title: MyA_hCF_1

description:
TT005 study
MyA-1_S15
Zhou_2023_SingleEnd_TranscriptMatrix.TPM.txt
Zhou_2023_SingleEnd_TranscriptMatrix.counts.txt
Zhou_2023_SingleEnd_TranscriptMatrix.length.txt


title: adult naked mole-rat anti-CD3 sorted splenocyte long-read PacBio scRNA-seq, replicate 3

status: Public on Nov 30 2023

type: SRA

city: South San Francisco

first: Nimrod

middle: Daniel

last: Rubinstein

state: CA

address: 1170 Veterans blvd

country: USA

institute: Calico

description:
mostly TCR RNA
10x Genomics
nmr_spleen.TCRs_2y_4

library_source: transcriptomic

data_processing:
PacBio SMRT LINK V11 software to generate circular consensus sequences (CCS), requiring a predicted accuracy ≥ Q20.
HetGla2.0 + GCF_000247695.1 and Heterocephalus_glaber_female 1.0 combined annotations
demultiplex.<sample_name>.bam is a file containing the CCS demultipled reads

molecule: total RNA

organism: Heterocephalus glaber

source_name: spleen

extract_protocol:
Spleens were removed by dissection, transferred to a sterile petri dish containing PBS with 5% FBS, and minced using surgical blades. Spleen fragments were then ground through 100 μm and 40 μm cell strainers, pelleted, and resuspended in the ACK lysis buffer as described in the thymus tissue collection section. Cell density and viability were determined using Countness II Cell Counter. Subsequently, splenocytes were resuspended at 1 million cells per ml of 0.04% BSA/PBS. In order to sort out the splenocyte T-cell subsets for constructing 10× GEM single-cell libraries, splenocytes were resuspended at 1 million cells per ml of FACS buffer (PBS with 1% FBS and 5mM EDTA).splenocytes were pre-incubated with the isotype control antibodies (100 ug/ml mIgG1 & 50 ug/ml rat IgG1) per 1 million cells/100ul FACS buffer for 10 minutes. Following that, cells were washed and resuspended at 2 million cells per 1 ml FACS buffer, and incubated with an anti-NMR CD3e (Abbvie-clone-5, Alexa 647, 1:100) and an anti-mouse CD11b (which cross reacts with the NMR CD11b,) (M1/70, R-PE, 5 ug/ml) on ice for 40 minutes. Cells were then washed and resuspended in the FACS buffer containing Sytox Blue Live/Dead dye for cell sorting using FACS BD Aria. Viable, single cells were gated, and the CD11b-/CD3e+ cells were collected for the generation of 10× GEM single-T-cell libraries.
Biotinylated lockdown probes targeting all constant regions of the four TCR loci were added tp the 10× Chromium Next Gen Single-Cell 3’ V3 3′-barcoded scRNA-seq cDNA libraries using the xGen Hybridization and Wash kit with customized Discovery Pools from Integrated DNA Technologies, Inc (IDT, Coralville, Iowa).500 ng of amplified cDNA was mixed with the blocking probes and xGen human Cot DNA, and the mixtures were dried down in a SpeedVac system (ThermoFisher). The hybridization and washing steps were performed according to the protocol from IDT. The hybridization and post-capture amplification steps were performed in a C1000 Touch Thermal Cycler (Bio-Rad Laboratories, Hercules, CA). Fourteen cycles were used for post-capture PCR amplification, and the amplified cDNA was evaluated using a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) with a high sensitivity chip.
Amplified cDNA at >200ng per sample was used to generate Pacific Biosciences (PB) SMRTcell libraries. Full-length PB sequencing was performed on the PB Sequel II platform at Histogenetics (Ossining, NY)

tag: tissue

value: spleen

tag: cell type

value: mostly spleen T cells

tag: age

value: 2 years

tag: Sex

value: male

tag: colony/strain

value: MS 61


title: HO-4T

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

data_processing:
Trimming adaptor sequences and removing reads of low quality were performed by cutadapt.
Quantified reads were aligned to the mouse genome (GRCh38) by STAR (v2.6.1a) and then gene-level read counts were generated based on the annotations of Gencode (v28).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes gene-level read counts.

organism: Homo sapiens

source_name: HBV positive HCC

extract_protocol:
Total RNA was extracted from tissue using an NucleoSpin RNA kit (MACHEREY-NAGEL, Düren, Germany).
Libraries were constructed using SureSelect Strand-Specific RNA kit according to the manufacturers

value: Hepatocellular carcinoma

tag: gender

value: M

value: mut

value: wt


title: Mabs-R Delta_Lsr2 Rep 3 RNA-seq

city: Montigny-le-Bretonneux

first: Frédéric

last: Crémazy

address: 2 avenue de la source de la Bièvre

country: France

institute: UVSQ/INSERM

data_processing:
Sequence reads were trimmed using fastp (v0.23.2).
Trimmed sequences were mapped on M. abscessus ATCC19977 reference genome using STAR (v2.7.6a).
Read count extraction was performed using FeatureCounts (V2.0.0).
Differential Expression Gene analysis was done using the SARtools package (v1.7.1) including DEseq2.
Assembly: NC_010397.1/GCF_000069185.1
Supplementary files format and content: Counts_DEG_analysis.xlsx: Excel file containing read counts, normalized read counts and DEG analysis results.

organism: Mycobacteroides abscessus

source_name: Mycobacterium

growth_protocol: Wild-type and lsr2 mutant strains were cultivated until they reached the exponential growth phase in 7H9 medium supplemented with 1% Glucose, until reaching an optical density (OD600) of approximately 0.6 or ~ 2.4 × 10^8 cells/mL.

extract_protocol:
For each strain, a total of 4.8 × 10^9 cells were collected, and the total RNA was extracted from three biological replicates using the Total RNA Miniprep kit (NEB).
After rRNA depletion, sequencing libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer’s instructions.

value: Mycobacterium

tag: morphotype

value: Rough

tag: genotype

value: Lsr2 KO

tag: strain


title: GFP_hCF_3

first: Farshad

last: Farshidfar

address: 171 Oyster Point Blvd Ste 500

institute: Tenaya Therapeutics Inc.

description:
TT005 study
GFP-3_S8
Zhou_2023_SingleEnd_TranscriptMatrix.TPM.txt
Zhou_2023_SingleEnd_TranscriptMatrix.counts.txt
Zhou_2023_SingleEnd_TranscriptMatrix.length.txt

data_processing:
Read alignment by Salmon (ver. 1.8.0)
tximport to generate gene expression matrix in Transcript Per Million (TPM)
Protein-coding genes identification by Ensembl human reference genome release 108
Exclusion of mitochondrial genes and renormalization to TPM.
Assembly: hg38 v.13
Supplementary files format and content: TXT

source_name: Cardiac Fibroblast

growth_protocol: Isolation of primary adult human and pig cardiac fibroblasts. Adult human or pig left ventricles were minced into small pieces and digested in cardiac fibroblast digestion medium (10μg/mL Liberase TH, 10 μg/mL Liberase TM, 1 unit/mL DNase I, 0.01% Polaxomer) for 1 h in 37ºC. After digestion, the cells were filtered through a 70 μM strainer into a 50 mL falcon tube. Cells were pelleted by spinning down for 5 min at 1200Å~g and placed in fibroblast growth medium. The medium was replaced every two days. Four days later, AHCFs or APCFs were frozen or re-plated for viral transduction.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to vender’s protocol. RNAs were retrotranscribed to cDNA using iScript Supermix™ (Bio-Rad). qPCR was performed using TaqMan. Gene Expression Master Mix (Thermo Scientific) mRNA levels were normalized by comparison to GAPDH mRNA.
100ng total RNA was extracted via polyA-tail specific protocol according to Illumina protocol. Sequencing libraries were generated using the TruSeq stranded RNA sample prep kit (Illumina). The libraries were sequenced as 75 bp single-end reads using an Illumina NovaSeq SP platform with an average of 35M reads per sample. Indexed libraries that met appropriate cut-offs for both quantity and quality were quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution was determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.6 ng/ul were used for sequencing.

treatment_protocol: AHCFs or APCFs were seeded into culture dishes or plates at a density of 5Å~103/cm2 in fibroblast growth medium (day -1). One day after plating cells (day 0), fibroblast growth medium was removed, and virus medium was added. One day after viral transduction (day 1), virus medium was replaced by iCM medium composed of 4 parts Dulbecco’s Modified Eagle’s Medium (DMEM) and 1-part Gibco. Media 199, 10% FBS, 1% nonessential amino acids, 1% penicillin/streptomycin, for every two days until day 4. On day 4, medium was changed to 75% iCM media and 25% RPMI + B27. On day 7, medium was changed to 50% iCM and 50% RPMI + B27. On day 11, medium was changed to 25% iCM and 75% RPMI + B27. On day 14, medium was changed to RPMI + B27+FFV (10ng/mL rhFGF, 15ng/ml rhFGF-10, and 5ng/mL rhVEGF) every day until day 21.

value: Cardiac Fibroblast

value: WT

tag: treatment

value: GFP cassette


title: old naked mole-rat anti-CD3 sorted splenocyte long-read PacBio scRNA-seq, replicate 1

description:
mostly TCR RNA
10x Genomics
nmr_spleen.TCRs_24y_1

value: 24 years


title: Mabs-R Delta_Lsr2 Rep 2 RNA-seq


title: adult naked mole-rat anti-CD3 sorted splenocyte long-read PacBio scRNA-seq, replicate 2

description:
mostly TCR RNA
10x Genomics
nmr_spleen.TCRs_2y_3

value: MS 74


title: GFP_hCF_2

description:
TT005 study
GFP-2_S7
Zhou_2023_SingleEnd_TranscriptMatrix.TPM.txt
Zhou_2023_SingleEnd_TranscriptMatrix.counts.txt
Zhou_2023_SingleEnd_TranscriptMatrix.length.txt


title: E12.5 mouse embryonic maxillary prominence_rep2

city: Shanghai

first: Jian

last: Sun

address: Quxi Road No.500

country: China

institute: Shanghai Ninth People's Hospital

data_processing:
The PE150 raw reads of RNA-Seq libraries were filtered by removing adaptor sequences, contamination and low-quality (phred quality < 20) reads. Reads quality was assessed using FastQC.
Sequenced reads were then mapped to the mm10 genome using STAR aligner version 2.7.3a. Reads were counted using htseq-count version 0.12.4 at the union mode.

organism: Mus musculus

source_name: maxillary prominence

growth_protocol: C57BL/6 mice were purchased from Shanghai Jihui Laboratory Animal Care Co.Ltd. All mice were maintained in SPF conditions at the Animal Center of the Ninth People’s hospital affiliated to Shanghai Jiaotong University School of medicine. Female and male mice between the ages of 8 to 12 weeks were used.

extract_protocol:
Total RNA was extracted using Trizol from freshly dissected maxillary prominence tissues from 7 littermates. For each developmental stage (E10.5, E11.5 and E12.5), three independent RNA samples were prepared. RNA purity was checked using the kaiaoK5500®Spectrophotometer (Kaiao, Beijing, China). RNA integrity and concentration were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
For each sample, 2 μg total RNA was used as input material for the library preparations. Sequencing libraries were then generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and eluted with EB buffer, followed by terminal repair, A-tailing and adapter ligation. The ligated products were retrieved and PCR amplification was performed to generate sequencing libraries. RNA concentration of library was measured using Qubit® RNA Assay Kit in Qubit® 3.0 to preliminary quantify and then dilute to 1ng/μl. Insert size was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA), and qualified insert size was accurately quantified using a StepOnePlusTM Real-Time PCR System. The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina HiSeq X ten platform and 150 bp paired-end reads were generated.

