title: HepG2_live119

source_name: HepG2 live119


title: HepG2_live116

status: Public on May 18 2021

type: SRA

city: Hong Kong

first: Xinlei

last: Wang

state: Hong Kong

address: Clear Water Bay, Sai Kung,

department: LIFS

country: China

institute: HKUST

library_source: transcriptomic

data_processing:
Index and adapter were trimmed in data downloaded form Basespace
Quality control was done using Fastqc
Alignment and quantification were done by mapping raw reads to GRCh38 using kallisto 0.46.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene expression/Transcript expression matrix(TPM)

molecule: total RNA

organism: Homo sapiens

source_name: HepG2 live116

growth_protocol: Both HepG2 and HCT-116 cell lines were culured with DMEM medium, supplemented with 1% Penicillin-Streptomycin and 10% Fetal Bovine Serum

extract_protocol: cDNA library was constructed using Smart-seq2 protocl, sequencing library was prepared using Illuminar Nextera DNA Library Prep Kit(Illumina, cat#FC-131-1096), we followed library contruction protocal provided by C1 Fluidigm(Fluidigm)

treatment_protocol: 80% methanol was used for cell fixation, fixed cells were stored in -80℃ for one week before further processing

tag: cell line


title: HepG2_live114

source_name: HepG2 live114


title: HepG2_live115

source_name: HepG2 live115


title: HepG2_fixed90

source_name: HepG2 fixed90


title: HepG2_fixed8

source_name: HepG2 fixed8


title: HepG2_fixed94

source_name: HepG2 fixed94


title: HepG2_live130

source_name: HepG2 live130


title: HepG2_fixed9

source_name: HepG2 fixed9


title: HepG2_fixed93

source_name: HepG2 fixed93


title: HepG2_fixed89

source_name: HepG2 fixed89


title: HepG2_fixed92

source_name: HepG2 fixed92


title: HepG2_fixed86

source_name: HepG2 fixed86


title: HepG2_live124

source_name: HepG2 live124


title: HepG2_fixed88

source_name: HepG2 fixed88


title: HepG2_live110

source_name: HepG2 live110


title: HepG2_live128

source_name: HepG2 live128


title: HepG2_live112

source_name: HepG2 live112


title: HepG2_live121

source_name: HepG2 live121


title: NKT.Sp Rep1

city: Bron

first: Sylvain

last: Mareschal

address: Centre de Biopathologie Est, 59 boulevard Pinel

department: NGS-HCL platform

country: France

institute: Hospices Civils de Lyon

library_source: genomic

data_processing:
Alignment and QC by the ENCODE pipeline (BigDataScript version 0.3.4, https://github.com/kundajelab/atac_dnase_pipelines).
Peak calling with MACS2 version 2.1.2 and the following parameters:  --gsize "hs" --bdg --qvalue 0.00001 --shift 75 --extsize 150 --nomodel --keep-dup all --call-summits –nolambda
Peak processing as described in Corces et al, Science 2018 (500 bp wide, overlap resolution, at least in 2 samples).
Reads per peak counted on sorted “tagAlign” files using bedtools coverage version 2.27.1.
Count normalization using edgeR version 3.24.3 (TMM).
Peak annotation using custom R scripts and Biomart exports from Ensembl (2020-11-19).
Genome_build: mm10
Supplementary_files_format_and_content: Two maps are provided :  - « NK_T_count-L_count-NKT » peaks were collected from NK and T cells and used only for counting in other samples (mPTCLs and NKT cells).  - « NK_T_L_count-NKT » peaks were collected from mPTCLs, NK and T cells and used only for counting in other samples.    Three files are provided with each map :  - « counts.txt » are raw counts in peaks.  - « CPM.txt » are log2 Counts Per Millions after normalization, as provided by EdgeR.  - « peaks.txt » provides annotation for each peak.

molecule: genomic DNA

organism: Mus musculus

source_name: NKT cells

extract_protocol:
10.000 cells were Facs-sorted and tagmented as previously described (Corces et al. Science 2018).
ATAC-seq libraries were constructed by ligating Nextera sequencing primers (Buenrostro et al. Nature 2015) using PCR amplification.

tag: strain

tag: genotype

value: WT

tag: phenotype

value: sorted on CD3+ CD1dTet(alpha Gal Cer)+ liver cells


title: HepG2_live111

source_name: HepG2 live111


title: HepG2_fixed84

source_name: HepG2 fixed84


title: HepG2_fixed91

source_name: HepG2 fixed91


title: NK.27-11+.Sp Rep1

source_name: NK cells

value: sorted on CD27- CD11b+ spleen NK cells


title: HepG2_fixed95

source_name: HepG2 fixed95


title: HepG2_live113

source_name: HepG2 live113


title: Total T cells.Sp Rep3

source_name: T cells

value: sorted on CD3+ thy1+ spleen cells


title: HepG2_fixed82

source_name: HepG2 fixed82


title: HepG2_fixed85

source_name: HepG2 fixed85


title: Total T cells.Sp Rep2


title: NKT.Sp Rep3


title: HepG2_fixed87

source_name: HepG2 fixed87


title: HepG2_fixed7

source_name: HepG2 fixed7


title: mPTCL 170506

source_name: mPTCL

value: sorted on liver cells


title: Total T cells.Sp Rep1


title: HepG2_fixed79

source_name: HepG2 fixed79


title: HepG2_fixed76

source_name: HepG2 fixed76


title: HepG2_fixed83

source_name: HepG2 fixed83


title: NKT.Sp Rep2


title: HepG2_fixed74

source_name: HepG2 fixed74


title: mPTCL 170612


title: mPTCL 170315


title: mPTCL 170303


title: HepG2_fixed72

source_name: HepG2 fixed72


title: HepG2_fixed73

source_name: HepG2 fixed73


title: HepG2_fixed71

source_name: HepG2 fixed71


title: HepG2_fixed6

source_name: HepG2 fixed6


title: HepG2_fixed70

source_name: HepG2 fixed70


title: mPTCL 170725


title: HepG2_fixed69

source_name: HepG2 fixed69


title: HepG2_fixed68

source_name: HepG2 fixed68


title: mPTCL 170518


title: Lucap 147 Tumor sample, total RNA, replicate2

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

country: USA

institute: FHCRC

data_processing:
Library strategy: RiboSeq
Sequencing was performed using an Illumina HiSeq 2500 in Rapid Run mode and employed a single-end, 50 base read length (SE50) sequencing strategy.
RNA-seq reads were aligned to the UCSC hg19 assembly using Tophat2 and counted for gene associations against the UCSC genes database with HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw values for each Sample.

source_name: Prostate cancer tissue

growth_protocol: Tissues were obtained as frozen chunks, and manually pulverized before lysis

extract_protocol:
Total RNA and ribosome-protected RNA were extracted following the protocol in the TruSeq Ribo Profile kit from Illumina
RNA libraries were prepared for sequencing following the protocol in the TruSeq Ribo Profile kit from Illumina

tag: tissue

value: tumor sample


title: HepG2_fixed67

source_name: HepG2 fixed67


title: Lucap 147 Tumor sample, total RNA, replicate1


description:
RPF RNA
Lucap 147 Tumor sample, Ribosome bound RNA, replicate2


title: HepG2_fixed77

source_name: HepG2 fixed77


description:
RPF RNA
Lucap 147 Tumor sample, Ribosome bound RNA, replicate1


title: mPTCL 170605


title: HepG2_fixed66

source_name: HepG2 fixed66


title: HepG2_fixed65

source_name: HepG2 fixed65


title: HepG2_fixed64

source_name: HepG2 fixed64


title: mPTCL 170615

source_name: mPTCL


title: A549 Cisplatin Post-Sort Proliferative#3

city: Concord, NSW

first: Kaitao

last: Lai

state: New South Wales

address: ANZAC Research Institute, Hospital Rd, Concord

department: Faculty of Medicine and Health

country: Australia

institute: Anzac Research Institute, The University Of Sydney

data_processing:
Illumina bcl2fastq 2.20.0.422 pipeline.
Cleaned sequence reads were then aligned against the Homo sapiens genome (Build version HG38).
The STAR aligner (v2.5.3a) was used to map reads to the genomic sequences.
Transcripts were assembled with the Stringtie tool v1.3.3 (http://ccb.jhu.edu/software/stringtie/) utilising the reads alignment with hg38 and reference annotation based assembly option (RABT).
edgeR (version 3.22.5) to perform differential expression analysis.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *_DESeq2_summarieOverlaps_with_normalized_read_counts.csv
Supplementary_files_format_and_content: *_edgeR_featureCounts_with_read_counts.csv
Supplementary_files_format_and_content: *_Heatmap_30genes.pdf

source_name: Adenocarcinomic human alveolar basal epithelial cells

growth_protocol: A549 cells were cultured in Advanced RPM containing 1% FCS and 1% GlutaMAX under standard tissue culture conditions (5% CO2, 20% O2). Cells were routinely monitored for mycoplasma and their identity confirmed by short tandem repeat profiling (Australian Genome Research Facility).

extract_protocol:
Total RNA was purified using miRNeasy Micro Kit from Qiagen and following the manufacture's protocol, including the optional DNase treatment. RNA quality was assessed by bioanalyzer and samples only considered when RIN>8. RNA concentration and quality were also measured by Qubit and Nanodrop. All samples with 260/280 >2.0 (nanophotometre).
TruSeq stranded RNA sample preparation protocol (Illumina). cDNA synthesis: mRNA was purified via oligo(dT) beads, fragmented with divalent cations and heat, 1st strand of cDNA was randomly primed, 2nd strand of cDNA was synthesised. cDNA library preparation: DNA fragment end repair (blunt ending of DNA fragments), 3' Adenylation of DNA fragments, Sequencing adapter ligation (T-A pairing of adapter and DNA fragments), Amplification of library via PCR.

treatment_protocol: Cells were treated with or without cisplatin (5 mg/mL) for 2 hr, and then allowed to recover for 3 days before harvesting for RNAseq analysis. Cell pellets were frozen in dry ice and stored at -80C.

tag: cell type

value: Lung adenocarcinoma cell line

tag: facs sorting

value: Post-sorted

value: Proliferative

tag: treatment

value: Cisplatin pulse


title: HepG2_fixed63

source_name: HepG2 fixed63


title: HepG2_fixed62

source_name: HepG2 fixed62


title: Microplast Rep2

city: Mumbai

first: Pooja

middle: Kamal

last: Melwani

state: Maharashtra

address: Mod Lab, Trombay

department: Radiation Biology & Health Science Division

country: India

institute: Bhabha Atomic Research Centre

description:
M2
Oligo dT enriched Mrna

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw read quality was checked using the FASTQC. Low quality reads and adapters were trimmed using the Trimmomatic. Clean reads were aligned to the human genome (hg38) using STAR Aligner. Gene counting was carried out using the HTSeq.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include raw counts estimated using the HTSeq.

growth_protocol: MCF-7 cells were cultured in DMEM medium supplemented with 10% fetal bovine serum and 1% antibiotic-antimycotic solution and maintained in a humidified atmosphere at 37°C in 5% CO2.

extract_protocol:
Total RNA was extracted from two biological replicates of microplasts enriched samples using RNeasy mini kit (Qiagen, Hilden, Germany). RNA concentration and integrity were determined with Nanodrop 1000 (Nanodrop, Wilmington, DE,USA) spectrophotometry.
Libraries were prepared using the TruSeq RNA sample prep kit V2 as per the manufacturer’s protocol (Illumina, San Diego, USA). Briefly, Poly(A) RNA was enriched from total RNA samples using oligo-dT attached beads and ds cDNA was prepared from enriched mRNA samples. cDNA from each sample was attached to a specific index adapter and the cDNA library was further amplified using index adapters. All the libraries were validated using Agilent Technologies2100 Bioanalyzer, normalised and pooled together. 100 base paired end sequencing was performed on Illumina HiSeq 2500 sequencing system at NCBS, Bangalore, India to get a minimum of 30 million reads per library.
Paired-end, unstranded.

treatment_protocol: MCF-7 cells were cultured in 50% MΦCM for 48 h. The cells were then washed with PBS and harvested using trypsin EDTA and centrifuged at 1000 g (5 min, 4°C) to remove the trypsin. Samples were resuspended in ice cold PBS and were kept on ice. A low-speed differential centrifugation protocol was used to isolate microplasts. The final supernatant was centrifuged at 1000 g (5 min, 4°C) to pellet the microplasts-enriched sample and resuspended in ice cold PBS. Microplasts purity was validated by flow cytometry (Cyflow Space, Sysmex) and microscopy.

