromium Single Cell 3’ v3 Reagent Kit, 10xGenomics).
Libraries were constructed according to the 10xGenomics sample preparation protocol (Chromium Single Cell 3’ v3 Reagent Kit, 10xGenomics).

tag: sequencing batch

value: batch 2

tag: index


title: HCC38_B2_scRNA


title: SUM229_B2_scRNA


title: HDQP1_B2_scRNA


title: SUM185_B2_scRNA


title: HCC2185_B2_scRNA


title: MDAMB157_PRRX1_ChIP_cond2


title: BY4741, control, rep1


title: EMG3_B2_scRNA


title: MDAMB157_PRRX1_ChIP_cond1


title: BY4741, 20h PeAfpA 1 ug/ml, rep1


title: BY4741, control, rep2


title: MFM223_B2_scRNA


title: Hs578_PRRX1_ChIP_Input_cond2


title: HCC1937_B2_scRNA


title: HCC1806_B2_scRNA


title: Hs578_PRRX1_ChIP_Input_cond1


title: Hs578_PRRX1_ChIP_cond2


title: HCC1187_B2_scRNA


title: Hs578_PRRX1_ChIP_cond1


title: DU4475_B2_scRNA


title: UACC3199_H3K27ac_ChIP_Input

extract_protocol:
Cells (5 × 10^6) were fixed with 1% paraformaldehyde for 10 min at room temperature. DSG was then removed and replaced with fixing buffer (50 mM HEPES-NaOH (pH 7.5), 100 mM NaCl, 1mM EDTA) containing 1% paraformaldehyde (Electron Microscopy Sciences, 15714) and cross-linked for 10 min at 37 °C. Crosslinking was quenched by adding glycine to a final concentration of 0.125 M. The cells were washed with ice-cold PBS, harvested in PBS. The nuclear fraction was extracted by first resuspending the pellet in 1 ml of lysis buffer (50 mM HEPES-NaOH (pH 8.0), 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) for 10 min at 4 °C. Cells were pelleted and washed in 1 ml of wash buffer (10 mM Tris-HCL (pH 8.0), 200 mM NaCl, 1 mM EDTA) for 10 min at 4 °C. Cells were then pelleted and resuspended in 1 ml of shearing buffer (10 mM Tris-HCl (pH 8), 1 mM EDTA, 0.1% SDS) and sonicated in a Covaris sonicator. Lysate was centrifuged for 5 min at 14,000 rpm to purify the debris. Then 100 µl of 10% Triton X-100 and 30 µl of 5M NaCl were added. The sample was then incubated with 20 µl of Dynabeads Protein G (LifeTechnologies,10003D) for 1 h at 4 °C. Primary antibodies were added to each tube, and immunoprecipitation (IP) was conducted overnight at 4 °C. Cross-linked complexes were precipitated with Dynabeads Protein G for 2 hr at 4 °C. The beads were then washed in low salt wash buffer (20 mM Tris-HCl pH 8, 150 mM NaCl, 10 mM EDTA, and 1% SDS) for 5 min at 4 °C, high salt wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) for 5 min at 4 °C and LiCl wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) for 5 min at 4 °C. DNA was eluted in elution buffer (100 mM sodium bicarbonate and 1% SDS). Cross-links were reversed overnight at 65 °C. RNA and protein were digested with 0.2 mg ml−1 RNase A for 30 min at 37 °C followed by 0.2 mg ml−1 Proteinase K for 1 h at 55 °C. DNA was purified with phenol-chloroform extraction and isopropanol precipitation.
ChIP-seq libraries were prepared using the Rubicon ThruPLEX DNA-seq Kit from 1 ng of purified ChIP DNA or input DNA according to the manufacturer’s protocol.


title: CAL51_B2_scRNA


title: Normal human 3D epidermis,  + IL-36G_003

type: RNA

city: Fukuoka

first: Emi

last: Sato

state: Fukuoka

address: 7-45-1 Nanakuma, Jounan-ku

country: Japan

institute: Fukuoka University Faculty of Medicine

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: 3D epidermis, 50ng IL-36G, 6d

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA from 3-D skin constructs was extracted using ISOGEN II (Nippon Gene, Toyama, Japan) and purified using the SV Total RNA Isolation System (Promega, Wisconsin, WI, USA) according to the manufacturers’ instructions.

treatment_protocol: Normal human epidermal keratinocytes (NHEK) were obtained from Lonza (Basel, Switzerland) and cultured as previously described (E. Sato et al., J. Invest. Dermatol. 2016,136,1449.).3-D skin constructs were prepared as previously described( Li J, Sen GL. J Vis Exp 2015; 106:e53280.). Recombinant human IL-17A and IL-17C were dissolved in distilled water (dH2O). The human skin

value: epiderimis

value: normal human epidermal  keratinocytes (NHEK)


title: Normal human 3D epidermis,  + IL-36B_003

source_name: 3D epidermis, 50ng IL-36B, 6d


title: Normal human 3D epidermis,  + IL-36B_002


title: Normal human 3D epidermis,  + IL-36G_001


title: CAL148_B2_scRNA


title: Normal human 3D epidermis,  + IL-36G_002


title: Normal human 3D epidermis,  + IL-36B_001


title: SUM185_H3K27ac_ChIP_Input


title: BT549_B1_scRNA

extract_protocol:
Cells were collected by trypsinization and processed according to the 10xGenomics sample preparation protocol (Chromium Single Cell 3’ v2 Reagent Kit, 10xGenomics).
Libraries were constructed according to the 10xGenomics sample preparation protocol (Chromium Single Cell 3’ v2 Reagent Kit, 10xGenomics).

value: batch 1


title: genomic DNA from 4013-TG6 (TNBC PDX)

type: genomic

description: genomic DNA from 4013-TG6

hyb_protocol: hybridisation to Illumina Infinium Human Methylation450K array was performed using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Data were preprocessed using the R package minfi {PMID: 24478339}, using the function preprocessIllumina with default parameters.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

growth_protocol: Tumors were induced by bilateral orthotopic mammary fat pad injection of 2 × 10^6 PDX cells suspended in 50 μl total volume of 50% DMEM media and 50% of Matrigel

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen ALLPrep according to standard instructions

tag: pdx model id


title: genomic DNA from 4195-TG5 (TNBC PDX)

description: genomic DNA from 4195-TG5


title: genomic DNA from IDC50X (TNBC PDX)

description: genomic DNA from IDC50X


title: SUM149_H3K27ac_ChIP_Input

tag: cell line


title: genomic DNA from 3936-TG5 (TNBC PDX)

description: genomic DNA from 3936-TG5


title: HCC1937_B1_scRNA


title: Normal human 3D epidermis,  + IL-36A_003

source_name: 3D epidermis, 50ng IL-36A, 6d


title: genomic DNA from HCI-002 (TNBC PDX)

description: genomic DNA from HCI-002


title: SUM229_H3K27ac_ChIP_Input

tag: antibody


title: HCC3153_B1_scRNA


title: genomic DNA from 2147-TG5 (TNBC PDX)

description: genomic DNA from 2147-TG5


title: SUM102_H3K27ac_ChIP_Input


title: genomic DNA from HCI-001 (TNBC PDX)

description: genomic DNA from HCI-001


title: genomic DNA from 4272-TG5 (TNBC PDX)

description: genomic DNA from 4272-TG5


title: genomic DNA from T272X (TNBC PDX)

description: genomic DNA from T272X


title: genomic DNA from HCI-009 (TNBC PDX)

description: genomic DNA from HCI-009


title: genomic DNA from BCM-3611 (TNBC PDX)

description: genomic DNA from BCM-3611


title: genomic DNA from UACC3199 (TNBC Cell line)

description: genomic DNA from UACC3199


title: HCC1806_B1_scRNA


title: Normal human 3D epidermis,  + IL-36A_001


title: PMC42_H3K27ac_ChIP_Input


title: genomic DNA from BCM-2665 (TNBC PDX)

description: genomic DNA from BCM-2665


title: Hs578_B1_scRNA


title: SUM1315_H3K27ac_ChIP_Input


title: MFM223_H3K27ac_ChIP_Input


title: Normal human 3D epidermis, control_002

source_name: 3D epidermis

value: control


title: Normal human 3D epidermis, control_003


title: genomic DNA from 5998-TG5 (TNBC PDX)

description: genomic DNA from 5998-TG5


title: Normal human 3D epidermis, control_001


title: genomic DNA from SUM159 (TNBC Cell line)

description: genomic DNA from SUM159


title: MDAMB231_B1_scRNA


title: BAT_rep2

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

description:
PPG4
snRNA-seq

data_processing:
Reads were aligned to the rat reference genome Rnor_6.0 (assembly GCA_000001895.4) using the 10x CellRanger v7.1.0 pipeline.
Commonly used python packages (i.e., numpy, pandas, matplotlib) were then used to do additional quality control, preprocessing, analyzing, and visualization of the data. Any nuclei that had less than 200 detected genes or genes that were detected in less than 3 cells were discarded. Cells that were found to be expressing greater than 10% mitochondrial genes were also discarded.
Ambient RNA and doublet removal was done using SoupX and scDblFinder, respectively.
To reduce technical variation between samples we did batch correction with the python package scVI.
Assembly: Rnor_6.0 (assembly GCA_000001895.4)
Supplementary files format and content: Matrix and tab-delimited files (barcodes.tsv, features.tsv, matrix.mtx).

molecule: nuclear RNA

organism: Rattus norvegicus

source_name: subscapular brown adipose tissue

extract_protocol:
Nuclei from frozen minced aortic perivascular adipose tissue or subscapular brown adipose tissue (~ 50 mg) were isolated with the Chromium Nuclei Isolation Kit (10X Genomics) according to manufacturer’s recommended protocol (CG000505, RevA), with a final resuspension in 50 µL Wash and Resuspension Buffer.
The 10X Chromium Next GEM Single Cell 3’ Reagent Kit v 3.1 (Dual Index) was used with a targeted cell recovery of 10,000 according to manufacturer’s recommended protocol (CG000315, Rev D).