treatment_protocol: On Embryo 10.5(E10.5), 11.5, or 12.5, pregnant C57BL/6 female were euthanized via isoflurane and cervical dislocation. Embryos were dissected from uterus and transferred ice-cold PBS in a 6-cm Petri dish using a disposable glass pipette. Intact maxillary prominences were carefully dissected out from embryos using fine forceps under a stereomicroscope and used for library construction as described below.

value: embryo 12.5

value: wild type


title: adult naked mole-rat anti-CD3 sorted splenocyte long-read PacBio scRNA-seq, replicate 1

description:
mostly TCR RNA
10x Genomics
nmr_spleen.TCRs_2y_2

value: spleen

value: mostly spleen T cells

value: 2 years

value: MS 60


title: Mabs-R Delta_Lsr2 Rep 1 RNA-seq


title: GFP_hCF_1

description:
TT005 study
GFP-1_S6
Zhou_2023_SingleEnd_TranscriptMatrix.TPM.txt
Zhou_2023_SingleEnd_TranscriptMatrix.counts.txt
Zhou_2023_SingleEnd_TranscriptMatrix.length.txt


title: old naked mole-rat anti-CD3 sorted splenocyte long-read PacBio scRNA-seq, replicate 2

description:
mostly TCR RNA
10x Genomics
nmr_spleen.TCRs_24y_2

value: male


title: E10.5 mouse embryonic maxillary prominence_rep1

value: embryo 10.5


title: E10.5 mouse embryonic maxillary prominence_rep3


title: CD_2wk, scRNA-seq

status: Public on Nov 29 2023

city: Kyoto

first: Shin-Ichi

last: Mae

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Center for iPS Cell Research and Application, Kyoto University

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (10x Genomics).
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Kidney

extract_protocol:
CD organoids generated from 2- and 6-week-cultured UBTCs were extracted from 10% Matrigel using Cell Recovery Solution on ice for 10 min. After aspiration of Cell Recovery Solution, the organoids were washed once with PBS and incubated in Accutasce for 5 min. The dissociated single cells were resuspended with 0.04% BSA/PBS.
Library was performed according to the manufacter's instructions (Single Cell 3’ Reagent Kit v3.1, 10x Genomics).

value: Kidney

tag: cell line

value: Collecting duct cells


title: patient 4, scRNAseq

city: Tokushima

first: atsushi

last: mitsuhashi

address: 3-18-15 Kuramoto-cho

department: Department of Respiratory Medicine and Rheumatology

institute: Tokushima university

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung adenocarcinoa

extract_protocol:
The tumor tissues surgically resected from lung adenocarcinoma patients were minced with scissors and incubated with RPMI including 1 mg/ml BSA (Sigma), 1 mg/ml collagenase A (Roche) and 10 U/ml DNase 1 (Roche) f. The number of whole cells was counted using a hemocytometer, and the suspended cells were labeled with PE conjugated anti-human CD45 antibody (Invitrogen). Dead cells were removed by ReadiDrop PI staining (Bio-Rad). Tumor-infiltrating CD45+ immune cells were sorted by LE-SH800BC (Sony).
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, isolated cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Lung adenocarcinoa

value: CD45+ cells


title: patient 3, scRNAseq

description: 10x Genomics


title: patient 2, scRNAseq

description: 10x Genomics


title: Mabs-S WT Rep 2 RNA-seq

value: Mycobacterium

value: Smooth


title: E10.5 mouse embryonic maxillary prominence_rep2


title: Input_RelA_R3

city: Los Angeles

first: Stephen

last: Smale

state: Ca

address: 6-730 MRL 675 Charles E. Young Drive South

department: MIMG

institute: University of California Los Angeles

library_source: genomic

data_processing:
Demultiplexed reads where mapped to the NCBI37/mm9 genome using Hisat2.
Binding site were identified using Homer peak-calling (FRD < 0.01) on uniquely mapped.
Binding sites were annotated to the closest gene (mm9).
Assembly: mm9
Supplementary files format and content: bedGraph files for each sample represent the strength of binding at each genomic location.

molecule: genomic DNA

source_name: BMDM

growth_protocol: Bone marrow was extracted from hip, femur, tibia, and fibula of wild type (C57/B16) mice. Cells were differentiated for 6-days in cell culture using 8%  M-CSG conditioned media.

extract_protocol:
Cellular fractionation was used to isolate nuclei. To capture NF-kB specificity, 1.0mM DSG and 1.0% Formaldehyde were used for crosslinking.  Chromatin shearing was done with either the Bioruptor or Covaris M220. Immunoprecipitation was performed with either anti-RelA, anti-cRel, or anti-p50 antibodies.
Libraries were constructed using the Kapa LTP Library Preparation Kit, according to manufacturers instructions.

treatment_protocol: Lipid A stimulation for 1.0h.

value: BMDM

value: Wild-type (C57/B16)

value: 1.0h Lipid A


title: p50_1.0h_R1


title: cRel_1.0h_R2


title: RelA_1.0h_R3


title: Input_p50_RelA_R1


title: Input_cRel_R1


title: RelA_1.0h_R1


title: RelA_1.0h_R2


title: cRel_1.0h_R1


title: Input_cRel_RelA_R2


title: CD_6wk, scRNA-seq


title: patient 1, scRNAseq

description: 10x Genomics


title: Input_cRel_R3


title: Input_p50_R3


title: p50_1.0h_R3


title: p50_1.0h_R2


title: cRel_1.0h_R3


title: MN_Full_red_2

city: Kunming

first: Yan

last: Qu

address: Kunming

institute: Southwest Forestry University

data_processing:
To obtain high-quality reads, Trimmomatic (v0.36) was used to remove reads with adapters and more than 20% of bases with a quality value of less than ten.
Transcripts were assembled using Trinity.
By mapping reads to the transcripts, only transcripts with correlation coefficients between replicate samples ≥ 0.8 were used for the following analysis.
All qualified transcripts were annotated to function databases, including NR, SwissProt, KEGG, and GO databases.
Only transcripts with an expression of ≥ 10 in at least one set of samples were used for subsequent analysis, and the average of the expression of all replicate samples was used as the gene expression.
Assembly: Mixed_camellia.fa
Supplementary files format and content: gene_FPKM.txt: Tab-delimited text file includes FPKM values or each Sample.

organism: Camellia reticulata

source_name: flowers

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) following the manufacturer's protocols, and mRNA was enriched using Oligo(dT) Magnetic Beads. RNA quality was analyzed using Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA), and RNA concentration was measured using a Qubit 2.0 Fluorometer (Life Technologies, CA, USA). RNA integrity was assessed by Agarose gel electrophoresis.
To prepare the RNA library, RNA was fragmented by the fragmentation buffer. First-strand cDNA was synthesized using N6 random primers, and then the second strand was synthesized to obtain the cDNA. The purified cDNA was modified by end-repair, A-tail, and ligation. After fragment size selection using AMPure XP beads, PCR amplification was performed to obtain the final sequencing library. Finally, all libraries were sequenced on the Illumina HiSeq platform.

value: flowers

tag: cultivar

value: Manao


title: MN_Full_red_3


title: MN_Full_red_1


title: HO-22T

value: Hepatocellular carcinoma

value: M

value: wt


title: MN_Full_white_3


title: MN_Full_white_2


title: Male_STAT5_High_replicate9_G74A_M1_outlier

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description:
Liver DNase-I released fragments
G74A_M1

data_processing:
READ MAPPING: DNase-seq reads were aligned to the mm9 mouse genome using Bowtie2 (Langmead et al 2009, Genome Biology) with default settings. Reads were filtered so that only uniquely-aligned reads were used for downstream analysis.
PEAK CALLING: Peaks were called using MACS2 (Zhang et al 2008, Genome Biology) with default parameters without filtering for PCR duplicates. Peaks were filtered to remove blacklisted regions (www.sites.google.com/site/anshulkundaje/projects/blacklists) and also regions called as peaks that contain only PCR duplicated reads.
Assembly: mm9
Supplementary files format and content: MACS2 output Excel files for both the combined-sample and individual replicate samples for each treatment group. Individual samples (listed above) were combined at the FASTQ file level and processed through a custom DNase-seq pipeline as described. A separate Excel file is provided for each treatment group. The first sheet of each Excel file contains the data for the combined sample and the subsequent sheets contain the data for the individual samples. Each sheet is organized in the following way: the MACS2 command and argument list is provided at the top (rows 1-18), columns A-C represent genomic coordinates of the indicated peak; column D is the DHS peak width, column E is the absolute peak summit position, column F is the pileup height at peak summit, column G is the  -log10(pvalue) for the peak summit, column H is the fold-change over background, column I is an integer score for display calculated as the -log10(qvalue), and column J is the peak name (unique identifier).
Supplementary files format and content: Note: the set of individual replicates that were combined is indicated in the name of the combined sample. For instance, for the Male_STAT5_High group, the combined sample is named "Male_Hi_combined", indicating that the Male_STAT5_High samples (n=8, listed above)  were combined. Similarly, for the Male_STAT5_Low group, the combined samples is named "Male_Lo_combined", indicating that the Male_STAT5_Low samples (n=10, listed above)  were combined. The name of each Excel sheet indicates the MACS2 DHS data for either the combined or individual replicate sample.

source_name: Liver

growth_protocol: Male CD1 mice (ICR strain), 8-10 weeks old, were purchased from Charles River Laboratories (Wilmington, MA) and kept on a 12-hour light/dark cycle with food and water without restriction.

extract_protocol:
DNA fragments were released from regions hypersensitive to DNase-I cutting and purified using a two step process: 1) sucrose gradient to isolate fragments less than 1-kb; followed by 2) SPRI bead purification to select DNA fragments 125-400 bp
Samples were prepared for sequencing with NEBNext Ultra DNA library prep kit for Illumina according to the manufacturer's directions (New England Biolabs).

treatment_protocol: Fresh livers were collected from individual untreated, pituitary-intact male mice. Portions of each liver were used to prepare a protein extract for analysis of liver STAT5 activity by electrophoretic mobility shift assay (EMSA) (Connerney et al., 2017) to identify individual mouse livers as STAT5-high activity (n = 8) and STAT5-low activity DNase-seq samples (n = 10) at the time the mice were euthanized.

value: CD-1 (Charles River)

value: Liver

value: Male

value: 8-10 weeks


title: Male_STAT5_High_replicate10_G74A_M2_outlier

description:
Liver DNase-I released fragments
G74A_M2


title: Male_STAT5_Low_replicate11_G92_M5_outlier

description:
Liver DNase-I released fragments
G92_M5


title: MN_Bud_3_1


title: MN_Bud_3_3


title: MN_Initial_1


title: MN_Initial_2


title: MN_Initial_3


title: SZT_Bud_1

value: Shizitou


title: SZT_Full_2


title: MN_Bud_3_2


title: MN_Bud_1_2


title: SZT_Bud_3


title: TZM_Full_2

value: Tongzimian


title: SZT_Bud_2


title: MN_Bud_1_3


title: MN_Full_white_1


title: MN_Bud_1_1


title: SZT_Full_3


title: TZM_Full_1


title: TZM_Full_3


title: TZM_Bud_3


title: TZM_Bud_2


title: TZM_Bud_1


title: Hediste diversicolor proboscis replicate 2 [HdPR2]

city: Caparica

first: Pedro

middle: M.

last: Costa

address: Campus de Caparica

department: Department of Life Sciences

country: Portugal

institute: NOVA School of Science and Technology, NOVA University of Lisbon

data_processing:
Data quality was assessed with the FastQC quality-control tool v0.11.9 for high throughput sequence data. Reads with low-quality and the Illumina adapter were trimmed by using TrimGalore v0.6.6.
Reads were combined and assembled with Trinity v2.6.6.
Coding regions within the assembled transcriptome were predicted using TransDecoder v5.5.0.
Reads were mapped against the respective assembled transcriptome with Kallisto v0.43.0.
The tximport v1.18.0 package was used to import the data into R, while edgeR v3.34.0 and limma v3.48.1 packages were used for identifing the differentially-expressed transcripts between organs for both species.
Supplementary_files_format_and_content: xlsx: Data frame with the predicted coding regions that were differentially-expressed between organs (log2 fold change, average log2 counts per million, likelihooh ratio statistics and FDR adjusted p-value, sequences and their length).
Supplementary_files_format_and_content: fasta: Nucleotidic sequences of the predicted coding regions that were differentially-expressed between the organs.