value: Macrophage conditioned medium

tag: sample type

value: Microplast


title: Microplast Rep1

description:
M1
Oligo dT enriched Mrna


title: mPTCL 161229


title: HepG2_fixed5

source_name: HepG2 fixed5


title: A549 Cisplatin Post-Sort Proliferative#1


title: HepG2_fixed61

source_name: HepG2 fixed61


title: HepG2_fixed58

source_name: HepG2 fixed58


title: A549 Cisplatin Post-Sort Proliferative#2


title: HepG2_fixed60

source_name: HepG2 fixed60


title: A549 Cisplatin Post-Sort Arrested#2

value: Arrested


title: A549 Cisplatin Pre-Sort#2

value: Pre-sorted

value: Asynchronous


title: A549 Cisplatin Post-Sort Arrested#1


title: A549 Cisplatin Pre-Sort#3


title: A549 Cisplatin Post-Sort Arrested#3


title: HepG2_fixed56

source_name: HepG2 fixed56


title: A549 Cisplatin Pre-Sort#1


title: HepG2_fixed55

source_name: HepG2 fixed55


title: A549 Control#2

value: Untreated


title: HepG2_fixed59

source_name: HepG2 fixed59


title: HepG2_fixed57

source_name: HepG2 fixed57


title: A549 Control#3


title: HepG2_fixed53

source_name: HepG2 fixed53


title: HepG2_fixed54

source_name: HepG2 fixed54


title: A549 Control#1


title: HepG2_fixed52

source_name: HepG2 fixed52


title: HepG2_fixed51

source_name: HepG2 fixed51


title: HepG2_fixed4

source_name: HepG2 fixed4


title: HepG2_fixed50

source_name: HepG2 fixed50


title: HepG2_fixed49

source_name: HepG2 fixed49


title: HepG2_fixed48

source_name: HepG2 fixed48


title: tgmel.73_WF_untreated

city: San Marcos

first: Yuan

last: Lu

state: TX

address: university drive

institute: Xiphophorus Genetic Stock Center

data_processing:
Adaptor sequences were first removed from raw sequencing files. Low quality section of sequencing reads, and low qulaity basecalls were further removed from raw sequencing files. All filtering steps were performed using a custom perl script.
Processed sequencing reads were mapped to medaka genome using Tophat2 (v.2.2.4)
FeatureCounts was used to qunatify sequencing reads that were mapped to gene models.
Genome_build: Ensembl release 92 oryzias latipes
Supplementary_files_format_and_content: comma seperated format/Sequncing read counts

organism: Oryzias latipes

source_name: whole fish

growth_protocol: Fertilized medaka eggs were collected from fish tanks that are dedicated for matings, and were transferred to rearing solution. After hatching, fries were transferred to regulatr fish tank and were maintained following animal facility protocol

extract_protocol:
Fish samples were homogenized in TRI reagent followed by addition of 200 μl/ml chloroform and the samples vigorously shaken and subjected to centrifugation at 12,000 g for 15 min at 4 °C. Total RNA was furhter purified using RNeasy mini RNA isolation kit (Qiagen, Valencia, CA, USA). Residual DNA was eliminated by incubating RNA samples with DNase for DNA digestion at 25°C for 15 min.Totall RNA concentration was determined using a Qubit 2.0 fluorometer (Life Technologies, Grand Island, NY, USA). RNA quality was verified on an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) to confirm that RIN scores were above 8.0 prior to sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Fish were placed in petri dish and were treated with vehicle control (saline, or DMSO), or Cisplatin/Trametinib for 5 days. An independent group of wild type and xmrk transgenic medaka that were not treated with vehicle or durg, but maintained under regular animal housing conditons were also inlcuded in the study.

value: xmrk transgenic

tag: age

value: 3-4 weeks old

tag: length

value: untreated


title: tgmel.74_WF_untreated


title: tgmel.77_WF_untreated


title: tgmel.75_WF_untreated


title: WT.72_WF_untreated

value: wild type


title: tgmel.76_WF_untreated


title: WT.71_WF_untreated


title: HepG2_fixed46

source_name: HepG2 fixed46


title: HepG2_fixed47

source_name: HepG2 fixed47


title: WT.70_WF_untreated


title: HepG2_fixed45

source_name: HepG2 fixed45


title: WT.69_WF_untreated


title: HepG2_fixed44

source_name: HepG2 fixed44


title: HepG2_fixed43

source_name: HepG2 fixed43


title: WT.68_WF_untreated


title: tgmel.67_WF_trametinib-20nM


title: HepG2_fixed41

source_name: HepG2 fixed41


title: tgmel.66_WF_trametinib-20nM


title: HepG2_fixed40

source_name: HepG2 fixed40


title: HepG2_fixed3

source_name: HepG2 fixed3


title: tgmel.64_WF_trametinib-20nM


title: tgmel.65_WF_trametinib-20nM


title: tgmel.63_WF_trametinib-20nM


title: HepG2_fixed42

source_name: HepG2 fixed42


title: HepG2_fixed39

source_name: HepG2 fixed39


title: tgmel.62_WF_trametinib-20nM


title: HepG2_fixed38

source_name: HepG2 fixed38


title: HepG2_fixed37

source_name: HepG2 fixed37


title: tgmel.60_WF_trametinib-20nM


title: HepG2_fixed34

source_name: HepG2 fixed34


title: HepG2_fixed33

source_name: HepG2 fixed33


title: HepG2_fixed32

source_name: HepG2 fixed32


title: tgmel.59_WF_trametinib-20nM


title: tgmel.57_WF_ctrl-DMSO

value: ctrl-DMSO


title: HepG2_fixed36

source_name: HepG2 fixed36


title: tgmel.58_WF_trametinib-20nM

source_name: whole fish


title: tgmel.55_WF_ctrl-DMSO


title: HepG2_fixed30

source_name: HepG2 fixed30


title: tgmel.56_WF_ctrl-DMSO


title: HepG2_fixed31

source_name: HepG2 fixed31


title: tgmel.54_WF_ctrl-DMSO


title: HepG2_fixed2

source_name: HepG2 fixed2


title: tgmel.53_WF_ctrl-DMSO


title: WT.52_WF_trametinib-20nM


title: WT.51_WF_trametinib-20nM


title: HepG2_fixed28

source_name: HepG2 fixed28


title: HepG2_fixed27

source_name: HepG2 fixed27


title: WT.50_WF_trametinib-20nM


title: HepG2_fixed29

source_name: HepG2 fixed29


title: tgmel.61_WF_trametinib-20nM


title: HepG2_fixed26

source_name: HepG2 fixed26


title: WT.48_WF_trametinib-20nM


title: WT.47_WF_ctrl-DMS0


title: HepG2_fixed25

source_name: HepG2 fixed25


title: HepG2_fixed23

source_name: HepG2 fixed23


title: HepG2_fixed35

source_name: HepG2 fixed35


title: WT.46_WF_ctrl-DMS0


title: HepG2_fixed22

source_name: HepG2 fixed22


title: WT.45_WF_ctrl-DMS0


title: HepG2_fixed20

source_name: HepG2 fixed20


title: HepG2_fixed1

source_name: HepG2 fixed1


title: HepG2_fixed19

source_name: HepG2 fixed19


title: WT.44_WF_ctrl-DMS0


title: HepG2_fixed18

source_name: HepG2 fixed18


title: WT.42_WF_cisplatin-70uM


title: WT.43_WF_ctrl-DMS0


title: WT.40_WF_cisplatin-70uM


title: HepG2_fixed17

source_name: HepG2 fixed17


title: WT.39_WF_cisplatin-70uM

source_name: whole fish


title: HepG2_fixed16

source_name: HepG2 fixed16


title: HepG2_fixed15

source_name: HepG2 fixed15


title: WT.36_WF_ctrl-saline

value: ctrl-saline


title: WT.37_WF_ctrl-saline


title: WT.49_WF_trametinib-20nM


title: HepG2_fixed14

source_name: HepG2 fixed14


title: HepG2_fixed12

source_name: HepG2 fixed12


title: WT.35_WF_ctrl-saline


title: HepG2_fixed11

source_name: HepG2 fixed11


title: WT.33_WF_ctrl-saline


title: HepG2_fixed10

source_name: HepG2 fixed10


title: WT.34_WF_ctrl-saline


title: tgmel.32_WF_cisplatin-70uM


title: HCT-116_live98

source_name: HCT-116 live98


title: WT.41_WF_cisplatin-70uM


title: HepG2_fixed21

source_name: HepG2 fixed21


title: HCT-116_live99

source_name: HCT-116 live99


title: tgmel.28_WF_cisplatin-70uM


title: HCT-116_live192

source_name: HCT-116 live192


title: HepG2_fixed13

source_name: HepG2 fixed13


title: tgmel.25_WF_cisplatin-70uM


title: tgmel.26_WF_cisplatin-70uM


title: WT.38_WF_cisplatin-70uM


title: tgmel.24_WF_cisplatin-70uM


title: tgmel.23_WF_cisplatin-70uM


title: tgmel.21_WF_cisplatin-70uM


title: HCT-116_live190

source_name: HCT-116 live190


title: HCT-116_live188

source_name: HCT-116 live188


title: HCT-116_live191

source_name: HCT-116 live191


title: HCT-116_live187

source_name: HCT-116 live187


title: tgmel.20_WF_cisplatin-70uM


title: HCT-116_live186

source_name: HCT-116 live186


title: HCT-116_live185

source_name: HCT-116 live185


title: HCT-116_live189

source_name: HCT-116 live189


title: HCT-116_live184

source_name: HCT-116 live184


title: tgmel.31_WF_cisplatin-70uM

source_name: whole fish


title: tgmel.17_WF_ctrl-saline


title: HCT-116_live183

source_name: HCT-116 live183


title: tgmel.18_WF_ctrl-saline


title: tgmel.16_WF_ctrl-saline


title: tgmel.15_WF_ctrl-saline


title: HCT-116_live182

source_name: HCT-116 live182


title: HCT-116_live179

source_name: HCT-116 live179


title: HCT-116_live178

source_name: HCT-116 live178


title: tgmel.14_WF_ctrl-saline


title: HCT-116_live177

source_name: HCT-116 live177


title: HCT-116_live176

source_name: HCT-116 live176


title: HCT-116_live175

source_name: HCT-116 live175


title: HCT-116_live174

source_name: HCT-116 live174


title: 72h treatment sample 3 [SCC40p8TGF72h]

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Demultiplexing of the intensity files using bcl2fastq version 2.17.1.14. Quality check was done via fastqc (v. 0.11.5, Babraham Bioinformatics)
Read alignment was performed using STAR aligner (v2.5.2a)
Read counting was performed using featureCounts (v1.5.0-p1)
Genome_build: hg38 version 89
Supplementary_files_format_and_content: tab-delimited text files with raw read count for each gene in each sample

source_name: UPCI-SCC-040_72h treatment

growth_protocol: Cells were cultured in MEM with Earle's salts, 2,2 g/L NaHCO3, stable glutamine, low-endotoxin medium (Merck, Germany) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Biochrom, Germany), 1% nonessential amino acids (NEAA) (PAN Biotech, Germany), 100 U/ml penicillin, and 100 μg/ml streptomycin (PAN Biotech, Germany) and incubated in a humidified chamber with 5% CO2 at 37°C.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions.
RNA-seq libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, Massachusetts, USA) with minor modifications in ligation and amplification.

treatment_protocol: Cells were treated with 5 ng/ml TGF-β1 in culture medium without FBS and penicillin/streptomycin for 48 or 72 h.

