title: LLC1_TIC, ADT- and HTO-derived cDNA

description:
10X Genomics
CITE-seq
Multiple instrument models: Illumina NextSeq 2000, Illumina NovaSeq 6000
LLC1_TIC_barcodes.tsv.gz
LLC1_TIC_features.tsv.gz
LLC1_TIC_matrix.mtx.gz

library_source: other

molecule: protein

value: tumor-infiltrating CD45+ cells


title: tumor-infiltrating NK cells, ICB treated mice

status: Public on Jun 20 2024

type: SRA

city: San Diego

first: John

middle: R

last: Teijaro

state: CA

address: 10550 North Torrey Pines Rd

department: Immunology and Microbial Science

country: USA

institute: The Scripps Research Institute

description:
RNA isolated from flow-sorted NK cells
bulk RNA-seq

library_source: transcriptomic

data_processing:
Raw data generated by Illumina sequencers were converted to FASTQ using cellranger mkfastq (10X Genomics) then subjected to quality control using fastqc and fastqcr.
Cell identification, cDNA counting and antibody-dependent tag counting were performed using cellranger v7.0.0 (10X Genomics) with the --include-intron=true option. The processed data uploaded are given as generated by cellranger count in the directory filtered_bc_feature_matrix.
For raw RNA-seq analysis, demultiplexed FASTQ files were aligned to the mouse genome (mm10) using STAR v2.7.6a with Ensembls v101 transcriptome annotations. The processed data provided are raw read counts generated by STAR.
Assembly: mm10
Supplementary files format and content: CITE-seq: count matrices generated by cellranger count
Supplementary files format and content: bulk RNA-seq: raw counts generated by STAR

molecule: polyA RNA

organism: Mus musculus

source_name: tumor

extract_protocol:
Single-cell suspensions were stained with CD45 antibody and viability dye, then live CD45+ cells sorted by flow cytometry. Individual sorted cell samples were stained using the TotalSeq-B hashtag antibodies (Biolegend) according to the manufacturer's specifications and the combined cells were stained using Biolegend's TotalSeq-B protein-targeted antibodies according to the manufacturer's protocol. Stained cells were subjected to library preparation using the 3' single-cell dual index transcriptome kit (10X Genomics) targeting 30,000 total cells. For bulk RNA-seq experiments, cells sorted by flow cytometry were subjected to RNA isolation using the Arcturus PicoPure kit (Thermo Scientific) followed by library preparation targeting polyA+ RNA.
The Chromium Single Cell 3' Reagent Kit v3.1 (Dual Index) (10X Genomics) was used according to the manufacturer's specifications. Bulk RNA-seq libraries were constructed using the SMARTer v4 kit (Takara Bio).
mRNA-derived libraries were constructed independently; a combined library containing hashtag and antibody dependent tag oligos was also constructed (ADT_library). For bulk RNA-seq experiments, polyA+ RNA was converted to cDNA, subjected to amplification and library preparation using SMARTer v4 (Takara) for Illumina single-end sequencing.
CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

tag: tissue

value: tumor

tag: cell type

value: tumor-infiltrating NK cells

tag: antibodies/tags


title: MUC4301

city: Munich

first: Stefanie

last: Eyerich

address: Biedersteinderstrasse 29

country: Germany

institute: Center of Allergy and Environment

data_processing:
STAR aligner with human genome reference hg38
Bioconductor package DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: .txt

molecule: total RNA

organism: Homo sapiens

source_name: lesional skin

growth_protocol: RNA analysis of skin biopsies, skin biopsies were stored at -80°C in RNAlater solution until RNA preparation

extract_protocol:
RNA from skin biopsies was isolated using the QIAzol Lysis Reagent (Qiagen) and miRNeasy Mini Kit (Qiagen) according to manufacturer’s protocol
RNASeq libraries were generated using the TruSeq Stranded Total RNA Kit (Illumina) with Ribo-Zero Depletion (rRNA Removal Mix) according to manufacturer’s high sample protocol. 200 ng of RNA was used as input. DNA was PCR amplified with Illumina primers for 13 cycles. Libraries were sequenced on the Illumina HiSeq 4000 as paired-end with a read length of 2x 150 bp and an average output of 40 Mio reads per sample and end following the manufacturer's protocols.

treatment_protocol: no treatment

tag: diagnosis

value: Atopic eczema

tag: patient id

tag: age

tag: gender

value: male

tag: batch id


title: EL4_TIC, ADT- and HTO-derived cDNA

description:
10X Genomics
CITE-seq
Multiple instrument models: Illumina NextSeq 2000, Illumina NovaSeq 6000
EL4_TIC_barcodes.tsv.gz
EL4_TIC_features.tsv.gz
EL4_TIC_matrix.mtx.gz


title: MUC4302

source_name: non-lesional skin


title: LLC1_TIC, mRNA-derived cDNA

library_source: transcriptomic single cell


title: tumor-infiltrating NK cells, vehicle treated mice


title: MC38_wt_BM_blood, ADT- and HTO-derived cDNA

description:
10X Genomics
CITE-seq
MC38_wt_BM_blood_barcodes.tsv.gz
MC38_wt_BM_blood_features.tsv.gz
MC38_wt_BM_blood_matrix.mtx.gz

source_name: bone marrow, blood

value: bone marrow, blood

value: bone marrow or blood CD45+ cells


title: EL4_TIC, mRNA-derived cDNA


title: MUC4300

value: female


title: MUC4299


title: MUC4298

value: psoriasis


title: MUC4294


title: MUC4297


title: MC38_wt_BM_blood, mRNA-derived cDNA


title: MC38_wt_TIC, mRNA-derived cDNA

description:
10X Genomics
CITE-seq
MC38_wt_TIC_barcodes.tsv.gz
MC38_wt_TIC_features.tsv.gz
MC38_wt_TIC_matrix.mtx.gz


title: Rep3 Mock 15 days

city: Uppsala

first: Van

last: Nguyen

address: Almas Allé 5

country: Sweden

institute: Uppsala University

description: processed data file: Read_Counts.txt

data_processing:
Sequencing was done by the company Novogene (UK) and we received the raw data
Filtering was done using SortmeRNA and Trimmomatic
Mapping was done against Picea abies genome v1.0 using STAR
Read counting was done using HTSeq-Count
Supplementary_files_format_and_content: Matrix table containing all raw counts of all samples

organism: Picea abies

source_name: Mock_15 days_Hypocotyl

growth_protocol: The Norway spruce seedlings were grown in the phytotron for 2 weeks.

extract_protocol:
Protocol from Azevedo 2003 – RNA extraction from needles of adult maritime pine
Libraries were prepared according to standard Illumina protocol

treatment_protocol: Hormone was applied once and samples were collected after 5, 10 and 15 days. Hormone concentration: BAP 135mM, IAA 50mM, combination BAP 135mM + IAA 50mM

