title: HDT2_S#D1_15:00

description: Gene expression of participant S#D1, sampling session HDT2, at 15:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session HDT2, at 15:00 hr


title: rapamycin-4.Input

status: Public on Mar 09 2024

type: SRA

city: Luzhou

first: Kai

last: Wang

address: No. 1, Section 1, Xianglin Road, Longmatan District

country: China

institute: Southwest Medical University

library_source: transcriptomic

data_processing:
First, clean reads of all libraries were aligned to the reference genome (HG19)  by Hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps.
GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes.
Assembly: hg19
Supplementary files format and content: excel and bed format file includs number of raw junction read for each sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: H460 cells were routinely cultured with DMEM medium containing 1% streptomycin/penicillin and 10% fetal bovine serum (FBS) in a 5% CO2 incubator.

extract_protocol:
Total RNA was extracted from H460 cells using an ultrapure total RNA extraction kit (Simgen, Hangzhou, China). 1.3ug total RNA was used for the construction of sequencing libraries.
The GenSeq® rRNA Removal Kit (GenSeq, Inc.) was used to remove ribosomal RNA (rRNA) from the sample. After the removal of rRNA, sequencing libraries were constructed using the GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) kit according to the manufacturer's instructions.

treatment_protocol: Autophagy was induced by treatment with 100nM rapamycin for 24h.

tag: cell line

tag: cell type

value: Human large cell lung cancer cell

tag: genotype

value: wild-type

tag: treatment

value: 100nM rapamycin


title: HC_M1P1_D15

city: Stanford

first: Wenfei

last: Sun

address: 318 Campus Dr.

country: USA

institute: Stanford University

description:
Smartseq
cell by gene matrix

data_processing:
Fastq reads were mapped with STAR(2.7.9a)
Assembly: mm10
Supplementary files format and content: Cell by gene matrix format

molecule: polyA RNA

organism: Mus musculus

source_name: posteromedial nucleus of the cortical amygdala

extract_protocol:
OligodT primers were used to enrich mRNA
Brain tissues were dissociated with Worthington Papain Digestion Kit RNA libraries were prepared using smart seq 2

treatment_protocol: Food Transmitted Food Preference paradigm

tag: tissue


title: HC_M1P1_E20

description:
Smartseq
cell by gene matrix

value: posteromedial nucleus of the cortical amygdala


title: OR female flies, 20 h post Staphylococcus aureus infection, rep4

city: Edinburgh

first: Pedro

last: Vale

state: Edinburgh

address: Ashworth Labs, Charlotte Auerbach Road

department: School of Biological Sciences

country: United Kingdom

institute: University of Edinburgh

data_processing:
Reads were trimmed using Cutadapt1 (version cutadapt-1.18-venv). Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA kit (AGATCGGAAGAGC). Reads after trimming were required to have a minimum length of 50.
Reads were aligned to the reference genome using STAR2 (version 2.7.3a) specifying paired-end reads
Reads were normalised using the weighted trimmed mean of M-values method5, passing ‘TMM’ as the method to the calcNormFactors method of edgeR.
Assembly: The reference used for mapping was the Drosophila melanogaster (BDGP6_ens107) combined with S. aureus (GCA_000013425.1), P. rettgeri (GCF_003204135.1) and DCV (NC_001834.1). The annotation used for counting was the standard GTF-format annotation for that reference.
Supplementary files format and content: Text file containing normalized read counts for genes in all samples (CPMs)

organism: Drosophila melanogaster

source_name: whole fly

growth_protocol: Drosophila melanogaster flies were grown from egg to adults at 25°C at LD12:12

extract_protocol:
RNA was extracted using TRI reagent (MRC, Fisher Scientific), according to manufacturer's protocol
Sequencing and initial bioinformatics analysis was carried out by Edinburgh Genomics, The University of Edinburgh, which is partly supported with core funding from the Natural Environment Research Council (UKSBS PR18037) and BBSRC (BB/T017864/1)
Libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep kits

treatment_protocol: 1-4 days old, mated females and males were infected with Staphylococcus aureus (PIG1) or  Providencia rettgeri (DSM4542) by pricking the flies with a tungsten needle dipped in bacterial solution (OD600=0.1). Samples were collected 8 and 20 hours after infecting the flies. Systemic infection with DCV was introduced to 2-5 days old, mated females and males by pricking as described with the bacterial infections. DCV inoculum of 10^8 viral particles was used. Samples were collected 3 days after the infection with DCV. As controls, uninfected flies of similar age were collected.

value: whole fly

tag: gender

value: female

value: OR


title: HDT2_S#B1_19:00

type: RNA

city: Guildford

first: Simon

last: Archer

address: Stag Hill

institute: University of Surrey

description: Gene expression of participant S#B1, sampling session HDT2, at 19:00 hr

hyb_protocol: Labeled cRNA (1.65 μg) was hy- bridized on a Whole Human Genome SurePrint G3 8x60k custom oligonucleotide microarray (G4102A, AMADID 085218; Agilent). Standard manufacturer’s in- structions for one-color gene-expression analysis were followed for labeling, hybridization and washing steps. Microarrays were hybridized at 65 °C for 17 h in an Agilent hybridization oven with rotisserie at 10 rpm. The microarrays were washed with Agilent Wash Buffer 1, prewarmed Wash Buffer 2 (37 °C), and acetonitrile, according to the manufacturer’s instructions. The last washing step was performed with Agilent Stabilization and Drying Solution for 30 s.

scan_protocol: The processed microarrays were scanned using an Agilent Microarray Scanner with a resolution of 5 μm, exploiting the extended dynamic range feature. The two images derived from each slide were scanned at 10% and 100% PMT and imported into the Agilent Feature Extraction software (v4.0.1.2.1) for image analysis.

data_processing: Log 2 values were quantile- normalized using the normalizeBetweenArrays function from R package limma (v3.46.0). Non-control 44k probes (all probes in microarray with GEO accession no. GPL15331) were were extracted resulting in a Gene Expression Matrix (GEM) of 41,619 transcripts in 637 samples. Transcripts flagged in any of the FE QC variables in less than 20% of the samples were retained for all analyses (n=27,154).

source_name: Peripherial_blood, participant S#B1, sampling session HDT2, at 19:00 hr

label_protocol: cRNA was synthesized and fluorescently labeled with Cy3-CTP from 100 ng of total RNA using the Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Whole blood was collected via an indwelling cannula

extract_protocol: Total RNA was isolated using a PAXgene Blood RNA Kit and a QiaCube robot (Qiagen, Hilden, Germany). The RNA was quantified and the A260/280 nm and A260/230 nm ratios were determined using a NanoDrop ND1000 spectrophotometer (Wilmington, DE). RNA quality was assessed using the Bioanalyzer 2100 (Agilent, Santa Clara, CA).

treatment_protocol: Whole peripheral blood (2.5 mL) was collected using PAXgene Blood RNA tubes (BD Biosciences) at selected time points.

tag: melatonin offset (decimal time)


title: con-1.Input

value: without any treatment


title: OR female flies, 20 h post Staphylococcus aureus infection, rep3


title: HC_M1P1_D13

description:
Smartseq
cell by gene matrix


title: MiaPaca-2_shPRMT1, RNA, rep2

city: Daejeon

first: Bomin

last: Ku

address: 335 Gwahak-ro

department: Biological Sciences

country: South Korea

institute: Korea advanced institute of science and technology (KAIST)

data_processing:
Libraries were sequenced on a NovaSeq 6000 with paired-end method (100bp).
Raw reads were trimmed using Trim_galore (v 0.6.7) and aligned to the hg19 genome using HISAT2 (v 2.2.1)
Trimmed reads were assembled and quantified using Stringtie (v 2.2.1) and normalized with Ballgown (v 2.26.0) and EdgeR (v3.36.0).
Bigwig files were generated using deeptools2 BamCoverage
Assembly: hg19
Supplementary files format and content: tab-delimited text file of RNA-seq

growth_protocol: DMEM, 10% fetal bovine serum, 2.5% horse serum, 1X penicillin/streptomycin. Cells were cultured at standard culture condition (37C, 5% CO2).

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min. Chromatin was sonicated for 10 min and subjected to immunoprecipitation with H3K27ac antibody.
Sequencing libraries were constructed with a TruSeq Standard Total RNA library Prep Gold Kit

value: pancreatic cancer


title: OR female flies, 20 h post Staphylococcus aureus infection, rep1


title: OR female flies, 20 h post Staphylococcus aureus infection, rep2


title: KSA2 male flies, 8 h post Staphylococcus aureus infection, rep4

value: male


title: MiaPaca-2_shNTC, RNA, rep1

value: shNTC


title: BDC2_S#D1_19:00

description: Gene expression of participant S#D1, sampling session BDC2, at 19:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session BDC2, at 19:00 hr


title: HDT2_S#B1_15:00

description: Gene expression of participant S#B1, sampling session HDT2, at 15:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session HDT2, at 15:00 hr


title: HC_M1P1_C9

description:
Smartseq
cell by gene matrix


title: HC_M1P1_C8

description:
Smartseq
cell by gene matrix


title: MiaPaca-2, input

library_source: genomic

data_processing:
Libraries were sequenced on a NovaSeq 6000 with paired-end method (150bp).
Raw reads were trimmed using Trim_galore (v 0.6.7) and aligned to the hg19 genome using Bowtie2 (v 2.4.4)
Duplicates were removed using Picard MarkDuplicates (v 2.26.3)
Peaks were called using MACS3 (v 3.0.0)
Bigwig files were generated using deeptools2 BamCoverage (v 3.5.1)
Assembly: hg19
Supplementary files format and content: BigWig file of ChIP-seq

molecule: genomic DNA

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min. Chromatin was sonicated for 10 min and subjected to immunoprecipitation with H3K27ac antibody.
Sequencing libraries were constructed with a TruSeq ChIP-seq Library Preparation Kit

tag: antibody


title: BDC2_S#B1_19:00

description: Gene expression of participant S#B1, sampling session BDC2, at 19:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session BDC2, at 19:00 hr


title: BDC2_S#D1_15:00

description: Gene expression of participant S#D1, sampling session BDC2, at 15:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session BDC2, at 15:00 hr


title: MiaPaca-2_shPRMT1, H3K27ac, rep2

value: ChIP with H3K27ac ab(ab4729)


title: HC_M1P1_D14

description:
Smartseq
cell by gene matrix


title: KSA2 male flies, 8 h post Staphylococcus aureus infection, rep2


title: MiaPaca-2_shPRMT1, RNA, rep1


title: BDC1_S#D1_11:00

description: Gene expression of participant S#D1, sampling session BDC1, at 11:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session BDC1, at 11:00 hr


title: HC_M1P1_C7

description:
Smartseq
cell by gene matrix


title: KSA2 male flies, 8 h post Staphylococcus aureus infection, rep1


title: BDC2_S#B1_15:00

description: Gene expression of participant S#B1, sampling session BDC2, at 15:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session BDC2, at 15:00 hr