value: oral squamous cell carcinoma (OSCC) cell line

tag: tissue source

value: Tongue

tag: passage

value: passage 8

value: TGF-ß1 treatment (72h)


title: 72h treatment sample 2 [SCC40p13TGF72h]

value: passage 13


title: tgmel.22_WF_cisplatin-70uM


title: 48h treatment sample 3 [SCC40p8TGF48h]

source_name: UPCI-SCC-040_48h treatment

value: TGF-ß1 treatment (48h)


title: Control sample 3 [SCC40p8TGF0h]

value: no TGF-ß1 treatment (control)


title: HCT-116_live173

source_name: HCT-116 live173


title: Control sample 1 [SCC40p12TGF0h]

value: passage 12


title: HCT-116_live172

source_name: HCT-116 live172


title: 72h treatment sample 1 [SCC40p12TGF72h]


title: HCT-116_live169

source_name: HCT-116 live169


title: 48h treatment sample 1 [SCC40p12TGF48h]


title: Control sample 2 [SCC40p13TGF0h]


title: HCT-116_live168

source_name: HCT-116 live168


title: HCT-116_live167

source_name: HCT-116 live167


title: HCT-116_live166

source_name: HCT-116 live166


title: HCT-116_live165

source_name: HCT-116 live165


title: HCT-116_live164

source_name: HCT-116 live164


title: P051 primary HCC

type: RNA

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

hyb_protocol: Total RNA was annealed with multiplexed tags to 770 target RNAs through a ligation reaction and purification step. NanoString technology is based on the direct molecular barcoding and digital detection of target molecules through the use of a color-coded probe pair. The probe pair consists of a Reporter Probe, which carries the signal on its 5' end, and a Capture Probe which carries a biotin on its 3' end.

scan_protocol: After hybridization, excess probes are washed away using a two step magnetic bead- based puri cation on the nCounter Prep Station. Magnetic beads derivatized with short nucleic acid sequences that are complementary to the Capture Probe and the Reporter Probes are used sequentially. First, the hybridization mixture containing target/probe complexes is allowed to bind to magnetic beads complementary to sequences on the Capture Probe. Wash steps are performed to remove excess Reporter Probes and non-target cellular transcripts. After washing, the Capture Probes and target/probe complexes are eluted o the beads and are hybridized to magnetic beads complementary to sequences on the Reporter Probe. An additional wash is performed to remove excess Capture Probes. Finally, the puried target/probe complexes are eluted o the beads and immobilized on the cartridge for data collection. After hybridization, excess probes are washed away using a two step magnetic bead- based puri cation on the nCounter Prep Station. Magnetic beads derivatized with short nucleic acid sequences that are complementary to the Capture Probe and the Reporter Probes are used sequentially. First, the hybridization mixture containing target/probe complexes is allowed to bind to magnetic beads complementary to sequences on the Capture Probe. Wash steps are performed to remove excess Reporter Probes and non-target cellular transcripts. After washing, the Capture Probes and target/probe complexes are eluted o the beads and are hybridized to magnetic beads complementary to sequences on the Reporter Probe. An additional wash is performed to remove excess Capture Probes. Finally, the purified target/probe complexes are eluted o the beads and immobilized on the cartridge for data collection.

data_processing: The raw code counts were normalized by the trimmed mean of M-values normalization method (TMM).

label: no label is used

source_name: Hepatocellular carcinoma

label_protocol: No label is used in Nanostring

extract_protocol: Total RNA were isolated from tumor tissues by using the AllPrep DNA/RNA Mini Kit (Qiagen) according to the manufacturer’s instructions.

value: primary HCC

tag: location

value: Liver


title: 48h treatment sample 2 [SCC40p13TGF48h]


title: HCT-116_live163

source_name: HCT-116 live163


title: HCT-116_live162

source_name: HCT-116 live162


title: HCT-116_live161

source_name: HCT-116 live161


title: P049 metastatic HCC

value: metastiatic HCC

value: Lung


title: P051 metastatic HCC


title: HCT-116_live159

source_name: HCT-116 live159


title: HCT-116_live160

source_name: HCT-116 live160


title: HCT-116_live170

source_name: HCT-116 live170


title: P049 primary HCC


title: P047 metastatic HCC


title: P047 primary HCC


title: HCT-116_live171

source_name: HCT-116 live171


title: HCT-116_live156

source_name: HCT-116 live156


title: P046 metastatic HCC


title: HCT-116_live155

source_name: HCT-116 live155


title: P048 primary HCC


title: HCT-116_live154

source_name: HCT-116 live154


title: P048 metastatic HCC


title: P046 primary HCC


title: P043 metastatic HCC


title: P045 primary HCC


title: P045 metastatic HCC


title: P040 metastatic HCC


title: P040 primary HCC


title: HCT-116_live153

source_name: HCT-116 live153


title: P043 primary HCC


title: HCT-116_live151

source_name: HCT-116 live151


title: HCT-116_live150

source_name: HCT-116 live150


title: HCT-116_live152

source_name: HCT-116 live152


title: P032 metastatic HCC


title: HCT-116_live149

source_name: HCT-116 live149


title: HCT-116_live157

source_name: HCT-116 live157


title: P029 metastatic HCC

source_name: Hepatocellular carcinoma


title: P031 metastatic HCC


title: P031 primary HCC


title: HCT-116_live148

source_name: HCT-116 live148


title: HCT-116_live146

source_name: HCT-116 live146


title: HCT-116_live145

source_name: HCT-116 live145


title: HCT-116_live144

source_name: HCT-116 live144


title: P029 primary HCC


title: HCT-116_live143

source_name: HCT-116 live143


title: HCT-116_live140

source_name: HCT-116 live140


title: HCT-116_live139

source_name: HCT-116 live139


title: P026 primary HCC


title: P026 metastatic HCC


title: P017 metastatic HCC


title: P017 primary HCC


title: HCT-116_live141

source_name: HCT-116 live141


title: HCT-116_live138

source_name: HCT-116 live138


title: P032 primary HCC


title: HCT-116_live147

source_name: HCT-116 live147


title: HCT-116_live137

source_name: HCT-116 live137


title: P011 primary HCC


title: P009 primary HCC


title: HCT-116_live136

source_name: HCT-116 live136


title: P010 primary HCC


title: HCT-116_live135

source_name: HCT-116 live135


title: P009 metastatic HCC


title: HCT-116_live134

source_name: HCT-116 live134


title: P004 metastatic HCC


title: HCT-116_live133

source_name: HCT-116 live133


title: HCT-116_live132

source_name: HCT-116 live132


title: P004 primary HCC

source_name: Hepatocellular carcinoma


title: HCT-116_live142

source_name: HCT-116 live142


title: P011 metastatic HCC


title: P010 metastatic HCC


title: P002 metastatic HCC


title: P002 primary HCC


title: P001 metastatic HCC


title: HCT-116_live130

source_name: HCT-116 live130


title: HCT-116_live131

source_name: HCT-116 live131


title: P001 primary HCC


title: HCT-116_live128

source_name: HCT-116 live128


title: HCT-116_live129

source_name: HCT-116 live129


title: P025 metastatic HCC


title: HCT-116_live127

source_name: HCT-116 live127


title: Neuron - KCl treatment, Input

city: Richardson

first: Zhenyu

last: Xuan

address: 800 West Campbell

institute: UT Dallas

data_processing:
BWA was used to map raw reads to mouse reference genome mm10 with default parameter setting.
Brg1 binding sites were detected by SICER 1.0 with default parameter setting.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bigWig; the columns in the peak files are chrom, start, end, ChIP_island_read_count, CONTROL_island_read_count, p_value, fold_change, FDR_threshold

source_name: neuron

growth_protocol: Primary cortical neurons were culture from E16.5 mouse embryo. Dissociated cortical neurons were plated on poly-L-ornithine- and fibronectin-coated wells. Culture media contained neurobasal plus with B27 plus supplement (Gibco).

extract_protocol:
Lysates were clarified from sonicated nuclei and BAF-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq following the manufacturer's protocols.

treatment_protocol: For depolarization, the cultures were pretreated with TTX (1 µM) and APV (100 µM) to inhibit spontaneous activation on 5 div and 50 mM KCl was added to the cultures for 1 h on 6 div.

value: Primary cultured cortical neurons

value: 50 mM KCl treated 1h

tag: chip antibody


title: Neuron - Basal, BRG1 IP

value: wild type

value: Basal level of KCl

value: J1 anti-BRG1/BRM


title: Non-responder_6

city: Iowa City

first: Benjamin

last: Hing

state: IA

address: 51 Newton Road, BSB 6-509

institute: University of Iowa

data_processing:
Reads were aligned using STAR (version 2.6.0a)
Alignments were processed using StringTie (version 1.3.5)
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: tab separated value file includes lengthScaledTPM value (scaled using the average transcript length over samples and then the library size) for each sample

source_name: Trigeminal ganglia

extract_protocol:
Trigeminal ganglia were dissected and flash frozen in liquid nitrogen.
RNA extraction and library preparation were performed by Genewiz. Library preparation was performed using poly A selection.

tag: Sex

value: Female


title: Neuron - Basal, Input


title: HCT-116_live126

source_name: HCT-116 live126


title: Neuron - KCl treatment, BRG1 IP


title: HCT-116_live125

source_name: HCT-116 live125


title: P025 primary HCC


title: P023 metastatic HCC


title: P023 primary HCC


title: P024 primary HCC


title: Non-responder_2

value: Male


title: P022 metastatic HCC


title: HCT-116_live124

source_name: HCT-116 live124


title: Non-responder_1


title: Responder_6


title: Responder_5


title: HCT-116_live123

source_name: HCT-116 live123


title: P024 metastatic HCC


title: P022 primary HCC


title: Responder_4


title: Non-responder_4


title: Non-responder_5


title: HCT-116_live120

source_name: HCT-116 live120


title: Responder_1


title: HCT-116_live119

source_name: HCT-116 live119


title: P7 crista ampullaris

first: Olivia

last: Bermingham-McDonogh

address: 1959  NE Pacific St box 357420

department: Biological Structure

institute: University of Washington

data_processing:
Base calling and sample were demultiplexing preformed by cellranger mkfastq (version in characteristics)
Sequences were alinged to genome and UMI counts were created using cellranger count (version in characteristics)
Spliced and unspliced matrices were created by running velocyto (0.17.17) on the cellranger output (E16 only)
Downstream analysis was preformed in R and python
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger count output

molecule: polyA RNA

source_name: crista ampullaris

extract_protocol:
Criste, including the ampullae were microdissected in ice-cold HBSS, then digested in type IV collagenase (37 C for 30 min), type II collagenase (37 C for 5 min) and papain (Worthington kit instructions) and strained using a cell-strainer
Chromium Single Cell 3’ Library & Gel Bead Kit v3 (10x Genomics; Pleasanton, CA) per the manufacturer’s instructions.

tag: developmental stage

tag: cellranger version

value: Cell Ranger 2.0.2

tag: 10x chemistry

value: Single Cell 3' v2


title: Responder_3

tag: strain


title: P3 crista ampullaris


title: P021 primary HCC


title: E18 crista ampullaris


title: HCT-116_live118

source_name: HCT-116 live118

tag: cell line


title: HCT-116_live117

source_name: HCT-116 live117


title: P020 metastatic HCC

source_name: Hepatocellular carcinoma

tag: tissue


title: P020 primary HCC


title: E16 crista ampullaris

value: Cell Ranger 3.0.2

value: Single Cell 3' v3


title: HCT-116_live116

source_name: HCT-116 live116


title: HCT-116_live122

source_name: HCT-116 live122


title: P021 metastatic HCC


title: P018 metastatic HCC


title: Responder_2


title: P018 primary HCC


title: HCT-116_live115

source_name: HCT-116 live115


title: Non-responder_3


title: P016 metastatic HCC


title: HCT-116_live114

source_name: HCT-116 live114


title: P016 primary HCC


title: P015 metastatic HCC


title: Sample 10_female_H3K27Ac_1st

city: Wakayama

first: Gen

last: Yamada

address: 811–1 Kimiidera

department: Institute of Advanced Medicine

country: Japan

institute: Wakayama Medical University

data_processing:
Read quality was checked for each sample using FASTQC version 0.11.5.
Reads were mapped to the reference mouse genome UCSC version mm10 using option ‘-k 2’ in Bowtie2 version 2.3.2.
Duplicate reads were excluded with SAMtools version 1.5.
Peak detection was done using the MACS algorithm version 2.1.1.20160309 with option '--to-large --nomodel'.
Genome_build: mm10
Supplementary_files_format_and_content: The BED files were genrated utiizing MACS algorithm.

growth_protocol: Pregnant ICR mice were housed in breeding cages followed with approved Wakayama Medical University guidelines. Noon on the day when the vaginal plug was detected was designed as E0.5.