tag: hormone

value: Mock

tag: period

value: 15 days

value: Hypocotyl


title: MC38_wt_TIC, ADT- and HTO-derived cDNA


title: MUC4293


title: MUC4292


title: Rep3 IAA 10 days

description: processed data file: Read_Counts.txt

source_name: IAA_10 days_Hypocotyl

value: IAA

value: 10 days


title: Rep3 IAA 15 days

description: processed data file: Read_Counts.txt

source_name: IAA_15 days_Hypocotyl


title: Rep3 Mock 10 days

description: processed data file: Read_Counts.txt

source_name: Mock_10 days_Hypocotyl


title: MUC4288


title: Rep3 Mock 5 days

description: processed data file: Read_Counts.txt

source_name: Mock_5 days_Hypocotyl

value: 5 days


title: MUC4291


title: MUC4287


title: Rep3 BAP+IAA 5 days

description: processed data file: Read_Counts.txt

source_name: BAP+IAA_5 days_Hypocotyl

value: BAP+IAA


title: Rep3 BAP 15 days

description: processed data file: Read_Counts.txt

source_name: BAP_15 days_Hypocotyl

value: BAP


title: MUC4286


title: MUC4285


title: Rep3 BAP 5 days

description: processed data file: Read_Counts.txt

source_name: BAP_5 days_Hypocotyl


title: MUC4277

value: Nummular Eczema


title: MUC4274


title: Rep3 BAP+IAA 10 days

description: processed data file: Read_Counts.txt

source_name: BAP+IAA_10 days_Hypocotyl


title: Rep3 IAA 5 days

description: processed data file: Read_Counts.txt

source_name: IAA_5 days_Hypocotyl


title: MUC4281


title: MUC4278


title: Rep2 Mock 15 days

description: processed data file: Read_Counts.txt


title: Rep3 BAP 10 days

description: processed data file: Read_Counts.txt

source_name: BAP_10 days_Hypocotyl


title: MUC4282


title: Rep2 Mock 10 days

description: processed data file: Read_Counts.txt


title: MUC4275


title: MUC4273


title: Rep2 IAA 15 days

description: processed data file: Read_Counts.txt


title: Rep2 IAA 10 days

description: processed data file: Read_Counts.txt


title: MUC4272


title: Rep2 Mock 5 days

description: processed data file: Read_Counts.txt


title: Rep2 BAP+IAA 15 days

description: processed data file: Read_Counts.txt

source_name: BAP+IAA_15 days_Hypocotyl


title: MUC4271


title: Rep2 IAA 5 days

description: processed data file: Read_Counts.txt


title: MUC4276


title: MUC4266


title: MUC4268


title: MUC4280


title: MUC4265


title: MUC4279


title: Rep2 BAP+IAA 5 days

description: processed data file: Read_Counts.txt


title: Rep2 BAP 10 days

description: processed data file: Read_Counts.txt


title: MUC4263


title: Rep2 BAP 5 days

description: processed data file: Read_Counts.txt


title: donor 531, RUNX3 KO, H3K27ac C&T

city: St. Louis

first: Jacqueline

last: Payton

state: MO

address: 660 S. Euclid Ave

department: Pathology and Immunology

institute: Washington University School of Medicine

library_source: genomic

data_processing:
fastq files were aligned to hg38 using bowtie2 and samtools using a pipeline adapted from PMID: 31232687.
bedgraph files were made from bam files using bedtools using a pipeline adapted from PMID: 31232687.
H3K27ac peaks were called by comparison of donor matched H3K27ac to IgG bedgraphs using SEACR PMID: 31300027.
Assembly: hg38
Supplementary files format and content: bedgraph files were made from bam files using bedtools using a pipeline adapted from PMID: 31232687.
Supplementary files format and content: bed files represent H3K27ac peaks that were called by comparison of donor matched H3K27ac to IgG bedgraphs using SEACR PMID: 31300027.
Library strategy: CUT&TAG

molecule: genomic DNA

source_name: peripheral blood

growth_protocol: HAB10 (RPMI 1640 medium + 10% human AB serum, 1x penicillin/streptomycin / glutamine / 1M HEPES buffer /NEAA / sodium pyruvate) + 5 ng/mL human IL-15

extract_protocol:
500,000 fresh whole cells were processed according to the Active Motif CUT&TAG-IT Assay kit (Active Motif, #53160)
500,000 fresh whole cells were processed according to the Active Motif CUT&TAG-IT Assay kit (Active Motif, #53160)

treatment_protocol: Cells were electroporated and cultured for 9 days in vitro in HAB10 + 5 ng/mL IL-15

value: peripheral blood

value: NK cell

tag: antibody

value: histone H3K27ac antibody (Active Motif #39134)

tag: antibody catalog

value: Guinea Pig anti-rabbit antibody (Active Motif anti-Rabbit kit, #53160)


title: Rep1 Mock 15 days

description: processed data file: Read_Counts.txt


title: donor 531, CRISPR control, H3K27ac C&T


title: MUC4262

value: male


title: Rep1 Mock 10 days

description: processed data file: Read_Counts.txt


title: Rep2 BAP+IAA 10 days

description: processed data file: Read_Counts.txt


title: MUC4261


title: MUC4267


title: MUC4260

value: Atopic eczema


title: donor 531, CRISPR control, IgG C&T

value: polyclonal rabbit IgG (Millipore Sigma #12-370)


title: Rep2 BAP 15 days

description: processed data file: Read_Counts.txt


title: Rep1 Mock 5 days

description: processed data file: Read_Counts.txt


title: donor 529, RUNX3 KO, IgG C&T


title: donor 529, RUNX3 KO, H3K27ac C&T


title: MUC4258

value: psoriasis


title: Rep1 IAA 15 days

description: processed data file: Read_Counts.txt


title: MUC4264

value: female


title: Rep1 IAA 10 days

description: processed data file: Read_Counts.txt


title: MUC4259


title: donor 529, CRISPR control, IgG C&T


title: Rep1 IAA 5 days

description: processed data file: Read_Counts.txt


title: Rep3 BAP+IAA 15 days

description: processed data file: Read_Counts.txt

value: 15 days


title: MUC4257


title: Rep1 BAP+IAA 15 days

description: processed data file: Read_Counts.txt

value: Hypocotyl


title: MUC4256


title: Rep1 BAP+IAA 10 days

description: processed data file: Read_Counts.txt


title: MUC4255


title: donor 435, CRISPR control, H3K27ac C&T


title: Rep1 BAP+IAA 5 days

description: processed data file: Read_Counts.txt


title: donor 435, CRISPR control, IgG C&T


title: donor 529, CRISPR control, H3K27ac C&T


title: MUC4254


title: malignant phyllodes tumor_rep5

type: RNA

city: Guangzhou

first: Shishi

last: He

address: 107 Yanjiang West Road

country: China

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

description: Biological replicate 5 of 6. Malignant fibroepithelial tumor , untreated.

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the manufacturers instructions. On completion of the fragmentation reaction, Agilent hybridization buffer was added to the fragmentation mixture and hybridized to microarrays for 16 hours at 60°C in a rotating hybridization oven.  After hybridization, microarrays were washed sequential.

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software.

source_name: Breast tumor, Malignant phyllodes tumor

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 4 ug RNA using the RNA Spike In Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: Tumor

tag: tissue type

value: Malignant phyllodes tumor


title: Rep1 BAP 15 days

description: processed data file: Read_Counts.txt


title: donor 431, RUNX3 KO, H3K27ac C&T


title: malignant phyllodes tumor_rep6

description: Biological replicate 6 of 6. Malignant fibroepithelial tumor , untreated.


title: malignant phyllodes tumor_rep3

description: Biological replicate 3 of 6. Malignant fibroepithelial tumor , untreated.


title: malignant phyllodes tumor_rep1

description: Biological replicate 1 of 6. Malignant fibroepithelial tumor , untreated.


title: malignant phyllodes tumor_rep4

description: Biological replicate 4 of 6. Malignant fibroepithelial tumor , untreated.


title: Rep1 BAP 10 days

description: processed data file: Read_Counts.txt

value: 10 days


title: donor 431, RUNX3 KO, IgG C&T


title: MUC4250


title: Rep1 BAP 5 days

description: processed data file: Read_Counts.txt

value: 5 days


title: donor 435, RUNX3 KO, H3K27ac C&T


title: benign phyllodes tumor_rep6

description: Biological replicate 6 of 6. Control benign fibroepithelial tumor , untreated.

source_name: Breast tumor, Benign phyllodes tumor

value: Benign phyllodes tumor


title: donor 431, CRISPR control, H3K27ac C&T


title: MUC4253

source_name: lesional skin


title: MUC4249

value: Nummular Eczema


title: 27TKP

city: Łódź

first: Jędrzej

last: Chrzanowski

state: łódzkie

address: Mazowiecka 15

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Lodz

data_processing:
Raw data was acquired from Illumina BaseSpace (Illumina, California, USA) using GenerateFASTQ v.2.0.1. Next, FASTQ files were processed using nf-core/rnaseq pipeline v.3.14.0 (Nextflow, doi: 10.1038/nbt.3820) following standard procedure. First, the adapters were trimmed using TrimGalore v.0.6.7 and cutadept v.3.4. Next, duplicates were marked and handled using the Mark Duplicatesfunction in Picard v.3.0.0. Trimmed and deduplicated FASTQ were aligned to the human reference genome (GRCh38.p13) with Salmon v.1.10.1 and STAR v.2.6.1d. The standard alignment protocol was followed, with homo sapiens NCBI version 108 GTF annotation file. Read counts were obtained using Salmon Quant v.1.10.1. Qualimap v.2.3 was applied to evalaute the quality control of alignment sequencing data against feature counts. At each step, FASTQC v.0.12.1 for quality control reporting and overall quality report was generated and integrated using MultiQC v.1.19. Read counts were normalized to the transcripts per million (TPM) using R v.4.0.3. Further downstream processing was performed in Python v.3.8.8, R v.4.0.3, Statistica v.13.3 (Tibco, CA, USA) and GSEA v.4.3.2 (Broad Institute, MA, USA)
Assembly: GRCh38.p13
Supplementary files format and content: RNAseq.merged.gene_count.csv - tab-separated files
Supplementary files format and content: RNAseq.merged.gene_TPM.csv

source_name: thymic adipose tissue

extract_protocol:
During the CABG procedure tissue samples are extracted from athymic adipose tissue and epicardial adipose tissue by a qualified cardiosurgeon. All tissue material was suspended in RNAlater soluton and stored frozen at -80°C. RNA was extracted from frozen tissue samples using RNeasy Mini Kit (Qiagen) following manufacturer's protocol.
Libraries were constructed using TruSeq Standard mRNA Librery Prep (Illumina, California, USA) following manufacturer's protocol. The RNAseq procedure was performed with NextSeq 500/550 High Output Kit v2.5 (300 Cycles; Illumina, California, USA) in accordance with the protocol provided by the manufacturer.