title: HC_M1P1_D12

description:
Smartseq
cell by gene matrix


title: HC_M1P1_D10

description:
Smartseq
cell by gene matrix


title: KSA2 female flies, 8 h post Staphylococcus aureus infection, rep4


title: MiaPaca-2_shNTC, RNA, rep2


title: HC_M1P1_C6

description:
Smartseq
cell by gene matrix


title: MiaPaca-2_shPRMT1, H3K27ac, rep1


title: HC_M1P1_C5

description:
Smartseq
cell by gene matrix


title: KSA2 female flies, 8 h post Staphylococcus aureus  infection, rep3


title: MiaPaca-2_shNTC, H3K27ac, rep2


title: KSA2 male flies, 8 h post Staphylococcus aureus infection, rep3


title: MiaPaca-2_shNTC, H3K27ac, rep1


title: HC_M1P1_C23

description:
Smartseq
cell by gene matrix


title: BDC1_S#D1_03:00

description: Gene expression of participant S#D1, sampling session BDC1, at 03:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session BDC1, at 03:00 hr


title: KSA2 female flies, 8 h post Staphylococcus aureus  infection, rep2


title: c3Seq_22NC_rep3

city: Wuhan

first: Rui

last: Xiao

state: Hubei

address: Medical Research Institute, Wuhan University

department: Medical Research Institute

institute: Wuhan University

data_processing:
C3’-seq reads were firstly trimmed using cutadapt (v3.4)73 to remove adaptor and dT sequence at 3’ end and aligned against the hg19 genome with STAR (2.6.0a);
Reads of low quality were filtered and the uniquely mapped reads were used;
Normalized bigwig was generated with bedtools.
Assembly: GRCh37 (hg19)
Supplementary files format and content: bigWig
Library strategy: C3'-Seq

extract_protocol:
Total RNA was isolated using TRIzol followed by two consecutive phenol-chloroform extractions and then precipitated by ethanol
Sheared RNA and RT-circulation-primer were used for reverse transcription,the cDNA circularization was performed using CircLigase II (epicenter, CL9021K) for 1 hour at 60 °C

value: Hepatocellular carcinom

value: WT


title: BDC1_S#D1_23:00

description: Gene expression of participant S#D1, sampling session BDC1, at 23:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session BDC1, at 23:00 hr


title: HC_M1P1_C22

description:
Smartseq
cell by gene matrix


title: KSA2 female flies, 8 h post Staphylococcus aureus  infection, rep1


title: BDC1_S#B1_11:00

description: Gene expression of participant S#B1, sampling session BDC1, at 11:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session BDC1, at 11:00 hr


title: c3Seq_22NC_rep2


title: OR male flies, 8 h post Staphylococcus aureus  infection, rep4


title: HC_M1P1_C21

description:
Smartseq
cell by gene matrix


title: BDC1_S#D1_07:00

description: Gene expression of participant S#D1, sampling session BDC1, at 07:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session BDC1, at 07:00 hr


title: HC_M1P1_C2

description:
Smartseq
cell by gene matrix


title: c3Seq_22KD_rep3

value: knockdown RBM22


title: OR male flies, 8 h post Staphylococcus aureus infection, rep3


title: HC_M1P1_C18

description:
Smartseq
cell by gene matrix


title: HC_M1P1_C17

description:
Smartseq
cell by gene matrix


title: OR male flies, 8 h post Staphylococcus aureus  infection, rep1


title: OR male flies, 8 h post Staphylococcus aureus infection, rep2


title: BDC1_S#B1_07:00

description: Gene expression of participant S#B1, sampling session BDC1, at 07:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session BDC1, at 07:00 hr


title: c3Seq_22KD_rep1


title: BDC1_S#B1_03:00

description: Gene expression of participant S#B1, sampling session BDC1, at 03:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session BDC1, at 03:00 hr


title: c3Seq_22KD_rep2


title: HC_M1P1_C14

description:
Smartseq
cell by gene matrix


title: POLR2A_Input_22NC2_5min

description: input DNA

data_processing:
ChIP-seq data were processed in accordance with ENCODE uniform transcription factor ChIP-seq pipeline (https://www.encodeproject.org/chip-seq/transcription_factor/).
Briefly, ChIP-seq reads were aligned to the GRCh37 human genome using BWA;
PCR duplicates and reads of low quality were filtered;
Normalized bigwig was generated with bedtools.
Assembly: GRCh37 (hg19)
Supplementary files format and content: bigWig

extract_protocol:
Nuclei were isolated and sonicated and lysates were cleared-up and applied for purification of protein-DNA complexes with antibodies.
Libraries were constructed using the VAHTSTM Universal DNA Library Prep Kit (Vazyme, ND606).


title: OR female flies, 8 h post Staphylococcus aureus infection, rep4


title: HC_M1P1_C13

description:
Smartseq
cell by gene matrix


title: OR female flies, 8 h post Staphylococcus aureus infection, rep3


title: HDT1_S#B1_19:00

description: Gene expression of participant S#B1, sampling session HDT1, at 19:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session HDT1, at 19:00 hr


title: POLR2A_Input_22NC2_20min

description: input DNA


title: c3Seq_22NC_rep1


title: BDC1_S#B1_23:00

description: Gene expression of participant S#B1, sampling session BDC1, at 23:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session BDC1, at 23:00 hr


title: HC_M1P1_C11

description:
Smartseq
cell by gene matrix

source_name: posteromedial nucleus of the cortical amygdala


title: POLR2A_Input_22NC2_10min

description: input DNA


title: OR female flies, 8 h post Staphylococcus aureus infection, rep2

source_name: whole fly


title: HC_M1P1_C10

description:
Smartseq
cell by gene matrix


title: HDT1_S#B1_15:00

description: Gene expression of participant S#B1, sampling session HDT1, at 15:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session HDT1, at 15:00 hr


title: OR female flies, 8 h post Staphylococcus aureus infection, rep1


title: BDC1_S#D1_19:00

description: Gene expression of participant S#D1, sampling session BDC1, at 19:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session BDC1, at 19:00 hr


title: HDT1_S#D1_19:00

description: Gene expression of participant S#D1, sampling session HDT1, at 19:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session HDT1, at 19:00 hr


title: BDC1_S#D1_15:00

description: Gene expression of participant S#D1, sampling session BDC1, at 15:00 hr

source_name: Peripherial_blood, participant S#D1, sampling session BDC1, at 15:00 hr


title: POLR2A_Input_22NC2_0min

description: input DNA


title: HDT1_S#B1_03:00

description: Gene expression of participant S#B1, sampling session HDT1, at 03:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session HDT1, at 03:00 hr


title: HC_M1P1_B9

description:
Smartseq
cell by gene matrix


title: POLR2A_Input_22NC1_5min

description: input DNA


title: KSA2 male flies, 20 h post Providencia rettgeri infection, rep4


title: HC_M1P1_B8

description:
Smartseq
cell by gene matrix


title: KSA2 male flies, 20 h post Providencia rettgeri infection, rep3


title: BDC1_S#B1_15:00

description: Gene expression of participant S#B1, sampling session BDC1, at 15:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session BDC1, at 15:00 hr


title: POLR2A_Input_22NC1_20min

description: input DNA


title: HC_M1P1_B7

description:
Smartseq
cell by gene matrix


title: BDC1_S#B1_19:00

description: Gene expression of participant S#B1, sampling session BDC1, at 19:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session BDC1, at 19:00 hr


title: KSA2 male flies, 20 h post Providencia rettgeri infection, rep2


title: HC_M1P1_B6

description:
Smartseq
cell by gene matrix


title: POLR2A_Input_22NC1_10min

description: input DNA


title: POLR2A_Input_22NC1_0min

description: input DNA


title: HC_M1P1_B5

description:
Smartseq
cell by gene matrix


title: KSA2 male flies, 20 h post Providencia rettgeri infection, rep1


title: R_S#C1_07:00

description: Gene expression of participant S#C1, sampling session R, at 07:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session R, at 07:00 hr


title: KSA2 female flies, 20 h post Providencia rettgeri infection, rep4


title: POLR2A_Input_22KD2_5min

description: input DNA


title: POLR2A_Input_22KD2_20min

description: input DNA


title: KSA2 female flies, 20 h post Providencia rettgeri infection, rep3


title: KSA2 female flies, 20 h post Providencia rettgeri infection, rep2


title: HC_M1P1_B23

description:
Smartseq
cell by gene matrix


title: POLR2A_Input_22KD2_10min

description: input DNA


title: R_S#C1_23:00

description: Gene expression of participant S#C1, sampling session R, at 23:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session R, at 23:00 hr


title: KSA2 female flies, 20 h post Providencia rettgeri infection, rep1


title: R_S#C1_03:00

description: Gene expression of participant S#C1, sampling session R, at 03:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session R, at 03:00 hr


title: HDT1_S#B1_07:00

description: Gene expression of participant S#B1, sampling session HDT1, at 07:00 hr

source_name: Peripherial_blood, participant S#B1, sampling session HDT1, at 07:00 hr


title: POLR2A_Input_22KD2_0min

description: input DNA


title: HC_M1P1_B20

description:
Smartseq
cell by gene matrix


title: R_S#A1_07:00

description: Gene expression of participant S#A1, sampling session R, at 07:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session R, at 07:00 hr


title: POLR2A_Input_22KD1_5min

description: input DNA


title: OR male flies, 20 h post Providencia rettgeri infection, rep4


title: OR male flies, 20 h post Providencia rettgeri infection, rep3


title: POLR2A_Input_22KD1_20min

description: input DNA


title: OR male flies, 20 h post Providencia rettgeri infection, rep2


title: HC_M1P1_B3

description:
Smartseq
cell by gene matrix


title: R_S#A1_23:00

description: Gene expression of participant S#A1, sampling session R, at 23:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session R, at 23:00 hr


title: POLR2A_Input_22KD1_10min

description: input DNA


title: HC_M1P1_B16

description:
Smartseq
cell by gene matrix


title: POLR2A_Input_22KD1_0min

description: input DNA


title: HDT3_S#C1_11:00

description: Gene expression of participant S#C1, sampling session HDT3, at 11:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session HDT3, at 11:00 hr


title: HC_M1P1_B22

description:
Smartseq
cell by gene matrix


title: HDT3_S#A1_07:00

description: Gene expression of participant S#A1, sampling session HDT3, at 07:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session HDT3, at 07:00 hr


title: HC_M1P1_B15

description:
Smartseq
cell by gene matrix

source_name: posteromedial nucleus of the cortical amygdala


title: OR female flies, 20 h post Providencia rettgeri infection, rep4

source_name: whole fly


title: R_S#A1_03:00

description: Gene expression of participant S#A1, sampling session R, at 03:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session R, at 03:00 hr


title: HDT3_S#A1_03:00

description: Gene expression of participant S#A1, sampling session HDT3, at 03:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session HDT3, at 03:00 hr