value: subscapular brown adipose tissue

value: brown adipose tissue

value: SS/HsdMcwiCrl

tag: age

value: week

tag: Sex

value: male

value: degree celsius

value: percent

value: polycarbonate cage

tag: bedding

value: aspen chip

tag: water

value: tap water

value: Teklad global 18% protein

value: Teklad

tag: disease

value: normal

value: Snap Frozen

value: Charles River Laboratory

value: Pentobarbital


title: genomic DNA from HCI-010 (TNBC PDX)

description: genomic DNA from HCI-010


title: genomic DNA from BCM-3107 (TNBC PDX)

description: genomic DNA from BCM-3107


title: PMC42_B1_scRNA

value: batch 1


title: taPVAT_rep2

description:
PPG3
snRNA-seq

source_name: thoracic aorta perivascular adipose tissue

tag: tissue

value: adipose tissue


title: Normal human 3D epidermis,  + IL-36A_002

value: epiderimis

value: normal human epidermal  keratinocytes (NHEK)

tag: treatment


title: MDAMB468_H3K27ac_ChIP_Input


title: CAL51_B1_scRNA


title: BAT_rep1

description:
PPG2
snRNA-seq

value: subscapular brown adipose tissue

value: brown adipose tissue

value: SS/HsdMcwiCrl

value: week


title: genomic DNA from SUM185 (TNBC Cell line)

description: genomic DNA from SUM185


title: genomic DNA from SUM229 (TNBC Cell line)

description: genomic DNA from SUM229


title: MDAMB157_H3K27ac_ChIP_Input


title: MDAMB436_H3K27ac_ChIP_Input


title: taPVAT_rep1

description:
PPG1
snRNA-seq

value: thoracic aorta perivascular adipose tissue

value: male

value: degree celsius

value: percent

value: polycarbonate cage


title: SUM1315_B1_scRNA


title: Hs578_H3K27ac_ChIP_Input


title: Her7-YFP, negative control

city: Lausanne

first: Andrew

middle: Charles

last: Oates

address: Station 19

department: SV IBI

country: Switzerland

institute: EPFL

data_processing:
library strategy: Cut&Tag
Paired reads were quality checked by FastQC (version 0.11.9) and aligned to the zebrafish genome assembly (GRCz.11 toplevel, Ensembl release 109) using Bowtie2 (version 2.5.1)
The resulting sam files were then converted into bam files, sorted and indexed using samtools (version 1.17) and visualized with the Integrated Genomics Viewer (IGV version 2.16.0).
Overlapping peak between the biological replicates was done using bedtools intersect (version 2.31.0)
The peak calling was performed, on the intersection between both replicates, using macs2 callpeak (version 2.2.7) with the following parameters: -g 1.5e+9 -f BAMPE -q 0.01 --keep-dup all.
Assembly: GRCz.11 toplevel, Ensembl release 109
Supplementary files format and content: bigWig, narrowPeak

organism: Danio rerio

source_name: whole embryo

extract_protocol:
The dissociated single cells were then washed three times and bound to activated Concanavalin A-coated magnetic beads. Cells were resuspended into 100 µl of antibody buffer (wash buffer containing 0.05% (wt/vol) digitonin (Dig), 2 mM EDTA and 0.1 % BSA). Antibody at 1mg.ml was added to a final concentration of 1:50 and cells were incubated overnight at 4°C on a nutator. The next day, cells were resuspended in 100 µl of Dig wash buffer (wash buffer containing 0.05% (wt/vol) Dig) containing the secondary antibody at a final concentration of 1:100 and incubated for 60min at room temperature. After incubation, beads/cells were washed three times with Dig-wash buffer to remove unbound antibody, followed by resuspension and incubation of beads/cells in 100 µl Dig-300 wash buffer (Dig wash buffer at 300 mM NaCl) with pA-Tn5 adapter complex (1:200 dilution), at room temperature for 1 h on a nutator. After two washes with Dig-300 wash buffer, beads/cells were resuspended in 100 µl tagmentation buffer (Dig-300 buffer containing 10mM Mgcl2) and incubated at 37°C for 1 hour. Tagmentation reaction was stopped by adding exactly 3.3µl 0.5M EDTA, 1µl 10% SDS and 1µl 20mg.ml Proteinase K followed by 60 min incubation at 55°C shaking at full speed (1300 rpm) to solubilize DNA fragments. Beads/cells were placed on a magnetic stand and the supernatant containing DNA fragments was transferred into a new tube for DNA purification (MinElute Qiagen, 28004).
Cut&Tag libraries for next generation sequencing were prepared by PCR reaction using the NEBnext HIFI 2x PCR master mix and indexed i5 and i7 10µM primers as previously described48. Samples were then cleaned up using the DNA Clean and concentrator-5 kit from Zymo. Libraries were pooled together and paired-end 76bp sequencing was done using the Illumina NextSeq 500 instrument for Tg(her1:her1-YFP) samples and the MiSeq instrument for Tg(her1:nls-mkate2,Her7:her7-YFP) samples.

value: whole embryo

tag: genotype


title: EMG3_dH3_dox_day_21_RNA

data_processing:
Raw RNA-seq reads were aligned to version hg19 of the human genome and gene count and FPKM values were obtained using the VIPER pipeline {Cornwell, 2018, PMID: 29649993}, with parameters (stranded: true, library_type: ‘fr-firststrand’, filter_mirna: true).
Assembly: hg19
Supplementary files format and content: counts table and FPKM table

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Mini Kit.
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500 ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to the manufacturer’s protocols.

treatment_protocol: cells were treated with 3ug/ml doxycycline to induce shRNA expression

tag: parental cell line

tag: prrx1 lentiviral vectors/recombinat dna

tag: condition

value: doxycycline


title: Her7-YFP, anti-H2AZ


title: genomic DNA from SUM149 (TNBC Cell line)

description: genomic DNA from SUM149


title: genomic DNA from SUM1315 (TNBC Cell line)

description: genomic DNA from SUM1315


title: EMG3_wt_no_dox_day_21_RNA

value: wild type

value: no doxycycline


title: Her7-YFP, anti-GFP rep2

value: anti-GFP


title: EMG3_dH3_no_dox_day_21_RNA


title: HDQP1_H3K27ac_ChIP_Input


title: HCC38_H3K27ac_ChIP_Input


title: Her7-YFP, anti-GFP rep1


title: EMG3_wt_dox_day_21_RNA


title: genomic DNA from PMC42 (TNBC Cell line)

description: genomic DNA from PMC42


title: HCC3153_H3K27ac_ChIP_Input


title: HCC70_H3K27ac_ChIP_Input


title: EMG3_dH3_no_dox_day_14_RNA


title: mosquito midgut -adpR KD, rep4

city: New Haven

first: Yu-Min

last: Chuang

state: CT

address: 1 Gilbert St TAC S410

department: Infectious disease

institute: Yale University

description: Sample 8

data_processing:
RNA samples were then submitted for library preparation using TruSeq (Illumina, San Diego, CA, USA)
Sequenced using Illumina HiSeq 2500 by paired-end sequencing
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
The transcript data was mapped with the A. gambiae PEST genome (AgamP4.13) downloaded from VectorBase (https://vectorbase.org/vectorbase/app/) and indexed using the kallisto-index.
Assembly: AgamP4.13
Supplementary files format and content: tpm-values-all-samples.txt

organism: Anopheles gambiae

source_name: midgut -adpR KD

extract_protocol:
Two days after a blood meal, the mosquitoes were collected for midgut dissection. Total RNA was purified.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: dsRNA (dsAdpR and dsGluc) microinjected A. gambiae mosquitoes were fed on P. berghei-infected Swiss Webster mice.

tag: strain

value: midgut

value: dsadpR injection

value: adiponectin receptor knockdown


title: mosquito midgut -adpR KD, rep3

description: Sample 7


title: HCC2185_H3K27ac_ChIP_Input


title: EMG3_dH3_dox_day_14_RNA


title: mosquito midgut -adpR KD, rep2

description: Sample 6


title: HCC1937_H3K27ac_ChIP_Input


title: genomic DNA from SUM102 (TNBC Cell line)

description: genomic DNA from SUM102


title: EMG3_wt_no_dox_day_14_RNA


title: HCC1806_H3K27ac_ChIP_Input


title: mosquito midgut -adpR KD, rep1

description: Sample 5


title: HCC1569_H3K27ac_ChIP_Input


title: HCC1395_H3K27ac_ChIP_Input


title: EMG3_dH3_no_dox_day_7_RNA


title: mosquito midgut -control, rep3

description: Sample 3

source_name: midgut -control

value: dsGluc injection

value: control


title: EMG3_dH3_dox_day_7_RNA


title: EMG3_wt_dox_day_14_RNA


title: mosquito midgut -control, rep2

description: Sample 2


title: HCC1143_H3K27ac_ChIP_Input


title: mosquito midgut -control, rep1

description: Sample 1


title: genomic DNA from MDAMB468 (TNBC Cell line)

description: genomic DNA from MDAMB468


title: EMG3_wt_no_dox_day_7_RNA


title: EMG3_wt_dox_day_7_RNA


title: genomic DNA from MDAMB231 (TNBC Cell line)

description: genomic DNA from MDAMB231


title: genomic DNA from MDAMB157 (TNBC Cell line)

description: genomic DNA from MDAMB157


title: FCIBC02_H3K27ac_ChIP_Input


title: SUM185_dH3_no_dox_day_21_RNA


title: genomic DNA from MDAMB436 (TNBC Cell line)

description: genomic DNA from MDAMB436


title: EMG3_H3K27ac_ChIP_Input


title: SUM185_dH3_dox_day_21_RNA


title: DU4475_H3K27ac_ChIP_Input


title: PiPSC_clone3_rep4

city: Calgary

first: Li-Fang (Jack)

last: Chu

state: Alberta

address: 2500 University Drive NW

country: Canada

institute: University of Calgary

description: ec.tsv, tpm.tsv

data_processing:
Basecalls were performed using illuminas bcl2fastq's version 2.17 for the Hiseq 3000 machine and NextSeq Demultiplex performed with native Dragen 3.8.4
Sequences were filtered and trimmed to remove low quality reads, adaptors, and other sequencing artificats
Sequencing reads were mapped to the Sus Scrofa Assembly Sscrofa11.1 (GCA_000003025.6) with bowtie 1.2.3
Gene expected couts were calculated using RSEM 1.2.3
Assembly: Sus Scrofa Assembly Sscrofa11.1 (GCA_000003025.6)
Supplementary files format and content: Processed data files are both in tab-seperated value format and contain expected counts (ec.tsv) and transcripts per million (tpm.tsv)

organism: Sus scrofa

source_name: PiPSC clone3

growth_protocol: Growth or differentiation medium as described in the assocaited study.