value: thymic adipose tissue

tag: diabetes diagnosis

value: Yes

tag: metformin use

tag: sglt2i use

tag: Sex

value: Male

tag: bmi [kg/m2]

tag: triglicerides [mmol/l]

tag: total cholesterol_[mmol/l]

tag: ldl [mmol/l]

tag: hdl [mmol/l]

tag: c-peptide [nmol/l]

tag: hba1c [mmol/mol]


title: malignant phyllodes tumor_rep2

description: Biological replicate 2 of 6. Malignant fibroepithelial tumor , untreated.

tag: tissue

tag: gender


title: benign phyllodes tumor_rep5

description: Biological replicate 5 of 6. Control benign fibroepithelial tumor , untreated.


title: 29TKN

source_name: epicardial adipose tissue

value: epicardial adipose tissue

value: No


title: MUC4246

source_name: non-lesional skin

tag: diagnosis

tag: patient id

tag: age

value: male

tag: batch id


title: benign phyllodes tumor_rep2

description: Biological replicate 2 of 6. Control benign fibroepithelial tumor , untreated.

tag: tissue type


title: benign phyllodes tumor_rep3

description: Biological replicate 3 of 6. Control benign fibroepithelial tumor , untreated.


title: GNF351-preteated IS-trained immunity-3, 6 days

city: Seoul

first: Hee Young

last: Kim

address: 103 Daehak-ro, Jongno-gu,

department: Department of Microbiology and Immunology

country: South Korea

institute: Seoul National University College of Medicine

description:
HC084_IS+G
Expression_Profile.GRCh37.transcript-2.xlsx

data_processing:
NovaSeq 6000 System User Guide Document # 1000000019358 (Illumina)
Sequence reads were trimmed using illumina trimmometric 0.38 program
Trimmed reads were aligned to the human GRCh37 (NCBI_105.20190906)
Assembly: GRch37(NCBI_105.20190906)
Supplementary files format and content: Excel file includes read count and FPKM

source_name: monocytes

growth_protocol:
10% human serum media
Purified monocytes were treated with IS for 24 h, followed by washing with pre-warmed PBS and incubation for another 5 days in RPMI medium supplemented with 10% human AB serum, 100 U/ml penicillin, and 100 μg/ml streptomycin.

extract_protocol:
Total RNA was prepared using RNA purification kit (Macherey-Nagel GmbH & Co.)
After RNA extraction, libraries for sequencing were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit and sequencing were performed using NovaSeq 6000 System User Guide Document # 1000000019358 (Illumina).

treatment_protocol: Purified monocytes were seeded on plates and were treated with IS 1 mM for 24 h, followed by washing with pre-warmed PBS and incubation for another 5 days. GNF351 10 μM were used for a 1 hr pre-treatment prior to the treatment with IS.

tag: cell type

value: monocytes

tag: treatment

value: GNF351-preteated IS-trained immunity


title: MUC4245

value: psoriasis


title: MUC4244


title: GNF351-preteated IS-trained immunity-2, 6 days

description:
HC069_IS+G
Expression_Profile.GRCh37.transcript-1.xlsx


title: GNF351-preteated IS-trained immunity-1, 6 days

description:
HC059_IS+G
Expression_Profile.GRCh37.transcript-1.xlsx


title: 25TKP

tag: diabetes diagnosis

tag: metformin use

tag: sglt2i use

tag: Sex


title: IS-induced trained immunity-3, 6 days

description:
HC084_IS
Expression_Profile.GRCh37.transcript-2.xlsx

value: IS-induced trained immunity


title: SI_LN_PP_Residual_ILC3_steady_rep2

city: New York City

first: Yiming

last: Huang

state: New York

address: 3960 Broadway

department: Department of Systems Biology

institute: Columbia University

data_processing:
Raw reads were processed by Cutadapt v2.1 to remove low-quality bases and TruSeq adapters
Remaining reads passing quality filtering were then analyzed by Kallisto v0.46.1 with default setting to quantify gene expression
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample
Supplementary files format and content: tab-delimited text file includes estimated reads count from pseudo-alignment for each Sample

source_name: SI

extract_protocol:
Total mRNA was isolated from 0.5 cm pieces of terminal ileum or distal colon, sorted CD4 T cells, or IECs from ileal scrapings after homogenization in Trizol using standard protocols.
RNA-seq libraries were constructed using Illumina Stranded mRNA Prep Ligation kit following manufacturer’s instructions

value: SI

tag: genotype

value: LN/PP residual ILC3

value: steady state


title: 27TKN

tag: bmi [kg/m2]

tag: triglicerides [mmol/l]

tag: total cholesterol_[mmol/l]

tag: ldl [mmol/l]

tag: hdl [mmol/l]


title: Colon_LN_PP_uninfected_WT_rep1

source_name: Colon

tag: tissue

value: Colon

value: LN/PP WT

value: uninfected


title: 25TKN

tag: c-peptide [nmol/l]

tag: hba1c [mmol/mol]


title: MUC4243

tag: diagnosis

tag: patient id

tag: age

tag: gender

tag: batch id


title: SI_LN_PP_Residual_ILC3_steady_rep1

tag: treatment


title: benign phyllodes tumor_rep1

description: Biological replicate 1 of 6. Control benign fibroepithelial tumor , untreated.

value: Tumor

tag: tissue type

value: Benign phyllodes tumor

value: female


title: fibroadenoma_rep3

description: Biological replicate 3 of 4. Control benign fibroepithelial tumor , untreated.

source_name: Breast tumor, Fibroadenoma

value: Fibroadenoma


title: Colon_LN_PP_uninfected_WT_rep2


title: benign phyllodes tumor_rep4

description: Biological replicate 4 of 6. Control benign fibroepithelial tumor , untreated.


title: fibroadenoma_rep4

description: Biological replicate 4 of 4. Control benign fibroepithelial tumor , untreated.


title: MUC4242


title: fibroadenoma_rep2

description: Biological replicate 2 of 4. Control benign fibroepithelial tumor , untreated.


title: IS-induced trained immunity-1, 6 days

description:
HC059_IS
Expression_Profile.GRCh37.transcript-1.xlsx

tag: cell type


title: control of trained immunity-3, 6 days

description:
HC084_con
Expression_Profile.GRCh37.transcript-2.xlsx

value: control of trained immunity


title: 23TKP

value: thymic adipose tissue

tag: diabetes diagnosis

value: No

tag: metformin use

tag: sglt2i use

tag: Sex

value: Male


title: Colon_LN_PP_Citro_infected_WT_D4_rep2

tag: genotype

value: Citro infected


title: MUC4241

value: psoriasis


title: Colon_LN_PP_Citro_infected_WT_D4_rep1


title: fibroadenoma_rep1

description: Biological replicate 1 of 4. Control benign fibroepithelial tumor , untreated.


title: IS-induced trained immunity-2, 6 days

description:
HC069_IS
Expression_Profile.GRCh37.transcript-1.xlsx

value: monocytes

value: IS-induced trained immunity


title: 23TKN

value: epicardial adipose tissue

tag: bmi [kg/m2]

tag: triglicerides [mmol/l]

tag: total cholesterol_[mmol/l]

tag: ldl [mmol/l]

tag: hdl [mmol/l]


title: MUC3754

tag: diagnosis

value: Atopic eczema

tag: patient id

value: male


title: 21TKP

tag: tissue

value: Yes

tag: c-peptide [nmol/l]

tag: hba1c [mmol/mol]


title: control of trained immunity-2, 6 days

description:
HC069_con
Expression_Profile.GRCh37.transcript-1.xlsx

tag: treatment


title: MUC3753

tag: age

tag: gender

tag: batch id


title: 66TKP

tag: diabetes diagnosis

tag: metformin use

tag: sglt2i use


title: 66TKN

tag: Sex

tag: bmi [kg/m2]


title: MUC3750


title: 44TKP

tag: triglicerides [mmol/l]

tag: total cholesterol_[mmol/l]


title: input-2, 6 days

data_processing:
Ilumina sequencing were performed using NovaSeq 6000 S4 Reagent Kit according to sequencing protocol of NovaSeq 6000 System User Guide Document # 1000000019358 v02.
Sequenced reads were trimmed using Trimmomatic software. Fragments were aligned to hg19 using Bowtie2 software.
Aligned fragments of H3K4me3-ChIP samples were concatenated into a single file to generate consistent peak ranges between samples using the makeTagDirectory function of Homer Suite.
The number of fragments in the peak was normalized to CPM and significance was compared using edgeR R-package
Assembly: hg19
Supplementary files format and content: bigWig (bw)

source_name: human monocyte-derived macrophage

extract_protocol:
Cells were crosslinked for 5 min with 1% formaldehyde at RT. After quenching and lysis, chromatin were sonicated using Bioruptor® (diagenode)
Purified DNA were prepared for DNA libraries using TruSeq DNA Sample Prep Kit according to Library Protocol TruSeq ChIP Sample Preparation Guide 15023092 Rev. B.