extract_protocol:
eExG were crosslinked with 20mM EGS (Thermo Fisher Scientific Inc.)  and 1% formaldehyde. Cross-linked chromatin was digested by MNase (Takara) and sonicated.
Immunoprecipitated DNA library for Ion Torrent was prepared in accordance with NEB Next Fast DNA Library Prep Set for Ion Torrent (NEW ENGLAND BioLabs. Inc). Immunoprecipitated DNA library for NextSeq was prepared in accordance with KAPA LTP Library preparation Kit (KAPA), SeqCap Adaptor Kit A (Roche), and Agencourt AMPure XP Beads (Beckman Coulter). High-thoughput sequencing was performed by using Ion Proton system (Thermo Fisher Scientific) and NextSeq 500 Desktop Sequencer (Illumina).

value: CD1 (ICR)

value: female

tag: embryonic day

tag: tissue/cell type

value: murine  embryonic external genitalia (eExG)

value: Anti-Histone H3 (acetyl K27)   (Abcam:4729)


title: Sample 8_male_H3K4me1_1st

value: male

value: Anti-Histone H3 (mono methyl K4)   (Abcam:8895)


title: Sample 7_male_input for H3K4me1_1st

source_name: male_input for H3K4me1


title: Sample 6_male_H3K27Ac_1st


title: HCT-116_live112

source_name: HCT-116 live112


title: Sample 5_male_input for H3K27Ac_1st

source_name: male_input for H3K27Ac


title: peripheric monocytes_6hr_3

city: Hefei

first: Lin

middle: lin

last: Jin

address: 443 Huangshan Road

institute: University of science and technology of China

hyb_protocol: Cy3-labeled cDNA were hybridized to Agilent Whole Human Genome  Microarray (4*44K) Design ID：014850.

scan_protocol: Fluorescence was detected using the Agilent Scanner G2505C (Agilent Technologies).

data_processing: Images were analyzed using Feature Extraction software (version V9.1.3, Agilent Technologies).

source_name: Peripheral blood stem cell-derived monocytes, 6h, replicate 3

label_protocol: RNA was amplified and labeling of CTP with cyanine-3 (cy3) was done with Agilent one-color labeling kits (Agilent Technologies).

extract_protocol: Cells were suspended in TRIzol and total RNA was extracted with an RNeasy MiniKit (Qiagen, Hilden, Germany).

treatment_protocol: After cultured 6 hours, monocytes were isolated from human cord blood mononuclear cells and peripheral blood stem cells

value: Peripheral blood stem cells by apheresis

tag: cell type

value: monocytes


title: peripheric monocytes_6hr_2

source_name: Peripheral blood stem cell-derived monocytes, 6h, replicate 2


title: peripheric monocytes_6hr_1

source_name: Peripheral blood stem cell-derived monocytes, 6h, replicate 1


title: cord blood monocytes_6hr_2

source_name: cord blood-derived monocytes, 6h, replicate 2

value: Cord blood


title: P014 metastatic HCC

value: metastiatic HCC

value: Lung


title: cord blood monocytes_6hr_1

source_name: cord blood-derived monocytes, 6h, replicate 1


title: cord blood monocytes_6hr_3

source_name: cord blood-derived monocytes, 6h, replicate 3


title: Sample 3_male input for AR_2nd

source_name: male input for AR


title: Sample 12_female_H3K4me1_1st


title: HCT-116_live108

source_name: HCT-116 live108


title: Sample 11_female_input for H3K4me1_1st

source_name: female_input for H3K4me1


title: HCT-116_live110

source_name: HCT-116 live110


title: HCT-116_live111

source_name: HCT-116 live111


title: Sample 1_male_input for AR_1st

source_name: male_input for AR


title: P014 primary HCC

source_name: Hepatocellular carcinoma

value: primary HCC

value: Liver


title: HCT-116_live113

source_name: HCT-116 live113


title: Sample 9_female_input for H3K27Ac_1st

source_name: female_input for H3K27Ac


title: Sample 2_male AR_1st

source_name: male AR

value: Anti-AR (N-20)  (Santa Cruz:sc-816)


title: P012 primary HCC


title: P015 primary HCC


title: P012 metastatic HCC


title: HCT-116_live107

source_name: HCT-116 live107


title: HCT-116_live106

source_name: HCT-116 live106


title: P006 metastatic HCC


title: HCC S31

scan_protocol: After hybridization, excess probes are washed away using a two step magnetic bead- based puri cation on the nCounter Prep Station. Magnetic beads derivatized with short nucleic acid sequences that are complementary to the Capture Probe and the Reporter Probes are used sequentially. First, the hybridization mixture containing target/probe complexes is allowed to bind to magnetic beads complementary to sequences on the Capture Probe. Wash steps are performed to remove excess Reporter Probes and non-target cellular transcripts. After washing, the Capture Probes and target/probe complexes are eluted o the beads and are hybridized to magnetic beads complementary to sequences on the Reporter Probe. An additional wash is performed to remove excess Capture Probes. Finally, the puried target/probe complexes are eluted o the beads and immobilized on the cartridge for data collection. After hybridization, excess probes are washed away using a two step magnetic bead- based puri cation on the nCounter Prep Station. Magnetic beads derivatized with short nucleic acid sequences that are complementary to the Capture Probe and the Reporter Probes are used sequentially. First, the hybridization mixture containing target/probe complexes is allowed to bind to magnetic beads complementary to sequences on the Capture Probe. Wash steps are performed to remove excess Reporter Probes and non-target cellular transcripts. After washing, the Capture Probes and target/probe complexes are eluted o the beads and are hybridized to magnetic beads complementary to sequences on the Reporter Probe. An additional wash is performed to remove excess Capture Probes. Finally, the puri ed target/probe complexes are eluted o the beads and immobilized on the cartridge for data collection.

data_processing: The raw code counts were normalized by the trimmed mean of M-values normalization method (TMM). Log2 normalized code count per million (CPM)

tag: gender

value: F

value: PD

value: No

tag: etiology

value: Other

tag: disease state

value: HCC patient with immune checkpoint inhibitor therapy

value: HCC tumor


title: HCC S30

value: M

value: PR

value: Yes

tag: age

value: HBV


title: HCT-116_live105

source_name: HCT-116 live105


title: 1o_plasmid

city: Farmington

first: Scott

last: Adamson

state: CT

address: 400 Farmington Ave

department: Genetics and Genome Sciences

institute: UConn Health

description: Amplicon DNA sequencing of plasmid pool midway through construction

data_processing:
Library strategy: RT-PCR sequencing (Vex-seq)
UMIs were extracted from read 2 using UMItools (v1.0.0) extract (with --bc-pattern=NNNNNNNNNN) using UMItools
Read pairs were aligned to variant specific references using hisat2 (2.1.0) with parameters -no-softclip --dta-cufflinks.
Duplicate reads were deduplicated using UMItools (v1.0.0) dedup.
Stringtie (v2.0.3) was used to detect novel splice junctions from aligned and deduplicated reads and all samples were merged
Pysam (v0.15.4) was used to extract junction counts from bam files for all stringtie detected junctions.
BWA-MEM (v0.7.17) was used to align plasmid DNA samples.
Samtools and htslb (v1.9) mpileup and bcftools were used to identify the number of novel variant reads and reference reads.
Genome_build: hg19
Supplementary_files_format_and_content: All processed data files are tab separated files. For the plasmid libraries, these contain total counts and counts of variant sequences (1o) as well as the allele frequency. For the Vex-seq libraries these are counts of included reads, excluded reads, percent spliced in, for each variant and identified isoform as well as characteristics about the splice junctions used (Stringtie outputs and pysam parsed junction counts).

organism: synthetic construct

source_name: pc-AT7-Glo1 plasmid with Vex-seq library in configuration 1o

growth_protocol: Cells were grown to a density of 0.7x10^6 for HepG2 and 1.0x10^6 for K562 and transfected with 5 micrograms of plasmid DNA

extract_protocol:
Total RNA was extracted 48 hours after transfection using Maxwell RSC simplyRNA kit (Promega).
cDNA was synthesized using Superscript III and a reporter-gene specific primer. Illumina primers and indices were added during PCR amplification.

tag: sequenced molecule

value: plasmid DNA


title: HCT-116_live104

source_name: HCT-116 live104


title: P006 primary HCC

tag: location


title: 2o_plasmid

description: Amplicon DNA sequencing of final plasmid pool

source_name: pc-AT7-Glo1 plasmid with Vex-seq library in configuration 2o


title: HCT-116_live103

source_name: HCT-116 live103


title: HCC S29

value: SD


title: Mouse neuron mutant Brg1 Basal

data_processing:
Tophat  (version 1.3.2) was used to map reads to mm9 with parameters of "--library-type fr-unstranded --segment-length 15 --solexa-quals -g 10".
Cufflink was used to quantify gene expression in RPKM with default parameter setting.
UCSC gene annotation of mm9 was used in Tophat mapping and  Cufflink quantification.
Genome_build: mm9
Supplementary_files_format_and_content: Text file with each column being RPKM of gene expression in each sample

source_name: neuron

extract_protocol:
Total RNA were expreact with TRIZOL and cleaned with a Qiagen RNeasy Kit.
RNA-seq libraries were prepared using the Illumina RNA-Seq Preparation Kit and sequenced on a HiSeq sequencer at the University of Texas Southwestern Sequencing Core Facility.

treatment_protocol: For depolarization, the cultures were pretreated with TTX (1 µM) and APV (100 µM) to inhibit spontaneous activation on 5 div and 50 mM KCl was added to the cultures for 6 h on 6 div.

tag: genotype

value: Brg1-cko (BAF53bCre Brg1F/F)

value: Primary cultured cortical neurons

tag: treatment

value: Basal level of KCl


title: Mouse neuron WT Brg1 KCl treated

value: wild type

value: 50 mM KCl treated 6h


title: Mouse neuron WT Brg1 Basal


title: HCT-116_live102

source_name: HCT-116 live102


title: HCT-116_live101

source_name: HCT-116 live101


title: Mouse neuron mutant Brg1 KCl treated


title: HCC S26


title: HCC S27


title: HCT-116_live100

source_name: HCT-116 live100


title: imPSCc2 LS rep2

city: Stockholm

first: Xinyuan

last: Liu

address: Hälsovägen 7

department: Department of Clinical Science, Intervention and Technology

country: Sweden

institute: Karolinska Institute

data_processing:
Reference genomes for human and mouse, GRCh38.87 and GRCm38.87 were downloaded from Ensembl and used to build respective indices for the species-based read classifier Xenome (1.0.1) and the short read aligner STAR (2.5.1b).
The program Xenome (1.0.1) was used to classify the fastq reads based on species origin using default settings.
Separated human and murine reads were subsequently aligned to their respective reference genomes by means of STAR (2.5.1b)  using default options with --sjdbGTFfile pointing to the respective reference annotation file and --outFilterMultimapNmax set to 1.
featureCounts from the package subread (1.5.2) was employed to quantify reads mapped to known features in the Ensembl database.
Genome_build: GRCh38.87 and GRCm38.87
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: mouse pancreatic stellate cells

growth_protocol: Panc1 and imPSCc2 were cultivated either under high serum condition with DMEM/F12 medium supplemented with 10% FBS (high serum) and 0.5% penicillin/streptomycin or low serum condition supplemented with 0.1% FBS, 0.3% bovine serum albumin (only for Panc1 cells) , insulin-transferrin-selenium-sodium pyruvate solution (ITS-A) (1/10 of the recommended concentration was used to adapt insulin to more physiological concentrations) and 0.5% penicillin/streptomycin in a humidified incubator at 37°C and 5% CO2. Both Panc1 and imPSCc2 were stepwise adapted to low serum condition over a course of 6–8 weeks.

extract_protocol:
Total RNA was extracted directly from monospheroids and heterospheroids for RNA-sequencing using the RNeasy PLUS kit (Qiagen).
Library preparations were conducted using NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB, E7760S), including a poly-A enrichment step by the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, E7490S). The End Repaired DNA was subjected to Agencourt AMPure XP bead clean-up and size selection (NEB, E6260). Libraries from the samples were multiplexed using NEBNext® Multiplex Oligos for Illumina® (NEB, Index Primers Set 1; E7335S).