title: HC_M1P1_B13

description:
Smartseq
cell by gene matrix


title: HC_M1P1_B14

description:
Smartseq
cell by gene matrix


title: POLR2A_ChIP_22NC2_5min

description: ChIP-seq data


title: POLR2A_ChIP_22NC2_20min

description: ChIP-seq data


title: OR female flies, 20 h post Providencia rettgeri infection, rep3


title: HDT3_S#C1_07:00

description: Gene expression of participant S#C1, sampling session HDT3, at 07:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session HDT3, at 07:00 hr


title: POLR2A_ChIP_22NC2_10min

description: ChIP-seq data


title: OR female flies, 20 h post Providencia rettgeri infection, rep2


title: HDT3_S#C1_19:00

description: Gene expression of participant S#C1, sampling session HDT3, at 19:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session HDT3, at 19:00 hr


title: HC_M1P1_A7

description:
Smartseq
cell by gene matrix


title: HDT3_S#A1_23:00

description: Gene expression of participant S#A1, sampling session HDT3, at 23:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session HDT3, at 23:00 hr


title: HC_M1P1_A6

description:
Smartseq
cell by gene matrix


title: POLR2A_ChIP_22NC2_0min

description: ChIP-seq data


title: OR male flies, 20 h post Providencia rettgeri infection, rep1


title: HDT3_S#C1_23:00

description: Gene expression of participant S#C1, sampling session HDT3, at 23:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session HDT3, at 23:00 hr


title: POLR2A_ChIP_22NC1_5min

description: ChIP-seq data


title: HC_M1P1_B18

description:
Smartseq
cell by gene matrix


title: HDT3_S#C1_15:00

description: Gene expression of participant S#C1, sampling session HDT3, at 15:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session HDT3, at 15:00 hr


title: HC_M1P1_A5

description:
Smartseq
cell by gene matrix


title: KSA2 male flies, 8 h post Providencia rettgeri infection, rep3

value: 8 h post Providencia rettgeri infection


title: R_S#A1_15:00

description: Gene expression of participant S#A1, sampling session R, at 15:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session R, at 15:00 hr


title: HC_M1P1_A4

description:
Smartseq
cell by gene matrix


title: POLR2A_ChIP_22NC1_20min

description: ChIP-seq data


title: HC_M1P1_A3

description:
Smartseq
cell by gene matrix


title: POLR2A_ChIP_22NC1_10min

description: ChIP-seq data


title: KSA2 male flies, 8 h post Providencia rettgeri infection, rep2


title: POLR2A_ChIP_22NC1_0min

description: ChIP-seq data


title: KSA2 male flies, 8 h post Providencia rettgeri infection, rep1


title: HDT3_S#A1_19:00

description: Gene expression of participant S#A1, sampling session HDT3, at 19:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session HDT3, at 19:00 hr


title: OR female flies, 20 h post Providencia rettgeri infection, rep1


title: HDT3_S#A1_15:00

description: Gene expression of participant S#A1, sampling session HDT3, at 15:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session HDT3, at 15:00 hr


title: HC_M1P1_A22

description:
Smartseq
cell by gene matrix


title: HC_M1P1_A21

description:
Smartseq
cell by gene matrix


title: POLR2A_ChIP_22KD2_20min

description: ChIP-seq data


title: HDT2_S#C1_11:00

description: Gene expression of participant S#C1, sampling session HDT2, at 11:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session HDT2, at 11:00 hr


title: KSA2 female flies, 8 h post Providencia rettgeri infection, rep3


title: HDT2_S#C1_03:00

description: Gene expression of participant S#C1, sampling session HDT2, at 03:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session HDT2, at 03:00 hr


title: KSA2 male flies, 8 h post Providencia rettgeri infection, rep4


title: R_S#A1_19:00

description: Gene expression of participant S#A1, sampling session R, at 19:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session R, at 19:00 hr


title: KSA2 female flies, 8 h post Providencia rettgeri infection, rep2


title: POLR2A_ChIP_22KD2_10min

description: ChIP-seq data


title: KSA2 female flies, 8 h post Providencia rettgeri infection, rep1


title: HC_M1P1_A20

description:
Smartseq
cell by gene matrix


title: POLR2A_ChIP_22KD2_0min

description: ChIP-seq data


title: HDT2_S#C1_23:00

description: Gene expression of participant S#C1, sampling session HDT2, at 23:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session HDT2, at 23:00 hr


title: OR male flies, 8 h post Providencia rettgeri infection, rep4


title: HC_M1P1_A2

description:
Smartseq
cell by gene matrix


title: HC_M1P1_A23

description:
Smartseq
cell by gene matrix


title: HDT2_S#A1_11:00

description: Gene expression of participant S#A1, sampling session HDT2, at 11:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session HDT2, at 11:00 hr


title: KSA2 female flies, 8 h post Providencia rettgeri infection, rep4


title: OR male flies, 8 h post Providencia rettgeri infection, rep3


title: POLR2A_ChIP_22KD1_20min

description: ChIP-seq data


title: HC_M1P1_A19

description:
Smartseq
cell by gene matrix

source_name: posteromedial nucleus of the cortical amygdala


title: POLR2A_ChIP_22KD2_5min

description: ChIP-seq data


title: HC_M1P1_A18

description:
Smartseq
cell by gene matrix


title: OR male flies, 8 h post Providencia rettgeri infection, rep1

source_name: whole fly


title: POLR2A_ChIP_22KD1_10min

description: ChIP-seq data


title: HC_M1P1_A17

description:
Smartseq
cell by gene matrix


title: POLR2A_ChIP_22KD1_0min

description: ChIP-seq data


title: HDT1_S#C1_07:00

description: Gene expression of participant S#C1, sampling session HDT1, at 07:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session HDT1, at 07:00 hr


title: HDT2_S#A1_07:00

description: Gene expression of participant S#A1, sampling session HDT2, at 07:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session HDT2, at 07:00 hr


title: HC_M1P1_A16

description:
Smartseq
cell by gene matrix


title: HDT1_S#C1_11:00

description: Gene expression of participant S#C1, sampling session HDT1, at 11:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session HDT1, at 11:00 hr


title: OR female flies, 8 h post Providencia rettgeri infection, rep4


title: POLR2A_ChIP_22KD1_5min

description: ChIP-seq data


title: HEXIM1_Input_NC_rep2

description: input DNA


title: OR female flies, 8 h post Providencia rettgeri infection, rep3


title: OR male flies, 8 h post Providencia rettgeri infection, rep2


title: HDT1_S#C1_23:00

description: Gene expression of participant S#C1, sampling session HDT1, at 23:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session HDT1, at 23:00 hr


title: HEXIM1_Input_NC_rep1

description: input DNA


title: OR female flies, 8 h post Providencia rettgeri infection, rep2


title: HDT1_S#A1_07:00

description: Gene expression of participant S#A1, sampling session HDT1, at 07:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session HDT1, at 07:00 hr


title: HEXIM1_Input_22KD_rep2

description: input DNA


title: OR female flies, 8 h post Providencia rettgeri infection, rep1


title: HEXIM1_Input_22KD_rep1

description: input DNA


title: HC_M1P1_A13

description:
Smartseq
cell by gene matrix


title: HC_M1P1_A12

description:
Smartseq
cell by gene matrix


title: HDT1_S#A1_03:00

description: Gene expression of participant S#A1, sampling session HDT1, at 03:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session HDT1, at 03:00 hr


title: HDT1_S#C1_03:00

description: Gene expression of participant S#C1, sampling session HDT1, at 03:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session HDT1, at 03:00 hr


title: HEXIM1_ChIP_NC_rep2

description: ChIP-seq data


title: BDC2_S#C1_11:00

description: Gene expression of participant S#C1, sampling session BDC2, at 11:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session BDC2, at 11:00 hr


title: KSA2 male flies, uninfected, rep3

value: uninfected


title: HDT1_S#A1_23:00

description: Gene expression of participant S#A1, sampling session HDT1, at 23:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session HDT1, at 23:00 hr


title: HC_M1P1_A10

description:
Smartseq
cell by gene matrix


title: KSA2 male flies, uninfected, rep2


title: HEXIM1_ChIP_NC_rep1

description: ChIP-seq data


title: G-6

city: Xi'an

first: Lele

last: Cheng

address: 277 West Yanta Road

institute: The First Affiliated Hospital of Xi’an Jiaotong University

data_processing:
Illumina Casava1.8 software used for basecalling.
clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Index of the reference genome was built using Hisat2 v2.1.0 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.1.0.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with abundance measurements for every gene and every sample

source_name: liver

extract_protocol:
Liver were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HFD+vehicle or HFD+GUDCA was treated for 1 week.

tag: strain

value: liver

value: GUDCA


title: KSA2 male flies, uninfected, rep4


title: HEXIM1_ChIP_22KD_rep2

description: ChIP-seq data


title: HC_M1P1_A14

description:
Smartseq
cell by gene matrix


title: G-5


title: KSA2 male flies, uninfected, rep1


title: HEXIM1_ChIP_22KD_rep1

description: ChIP-seq data


title: G-4


title: KSA2 female flies, uninfected, rep4


title: CDK9_Input_NC_rep2

description: input DNA


title: BDC2_S#A1_07:00

description: Gene expression of participant S#A1, sampling session BDC2, at 07:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session BDC2, at 07:00 hr


title: KSA2 female flies, uninfected, rep3


title: V-3

value: Vehicle


title: V-2


title: KSA2 female flies, uninfected, rep2


title: BDC2_S#A1_03:00

description: Gene expression of participant S#A1, sampling session BDC2, at 03:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session BDC2, at 03:00 hr


title: CDK9_Input_22KD_rep2

description: input DNA


title: KSA2 female flies, uninfected, rep1


title: OR male flies, uninfected, rep4


title: HDT2_S#C1_19:00

description: Gene expression of participant S#C1, sampling session HDT2, at 19:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session HDT2, at 19:00 hr


title: shLin28a32

city: yangling

first: Wu

last: Xiaolong

state: Shannxi

address: College of Veterinary MedicineShaanxi Centre of Stem Cells Engineering and Techn

department: College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology

institute: Northwest A&F University

data_processing:
BGIseq500 platform used for basecalling.
Align clean reads to the reference genes by using Bowtie2 to get the alignment result
The sequencing data was filtered with SOAPnuke (v1.5.2).
The expression level of gene was calculated by RSEM (v1.2.12).
Genome_build: GCF_000003025.6_Sscrofa11.1
Supplementary_files_format_and_content: Matrix table with raw gene counts and FPKM values for every gene and every sample

organism: Sus scrofa

source_name: porcine induced pluripotent stem cells

extract_protocol:
1.Total RNA was extracted using RNAiso Plus reagent; 2.mRNA enrichment and purification: Oligo dT Selection to enrich the mRNA; 3.RNA fragmentation and cDNA synthesis; 4.End repair, add A and adaptor ligation; 5.PCR; 6.Circularization and make DNB.
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols

tag: development stage

tag: breed

value: Bamei black pig

value: induced pluripotent stem cells


title: CDK9_Input_22KD_rep1

description: input DNA


title: BDC2_S#A1_11:00

description: Gene expression of participant S#A1, sampling session BDC2, at 11:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session BDC2, at 11:00 hr


title: BDC2_S#C1_23:00

description: Gene expression of participant S#C1, sampling session BDC2, at 23:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session BDC2, at 23:00 hr


title: CDK9_ChIP_NC_rep1

description: ChIP-seq data


title: OR male flies, uninfected, rep3

source_name: whole fly

value: whole fly


title: CDK9_Input_NC_rep1

description: input DNA


title: HDT2_S#A1_19:00

description: Gene expression of participant S#A1, sampling session HDT2, at 19:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session HDT2, at 19:00 hr


title: HDT2_S#C1_15:00

description: Gene expression of participant S#C1, sampling session HDT2, at 15:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session HDT2, at 15:00 hr


title: shNC2

value: Negative Control


title: CDK9_ChIP_NC_rep2

description: ChIP-seq data


title: shNC1


title: CDK9_ChIP_22KD_rep2

description: ChIP-seq data


title: OR male flies, uninfected, rep2

value: OR


title: BDC2_S#A1_23:00

description: Gene expression of participant S#A1, sampling session BDC2, at 23:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session BDC2, at 23:00 hr


title: OR male flies, uninfected, rep1


title: HC_M1P1_B19

description:
Smartseq
cell by gene matrix

source_name: posteromedial nucleus of the cortical amygdala


title: CDK9_ChIP_22KD_rep1

description: ChIP-seq data


title: conrep3C

city: Grand Rapids

first: Robert

last: Fillinger

state: Michigan

address: 333 Bostwick Ave NE

institute: Van Andel Institute

data_processing:
Takara's cogentAP
STAR alignment
kallisto pseudo alignment (QC)
Assembly: WBcel235
Supplementary files format and content: comma separated value (CSV) containing differentially expressed genes (e.g. significance, fold change) of transcriptomes between treatment groups

organism: Caenorhabditis elegans

source_name: oocyte

growth_protocol: animals were raised on NGM under standard culture conditions

extract_protocol:
C. elegans mothers were cultured from the adolescent L4 stage until the first day of adulthood on control NGM culture or on osmotic stress 300mM NaCl culture. The mature oocytes were then dissected and collected in SMART seq buffer.
SMARTer Stranded Total RNA-Seq Kit v3 - Pico

treatment_protocol: adolescent C. elegans mothers were transferred to NGM with a 300mM NaCl concentration until day 1 of adulthood

value: oocyte

value: control NGM culture


title: OR female flies, uninfected, rep4

value: female


title: BDC2_S#C1_19:00

description: Gene expression of participant S#C1, sampling session BDC2, at 19:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session BDC2, at 19:00 hr


title: shLin28a31


title: SPT5_Input_NC_rep2

description: input DNA


title: OR female flies, uninfected, rep3


title: conrep3B


title: HDT2_S#A1_23:00

description: Gene expression of participant S#A1, sampling session HDT2, at 23:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session HDT2, at 23:00 hr


title: SPT5_Input_NC_rep1

description: input DNA


title: OR female flies, uninfected, rep2


title: conrep3A


title: BDC2_S#C1_15:00

description: Gene expression of participant S#C1, sampling session BDC2, at 15:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session BDC2, at 15:00 hr


title: conrep2C


title: OR female flies, uninfected, rep1


title: SPT5_Input_22KD_rep1

description: input DNA


title: BDC1_S#C1_07:00

description: Gene expression of participant S#C1, sampling session BDC1, at 07:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session BDC1, at 07:00 hr


title: SPT5_Input_22KD_rep2

description: input DNA


title: BDC2_S#A1_19:00

description: Gene expression of participant S#A1, sampling session BDC2, at 19:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session BDC2, at 19:00 hr


title: BDC2_S#A1_15:00

description: Gene expression of participant S#A1, sampling session BDC2, at 15:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session BDC2, at 15:00 hr


title: conrep2B


title: MiaPaca-2_shPRMT1, rep2

data_processing:
Libraries were sequenced on a Illumina platform with paired-end method (150bp).
Raw reads were trimmed using Trim_galore (v 0.6.7) and aligned to the hg19 genome using Bowtie2 (v 2.4.4)
Duplicates were removed using Picard MarkDuplicates (v 2.26.3)
Peaks were called using MACS3 (v 3.0.0)
Bigwig files were generated using deeptools2 BamCoverage (v 3.5.1)
Assembly: hg19
Supplementary files format and content: BigWig file of ATAC-seq

extract_protocol:
Cells were lysed, and nuclei pellets were transposed for 30min at 37C.
Sequencing libraries were constructed with a Active Motif ATAC-seq Kit, as per manufacturrer's instructions.

value: pancreatic cancer


title: SPT5_ChIP_NC_rep2

description: ChIP-seq data

value: Hepatocellular carcinom


title: BDC1_S#C1_03:00

description: Gene expression of participant S#C1, sampling session BDC1, at 03:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session BDC1, at 03:00 hr


title: MiaPaca-2_shPRMT1, rep1


title: conrep2A


title: BDC1_S#C1_23:00

description: Gene expression of participant S#C1, sampling session BDC1, at 23:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session BDC1, at 23:00 hr


title: SPT5_ChIP_NC_rep1

description: ChIP-seq data

value: WT


title: conrep1B


title: MiaPaca-2_shNTC, rep2

value: shNTC


title: conrep1C


title: BDC1_S#A1_11:00

description: Gene expression of participant S#A1, sampling session BDC1, at 11:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session BDC1, at 11:00 hr


title: MiaPaca-2_shNTC, rep1


title: SPT5_ChIP_22KD_rep1

description: ChIP-seq data

value: knockdown RBM22


title: BDC1_S#A1_07:00

description: Gene expression of participant S#A1, sampling session BDC1, at 07:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session BDC1, at 07:00 hr


title: 300rep3A

value: 300mM NaCl culture


title: POLR2G_Input_NC_rep2

description: input DNA


title: HET-TEC-19081 RNAseq

city: Phoenix

first: Ying-Wei

last: Lan

address: 475 N. 5th Street

department: Child Health

institute: The University of Arizona College of Medicine-Phoenix

data_processing:
RNA from endothelial cells isolated from bleomycin-treated control and endFoxf1+/- mouse lungs were used for RNA-seq analysis. RNeasy Mini kit (Qiagen) was used to isolate total RNA from total lung lysates or isolated endotheilal populations. mRNAs of specific genes were analyzed by qRT–PCR using the StepOnePlus Real-Time PCR system (Applied Biosystems) Next-generation sequencing of equimolar pools of cDNA libraries was performed using a single read 75 rapid flow cell on a HiSeq 2500 sequencing platform (Illumina), generating greater than 20 million raw reads per sample. The raw sequenced reads were aligned from FASTQ files to the mouse genome build GRCm38/mm10 and the UCSC reference transcriptome (http://ccb.jhu.edu/software/tophat/index.shtml) using “Cufflinks” .
The expression profile of samples were quantified using SUBREAD
Differential expression was assessed using the R package DEseq2.
Assembly: mm10
Supplementary files format and content: For RNA-seq excel file lists TPM  for genes in control and endFoxf1+/-

source_name: Lung

growth_protocol: Mice were housed in barrier and all experiments were performed in accordance with approved IACUC protocols.

extract_protocol:
total RNA was extracted from FACS-sorted endothelial cells using the Qiagen QIAquick RNA isolation kit.
Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation Kit (Illumina).

treatment_protocol: RNAseq was performed on cells isolated  21 days post tumor cell injection.

value: Lung

value: FACS-sorted lung endothelial cells (CD45-CD31+)


title: HET-TEC-19082 RNAseq


title: 300rep3C


title: HET-TEC-19083 RNAseq


title: HET-TEC-19079 RNAseq


title: POLR2G_Input_22KD_rep1

description: input DNA


title: 300rep2C


title: POLR2G_ChIP_NC_rep2

description: ChIP-seq data


title: POLR2G_Input_22KD_rep2

description: input DNA


title: 300rep2B


title: conrep1A


title: ConTEC-19077 RNAseq

value: control


title: SPT5_ChIP_22KD_rep2

description: ChIP-seq data


title: BDC1_S#A1_23:00

description: Gene expression of participant S#A1, sampling session BDC1, at 23:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session BDC1, at 23:00 hr


title: HDT1_S#C1_19:00

description: Gene expression of participant S#C1, sampling session HDT1, at 19:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session HDT1, at 19:00 hr


title: POLR2G_ChIP_NC_rep1

description: ChIP-seq data


title: HDT1_S#A1_19:00

description: Gene expression of participant S#A1, sampling session HDT1, at 19:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session HDT1, at 19:00 hr


title: HDT1_S#A1_15:00

description: Gene expression of participant S#A1, sampling session HDT1, at 15:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session HDT1, at 15:00 hr


title: BDC1_S#A1_03:00

description: Gene expression of participant S#A1, sampling session BDC1, at 03:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session BDC1, at 03:00 hr


title: 300rep3B

source_name: oocyte


title: POLR2G_Input_NC_rep1

description: input DNA


title: BDC1_S#C1_19:00

description: Gene expression of participant S#C1, sampling session BDC1, at 19:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session BDC1, at 19:00 hr


title: 300rep2A


title: ConTEC-19076 RNAseq


title: 300rep1B


title: ConTEC-19078 RNAseq


title: HDT2_S#A1_15:00

description: Gene expression of participant S#A1, sampling session HDT2, at 15:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session HDT2, at 15:00 hr


title: HDT1_S#C1_15:00

description: Gene expression of participant S#C1, sampling session HDT1, at 15:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session HDT1, at 15:00 hr


title: POLR2G_ChIP_22KD_rep1

description: ChIP-seq data


title: BDC1_S#C1_15:00

description: Gene expression of participant S#C1, sampling session BDC1, at 15:00 hr

source_name: Peripherial_blood, participant S#C1, sampling session BDC1, at 15:00 hr


title: 300rep1A


title: Thymic stromal cells, IRF6flox, scRNAseq

status: Public on Mar 08 2024

city: Bethesda

first: Michael

middle: C

last: Kelly

state: MD

address: 41 Center Drive

department: Center for Cancer Research

institute: NCI

description:
10x Genomics
SCAF2439_IRF6flox

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v6.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: filtered scRNA-seq expression matrices in hdf5 format

source_name: Thymic stromal cells

extract_protocol:
Single cell suspensions were generated from target tissues from specific genotype mice. For venus-positive or venus-negative cell populations, cells were sorted by FACs into collection tubes. Cell suspensions were stored on ice, counted and viabilities checked prior to be loaded on the 10x Genomics chromium platform for single cell partitioning, lysis, and reverse transciption of mRNA into cDNA libraries.
Library constructionwas performed according to the manufacter’s instructions (Single Cell 3’ v3 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscribed to cDNA, which contains a partial Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Thymic stromal cells


title: Participant 337061

type: genomic

city: Santa Cruz

first: Audrie

last: Lin

state: CA

address: METX, 1156 High St.