molecule: polyA RNA

organism: Hediste diversicolor

source_name: Muscular region of proboscis

extract_protocol:
RNA was isolated from whole-tissue preserved in RNAlater using the RNeasy Mini Kit (Qiagen) combined with on-column DNA digestion with the RNase-Free DNase set (Qiagen).
Library preparation was done using Stranded mRNA Library Preparation Kit and the generated RNA fragments were sequenced in an Illumina Novaseq platform, using 150bp paired-end sequencing reads: 100M for samples HdG2 and HdPR2, 40M for the remaining.

value: Muscular region of proboscis


title: Hediste diversicolor proboscis replicate 3 [HdPR3]


title: LvOvary

city: Providence

first: Nathalie

last: Oulhen

state: RI

address: 185 meeting street

institute: Brown university

description: single cell mRNA

data_processing:
Single cell encapsulation was performed using the Chromium Single Cell Chip B kit on the 10x Genomics Chromium Controller. Single cell cDNA and libraries were prepared using the Chromium Single Cell 3′ Reagent kit v3.1 Chemistry. Libraries were sequenced by Genewiz/Azenta on the Illumina NovaSeq. Single-cell unique molecular identifier (Fujii et al., 2009) counting (counting of unique barcodes given to individual transcript molecules) was performed using Cell Ranger from 10x Genomics. The reference files were generated for each species using CellRanger mkref (Spur-4.2, Lvar3, and Pm v3 assembly available on echinobase). Cellranger gene expression matrices were further analyzed using the R package Seurat (Stuart et al., 2019). Individual datasets were normalized by scaling gene expression in each cell by total gene expression. tSNE analysis was performed with the following parameters: dimension 15 and resolution 0.5. Cell cluster marker genes for single cell RNA sequencing datasets were extracted using the FindMarkers function in Seurat (using R) and were then sorted based on the pct1/pct2 ratio.
Assembly: Spur-4.2, Lvar3, Pm v3 assembly available on echinobase
Supplementary files format and content: tab-delimited text files include matrices that contain UMI-corrected counts for each cell and integrated seurat object

organism: Lytechinus variegatus

source_name: Ovary

extract_protocol: Single cell encapsulation was performed using the Chromium Single Cell Chip B kit on the 10x Genomics Chromium Controller. Single cell cDNA and libraries were prepared using the Chromium Single Cell 3’ Reagent kit v3 Chemistry. Libraries were sequenced by Genewiz on the Illumina Hiseq (2x150 bp paired-end runs).

value: ovary


title: SZT_Full_1


title: Hediste diversicolor glands replicate 2 [HdG2]

source_name: Glandular region of proboscis

value: Glandular region of proboscis


title: Hediste diversicolor glands replicate 3 [HdG3]


title: Hediste diversicolor glands replicate 1 [HdG1]


title: mycelia -MNase_1617_rep1_IP

city: Hangzhou

first: mengting

last: xu

state: ZheJiang

address: Zhejiang University

institute: mengtingxu

data_processing:
High-throughput sequencing was carried out using Illumina Hiseq-PE150 by Novogene Corporation (Beijing, China) for Illumina (Langmead et al., 2009).
The clean read pairs were mapped to the reference genome with Bowtie2 (Version 2.3.5) (Langmead and Salzberg, 2012)
Enriched peaks were called by HOMER (Version 4.9.1) with default parameters (Heinz, 2010).
Assembly: MG8
Supplementary files format and content: peak text files
Supplementary files format and content: bedGraph

organism: Pyricularia oryzae

growth_protocol: The Pyricularia oryzae strains were grown on CM medium at 28℃ in the dark for 2 days, followed by growth under continuous lights for 5 days. Then taking 10-12 pieces of mycelia and culture them in liquid CM medium for 2 days.The mycelia were harvested by 2-3 layers of Miracloth.

extract_protocol:
The ChIP experiments with mycelia cultured in liquid CM for 2 days were conducted as previous reports with minor modification (He et al., 2018; Tao et al., 2017). Briefly, 1.0 g mycelia were crosslinked with 1% formaldehyde for 20 mins and stopped with 125 mM glycine for 5 mins at room temperature. Samples were ground with liquid nitrogen and resuspended in nuclei isolating buffer. Subsequently the precipitated nuclei were used to total chromatin extraction with 1mL lysis buffer. The lysis chromatin was sonicated into DNA fragments between 200-500 bp using Diagenode Bioruptor. 20μL chromatin was used to input DNA extraction and the remainder was pre-cleared with 10μL protein A Dynabeads (Thermofisher, 10001D) for 1 hour. Subsequently the chromatin was incubated with anti-H3K27me3 (Abcam, ab6002) or anti-H3K4ac (Active Motif, 39381) overnight at 4°C. Another 20μL protein A Dynabeads was used capture protein-DNA mixture and followed by three washing. Protein-DNA mixture was reverse-crosslinked, and DNA was recovered with phenol-chloroform extraction. The recovery DNA was used as template for followed ChIP-qPCR and ChIP-seq. Two biological repeats were conducted.
The purified DNA was used as libraries construction with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L).

treatment_protocol: The mycelia were crosslinked with 1% formaldehyde for 20 mins and stopped with 125 mM glycine for 5 mins at room temperature.

value: mycelia

value: mutant

value: MNase


title: mycelia -MNase_1617_rep2_IP


title: mycelia -MNase_WT_rep1_IP

value: wild type


title: mycelia - N1617MRG-GFP_rep2_IP

value: complement

value: GFP


title: mycelia - H3K36me2_eed_rep2_IP

source_name: eed

value: eed


title: mycelia - N1617CD-GFP_rep1_IP


title: mycelia - N1617GFP_rep1_IP


title: mycelia - H3K36me2_WTn_rep2_IP


title: mycelia - N1617CD-GFP_Input


title: mycelia - H3K36me2_kmt6_rep1_IP


title: mycelia - H3K36me2_eed_rep1_IP


title: mycelia - N1617MRG-GFP_Input


title: mycelia - H3K36me2_kmt6_rep2_IP


title: mycelia - N1617MRG-GFP_rep1_IP


title: mycelia - N1617GFP_rep2_IP


title: mycelia - N1617CD-GFP_rep2_IP


title: mycelia - N1617GFP_Input


title: mycelia - H3K36me2_WTn_rep1_IP


title: mycelia - H3K36me2_1617_rep2_IP


title: mycelia -MNase_WT_rep2_IP


title: mycelia - H3K36me2_1617_rep1_IP


title: Hediste diversicolor proboscis replicate 1 [HdPR1]


title: mycelia - H3K36me2_WT_rep2_IP


title: mycelia - H3K36me2_WT_rep1_IP


title: mycelia - H3K36me3_1617_rep1_IP


title: mycelia - H3K36me3_WT_rep2_IP


title: ash1set2 mycelia 2 days rep3

data_processing:
RNAs were sequenced separately at Novogene, using Illumina Hiseq X-Ten with Hiseq-PE150 strategy.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The clean reads were mapped to the reference genome of M. oryzae (MSU release 7) using TopHat software with default settings (Daehwan Kim, 2013). For analysis of differential expression, the assembled transcripts from three independent biological replicates in the WT and deletion mutants were included and compared using Cuffdiff with default settings (Trapnell et al., 2010).
To calculate the significance of the overlap of two sets of genes, P value with Fisher’s exact test for overlapping was performed with online test (the total number of genes in the M. oryzae genome used was 14317). (http://nemates.org/MA/progs/overlap_stats.html).
Assembly: MG8
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: mycelia

growth_protocol: The Magnaporthe oryzae strains were grown on CM medium at 28℃ in the dark for 2 days, followed by growth under continuous lights for 5 days. Then taking 4-5 pieces of mycelia and culture them in liquid CM medium for 2 days.The mycelia were harvested by 2-3 layers of Miracloth.

extract_protocol:
Total RNA was extracted from mycelia cultured in the liquid CM for 2 days from three biological repeats using the TRIzol (Invitrogen, USA) reagent according to the manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ash1set2 mutant


title: mycelia - H3K36me3_1617_rep2_IP


title: ash1set2 mycelia 2 days rep2


title: ash1set2 mycelia 2 days rep1


title: set2 mycelia 2 days rep3

value: set2 mutant


title: ash1 mycelia 2 days rep3

value: ash1 mutant


title: set2 mycelia 2 days rep1


title: 17 mycelia 2 days rep2

data_processing:
RNAs were sequenced separately at Novogene, using Illumina NovaSeq 6000 with Hiseq-PE150 strategy.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The clean reads were mapped to the reference genome of M. oryzae (MSU release 7) using TopHat software with default settings (Daehwan Kim, 2013). For analysis of differential expression, the assembled transcripts from three independent biological replicates in the WT and deletion mutants were included and compared using Cuffdiff with default settings (Trapnell et al., 2010).
To calculate the significance of the overlap of two sets of genes, P value with Fisher’s exact test for overlapping was performed with online test (the total number of genes in the M. oryzae genome used was 14317). (http://nemates.org/MA/progs/overlap_stats.html).
Assembly: MG8
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample


title: 17 mycelia 2 days rep1


title: mycelia - H3K27ac_1617_rep1_IP


title: mycelia - H3K27me3_1617_rep2_IP


title: mycelia - H3K27ac_1617_rep2_IP


title: WT mycelia 2 days rep1


title: 16 mycelia 2 days rep2


title: 1617 mycelia 2 days rep2


title: 1617 mycelia 2 days rep3


title: 16 mycelia 2 days rep1


title: set2 mycelia 2 days rep2


title: 16 mycelia 2 days rep3


title: WT mycelia 2 days rep2


title: 1617 mycelia 2 days rep1


title: mycelia - H3K27me3_WT_rep1_IP


title: mycelia - H3K27me3_WT_rep2_IP


title: mycelia - H3K27ac_WT_rep2_IP


title: mycelia - H3K27ac_WT_rep1_IP


title: WT mycelia 2 days rep3


title: 17 mycelia 2 days rep3


title: mycelia - H3K36me3_WT_rep1_IP


title: mycelia - H3K27me3_1617_rep1_IP


title: ash1 mycelia 2 days rep1


title: ash1 mycelia 2 days rep2


title: WT mycelia 2 days rep1

value: B157 wild type


title: mycelia - H3K36me2_ash1set2_Repeat2_IP


title: mycelia - H3K36me2_ash1set2_Repeat1_IP


title: mycelia - H3K36me3_ash1set2_rep2_IP


title: mycelia - H3K36me2_WT_rep2_IP


title: mycelia - H3K36me2_WT_rep1_IP


title: mycelia - H3K36me2_set2_rep2_IP


title: mycelia - H3K36me3_WT_rep2_IP


title: mycelia - H3K36me3_set2_rep2_IP


title: mycelia - H3K36me2_WT_Repeat2_IP


title: mycelia - H3K36me2_ash1_rep2_IP


title: mycelia - H3K36me2_set2_rep1_IP


title: mycelia - H3K36me2_ash1_rep1_IP


title: mycelia - H3K27me3_set2_rep2_IP


title: mycelia - H3K27me3_set2_rep1_IP


title: mycelia - H3K27me3_ash1_rep2_IP


title: mycelia - H3K36me3_ash1_rep2_IP


title: mycelia - H3K27me3_ash1_rep1_IP


title: mycelia - H3K27me3_ash1set2_rep1_IP


title: mycelia - H3K36me3_WT_rep1_IP


title: mycelia - H3K36me3_set2_rep1_IP


title: mycelia - H3K36me3_ash1_rep1_IP


title: mycelia - H3K27me3_WT_rep2_IP


title: mycelia - H3K27me3_ash1set2_rep2_IP


title: WT mycelia 2 days rep2


title: mycelia - H3K36me2_WT_Repeat1_IP


title: mycelia - H3K36me3_ash1set2_rep1_IP


title: mycelia - H3K27me3_WT_rep1_IP


title: CUT&RUN NFAT5 whole kidney, rep 2

city: Saint Louis

first: Nicolas

last: Ledru

state: MO

address: 660. S Euclid Ave., CB 8118

institute: Washington University in St. Louis

description:
CUT&RUN sequencing using CUTANA (Epicypher, 14-1048)
wholekidney_nfat5_peaks.broadPeak