treatment_protocol: Panc1 and imPSCc2 were trypsinized and grown either as monospheroids (2500 imPSCc2 or Panc1 cells) or heterospheroids (500 Panc1 cells and 2000 imPSCc2 in high serum; 1250 Panc1 cells and 1250 imPSCc2 in low serum) in non-treated, round-bottom 96-well microplates in DMEM/F12 medium supplemented with either 10% FBS (“high serum” condition) or 0.1% FBS, 0.3% BSA and ITS-A (“low serum” condition), and 0.5% penicillin/streptomycin as well as 0.24% methyl cellulose at 37°C and 5% CO2 humidified condition

tag: tag

value: low serum

value: mouse pancreatic stellate cells


title: imPSCc2 LS rep3


title: imPSCc2 LS rep4


title: imPSCc2 LS rep1


title: HCC S25


title: HCT-116_fixed9

data_processing:
Index and adapter were trimmed in data downloaded form Basespace
Quality control was done using Fastqc
Alignment and quantification were done by mapping raw reads to GRCh38 using kallisto 0.46.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene expression/Transcript expression matrix(TPM)

source_name: HCT-116 fixed9


title: HCC S24

source_name: Hepatocellular carcinoma

value: No


title: HCT-116_fixed96

source_name: HCT-116 fixed96


title: HCC S23

value: F

value: PD


title: HCT-116_fixed95

source_name: HCT-116 fixed95


title: HCC S22

value: HCC patient with immune checkpoint inhibitor therapy

value: HCC tumor


title: LV58: HFD+TXN, biological replicate 9

city: Corvallis

first: Adrian

middle: F

last: Gombart

state: OR

address: Linus Pauling Science Center

department: Linus Pauling Institute/Biochemistry and Biophysics

institute: Oregon State University

description:
TXN58
single-end, two raw files were generated from two separate Illumina runs

data_processing:
Two reads from separate Illumina runs were concatenated into one.
Concatenated reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, using bbduk with parameters k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=20 minlength=20
Sequences then mapped to GRCm38 using STAR version 37.95
BAM files were then converted to raw counts and genes were annotated using Rsamtools (v.2.6.0), GenomicFeatures (1.42.1), GenomicAlignments (v.1.26.0), Mus.musculus (v.1.3.1) in R.
Genes whose names contain "ribosomal protein", "RIKEN", "predicted gene", "pseudogene", "cDNA sequence", "nuclear encoded rRNA", "microRNA",  "DNA segment", "uncharacterized", "pre-RNA", "20S rRNA",  "non-protein coding" were removed.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: liver

extract_protocol:
Liver were removed, flash frozen in liquid N2 and stored at -80C until day of RNA isolation; total RNA was harvested using Direct-zol RNA Miniprep Plus kit (Zymo Research).
RNA purity and integrity were evaluated using a Bioanalyzer RNA 6000 Nano chip (Agilent Technologies). Lexogen QuantSeq 3'mRNA-Seq Library Prep Kit-FWD for Illumina sequencing was used with 325 ng of total RNA for the construction of sequencing libraries.
Library preparation was started by oligo(dT) priming, with primers already containing the Illumina-compatible linker sequence for Read 2. After firststrand synthesis, the RNA was removed before random primers that contained the corresponding Illumina-compatible linker sequence for Read 1 initiated the second-strand synthesis.
Second strand synthesis was followed by a magnetic bead-based purification step. The libraries were PCR amplified introducing sequences required for cluster generation and i7 and i5 dual indices (Lexogen i7 6 nt Index Set and Lexogen i5 6 nt Unique Dual Indexing Add-on Kit) for 16-20 PCR cycles with the optimal number predetermined by qPCR with the PCR Add-on Kit for Illumina (Lexogen GmbH). After a second magnetic bead-based purification, libraries were quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and sized using an Agilent High Sensitive D5000 Screen Tape (Agilent Technologies) to determine molarity. Equal molar amounts of the libraries were multiplexed and then sequenced on an Illumina Hiseq3000 platform (Illumina, San Diego, CA, USA) at the Center for Genome Research and Biocomputing, Oregon State University using single-end sequencing with 100-bp reads.

tag: Sex

value: male

value: 26 weeks

value: liver

value: HFD+TXN


title: LV57: HFD+TXN, biological replicate 8

description:
TXN57
single-end, two raw files were generated from two separate Illumina runs


title: LV56: HFD+TXN, biological replicate 7

description:
TXN56
single-end, two raw files were generated from two separate Illumina runs


title: HCT-116_fixed94

source_name: HCT-116 fixed94

extract_protocol: cDNA library was constructed using Smart-seq2 protocl, sequencing library was prepared using Illuminar Nextera DNA Library Prep Kit(Illumina, cat#FC-131-1096), we followed library contruction protocal provided by C1 Fluidigm(Fluidigm)


title: HCC S21

value: M

value: SD

value: Yes

value: HBV


title: imPSCc2 HS rep1

value: high serum


title: LV55: HFD+TXN, biological replicate 6

description:
TXN55
single-end, two raw files were generated from two separate Illumina runs


title: imPSCc2 HS rep4


title: imPSCc2 HS rep3


title: imPSCc2 HS rep2

description: outlier, not included in analysis


title: HCC S20


title: HCT-116_fixed92

source_name: HCT-116 fixed92


title: HCC S19

value: PR

value: HCV


title: LV54: HFD+TXN, biological replicate 5

description:
TXN54
single-end, two raw files were generated from two separate Illumina runs


title: HCC S18


title: HCT-116_fixed90

source_name: HCT-116 fixed90


title: HCC S16


title: HCC S17


title: LV53: HFD+TXN, biological replicate 4

description:
TXN53
single-end, two raw files were generated from two separate Illumina runs


title: LV52: HFD+TXN, biological replicate 3

description:
TXN52
single-end, two raw files were generated from two separate Illumina runs


title: LV45: HFD+HXN, biological replicate 9

description:
HXN45
single-end, two raw files were generated from two separate Illumina runs

value: HFD+HXN


title: HCT-116_fixed8

source_name: HCT-116 fixed8


title: D39 ΔbgaA:: PspxB-metR-3×flag no methionine Input 2

city: Beijing

first: Jing-Ren

last: Zhang

state: Beijing

address: Room 312, Renhuan Building, Tsinghua University

department: School of Medicine

institute: Tsinghua University

data_processing:
Base calliing: Illumina Casava software version 1.8
Quality control: FastQC v0.11.8
Trimming:  TrimGalore-0.6.6
S. pneumoniae reads were mapped with Bowtie2-2.4.1, and then Picard was used for duplicates removal
Peaks were defined using BELT algorithm, quantification of ChIP peaks against input was calculated by featureCounts, TPM calculation of individual peaks was using a custom script
Genome_build: Streptococcus pneumoniae D39 (accession NC_008533.2, assembly  GCA_000014365.2) was used directly in the analysis.
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each sample.

organism: Streptococcus pneumoniae D39

source_name: D39 ΔbgaA:: PspxB-metR-3×flag cultured in CDM without methionine till OD620=0.2 (replicate 2 of Input)

growth_protocol: Culture D39 ΔbgaA:: PspxB-metR-3×flag in THY to OD620 = 0.5. Then wash twice with Ringer’s solution. Resuspend bacteria pellet in CDM without methionine to OD620 = 0.5. Then dilute the corresponding bacteria in 200 mL CDM without methionine (1:20 dilution) and grow until OD 0.2.

extract_protocol:
The culture was grown to OD620 0.2 before being washed being mixed with 1% formaldehyde in the fixation buffer at a volume ratio of 1:10 to crosslink interacting bacterial protein-DNA molecules. The mixture was gently rotated for 30 min at room temperature, quenched 1:3 (v/v) with 1 M Tris, pH 8.0, for 10 min, pelleted by centrifugation at 4°C, washed twice in ice-cold PBS by centrifugation, and snap-frozen in liquid nitrogen.  The cell pellets were then resuspended in 2 ml ice-cold lysis buffer in a 5-ml round-bottom tube, and sonicated on ice for 55 X 5 seconds with an interval of 20 seconds to break down genomic DNA using Sonics Vibracell VC750 with 30 % amplitude.  After centrifugation at 4°C, the supernatants were divided into the 200 μl input control and 800 μl immunoprecipitation (IP) sample.  The IP sample was mixed with the lysis buffer with 10 μg anti-FLAG antibody (Sigma) on a rotating wheel for 8 h at 4 °C, and subsequently with protein G-coupled Dynabeads (Invitrogen) for 10 h at 4 °C.  Beads were isolated on a magnet, sequentially washed with the lysis and wash buffers by centrifugation, resuspended in 520 µl TES buffer, and incubated at 65 °C for 4 h to de-crosslink and elute DNA fragments from beads.  The input sample was supplemented with 300 µl TES and 20 µl 10 % SDS and incubated at 65 °C for 4 h.  Both the IP and input samples were treated with 12.5 μl Proteinase K (20 mg/ml in TE) before DNA was purified by sequential treatment with phenol, chloroform, and ethanol.  DNA pellets were dissolved in 100 μl TE (pH 8.0) for 15 min at 65 °C.  The DNA samples were verified by DNA gel electrophoresis and used to construct libraries.
The purified DNA was used for ChIP-seq library preparation. The library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: antibiotic resistance

value: rpsL1 (StreptomycinR)

tag: od620 for bacteria collection


title: LV49: HFD+TXN, biological replicate 1

description:
TXN49
single-end, two raw files were generated from two separate Illumina runs

tag: strain


title: D39 ΔbgaA:: PspxB-metR-3×flag no methionine Input 1

source_name: D39 ΔbgaA:: PspxB-metR-3×flag cultured in CDM without methionine till OD620=0.2 (replicate 1 of Input)


title: LV46: HFD+HXN, biological replicate 10

description:
HXN46
single-end, two raw files were generated from two separate Illumina runs

tag: tissue


title: HCT-116_fixed89

first: Xinlei

last: Wang

address: Clear Water Bay, Sai Kung,

institute: HKUST

source_name: HCT-116 fixed89

tag: cell line


title: LV51: HFD+TXN, biological replicate 2

description:
TXN51
single-end, two raw files were generated from two separate Illumina runs


title: LV44: HFD+HXN, biological replicate 8

description:
HXN44
single-end, two raw files were generated from two separate Illumina runs


title: Sample 4_male AR_2nd

source_name: male AR

value: CD1 (ICR)

tag: embryonic day

tag: tissue/cell type

value: murine  embryonic external genitalia (eExG)

tag: chip antibody

value: Anti-AR (N-20)  (Santa Cruz:sc-816)


title: D39 ΔbgaA:: PspxB-metR-3×flag no methionine IP 2

source_name: D39 ΔbgaA:: PspxB-metR-3×flag cultured in CDM without methionine till OD620=0.2 (replicate 2 of IP)


title: LV43: HFD+HXN, biological replicate 7

description:
HXN43
single-end, two raw files were generated from two separate Illumina runs


title: HCT-116_fixed91

source_name: HCT-116 fixed91


title: D39 ΔbgaA:: PspxB-metR-3×flag no methionine IP 1

source_name: D39 ΔbgaA:: PspxB-metR-3×flag cultured in CDM without methionine till OD620=0.2 (replicate 1 of IP)


title: HCT-116_live158

source_name: HCT-116 live158


title: HCT-116_fixed88

source_name: HCT-116 fixed88


title: 8: darG-depleted Rep 3

city: Guildford

first: Graham

last: Stewart

address: University of Surrey

department: Faculty of Health and Medical Sciences

country: United Kingdom

institute: University of Surrey

data_processing:
Sequence reads were trimmed to remove possible adaptoer sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Mycobacterium Bovis BCG Pasteur_1173P2 reference genome available on ENSEMBL using Bowtie2 aligner v.2.2.6. BAM files were generated as a result of this step.
Unique hit counts were calculated by using featureCounts from the Subread package v.1.5.2.  The hit counts were summarized and reported using the gene_ID feature in the annotation file.  Only unique reads that fell within gene regions were counted.
Genome_build: AM408590.1

organism: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2

source_name: Bacilli in liquid culture

growth_protocol: Growth of bacilli in shaking liquid medium (7H9 supplemented with tween 80, glycerol and OADC)

extract_protocol:
Bacilli were pelleted and preserved with RNA Later, then extracted with Tri Reagent and Zymo RNA clean and concentrate columns with two on column DNAse digestion steps.
RNA Seq libraries were prepared for sequencing using standard Illumina protocols, by GENEWIZ (Brooks Life Science)

treatment_protocol: Untreated for 48h, treated with ATC 200ng/ml for 48 to deplete darG, or treatement with mitomycin C 20ng/ml for the final 24 hours

value: BCG Pasteur 1173P2

value: ATC induction of darG-CRISPRi for 48h


title: LV41: HFD+HXN, biological replicate 5

description:
HXN41
single-end, two raw files were generated from two separate Illumina runs