department: Microbiology and Environmental Toxicology

institute: University of California, Santa Cruz

description:
093016-(5)_A8063FS3_B96_1060; 093016-(7)_A1343FS3-B96_1060; 100316-(2)_A749FS_B96_1060; 100316-(3)__A1342FS_B96_1060
sample_type: E1W01

data_processing: Percent DNA methylation for each CpG site and sample being sequenced

source_name: saliva DNA methylation

extract_protocol:
Saliva samples were collected using the Oragene kit (OGR-575). DNA was extracted from 200 µL saliva using DNAdvance (Beckmen Coulter) with the Biomek FXP liquid handler (Beckman Coulter) at EpigenDx (Hopkinton, MA). The NanoDrop 2000 (ThermoFisher Scientific) was used to quantify the extracted DNA by OD260/280.
EpigenDx carried out pyrosequencing of bisulfite-treated DNA. Briefly, 500 ng of extracted genomic DNA was bisulfite treated using the EZ DNA Methylation kit (Zymo Research, Inc., CA). The kit protocol was followed for purification and elution of the bisulfite treated DNA (final elution volume of 46 µL). PCR amplification was achieved using 1 µL of bisulfite treated DNA and 0.2 µM of each primer. To purify the final PCR product using sepharose beads, one primer was biotin-labeled and purified by high performance liquid chromatography. After being bound to Streptavidin Sepharose HP (GE Healthcare Life Sciences), the immobilized PCR products were purified, washed, denatured with a 0.2 µM NaOH solution, and rewashed using the Pyrosequencing Vacuum Prep Tool (Pyrosequencing, Qiagen), according to the manufacturer’s instructions. Purified single stranded PCR products were annealed to 0.5 µM of sequencing primer. Following the manufacturer’s protocol, 10 µL of the PCR products were pyrosequenced on the PSQ96 HS System (Pyrosequencing, Qiagen). QCpG software (Pyrosequencing, Qiagen) was used to analyze the methylation status of each locus (CpG site) individually as an artificial C/T SNP. To calculate the methylation level at each CpG site, the following formula was used: the percentage of methylated alleles divided by the sum of all methylated and unmethylated alleles. To obtain the mean methylation level, the methylation levels of all measured CpG sites within the targeted region of the gene were used. To ensure detection of incomplete bisulfite conversion of the DNA, each experiment used non-CpG cytosines as internal controls. Other controls in each PCR included unmethylated and methylated DNA. To test for bias, unmethylated control DNA was combined with in vitro methylated DNA at several ratios (0%, 5%, 10%, 25%, 50%, 75%, and 100%), the mixed products were bisulfite-modified and underwent PCR, followed by pyrosequencing analysis.

tag: age in months

tag: Sex

tag: treatment arm

value: Nutrition + WSH

tag: dna concentration (ng/ul)

tag: box

tag: box position

tag: ^sample


title: Participant 302051

value: Control


title: Participant 282041


title: Participant 282071


title: Participant 503011


title: Participant 503081


title: Participant 503021


title: BDC1_S#A1_15:00

description: Gene expression of participant S#A1, sampling session BDC1, at 15:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session BDC1, at 15:00 hr


title: BDC1_S#A1_19:00

description: Gene expression of participant S#A1, sampling session BDC1, at 19:00 hr

source_name: Peripherial_blood, participant S#A1, sampling session BDC1, at 19:00 hr


title: Participant 503071


title: Participant 503031


title: Participant 504031


title: Participant 504061


title: POLR2G_ChIP_22KD_rep2

description: ChIP-seq data

tag: cell line

tag: cell type


title: HC_M1P1_A15

description:
Smartseq
cell by gene matrix

source_name: posteromedial nucleus of the cortical amygdala


title: ConTEC-19075  RNAseq

tag: genotype


title: Participant 504011


title: Participant 504051


title: Participant 504041


title: Participant 553081


title: Participant 504081


title: Participant 552011


title: Participant 504021


title: Participant 286021


title: Participant 503041


title: Participant 286051


title: Participant 286061


title: Participant 286031


title: Participant 503051


title: Participant 288031


title: Participant 288071


title: Participant 288051


title: Participant 288021


title: Participant 518071


title: Participant 299051


title: Participant 333041


title: Participant 518021


title: Participant 518011


title: Participant 288011


title: Participant 518031


title: Participant 518051


title: Participant 554081


title: Participant 294061


title: Participant 294041


title: Participant 518081


title: Participant 294021


title: Participant 294051


title: Participant 299031


title: Participant 299061


title: Participant 302011


title: Participant 302021


title: Participant 299071


title: Participant 302041


title: Participant 302081


title: Participant 299011


title: Participant 302061


title: Participant 321081


title: Participant 321021


title: Participant 321041


title: Participant 321061


title: Participant 288041


title: Participant 524031


title: Participant 302071


title: Participant 321011


title: Participant 524021


title: Participant 524071


title: Participant 524081


title: Participant 524051


title: Participant 524041


title: Participant 551031


title: Participant 551071


title: Participant 551061


title: Participant 294031


title: Participant 551021


title: V-1

source_name: liver

tag: tissue

value: liver

tag: treatment

value: Vehicle


title: Participant 294081


title: Participant 294071


title: Participant 333021


title: Participant 333061


title: Participant 333071


title: Participant 333051


title: Participant 335071


title: Participant 333011


title: Participant 335041


title: Participant 335011


title: Participant 339081


title: Participant 339051


title: Participant 339061


title: Participant 532021


title: Participant 532061


title: Participant 532041


title: Participant 543011


title: Participant 546031

description:
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sample_type: E1W01


title: Participant 532011


title: Participant 294011


title: Participant 553061


title: Participant 553031


title: Participant 553051


title: Participant 553011


title: Participant 553041


title: Participant 289021


title: Participant 289061


title: Participant 289031


title: Participant 339031


title: Participant 289081


title: Participant 339021


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title: Participant 340061


title: Participant 340021


title: Participant 340011


title: Participant 340071


title: Participant 340051


title: Participant 553021


title: Participant 353021


title: Participant 356051


title: Participant 344021


title: Participant 356031


title: Participant 356021


title: Participant 543071


title: Participant 543041


title: Participant 543061


title: Participant 554061


title: Participant 340081


title: Participant 289071


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title: Participant 561011


title: Participant 632061


title: Participant 353051


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title: Participant 344011


title: Participant 344051


title: Participant 546081


title: Participant 561021


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title: Participant 564061


title: Participant 554071


title: Participant 543021


title: Participant 564051


title: Participant 644071


title: Participant 564081


title: Participant 644031


title: Participant 353071


title: Participant 564041


title: Participant 561041


title: Participant 546071


title: Participant 564021


title: Participant 546041


title: Participant 546061


title: Participant 353031


title: Participant 546021


title: Participant 546051


title: Participant 563071


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title: Participant 601081


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title: Participant 353061


title: Participant 612011


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title: Participant 612061


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title: Participant 348021


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title: Participant 552041


title: Participant 552031


title: Participant 563021


title: Participant 552021


title: Participant 574051


title: Participant 574041


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title: Participant 621021

description:
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sample_type: E1W01


title: Participant 621011


title: Participant 621031


title: Participant 621081


title: Participant 621051


title: Participant 621071


title: Participant 621041


title: Participant 563061


title: Participant 353081


title: Participant 621061


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title: Participant 563081


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title: Participant 575051


title: Participant 575041


title: Participant 575081


title: Participant 576031


title: Participant 563031


title: Participant 576071


title: Participant 339011


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title: Participant 576041


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title: Participant 570081


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title: Participant 588011


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title: Participant 592031


title: Participant 337011


title: Participant 594031


title: Participant 532051


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title: Participant 337071


title: Participant 592081


title: Participant 592021


title: Participant 592071


title: Participant 588081


title: Participant 594011


title: Participant 591071


title: Participant 596021


title: Participant 596061


title: Participant 591021


title: Participant 596051

description:
092116-(5)_A749FS_B96_1057; 092216-(1)_A1342,1343_Row 8_B1054,7,8; 092216-(2)_A8063FS3_B96_1054,1057,1058_Row 8; 092316-(2)_A1342FS_B96_1057_Row 1-7; 092616-(3)_A8063FS3_B96_1057_Row 1-7
sample_type: E1W01


title: Participant 816021


title: Participant 817051


title: Participant 817031


title: Participant 337031


title: Participant 817041


title: Participant 594021


title: Participant 356071


title: Participant 817061


title: Participant 356041


title: Participant 666051


title: Participant 596071


title: Participant 666041


title: Participant 356061


title: Participant 596031


title: Participant 666031


title: Participant 687021


title: Participant 687011


title: Participant 687081


title: Participant 689041


title: Participant 596011


title: Participant 689021


title: Participant 689051


title: Participant 689061


title: Participant 346071


title: Participant 346081


title: Participant 687071


title: Participant 689022


title: Participant 666021


title: Participant 689081


title: Participant 346021


title: Participant 658071


title: Participant 658021


title: Participant 816061


title: Participant 346031


title: Participant 687061


title: Participant 649031


title: Participant 816081


title: Participant 658031


title: Participant 649021


title: Participant 649041


title: Participant 649061


title: Participant 649052


title: Participant 658051


title: Participant 649011


title: Participant 658061


title: Participant 689011


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title: Participant 676071


title: Participant 676031


title: Participant 676011


title: Participant 676081


title: Participant 676021


title: Participant 816041


title: Participant 676061


title: Participant 733071


title: Participant 713011


title: Participant 737041


title: Participant 737071


title: Participant 737021

value: EMPTY


title: Participant 733011


title: Participant 733031


title: Participant 733061


title: Participant 748051


title: Participant 737011


title: Participant 748011


title: Participant 676051


title: Participant 748021


title: Participant 748071


title: Participant 748041


title: Participant 748031


title: Participant 756031

description:
092016-(1)_A749FS_B96_1056; 092016-(3)_A1342FS_B96_1056; 092016-(4)_A8063FS3_B96_1056; 092816-(3)_A1343FS3_B96_1056
sample_type: E1W01