treatment_protocol: Purified monocytes were seeded on plates and were treated with IS 1 mM for 24 h, followed by washing with pre-warmed PBS and incubation for another 5 days.

tag: cell type

value: human monocyte-derived macrophage

value: control

tag: chip antibody


title: MUC3743

tag: diagnosis

value: Nummular Eczema

tag: patient id


title: IS-2, H3K4me3, 6 days

value: IS


title: Colon_LN_PP_Citro_infected_WT_D4_rep3

tag: tissue

value: Colon

tag: genotype

value: LN/PP WT


title: MUC3749


title: input-1, 6 days

tag: treatment


title: Colon_LN_PP_Citro_infected_CD4_D4_rep3

value: LN/PP CD4(dILC3)


title: MUC3744

tag: age


title: control of trained immunity-1, 6 days

description:
HC059_con
Expression_Profile.GRCh37.transcript-1.xlsx

value: control of trained immunity


title: SI_LN_PP_uninfected_WT_rep1

value: SI

value: uninfected


title: Colon_LN_PP_Citro_infected_CD4_D4_rep2

value: Citro infected


title: 34TKN

value: No

value: Male

tag: ldl [mmol/l]

tag: hdl [mmol/l]

tag: c-peptide [nmol/l]

tag: hba1c [mmol/mol]


title: Colon_LN_PP_Citro_infected_CD4_D4_rep1


title: 44TKN

value: epicardial adipose tissue

tag: diabetes diagnosis

tag: metformin use

tag: sglt2i use


title: MUC3732

tag: gender

tag: batch id


title: control-2, H3K4me3, 6 days

tag: cell type


title: SI_LN_PP_uninfected_WT_rep2


title: MUC3731


title: SI_LN_PP_Citro_infected_WT_D4_rep1


title: 29TKP

value: thymic adipose tissue

tag: Sex

tag: bmi [kg/m2]

tag: triglicerides [mmol/l]

tag: total cholesterol_[mmol/l]


title: MUC3728

tag: diagnosis

tag: patient id

value: male


title: control-1, H3K4me3, 6 days

tag: treatment

tag: chip antibody


title: 21TKN

tag: tissue

value: Yes

tag: ldl [mmol/l]

tag: hdl [mmol/l]


title: MDA-MB-435 cells, CPYPP

city: Taichung

first: Ling-Chu

last: Chang

state: -- select state --

address: 6F, No. 350, Jingmao 1st Road, Beitun Dist.,

department: Center for Molecular Medicine

country: Taiwan

institute: China Medical University Hospital

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Alignment: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1).
Expression analysis: In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis: Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <= 0.05 to detect differential expressed ones.
Assembly: GRCh37.p13
Supplementary files format and content: tab-delimited text file induces raw counts for each sample

source_name: melanoma cells

growth_protocol: MDA-MB-435 cells were cultured in DMEM/F12 medium supplemented with 10% (v/v) FBS, 100 U/ml penicillin, and 100 μg/ml streptomycin. Cells were maintained at 37°C in a humidified incubator containing 5% CO2.

extract_protocol:
Total RNA was isolated using TRIzol™ Reagent (ThermoFisher).
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

treatment_protocol: MDA-MB-435 cells were treated with 10 μM CPYPP for 6 hours.

value: melanoma cells

tag: cell line

tag: genotype

value: WT

value: CPYPP, 6 hours


title: MUC3727

value: Nummular Eczema

tag: age


title: MDA-MB-435 cells, control

value: Control


title: 63TKP

tag: diabetes diagnosis

tag: metformin use

tag: sglt2i use

value: Female

tag: c-peptide [nmol/l]

tag: hba1c [mmol/mol]


title: 34TKP

tag: Sex

tag: bmi [kg/m2]

tag: triglicerides [mmol/l]


title: IS-1, H3K4me3, 6 days

tag: cell type

value: human monocyte-derived macrophage

value: IS


title: MUC3726

tag: diagnosis

tag: patient id

tag: gender

value: female

tag: batch id


title: 63TKN

tag: tissue

tag: total cholesterol_[mmol/l]

tag: ldl [mmol/l]

tag: hdl [mmol/l]


title: SI_LN_PP_Citro_infected_CD4_D4_rep1

value: SI

tag: genotype

value: LN/PP CD4(dILC3)

tag: treatment


title: MUC3724

tag: age


title: 33TKP

tag: diabetes diagnosis

value: No

tag: metformin use

tag: sglt2i use

tag: c-peptide [nmol/l]


title: MDA-MB-231 cells, control

source_name: breast cancer cells

value: breast cancer cells

tag: cell line


title: SI_LN_PP_Citro_infected_CD4_D4_rep2

value: Citro infected


title: 33TKN

value: epicardial adipose tissue

tag: Sex

value: Male

tag: bmi [kg/m2]

tag: triglicerides [mmol/l]

tag: hba1c [mmol/mol]


title: MUC3725

tag: diagnosis

tag: patient id

tag: gender

tag: batch id


title: SI_LN_PP_Citro_infected_CD4_D4_rep3

tag: tissue


title: MDA-MB-231 cells, CPYPP

tag: cell type

tag: genotype


title: MUC3723

tag: age

value: male


title: SCN5A_knockdown_1

city: Taipei

first: Iqra

last: Mushtaq

state: Taipei

address: Wuxing street

institute: Taipei Medical Univ-3014874 - Taipei

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mirbase using Subread v2.0.1
Assembly: mirbase
Supplementary files format and content: Tab-delimited text file with normalized counts for every miRNA and every sample

source_name: Heart

growth_protocol: Human cardiac fibroblasts were cultured in fibroblasts medium-2 with 10% v/v heat inactivated fetal bovine serum, and antibiotics in 5% v/v CO2 at 37°C.

extract_protocol:
RNA was extracted using Trizol reagent (Invitrogen), 1.0 ug of total RNA was used to contruct sequence liabraries
small RNA libraries were prepared for sequencing using standard NEBNext protocols

treatment_protocol: SCN5A gene was knocked down using lentivrus shRNA system

value: Heart

value: human cardiac fibroblasts

value: SCN5A knockdown


title: SCN5A_knockdown_2


title: SI_LN_PP_Citro_infected_WT_D4_rep2

value: LN/PP WT

tag: treatment


title: SI_LN_PP_STOP_steady_rep1

value: LN/PP STOP

value: steady state


title: SCN5A_Cont_2

value: wild type


title: MUC3720

value: Nummular Eczema


title: SI_LN_PP_STOP_steady_rep2


title: MUC3719


title: SI_LN_PP_CD4_steady_rep1


title: SI_LN_PP_Citro_infected_WT_D4_rep3


title: SCN5A_Cont_1


title: MUC3718


title: xGen rRNA depletion

city: Uchinada

first: Hiroki

last: Ura

state: Ishikawa

address: 1-1 Daigaku

country: Japan

institute: Kanazawa Medical University Hospital

data_processing:
The fastq files were generated using bcl2fastq software.
Sequenced reads were mapped to hg38 using HISAT2 (v2.1.0) with default parameter.
Reads Per Kilobase of exon per Megabase of library size (RPKM)  and Transcripts per Million (TPM) were calcurated by StringTie (v1.3.4d) with default parameter.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM and TPM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: KMUGMCi001 hiPSCs were maintainded in StemFIt AK02N in humidiffered atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted with TRIzol reagent according to manufacturer’s instructions.
RNA libraries for RNA-Seq were prepared using each NEBNext Ultra II directional RNA Library Prep Kit for Illumina, SMART-Seq Stranded Kit, IDT xGen Broad-Range RNA Library Prep Kit and GenNext RamDA-seq Single Cell Kit according manufacturer's instructions.