extract_protocol:
Total RNA are extracted using QIAGEN Rneasy Plus Mini Kit
The ligation-mediated sequencing protocol was used to prepare and index cDNA libraries (Hou et al 2015)

value: PiPSC clone3

tag: cell type

value: Pig iPS cells

tag: time

tag: differentiation status

value: PiPS-EP5 minusPD minusA83 c18 p15


title: PiPSC_clone3_rep2

description: ec.tsv, tpm.tsv

tag: cell line


title: CAL851_H3K27ac_ChIP_Input

tag: antibody


title: SUM185_wt_no_dox_day_21_RNA


title: genomic DNA from Hs578 (TNBC Cell line)

description: genomic DNA from Hs578


title: PiPSC_clone3_rep3

description: ec.tsv, tpm.tsv


title: genomic DNA from HDQP1 (TNBC Cell line)

description: genomic DNA from HDQP1


title: SUM185_wt_dox_day_21_RNA


title: CAL148_H3K27ac_ChIP_Input


title: SUM185_dH3_no_dox_day_14_RNA


title: CAL120_H3K27ac_ChIP_Input


title: PiPSC_clone2_rep3

description: ec.tsv, tpm.tsv

source_name: PiPSC clone2

value: PiPSC clone2

value: PiPS-EP5 minusPD minusA83 c12 p10


title: SUM185_dH3_dox_day_14_RNA


title: genomic DNA from HCC3153 (TNBC Cell line)

description: genomic DNA from HCC3153


title: genomic DNA from HCC38 (TNBC Cell line)

description: genomic DNA from HCC38


title: SUM185_wt_no_dox_day_14_RNA


title: UACC3199_H3K27ac_ChIP

value: anti-H3K27ac (Diagenode, C15410196)


title: genomic DNA from HCC70 (TNBC Cell line)

description: genomic DNA from HCC70


title: mosquito midgut -control, rep4

description: Sample 4


title: PiPSC_clone3_rep1

description: ec.tsv, tpm.tsv


title: SUM185_wt_dox_day_14_RNA


title: PiPSC_clone2_rep1

description: ec.tsv, tpm.tsv


title: genomic DNA from HCC1569 (TNBC Cell line)

description: genomic DNA from HCC1569


title: SUM229_H3K27ac_ChIP


title: genomic DNA from MFM223 (TNBC Cell line)

description: genomic DNA from MFM223


title: genomic DNA from HCC1937 (TNBC Cell line)

description: genomic DNA from HCC1937


title: BT549_H3K27ac_ChIP_Input


title: SUM185_dH3_no_dox_day_7_RNA


title: genomic DNA from HCC2185 (TNBC Cell line)

description: genomic DNA from HCC2185


title: PiPSC_clone1_rep4

description: ec.tsv, tpm.tsv

source_name: PiPSC clone1

value: PiPSC clone1

value: PiPS-EP1 minusPD c4 p11


title: SUM185_H3K27ac_ChIP


title: HCC1187_H3K27ac_ChIP_Input


title: genomic DNA from HCC1806 (TNBC Cell line)

description: genomic DNA from HCC1806


title: plasma exosomes from 5 CCS patients, CCS group sample 3

first: Xiaoyan

last: Liu

address: 8 Gongren Tiyuchang Nanlu, Chaoyang District

institute: Beijing Chao-Yang Hospital

data_processing:
Illumina Bcl2FastQ software used for basecalling.
Raw reads were treated with Trimmomatic tools(V0.36) to remove adapters. Following reads quality control:Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15, drop reads which are less than 35% of initiation read length. Then reads quality was inspected using the FastQC software then output statistical result.
Tophat-fusion were used to detect circRNAs，According to the splicing sequence GT/AG, the circRNAs is accurately identified after the initial results are corrected. Reads were mapped to human reference genome GRCh37/hg19 (http://genome.ucsc.edu/) by Tophat, respectively.
Back-spliced junction reads identified in Tophat-fusion were combined and scaled to RPM (Reads Per Million mapped reads). The total number of reads spanning back-spliced junctions was used as an absolute measure of circRNA abundance.
To estimate the relative expression of a circRNA, we counted the total number of reads mapped to the human reference genome in each sample and normalized the number of reads spanning the back-spliced junction to RPM.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include count values for each Sample
Supplementary files format and content: tab-delimited text files include RPM values for each Sample

source_name: plasma

extract_protocol:
Plasma exosomal RNA were extracted using a commercial kit (Qiagen Inc, 217184, Dusseldorf, Germany) according to the manufacturer's instructions and quantified from the OD260/280 read by NanoDrop ND-1000 instrument.
RNA libraries for RNA seq were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina following the manufacture's protocol.

value: plasma

tag: group

value: chronic coronary syndrome


title: genomic DNA from EMG3 (TNBC Cell line)

description: genomic DNA from EMG3


title: PiPSC_clone1_rep3

description: ec.tsv, tpm.tsv


title: plasma exosomes from 5 CCS patients, CCS group sample 2


title: SUM149_H3K27ac_ChIP


title: SUM185_wt_no_dox_day_7_RNA

value: wild type

value: no doxycycline


title: plasma exosomes from 5 CCS patients, CCS group sample 1


title: SUM185_dH3_dox_day_7_RNA

value: doxycycline


title: SUM185_wt_dox_day_7_RNA


title: genomic DNA from HCC2157 (TNBC Cell line)

description: genomic DNA from HCC2157


title: genomic DNA from HCC1143 (TNBC Cell line)

description: genomic DNA from HCC1143


title: PiPSC_clone1_rep2

description: ec.tsv, tpm.tsv


title: SUM102_H3K27ac_ChIP


title: SUM1315_H3K27ac_ChIP


title: genomic DNA from DU4475 (TNBC Cell line)

description: genomic DNA from DU4475


title: plasma exosomes from 5 NCCP patients, control group sample 3


title: genomic DNA from HCC1187 (TNBC Cell line)

description: genomic DNA from HCC1187


title: pFib_rep1

description: ec.tsv, tpm.tsv

source_name: Pig fibroblasts

value: Pig fibroblasts


title: plasma exosomes from 5 NCCP patients, control group sample 2


title: pFib_rep4

description: ec.tsv, tpm.tsv


title: plasma exosomes from 5 NCCP patients, control group sample 1


title: PMC42_H3K27ac_ChIP


title: pFib_rep3

description: ec.tsv, tpm.tsv


title: MFM223_H3K27ac_ChIP


title: MFM223_dH3_dox_day_21_RNA


title: pFib_rep2

description: ec.tsv, tpm.tsv


title: MFM223_dH3_no_dox_day_21_RNA


title: MFM223_wt_no_dox_day_21_RNA


title: MDAMB468_H3K27ac_ChIP


title: genomic DNA from HCC1395 (TNBC Cell line)

description: genomic DNA from HCC1395


title: pNPC_day24_rep3

description: ec.tsv, tpm.tsv

source_name: PiPSC clone 8

value: PiPSC clone 8

value: Day 24

value: PiPSC8 differentiated to neuro progenitor cells at day24


title: MFM223_wt_dox_day_21_RNA

source_name: breast cancer cells


title: genomic DNA from CAL148 (TNBC Cell line)

description: genomic DNA from CAL148


title: N2, CeMbio, neomycin, 3

city: Albany

first: Dan

middle: Jinwon

last: Kim

state: CA

address: 675 kula gulf way

department: Integrative Biology

institute: University of California, Berkeley

data_processing:
Kallisto was employed on both paired end reads to identify and quantify transcripts, and DESeq2 was used to identify differentially expressed genes, using false discovery rate corrected p-value cutoff of 0.05
Assembly: WBcel235
Supplementary files format and content: tab-separate values files include TPM values for each sample

organism: Caenorhabditis elegans

source_name: metagenomics

growth_protocol: Germ-free and synchronized populations of arrested L1 larvae were obtained by bleaching gravid worms to release eggs, hatching eggs on nematode growth medium (NGM) without food, and then raising worms to  Gravid at 20°C on plates with bacterial monocultures or communities.

extract_protocol:
RNA was extracted using with Trizol (Invitrogen). Genomic DNA contamination was removed using Turbo DNase (Qiagen).
Messenger RNA was purified from total RNA using poly-T oligo attached magnetic beads, followed by cDNA synthesis from mRNA fragments using random hexamer primers prepared by Novogene

treatment_protocol: Gravid worms were washed three times with 15mL filtered M9 and transferred to NGM plates seeded with E. coli with or without  0.25 mg/ml neomycin for 8 hours, following which 100-150 worms (per group, per replicate) were washed off, washed three times with M9 solution and used for RNA extraction

value: metagenomics

value: WT

value: 0.25ml/mg Neomycin


title: N2, CeMbio, neomycin, 2


title: genomic DNA from CAL851 (TNBC Cell line)

description: genomic DNA from CAL851


title: pNPC_day24_rep2

description: ec.tsv, tpm.tsv

value: Pig iPS cells


title: MFM223_dH3_no_dox_day_14_RNA


title: MDAMB436_H3K27ac_ChIP


title: pNPC_day24_rep1

description: ec.tsv, tpm.tsv


title: MDAMB157_H3K27ac_ChIP


title: N2, CeMbio, neomycin, 1


title: N2_CeMbio, no antibiotic,2


title: genomic DNA from FCIBC02 (TNBC Cell line)

description: genomic DNA from FCIBC02


title: HDQP1_H3K27ac_ChIP


title: Hs578_H3K27ac_ChIP


title: N2_CeMbio, no antibiotic,3


title: MFM223_wt_dox_day_14_RNA


title: pCardio_day9_rep2

description: ec.tsv, tpm.tsv

value: Day 9

value: PiPSC8 differentiated to beating cardiomyocytes at day9


title: N2_CeMbio, no antibiotic,1


title: MFM223_dH3_dox_day_14_RNA


title: HCC70_H3K27ac_ChIP

value: anti-H3K27ac (Diagenode, C15410196)


title: MFM223_dH3_no_dox_day_7_RNA


title: genomic DNA from CAL120 (TNBC Cell line)

description: genomic DNA from CAL120


title: N2,OP50,neomycin,3


title: pEC_day6_rep3

description: ec.tsv, tpm.tsv

value: Day 6

value: PiPSC8 differentiated to endothelial cells at day6


title: HCC38_H3K27ac_ChIP


title: genomic DNA from CAL51 (TNBC Cell line)

description: genomic DNA from CAL51


title: pCardio_day9_rep1

description: ec.tsv, tpm.tsv


title: HCC3153_H3K27ac_ChIP


title: pCardio_day9_rep3

description: ec.tsv, tpm.tsv


title: MFM223_dH3_dox_day_7_RNA


title: N2,OP50,neomycin,2


title: PiPSC_clone2_rep4

description: ec.tsv, tpm.tsv

value: PiPSC clone2

value: PiPS-EP5 minusPD minusA83 c12 p10


title: genomic DNA from BT549 (TNBC Cell line)