title: Participant 756071


title: Participant 791071


title: Participant 756011


title: Participant 748061


title: Participant 766081


title: Participant 773081


title: Participant 791011


title: Participant 773051


title: Participant 773031


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title: Participant 773011


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title: Participant 594081


title: Participant 791041


title: Participant 773041


title: Participant 793041


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title: Participant 766042


title: Participant 766051


title: Participant 782041


title: Participant 782031


title: Participant 782081


title: Participant 782021


title: Participant 782051


title: Participant 782011


title: Participant 801031


title: Participant 801081


title: Participant 824061


title: Participant 878061


title: Participant 876061


title: Participant 793021


title: Participant 845061


title: Participant 886031


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title: Participant 766041


title: Participant 766061


title: Participant 809021


title: Participant 809051


title: Participant 809071


title: Participant 844021


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title: Participant 737081


title: Participant 844011


title: Participant 847061


title: Participant 844061


title: Participant 847011


title: Participant 848011


title: Participant 848041


title: Participant 737061


title: Participant 862071


title: Participant 801021


title: Participant 848071


title: Participant 848031


title: Participant 848081


title: Participant 878011


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title: Participant 948081


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title: Participant 820031


title: Participant 847071


title: Participant 847021


title: Participant 853021


title: Participant 856031


title: Participant 856021


title: Participant 847051


title: Participant 856061


title: Participant 853041


title: Participant 856041


title: Participant 862061


title: Participant 862021


title: Participant 862011


title: Participant 862051


title: Participant 862041


title: Participant 867051


title: Participant 848051


title: Participant 867031


title: Participant 867071


title: Participant 867081


title: Participant 867061


title: Participant 924041


title: Participant 871051

description:
092116-(3)_A749_1342_1343_8063_BS_1061; 092716-(3)_A1342_B1061; 092916-(4)_A8063_A1343_BS1061
sample_type: E1W01


title: Participant 871081

description:
092016-(5)_A749FS_B96_1055; 092116-(2)_A1342FS_B96_1055; 092116-(4)_A8063FS_B96_1055; 092816-(2)_A1343FS3_B96_1055
sample_type: E1W01


title: Participant 871061


title: Participant 871041


title: Participant 871011


title: Participant 871021


title: Participant 871071


title: Participant 876041


title: Participant 876011


title: Participant 878021


title: Participant 824041


title: Participant 876021


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title: Participant 888071


title: Participant 861061


title: Participant 878071


title: Participant 876051


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title: Participant 886021


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title: Participant 886051


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title: Participant 888031


title: Participant 888051


title: Participant 888061


title: Participant 886011


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title: Participant 890011


title: Participant 897041


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title: Participant 897081


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title: Participant 898031


title: Participant 907041


title: Participant 898061


title: Participant 897021


title: Participant 897061


title: Participant 907021


title: Participant 838051


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title: Participant 901021


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title: Participant 838021


title: Participant 845051


title: Participant 845011


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title: Participant 898011


title: Participant 898021


title: Participant 898071


title: Participant 898051


title: Participant 906011


title: Participant 906021


title: Participant 906081


title: Participant 906031


title: Participant 911021


title: Participant 911011


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title: Participant 911071


title: Participant 911061


title: Participant 935061


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title: Participant 935071


title: Participant 906051


title: Participant 845021


title: Participant 911081


title: Participant 882031


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title: Participant 906071


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title: Participant 915061


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title: Participant 915071


title: Participant 915081


title: Participant 913021


title: Participant 919061


title: Participant 922081


title: Participant 911041


title: Participant 915041


title: Participant 922021

description:
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sample_type: E1W01


title: Participant 922071


title: Participant 937071


title: Participant 922061


title: Participant 922041


title: Participant 922031


title: Participant 929051


title: Participant 929041


title: Participant 929071


title: Participant 929081


title: Participant 939031


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title: Participant 852031


title: Participant 852011


title: Participant 852071


title: Participant 852041


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title: Participant 861031


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title: Participant 947081


title: Participant 947071


title: Participant 948031


title: Participant 947041


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title: Participant 894051


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title: Participant 901061


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title: Participant 882011


title: Participant 927031

description:
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sample_type: E1W01


title: Participant 894061


title: Participant 927081


title: Participant 919071


title: Participant 927051


title: Participant 927061


title: Participant 927021


title: Participant 940031


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title: Participant 970031


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title: Participant 972071


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title: Participant 994051


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title: Participant 955031


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title: Participant 955021


title: Participant 955061


title: Participant 955011


title: Participant 940071


title: Participant 955041


title: Participant 999081


title: Participant 977061


title: Participant 977051


title: Participant 960061


title: Participant 955071


title: Participant 977041


title: Participant 977021


title: Participant 982011


title: Participant 977031


title: Participant 977011


title: Participant 983061


title: Participant 977081


title: Participant 999061


title: Participant 944031


title: Participant 983021


title: Participant 960011


title: Participant 944051


title: Participant 972061


title: NPC_E7KI-2 (rep-2)

city: LOS ANGELES

first: Chia-ho

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

institute: UCLA

data_processing:
Adapter (CTGTCTCTTATA) was trimmed using Cutadapt. Trimmed reads were aligned to mm10 using STAR.  Peak calling was performed using MACS3 with --nomodel -g mm --keep-dup all -q 0.01 --llocal 10000. Bigwig files were generaed using deeptools bamCoverage (--outFileFormat bigwig --binSize 10 --normalizeUsing RPKM -p 20).
Assembly: mm10
Supplementary files format and content: bigwig

source_name: HBG3 ES cell line-derived NPC

extract_protocol: not provided

value: HBG3 ES cell line-derived NPC

value: Neural  Progenitor Cell (NPC)

value: Dpf2 E7-KI

value: Differentiation to NPC


title: NPC_E7KI-3 (rep-3)


title: Participant 982061


title: Participant 982031


title: NPC_E7KI-1 (rep-1)


title: NPC_E7KO-3 (rep-3)

value: Dpf2 E7-KO


title: Participant 982071


title: NPC_E7KO-2 (rep-2)


title: Participant 982051


title: NPC_E7KO-1 (rep-1)


title: Participant 985031


title: Participant 985021


title: NPC_WT-3 (rep-3)

value: WT


title: NPC_WT-2 (rep-2)


title: ESC_E7KI-3 (rep-3)

source_name: HBG3 ES cell line

value: HBG3 ES cell line

value: Embryonic stem cell (ESC)

value: Stem cell maintenance


title: NPC_WT-1 (rep-1)


title: Participant 985011


title: Participant 985061


title: Participant 985081


title: ESC_E7KO-3 (rep-3)


title: Participant 985071


title: ESC_E7KO-2 (rep-2)


title: Participant 934031


title: Participant 934071


title: ESC_WT-2 (rep-2)


title: ESC_WT-3 (rep-3)


title: Participant 982041


title: Participant 944011


title: ESC_WT-1 (rep-1)


title: Participant 944021


title: AS3

city: boston

first: Shizhong

last: Ke

state: Massachusetts

address: 3 BLACKFAN CIRCLE, CLS0428D

institute: Beth Israel Deaconess Medical Center (BIDMC)

data_processing:
Quality Control (QC) of Raw Data: The first step is to check the quality of the raw sequence data.
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped to GrCM38/mm10
raw counts of sequencing reads extraction and normalization were performed
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts of sequencing reads for each sample

source_name: Mouse breast cancer

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Mouse breast cancer

value: Combination


title: AS2


title: AS1


title: Participant 969051


title: S3

value: Sulfopin


title: Participant 969081

value: Nutrition + WSH


title: ESC_E7KI-1 (rep-1)


title: Participant 960051


title: Participant 969071


title: Participant 969031


title: Participant 985051

value: Control


title: S1


title: A3

value: Abemaciclib


title: Participant 934021


title: Participant 969061


title: ESC_E7KO-1 (rep-1)


title: Participant 969041


title: A1


title: Participant 990041


title: S2


title: Participant 934011


title: CON2

value: Vehicle


title: Participant 990021


title: Participant 990031


title: CON3


title: Participant 990071


title: CON1


title: Participant 992081


title: Participant 992031


title: Participant 992041


title: Female, thyroids, Mix (BPA, BPS, and BPF) 500mg/kg/day, rep 1

first: Soontag

last: Jung

address: 141 Gajeong-ro, Yuseong-gu

department: Developmental and reproductive toxicology

institute: Korea Institute of Toxicology

data_processing:
The RNA-seq reads were trimmed using BBDuk tool and quality checked with FastQC
Clean reads were mapped to the reference genome using Bowtie2.
The raw read counts were calculated from unique and multiple alignments using Bedtools.
The raw read count data were normalized by trimmed mean of M-values (TMM) method  using edgeR
Assembly: rn6
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Rattus norvegicus

source_name: thyroids

extract_protocol:
Total RNA was extracted from all tissues using TRIzol
RNA libraries for RNA-seq were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit following manufactuer's protocols

value: thyroids

value: Sprague-Dawley rat

value: Female

tag: age

value: PND 63


title: Participant 992021


title: Female, thyroids, BPA 500mg/kg/day, rep 3


title: Female, thyroids, vehicle control, rep 3


title: Female, thyroids, BPA 500mg/kg/day, rep 2


title: Female, thyroids, BPA 500mg/kg/day, rep 1


title: ESC_E7KI-2 (rep-2)

value: Dpf2 E7-KI


title: Participant 960031


title: Participant 960041


title: Female, thyroids, vehicle control, rep 2


title: Participant 990061


title: Participant 960021


title: Female, thyroids, vehicle control, rep 1


title: A2


title: Female, ovaries, Mix (BPA, BPS, and BPF) 500mg/kg/day, rep 3

source_name: ovaries

value: ovaries


title: Female, thyroids, Mix (BPA, BPS, and BPF) 500mg/kg/day, rep 3


title: Female, ovaries, Mix (BPA, BPS, and BPF) 500mg/kg/day, rep 2


title: Female, thyroids, Mix (BPA, BPS, and BPF) 500mg/kg/day, rep 2


title: Participant 983011


title: Participant 983071


title: Participant 983051


title: Female, ovaries, BPA 500mg/kg/day, rep 2


title: Female, ovaries, BPA 500mg/kg/day, rep 3


title: Female, ovaries, BPA 500mg/kg/day, rep 1


title: Participant 989011


title: Participant 989061


title: Female, ovaries, Mix (BPA, BPS, and BPF) 500mg/kg/day, rep 1


title: Female, ovaries, vehicle control, rep 3


title: Participant 992051


title: Participant 989081


title: Participant 999071


title: Female, ovaries, vehicle control, rep 2


title: Female, ovaries, vehicle control, rep 1


title: Participant 999011


title: Female, liver, Mix (BPA, BPS, and BPF) 500mg/kg/day, rep 1

value: liver


title: Female, liver, BPA 500mg/kg/day, rep 3


title: Participant 983031


title: Female, liver, BPA 500mg/kg/day, rep 1


title: S18C_448AP

city: Munich

first: Hans

middle: Carlo

last: Maurer

state: Bavaria

address: Ismaninger Str. 22

department: II. Medizinische Klinik

country: Germany

institute: Klinikum rechts der Isar

description:
R1 fastq file: cDNA; R2 fastq file: barcode/UMI
448AP_human_counts.txt

data_processing:
Dropseq (v1.0) – see Macosko et al., PMID: 26000488.
Assembly: Mouse GRCm38 and Human GRCh38, respectively.
Supplementary files format and content: Tab-delimited files contain raw counts for each sample

source_name: Human PDAC Cells

extract_protocol:
Qiagen RNeasy Plus Micro Kit (Nr. 74034)
RT and template switch with primers containing Barcode, UMI and adapter. Full length amplification of the cDNA. Fragmentation and Adapter ligation with NEB Ultra II FS kit and final amplification of the 3’-end with Illumina overhangs. Sequencing of cDNA in Read1 and sequencing of Barcode and UMI in Read2.