data_processing:
Sequencing was performed on an Illumina NovaSeq instrument (150 bp, paired end). Fastq files were trimmed with Trim Galore (Cutadapt v2.8) and aligned with Bowtie2 (v2.3.5.1)
Peak calling was performed with MACS2 (v2.2.7.1). IgG fastq files were inputted to MACS2 as negative control samples.
Assembly: hg38
Supplementary files format and content: MACS2-called peak lists are provided for H3K4me3 CUT&RUN and H3K27ac CUT&RUN sequencing in BED format.
Library strategy: CUT&RUN

source_name: Adult human kidney

extract_protocol:
CUT&RUN was performed with the CUTANA kit (Epicyper, 14-1048). Cell cultures were fixed with 0.5% formaldehyde for 1 minute at room temperature, then quenched with glycine to a final concentration of 125mM. Cells were scraped from dishes then spun down at 500g for 5 minutes. Cell pellets were resuspended in PBS with 1% BSA, counted, spun down again, and resuspended again. 500,000 cells in 100 ul wash buffer were incubated with Concanavalin A-conjugated paramagnetic beads, then 1 ug of antibody was added to each sample. Bulk human kidney CUT&RUN was performed on one healthy and one CKD sample. Samples were cut into <2 mm pieces and homogenized using Dounce loose head homogenizers. Samples were then filtered through a 200µm cell strainer and homogenized in the Dounce tight head homogenizers. Samples were incubated on ice for 5 minutes, then filtered through a 40µm cell strainer, centrifuged at 500g for 5 minutes at 4°C. The resuspended pellet was then washed with 4ml of lysis buffer and incubated for 5 minutes at 4°C. Then the sample was centrifuged again and resuspended, then filtered through a 5µm cell strainer to generate an unfixed nuclei suspension. Remaining steps were manufacturer instructions for cross-linked samples.
Library preparation was performed with NEBNext ULTRA II DNA Library Prep Kit for Illumina (New England BioLabs, E7645S)

value: adult human kdiney

tag: cut&run antibody

value: NFAT5 (Thermo Fisher Scientific, PA1-023)

value: untreated


title: CUT&RUN IgG whole kidney, rep 2

description: CUT&RUN sequencing using CUTANA (Epicypher, 14-1048), negative control used when calling peaks for other whole kidney samples

value: IgG (Epicypher, 13-0042)


title: CUT&RUN IgG whole kidney, rep 1


title: SNU-398 cells, overexpression EMX1-X1 1

city: Guangzhou

first: Dongsheng

last: Wen

state: Guangdong

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

description:
OX7
raw_counts.txt

data_processing:
The bcl2Fastq software (version 2.1.7), with default parameter, converts basecalls from Illumina High Throughput Sequencing (HTS) machines to fastQ files containing sequence information ready for further analysis.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp with default parameter (version 0.23.4)
Trimmed sequence reads were mapped to hg38 using STAR software with default parameter(version 2.7.10b)
Read count extraction using featureCounts (version 2.0.6) in pair-end mode
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: The SNU-398 cells were cultured in RPMI1640 (CORNING) with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. The cells were maintained in a humidified incubator with 5% CO2 at 37℃.

extract_protocol:
In brief, RNA was extracted using TRIZOL/Chlorophorm/Phenol method.
The Illumina RNA Library Prep kit (NEBNext® UltraTM) was used. The libraries were tagged with unique adapter indexes. Final libraries were validated on the Agilent 2100 Bioanalyzer, quantified via qRT-PCR, pooled at equimolar ratios, diluted, denatured, and loaded onto an Illumina novaseq 6000

treatment_protocol: The SNU-398 cell line was stably overexpressed with EMX1-FL or EMX1-X1 using lentiviral transfection, followed by puromycin-resistant screening.

value: hepatocellular carcinoma

value: EMX1-X1 overexpression

value: Puromycin-resistant screening


title: SNU-398 cells, overexpression EMX1-X1 2

description:
OX8
raw_counts.txt


title: UZH2_500nM_1

city: shanghai

first: huang

last: yuting

address: 555 Zu Chong Road

institute: Shanghai Jiaotong University

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp.
We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38
The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file incudes FPKM and  raw counts for each Sample

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: 500nM UZH2


title: UZH2_500nM_2


title: WD6305_500nM_2


title: CUT&RUN HIVEP2 primary RPTEC, rep 3

description:
CUT&RUN sequencing using CUTANA (Epicypher, 14-1048)
hivep2_peaks.broadPeak

source_name: primary renal proximal epithelial cells

value: Human renal proximal tubule epithelial cells (Lonza, CC-2553)

value: HIVEP2 (Thermo Fisher Scientific, PA5-100576)


title: CUT&RUN NFAT5 primary RPTEC, rep 1

description:
CUT&RUN sequencing using CUTANA (Epicypher, 14-1048)
nfat5_peaks.broadPeak


title: CUT&RUN NFAT5 whole kidney, rep 1


title: RNA-seq of CREB5 siRNA-treated primary RPTEC, rep 3

data_processing:
Illumina bcl files were demultiplexed and processed to generate fastq files.
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read. Reads were aligned to the Ensembl release 101 assembly with STAR v2.7.9a. Sequencing performance was assessed for the total number of aligned reads and uniquely aligned reads, as well as features detected. Gene counts were calculated from uniquely aligned unambiguous reads by Subread:featureCount v2.0.3. Gene counts were then adjusted for differences in library size with TMM normalization size factors.
Assembly: hg38
Supplementary files format and content: The all_rnaseq_gene_counts.tsv file contains gene counts for each siRNA sample sequenced for this manuscript. Sample names sample.hiv1-3 correspond to HIVEP2 siRNA treatment, sample.cr1-3 correspond to CREB5 siRNA treatment, sample.pp1-3 correspond to PPARA siRNA treatment, sample.nf1-3 correspond to NFAT5 siRNA treatment, and sample.nt1-3 correspond to non-targeting control siRNA treatment.

source_name: primary human renal proximal epithelial cells

extract_protocol:
RNA was extracted from the proximal tubule cell cultures with the RNeasy Mini Kit (Qiagen, 74104) following manufacturer instructions.
Total RNA integrity was determined by Agilent 4200 Tapestation. Library preparation was performed with 0.5-1 ug of total RNA. Ribosomal RNA was removed by RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was fragmented in reverse transcriptase buffer and heated to 94 degrees for 8 minutes. mRNA was then reverse transcribed using SuperScript III RT enzyme (Life Technologies, per manufacturer’s instructions) and random hexamers to produce cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, and had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using a 2x150bp configuration.

treatment_protocol: Non-targeting or NFAT5-targeting siRNA transfection was performed with RNAiMAX (Thermo Fisher, 13778075). At 48 hours following transfection, cells were harvested.

value: CREB5 siRNA (Horizon Discovery, L-008436-00)


title: RNA-seq of PPARA siRNA-treated primary RPTEC, rep 3

value: PPARA siRNA (Horizon Discovery, L-003434-00)


title: CUT&RUN NFAT5 primary RPTEC, rep 2


title: RNA-seq of PPARA siRNA-treated primary RPTEC, rep 2


title: RNA-seq of CREB5 siRNA-treated primary RPTEC, rep 1


title: RNA-seq of HIVEP2 siRNA-treated primary RPTEC, rep 3

value: HIVEP2 siRNA (Horizon Discovery, L-015324-00)


title: RNA-seq of PPARA siRNA-treated primary RPTEC, rep 1


title: RNA-seq of HIVEP2 siRNA-treated primary RPTEC, rep 1


title: RNA-seq of CREB5 siRNA-treated primary RPTEC, rep 2


title: DMSO_2

value: DMSO


title: WD6305_500nM_1


title: SNU-398 cells, overexpression EMX1-FL 3

description:
OE6
raw_counts.txt

value: EMX1-FL overexpression


title: SNU-398 cells, overexpression EMX1-FL 2

description:
OE5
raw_counts.txt


title: CUT&RUN HIVEP2 primary RPTEC, rep 1


title: SNU-398 cells, overexpression EMX1-X1 3

description:
OX9
raw_counts.txt


title: DMSO_1


title: SNU-398 cells, overexpression control 3

description:
OV3
raw_counts.txt

value: Wild type


title: SNU-398 cells, overexpression control 2

description:
OV2
raw_counts.txt


title: SNU-398 cells, overexpression EMX1-FL 1

description:
OE4
raw_counts.txt


title: E774E, pre-vaccination of case group, scRNAseq

first: Xiaoyu

last: Liu

address: 639 Manufacturing Board Road

description: 10x Genomics

data_processing:
Cell Ranger (v6.1.1, 10X Genomics)
Assembly: GRCh38
Supplementary files format and content: Filtered single-cell gene expression matrix
Supplementary files format and content: Associated cell barcodes
Supplementary files format and content: Associated gene features

source_name: peripheral blood

extract_protocol:
5 ml of fresh peripheral blood was drawn per individual, mixed with 5 ml of phosphate-buffered saline (PBS), and then gently layered over 5 ml of Ficoll (GIBCO, USA) in a Falcon tube.   Samples were centrifuged at 400g for 30 min without brake.   After centrifugation, PBMCs in the white layer were carefully transferred to a new tube.   After being washed with PBS twice, samples were then centrifuged at 400g for 10 min, and the pellets were resuspended with cryopreservation medium [1 ml of fetal bovine serum supplemented with 120 μl of dimethyl sulfoxide (DMSO)] for long-term storage in liquid nitrogen. Cell viability was assessed by trypan blue staining and the samples (cell viability >90%) were prepared using a 10 × Genomics Single Cell 30 v2 Reagent Kit according to the manufacturer's instructions.
To perform single-cell RNA sequencing (scRNA-seq), thawed PBMCs were captured using the 10X Chromium system (10X Genomics, USA) according to the manufacturer's protocol. GEMs are generated by mixing the Master Mix with cells, and partitioning oil on chromium next GEM Chip G (10X Genomics, Cat# PN-2000177). The gel beads are dissolved and lysed copartitioned cells to release oligonucleotides, the latter are mixed with cell lysate and a Master Mix, poly-adenylated mRNA is reversed transcription to 10X full-length cDNA. Recycle and purify the GEMs by Dynabeads MyOneTM SILANE (10X Genomics, Cat# PN-2000048) cleanup mix and Buffer EB (Qiagen, Cat# 19086), and then break the GEMs and recover pooled post-GEM-RT. Amplify 10X barcoded full-length cDNA via PCR with primers against common 50 and 30 ends.  cDNA amplifications are purified using the SPRIselect Reagent Kit (Beckman Coulter, Cat# B23318), and then the quality test of cDNA amplifications is performed on a 2100 Bioanalyzer instrument (Agilent, Cat# SD-UF0000034 Rev. D).