description: genomic DNA from BT549


title: MFM223_wt_no_dox_day_7_RNA

value: wild type

value: no doxycycline


title: pEC_day6_rep2

description: ec.tsv, tpm.tsv


title: N2,OP50,neomycin,1


title: HCC2185_H3K27ac_ChIP


title: PiPSC_clone2_rep2

description: ec.tsv, tpm.tsv


title: N2,OP50,no antibiotic,3


title: MFM223_wt_dox_day_7_RNA

value: doxycycline


title: HCC1937_H3K27ac_ChIP


title: pSomite_day3_rep3

description: ec.tsv, tpm.tsv

value: PiPSC clone 8

value: Day 3

value: PiPSC8 differentiated to somite with S2LDN medium at day3


title: N2,OP50,no antibiotic,2

value: metagenomics


title: pSomite_day3_rep1

description: ec.tsv, tpm.tsv


title: HCC3153_dH3_dox_day_21_RNA


title: pEC_day6_rep1

description: ec.tsv, tpm.tsv


title: HCC1395_H3K27ac_ChIP


title: HCC1569_H3K27ac_ChIP


title: HCC3153_wt_no_dox_day_21_RNA


title: O157:H7 infected RSE_3

city: Gainesville

first: Subhashinie

last: Kariyawasam

state: Florida

address: 1945 SW 16th Ave

department: Comparative, Diagnostic, and Population Medicine

institute: University of Florida

data_processing:
CLC Genomics workbench v.23.0.4
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC-genomics bench work
Read count extraction and normalization were performed using CLC genomics workbench
Supplementary files format and content: fataq.gz file includes raw counts for each sample
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

organism: Escherichia coli

source_name: Infection

growth_protocol: CCD 841 (ATCC CRL-1790)were grown at 37°C with 5% CO2, in Eagle's Minimum Essential Medium. RSE cells were isolated from healthy cattle and maintained at 37°C with 5% CO2 in Dulbecco's Modified Eagle's Medium (DMEM)

extract_protocol:
Total RNA was extracted using RiboPure™ RNA Purification Kit (Invitrogen™). Bacterial RNA was separated from total RNA via mammalian RNA depletion using MICROBEn-rich™ Kit (Invitrogen™). Host depleted samples further processed for rRNA depletion to enrich bacterial mRNA using using MICROBExpress™ Bacterial mRNA Enrichment Kit (Invitrogen™). All steps were carried out according to the manufacturer’s instructions. Quality and concentration of RNA samples in each step was measured using NanoDrop™ 2000/2000c Spectrophotometer (Thermo Scientific™).
Library preparation was done using NEBNext Ultra RNA Library Prep Kit for Illumina as per manufacturer’s recommendations

treatment_protocol: After reaching confluency of 106 cells, E. coli O157:H7 were added from overnight culture at a MOI of 20 to each cell lines and incubated 6 hours

tag: infection

value: BovineRecto anal junction squamous epithelial

value: WT


title: N2,OP50,no antibiotic,1


title: HCC1806_H3K27ac_ChIP

data_processing:
Reads were aligned to hg19 with BWA-mem v0.7.17 (http://bio-bwa.sourceforge.net).
Duplicates were removed using Picard MarkDuplicates v2.18.17 (http://broadinstitute.github.io/picard/), with parameters (REMOVE_DUPLICATES=TRUE, VALIDATION_STRINGENCY=LENIENT).
ChIP-signal was quantified and peaks were called using MACS2 v2.1.2 {Zhang, 2008, PMID:18798982}, with parameters (--SPMR -B --keep-dup=1 --extsize=146 --nomodel, -q 0.05).
Assembly: hg19
Supplementary files format and content: bigwig of signals & bed files of called peaks


title: HCC3153_wt_dox_day_21_RNA


title: pPSM_day2_rep2

description: ec.tsv, tpm.tsv

value: Pig iPS cells

value: Day 2

value: PiPSC8 differentiated to presomitic mesoderm with S1LDN medium at day2


title: HCC3153_dH3_no_dox_day_14_RNA


title: pPSM_day2_rep3

description: ec.tsv, tpm.tsv


title: pSomite_day3_rep2

description: ec.tsv, tpm.tsv


title: HCC1187_H3K27ac_ChIP

value: anti-H3K27ac (Diagenode, C15410196)


title: HCC1143_H3K27ac_ChIP


title: O157:H7 infected RSE_2


title: O157:H7 infected RSE_1


title: HCC3153_dH3_no_dox_day_21_RNA


title: pPSM_day2_rep1

description: ec.tsv, tpm.tsv


title: FCIBC02_H3K27ac_ChIP


title: HCC3153_dH3_dox_day_14_RNA


title: O157:H7 infected CCD841_3

value: human colonic epithelial cell


title: O157:H7 infected CCD841_2


title: pMesendoderm_day1_rep3

description: ec.tsv, tpm.tsv

value: Day 1

value: PiPSC8 differentiated to primitive streak/mesendoderm with E8A100ch3 at day1


title: pMesendoderm_day1_rep2

description: ec.tsv, tpm.tsv


title: HCC3153_wt_dox_day_14_RNA


title: EMG3_H3K27ac_ChIP


title: O157:H7 infected CCD841_1


title: pMesendoderm_day1_rep1

description: ec.tsv, tpm.tsv


title: O157:H7 in media_3


title: CAL148_H3K27ac_ChIP


title: HCC3153_dH3_dox_day_7_RNA


title: PiPSC_day0_rep2

description: ec.tsv, tpm.tsv

value: Day 0

value: undifferentiated PiPSC8 (MEF-feeder removed.)


title: CAL851_H3K27ac_ChIP


title: HCC3153_wt_no_dox_day_7_RNA

value: wild type

value: no doxycycline


title: PiPSC_day0_rep3

description: ec.tsv, tpm.tsv

value: PiPSC clone 8


title: CAL120_H3K27ac_ChIP


title: O157:H7 in media_2


title: HCC3153_wt_dox_day_7_RNA

value: doxycycline


title: PiPSC_day0_rep1

description: ec.tsv, tpm.tsv


title: O157:H7 in media_1


title: BT549_H3K27ac_ChIP


title: TFH, KO, rep1

status: Public on Nov 08 2023

city: Pohang

first: Jiho

last: Park

address: 77, Cheongam-ro

country: South Korea

institute: POSTECH

data_processing:
Reads for each sample were mapped to the reference genome (mm10) by Tophat (v2.0.13).
The aligned were added to Cuffdiff (v2.2.0) to report differentially expressed genes.
For library normalization and dispersion estimation, geometric and pooled methods were applied.
The FPKM (Fragments Per Kilobase of transcript per Million Mapped reads) value is used as a normalization value.
Assembly: mm10
Supplementary files format and content: List of differentially expressed genes (DEGs) between WT and ETV5-deficient TFH cells are presented in DEG_data.xlsx file. KO versus WT fold change, p-value and FPKM value are shown in DEG_data.xlsx file.

organism: Mus musculus

source_name: Spleen

extract_protocol:
TFH cells (CD4+CD44+CXCR5+PD-1+) from the spleen of WT and Etv5f/f;Cd4-Cre mice were sorted by a MoFlo-XDP (Beckman Coulter). Total RNA was extracted with TRIzol (GeneAll) according to the manufacturer's instruction.
The library for RNA sequencing was generated using the Truseq stranded mRNA library prep kit (Illumina)

value: Spleen

value: TFH cell (CD4+CD44+CXCR5+PD-1+)


title: HCC3153_wt_no_dox_day_14_RNA


title: TFH, WT, rep2


title: TFH, WT, rep1


title: DU4475_H3K27ac_ChIP


title: HCC3153_dH3_no_dox_day_7_RNA


title: FP3O

city: Fort Collins

first: Ana-Clara

last: Bobadilla

state: Colorado

address: 1350 Centre Ave

department: Biomedical Sciences

institute: Colorado State University

description: Female Prefrontal Cortex Overlapping Replicate 3

data_processing:
Raw sample files in fastq form were trimmed for Takara library prep adaptations using the "CutAdapt" R package, followed by FASTQC analysis to confirm proper trimming. Samples were mapped to mouse transcriptome (grc39) using "Salmon" R package. Output counts from mapping were further normalized and analyzed for differentially expressed genes (DEG) utilizing "tximport" and "DESeq2" R packages.
Assembly: grc39
Supplementary files format and content: tab-delimited text files with ensemble gene name, length, effective length, TPM, numreads

source_name: Brain

extract_protocol:
Whole brains were extracted from euthanized mice (5% isoflurane exposure followed by cervical dislocation) and incubated for 5 minutes on ice in cellular stabilizing solution: 45% HEBG medium (2% 50X B27 (Thermo Fisher; 17504044) and 0.25% 100X Glutamax (Thermo Fisher; 35050061) per 1 mL of Hibernate E-Minus Phenol Red (Thermo Fisher; NC1506837)), 45% artificial cerebral spinal fluid (aCSF;  7.13 g/L NaCl (Sigma-Aldrich; S9888-500G), 0.23 g/L KCl (Sigma-Aldrich; P3911-25G), 0.14 g/L MgSO4 (Sigma-Aldrich; 746452-500G), 0.19 g/L CaCl2 (Sigma-Aldrich; C33067-100G), 0.048 g/L NaH2PO4 (Millipore-Sigma; 10049-21-5), 2.1 g/L NaHCO3 (Millipore-Sigma; 144-55-8), 1 L diH2O adjusted for dry reagent volumes), 9.97% RNAlater (Thermo Fisher; AM7020), and 0.03% RNaseOUT (Thermo Fisher; 10777019). Brain sections (1.94-0.64 bregma; 1.5 mm thickness) containing the nucleus accumbens core and prefrontal cortex were cut using a brain matrix (0.5 mm spaced slits) kept cold at -20°C with ice-cold razors. Punches of brain tissue were made using a 1 mm core puncher for each nucleus accumbens bilateral region and 1.5 mm sized punches for the prefrontal cortex. Brain regions from three mice per sex were pooled together for adequate RNA collection. Brain punches were immediately placed in enzymatic dissociation solution (2mg/mL papain (Worthington; LS003120) diluted in 1 mL HEBG with 0.125% 100x Glutamax – heated in 30C water bath for 10 minutes before immediately placing on ice for brain punches) on ice for 20 minutes. Mechanical trituration while incubating in papain solution was carried out using 10x syringe fluctuations with a 23G needle followed by a 27G needle. Caution is taken to not introduce air bubbles during syringe fluctuations that otherwise rupture cell membranes. Tissue was centrifuged for 3 minutes at 1000 rcf at 4°C, and the supernatant was carefully discarded via pipette, leaving ~20 uL medium to prevent significant cell loss. Cells were slowly resuspended via pipette with 500 uL of 4°C HEBG medium and then filtered through a 40 um cell strainer. Semi-permeabilization was carried out by adding 500 uL of -20°C ethyl acetate (95% ethanol; 5% acetate) to the 500 uL of HEBG medium with cells for a final 50% ethyl acetate concentration. Tubes were slowly inverted by hand for 1 minute briefly before centrifuging for 5 min at 1000 rcf in 4°C. The supernatant was discarded carefully via pipette leaving ~20 uL to prevent cellular loss and cells are resuspended gently via pipette in 500 uL of 4°C HEBG medium with neuronal (NeuN-Alexafluor-405; conc. 5:500; Novus Biologicals; NBP1-92693AF405) and cFos-labeling conjugated antibodies (cFos-Alexafluor-488; conc. 5:500; Novus Biologicals; NBP2-50037AF488). Cells were incubated at 4°C while rotating in the dark for 45 minutes. Cells were centrifuged for 5 minutes at 1000 rcf at 4°C, and the supernatant was carefully discarded via pipette, leaving ~20 uL medium to prevent significant cell loss. Cells were resuspended in 1 mL of 4°C HEBG medium and filtered with a 40 um cell strainer into a sterile 5 mL FACS tube and kept at 4°C. Cells were then sorted for neuronal and reward-specific tags (neuron – immunolabeled NeuN; cocaine – endogenous tdTomato; sucrose – immunolabeled cFos; overlap – tdTomato/cFos) using FACS (FACSMelody; FACSChorus Software 100-um nozzle; BD Biosciences). 80k-100k events per reward-specific population were sorted directly into the RLT buffer (RNeasy Mini Kit; Qiagen; 74104) for downstream RNA extraction using RNeasy Mini Kit. RNA samples were kept at -80°C until downstream RNA sequencing.
RNA samples underwent library preparation and next-generation RNA sequencing at the University of Colorado Anschutz Medical Campus Genomics and Microarray Core. Low-input ribosome depleted (SMART-seq; Takara Bio; library size: 200-500bp) library prep was used for downstream paired-end 2x150bp RNA sequencing at a 50 million read depth using NovaSEQ 6000 (Illumina).