value: Human PDAC Cells

tag: cell line_id

tag: media

value: Basal Branching PDO Media

tag: batch

tag: replicate

tag: dimension

tag: day

tag: environment

value: collagen


title: HiC_DMSO

city: Amsterdam

first: Mikhail

last: Magnitov

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

description: Lane1 run was sequenced on Illumina MiSeq, Lane 2 run was sequenced on NextSeq 550

data_processing:
ChIP-seq: ZFP143 ChIP-seq reads were mapped to the mm10 mouse reference genome assembly using bwa mem. Calibrated CTCF ChIP-seq reads were mapped to the mm10 mouse and hg38 human reference genome assemblies using bwa mem. Uniquely mapped reads with MAPQ > 10 mapped in proper read pairs were selected using SAMtools. Duplicate reads were filtered out using the Picard “MarkDuplicates” function. Scaling factors for calibrated CTCF ChIP-seq normalisation were calculated as described previously (Greulich et al., 2021). The bigwig coverage tracks were generated using the “bamCoverage” and "bamCompare" functions from the deepTools. TT-seq: TT-seq reads were mapped to the mm10 mouse reference genome assembly using STAR with GENCODE vM25 gene annotation. Uniquely mapped reads with MAPQ > 10 were selected using SAMtools. Duplicate reads were filtered out using the Picard “MarkDuplicates” function. The reads were split by strand using SAMtools as described previously (Gregersen et al., 2020). Gene counts were obtained using the ”htseq-count” function from HTSeq. Bigwig coverage tracks were generated separately for forward and reverse strands using the "bamCoverage" function from deepTools. Hi-C: Hi-C reads were mapped to the mm10 mouse reference genome assembly using bwa mem with the Open2C distiller-nf pipeline. Mapped reads were parsed using pairtools with the “walks-policy” parameter set to “mask” and the “max_mismatch_bp” parameter set to 1. Read pairs were then binned into Hi-C contact matrices. Iterative correction of the matrices and removal of low coverage bins was performed using the "balance" function from cooler. 4C-seq: 4C-seq reads were processed as previously described (Haarhuis et al., 2017; van de Werken et al., 2012) using custom R scripts. The sequencing data were demultiplexed per viewpoint and mapped to the mm10 mouse reference genome assembly using the bwa aln and bwa samse. To generate the read counts per RE fragment, for each fragment we counted the number of mapped reads that have the same start or end coordinates as the fragment. To obtain 4C contact profiles, the counts were normalised to the total number of overlaps detected per million reads. ATAC-seq: ATAC-seq reads were mapped to the mm10 mouse reference genome assembly bwa mem. Uniquely mapped reads that were not mapped to mitochondrial DNA and had MAPQ > 10 were selected using SAMtools. Duplicate reads were filtered out using the Picard “MarkDuplicates” function. RNA-seq: RNA-seq reads were mapped to the mm10 mouse reference genome assembly using STAR with GENCODE vM25 gene annotation. Read counts per gene were obtained using the "quantMode" parameter in STAR.
Assembly: mm10
Supplementary files format and content: ChIP-seq: normalized signal tracks in bigWig format; peaks in BED format. TT-seq: normalized signal tracks in bigWig format; read counts per gene in TXT format. Hi-C: contact matrices in MCOOL and HIC formats. 4C-seq: viewpoint coordinates in TXT format; normalized coverage per fragment in TSV format. RNA-seq: read counts per gene in TXT format.

growth_protocol: Mouse Embryonic Stem Cells E14Tg2A (129/Ola) cell lines were cultured on 0.1% gelatin-coated plates in serum-free DMEM/F12 (Gibco) and Neurobasal (Gibco) medium (1:1) supplemented with N-2 (Gibco), B-27 (Gibco), BSA (0.05%, Gibco), 10 × 4 U of Leukaemia Inhibitory Factor (LIF) (Millipore), MEK inhibitor PD0325901 (1 μM, Selleckchem), GSK3-β inhibitor CHIR99021 (3 μM, Cayman Chemical) and 1-Thioglycerol (1.5 × 10−4 M, Sigma-Aldrich). The cell lines were passaged every 2 days in daily culture.

extract_protocol:
ChIP-seq: Chromatin was cross-linked using 1% FA final concentration. Chromatin was sheared on a Bioruptor Plus sonication instrument and immunoprecipitated by different antibodies. DNA was purified using the MiniElute PCR purification kit from Qiagen. TT-seq: Libraries for TTchem-seq were prepared following a published protocol (Gregersen et al., 2020). Cells were labelled with 2 mM of the uridine analog 4-thiouridine (4sU) for 10 min. Total RNA was isolated and fragmented. The 4sU-biotin labelled RNA was enriched using µMacs Streptavidin Kit (Miltenyi). Hi-C: Hi-C data were generated using as a previous published protocol (Rao et al., 2014) with minor modifications (Haarhuis et al., 2017). Cells were harvested and crosslinked using 2% formaldehyde. Crosslinked DNA was digested in nucleus using MboI (NEB), and biotinylated nucleotides were incorporated at the restriction overhangs and joined by blunt-end ligation. The ligated DNA was enriched in a streptavidin pull-down 4C-seq: 4C-seq was performed as previously described (Geeven et al., 2018; van de Werken et al., 2012) using a two-step PCR method for indexing described first in (Haarhuis et al., 2017). MboI (NEB) was used as the first restriction enzyme and Csp6I (NEB) as the second restriction enzyme. ATAC-seq: Cells were washed in cold PBS and subjected to lysis using a 2x lysis buffer. Subsequently, the cells were centrifuged, and the resulting pellet was treated with 2xTD buffer and 2 uL of transposon mix. RNA-seq: RNA was first isolated using standard RNA isolation procedure from Qiagen RNeasy Mini Kit (Qiagen), including a DNaseI treatment.
ChIP-seq: Libraries were prepared following the KAPA HTP Library Preparation Kit (Roche). TT-seq: Libraries were prepared using KAPA RNA HyperPrep and KAPA Dual-Indexed Adapter kits (Roche) using dual indexing adapters. Hi-C: Hi-C libraries were prepared using a standard end-repair and A-tailing method. 4C-seq: 4C-seq libraries were prepared using a two-step PCR method for indexing described first in (Haarhuis et al., 2017). ATAC-seq: PCR amplification was conducted using KAPA HiFi HotStart ReadyMix (Roche). Fragments ranging from 200 to 700 bp were purified utilising AMPure XP beads (Beckman Coulter). RNA-seq: Libraries were prepared following the TruSeq Stranded mRNA kit (Illumina) with TruSeq RNA Single Indexes set A (Illumina).

treatment_protocol: For the knock-in of the FKBP sequence at the genes of interest, cells were transfected with the plasmids containing the gRNA sequence and the donor plasmid designed to include the FKBP-2xHA-P2A-GFP in between two homology arms for the gene of interest. To induce ZFP143 degradation, the cells were treated with 500 nM dTAG-V1 or DMSO as a control.

value: Embryonic Stem Cell

value: DMSO


title: S18A_448AP


title: S18B_448AP


title: HiC_dTAG_6H

tag: time


title: Female, liver, vehicle control, rep 3

tag: strain

tag: Sex


title: S16C_448AP

value: PDO Full Media


title: Female, liver, vehicle control, rep 2


title: S16B_448AP


title: S12C_448AP


title: Female, liver, vehicle control, rep 1


title: Female, kidney, Mix (BPA, BPS, and BPF) 500mg/kg/day, rep 3

source_name: kidney

value: kidney


title: Female, kidney, Mix (BPA, BPS, and BPF) 500mg/kg/day, rep 2


title: S12B_448AP


title: Mouse colon organoid_2, HNF4AOE

city: New York

first: Sanlan

last: Li

state: NY

address: 1300 York Avenue

institute: Weill Cornell Medicine

description:
HNF4AOE2
hnf4aOE_raw_counts.csv

data_processing:
Briefly, reads alignment was performed by STAR package,the raw count tables were generated by featureCounts
Assembly: mm10
Supplementary files format and content: Comma Separated Values (CSV) file containing raw counts for the samples

source_name: colon organoid

growth_protocol: Mouse colon orgnoid lines were cultured and maintained in mouse colon 3D medium contraining 60% condition medium and appropriate small molecules in Advanced DMEM/F12 base medium at 37 degree incubator with 5% CO2.

extract_protocol:
We used and followed Qiagen micro RNA extraction kit protocol to extract the RNA
The library construction strategy was non-directional eukaryotic mRNA library by using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina.

treatment_protocol: 48h after infected with control virus or HNF4A virus, the mouse colon organoids were selected by puromycin (1ug/mL) for 6 days and differentiated in mouse colon differentiation medium for 4 days before harvesting samples for RNA extraction.

value: colon organoid

value: colon epithelial cells

value: HNF4A OE

value: epithelial differentiation


title: S10B_448AP


title: S16A_448AP


title: Participant 999051

tag: age in months

tag: treatment arm

value: Nutrition + WSH

tag: dna concentration (ng/ul)

tag: box

tag: box position

tag: ^sample


title: S10C_448AP

tag: cell type


title: Mouse colon organoid_1, HNF4AOE

description:
HNF4AOE1
hnf4aOE_raw_counts.csv

tag: tissue

tag: genotype

tag: treatment


title: Female, kidney, BPA 500mg/kg/day, rep 2

value: Sprague-Dawley rat

value: Female

tag: age


title: Female, liver, Mix (BPA, BPS, and BPF) 500mg/kg/day, rep 2

value: PND 63


title: Female, liver, Mix (BPA, BPS, and BPF) 500mg/kg/day, rep 3


title: Female, kidney, Mix (BPA, BPS, and BPF) 500mg/kg/day, rep 1


title: S10A_448AP

tag: cell line_id

tag: media

tag: batch

tag: replicate

tag: dimension


title: S6C_448AP

tag: day

tag: environment


title: S12A_448AP


title: Female, kidney, BPA 500mg/kg/day, rep 1

tag: strain

tag: Sex


title: Female, kidney, vehicle control, rep 2


title: Mouse colon organoid_1, Control virus

description:
H174CON1
hnf4aOE_raw_counts.csv

value: WT


title: Female, kidney, vehicle control, rep 1


title: S6A_448AP


title: S4B_448AP


title: Col:ore15-2_Rep3

city: Hyeonpung-eup

first: Hyunsu

last: Park

state: Dalseong-gun, Daegu

address: E4-620, 333, Techno jungang-daero

department: New biology

institute: DGIST

description: Sample 3

data_processing:
The quality of the raw sequences of each sample was analyzed by FastQC
Raw files were trimmed using cutadapt v1.1079. The resulting reads were aligned to the Arabidopsis thaliana genome (TAIR10) using TopHat v2.1.181.
The number of reads aligned against the annotated genes was calculated using HTSeq v0.6.182
Reads Per Kilobase of transcript per Million mapped reads (RPKM) normalization was applied to the read counts, as described previously.
Genome_build: Arabidopsis_thaliana.TAIR10.31
Supplementary_files_format_and_content: Tab-delimited text files including counts or RPKM values for the individual samples

organism: Arabidopsis thaliana

source_name: T-DNA insertion line of ORE15, Columbia-0 background

growth_protocol: ORE15 mutants used in this study were generated in the Arabidopsis thaliana ecotype Columbia (Col) background (wild type). After stratification for at least 2 days at 4°C in the dark, the seeds were sown in plates. containing half-strength Murashige and Skoog (½ MS) media supplemented with 0.5% sucrose, 0.5 g/L 4-morpholineethanesulfonic acid (MES), and 0.8% agar (pH 5.7). The plates were placed vertically in an environmentally controlled growth room at 22°C under continuous 80 μmol m−2 s−1 light intensity.