value: human iPSC


title: xGen mRNA capture


title: MUC3717


title: SI_LN_PP_CD4_steady_rep2

value: SI


title: ChIP input, 24h starvation, HEK293T, Rep2

city: Zürich

last: Jonas

state: Zürich

address: Otto-Stern-Weg 5

department: Biology

country: Switzerland

institute: ETH Zurich

data_processing:
FastQC quality control, Trimmomatic adapter trimming (parameters: ILLUMINACLIP:NexteraPE-PE.fa:1:30:4:1:true TRAILING:3 MINLEN:20)
Bowtie alignment (parameters: -X2000 (maximal fragment length) and -very-sensitive)
Removal of duplicate reads and reads with map quality score <10 with Picard tools
MACS2 peak calling with q-value<0.05
Assembly: hg38
Supplementary files format and content: bigwig files contain reads normalized by total library size (RPKM)
Supplementary files format and content: narrow.peak files contain MACS2 called peaks based on two replicates, using the respective input sample as a control

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% fetal calf serum (FCS) and antibiotics in a humidified atmosphere with 5% CO2 at 37C. For starvation conditions, cells were grown in glucose-free medium for 24 hours before harvesting. For HDGF depletion, HDGF was depleted using HDGF-specific siPOOLs for 72 hours before harvesting.

extract_protocol:
Cells were fixed using 1% formaldehyde for 5 min. The crosslinking reaction was quenched with 125mM glycine. Cells were lysed in swelling buffer 5mM PIPES pH8; 85mM KCL; 0,5% IGEPAL + protease inhibitors). Chromatin was sonicated on a Diagenode Bioruptor300 for 30 min (30s ON/ 30s OFF) on the high setting.
At least 20 mg of DNA were used for library preparation using the NEBNext Ultra DNA library prep kit.
ChIPseq, 150 bp paired-end reads

value: Human embryonic kidney

value: Wild type

tag: chip antibody


title: RNA-seq_hda6_16-hr_rep3

city: University Park

first: Ha Eun

last: Jeh

state: PA

address: 362 Frear N Bldg

institute: Penn State University

data_processing:
Raw RNA sequencing data was trimmed using Trim Galore! (v0.6.6, --length 30) with Cutadapt (v2.8)
Aligned to the TAIR10 reference genome using STAR (v2.7.10a,--twopassMode Basic -- outFilterMultimapNmax 1).
Read count data was generated with QoRTs (v1.3.6, --minMAPQ 25).
Assembly: TAIR10
Supplementary files format and content: Each row contains read count data with  <GeneID> <read count>

organism: Arabidopsis thaliana

source_name: leaf at bolting stage

growth_protocol: Seeds were stratified in water at 4 ⁰C for 2 - 3 d and sown on soil and grown in growth chambers with 22/20 ⁰C with 12-hr or 16-hr daylength and 120 − 150 μmol m−2 s−1 light.

extract_protocol:
DNA was extracted with NucleoSpin Plant II Kit (Macherey-Nagel, Germany).
Library was constructed and sequenced as paired-end 150-bp

treatment_protocol: For the heat stress experiment, plants were grown at normal condition (22/20 ⁰C) for 10 days for germination. Then, treatment plants were moved to 28/26 ⁰C.

value: leaf at bolting stage

tag: ecotype

value: 16-hr, no heat


title: MUC3714

value: psoriasis

value: female


title: SMART-Seq rRNA depletion RIN 1


title: SMART-Seq rRNA depletion RIN 4


title: RNA-seq_hda6_16-hr_rep1


title: INTS13 ChIP, 24h starvation, HEK293T, Rep2

value: INTS13 (Proteintech, #19892-1-AP)


title: SMART-Seq rRNA depletion 1 ng


title: ChIP input, 24h starvation, HEK293T, Rep1


title: xGen rRNA depletion RIN 1


title: INTS13 ChIP, 24h starvation, HEK293T, Rep1


title: RNA-seq_wildtype for hda6_16-hr_rep3


title: RNA-seq_hda6_16-hr_rep2


title: SMART-Seq rRNA depletion 300 ng


title: RNA-seq_wildtype for hda6_16-hr_rep2


title: MUC3707


title: xGen rRNA depletion RIN 4


title: HDGF ChIP, 24h starvation, HEK293T, Rep2

value: HDGF (Proteintech, #11344-1-AP)


title: HDGF ChIP, 24h starvation, HEK293T, Rep1


title: MUC3706

value: male


title: RamDA-Seq RIN 1


title: RNA-seq_wildtype for hda6_16-hr_rep1


title: siFBL C4-2  rep2_6h

city: Boston

first: Yanqiang

last: Li

state: MA

address: 300 Longwood Ave.

department: Cardiology Department

institute: Boston Children's Hospital

data_processing:
To estimate mRNA half-lives, we followed a published SLAM-seq protocol. Initially, raw reads in fastq files underwent quality checking and trimming using TrimGalore (https://github.com/FelixKrueger/TrimGalore). Subsequently, these reads were processed with slamdunk (v0.4.3)84.
The mRNA half-life estimation Half-life values per gene were averaged over three replicates per condition, following the pipeline from https://github.com/melonheader/HLEB85. We also calculated a filtered version that averaged only over data from those replicates where the calculated pseudo-R2 values were >0.95 (providing evidence for good model fits) and considered those values as ‘stringently’ filtered where at least 2 replicates remained after filtering and where the standard deviation of the considered half-life values was < 1.
Assembly: hg38
Supplementary files format and content: Uracil to cytosine conversions per sample were quantified using the SLAMdunk software

source_name: C4-2 Cell line

growth_protocol: The human prostate cancer cell line C4-2 was a gift from L. Chung at Cedars-Sinai Medical Center and were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS). The cells were maintained at 37 °C and 5% CO2 in a humidified atmosphere and were authenticated and routinely screened for Mycoplasma.

extract_protocol:
Total RNA (two replicates at siCTRL, siFBL at  0h, 6h,12h,24h) was isolated from C4-2 cells RNA  by Trizol (Thermo), and the 4-thiol groups present on S4U-labeled transcripts were alkylated with iodoacteamide.
The mRNA degradation kinetics was measured using SLAM-seq Kinetics Kit: Catabolic Kinetics Module (LEXOGEN) by following the manufacturer’s protocol. In general, control or FBL-deficient C4-2 cells were cultivated in 1640 medium containing 100 μM 4-thiouridine (S4U) for a continuous 24-hour duration. Subsequently, the S4U-containing medium was exchanged by medium with an excess (10 mM) of unmodified uridine (U), and cell samples were collected at the specific time-points. The reference point for these time-points was set at 0 hour, corresponding to the moment of S4U removal. RNA isolation was performed on all collected samples by Trizol (Thermo), and the 4-thiol groups present on S4U-labeled transcripts were alkylated with iodoacteamide.
The libraries were generated from 70-200 ng of input RNA using QuantSeq 3’ mRNA-Seq Library Prep Kit (LEXOGEN).