value: Brain

value: Neuron

tag: Sex

value: female

tag: neuron population

value: Overlapping

tag: region

value: Prefrontal-cortex

tag: replicate

value: Dual Cocaine and Sucrose Self-Administration


title: FP3NonEns

description: Female Prefrontal Cortex Nonensemble Replicate 3

tag: tissue

value: Nonensemble

tag: treatment


title: FP3C

description: Female Prefrontal Cortex Cocaine-seeking Replicate 3

value: Cocaine-seeking

tag: genotype


title: FP3Naive

description: Female Prefrontal Cortex Naive Replicate 3

value: Naïve


title: TFH, KO, rep2


title: FP2O

description: Female Prefrontal Cortex Overlapping Replicate 2


title: FP2S

description: Female Prefrontal Cortex Sucrose-seeking Replicate 2

value: Sucrose-seeking


title: FP2NonEns

description: Female Prefrontal Cortex Nonensemble Replicate 2


title: FP2C

description: Female Prefrontal Cortex Cocaine-seeking Replicate 2


title: FP1O

description: Female Prefrontal Cortex Overlapping Replicate 1


title: FP1S

description: Female Prefrontal Cortex Sucrose-seeking Replicate 1


title: MFM223_wt_no_dox_day_14_RNA

tag: parental cell line

tag: prrx1 lentiviral vectors/recombinat dna


title: FP2Naive

description: Female Prefrontal Cortex Naive Replicate 2


title: FP1Naive

description: Female Prefrontal Cortex Naive Replicate 1


title: FN3S

description: Male Prefrontal Cortex Sucrose-seeking Replicate 3

value: Nucleus-accumbens-core


title: FP1C

description: Female Prefrontal Cortex Cocaine-seeking Replicate 1


title: FN3NonEns

description: Male Prefrontal Cortex Nonensemble Replicate 3


title: FN2S

description: Male Prefrontal Cortex Sucrose-seeking Replicate 2


title: FN3Naive

description: Male Prefrontal Cortex Naive Replicate 3


title: FN3O

description: Male Prefrontal Cortex Overlapping Replicate 3


title: FP3S

description: Female Prefrontal Cortex Sucrose-seeking Replicate 3


title: FN2O

description: Male Prefrontal Cortex Overlapping Replicate 2


title: FN2Naive

description: Male Prefrontal Cortex Naive Replicate 2


title: FN2C

description: Male Prefrontal Cortex Cocaine-seeking Replicate 2


title: FN1S

description: Male Prefrontal Cortex Sucrose-seeking Replicate 1


title: FN2NonEns

description: Male Prefrontal Cortex Nonensemble Replicate 2


title: FN1NonEns

description: Male Prefrontal Cortex Nonensemble Replicate 1


title: FN1O

description: Male Prefrontal Cortex Overlapping Replicate 1


title: FN1C

description: Male Prefrontal Cortex Cocaine-seeking Replicate 1


title: MP3O

description: Female Nucleus Accumbens Core Overlapping Replicate 3


title: FP1NonEns

description: Female Prefrontal Cortex Nonensemble Replicate 1


title: MP3S

description: Female Nucleus Accumbens Core Sucrose-seeking Replicate 3


title: FN3C

description: Male Prefrontal Cortex Cocaine-seeking Replicate 3


title: MP3NonEns

description: Female Nucleus Accumbens Core Nonensemble Replicate 3

value: male


title: MP2S

description: Female Nucleus Accumbens Core Sucrose-seeking Replicate 2


title: MP3C

description: Female Nucleus Accumbens Core Cocaine-seeking Replicate 3


title: MP2O

description: Female Nucleus Accumbens Core Overlapping Replicate 2


title: MP1Naive

description: Female Nucleus Accumbens Core Naive Replicate 1


title: MP1S

description: Female Nucleus Accumbens Core Sucrose-seeking Replicate 1


title: MP1NonEns

description: Female Nucleus Accumbens Core Nonensemble Replicate 1


title: MP2C

description: Female Nucleus Accumbens Core Cocaine-seeking Replicate 2


title: MP2NonEns

description: Female Nucleus Accumbens Core Nonensemble Replicate 2


title: MP1O

description: Female Nucleus Accumbens Core Overlapping Replicate 1


title: MP2Naive

description: Female Nucleus Accumbens Core Naive Replicate 2


title: MN3S

description: Male Nucleus Accumbens Core Sucrose-seeking Replicate 3


title: MN3O

description: Male Nucleus Accumbens Core Overlapping Replicate 3


title: MN3NonEns

description: Male Nucleus Accumbens Core Nonensemble Replicate 3


title: MP1C

description: Female Nucleus Accumbens Core Cocaine-seeking Replicate 1


title: MN3Naive

description: Male Nucleus Accumbens Core Naive Replicate 3


title: MN2O

description: Male Nucleus Accumbens Core Overlapping Replicate 2


title: MN2S

description: Male Nucleus Accumbens Core Sucrose-seeking Replicate 2


title: MN3C

description: Male Nucleus Accumbens Core Cocaine-seeking Replicate 3


title: FN1Naive

description: Male Prefrontal Cortex Naive Replicate 1


title: MN2NonEns

description: Male Nucleus Accumbens Core Nonensemble Replicate 2


title: MN2Naive

description: Male Nucleus Accumbens Core Naive Replicate 2


title: MN2C

description: Male Nucleus Accumbens Core Cocaine-seeking Replicate 2


title: MN1O

description: Male Nucleus Accumbens Core Overlapping Replicate 1


title: MN1S

description: Male Nucleus Accumbens Core Sucrose-seeking Replicate 1


title: MN1Naive

description: Male Nucleus Accumbens Core Naive Replicate 1


title: MN1NonEns

description: Male Nucleus Accumbens Core Nonensemble Replicate 1


title: MP3Naive

description: Female Nucleus Accumbens Core Naive Replicate 3


title: MN1C

description: Male Nucleus Accumbens Core Cocaine-seeking Replicate 1


title: LIMP-RES-P1-0125-buccal

city: Washington,DC

first: Nino

last: Gustavo

state: Washington,DC,

address: Sheikh Zayed Campus,111 Michigan Avenue,

department: Center for Precision Medicine and Genomics Research

institute: Childrens National Hospital

hyb_protocol: Samples were whole-genome amplified, enzymatically fragmented, and hybridized to BeadChip array using the Infinium MethylationEPIC BeadChip kit according to the manufacturer’s protocol (Illumina).

scan_protocol: Hybridized methylation arrays were scanned using the iScan system (Illumina) at Georgetown University’s Genomics & Epigenomics Shared Resource Core in Washington, DC and the NextSeq550 (Illumina) using the BeadChip scanning protocol and adapter at Children's National Research Institute Genomic's Core in Washington, DC.

data_processing: Raw intensity values (idat files) were generated from each EPIC BeadChip row using the iScan system. All statistical analysis was done using R (version 4.2.2) and Bioconductor packages.

source_name: newborn pandemic case male

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was isolated from collected Genotek OC175 buccal swabs using the L2Prep-It kit. DNA concentration was determined by the Qubit fluorometer Broad Range dsDNA kit. DNA was bisulfite converted using Zymo Methylation Lightning Kit.

tag: clincal phenotype

value: pandemic case

tag: newborn sex

tag: gestational age at collection

value: buccal swab


title: LIMP-RES-P1-0112-buccal

source_name: newborn pandemic case female


title: LIMP-RES-P1-0049-buccal


title: LIMP-RES-P1-0096-buccal


title: LIMP-RES-P1-0076-buccal


title: LIMP-RES-P1-0007-buccal


title: LIMP-RES-P1-0028-buccal


title: LIMP-RES-P1-0054-buccal


title: LIMP-RES-P1-0118-buccal


title: LIMP-RES-P1-0021-buccal


title: LIMP-RES-P1-0020-buccal


title: LIMP-RES-P1-0090-buccal


title: LIMP-RES-P1-0070-buccal


title: LIMP-RES-P1-0107-buccal


title: LIMP-RES-P1-0098-buccal


title: LIMP-RES-P1-0082-buccal


title: LIMP-RES-P1-0056-buccal


title: LIMP-RES-P1-0064-buccal


title: LIMP-RES-P1-0022-buccal


title: LIMP-RES-P1-0099-buccal


title: LIMP-RES-P1-0047-buccal


title: LIMP-RES-P1-0051-buccal


title: LIMP-RES-P1-0059-buccal


title: LIMP-RES-P1-0066-buccal


title: LIMP-RES-P1-0015-buccal


title: LIMP-RES-P1-0057-buccal


title: LIMP-RES-P1-0006-buccal


title: LIMP-RES-P1-0014-buccal


title: Spec-seq_r90w_2m

city: Saint Louis

first: Shiming

last: Chen

state: Missouri

address: 517 South Euclid Avenue

department: Department of Ophthalmology & Visual Sciences

institute: Washington University in St Louis

library_source: other

data_processing:
Reads with any mismatch in the Spec-seq library conserved regions were discarded prior to quantification.
The ratio of individual sequence in bound and unbound reads was calculated as a measurement of relative binding affinity compared to the consensus sequence.
The relative binding energy was then derived from the natural logarithm of the relative binding affinity and represented in kcal/mol units.
Supplementary files format and content: Text files with normalized read counts in bound and unbound fraction and the derived relative binding affinity and relative binding energy.
Library strategy: Spec-seq (amplicon based sequencing)

molecule: other

organism: synthetic construct

source_name: synthetic construct

extract_protocol:
After EMSA, Spec-seq libraries from both bound and unbound bands were eluted from the excised Tris-glycine gel.
Sequencing adapters and primers were added to both ends of the Spec-seq library using two-step PCR.