tag: group

value: elevated group (E)

tag: individual

value: peripheral blood

value: Mononuclear cells

value: pre-vaccination


title: C71E, pre-vaccination of control group, scRNAseq

description: 10x Genomics

value: control group (C)


title: C744EF, post-vaccination of control group, scRNAseq

description: 10x Genomics

value: post-vaccination


title: C199EF, post-vaccination of control group, scRNAseq

description: 10x Genomics


title: E921EF, post-vaccination of case group, scRNAseq

description: 10x Genomics


title: E921E, pre-vaccination of case group, scRNAseq

description: 10x Genomics


title: INMG3

city: Bremerhaven

first: Cyril

last: Degletagne

address: Am Handelshafen

department: Functional Ecology

country: Germany

institute: Alfred Wegener Institute

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger v7.0.1 pipeline to generate FASTQ files.
Sequences were aligned to the hg38 genome to gene expression count using 10X Space Ranger v1.3.0 with defaults settings and Visium transcriptome probe set v1.
Gene expression level of RefSeq coding genes were quantified using Space Ranger's default settings.
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene Ids
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: spatial transcriptomics

source_name: muscle

extract_protocol: Visium FFPE v1 protocol

value: muscle

tag: diagnosis

value: granulomatous myositis associated with multisystemic sarcoidosis


title: C744E, pre-vaccination of control group, scRNAseq

description: 10x Genomics


title: E735EF, post-vaccination of case group, scRNAseq

description: 10x Genomics


title: RNA-seq of HIVEP2 siRNA-treated primary RPTEC, rep 2


title: control siRNA bio rep 2

city: Columbus

first: Laszlo

last: Farkas

state: OH

address: 473 W 12th Avenue

institute: The Ohio State University

data_processing:
Rosalind.bio
Reads were trimmed using cutadap
Quality scores were assessed using FastQC
Reads were aligned to the Homo sapiens genome build GRCh38 using STAR
Individual sample reads were quantified using Htseq (9) and normalized via Relative Log Expression (RLE) using DESeq2 R library. Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step using RseQC. Deseq2 was also used to calculate fold changes and p-values and perform optional covariate correction.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes normalized counts for each sample

source_name: lung

growth_protocol: Human pulmonary artery endothelial cells were cultured in complete EGM-2MV media (Lonza CC-3162) in a cell culture incubator at 37°C with 5% CO2 and 100% humidity.

extract_protocol:
RNA was isolated using the miRNAeasy kit (Qiagen, 217084) according to the manufacturer’s instructions.
RNA sequencing was performed in the Genomic Shared Resource at The Ohio State University using NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina, NEBNext rRNA Depletion Kit, NEBNext Multiplex Oligos for Illumina Unique Dual Index Primer Pairs. 100 ng total RNA (quantified using Qubit Fluorometer) was used as library input. Fragmentation time was 10 min and PCR was done 11x. Libraries were sequenced with Novaseq SP Pair_end 150 bp format.

treatment_protocol: For siRNA-mediated knockdown of RAB7, PAECs were transfected with 50 nM RAB7 or control siRNA using GenMute Reagent (SL100568, SignaGen). The following siRNAs were used: RAB7 siRNA (IDT, NM_004637 13.2), control siRNA (IDT, 51-01-14-04). After 24h, siRNA was removed, and RNA was isolated  48h after transfection.

value: lung

value: pulmonary artery endothelial cell

value: endothelial cell

value: control

value: control siRNA


title: INMG2


title: RAB7 siRNA bio rep 1

value: RAB7 siRNA


title: RAB7 siRNA bio rep 3


title: RAB7 siRNA bio rep 2


title: SKMES sh643, biol rep 3

city: Poznan

first: Marta

last: Machnik

state: Wielkopolska

address: Rokietnicka 8

department: Chair of Medical Biotechnology

country: Poland

institute: Poznan University of Medical Sciences

description:
sample_4-3
SKMES shZNF643 Expression_Profile.GRCh38.gene.xlsx
SKMES shZNF643 Expression_Profile.GRCh38.transcript.xlsx

data_processing:
Trimmed reads were mapped to the UCSC hg38 human reference genome with HISAT2.
Known genes and transcripts were assembled with StringTie based on the reference genome model.
After assembly, the abundance of gene/transcript was calculated in the read count and normalized value as FPKM/TPM (Fragments/Transcript Per Kilobase of transcript per Million mapped reads) for a sample.
Assembly: USCS hg38
Supplementary files format and content: xlsx data file containing read counts, FPKMs and TPMs for all samples for each analyzed gene
Supplementary files format and content: xlsx data file containing read counts, FPKMs and TPMs for all samples for each analyzed transcript

source_name: SKMES

growth_protocol: Lung cancer cells received DMEM F-12 medium (Biowest, Nuaillé, France) with 10% FBS (EURx, Gdansk, Poland) and 1% penicillin-streptomycin (Biowest, Nuaillé, France). The cells were cultured in a suitable incubator at 37°C in 5% CO2. Trypsin (Biowest, Nuaillé, France) at the appropriate concentration was used to detach the cells during passaging.

extract_protocol:
RNA was isolated from 3 biological replicates of H2073 and SKMES cells (WT, shLUC, sh643) with GeneMATRIX Universal RNA Purification Kit (EurX) according to the manufacturer’s protocol.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LT Sample Prep Kit according to TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E.

treatment_protocol: shZNF643 and shLUC cancer cells were transduced with lentiviral vectors carrying shRNA sequences complementary to ZNF643 mRNA or complementary to luciferase (5’-CAGCGATGACGAAATTCTTAG-3’) as a control (respectively). We used a mix of three different shZNF643 sequences (5'- GCCTTACAGAATGATATTTCG -3'; 5'- GGCCTAATGATGGAAAGATTT -3'; 5'- GCAGCATGTATTCCACCTTGG -3') to obtain the most efficient level of gene knockdown (shZNF643). Lentiviral particles were prepared by 2nd generation system in HEK-293T cells, using psPAX2 and pMD2.G packaging plasmid and pLV-THEM-GP transfer vector.

value: SKMES

value: established cell line of human lung squamous cell carcinoma

value: shRNA targeting  ZNF643 mRNA


title: SKMES sh643, biol rep 1

description:
sample_4-1
SKMES shZNF643 Expression_Profile.GRCh38.gene.xlsx
SKMES shZNF643 Expression_Profile.GRCh38.transcript.xlsx


title: E735E, pre-vaccination of case group, scRNAseq

description: 10x Genomics

value: elevated group (E)


title: control siRNA bio rep 3


title: control siRNA bio rep 1


title: SNU-398 cells, overexpression control 1

description:
OV1
raw_counts.txt

value: hepatocellular carcinoma

value: Wild type

value: Puromycin-resistant screening


title: SKMES shLUC, biol rep 3

description:
ctrl_2-3
SKMES shZNF643 Expression_Profile.GRCh38.gene.xlsx
SKMES shZNF643 Expression_Profile.GRCh38.transcript.xlsx

value: control shRNA sequence


title: C71EF, post-vaccination of control group, scRNAseq

description: 10x Genomics

value: control group (C)

value: peripheral blood

value: Mononuclear cells

value: post-vaccination


title: C199E, pre-vaccination of control group, scRNAseq

description: 10x Genomics

value: pre-vaccination


title: E774EF, post-vaccination of case group, scRNAseq

description: 10x Genomics


title: SKMES shLUC, biol rep 1

description:
ctrl_2-1
SKMES shZNF643 Expression_Profile.GRCh38.gene.xlsx
SKMES shZNF643 Expression_Profile.GRCh38.transcript.xlsx


title: SKMES shLUC, biol rep 2

description:
ctrl_2-2
SKMES shZNF643 Expression_Profile.GRCh38.gene.xlsx
SKMES shZNF643 Expression_Profile.GRCh38.transcript.xlsx


title: SKMES WT, biol rep 3

description:
ctrl_1-3
SKMES shZNF643 Expression_Profile.GRCh38.gene.xlsx
SKMES shZNF643 Expression_Profile.GRCh38.transcript.xlsx

value: unmodified


title: SKMES WT, biol rep 2

description:
ctrl_1-2
SKMES shZNF643 Expression_Profile.GRCh38.gene.xlsx
SKMES shZNF643 Expression_Profile.GRCh38.transcript.xlsx


title: H2073 sh643, biol rep 1

description:
S4_1
H2073 shZNF643 Expression_Profile.GRCh38.gene.xlsx
H2073 shZNF643 Expression_Profile.GRCh38.transcript.xlsx

value: established cell line of human lung adenocarcinoma


title: H2073 shLUC, biol rep 3

description:
K2_3
H2073 shZNF643 Expression_Profile.GRCh38.gene.xlsx
H2073 shZNF643 Expression_Profile.GRCh38.transcript.xlsx


title: SKMES sh643, biol rep 2

description:
sample_4-2
SKMES shZNF643 Expression_Profile.GRCh38.gene.xlsx
SKMES shZNF643 Expression_Profile.GRCh38.transcript.xlsx


title: H2073 sh643, biol rep 3

description:
S4_3
H2073 shZNF643 Expression_Profile.GRCh38.gene.xlsx
H2073 shZNF643 Expression_Profile.GRCh38.transcript.xlsx


title: H2073 WT, biol rep 1

description:
K1_1
H2073 shZNF643 Expression_Profile.GRCh38.gene.xlsx
H2073 shZNF643 Expression_Profile.GRCh38.transcript.xlsx


title: H2073 shLUC, biol rep 1

description:
K2_1
H2073 shZNF643 Expression_Profile.GRCh38.gene.xlsx
H2073 shZNF643 Expression_Profile.GRCh38.transcript.xlsx


title: WT Input biol repl 1

city: Poznań

first: Urszula

last: Oleksiewicz

state: Greater Poland

address: Rokietnicka 8, Medical Biology Center

data_processing:
Read quality control was performed with the FastQC software
Trimming was by Novogene: “The procedure for data trimming is in the following: (1) Discard the reads with low quality (proportion of low quality bases larger than 50%); (2) Discard the reads with N ratio (unsure base) larger than 15%; (3) Discard the reads with adaptor at the 5’-end; (4) Discard the reads without adaptor and inserted fragment at the 3’-end; (5) Trim the adapter sequence at the 3’-end; (6) Discard the reads whose length are less than 18nt after trimming.”
MAPQ  was used to assess mapping quality
The peaks were called with MACS2 software and annotated with PeakAnnotator
DREME tool was applied to search for significant motif sequences related to the peaks
Assembly: USCS hg38
Supplementary files format and content: bigWig files (ChIP, Input samples) and narrowPeaks files (ChIP)

growth_protocol: SKMES ZNF643-OE received DMEM F-12 medium (Biowest, Nuaillé, France) with 10% FBS (EURx, Gdansk, Poland) and 1% penicillin-streptomycin (Biowest, Nuaillé, France). The cells were cultured in a suitable incubator at 37°C in 5% CO2. Trypsin (Biowest, Nuaillé, France) at the appropriate concentration was used to detach the cells during passaging.

extract_protocol:
Chromatin immunoprecipitation (ChIP) was carried out with the HighCell# ChIP Kit (Diagenode, Belgium) with minor modifications. Briefly, after induction of ZNF643 overexpression in the SKMES cell line, the cells were harvested, and counted. We used 10 mln cells for crosslinking with 1% methanol-free formaldehyde (Invitrogen, UA) for 8 min in RT. The fixation was stopped with glycine, and after extraction of cell nuclei, the samples were subjected to fragmentation with the Bioruptor sonicator (Diagenode, Belgium) by applying four runs consisting of ten cycles (30 s on / 30 s off) followed by short vortexing after each cycle. After sonication, the lysates were spun and purified on 50 µl pre-washed Pierce™ Protein A Agarose beads (Invitrogen, USA) for 2.5 h at 4 °C. After purification, the lysates were centrifuged and transferred onto the magnetic beads covered previously with 2 µg rabbit anti-HA ChIP-grade antibody (#ab9110, Abcam, USA). The immunoprecipitation was performed at 4 °C overnight with gentle rotation (40 rpm). For DNA elution and decrosslinking, we utilized the iPURE kit (Diagenode, Belgium) according to the producer's instructions.
The DNA fragments were repaired, dA-tailed, ligated to sequencing adaptors, size selected and PCR amplified.