value: C4-2 Cell line

value: prostate cancer

tag: sirna

value: siFBL

tag: time point


title: RamDA-Seq RIN 4

tag: cell line


title: MUC3713


title: RNA-seq_msh1_16-hr_rep3


title: siFBL C4-2  rep2_24h


title: xGen RIN 1


title: MUC3696


title: MUC3708


title: xGen RIN 4


title: siFBL C4-2  rep2_12h


title: siFBL C4-2  rep2_0h


title: MUC3693


title: siFBL C4-2  rep1_6h


title: RNA-seq_msh1_16-hr_rep1


title: RNA-seq_msh1_16-hr_rep2


title: MUC3695


title: SMART-Seq RIN 4


title: SMART-Seq RIN 1


title: RNA-seq_cue1_16-hr_rep3


title: RNA-seq_cue1_16-hr_rep2


title: RamDA-Seq 10 pg


title: MUC3690


title: siFBL C4-2  rep1_12h


title: RNA-seq_cue1_16-hr_rep1


title: RamDA-Seq 1 ng


title: MUC3689


title: RNA-seq_wildtype_16-hr_rep3


title: MUC3705


title: MUC3688


title: siFBL C4-2  rep1_0h


title: RNA-seq_wildtype_16-hr_rep2


title: MUC3687


title: xGen 100 ng


title: MUC3694


title: siCTRL C4-2  rep2_6h

value: siCTRL


title: SMART-Seq 10 pg


title: MUC3686


title: RNA-seq_wildtype_16-hr_rep1

value: wild type


title: siCTRL C4-2  rep2_24h


title: RNA-seq_sal1_12-hr_rep2

value: 12-hr, no heat


title: MUC3685

value: Nummular Eczema


title: SMART-Seq 1 ng

value: human iPSC


title: siFBL C4-2  rep1_24h


title: MUC3682


title: siCTRL C4-2  rep2_0h


title: siCTRL C4-2  rep2_12h


title: Standard RNA-Seq rep2


title: Standard RNA-Seq KAPA


title: RNA-seq_sal1_12-hr_rep1


title: Standard RNA-Seq rep1


title: RNA-seq_wildtype for sal1_12-hr_rep3


title: siCTRL C4-2  rep1_6h


title: MUC3676


title: siCTRL C4-2  rep1_24h


title: xGen 1 ng


title: MUC3681


title: S24_67TKP

data_processing:
Raw data was acquired from Illumina BaseSpace (Illumina, California, USA) using GenerateFASTQ v.2.0.1. Next, FASTQ files were processed using nf-core/rnaseq pipeline v.3.14.0 (Nextflow, doi: 10.1038/nbt.3820) following standard procedure. First, the adapters were trimmed using TrimGalore v.0.6.7 and cutadept v.3.4. Next, duplicates were marked and handled using the Mark Duplicatesfunction in Picard v.3.0.0. Trimmed and deduplicated FASTQ were aligned to the human reference genome (GRCh38.p13) with Salmon v.1.10.1 and STAR v.2.6.1d.  The standard alignment protocol was followed, with homo sapiens NCBI version 108 GTF annotation file. Read counts were obtained using Salmon Quant v.1.10.1. Qualimap v.2.3 was applied to evalaute the quality control of alignment sequencing data against feature counts. At each step, FASTQC v.0.12.1 for quality control reporting and overall quality report was generated and integrated using MultiQC v.1.19. Read counts were normalized to the transcripts per million (TPM) using R v.4.0.3. Further downstream processing was performed in Python v.3.8.8, R v.4.0.3, Statistica v.13.3 (Tibco, CA, USA) and GSEA v.4.3.2 (Broad Institute, MA, USA)
Assembly: GRCh38.p13
Supplementary files format and content: RNAseq.merged.gene_count.csv - tab-separated files
Supplementary files format and content: RNAseq.merged.gene_TPM.csv

value: thymic adipose tissue

tag: diabetes diagnosis

value: Yes

tag: metformin use

tag: sglt2i use

tag: Sex

value: Male

tag: bmi [kg/m2]

tag: total cholesterol_[mmol/l]

tag: ldl [mmol/l]

tag: hdl [mmol/l]

tag: c-peptide [nmol/l]


title: RNA-seq_wildtype for sal1_12-hr_rep2

tag: tissue

value: leaf at bolting stage

tag: genotype


title: siCTRL C4-2  rep1_12h

tag: cell type


title: RNA-seq_sal1_12-hr_rep3

tag: treatment


title: S23_67TKN

value: epicardial adipose tissue

tag: triglicerides [mmol/l]

tag: hba1c [mmol/mol]


title: MUC3675

tag: diagnosis

tag: patient id

tag: age

tag: gender

value: female

tag: batch id


title: RNA-seq_wildtype for sal1_12-hr_rep1

tag: ecotype


title: siCTRL C4-2  rep1_0h

tag: cell line

tag: sirna

tag: time point


title: MUC3674


title: MUC3673


title: msh1hda6 Gen2_12-hr_rep5

data_processing:
Raw whole-genome bisulfite sequencing data was trimmed using Trim Galore! (v0.6.6) with Cutadapt (v2.8)
Aligned to the TAIR10 reference genome using Bismark (v0.23.1) with Bowtie 2 (v3.5.1) and Samtools (v1.10).
Assembly: TAIR10
Supplementary files format and content: Each row contains read count data with <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context> in txt format

extract_protocol:
DNA was extracted with NucleoSpin Plant II Kit (Macherey-Nagel, Germany).
Library was constructed and sequenced as paired-end 100-bp for the Batch 1 (WT_12h, cue1_12h, hda6_12h) and paired-end 150-bp for other batches


title: S19_49TKN

tag: diabetes diagnosis

tag: metformin use

tag: sglt2i use

tag: Sex

tag: bmi [kg/m2]

tag: total cholesterol_[mmol/l]

tag: ldl [mmol/l]

tag: hdl [mmol/l]


title: msh1hda6 Gen2_12-hr_rep4

tag: tissue

tag: genotype

tag: treatment


title: S20_49TKP

tag: triglicerides [mmol/l]

tag: c-peptide [nmol/l]

tag: hba1c [mmol/mol]


title: MUC3671

tag: diagnosis

value: psoriasis

tag: patient id

tag: age

tag: gender

tag: batch id


title: S18_39TKP

tag: diabetes diagnosis

value: No

tag: metformin use

tag: sglt2i use


title: Human kidney medulla, Hi-C, rep2

city: New Haven

first: Haikuo

state: CT

address: 55 Prospect St

institute: Washington University in St. Louis

data_processing:
Preprocessing of paired-end raw .fastq files of Hi-C sequencing data were performed with Juicer v1.6, including genome alignment, read sorting, duplicate removal and generation of .hic contact matrices, with resolutions of 5K, 10K, 25K, 50K, 100K, 250K, 500K, 1000K and 2500K bases.
Assembly: Human hg19 (primary assembly of GRCh37) was used as the reference genome.
Supplementary files format and content: .hic Hi-C contact matrices

source_name: Kidney

extract_protocol:
We extracted nuclei from tissues and used the nuclear suspensions for library preparation (1 million nuclei for each Hi-C reaction).
Hi-C library preparation was performed with the Arima Library Prep Kit v2 (A303011, Arima Genomics).
Hi-C and CUT&RUN on the same nuclear suspension pool

value: Kidney

tag: kidney region

value: medulla


title: msh1hda6 Gen2_12-hr_rep2

tag: cell line


title: msh1hda6 Gen2_12-hr_rep3


title: Human kidney papilla, Hi-C, rep2

value: papilla


title: S17_39TKN

tag: Sex

tag: bmi [kg/m2]

tag: total cholesterol_[mmol/l]

tag: ldl [mmol/l]

tag: hdl [mmol/l]


title: MUC3670

data_processing:
STAR aligner with human genome reference hg38
Bioconductor package DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: .txt


title: MUC3672


title: Human kidney medulla, Hi-C, rep1

tag: tissue


title: msh1hda6 Gen2_12-hr_rep1

tag: genotype

tag: treatment


title: Human kidney cortex, Hi-C, rep2

value: cortex


title: S16_36TKP

tag: triglicerides [mmol/l]

tag: c-peptide [nmol/l]

tag: hba1c [mmol/mol]


title: MUC3669

tag: diagnosis

tag: patient id

tag: age

tag: gender

tag: batch id


title: hda6 Gen3_12-hr_rep5

tag: cell line


title: MUC2952

value: Atopic eczema

value: male


title: S15_36TKN

tag: diabetes diagnosis

tag: metformin use

tag: sglt2i use

tag: Sex


title: Human kidney cortex, Hi-C, rep1

tag: kidney region


title: hda6 Gen3_12-hr_rep4

tag: tissue

value: 12-hr, no heat


title: S12_19TKP

tag: bmi [kg/m2]

tag: total cholesterol_[mmol/l]

tag: ldl [mmol/l]

tag: hdl [mmol/l]


title: Human kidney papilla, CUT&RUN IgG, rep2

data_processing:
The paired-end raw .fastq files of CUT&RUN sequencing data were first trimmed with TrimGalore v0.6.10. The reads were aligned to the hg19 genome or the E. coli genome (E. coli strain K12, MG1655) with Bowtie2 v2.3.5.1. The .sam files post hg19 genome alignment were sorted and indexed with samtools v1.10.24. The .bam files of two replicates of the same kidney anatomic regions can be merged with samtools for downstream analysis. Bigwig file were generated with bamCoverage v3.5.4 and the fraction of E. coli reads was considered for data normalization.
Assembly: Human hg19 (primary assembly of GRCh37) was used as the reference genome.
Supplementary files format and content: .bw
Library strategy: CUT&RUN

extract_protocol:
We extracted nuclei from tissues and used the nuclear suspensions for library preparation (500K for each CUT&RUN reaction).
CUT&RUN library preparation was performed with the NEBNext® Ultra™ II DNA Library Prep Kit.

tag: chip antibody

value: IgG


title: hda6 Gen3_12-hr_rep3

tag: genotype

tag: treatment


title: S11_19TKN

tag: triglicerides [mmol/l]

tag: c-peptide [nmol/l]

tag: hba1c [mmol/mol]


title: MUC2951

extract_protocol:
RNA from skin biopsies was isolated using the QIAzol Lysis Reagent (Qiagen) and miRNeasy Mini Kit (Qiagen) according to manufacturer’s protocol
RNASeq libraries were generated using the TruSeq Stranded Total RNA Kit (Illumina) with Ribo-Zero Depletion (rRNA Removal Mix) according to manufacturer’s high sample protocol. 200 ng of RNA was used as input. DNA was PCR amplified with Illumina primers for 13 cycles. Libraries were sequenced on the Illumina HiSeq 4000 as paired-end with a read length of 2x 150 bp and an average output of 40 Mio reads per sample and end following the manufacturer's protocols.