tag: peptide

value: CRX R90W HD

tag: emsa band

value: bound

tag: molecule type

value: synthetic DNA


title: LIMP-RES-P1-0110-buccal


title: Spec-seq_r90w_1m


title: Spec-seq_r90w_1f

value: unbound


title: Spec-seq_k88n_2m

value: CRX K88N HD


title: Spec-seq_k88n_1m


title: Spec-seq_e80a_2m

value: CRX E80A HD


title: Spec-seq_e80a_2f


title: Spec-seq_k88n_2f


title: Spec-seq_e80a_1m


title: Spec-seq_k88n_1f


title: LIMP-RES-P1-0040-buccal


title: Spec-seq_e80a_1f


title: Spec-seq_wt_2f

value: WT CRX HD


title: Spec-seq_wt_1m


title: Spec-seq_wt_1f


title: Spec-seq_wt_2m


title: T3-T4 Tumor_(LN negative patient 08) [RT2107138149-1]

city: Guangzhou

first: Zhenyuan

last: Li

address: 1838th North Guangzhou Avenue, Southern Medical University

institute: Southern Medical University

data_processing:
sequencing reads was filtered using fastp version 0.23.2 (default parameter)
sequending reads was aligned to the referecence sequence using salmon version 1.9.0. (default parameter)
R version 4.2.2 was used in downstream analysis
tximport version 1.26.1 was used to import the output of salmon and TPM normalization
DESeq2 version 1.38.3 was used to identify differentlially expressed genes
Assembly: hg38
Supplementary files format and content: A comma-separated TPM expression matrix, with rows as gene ENSEMBL IDs and columns as samples

source_name: primary tumor

extract_protocol:
The samples were collected from patients who underwent surgery at the Nanfang Hospital of Southern Medical University (Guangzhou, China) between December 2020 and December 2021. All samples were immediately snap-frozen in liquid nitrogen and stored at −80 °C until required.
The extracted total RNA is subjected to quality checks for purity, quantity and integrity (RIN). Isolation: Because eukaryotic mature mRNA has a ploy(A) tail and other RNAs do not, oligo dT magnetic beads can be used to specifically bind to the poly(A) tail of mRNA to remove other RNAs. fragmentation: Fragmentation of purified mRNA with reagents (fragmentation reagent). cDNA first strand synthesis Random hexamer primer, reverse transcriptase to synthesise cDNA using mRNA as template. cDNA second strand synthesis: Second strand synthesis and deletion of mRNA to produce double-stranded cDNA (ds cDNA). Purification of double-stranded cDNA: end repair of double-stranded cDNA. Ends are patched and the repaired cDNA is then purified. ds cDNA 3' end is added with A (dA - tailing). The ligand: each ligand has an index (6bp) and different libraries can be built using different indexes. PCR enrichment of the libraries: After amplification and purification, the libraries will be checked and ready for sequencing.

value: primary tumor


title: T3-T4 Normal_(LN negative patient 08) [RT2107138148-1]

source_name: normal adjacent tissue

value: normal adjacent tissue


title: T3-T4 Tumor_(LN negative patient 07) [RT2107138147-1]


title: T3-T4 Normal_(LN negative patient 07) [RT2107138146-1]


title: T1-T2 Normal_(LN negative patient 06) [RT2107138144-1]


title: T1-T2 Tumor_(LN negative patient 06) [RT2107138145-1]


title: T3-T4 Tumor_(LN negative patient 04) [RT2107138141-1]


title: T1-T2 Tumor_(LN negative patient 05) [RT2107138143-1]


title: T1-T2 Normal_(LN negative patient 05) [RT2107138142-1]


title: T3-T4 Normal_(LN negative patient 04) [RT2107138140-1]


title: T3-T4 Tumor_(LN negative patient 03) [RT2107138139-1]


title: T3-T4 Normal_(LN negative patient 03) [RT2107138138-1]


title: T1-T2 Normal_(LN negative patient 02) [RT2107138136-1]


title: T3-T4 Metastatic lymph node (LN positive patient 08) [RT2107138133-1]

source_name: Metastasis lymph nodes

value: Metastasis lymph nodes


title: T1-T2 Normal_(LN negative patient 01) [RT2107138134-1]


title: T3-T4 Tumor_(LN positive patient 08) [RT2107138132-1]


title: T3-T4 Normal_(LN positive patient 08) [RT2107138131-1]


title: T1-T2 Tumor_(LN negative patient 01) [RT2107138135-1]


title: LIMP-CTL-P1-2257-buccal

source_name: newborn pre-pandemic healthy control female

value: pre-pandemic control

value: female


title: T3-T4 Tumor_(LN positive patient 07) [RT2107138129-1]


title: T1-T2 Tumor_(LN positive patient 06) [RT2106133228-2]


title: T3-T4 Metastatic lymph node_(LN positive patient 07) [RT2107138130-1]


title: T1-T2 Metastatic lymph node_(LN positive patient 06) [RT2106133229-1]


title: T3-T4 Normal_(LN positive patient 07) [RT2107138128-1]


title: T1-T2 Normal_(LN positive patient 06) [RT2106133227-2]


title: T1-T2 Metastatic lymph node (LN positive patient 05) [RT2106133226-1]


title: LIMP-CTL-P1-2235-buccal

source_name: newborn pre-pandemic healthy control male


title: T1-T2 Tumor (LN positive patient 05) [RT2106133225-2]


title: Spec-seq_r90w_2f


title: T1-T2 Normal_(LN positive patient 05) [RT2106133224-2]


title: T1-T2 Metastatic lymph node (LN positive patient 04) [RT2106133220-1]


title: old_females_pred_GR_3

city: Cincinnati

first: Mattia

last: Quattrocelli

state: OH

address: 240 Sabin Way

institute: Cincinnati Children's Hospital Medical Center

data_processing:
A quality control check on the generated fastq ﬁles was performed using FastQC.
Peak analysis was conducted using HOMER software (v4.10, 70; standard commands) after aligning fastq files to the mm10 mouse genome using bowtie2 71.
Assembly: mm10
Supplementary files format and content: bedgraph file of peaks (raw counts)

source_name: quadriceps

extract_protocol:
Quadriceps muscles were cryopowdered using a liquid nitrogen-cooled Retsch Cryomill. The cryopow-dered tissue was then fixed in 10 ml 1% PFA for 30 minutes at room temperature with gentle nutation. Fixation was quenched 1ml of 1.375M glycine (Cat # BP381-5, Fisher Scientific, Waltham, MA) with gentle nutation for 5 minutes at room temperature. After centrifugation at 3000g for 5 minutes at 4°C, the pellet was resuspended in cell lysis buffer as per reported conditions 69, supplementing the cell lysis buffer with 3mg/ml cytochalasin B and rotating for 10 minutes at 4°C.  Nuclei were pelleted at 300g for 10 min at 4°C, and subsequently processed fol-lowing the reported protocol with the adjustment of adding 3µg/ml cytochalasin B into all solutions for chromatin preparation and sonication, antibody incubation, and wash steps.  Chromatin was then sonicated for 15 cycles (30 sec, high power; 30 sec pause; 500µl volume) in a water bath sonicator set at 4°C (Bioruptor 300; Dia-genode, Denville, NJ).  After centrifuging at 10000g for 10 minutes at 4°C, sheared chromatin was checked on agarose gel for a shear band comprised between ~150 and ~600bp. Two µg of chromatin was kept for pooled input controls, whereas ~50µg chromatin were used for each pull-down reaction in a final volume of 2ml rotating at 4°C overnight. Primary antibody: rabbit polyclonal anti-GR (ABclonal #A2164). Chromatin complexes were precipitated with 100µl Dynabeads M-280 (sheep anti-rabbit #11203D; Thermo Scientific, Waltham, MA).  After washes and elution, samples were treated with proteinase K (cat #19131; Qiagen, Hilden, Germany) at 55°C and cross-linking was reversed through overnight incubation at 65°C. DNA was purified using the MinElute puri-fication kit (cat #28004; Qiagen, Hilden, Germany), quantitated using Qubit reader and reagents.
Library preparation and sequencing were conducted at the CCHMC DNA sequencing Core. Up to 30 ng of post-Immunoprecipitation dsDNA as measured by Invitrogen™ Qubit™ high- sensitivity spectroﬂuorometric measurement was made into Illumina-compatible NGS libraries using the ThruPLEX® DNA-Seq kit from Takara Bio Inc.
Each created library was dual-indexed with 8-base molecular barcodes for high level mul5plexing. Libraries were made with 13 cycles of PCR ampliﬁcation.

value: quadriceps

tag: age

value: old

value: weekly pred


title: old_females_pred_GR_2


title: LIMP-CTL-P1-2253-buccal


title: LIMP-RES-P1-0003-buccal

value: pandemic case

value: male


title: T3-T4 Metastatic lymph node (LN positive patient 03) [RT2106133217-1]


title: T1-T2 Normal (LN positive patient 04) [RT2106133219-1]


title: T1-T2 Tumor_(LN positive patient 04) [RT2106133218-1]


title: old_females_veh_GR_1

value: vehicle


title: T3-T4 Tumor_(LN positive patient 03) [RT2106133216-1]


title: old_females_veh_GR_2


title: old_females_input

value: pooled


title: old_females_veh_GR_3


title: T3-T4 Metastatic lymph node_(LN positive patient 02) [RT2106133214-1]


title: T3-T4 Tumor (LN positive patient 02) [RT2106133213-1]


title: young_females_pred_GR_2

value: young


title: young_females_pred_GR_3


title: old_females_pred_GR_1


title: LIMP-RES-P1-0005-buccal

value: buccal swab


title: T3-T4 Normal (LN positive patient 02) [RT2106133212-1]


title: young_females_pred_GR_1


title: T1-T2 Tumor_(LN negative patient 02) [RT2107138137-1]


title: LIMP-CTL-P1-2239-buccal


title: T1-T2 Metastatic lymph node_(LN positive patient 01) [RT2106133211-1]


title: T1-T2 Normal_(LN positive patient 01) [RT2106133209-1]


title: LIMP-CTL-P1-2246-buccal


title: young_females_veh_GR_2


title: 7PM petunia corolla chromatin, H3K36me3 ChIP, replicate 3

city: West Lafayette

first: Ryan

last: Patrick

state: Indiana

address: 625 Agriculture Mall Dr

institute: Purdue University

data_processing:
Adapter sequences were trimmed with Cutadapt and reads were aligned the Petunia axillaris genome with Bowtie2.
Convergent aligned read pairs were converted into fragment bed files which were used for island calling using SICER V1.1.
Dynamic islands between 7PM and 7AM for each replicate were determined, using with a corresponding input background. FDR cutoff of below 0.01 and fold-change cutoff of 2 or greater.
Input replicates 1 and 2 were used for for H3K4me3, H3K9ac, and H3K27ac background, while input replicates 1 and 3 were used for H3K36me3 replicates
Assembly: Petunia axillaris draft genome sequence v1.6.2
Supplementary files format and content: SICER dynamic island output files (bed format)

organism: Petunia x hybrida

source_name: corolla

growth_protocol: Petunia were grown under normal greenhouse conditions, with a 14h light and 10h dark cycle. Light period was from 6AM to 8PM.