treatment_protocol: To obtain ZNF643 overexpression (ZNF643-OE) in the SKMES cancer cell line, we used an HA-tagged ZNF643 coding sequence delivered with a pEXPpSIN-TRE-GW-ZNF643-3xHA lentiviral plasmid, kindly gifted by Prof. Didier Trono from the École Polytechnique Fédérale de Lausanne (Lausanne, Switzerland). ZNF643 overexpression was induced with 2 µg/ml doxycycline (Sigma Aldrich).

value: squamous cell lung cancer

value: 2 µg/ml doxycycline for 48 h


title: BT549 cells, MB3 treatment, BioRep2

city: Odense

first: Simon

middle: Toftholm

last: Jakobsen

state: Syddanmark

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Sequencing data was demulitplexed using bcl2fastq before aligned to the human genome version GRCh38.
Samtools was used to remove low quality read.
FeatureCounts were used to quantify raw read coverage before further analysis was performed using DESeq2.
Assembly: hg38
Supplementary files format and content: DEseq2 normalized gene counts

source_name: Cell line

growth_protocol: BT549 cells were maintained in RPMI supplemented with 10% FBS and antibiotics and culutred at 37oC and 5% CO2

extract_protocol:
Total RNA was harvested from cells with Tri-reagent (Sigma-Aldrich, 93289) and purified with chloroform on EconoSpin Columns (EconoSpin, 1910). Ribosomal RNA was depleted using the NEBNext rRNA depletion kit (Biolabs, E6310) before the library was prepared with the NEBNext RNA Library Prep kit (Biolabs, E7540).
Samples were sequenced on a NovaSeq 6000 (Illumina) to reach approximately 25M paired-end reads per sample.

treatment_protocol: 100μM MB-3 (dissolved in DMSO) for 3hr

value: Cell line

value: TNBC

value: WT


title: ZNF643 Input biol rep 1

value: SKMES


title: WT ChIP biol rep 1

tag: antibody

value: rabbit anti-HA ChIP-grade antibody (#ab9110, Abcam)


title: ZNF643 ChiP biol rep 2


title: BT549 cells, MED3 treatment, BioRep1

tag: tissue


title: H2073 WT, biol rep 3

description:
K1_3
H2073 shZNF643 Expression_Profile.GRCh38.gene.xlsx
H2073 shZNF643 Expression_Profile.GRCh38.transcript.xlsx

tag: cell type


title: BT549 cells, VEH treatment, BioRep3 #2

value: VEH


title: WT ChIP biol rep 2


title: BT549 cells, VEH treatment, BioRep1 #2


title: H2073 WT, biol rep 2

description:
K1_2
H2073 shZNF643 Expression_Profile.GRCh38.gene.xlsx
H2073 shZNF643 Expression_Profile.GRCh38.transcript.xlsx


title: BT549 cells, VEH treatment, BioRep2 #2


title: ZNF643 Input biol rep 2


title: Input, MCF7, Fulv

data_processing:
Sequencing data was demulitplexed using bcl2fastq before aligned to the human genome version GRCh38.
Samtools was used to remove PCR duplicates and low quality reads, before MACS2 was used to call peaks using defult settings.
Homer was used to generate files for plotting the data of the regions of interest.
Assembly: hg38
Supplementary files format and content: RPKM normalized bigwig files the ChIP-seq data or MACS2 called peaks in narrowPeak format

extract_protocol:
In brief, for each chromatin immunoprecipitation cells of two 15cm plates were crosslinked at RT using 2mM disuccinimidyl glutarate (DSG) for 20min followed by 1% formaldehyde for 10min, which was quenched in 0.1M glycine for 10min. Cells were washed twice in cold PBS and scraped off the plates in cold PBS containing protease inhibitors (Roche, Complete 11836170001 and Halt, Thermo Scientific, 78438). Crosslinked material was resuspended in lysis buffer 1 (50mM Hepes-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100) for 10min followed by 5min in lysis buffer 2 (10mM Tris-HCL pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA) before resuspending in lysis buffer 3 (10mM Tris-HCL pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0,5% N-lauroylsarcosine). Samples were sonicated using Covaris Ultrasonicator ME220 until DNA fragments had a size between 150-500bp. Chromatin was immunoprecipitated overnight using protein A coated dynabeads (Dynabeads, 10002D) with specific antibodies. After washing the beads, chromatin was eluted and decrosslinked by incubating at 65oC over-night in elution buffer (50mM Tris-HCL, 10mM EDTA, 1% SDS). Samples were treated with RNase A (20ng/mL) for 1h followed by proteinase K (200ng/mL) for 2h before DNA was purified by standard phenol-chloroform purification.
Purified DNA was submitted to library preparation using NEBNext Ultra II DNA Library Prep Kit (New England BioLabs, E765). The samples were sequenced on a NovaSeq 6000 (Illumi-na) to reach approximately 25M paired-end reads per sample.

treatment_protocol: 40μM KJ-PYR-9, 10μM MYC-MI6 or 10μM MYCi975  (dissolved in DMSO) for 3hr or 100nM Fulvestrant (dissolved in water) for 1hr

value: ER+

value: Fulvestrant


title: WT Input biol rep 2


title: H2073 shLUC, biol rep 2

description:
K2_2
H2073 shZNF643 Expression_Profile.GRCh38.gene.xlsx
H2073 shZNF643 Expression_Profile.GRCh38.transcript.xlsx

value: control shRNA sequence


title: Input, MCF7, Veh

value: Veh


title: SKMES WT, biol rep 1

description:
ctrl_1-1
SKMES shZNF643 Expression_Profile.GRCh38.gene.xlsx
SKMES shZNF643 Expression_Profile.GRCh38.transcript.xlsx

value: established cell line of human lung squamous cell carcinoma


title: MYC, MCF7, Veh, BioRep3

value: Cell Signaling, 13987


title: H2073 sh643, biol rep 2

description:
S4_2
H2073 shZNF643 Expression_Profile.GRCh38.gene.xlsx
H2073 shZNF643 Expression_Profile.GRCh38.transcript.xlsx

value: shRNA targeting  ZNF643 mRNA


title: MYC, MCF7, Fulv, BioRep2


title: MYC, MCF7, Fulv, BioRep1


title: ZNF643 ChiP biol rep 1


title: MYC, MCF7, Veh, BioRep2


title: MYC, MCF7, Fulv, BioRep3


title: Input, BT549 cells, MYCMI-6


title: Input, BT549 cells, Veh #2


title: H3K9ac ChIP, BT549 cells Veh, BioRep3

value: Abcam, Ab4441


title: H3K9ac ChIP, BT549 cells MYCi975, BioRep2


title: H3K9ac ChIP, BT549 cells MYCi975, BioRep1


title: GCN5 ChIP, BT549 cells MYCi975, BioRep3

value: Abcam, Ab217876


title: GCN5 ChIP, BT549 cells Veh, BioRep3


title: GCN5 ChIP, BT549 cells Veh, BioRep2


title: H3K9ac ChIP, BT549 cells Veh, BioRep2


title: GCN5 ChIP, BT549 cells MYCi975, BioRep1


title: BRD4 ChIP, BT549 cells MYCi975, BioRep3

value: Bethyl Laboratories, A301-985A


title: GCN5 ChIP, BT549 cells MYCi975, BioRep2


title: BRD4 ChIP, BT549 cells MYCi975, BioRep1


title: BRD4 ChIP, BT549 cells MYCi975, BioRep2


title: BRD4 ChIP, BT549 cells MYCMI-6, BioRep3


title: BT549 cells, MB3 treatment, BioRep3


title: GCN5 ChIP, BT549 cells, Veh, BioRep1


title: Input, BT549 cells, MYCi975


title: MYC, MCF7, Veh, BioRep1


title: BRD4 ChIP, BT549 cells MYCMI-6, BioRep1


title: BRD4 ChIP, BT549 cells, Veh, BioRep1


title: BRD4 ChIP, BT549 cells Veh, BioRep2


title: MYC ChIP, BT549 cells MYCi975, BioRep1


title: MYC ChIP, BT549 cells MYCi975, BioRep3


title: MYC ChIP, BT549 cells MYCi975, BioRep2


title: BRD4 ChIP, BT549 cells MYCMI-6, BioRep2


title: MYC ChIP, BT549 cells MYCMI-6, BioRep3


title: MYC ChIP, BT549 cells, Veh, BioRep1 #2


title: MYC ChIP, BT549 cells MYCMI-6, BioRep1


title: MYC ChIP, BT549 cells Veh, BioRep2


title: H3K9ac ChIP, BT549 cells, Veh, BioRep1


title: MYC ChIP, BT549 cells MYCMI-6, BioRep2


title: Total POL II ChIP, BT549 cells MYCi975, BioRep1

value: C15100055, Diagnode


title: Total POL II ChIP, BT549 cells MYCi975, BioRep2

value: Cell line


title: Total POL II ChIP, BT549 cells MYCMI-6, BioRep1

value: TNBC


title: Total POL II ChIP, BT549 cells MYCMI-6, BioRep2


title: Total POL II ChIP, BT549 cells KJ-PYR-9, BioRep2


title: Total POL II ChIP, BT549 cells Veh, BioRep4


title: Mon-Mac-6_WD6305_3

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp.
We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38.
The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: GRCh38
Supplementary files format and content: *.txt: Tab-delimited text file incudes FPKM and raw counts for each Sample.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.


title: Total POL II ChIP, BT549 cells Veh, BioRep5


title: Total POL II ChIP, BT549 cells, Veh, BioRep1


title: Total POL II ChIP, BT549 cells KJ-PYR-9, BioRep1


title: Total POL II ChIP, BT549 cells Veh, BioRep2


title: Mon-Mac-6_WD6305_2


title: Mon-Mac-6_DMSO_3

value: DMSO


title: Mon-Mac-6_DMSO_2


title: WT mycelia 2 days rep3

value: mycelia

value: B157 wild type


title: Mon-Mac-6_WD6305_1


title: Mon-Mac-6_DMSO_1


title: 15685_D_11PCW

city: Newcastle Upon Tyne

first: Majlinda

last: Lako

address: International Centre for Life, Central Parkway

department: Institute of Genetic Medicine and Institute for Ageing

country: United Kingdom

institute: Newcastle University

description:
15685_11PCW_counts.csv
15685_11PCW_md.csv

data_processing:
Spaceranger version 1.0 was used to demulitplex the data, generate gene expression matrices by aligning the FASTQs to GRCH38.
The pipeline was also used to calculate spot co-ordinates using fiducial detection and to identify the spots covered by the tissue. The results from Spaceranger were imported into R using Spaniel (version 1.12). The data from each sample, which was derived from 4 consecutive sections within the tissue, was normalised and clustered, with a resolution of 0.5, using Seurat as described in the scRNA analysis section.
Supplementary files format and content: csv, png, json
Library strategy: Spatial Transcriptomics

source_name: Eye

extract_protocol:
Fresh frozen sections of four fetal retina samples of 8, 10, 11 and 13PCW were used for the spatial transcriptome analyses performed with the Visium Spatial Gene Expression kit from 10XGenomics. First the tissue optimisation was performed defining 30 minutes as the most optimal permeabilization time window. The spatial transcriptomic procedure was performed according to manufacturer’s instructions. Four tissue sections from each sample were carefully placed into the four capture areas, fixed, haematoxylin and eosin stained and images in order to preserve histological information. This makes it possible to overlay the cell tissue image and the gene expression data in a later step. After permeabilization, reverse transcription reagents were added on top of the tissues. The tissues were subsequently removed, leaving the cDNA coupled to the arrayed oligonucleotides on the slide.
The cDNA-RNA hybrids were cleaved off the chip and the sequencing libraries were prepared. The sequencing depth varied between 25,000,000 and 150,000,000 million reads.