value: male

value: 26 weeks


title: HCC S10

source_name: Hepatocellular carcinoma

tag: gender

tag: etiology

value: HCC patient with immune checkpoint inhibitor therapy

value: HCC tumor


title: HCC S08

value: M

tag: age

tag: disease state


title: 9: Mitomycin C treated Rep 3

value: Mitomycin C treatment for 24h


title: human_OE_rep1

type: genomic

city: shanghai

first: sun

middle: tong

last: xin

address: xinjunhuanlu

institute: oebiotech

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human  MethylationEPIC(850K) BeadChip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: human osteoarthritis cell rep1

label_protocol: Standard Illumina Protocol

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

tag: cell type

value: human osteoarthritis cell


title: HCT-116_fixed85

city: Hong Kong

source_name: HCT-116 fixed85


title: HCT-116_fixed86

source_name: HCT-116 fixed86


title: LV39: HFD+HXN, biological replicate 3

description:
HXN39
single-end, two raw files were generated from two separate Illumina runs

source_name: liver

value: liver


title: human_OE_rep3

source_name: human osteoarthritis cell rep3


title: 6: Mitomycin C treated Rep 2


title: HCT-116_fixed84

source_name: HCT-116 fixed84


title: LV38: HFD+HXN, biological replicate 2

description:
HXN38
single-end, two raw files were generated from two separate Illumina runs


title: HCC S12

value: SD

value: Yes

value: HBV


title: HCC S14

value: PD

value: No


title: HCT-116_fixed87

source_name: HCT-116 fixed87


title: LV40: HFD+HXN, biological replicate 4

description:
HXN40
single-end, two raw files were generated from two separate Illumina runs

value: HFD+HXN


title: 7: Untreated Rep 3

value: Growth in medium for 48h


title: HCC S11

value: PR

value: HCV


title: 5: darG-depleted Rep 2

value: BCG Pasteur 1173P2

value: ATC induction of darG-CRISPRi for 48h


title: human_NC_rep1

source_name: human normal cell rep1

value: human normal cell


title: HCC S06

value: HCC patient with immune checkpoint inhibitor therapy

value: HCC tumor


title: LV37: HFD+HXN, biological replicate 1

description:
HXN37
single-end, two raw files were generated from two separate Illumina runs

value: male

value: 26 weeks


title: human_NC_rep3

source_name: human normal cell rep3


title: human_NC_rep2

source_name: human normal cell rep2


title: human_OE_rep2

source_name: human osteoarthritis cell rep2

value: human osteoarthritis cell


title: HCC S02

value: M

value: SD

value: Other


title: 4: Untreated Rep 2


title: HCT-116_fixed82

source_name: HCT-116 fixed82


title: LV22: HFD, biological replicate 10

description:
HFD22
single-end, two raw files were generated from two separate Illumina runs

value: liver

value: HFD


title: HCT-116_fixed83

source_name: HCT-116 fixed83


title: HCC S01

value: PD

value: No

value: HBV


title: 3: Mitomycin C treated Rep 1

value: Mitomycin C treatment for 24h


title: HCT-116_fixed81

source_name: HCT-116 fixed81


title: LV20: HFD, biological replicate 8

description:
HFD20
single-end, two raw files were generated from two separate Illumina runs


title: 2: darG-depleted Rep 1

value: BCG Pasteur 1173P2


title: HCC S03

value: HCV


title: HCT-116_fixed80

source_name: HCT-116 fixed80


title: 1: Untreated Rep 1

source_name: Bacilli in liquid culture

value: Growth in medium for 48h


title: HCT-116_fixed7

source_name: HCT-116 fixed7


title: Kidney CI-AKI Rep3

city: Fuzhou

first: Zhiqing

state: Fujian

address: NO. 156, North Xierhuan Road

department: Department of Cardiology

institute: 900 Hospital of the Joint Logistics Team

data_processing:
Sequenced raw reads were preprocessed by removing rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads with Seqtk (https:// github.com/lh3/seqtk).
Obtained clean reads were mapped to the Rat rn6 reference genome with two mismatches by Hisat2 (version 2.0.4). After genome mapping, Cufflinks v2.1.1 was run with a reference annotation to generate FPKM (fragments per kilobase of exon model per million mapped reads)values for known gene models.
The p-value significance threshold was set by the false discovery rate (FDR) strictly controlled using the Benjamini and Hochberg algorithm. The fold-changes were estimated according to the FPKM in each sample. Differentially expressed genes were identified using Cuffdiff with the following filter criteria: FDR≤0.05 and fold-change≥2.
Genome_build: rn6

organism: Rattus norvegicus

source_name: kidney

growth_protocol: The three-month-old male Sprague-Dawley rats (Fujian Medical University breed, China), weighing approximately 250 g at the start of the experiment, were used and kept in individual cages under controlled conditions of light (12 hours/12 hours light/dark cycle) and temperature (21~23℃), with free access to tap water and standard rat chow for a 7-day adaptive period.

extract_protocol:
Total RNA was extracted using mirVanaTM miRNA Isolation Kit (Cat# AM1561, Ambion)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Briefly, rats were deprived of water for 48 hours and then anaesthetized by pentobarbital sodium (40 mg/kg, ip.). Catheters were palced in the right femoral vein and the common carotid artery (24 G×21 mm, SPECATH, Foshan, China), and a baseline arterial blood sample was drawn (1 ml) for determination of SCr. Then, INDO was administreted intravenously (10 mg/kg, iv.), and followed after 15 minuters by L-NAME (10 mg/kg, iv.). Another 15 minuters later, rats were randomized to receive iopromide (CI-AKI group) or normal saline (control group) via the carotid artery cannulation (7.8 ml/kg, ia.). The rats were then allowed to recover in individual cages with free access to tap water and standard chow. Approximately 12 hours after iopromide injection, the blood sample for the measurement of postoperative SCr was obtained under anesthesia. The kidney tissue for RNA-sequencing or qRT-PCR validation was then harvested immediately and stored in the RNAsafty Reagent (Bohao, Shanghai, China) at 4 degrees Celsius overnight, before tansfered to an minus 20 degrees Celsius refrigerator. Part of the kidney tissue, containing cortex and medulla, were fixed in 10 % neutral formalin liquid for histological analysis. The sections of kidney tissue were stained with hematoxylin and eosin, and the Paller scores were calculated to determind the severity of the tubular injury. In the end, the rats were sacrificed with an overdose of pentobarbital anesthesia (200 mg/kg, ip.).

value: Sprague-Dawley

value: kidney

value: three-month-old

tag: diagnosis

value: contrast-induced acute kidney injury


title: LV18: HFD, biological replicate 6

description:
HFD18
single-end, two raw files were generated from two separate Illumina runs

value: male

value: 26 weeks

tag: treatment


title: HCT-116_fixed79

source_name: HCT-116 fixed79


title: LV19: HFD, biological replicate 7

description:
HFD19
single-end, two raw files were generated from two separate Illumina runs


title: Kidney CI-AKI Rep2


title: Kidney CI-AKI Rep1


title: HCT-116_fixed78

source_name: HCT-116 fixed78


title: LV17: HFD, biological replicate 5

description:
HFD17
single-end, two raw files were generated from two separate Illumina runs

source_name: liver


title: E12_Liver

city: Montreal

first: Anna

middle: K.

last: Naumova

state: Quebec

address: 2155 rue Guy

department: Departments of Obstetrics and Gynecology and Human Genetics

country: Canada

institute: McGill University

data_processing:
Sequenced reads were trimmed for adapters and low-quality bases with Trimmomatic (v0.36).
Trimmed reads were aligned to the GRCm38 reference genome using the STAR two-pass method (v2.7.3a).
Raw count matrix generated from alignment files using HTSeq-count (v0.6.0).
Data quality was assessed using RNAseqQC (v1.1.8).
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA was isolated using TRIzol Reagent (Thermo Fisher Scientific, MA, US) according to the manufacturer's instructions and followed by purification using the RNeasy MinElute Cleanup Kit (Qiagen, NL).
Libraries were prepared using the Illumina TruSeq library prep kit according to manufacturer's instructions. Briefly, ribosomal RNA was depleted using Ribo-Zero rRNA Removal Mix beads and then fragmented. Then, cDNA is synthesized from the RNA fragments, one strand at a time. After cDNA synthesis, 3' ends are adenylated and then sequencing adapters are ligated to te 3' end. PCR is peformed to enrich cDNA fragments, after which library concentration is determined using qPCR and size distribution is measured with Caliper LabChip Hisens chips. Final products are pooled and used for sequencing.

value: Female

tag: genotype

value: homozygous Esr1 knockout

value: Liver


title: E47_Liver

tag: Sex


title: Kidney Control Rep3

value: control


title: E31_Liver


title: HCT-116_fixed77

source_name: HCT-116 fixed77


title: LV21: HFD, biological replicate 9

description:
HFD21
single-end, two raw files were generated from two separate Illumina runs

value: liver

value: HFD


title: Kidney Control Rep2


title: E22_Liver


title: Kidney Control Rep1


title: HCT-116_fixed76

source_name: HCT-116 fixed76


title: LV16: HFD, biological replicate 4

description:
HFD16
single-end, two raw files were generated from two separate Illumina runs


title: LV15: HFD, biological replicate 3

description:
HFD15
single-end, two raw files were generated from two separate Illumina runs


title: HCT-116_fixed75

source_name: HCT-116 fixed75


title: HCT-116_fixed74

source_name: HCT-116 fixed74


title: E14_Liver


title: E35_Liver

value: Male


title: E30_Liver


title: HCT-116_fixed73

source_name: HCT-116 fixed73


title: EPO-2

city: jinan

first: meng

last: zhang

address: Jinan 250012, Shandong, China

institute: Shandong University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the mm10 genome assembly using Tophat version 2.0.6 with parameters: -r 100 -I 50000  --max-segment-intron 50000 -a 10 -g 10
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using DEGseq function package in R program version 2.10.0
Genome_build: UCSC mm10
Supplementary_files_format_and_content: raw fragment counts for each Sample

source_name: Aorta

extract_protocol:
A total of 3μg RNA per sample was used as input material for RNA sample preparations.
Sequencing libraries were generated by using the NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA). First-strand cDNA was synthesized by using a random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second-strand cDNA synthesis involved use of DNA polymerase I and RNase H. Then cDNA samples were amplified by PCR, and the products were purified (AMPure XP system). Library quality was assessed by using the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples involved using a cBot Cluster Generation System with the TruSeq PE Cluster Kit v3-cBot-HS (Illumina). After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125/150-bp paired-end reads were generated.

treatment_protocol: The vehicle group mice received intraperitoneal injection of saline and the EPO group mice received intraperitoneal recombinant human EPO (3SBIOINC, Shenyang, China) injection of 5,000IU/kg/day, for 4 weeks. All mice underwent euthanasia after 4 weeks’ infusion and aortic tissues were extracted for further investigation.

value: Apoe-/- mice

value: aorta

value: treated with EPO for 4 weeks


title: EPO-3


title: LV13: HFD, biological replicate 1

description:
HFD13
single-end, two raw files were generated from two separate Illumina runs


title: EPO-1


title: LV10: LFD, biological replicate 10

description:
LFD10
single-end, two raw files were generated from two separate Illumina runs

value: LFD


title: HCT-116_fixed72

source_name: HCT-116 fixed72


title: Vehicle-3

value: treated with saline for 4 weeks


title: E5_Liver


title: LV08: LFD, biological replicate 8

description:
LFD08
single-end, two raw files were generated from two separate Illumina runs


title: HCT-116_fixed71

source_name: HCT-116 fixed71


title: E27_Liver


title: LV09: LFD, biological replicate 9

description:
LFD09
single-end, two raw files were generated from two separate Illumina runs


title: Vehicle-2


title: E39_Liver

value: wild type


title: Vehicle-1


title: HCT-116_fixed70

source_name: HCT-116 fixed70


title: E23_Liver


title: E16_Liver


title: HCT-116_fixed6

source_name: HCT-116 fixed6


title: LV14: HFD, biological replicate 2

description:
HFD14
single-end, two raw files were generated from two separate Illumina runs


title: AA rep3

city: Stony Brook

first: Sandeep

last: Mallipattu

state: NY

address: 101 Nicolls Road

department: Department of Medicine

institute: Stony Brook University

data_processing:
Raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
Raw RNA-seq data was quantified to gene-level counts using Kallisto (Bray et al., 2016) with the ARCHS4 pipeline (Lachmann et al., 2017)
Raw counts were normalized to log10-Counts Per Million (logCPM) by dividing each column by the total sum of its counts followed by the application of a log10-transform.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file containing logCPM values for all samples

source_name: proximal tubule S2/S3 segments

extract_protocol:
Mice were perfused with PBS, kidneys removed and stored in RNAlater. Mouse kidneys were sliced and tubule microdissection was performed in ice-cold dissection solution (135 mM NaCl, 1 mM Na2HPO4, 1.2 mM Na2SO4, 1.2 mM MgSO4, 5 mM KCl, 2 mM CaCl2, 5.5 mM glucose, 5 mM HEPES, 0.1% BSA; pH 7.4) using a Leica MZ12.5 stereomicroscope equipped with Leica MC170 HD microscope camera and ThermaZone cooling device. Five to ten S2/S3 PT tubules were pooled together from each kidney and washed with PBS in a separate petri dish. RNA was extracted using PicoPure RNA kit (Applied Biosystems).
cDNA was prepared using TruSeq Stranded mRNA Sample Preparation kit (Illumina, San Diego, CA), according to the manufacturer’s instructions.