extract_protocol:
Petunia corolla tissue was crosslinked in 1% formaldehyde under vaccuum. Nuclei were isolated resuspended in lysis buffer, followed by sonication. Chromatin was immunoprecipitated, decrosslinked, and purified by phenol-chloroform extraction.
Libraries were constructed using NEBNext multiplex oligos (New England Biolabs)

tag: cultivar

value: Mitchell

value: corolla

tag: chip antibody

tag: timepoint


title: T1-T2 Tumor_(LN positive patient 01) [RT2106133210-1]


title: young_females_veh_GR_3

tag: Sex


title: LIMP-CTL-P1-2224-buccal


title: young_females_veh_GR_1


title: LIMP-CTL-P1-2217-buccal


title: LIMP-CTL-P1-2222-buccal


title: young_females_input


title: old_males_pred_GR_3


title: old_males_pred_GR_2


title: 7AM petunia corolla chromatin, H3K36me3 ChIP, replicate 3


title: LIMP-CTL-P1-2230-buccal


title: 7AM petunia corolla chromatin, H3K36me3 ChIP, replicate 1


title: LIMP-CTL-P1-2238-buccal


title: 7PM petunia corolla chromatin, H3K27ac ChIP, replicate 2


title: old_males_veh_GR_3


title: 7PM petunia corolla chromatin, H3K27ac ChIP, replicate 1


title: old_males_veh_GR_2


title: old_males_pred_GR_1


title: old_males_veh_GR_1


title: 7AM petunia corolla chromatin, H3K27ac ChIP, replicate 1


title: 7PM petunia corolla chromatin, H3K9ac ChIP, replicate 2


title: old_males_input


title: 7PM petunia corolla chromatin, H3K9ac ChIP, replicate 1


title: 7AM petunia corolla chromatin, H3K9ac ChIP, replicate 1


title: 7AM petunia corolla chromatin, H3K9ac ChIP, replicate 2


title: young_males_pred_GR_2


title: 7AM petunia corolla chromatin, H3K27ac ChIP, replicate 2


title: young_males_veh_GR_3


title: 7PM petunia corolla chromatin, H3K4me3 ChIP, replicate 2


title: 7PM petunia corolla chromatin, H3K4me3 ChIP, replicate 1


title: 7PM petunia corolla chromatin, H3K36me3 ChIP, replicate 1


title: young_males_pred_GR_1


title: young_males_pred_GR_3


title: young_males_veh_GR_2


title: young_males_input


title: 7AM petunia corolla chromatin, H3K4me3 ChIP, replicate 1


title: young_males_veh_GR_1


title: 7PM petunia corolla chromatin, replicate 3


title: 7PM petunia corolla chromatin, replicate 2


title: 7AM petunia corolla chromatin, H3K4me3 ChIP, replicate 2


title: MeCP2_P900L_B1

city: St. Louis

first: Diana

middle: Christian

last: Beard

address: 660 S. Euclid Ave.

department: Neuroscience

institute: Washington University in St. Louis

data_processing:
ChIP-seq reads were mapped to the mm9 genome using bowtie2 alignment and reads were extended based on library sizes and deduplicated.
Bedtools coverage -counts parameter was used to quantify ChIP signal
Assembly: mm9
Supplementary files format and content: bed

source_name: Cortex

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using the S220 Ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) and complemented with the Accel-NGS 2S Set A adapters. Up to 4ng of DNA was used as starting material. Libraries were amplified using 11-14 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent DNA D1000 Screentape Assay Kit.

value: Cortex

tag: strain

value: Male

value: Rabit anti-MeCP2:Chen et al.


title: MeCP2_P900L_B2

tag: tissue


title: MeCP2_rWT_B2


title: 7AM petunia corolla chromatin, replicate 3


title: 7PM petunia corolla chromatin, replicate 1


title: MeCP2_R878H_B2


title: LIMP-CTL-P1-2227-buccal


title: 7AM petunia corolla chromatin, replicate 2


title: 7AM petunia corolla chromatin, replicate 1


title: MeCP2_R878H_B1


title: MeCP2_rWT_B1


title: MeCP2_pWT_B1


title: MeCP2_pWT_B2


title: PBMC, Baseline, Strong Responder (SR), PREV99

city: Farmington

first: Duygu

last: Ucar

address: 10 Discovery Dr

institute: The Jackson laboratory for Genomic Medicine

data_processing:
Illumina base call files for all libraries were converted to FASTQs using bcl2fastq v2.20.0.422 (Illumina) and FASTQ files associated with the gene expression libraries were aligned to the GRCh38 reference assembly with v32 annotations from GENCODE (10x Genomics GRCh38 reference 2020-A) using the version 6.1.2 Cell Ranger multi pipeline (10x Genomics).
Assembly: GRCh38
Supplementary files format and content: Transcriptomic counts matrices in Matrix Market CSR format.  Rows correspond to features in the order provided in features.tsv/features.tsv and columns correspond to cell-barcodes in the order provided in barcodes.tsv.

source_name: blood

extract_protocol:
PBMCs were thawed quickly at 37oC and in DMEM supplemented with 10% FBS. Post-thawing, cells were washed and suspended in PBS containing 0.04% BSA and immediately processed as follows. Cell viability was assessed on a Countess II automated cell counter (ThermoFisher).
10x Genomics 3' single cell RNA-seq
12,000 cells (~4,000 cells from each hashtagged sample) were loaded onto one lane of a 10 Genomics Chromium X. Single cell capture, barcoding and library preparation were performed using the 10x Chromium platform version 3.1 chemistry and according to the manufacturer’s protocol (#CG000388). cDNA and libraries were checked for quality on Agilent 4200 Tapestation and ThermoFisher Qubit Fluorometer, quantified by KAPA qPCR, and sequenced using 13% of an Illumina NovaSeq 6000 S4 v1.5 200 cycle flow cell lane, with a 28-10-10-90 asymmetric read configuration, targeting 6,000 barcoded cells with a minimum sequencing depth of 50,000 read pairs per cell.

tag: figure ids

value: blood

tag: cell type

value: PBMCs

tag: response status

value: Strong Responder (SR)

tag: age (in years)


title: PBMC, Baseline, Strong Responder (SR), PREV72


title: PBMC, Baseline, Weak Responder (WR), PREV89

value: Weak Responder (WR)


title: PBMC, Baseline, Strong Responder (SR), PREV71

value: female


title: PBMC, Baseline, Strong Responder (SR), PREV36


title: PBMC, Baseline, Weak Responder (WR), PREV45


title: PBMC, Baseline, Weak Responder (WR), PREV66


title: K4-M-20

data_processing:
A quality control check on the fastq files was performed using FastQC.
Upon passing basic quality metrics, the reads were trimmed to remove adapters and low-quality reads using default parameters in Trimmomatic 75 [Version 0.33].
The trimmed reads were then mapped to mm10 reference genome using default parameters with strandness (R for single-end and RF for paired-end) option in Hisat2 76 [Version 2.0.5].
In the next step, transcript/gene abundance was determined using kallisto 77 [Version 0.43.1].
We first created a transcriptome index in kallisto using Ensembl cDNA sequences for the reference genome. This index was then used to quantify transcript abundance in raw counts and counts per million (CPM).
Assembly: mm10
Supplementary files format and content: csv table containing isoform CPM

extract_protocol:
RNA-seq was conducted on RNA extracted from quadriceps muscle. Total RNA was extracted from cryo-pulverized quadriceps muscles with Trizol (#15596026; Thermo Fisher Scientific, Waltham, MA) and re-purified using the RNeasy Mini Kit (Cat #74104; Qiagen, Germantown, MD). RNA-seq was performed at the DNA Core (CCHMC) blinded to treatment groups.
150 to 300 ng of total RNA determined by Qubit (Cat#Q33238; Invitro-gen, Waltham, MA) high-sensitivity spectrofluorometric measurement was poly-A selected and reverse tran-scribed using Illumina’s TruSeq stranded mRNA library preparation kit (Cat# 20020595; Illumina, San Diego, CA).
Each sample was fitted with one of 96 adapters containing a different 8 base molecular barcode for high level multiplexing. After 15 cycles of PCR amplification, libraries were sequenced.

value: quadriceps

tag: genotype

value: WT

tag: treatment

value: weekly pred


title: K4-F-22

value: old


title: K4-F-21

value: vehicle


title: K4-F-24

value: young


title: PBMC, Baseline, Weak Responder (WR), PREV31

value: male


title: LIMP-CTL-P1-2216-buccal

tag: clincal phenotype

value: pre-pandemic control

tag: newborn sex

tag: gestational age at collection

value: buccal swab


title: K4-M-18


title: K4-F-23


title: PBMC, Baseline, Strong Responder (SR), PREV18


title: PBMC, Baseline, Weak Responder (WR), PREV23


title: K4-M-17


title: K4-M-19


title: PBMC, Baseline, Strong Responder (SR), PREV10


title: PVAX16_Baseline

data_processing:
Raw BCL files generated by the sequencer were converted to FASTQ files. CASAVA was used to generate FASTQ files for RNAseq data. Trimmomatic (version 0.33) was used to remove adapters, leading and trailing low-quality bases.  Reads less than 36 bases long were dropped. Reads with more than 50% low-quality bases overall were filtered out. The remaining high-quality reads were then used for expression estimation. Alignment estimation of gene expression levels using the EM algorithm for paired-end read data was performed using RSEM (package version 1.2.12); default settings were used for alignment. RSEM uses bowtie2 as aligner to align the mapped reads against the hg38 reference genome. Data quality control was performed using Picard (version 1.95) and bamtools to obtain general alignment statistics from the bam file.
Gene expression values from PBMC RNA-seq data were converted into count-per-million (cpm) using edgeR R package (version 3.28.1)113. Genes with cpm values less than 0.5 across all samples were filtered out from the rest of the analyses. Differential gene expression analyses were conducted using generalized linear models (as implemented in the edgeR package) using the default TMM normalization.
Assembly: hg38
Supplementary files format and content: tab delimited text file includes raw counts for each sample
Supplementary files format and content: tab delimited text file includes counts per million (in log2) for each sample

source_name: Blood

extract_protocol:
Total RNA was isolated from PBMCs using the Qiagen RNeasy Mini Kit (Qiagen) or  Arcturus PicoPure (Life Technologies) kits following manufacturer’s protocols.
RNA-seq libraries were prepared with KAPA mRNA HyperPrep kit (Roche) according to manufacturer’s instruction.