value: Eye

tag: developmental stage


title: 14749_B_13PCW

description:
14749_13PCW_counts.csv
14749_13PCW_md.csv


title: 15685_B_11PCW


title: 14749_C_13PCW


title: 14749_D_13PCW


title: 15685_C_11PCW


title: Total POL II ChIP, BT549 cells, Veh, BioRep3


title: 15870_B_10PCW

description:
15870_10PCW_counts.csv
15870_10PCW_md.csv


title: 15870_A_10PCW


title: 15685_A_11PCW


title: 15817_B_8PCW

description:
15817_8PCW_counts.csv
15817_8PCW_md.csv


title: 15817_C_8PCW

description:
15817_8PCW_counts.csv
15817_8PCW_md.csv


title: 15870_C_10PCW


title: P2017_RNA_04HT-29/B6-GR/MRTcdA-treated  [9401_S120]

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

institute: Berlin Institute of Health, Charité Medical University of Berlin

data_processing:
Illumina Casava1.8 software used for basecalling
Sequenced reads were mapped to human genome (GRCh38.p7) using STAR (v2.7.8a) using Gencode annotation v. 25.
Raw counts were filtered for genes with less than 5 counts in at least 3 samples, or less than 10 counts in total.
Differential gene expression was performed in R using DESeq2 (v1.30.1).
Assembly: GRCh38.p7
Supplementary files format and content: Excel file containing raw counts, RLD normalized counts, and annotation.

source_name: intestinal epithelial cell monolayers

extract_protocol:
Epithelial cells were immediately frozen in liquid nitrogen and RNA was harvested with mirVana miRNA Isolation Kit using the Total RNA isolation procedure. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols for TruSeq stranded mRNA libraries.

value: intestinal epithelial cell monolayers

value: colon, carcinoma cell line

value: TcdA-treated


title: P2017_RNA_08HT-29/B6-GR/MRTcdB-treated  [9405_S124]

value: TcdB-treated


title: P2017_RNA_05HT-29/B6-GR/MRTcdA-treated  [9402_S121]


title: P2017_RNA_09HT-29/B6-GR/MRTcdB-treated  [9406_S125]


title: P2017_RNA_03HT-29/B6-GR/MRcontrol  [9400_S119]

value: control


title: 14749_A_13PCW


title: P2017_RNA_01HT-29/B6-GR/MRcontrol  [9398_S117]


title: P2017_RNA_06HT-29/B6-GR/MRTcdA-treated  [9403_S122]


title: P2017_RNA_02HT-29/B6-GR/MRcontrol  [9399_S118]


title: 15817_A_8PCW

description:
15817_8PCW_counts.csv
15817_8PCW_md.csv


title: 15870_D_10PCW


title: BT549 cells, siCtl treatment, BioRep3

data_processing:
Sequencing data was demulitplexed using bcl2fastq before aligned to the human genome version GRCh38.
Samtools was used to remove low quality read.
FeatureCounts were used to quantify raw read coverage before further analysis was performed using DESeq2.
Assembly: hg38

treatment_protocol: 40μM KJ-PYR-9 (dissolved in DMSO) for 3hr or SMARTpool siRNA targeting MYC was used to KD MYC for 72h

value: WT

value: siCtl


title: BT549 cells, siMYC treatment, BioRep2

value: siMYC


title: BT549 cells, KJ-PYR-9 + DEX treatment, BioRep1

value: KJ-PYR-9 + DEX


title: BT549 cells, siMYC treatment, BioRep3


title: BT549 cells, siMYC treatment, BioRep1


title: BT549 cells, siCtl treatment, BioRep2


title: BT549 cells, KJ-PYR-9 + DEX treatment, BioRep2


title: BT549 cells, KJ-PYR-9 + DEX treatment, BioRep3


title: BT549 cells, siCtl treatment, BioRep1


title: BT549 cells, KJ-PYR-9 treatment, BioRep3


title: BT549 cells, KJ-PYR-9 treatment, BioRep2


title: 15817_D_8PCW

description:
15817_8PCW_counts.csv
15817_8PCW_md.csv


title: BT549 cells, VEH treatment, BioRep1

value: VEH


title: BT549 cells, KJ-PYR-9 treatment, BioRep1


title: BT549 cells, VEH treatment, BioRep3


title: BT549 cells, VEH treatment, BioRep2


title: Input, BT549 cells, JQ1

treatment_protocol: 40μM KJ-PYR-9 (dissolved in DMSO) for 3hr, SMARTpool siRNA targeting MYC or GCN5 was used to KD MYC for 72h, 0,5μM DEX treatment for 2hr


title: Input, BT549 cells, Veh

value: Veh


title: BT549 cells, DEX treatment, BioRep3

value: Cell line

value: DEX


title: BRD4, BT549 cells, Veh, BioRep1

value: TNBC

value: Bethyl Laboratories, A301-985A


title: BRD4, BT549 cells, Veh, BioRep2


title: BRD4, BT549 cells, JQ1, BioRep3


title: BRD4, BT549 cells, JQ1, BioRep1


title: BRD4, BT549 cells, Veh, BioRep3


title: RNAPII S5p, BT549 cells, JQ1, BioRep2

value: Cell Signaling, 13523


title: P2017_RNA_07HT-29/B6-GR/MRTcdB-treated  [9404_S123]


title: BRD4, BT549 cells, JQ1, BioRep2


title: BT549 cells, DEX treatment, BioRep2


title: RNAPII S5p, BT549 cells, Veh, BioRep3


title: RNAPII S5p, BT549 cells, JQ1, BioRep1


title: RNAPII S5p, BT549 cells, Veh, BioRep1


title: H3K9ac, BT549 cells, siGCN5, BioRep2

value: Abcam, Ab4441


title: H3K9ac, BT549 cells, siGCN5, BioRep1


title: H3K9ac, BT549 cells, siGCN5, BioRep3


title: Input, BT549 cells, siGCN5


title: RNAPII S5p, BT549 cells, Veh, BioRep2


title: H3K9ac, BT549 cells, siCtl, BioRep3


title: H3K9ac, BT549 cells, siCtl, BioRep1


title: H3K9ac, BT549 cells, siCtl, BioRep2


title: BRD4, BT549 cells, siGCN5, BioRep1


title: BRD4, BT549 cells, siGCN5, BioRep3


title: Input, BT549 cells, siCtl


title: RNAPII S5p, BT549 cells, siCtl, BioRep3


title: BRD4, BT549 cells, siCtl, BioRep1


title: RNAPII S5p, BT549 cells, siGCN5, BioRep1


title: RNAPII S5p, BT549 cells, siGCN5, BioRep2


title: BRD4, BT549 cells, siCtl, BioRep2


title: RNAPII S5p S5p, BT549 cells, siCtl, BioRep1


title: BRD4, BT549 cells, KJPYR9, BioRep2


title: BRD4, BT549 cells, Veh, BioRep3_B663


title: BRD4, BT549 cells, Veh, BioRep2_B662


title: BRD4, BT549 cells, KJPYR9, BioRep3


title: BRD4, BT549 cells, KJPYR9, BioRep1


title: BRD4, BT549 cells, Veh, BioRep1_B661


title: GCN5, BT549 cells, KJPYR-9, BioRep1

value: Abcam, Ab217876


title: GCN5, BT549 cells, KJPYR-9, BioRep3


title: GCN5, BT549 cells, Veh, BioRep3


title: GCN5, BT549 cells, KJPYR-9, BioRep2


title: GCN5, BT549 cells, Veh, BioRep1


title: uncastrated boar [C27-Lm]

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

data_processing:
Fastq files were analysed with docker4seq package. In brief, fastq files quality was evaluated with fastqc. Fastq were trimmed with Skewer and mapped with STAR 2.5 against Sus scrofa genome retrieved from EMBL repository. Differential expression analysis was performed with DEseq2.
Assembly: Sscrofa11.1
Supplementary files format and content: raw counts, tab delimited

organism: Sus scrofa

source_name: uncastrated boar

extract_protocol:
RNeasy Plus Universal Mini Kit (Qiagen)
TruSeq stranded mRNA library preparation kit (Illumina)

treatment_protocol: i.m. injections of 4 mg/kg b.w. of Sustanon (250 mg/ml) (T) or undergo i.m. injections of 5 mg/kg b.w. of Myodin (25 mg/ml) (N).

value: Liver


title: uncastrated boar [C25-Lm]


title: Input, BT549 cells, KJPYR9


title: GCN5, BT549 cells, Veh, BioRep2


title: sow [C18-Lf]

source_name: sow


title: sow [C16-Lf]


title: castrated boar [C14-Lmc]

source_name: castrated boar


title: castrated boar [C15-Lmc]


title: Input_D, BT549 cells, Veh


title: H3K9ac, BT549 cells, KJPYR9, BioRep2


title: H3K9ac, BT549 cells, KJPYR9, BioRep1


title: uncastrated boar + Myodin [N22-Lm]

source_name: uncastrated boar + Myodin

value: Myodin


title: castrated boar [C13-Lmc]


title: uncastrated boar + Myodin [N23-Lm]


title: uncastrated boar + Myodin [N24-Lm]


title: H3K9ac, BT549 cells, Veh, BioRep2


title: H3K9me2, BT549 cells, Veh, BioRep2

value: Abcam, Ab176882


title: H3K9ac, BT549 cells, Veh, BioRep1


title: sow [C17-Lf]


title: H3K9me2, BT549 cells, KJPYR9, BioRep2


title: sow + Myodin [N11-Lf]

source_name: sow + Myodin


title: H3K9me2, BT549 cells, KJPYR9, BioRep1


title: H3K9me2, BT549 cells, Veh, BioRep1


title: castrated boar + Myodin [N9-Lmc]

source_name: castrated boar + Myodin


title: H3K9me1, BT549 cells, KJPYR9, BioRep2

value: Abcam, Ab9045


title: H3K9me1, BT549 cells, KJPYR9, BioRep1


title: castrated boar + Myodin [N8-Lmc]


title: H3K9me1, BT549 cells, Veh, BioRep2


title: uncastrated boar + Sustanon [T20-Lm]

source_name: uncastrated boar + Sustanon

value: Sustanon


title: H3K9me1, BT549 cells, Veh, BioRep1


title: sow + Myodin [N12-Lf]


title: uncastrated boar + Sustanon [T19-Lm]


title: KDM3A, BT549 cells, KJPYR9, BioRep2

value: Bethyl Laboratories, A301-538A


title: sow + Sustanon [T4-Lf]

source_name: sow + Sustanon


title: KDM3A, BT549 cells, KJPYR9, BioRep1


title: castrated boar + Sustanon [T3-Lmc]

source_name: castrated boar + Sustanon


title: castrated boar + Sustanon [T2-Lmc]


title: RNAPII S5p, BT549 cells, KJPYR9, BioRep2


title: RNAPII S5p, BT549 cells, Veh, BioRep4


title: sow + Sustanon [T5-Lf]


title: RNAPII S5p, BT549 cells, Veh, BioRep3_A003


title: rad21 homozygous tailbud, Wnt stimulation, replicate 4

city: Dunedin

first: Julia

last: Horsfield

address: 56 Hanoverstr

department: Pathology

country: New Zealand

institute: Otago University

data_processing:
Cutadapt (trimming adapter sequences)
HISAT2 and SAMtools (read alignment)
FeatureCounts (generating fragment count matrices)
The DESeq2 (differential gene expression)
Assembly: GRCz11
Supplementary files format and content: CountMatrix_tailbudRNAseq.tsv :  a tsv containig counts for all 32 samples generated using FeatureCounts
Supplementary files format and content: signDGE_by_genotype_treatment.xlsx : an excell file with the DESeq2 results for each of 8 sample groups

organism: Danio rerio

source_name: tailbud

growth_protocol: E3 media 28 C

extract_protocol:
RNA was extracted from the pools of 80 tailbuds per sample using the RNeasy Micro kit (74104; Qiagen, Germany)
Libraries were prepared from 250 ng of total RNA using the TruSeq Stranded mRNA Library Prep kit (Illumina, USA) and TruSeq RNA CD Index Plate (Illumina, USA)