value: S2/S3 kidney proximal tubules segments


title: LV07: LFD, biological replicate 7

description:
LFD07
single-end, two raw files were generated from two separate Illumina runs


title: AA rep2


title: HCT-116_fixed69

source_name: HCT-116 fixed69


title: LV04: LFD, biological replicate 4

description:
LFD04
single-end, two raw files were generated from two separate Illumina runs


title: E36_Liver


title: HCT-116_fixed93

source_name: HCT-116 fixed93


title: HCT-116_fixed67

source_name: HCT-116 fixed67


title: HCT-116_fixed68

source_name: HCT-116 fixed68


title: DMSO rep3


title: LV05: LFD, biological replicate 5

description:
LFD05
single-end, two raw files were generated from two separate Illumina runs


title: E24_Liver


title: LV03: LFD, biological replicate 3

description:
LFD03
single-end, two raw files were generated from two separate Illumina runs


title: HCT-116_fixed66

source_name: HCT-116 fixed66


title: AA rep1


title: LV02: LFD, biological replicate 2

description:
LFD02
single-end, two raw files were generated from two separate Illumina runs

source_name: liver


title: HCT-116_fixed65

source_name: HCT-116 fixed65


title: B15_L1_803D73

first: Qiu

last: Xie

address: No.1 Shuaifuyuan Wangfujing Dongcheng District

institute: Peking Union Medical College Hospital

data_processing:
Raw data were trimmed using TrimGalore version 0.6.5.
RNA-seq reads were aligned to the mm10 genome assembly using STAR version 2.7.3a.
Low mapping quality reads were removed using Samtools version 1.7.
Gene expression was calculated using Cufflinks version 2.2.1 and differentially expressed genes were called using Cuffdiff version 2.2.1.
Genome_build: mm10

source_name: Uqcc3-depleted 2-cell embryo

growth_protocol: All animal experiments followed the rules and guidelines of the local animal ethical committee and the Animal Care and Use Committee of Peking Union Medical College Hospital. The study protocol was approved by the Animal Care and Use Committee of Peking Union Medical College Hospital. Female and male C57BL/6N mice were purchased from Vital River Laboratory Animal Technology Co Ltd, and were housed in ventilated cages on a 12-h light/dark cycle at constant temperature (22 °C) and under controlled humidity.

extract_protocol:
The embryos were lysed and used for cDNA synthesis using a single-cell full-length mRNA-amplification kit for sequencing (Vazyme, N712). Reagents for first-strand cDNA synthesis were thawed on ice, vortexed to mix, briefly centrifuged to form pellets, and then placed on ice. A sample buffer was prepared as follows: 18 µL lysis buffer; 2 µL RNase inhibitor; 1 µL Oligo(dT) VN primer, 1 µL dNTP mix for annealing reaction. Reverse transcription reaction solution was prepared as follows: first-strand buffer 2 µL; DTT 0.5 µL; RNase inhibitor 0.5 µL; 5’ TS oligo primer 1 µL; sc reverse transcriptase 1 µL. The solution was mixed thoroughly in a thermal cycler under following conditions: 42 °C for 90 min, 70 °C for 15 min, and 4 °C holds. Then, full-length cDNA amplification was performed using first-strand cDNA synthesis products (10 µL), PCR primers (0.5 µL), and 2 × amplification mix (12.5 µL). A PCR instrument (ABI, Veriti) was used to run the following program: 98 °C for 1 min, (98 °C for 10 sec; 65 °C for 15 sec, 72 °C for 6 min) × 18 cycles, and 72 °C for 5 min. Purification of cDNA amplification products was performed using magnetic beads.
After detection of cDNA amplification products using an Agilent 2100 bioanalyzer, 1 ng cDNA was used as the starting material, and the TruePrep DNA Library Prep Kit V2 for Illumina® (Vazyme, #TD503) was used as described above. With 1 ng DNA fragment, we amplified DNA with 15 rounds under the following conditions: 72 °C for 30 min, 98 °C for 30 s, (98 °C for 15 s, 60 °C for 30 s, 72 °C for 3 min) × 15 cycles, 72 °C for 5 min, and 4 °C hold. DNA clean beads were used for size selection. The libraries were sequenced on NovaSeq6000 with paired-end 150 bp reads (Illumina, NovaSeq6000).

treatment_protocol: 8 week-old female mice were randomly divided into two groups. One group were injected with SiRNA-select negative control (5uM) (s4390843, Thermo) at 8hpi; and the other group were injected with SiRNA-Uqcc3(5uM) (s98785, Thermo) at 8hpi.The injected embryos with normal morphology were harvested at the late 2-cell stage for RNA-seq.

tag: developmental stage

value: embryo

value: siRNA-treated (Uqcc3-depleted)


title: LV06: LFD, biological replicate 6

description:
LFD06
single-end, two raw files were generated from two separate Illumina runs

value: male

value: 26 weeks


title: DMSO rep1


title: B14_L2_802D73


title: LV01: LFD, biological replicate 1

description:
LFD01
single-end, two raw files were generated from two separate Illumina runs


title: Panc1/imPSCc2 LS  rep4

organism:
Homo sapiens
Mus musculus

source_name: human pancreatic cancer cells; mouse pancreatic stellate cells

tag: tag

value: low serum


title: HCT-116_fixed64

source_name: HCT-116 fixed64


title: B4_L2_804F10 and B4_L4_804F10

source_name: 2-cell embryo

tag: strain


title: HCT-116_fixed63

source_name: HCT-116 fixed63


title: PTKO AA 6wk rep3

data_processing:
Raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
Raw RNA-seq data was quantified to gene-level counts using Kallisto (Bray et al., 2016) with the ARCHS4 pipeline (Lachmann et al., 2017)
Raw counts were normalized to log10-Counts Per Million (logCPM) by dividing each column by the total sum of its counts followed by the application of a log10-transform.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file containing CPM values for all samples

source_name: Kidney cortex

extract_protocol:
Mice were perfused with PBS, kidneys removed and stored in RNAlater. RNA was extracted using the RNeasy kit (Qiagen) and DNase treated.
cDNA was prepared using TruSeq Stranded Total RNA Sample Preparation kit (Illumina, San Diego, CA), according to the manufacturer’s instructions.

tag: tissue

value: Kidney cortex


title: PTKO AA 6wk rep2


title: Panc1/imPSCc2 LS  rep3

value: human pancreatic cancer cells; mouse pancreatic stellate cells


title: B3_L2_803F10


title: HCT-116_fixed62

source_name: HCT-116 fixed62

tag: cell line


title: Panc1/imPSCc2 LS  rep2


title: PTKO AA 6wk rep1


title: E15_Liver

value: Liver


title: HCT-116_fixed61

source_name: HCT-116 fixed61


title: pool LN (Well 1)

city: San Francisco

first: Tippi

last: MacKenzie

state: California

address: 550 16th Street

department: Surgery, Pediatrics, Center for Maternal-Fetal Precision Medicine

institute: University of California, San Francisco

description: Well 1 of Pool LN. Pool LN consisted of cells isolated from udLN and brLN tissues of two Aire-DTR mice and one WT mouse.

data_processing:
Psuedoalignment was preformed using the kallisto|bustools pipeline.
Reads were demultiplexed using tag count matrices from barcoding experiment that were generated with kITE and kallisto|bustools.
Cell barcodes a) with more than 5% mitochondrial reads, or b) with a total number of counts or number of genes above the 99.5 percentile or c) with less than 10 observed counts were removed from each batch. Uterus samples were also filtered from the dataset due to a low number of detected cells.
Gene counts were normalized to 10,000 counts/cell and were log1p-transformed.
Highly variable genes were calculated using the scanpy function highly_variable_genes using Seurat flavor with the default parameters (min_mean=0.0125, max_mean=3 and min_disp=0.5). Only highly variable genes are present in the processed data files.
The number of counts per cell was regressed out and the gene expression matrix was scaled using scanpy function scale with max_value=10
CD4+ Effector cells were isolated and reclustered by re-running the normalization, log-transformation, highly-variable gene calculation, and scaling on the raw data from CD4+ effector cells.
Software versions: kallisto (0.46.1), bustools (0.40.0), kITE (https://github.com/pachterlab/kite), scanpy (1.7.0)
Genome_build: GRCm38
Supplementary_files_format_and_content: *.obs.txt.gz = mapping file of cellular barcodes
Supplementary_files_format_and_content: *.genes.txt.gz = genes of corresponding .mtx gene count matrix
Supplementary_files_format_and_content: *.mtx = gene barcode matrices
Supplementary_files_format_and_content: mackenziet_airedtr_raw_data.* files are the raw counts
Supplementary_files_format_and_content: mackenziet_airedtr_processed_data.* files are the processed data files
Supplementary_files_format_and_content: mackenziet_airedtr_CD4.* files are the processed data files for CD4+ effector cells

source_name: CD45+ CD3+ cells

extract_protocol:
For single cell RNA sequencing, lymphocytes were prepared by mashing lymph nodes, which were then filtered through a 70-micron cell-strainer. The maternal uterus was minced with razor blades and digested for 15 minutes at 37C with 5% CO2 in 2mg/mL collagenase D (Roche, Basel, Switzerland) and 10ug/mL DNase I recombinant (Roche, Basel, Switzerland). Digested cells were resuspended in cold FACS buffer (DPBS containing 0.5% BSA and 0.2 mM EDTA) and filtered through a 70-micron cell-strainer. Density-gradient centrifugation was used to enrich for lymphocyte cells, using a three-layer Percoll PLUS gradient (Sigma) with specific gravities of 1.115, 1.065, and 1.0. Cells isolated from between the 1.065 and 1.115 layer were resuspended in anti-Fc receptor blocking antibody clone 2.4G2 for 10 minutes, then incubated on ice for 30 minutes with antibody cocktail. Live, CD45+ CD3+ cells were sorted into PBS with 2% BSA following the 10x Genomics protocol for multiplexing and single cell sequencing
Single Cell 3′ Library Kit V3 (10× Genomics).
droplet-based single cell RNA-Seq

tag: cell pool

value: pool LN

value: uterine-draining lymph node+ brachial lymph node

value: CD45+ CD3+ cells

value: mixed sample (non-demultiplexed) representing Aire-DTR and WT


title: fl/fl AA 6wk rep3


title: DMSO rep2

source_name: proximal tubule S2/S3 segments


title: pool LN (Well 2)

description: Well 2 of Pool LN. Pool LN consisted of cells isolated from udLN and brLN tissues of two Aire-DTR mice and one WT mouse.


title: Panc1/imPSCc2 HS rep4

value: high serum


title: pool2-2 (Well 2)

description: Well 2 of Pool 2. Pool 2 consisted of cells isolated from uterus, udLN and brLN tissues of one Aire-DTR mouse and one WT mouse. Mice in Pool 2 are unique from mice in Pool 1.

value: pool 2

value: uterus + uterine-draining lymph node+ brachial lymph node


title: Panc1/imPSCc2 LS  rep1


title: Panc1/imPSCc2 HS rep3

description: Panc1 in heterospheroid: outlier, not included in analysis


title: fl/fl AA 6wk rep2


title: HCT-116_fixed5

department: LIFS

source_name: HCT-116 fixed5


title: fl/fl AA 6wk rep1


title: pool2-1 (Well 1)

description: Well 1 of Pool 2. Pool 2 consisted of cells isolated from uterus, udLN and brLN tissues of one Aire-DTR mouse and one WT mouse. Mice in Pool 2 are unique from mice in Pool 1.