tag: figureid

value: Blood

tag: time

value: Baseline

value: Pneumovax -23


title: K4-F-15

tag: age


title: PREV71_Day10

value: Prevnar -13

value: Female


title: K4-F-13


title: K4-F-14


title: PREV66_Day1

value: PBMCs

value: Male


title: PVAX87_Day60


title: K4-F-11

value: female


title: PREV18_Day1


title: K4-F-10

value: quadriceps


title: T3-T4 Normal_(LN positive patient 03) [RT2106133215-1]

value: normal adjacent tissue


title: K4-F-9

value: WT


title: PREV71_Baseline


title: PREV89_Day10


title: PREV31_Day10


title: K4-M-8

value: weekly pred


title: PVAX90_Day10


title: K4-M-7


title: PVAX90_Day1


title: K4-M-5

value: vehicle


title: PVAX75_Baseline


title: PVAX25_Day10


title: K4-M-4

value: old


title: K4-M-3

value: male


title: K4-F-16

value: young


title: PVAX25_Baseline


title: PVAX76_Baseline


title: K4-M-1


title: PVAX38_Baseline


title: K4-M-2


title: K4-F-12


title: PVAX87_Day10


title: PVAX61_Baseline


title: WT_Crypt_Input

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Rd

department: Genetics

institute: Rutgers, the State University of New Jersey

data_processing:
FastQC (v0.11.3) was used to check the quality of raw sequencing reads.
Alignment to the mouse reference genome (MGSCv37/mm9) was done using bowtie2 (v2.2.6) (30) and alignments were sorted using Samtools (v0.1.19).
When required, Picard’s MergeSamFiles was used to merge replicate bam files (http://broadinstitute.github.io/picard).
deepTools2 (31) bamCoverage (v2.4.2) was used to generate RPKM-normalized bigwig files from individual and merged bam files.
Raw gene-level counts data for each region was obtained using featureCounts from the Subread package (v2.03).
DESeq2 (v1.36.0) was applied to counts data for differential analyses.
Assembly: mm9
Supplementary files format and content: Bigwig files for each sample
Supplementary files format and content: Merged bigwig files from replicates of each group
Supplementary files format and content: Counts output from FeatureCounts (txt files)
Supplementary files format and content: Differential enrichment analysis was generated as a csv file by DESeq2

source_name: duodenal epithelium

extract_protocol:
The initial third of the small intestine (duodenum) was dissected and opened longitudinally to wash the inter-lumen space and expose epithelial cells. Tissue was cut into 1-inch pieces and rinsed with ice-cold PBS. Tissue was treated with 3mM EDTA/PBS for 25 minutes for mutant mice and 35 minutes for wild-type, with changes in EDTA solution at the initial 5- and 10-minute time points. Mechanical force was applied to release the epithelial cell layer from the underlying mesenchyme. Crypts and villi were separated with a 70uM filter. The smaller crypts pass through the pores of the filter while the larger villi stay on top. Both crypts and villi were collected from wild-type mice, while only villi were collected from Hnf4 mutant mice.  Cells were washed twice with ice-cold PBS and pelleted by centrifugation at 300 rcf at 4°C. Crypt and villus cell pellets were cross-linked with 1% formaldehyde (Sigma, F8775) at 4°C for 10 min and then at 25°C for 50 min. Cells were pelleted and washed with ice-cold PBS twice by centrifugation at 300g at 4°C. Fixed cells were lysed in 3X volume of lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl pH 8.0, 1X protease inhibitor cocktail (G-Biosciences, 786-433). Cells were sonicated for 35 minutes using a Diagenode Bioruptor to shear chromatin to 200-500bp. Protein A/G beads (Invitrogen, 10001D and 10004D) were washed with 1% BSA in PBS and pre-loaded with Anti-RNA polymerase II antibody (Millipore,05-623, Lot 3506610). Antibody-conjugated beads were washed twice with 1% BSA and incubated with sheared chromatin in dilution buffer (1% Triton X -100, 2mM EDTA, 150mM NaCl, 20mM Tris-HCl, pH 8.0). The final concentration of SDS in the sonicate was 0.26%. Chromatin and beads were incubated on a rotator at 4°C overnight. Chromatin-bound, antibody-conjugated beads were collected by magnetic separation. Unbound chromatin was discarded. Beads were washed five times with RIPA buffer (50mM HEPES pH 7.6, 1mM EDTA, 0.7% Sodium deoxycholate, 1% NP-40, 0.5M LiCl), and once with TE buffer (10mM Tris, 0.1mM EDTA). Cross-links were reversed in buffer containing 0.1M NaHCO3 and 1% SDS overnight at 37°C to release ChIP DNA. DNA was column purified using the MinElute PCR purification kit (Qiagen, 28004) and quantified using Picogreen (Invitrogen, P7581). Libraries were prepared using the ThruPLEX DNA-Seq kit (Takara, R400675) and DNA Unique Dual Index Kit (Takara, R400666).
ThruPLEX DNA-Seq kit (Takara, R400675)

treatment_protocol: Hnf4 DKO mice were injected i.p. with tamoxifen (50mg/kg/day) for 2 consecutive days and were sacrificed 1 day after last injection.. WT mice received vehicle injections of 10% ethanol and 90% corn oil without tamoxifen.

value: duodenal epithelium

value: adult crypt cells

value: oil vehicle


title: Hnf4DKO_Villi_PolIIChIP_rep3

value: adult villus cells

value: Hnf4{alpha}{gamma} DKO

value: Tamoxifen


title: Hnf4DKO_Villi_PolIIChIP_rep2


title: PVAX16_Day10

value: Blood

value: PBMCs

value: Pneumovax -23


title: K4-M-6

value: quadriceps


title: PVAX38_Day1

value: Female


title: Hnf4DKO_Villi_PolIIChIP_rep1


title: PREV10_Day1

value: Prevnar -13

value: Male


title: PREV71_Day60


title: WT_Crypt_PolIIChIP_rep3

value: WT


title: PREV31_Day1


title: PVAX44_Baseline

value: Baseline


title: WT_Crypt_PolIIChIP_rep2


title: WT_Crypt_PolIIChIP_rep1


title: PREV18_Day60


title: Hnf4DKO_Villi_Input


title: PVAX25_Day1


title: WT_Villi_PolIIChIP_rep3


title: WT_Villi_PolIIChIP_rep1


title: WT_Villi_PolIIChIP_rep2


title: PVAX38_Day10


title: PVAX76_Day60


title: PREV18_Day10


title: PVAX90_Day60


title: WT_Villi_Input


title: PVAX76_Day1


title: 705, RMC-6272, 3nM, Rep3

city: Boston

first: Heng

last: Du

address: 45 Francis St

institute: Brigham and Women's Hospital

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp.
clean data (clean reads) were obtained by removing reads containing adapter and poly-N. Q20, Q30 and GC content of the clean data were calculated
sequences and reads with low quality from raw data
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
FeatureCounts was used to count the read numbers mapped of each gene.
Assembly: mm10/hg38
Supplementary files format and content: tab-delimited text file including raw counts
Supplementary files format and content: tab-delimited text file including RPKM values

growth_protocol: Cells were maintained in DMEM medium supplemented with 10% fetal bovine serum (FBS), 100 units/ml of penicillin and streptomycin, and incubated at 37℃ in 5% CO2.

extract_protocol:
Total RNA was extracted using a RNeasy mini kit (Qiagen, #74104).
1 μg RNA per sample was used for cDNA library preparation using the NEBNextÒ UltraTM RNA Library Prep Kit for Illumina (NEB, USA)

treatment_protocol: Cells were treated with DMSO, Rapamycin (10 nM), or RMC-6272 (3 nM) for 24h (triplicates per condition).

tag: cell line

value: Renal cell carcinoma

value: Tsc2 null

tag: concentration

value: 3 nM


title: 705, Rapamycin, 10nM, Rep3

value: Rapamycin

value: 10 nM


title: 705, RMC-6272, 3nM, Rep1


title: 705, RMC-6272, 3nM, Rep2


title: 705, Rapamycin, 10nM, Rep2


title: PREV36_Baseline

tag: Sex


title: 705, Rapamycin, 10nM, Rep1


title: PVAX25_Day60


title: PVAX44_Day60


title: 705, Ctrl, Rep3

value: DMSO


title: 705, Ctrl, Rep2


title: PREV89_Day1


title: 705, Ctrl, Rep1


title: PREV71_Day1


title: PREV18_Baseline


title: MEF, 6h IFNb, Tn5hc

city: Heidelberg

first: Isabelle

last: Seufert

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

description: 10x Genomics

data_processing:
Demultiplexing, barcode processing, genome mapping and aggregation were conducted using the Cell Ranger ATAC software v2.0.0 (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac).
Assembly: mm10-2020-A
Supplementary files format and content: h5 single cell peak count matrix, tab-separated fragment file, comma-separated single cell info file

source_name: Mouse embryonic fibroblasts

growth_protocol: MEFs were incubated at 37°C and 5% CO2. Media was DMEM (Gibco, 11880-28), 10% FCS (PAN-Biotech; P30-3602), 1x L-Glutamine (PAN-Biotech, P04-80050), 1x PenStrep (PAN-Biotech, P06-07050).

extract_protocol: Libraries were prepared according to the Chromium single-cell ATAC v1.1 protocol (10x Genomics) using the provided Tn5 (10xTn5), an in-house loaded Tn5 at high concentration (Tn5hc) or a dilution of Tn5hc to 30 % activity (Tn5hc 30 %).

treatment_protocol: All cells were treated with 500 U/ml of self-made interferon beta (16.6 U/µl) for 6 hours.

value: Mouse embryonic fibroblasts

tag: strain


title: PREV89_Baseline

tag: tissue