tag: diagnosis

tag: patient id

tag: age

tag: gender

tag: batch id


title: Human kidney papilla, Hi-C, rep1

tag: kidney region


title: Human kidney papilla, CUT&RUN IgG, rep1

tag: tissue


title: hda6 Gen3_12-hr_rep2

tag: cell line


title: MUC2950

value: Nummular Eczema


title: Human kidney papilla, CUT&RUN H3K4me3, rep2


title: S10_17TKP

value: thymic adipose tissue

tag: diabetes diagnosis

tag: metformin use

tag: sglt2i use

tag: Sex

value: Female

tag: bmi [kg/m2]

tag: total cholesterol_[mmol/l]


title: MUC2949


title: Human kidney papilla, CUT&RUN H3K4me3, rep1

tag: chip antibody


title: hda6 Gen3_12-hr_rep1

tag: genotype

tag: treatment


title: S8_16TKP

tag: triglicerides [mmol/l]

tag: ldl [mmol/l]

tag: hdl [mmol/l]

tag: c-peptide [nmol/l]

tag: hba1c [mmol/mol]


title: MUC2946

tag: diagnosis

tag: patient id

tag: age

tag: gender

tag: batch id


title: Human kidney papilla, CUT&RUN H3K27me3, rep2

tag: tissue

tag: kidney region


title: S9_17TKN

tag: diabetes diagnosis

tag: metformin use

tag: sglt2i use

tag: Sex

tag: bmi [kg/m2]


title: wildtype for hda6 Gen3, msh1hda6 Gen2_12-hr_rep5

tag: cell line

tag: genotype

value: wild type

tag: treatment


title: MUC2944


title: wildtype for hda6 Gen3, msh1hda6 Gen2_12-hr_rep4

value: leaf at bolting stage


title: Human kidney papilla, CUT&RUN H3K27me3, rep1

tag: chip antibody


title: MUC2945


title: wildtype for hda6 Gen3, msh1hda6 Gen2_12-hr_rep3


title: S7_16TKN

value: epicardial adipose tissue

tag: triglicerides [mmol/l]

tag: total cholesterol_[mmol/l]

tag: ldl [mmol/l]

tag: hdl [mmol/l]

tag: c-peptide [nmol/l]

tag: hba1c [mmol/mol]


title: S6_15TKP

tag: tissue

value: Yes


title: MUC2943

tag: diagnosis

tag: patient id

tag: age

tag: gender

tag: batch id


title: Human kidney medulla, CUT&RUN IgG, rep2

tag: kidney region


title: wildtype for hda6 Gen3, msh1hda6 Gen2_12-hr_rep2

tag: cell line


title: Human kidney medulla, CUT&RUN IgG, rep1


title: MUC2917


title: Human kidney medulla, CUT&RUN H3K4me3, rep2


title: MUC2916


title: wildtype for hda6 Gen3, msh1hda6 Gen2_12-hr_rep1

tag: genotype


title: hda6_12-hr_heat_flowering_rep3

source_name: leaf at flowering stage

value: leaf at flowering stage

tag: treatment

value: 12-hr, heat


title: S5_15TKN

tag: diabetes diagnosis

tag: metformin use

tag: sglt2i use

value: No

tag: Sex

tag: bmi [kg/m2]


title: S3_3TKN

tag: triglicerides [mmol/l]

tag: total cholesterol_[mmol/l]

tag: ldl [mmol/l]

tag: hdl [mmol/l]

tag: c-peptide [nmol/l]


title: MUC2914

tag: diagnosis

tag: patient id

tag: age

value: female


title: S2_1TKP

tag: tissue

value: Male

tag: hba1c [mmol/mol]


title: hda6_12-hr_heat_flowering_rep1

tag: cell line

tag: genotype


title: MUC2913

tag: gender

tag: batch id


title: S1_1TKN

tag: diabetes diagnosis

tag: metformin use

tag: sglt2i use


title: Human kidney medulla, CUT&RUN H3K27me3, rep2

value: Kidney

tag: kidney region

value: medulla

tag: chip antibody


title: MUC2911

value: Atopic eczema

value: male


title: hda6_12-hr_control_flowering_rep3

tag: treatment

value: 12-hr, no heat


title: hda6_12-hr_control_flowering_rep2


title: ChIP input, control depletion, HEK293T, Rep1

tag: cell type

value: Human embryonic kidney

value: Wild type


title: Human kidney cortex, CUT&RUN IgG, rep1

value: cortex

value: IgG


title: ChIP input, control depletion, HEK293T, Rep2


title: MUC2910


title: Human kidney cortex, CUT&RUN IgG, rep2


title: S4_3TKP

value: thymic adipose tissue

tag: Sex

value: Female

tag: bmi [kg/m2]

tag: triglicerides [mmol/l]

tag: total cholesterol_[mmol/l]

tag: ldl [mmol/l]

tag: hdl [mmol/l]

tag: c-peptide [nmol/l]


title: INTS13 ChIP, ctrl depletion, HEK293T, Rep2

tag: cell line

tag: genotype

value: INTS13 (Bethyl Laboratories #A303-575A)


title: Human kidney cortex, CUT&RUN H3K4me3, rep2

tag: tissue


title: hda6_12-hr_control_flowering_rep1

value: leaf at flowering stage


title: hda6_16-hr_rep3

value: leaf at bolting stage

value: 16-hr, no heat


title: INTS13 ChIP, ctrl depletion, HEK293T, Rep1


title: Human kidney medulla, CUT&RUN H3K4me3, rep1


title: MUC2906

tag: diagnosis

tag: patient id

tag: age

tag: gender

tag: batch id


title: Human kidney cortex, CUT&RUN H3K4me3, rep1

tag: kidney region

tag: chip antibody


title: hda6_12-hr_heat_flowering_rep2

tag: treatment

value: 12-hr, heat


title: HDGF ChIP, ctrl depletion, HEK293T, Rep2

tag: cell type

value: HDGF (Proteintech, #11344-1-AP)


title: Human kidney medulla, CUT&RUN H3K27me3, rep1

value: Kidney


title: MUC2905


title: hda6_16-hr_rep1


title: HDGF ChIP, ctrl depletion, HEK293T, Rep1


title: Human kidney cortex, CUT&RUN H3K27me3, rep1


title: wildtype for hda6_16-hr_rep3

value: wild type


title: MUC2903

value: Atopic eczema


title: MUC2908

value: male


title: Neuron DIV60 fAD AD25 2

city: Montreal

first: Gilbert

last: Bernier

state: Quebec

address: 5690 rosemont boulevard

country: Canada

institute: HMR

description:
AD25D33.sam
readcount DIV60 fAD Vs CTL.xlsx

data_processing:
Base-calling and feature count were done using Illumina software. For differential expression analysis, Dseq2 was used on the R program.
Assembly: HG38
Supplementary files format and content: readcounts

growth_protocol: the iPSC were differentiated into adult neurons using the method desribed in Flamier at al 2018

extract_protocol:
the RNA was extracted using Quiagen RNA kits according to the manufacturer instructions.
cDNA was prepared according to the manufacturer’s instructions (NEB library).

value: Neurons

value: fAD


title: MUC2902


title: Neuron DIV60 fAD AD25 1

description:
AD25D32.sam
readcount DIV60 fAD Vs CTL.xlsx


title: ChIP input, HDGF depletion, HEK293T, Rep1

value: Human embryonic kidney

value: Wild type (HDGF depletion)


title: MUC2900


title: INTS13 ChIP, HDGF depletion, HEK293T, Rep2


title: MUC2907


title: MUC2899


title: wildtype for hda6_16-hr_rep2


title: hda6_16-hr_rep2


title: msh1/hda6 Gen1_12-hr_control_nonflowering_rep3

value: 12-hr, no heat


title: Neuron DIV60 fAD AD24 2

description:
AD24D32.sam
readcount DIV60 fAD Vs CTL.xlsx


title: MUC2898


title: INTS13 ChIP, HDGF depletion, HEK293T, Rep1


title: Human kidney cortex, CUT&RUN H3K27me3, rep2

value: cortex


title: msh1/hda6 Gen1_12-hr_control_nonflowering_rep2


title: Neuron DIV60 fAD AD24 1

description:
AD24D31.sam
readcount DIV60 fAD Vs CTL.xlsx


title: Talaromyces marneffei ATCC18224 Y3(fungus)

city: nanning

first: jing

last: dan

state: Guangxi

address: Shuangyong Road, Qingxiu District,Nanning, 530021,China

institute: guangxi medicial university

data_processing:
Trimmomatic
Raw reads are data filtered using the Trimmomatic (v0.39) tool (parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36). Filtered reads were compared to the reference genome using STAR (version 2.7.9a) (parameters: -runThreadN 30 -alignIntronMax 100000 - chimSegmentReadGapMax parameter 3 -alignSJstitchMismatchNmax 5 -1 5 5).
Calculating expression using featureCounts (v1.6.5)
Assembly: GCF_000001985.1
Supplementary files format and content: text file includes readcount for each sample

organism: Talaromyces marneffei

growth_protocol: T. marneffei ATCC18224 was expanded in 37℃ for 14 days, with 200-220 rpm rotation in RPMI 1640 medium plus 10% FBS (Fetal Bovine Serum).