extract_protocol:
Total RNA was extracted from 0.5 cm tips of primary roots of Col and ore15-2 seedlings at 5 DAP (n = 2 seedlings per genotype)(Welgene, Korea). The RNA integrity number (RIN) of each total RNA sample was calculated using the Agilent 2100 BioAnalyzer System, and samples with a RIN 6.7 or higher were selected for RNA-seq. Next, poly(A) mRNA was purified from 1 µg of total RNA of each sample, according to the manufacturer’s standard protocols.
The purified mRNA was fragmented using the Illumina TruSeq™ Stranded mRNA LT Sample Prep Kit and reverse transcribed using Superscript III reverse transcriptase. then, sequenced on the Illumina HiSeq 2500 platform.

treatment_protocol: To perform phytohormone treatments, seedlings at 5 DAP were transferred from ½ MS media to ½ MS media (control) or ½ MS media supplemented with the indicated concentrations of IAA or BA and grown for 24 h.

tag: ecotype

value: Columbia-0 background

value: T-DNA insertion line of ORE15

value: 0.5 cm root tips

value: Root Meristem Stem cell

value: 5 days after planting


title: S4A_448AP

value: Human PDAC Cells

value: collagen


title: Male, thyroids, Mix (BPA, BPS, and BPF) 500mg/kg/day, rep 2

value: thyroids

value: Male


title: Col:ore15-2_Rep2

description: Sample 2


title: Male, thyroids, Mix (BPA, BPS, and BPF) 500mg/kg/day, rep 3


title: Col_Rep3

description: Sample 6

source_name: wildtype, Columbia-0 background

value: wildtype


title: Col:ore15-2_Rep1

description: Sample 1


title: Col_Rep2

description: Sample 5


title: Col_Rep1

description: Sample 4


title: S-46B_536APe

description:
R1 fastq file: cDNA; R2 fastq file: barcode/UMI
536APe_mouse_counts.txt

source_name: Murine PDAC Cells

value: Murine PDAC Cells

tag: morphology

value: tree-like

value: KC

value: untreated


title: Male, thyroids, BPA 500mg/kg/day, rep 2

value: Sprague-Dawley rat


title: S-46A_536APe


title: S-44B_536APe

value: thick branched


title: S-44C_536APe


title: Male, thyroids, BPA 500mg/kg/day, rep 3

value: PND 63


title: S-46C_536APe


title: Male, thyroids, BPA 500mg/kg/day, rep 1


title: S-42C_536APe

value: cystic branched


title: S-44A_536APe


title: S4C_448AP

value: PDO Full Media


title: S6B_448AP

value: Basal Branching PDO Media


title: Female, liver, BPA 500mg/kg/day, rep 2

value: liver

value: Female


title: Male, thyroids, vehicle control, rep 3


title: S-42B_536APe


title: Male, thyroids, vehicle control, rep 2


title: S-42A_536APe


title: S-40B_536APe

value: TEBBO


title: Male, thyroids, vehicle control, rep 1


title: Male, thyroids, Mix (BPA, BPS, and BPF) 500mg/kg/day, rep 1


title: S-38A_536APe

value: bulk population

value: collagen


title: S-38C_536APe


title: Male, testes, Mix (BPA, BPS, and BPF) 500mg/kg/day, rep 2

source_name: testes

value: testes

value: Male


title: Male, testes, Mix (BPA, BPS, and BPF) 500mg/kg/day, rep 3


title: S-38B_536APe

value: Murine PDAC Cells


title: S-10A_536APe

value: tree-like

value: AZD5153+Poziotinib treated


title: S-10C_536APe

value: KC


title: S-10B_536APe


title: S-40A_536APe

value: untreated


title: S-8C_536APe

value: thick branched


title: Male, testes, Mix (BPA, BPS, and BPF) 500mg/kg/day, rep 1

value: Sprague-Dawley rat

value: PND 63


title: S-10Aold_536APe


title: Male, testes, BPA 500mg/kg/day, rep 3


title: S-8B_536APe


title: Mouse colon organoid_2, Control virus

description:
H174CON2
hnf4aOE_raw_counts.csv

value: colon organoid

value: colon epithelial cells

value: WT

value: epithelial differentiation


title: S-6C_536APe

value: cystic branched


title: Male, testes, BPA 500mg/kg/day, rep 2


title: Male, testes, BPA 500mg/kg/day, rep 1


title: S-8A_536APe


title: S-6B_536APe


title: Que, cultured, 24h, rep3

city: Beijing

first: sa

last: du

institute: Peking University School of Stomatology

description:
three dimensional culture
HPS-3

data_processing:
The llumina Novaseq 6000 platform was used to sequence the libraries.
Fastp1 was used to manipulate the raw reads in fastq format, removing low quality reads to obtain clean reads.
HISAT22 was applied to map the clean reads to the reference genome.
Calculate FPKM3 for each gene and obtain read counts for each gene using HTSeq-count4.
Assembly: HISAT22
Supplementary files format and content: Calculate FPKM3 for each gene and obtain read counts for each gene using HTSeq-count4.

growth_protocol: RAW264.7 were cultured at 37 °C in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco), 100 mg/mL penicillin, and 100 mg/mL streptomycin (Gibco) in a 5% CO2 atmosphere.

extract_protocol:
The hydrogel containing macrophages was frozen in liquid nitrogen. After adding the TRIzol solution (Invitrogen), the samples were thoroughly ground with a glass grinder.
The libraries were then built using the VAHTS Universal V6 RNA-seq Library Preparation Kit according to the manufacturer’s instructions.

treatment_protocol: Cells were suspended in PVA solution (7 wt% PVA in DMEM solution) at a final density of 2 million cells/mL. P1 solution (8 wt% P1 in DMEM solution) for solubilizing flavonoids was prepared. Equal volumes of these two solutions were mixed at room temperature to obtain Gel-Fla. Subsequently, they were transferred to a humidified incubator under standard cultivation conditions (37 °C, 5% CO2).

value: Que

tag: cell line

value: macrophage cells


title: Que, cultured, 24h, rep2

description:
three dimensional culture
HPS-2

tag: cell type


title: S-40C_536APe

value: TEBBO

value: collagen


title: S-6A_536APe

value: Murine PDAC Cells


title: Male, testes, vehicle control, rep 3

tag: tissue

value: testes

value: Male


title: Que, cultured, 24h, rep1

description:
three dimensional culture
HPS-1

tag: genotype


title: S-4B_536APe

value: KC

tag: treatment

value: AZD5153+Poziotinib treated


title: S-2C_536APe

value: bulk population


title: Cat, cultured, 24h, rep3

description:
three dimensional culture
ECS-3

value: Cat


title: Male, liver, Mix (BPA, BPS, and BPF) 500mg/kg/day, rep 3

value: liver

value: Sprague-Dawley rat

tag: age

value: PND 63


title: S-54C_536APm

description:
R1 fastq file: cDNA; R2 fastq file: barcode/UMI
536APm_mouse_counts.txt

tag: cell line_id

value: star-like

value: untreated


title: S-4A_536APe


title: Cat, cultured, 24h, rep2

description:
three dimensional culture
ECS-2

value: WT


title: S-2A_536APe


title: Male, liver, Mix (BPA, BPS, and BPF) 500mg/kg/day, rep 2


title: Cat, cultured, 24h, rep1

description:
three dimensional culture
ECS-1


title: 2H myr, cultured, 24h, rep3

description:
three dimensional culture
EQYMS-3

value: 2H myr


title: S-54B_536APm


title: S-52C_536APm

value: firework


title: Male, liver, Mix (BPA, BPS, and BPF) 500mg/kg/day, rep 1


title: S-50C_536APm

value: branched mesenchymal


title: S-52B_536APm

value: collagen


title: S-4C_536APe

value: Murine PDAC Cells

value: TEBBO


title: Male, liver, BPA 500mg/kg/day, rep 3

value: Male


title: S-50A_536APm

value: KC


title: 2H myr, cultured, 24h, rep1

description:
three dimensional culture
EQYMS-1

value: macrophage cells


title: Male, liver, BPA 500mg/kg/day, rep 2


title: 2H myr, cultured, 24h, rep2

description:
three dimensional culture
EQYMS-2


title: S-52A_536APm


title: S-48C_536APm

value: bulk population


title: S-50B_536APm


title: Male, testes, vehicle control, rep 2

value: testes


title: Male, liver, BPA 500mg/kg/day, rep 1

value: liver


title: Male, testes, vehicle control, rep 1

value: Sprague-Dawley rat


title: S-48B_536APm


title: S-2B_536APe

value: AZD5153+Poziotinib treated


title: Myr, cultured, 24h, rep2

description:
three dimensional culture
YMS-2

value: Myr


title: S-54A_536APm

value: star-like

value: untreated


title: S-48A_536APm


title: Male, liver, vehicle control, rep 3

value: PND 63


title: S-31C_536APm

value: RO5126766 treated


title: Myr, cultured, 24h, rep1

description:
three dimensional culture
YMS-1

value: WT


title: S-31B_536APm

value: collagen


title: Male, liver, vehicle control, rep 2


title: S-31A_536APm

value: Murine PDAC Cells


title: S-30C_536APm

value: firework


title: S-30B_536APm


title: Male, kidney, Mix (BPA, BPS, and BPF) 500mg/kg/day, rep 3

value: kidney

value: Male


title: S-29_536APm

value: branched mesenchymal

value: KC


title: S-30A_536APm


title: Myr, cultured, 24h, rep3

description:
three dimensional culture
YMS-3

value: macrophage cells


title: Gel, cultured, 24h, rep2

description:
three dimensional culture
PBS-2

value: Gel


title: S-27C_536APm


title: S-28C_536APm

value: bulk population


title: Male, kidney, Mix (BPA, BPS, and BPF) 500mg/kg/day, rep 2

value: Sprague-Dawley rat


title: S-28B_536APm


title: Gel, cultured, 24h, rep1

description:
three dimensional culture
PBS-1


title: S-28A_536APm