title: Panc1/imPSCc2 HS rep2


title: HCT-116_fixed59

source_name: HCT-116 fixed59


title: HCT-116_fixed58

source_name: HCT-116 fixed58


title: pool1-2 (Well 2)

description: Well 2 of Pool 1. Pool 1 consisted of cells isolated from uterus, udLN and brLN tissues of one Aire-DTR mouse and one WT mouse.

value: pool 1


title: PTKO AA 3wk rep3


title: PTKO AA 3wk rep2


title: Panc1/imPSCc2 HS rep1


title: PTKO AA 3wk rep1


title: NH200 EN1 siRNA + TGF SP1 IP

city: Würzburg 97074

first: Chunguang

last: Liang

state: Bayern

address: Bioinformatik, Biozentrum, Uni Würzburg, Am Hubland

department: Bioinformatics

institute: Biozentrum

data_processing:
read alignment using Bowtie2
peak calling with MACS2
quality control using ChIPQC
annotation by ChIPpeakAnno and ChIPseeker
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: bed

source_name: Dermal fibroblasts

growth_protocol: The fibroblasts were cultured in DMEM-F12 with 10% FBS, 1% penicillin-streptomycin, 2 mM l-glutamine and 2.5 μg ml−1 amphotericin B until reaching 90% confluence. For the experiment, fibroblasts of passage 6 were used. 5 T175 flasks or approximately 10*106 cells were used for each immunoprecipitation reaction.

extract_protocol:
ChIP assays, including purification of the enriched DNA, were performed using the ChIP-IT High Sensitivity Kit (Active Motif). 20-30 μg of sonificated chromatin extract was incubated with 1 µg of antibodies against EN1 or SP1.
Libraries were prepared according to standard Illumina protocols

treatment_protocol: The cells were treated with siRNA targeting EN1 or control, non-targeting siRNA by nucleofection. One day later, the cells were serum-starved, and after further 24 hours the cells were stimulated with 10 ng/ml of TGFβ and incubated for further 24 hours.

value: Human dermal fibroblasts

value: TGFbeta

tag: phenotype

value: knockdown of EN1

value: SP1 (#9389S, Cell Signaling)


title: HCT-116_fixed60

source_name: HCT-116 fixed60


title: fl/fl AA 3wk rep3


title: NH200 nT siRNA + TGF SP1 IP

value: unchanged

tag: chip antibody


title: HCT-116_fixed56

source_name: HCT-116 fixed56


title: NH200 EN1 siRNA + TGF EN1 IP

value: EN1 (NBP2-57757, Novus Biologicals)


title: fl/fl AA 3wk rep2

value: Kidney cortex


title: HCT-116_fixed54

source_name: HCT-116 fixed54


title: fl/fl AA 3wk rep1


title: NH200 EN1 siRNA + TGF input

value: input


title: KO brain (mouse C)

city: Chicago

first: Caraline

last: Sepich

state: IL

address: 929 E 57th Street

department: Chemistry

institute: University of Chicago

data_processing:
Base calling was performed with Illumina bcl2fastq software.
Quality of sequenced reads was assessed with FastQC v0.11.5.
Adapter trimming and quality filtering were performed with Trimmomatic in single-end mode with options LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, and MINLEN:36.
Reads were then aligned to the mm10 genome using STAR 2.7.3a.
Read counts mapping to each gene were obtained using FeatureCounts with options -s 2, -g gene_id, and -t exon.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Sepich-Poore_METTL5_mouse_counts.txt: Tab-delimited text file includes gene ID, gene location, and transcript counts from each sample; raw counts.

source_name: KO mouse C brain

extract_protocol:
Mouse organs were collected immediately upon sacrifice, washed in ice-cold PBS, placed in ~4 volumes of Trizol (Invitrogen), and then sonicated using a hand-held sonicator (OMNI International) with a few brief pulses until there were no more visible chunks. Samples were stored at -80ºC until use.
Libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v2 (Takara) per manufacturer’s instructions and sequenced on a NovaSeq6000 with 100 bp single-end reads.

value: brain

value: METTL5 KO

tag: mouse

value: C


title: KO brain (mouse F)

source_name: KO mouse F brain

value: F


title: HCT-116_fixed53

source_name: HCT-116 fixed53


title: WT brain (mouse D)

source_name: WT mouse D brain

value: WT

value: D


title: NH200 nT siRNA + TGF input


title: HCT-116_fixed52

source_name: HCT-116 fixed52


title: PTKO DMSO rep2

source_name: Kidney cortex


title: WT brain (mouse E)

source_name: WT mouse E brain

value: E


title: HCT-116_fixed55

source_name: HCT-116 fixed55


title: HCT-116_fixed57

source_name: HCT-116 fixed57


title: pool1-1 (Well 1)

description: Well 1 of Pool 1. Pool 1 consisted of cells isolated from uterus, udLN and brLN tissues of one Aire-DTR mouse and one WT mouse.

source_name: CD45+ CD3+ cells

value: uterus + uterine-draining lymph node+ brachial lymph node

value: CD45+ CD3+ cells

value: mixed sample (non-demultiplexed) representing Aire-DTR and WT


title: HCT-116_fixed51

source_name: HCT-116 fixed51


title: WT brain (mouse B)

source_name: WT mouse B brain

value: B


title: NH198 EN1 siRNA + TGF SP1 IP

value: Human dermal fibroblasts

value: TGFbeta

value: knockdown of EN1


title: LV42: HFD+HXN, biological replicate 6

description:
HXN42
single-end, two raw files were generated from two separate Illumina runs

source_name: liver

value: male

value: 26 weeks

value: liver

value: HFD+HXN


title: KO liver (mouse F)

source_name: KO mouse F liver

value: METTL5 KO


title: HCT-116_fixed50

source_name: HCT-116 fixed50


title: NH198 nT siRNA + TGF SP1 IP

source_name: Dermal fibroblasts

value: unchanged

value: SP1 (#9389S, Cell Signaling)


title: KO liver (mouse C)

source_name: KO mouse C liver

value: C


title: KO brain (mouse A)

source_name: KO mouse A brain

value: brain

value: A


title: fl/fl DMSO rep3

value: Kidney cortex


title: NH200 nT siRNA + TGF EN1 IP

value: EN1 (NBP2-57757, Novus Biologicals)


title: HCT-116_fixed4

source_name: HCT-116 fixed4


title: PTKO DMSO rep3


title: KO liver (mouse A)

source_name: KO mouse A liver


title: HCT-116_fixed49

source_name: HCT-116 fixed49


title: fl/fl DMSO rep2


title: NH198 nT siRNA + TGF EN1 IP


title: NH198 EN1 siRNA + TGF EN1 IP


title: fl/fl DMSO rep1


title: WT liver (mouse E)

source_name: WT mouse E liver

value: WT

value: E


title: NH198 EN1 siRNA + TGF input

value: Human dermal fibroblasts

value: input


title: EPID17_840 [H5CV7BBXY_1_SI-GA-H2]

city: Barcelona

first: Laudanna

last: Carmelo

state: Barcelona

address: Baldiri i Reixac, 10

department: Aging and Metabolism

country: Spain

institute: Institute for Research in Biomedicine (IRB-Barcelona)

description:
H5CV7BBXY_SI-GA-H2
raw.counts.KO2.csv.gz

data_processing:
Sequencing of cDNA libraries was carried out on a HiSeq 4000 sequencer (Illumina) to obtain approximately 25,000-50,000 paired-end 75 bp reads per cell, respectively.
Alignment of scRNAseq analyses was completed utilizing 10x Genomics Cell Ranger pipeline (version 2.2.0).
Each library was aligned to an indexed mm10 genome (USCS) using Cell Ranger Count and processed using the Seurat pipeline (version 3.0.1) in R (version 3.5.2).
Genome_build: mm10
Supplementary_files_format_and_content: raw_counts

source_name: Mammary gland cells

extract_protocol:
Cell concentration and viability were verified by counting with a TC20™ Automated Cell Counter (Bio-Rad Laboratories, S.A). Cells were partitioned into Gel Bead-In-Emulsions with a Target Cell Recovery of 5000 cells.
cDNA sequencing libraries were prepared using the NextGEM Single-cell 3’ mRNA kit (V3; 10X Genomics) following manufacturer's instructions.

value: Total mammary epithelium

tag: replicate


title: HCT-116_fixed47

state: Hong Kong

source_name: HCT-116 fixed47


title: PTKO DMSO rep1

source_name: Kidney cortex


title: NH140 EN1 siRNA + TGF SP1 IP

value: TGFbeta

value: knockdown of EN1


title: HCT-116_fixed46

source_name: HCT-116 fixed46


title: NH198 nT siRNA + TGF input


title: WT liver (mouse B)

source_name: WT mouse B liver

value: liver

value: B


title: ESCs, PB-Ss18-8h

city: hangzhou

first: kuang

last: junqi

address: No.18 Shilongshan Road

institute: westlake University

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
The ChIP-seq datasets were aligned to the mouse Genome mm10 using Bowtie2 (version 2.2.5) with the parameters --very-sensitive --end-to-end --no-unal.
Bowtie2 SAM output files were converted to sorted BAM files using SAMtools. Multiple mapped reads were discarded. When multiple reads mapped to the same genomic position, only one read were retained.
The samtools and bedtools suites were used to generate bigwig files for visualization in the IGV browser
Peaks were called using MACS2 software with the default parameters.
Genome_build: mm10

source_name: mouse embryonic stem cells(mESCs)

growth_protocol: Mouse ESCs were cultured on feeder free with mESC-2i medium (DMEM, 15%FBS, NEAA, GlutaMAX, PD0325901, Chir99021, LIF)

extract_protocol:
protein-DNA complexes were isolated with antibody and Tn5-proteinA/G.
The ChIP DNA library for sequencing was constructed with NovoNGS CUT&Tag 2.0 High-Sensitivity Kit  for Illumina (novoprotein) according to manufacturer’s instructions

treatment_protocol: Treated with 2µg/ml doxycycline or small molecules PFI-3 and BI-9564.

value: OG2 transgenetic mouse embryonic stem cells(OG2ES)

value: CST no 21792

value: treated with PFI-3&BI-9564 8h


title: WT liver (mouse D)

source_name: WT mouse D liver

value: D


title: HCT-116_fixed45

source_name: HCT-116 fixed45


title: NH140 nT siRNA + TGF SP1 IP

value: unchanged

value: SP1 (#9389S, Cell Signaling)


title: ESCs, PB-Jun-8h

value: Abcam, ab31419


title: NH140 EN1 siRNA + TGF EN1 IP

value: EN1 (NBP2-57757, Novus Biologicals)


title: EPID17_840 [CD2ALANXX_6_SI-GA-H2]

description:
CD2ALANXX_SI-GA-H2
raw.counts.KO2.csv.gz


title: ESCs, PB-K27ac-8h

value: Abcam, ab4729


title: EPID17_840 [CD2ALANXX_7_SI-GA-H2]


title: NH140 EN1 siRNA + TGF input


title: ESCs, DMSO-Ss18-8h

value: treated with DMSO 8h


title: HCT-116_fixed42

source_name: HCT-116 fixed42


title: EPID17_838 [H5CV7BBXY_1_SI-GA-G2]

description:
H5CV7BBXY_SI-GA-G2
raw.counts.WT2.csv.gz

value: Ctrl


title: HCT-116_fixed48

source_name: HCT-116 fixed48


title: NH140 nT siRNA + TGF EN1 IP

source_name: Dermal fibroblasts

value: Human dermal fibroblasts


title: ESCs, DMSO-Jun-8h


title: EPID17_840 [H5CV7BBXY_2_SI-GA-H2]

value: Total mammary epithelium


title: EPID17_840 [CD2ALANXX_8_SI-GA-H2]


title: NH140 nT siRNA + TGF input

value: TGFbeta

value: input


title: ESCs, DMSO-K27ac-8h


title: EPID17_838 [CD2ALANXX_7_SI-GA-G2]

description:
CD2ALANXX_SI-GA-G2
raw.counts.WT2.csv.gz


title: HCT-116_fixed3

source_name: HCT-116 fixed3


title: ESCs, Brg1-ChIP-WT-8h

value: CST no 52251

value: treated with doxycycline for 8h


title: HCT-116_fixed44

source_name: HCT-116 fixed44