treatment_protocol: 2.5 μM 6-bromoindirubin-3’-oxime in E3 media from 4 hpf till tailbud disection

value: tailbud

value: homozygous rad21 mutant

value: Wnt signaling stimulation


title: rad21 heterozugous tailbud, Wnt stimulation, replicate 4

value: heterozygous rad21 mutant


title: RNAPII S5p, BT549 cells, Veh, BioRep2_A002

value: Cell line

value: Veh


title: RNAPII S5p, BT549 cells, Veh, BioRep1_A001

value: TNBC


title: rad21 homozygous tailbud, no treatment, replicate 4


title: RNAPII S5p, BT549 cells, KJPYR9, BioRep3


title: stag2b tailbud, no treatment, replicate 4

value: homozygous stag2b mutant


title: KDM3A, BT549 cells, Veh, BioRep2


title: stag2b tailbud, Wnt stimulation, replicate 4


title: rad21 heterozugous tailbud, no treatment, replicate 4


title: sow + Sustanon [T6-Lf]


title: Wild type tailbud, Wnt stimulation, replicate 4

value: wild type


title: RNAPII S2p, BT549 cells, KJPYR9, BioRep3

value: Cell Signaling, 13499


title: RNAPII S2p, BT549 cells, KJPYR9, BioRep4


title: KDM3A, BT549 cells, Veh, BioRep1


title: Wild type tailbud, no treatment, replicate 4


title: RNAPII S5p, BT549 cells, Veh, BioRep5

value: Cell Signaling, 13523


title: RNAPII S5p, BT549 cells, KJPYR9, BioRep1


title: rad21 heterozugous tailbud, Wnt stimulation, replicate 3


title: RNAPII S2p, BT549 cells, KJPYR9, BioRep1


title: rad21 heterozugous tailbud, no treatment, replicate 3


title: RNAPII S2p, BT549 cells, Veh, BioRep4


title: rad21 homozygous tailbud, Wnt stimulation, replicate 3


title: RNAPII S2p, BT549 cells, Veh, BioRep5


title: stag2b tailbud, Wnt stimulation, replicate 3


title: stag2b tailbud, no treatment, replicate 3


title: RNAPII S2p, BT549 cells, Veh, BioRep2


title: RNAPII S2p, BT549 cells, Veh, BioRep3


title: RNAPII S2p, BT549 cells, KJPYR9, BioRep2


title: Input, KJPYR9+Dex, BT549 cells

value: KJ-PYR-9 + Dex


title: RNAPII S2p, BT549 cells, Veh, BioRep1


title: Wild type tailbud, Wnt stimulation, replicate 3


title: rad21 homozygous tailbud, Wnt stimulation, replicate 2


title: rad21 homozygous tailbud, no treatment, replicate 3


title: MED1 ChIP, BT549 cells, KJPYR9+Dex, BioRep3

value: Bethyl Laboratories, A300-793A


title: MED1 ChIP, BT549 cells, KJPYR9+Dex, BioRep1


title: Wild type tailbud, no treatment, replicate 3


title: MED1 ChIP, BT549 cells, KJPYR9+Dex, BioRep2


title: rad21 heterozugous tailbud, no treatment, replicate 2


title: rad21 homozygous tailbud, no treatment, replicate 2


title: Input, KJPYR9, BT549 cells_9832


title: MED1 ChIP, BT549 cells, KJPYR9, BioRep3_9806


title: stag2b tailbud, Wnt stimulation, replicate 2


title: MED1 ChIP, BT549 cells, KJPYR9, BioRep2_9807


title: stag2b tailbud, no treatment, replicate 2


title: MED1 ChIP, BT549 cells, KJPYR9, BioRep1_9816


title: rad21 heterozugous tailbud, Wnt stimulation, replicate 2


title: Wild type tailbud, Wnt stimulation, replicate 2


title: rad21 homozygous tailbud, Wnt stimulation, replicate 1


title: MED1 ChIP, BT549 cells, Dex, BioRep1_9818

value: Dex


title: MED1 ChIP, BT549 cells, Dex, BioRep3_9814


title: Wild type tailbud, no treatment, replicate 2


title: rad21 heterozugous tailbud, Wnt stimulation, replicate 1


title: Input, Veh, BT549 cells_9830


title: RNAPII S5p S5p, BT549 cells, siCtl, BioRep2

value: siCtl


title: rad21 homozygous tailbud, no treatment, replicate 1


title: stag2b tailbud, no treatment, replicate 1


title: rad21 heterozugous tailbud, no treatment, replicate 1


title: MED1 ChIP, BT549 cells, Veh, BioRep1_9821


title: MED1 ChIP, BT549 cells, Veh, BioRep2_9819


title: Input, BT549 cells, Dex, BioRep3


title: Wild type tailbud, Wnt stimulation, replicate 1


title: stag2b tailbud, Wnt stimulation, replicate 1


title: Input, BT549 cells, Dex, BioRep1


title: MED1 ChIP, BT549 cells, Dex, BioRep2_9810


title: Wild type tailbud, no treatment, replicate 1


title: Input, BT549 cells, Veh, BioRep1


title: GR ChIP, BT549 cells, Dex, BioRep3

value: Cell Signaling, D6H2L


title: ST RNAseq of PT 1

city: Davis

first: Michael

last: Mienaltowski

address: One Shields Ave

department: Animal Science

institute: University of California Davis

data_processing:
library strategy: 10x Visium Spatial transcriptome
Space Ranger 1.31 to process FASTQ files
Space Ranger files read into R for Seurat analysis
Assembly: Rattus norvegicus (Rnor_6.0 (GCA_000001895.4)
Supplementary files format and content: cloupe files for visualization and analysis of data in Loupe Browser
Supplementary files format and content: h5 files are matrix files from Space Ranger that compress expression data into another accessible form
Supplementary files format and content: spatial_enrichment.csv files feature spatial autocorrelation analysis using Moran's I in CSV format.
Supplementary files format and content: aligned_fiducials.jpg files are aligned fiducials QC image
Supplementary files format and content: detected_tissue_image.jpg are QC images for detected tissue sections
Supplementary files format and content: scalefactors_json.json files contain scale conversion factors for spot diameter and coordinates at various image resolutions
Supplementary files format and content: image.png files are high and low resolution image files of tissue sections
Supplementary files format and content: tissue_positions.csv are CSV containing spot barcode; if the spot was called under (1) or out (0) of tissue, the array position, image pixel position x, and image pixel position y for the full resolution image.

organism: Rattus norvegicus

source_name: Patellar tendon

extract_protocol:
Frozen-sectioned tissue was methanol fixed. Tissue permeabilized, and RNA library preparation done using 10x Visium Spatial Gene Expression Reagent Kit.
10x Visium Spatial Gene Expression Reagent Kit

value: Patellar tendon

tag: Sex

value: male

value: Sprague-Dawley WT


title: BRD4, BT549 cells, siGCN5, BioRep2

value: Bethyl Laboratories, A301-985A


title: Sample_96

city: Tromsø

first: Ilona

last: Urbarova

address: Hansine Hansens veg 18

department: Department of Community Medicine

country: Norway

institute: UiT The Arctic University of Norway

data_processing:
FASTQ files were created using bcl2fastq 2.17 (Illumina, Inc., San Diego, CA, USA).
The sequencing reads in the individual FASTQ files from NLCB cohort were trimmed and quality filtered using cutadapt-1.2.1.
Trimmed reads were mapped to the human genome (hg38) using STAR aligner and counted using featureCounts.
mRNA read counts were normalized using reads per million (RPM) normalization and log2 transformation (voom from limma).
The count matrix was filtered based on Reads Per Million (RPM) values using following filtering criteria: rowSums(rpm(matrix)) > ncol(matrix) * 2 and annotated using AnnotationDbi R package v1.52.0 (org.Hs.eg.db human database).
Genome_build: GRCh38

source_name: Whole blood

extract_protocol:
Inclusion criteria were: (i) patients with suspected LC that will during routine examination have a biopsy or blood samples taken, (ii) patients with relapse of LC, (iii) patients aged 18 years or more, (iv) written informed consent, (v) sampling does not imply significant delay of treatment, and (vi) sampling does not imply a significantly increased risk compared to routine diagnostic sampling. The recruited participants included individuals that were symptomatic of lung cancer, but not all were diagnosed with a confirmed lung cancer diagnosis and for those that were confirmed, the study sample comprised patients of any histological subtype and stage. Symptomatic persons with a CT scan which indicated LC but who during diagnostic follow-up were not diagnosed with lung cancer are hereafter referred to as FalsePos (“false positives”). During diagnostic workup of patients with suspected LC, blood samples were collected together with phenotype data. None of the patients had started cancer treatment at the time of sampling. Phenotype data were collected from questionnaires and electronic health records from the hospital. PAXgene tubes were collected and stored at -80°C.  Total RNA was extracted from PAX tubes using the Qiagen PAXgene Blood miRNA Kit (Qiagen, MD, USA) in combination with an automated Qiacube system according to manufacturer’s instructions.
RNA quantity, quality and purity were evaluated using Qubit (Thermo Fisher Scientific, MA, USA), Bioanalyzer (Agilent, CA, USA) and NanoDrop (Thermo Fisher Scientific, MA, USA). 400 ng of total RNA was then incubated with magnetic beads coated with oligo-dT, then all other RNAs except mRNA were removed by washing. RNA sequencing libraries for samples from NLCB cohort were generated using the Lexogen SENSE mRNA-Seq library prep kit according to manufacturer’s instructions (Lexogen GmbH, Vienna, Austria). In brief, library preparation was initiated by random hybridization of starter/stopper heterodimers to the poly(A) RNA still bound to the magnetic beads. These starter/stopper heterodimers contain Illumina-compatible linker sequences. A single-tube reverse transcription and ligation reaction extends the starter to the next hybridized heterodimer, where the newly-synthesized cDNA insert was ligated to the stopper. Second-strand synthesis was performed to release the library from the beads. The resulting double-stranded library was purified and amplified (12 PCR cycles) after adding the adaptors and indexes. Finally, libraries were quantitated by qPCR using KAPA Library Quantification Kit (Kapa Biosystems, Inc., MA, USA) and validated using Agilent High Sensitivity DNA Kit on a Bioanalyzer (Agilent Technologies, CA, USA). The size range of the DNA fragments were measured to be in the range of 200-600 bp with average library size 300 bp.   Prior to sequencing, the libraries were quantified (KAPA Library Quantification Kit (Illumina/ABI Prism), normalized and pooled. Quantitated libraries were further diluted to 2.3 pM and subject to clustering by a cBot Cluster Generation System prior to sequencing on one HiSeq4000 flowcell (Illumina Inc. San Diego, CA, USA), according to manufacturer’s instructions. Finally, single-end read sequencing was performed for 50 cycles on an Illumina HiSeq4000 instrument, in accordance with the manufacturer’s instructions (Illumina, Inc., San Diego, CA, USA).

value: Whole blood

value: Advanced

tag: histology

value: Other

tag: agescaled

tag: smokingstatus

value: Ever

tag: survival


title: Sample_97

value: FalsePos


title: Input, Dex, BT549 cells

value: Cell line

value: TNBC


title: Input, BT549 cells, Veh, BioRep3

value: Veh


title: GR ChIP, BT549 cells, Veh, BioRep3


title: Sample_98

value: female

value: Early


title: GR ChIP, BT549 cells, Dex, BioRep2


title: Input, BT549 cells, Veh, BioRep2


title: Sample_99


title: Sample_95

value: Never


title: Input, BT549 cells, Dex, BioRep2

value: Dex


title: Sample_94

value: AD


title: GR ChIP, BT549 cells, Veh, BioRep2

value: Cell Signaling, D6H2L


title: GR ChIP, BT549 cells, Veh, BioRep1


title: ST RNAseq of PT 2

value: Patellar tendon

value: male

tag: genotype


title: Sample_93


title: Sample_92

value: Middle

value: SQ