extract_protocol:
RNA was harvested using TIANGEN Polysaccharides and Polyphenolics rich kit
Enrichment of mRNA with polyA tail through Oligo (dT) magnetic beads

treatment_protocol: Fungus was precipitated with centrifuge of 14000 g for 10 minutes

tag: strain

value: WT


title: MUC2897


title: msh1/hda6 Gen1_12-hr_control_nonflowering_rep1


title: ChIP input, HDGF depletion, HEK293T, Rep2


title: Talaromyces marneffei ATCC18224 Y1(fungus)


title: MUC2894


title: Neuron DIV60 fAD AD21 2

description:
AD21D32.sam
readcount DIV60 fAD Vs CTL.xlsx


title: wildtype for hda6_16-hr_rep1


title: Neuron DIV60 fAD AD24 3

description:
AD24D33.sam
readcount DIV60 fAD Vs CTL.xlsx


title: MUC2895


title: MUC2893

value: female


title: MUC2892


title: Neuron DIV60 fAD AD20 3

description:
AD20D33.sam
readcount DIV60 fAD Vs CTL.xlsx


title: hda6 Gen2_12-hr_control_nonflowering_rep1


title: Neuron DIV60 fAD AD21 1

description:
AD21D31.sam
readcount DIV60 fAD Vs CTL.xlsx


title: WT Week7 2

city: San Francisco

first: Christina

last: Homer

address: 513 Parnassus Ave, S472

institute: University of California, San Francisco

description: Coccidioides posadasii Silveira

data_processing:
Estimated counts of each transcript were calculated for each sample by alignment-free comparison against the predicted mRNA for the published Silveira genome (de Melo Teixeira et al 2022, PMID 35137016) using KALLISTO version 0.46.2 (Bray et al 2016, PMID 27043002)
Assembly: Silveira genome (de Melo Teixeira et al 2022, PMID 35137016)
Supplementary files format and content: Processed data are Kallisto output files with estimated counts per gene.

organism: Coccidioides posadasii

source_name: liquid culture

growth_protocol: All samples are arthroconidia (spores). Arthroconidia were generated on 2x GYE agar (2% Dextrose (Fisher), 1% Yeast extract (Gibco), 1.5% Bacto-Agar (BD)) + Penicillin/Streptomycin (100 U/ml penicillin and 100 g/ml streptomycin, UCSF Media Core) in T225 tissue culture flasks for 4-6 weeks at 30˚C, 25˚C, or 37˚C. Arthroconidia were then collected through scraping and washing as previously described (Mead et al 2020, PMID 32894648).

extract_protocol:
5x10^7 arthroconidia were placed in Trizol LS (Ambion) and bead beat for 2 min. RNA was extracted using the Direct-zol RNA Miniprep Plus isolation kit (Zymo) with on-column DNAse digestion step extended for 15 min.
Sequencing libraries were prepared using the Ultra II Directional RNA Library Prep kit with dual-indexed multiplexing barcodes, with total RNA as the input, omitting the polyA selection step. Library quality and adaptor dimer contamination were analyzed using Agilent High Sensitivity DNA Chip. An additional round of library size selection was performed using homemade Serapure size selection beads (Rohland et al 2012, PMID 22267522) for libraries containing significant adaptor dimers.

treatment_protocol: For samples labeled 'Week 0-7', arthroconidia generated from 30˚C growth coniditions were incubated at 4˚C in PBS for the specified number of weeks prior to RNA harvest.

value: liquid culture

value: Week7 at 4C

tag: replicate


title: Neuron DIV60 fAD AD20 2

description:
AD20D32.sam
readcount DIV60 fAD Vs CTL.xlsx


title: MUC2841

city: Munich

address: Biedersteinderstrasse 29

institute: Center of Allergy and Environment

value: psoriasis


title: hda6 Gen2_12-hr_control_nonflowering_rep2

value: leaf at bolting stage


title: wildtype_12-hr_heat_flowering_rep1

value: leaf at flowering stage

value: 12-hr, heat


title: MUC2840

source_name: lesional skin


title: wildtype_12-hr_heat_flowering_rep2

value: wild type


title: WT Week7 3

description: Coccidioides posadasii Silveira


title: WT Week5 3

description: Coccidioides posadasii Silveira

value: Week5 at 4C


title: Talaromyces marneffei ATCC18224 Y2(fungus)


title: MUC2837

value: Atopic eczema


title: WT Week5 2

description: Coccidioides posadasii Silveira


title: wildtype_12-hr_heat_flowering_rep3


title: Neuron DIV60 fAD AD7 2

description:
AD75_2.sam
readcount DIV60 fAD Vs CTL.xlsx

value: Neurons


title: wildtype_12-hr_control_nonflowering_rep3


title: hda6 Gen2_12-hr_control_nonflowering_rep3


title: WT Week7 1

description: Coccidioides posadasii Silveira


title: Neuron DIV60 fAD AD20 1

description:
AD20D31.sam
readcount DIV60 fAD Vs CTL.xlsx

value: fAD


title: WT Week3 3

description: Coccidioides posadasii Silveira

value: Week3 at 4C


title: MUC2836


title: wildtype_12-hr_control_nonflowering_rep2


title: Neuron DIV60 fAD AD7 1

description:
AD75_1.sam
readcount DIV60 fAD Vs CTL.xlsx


title: Neuron DIV60 CTL GB14 2

description:
GB14_2.sam
readcount DIV60 fAD Vs CTL.xlsx


title: Neuron DIV60 fAD AD21 3

description:
AD21D33.sam
readcount DIV60 fAD Vs CTL.xlsx


title: MUC2822


title: WT Week3 2

description: Coccidioides posadasii Silveira


title: wildtype_12-hr_control_nonflowering_rep1


title: MUC2821


title: wildtype_12-hr_control_flowering_rep3


title: WT Week3 1

description: Coccidioides posadasii Silveira


title: Neuron DIV60 CTL GB2 4

description:
G2_P30_2.sam
readcount DIV60 fAD Vs CTL.xlsx


title: MUC2820


title: wildtype_12-hr_control_flowering_rep2


title: Neuron DIV60 CTL GB2 3

description:
G2_P30_1.sam
readcount DIV60 fAD Vs CTL.xlsx


title: WT Week2 3

description: Coccidioides posadasii Silveira

value: Week2 at 4C


title: MUC2819


title: wildtype_12-hr_control_flowering_rep1

value: 12-hr, no heat


title: WT Week2 2

description: Coccidioides posadasii Silveira


title: Neuron DIV60 CTL GB2 2

description:
GB21_2.sam
readcount DIV60 fAD Vs CTL.xlsx


title: hda6 Gen2_16-hr_rep3

value: 16-hr, no heat


title: WT Week2 1

description: Coccidioides posadasii Silveira

value: WT


title: MUC2817

value: male


title: WT Week5 1

description: Coccidioides posadasii Silveira

value: liquid culture


title: MUC2818


title: hda6 Gen2_16-hr_rep2


title: Neuron DIV60 CTL GB2 1

description:
GB21_1.sam
readcount DIV60 fAD Vs CTL.xlsx


title: WT Week1 3

description: Coccidioides posadasii Silveira

value: Week1 at 4C


title: Neuron DIV60 CTL GB1 1

description:
G1_P30_1.sam
readcount DIV60 fAD Vs CTL.xlsx


title: WT Week1 2

description: Coccidioides posadasii Silveira


title: MUC2816

value: psoriasis


title: hda6 Gen2_16-hr_rep1

value: leaf at bolting stage


title: Neuron DIV60 CTL GB1 2

description:
G1_P30_2.sam
readcount DIV60 fAD Vs CTL.xlsx


title: MUC2815


title: Neuron DIV60 CTL GB14 1

description:
GB14_1.sam
readcount DIV60 fAD Vs CTL.xlsx


title: msh1_16-hr_rep3


title: iPSC fAD AD25 2

description:
AD25PS2
readcount iPSC fAD Vs CTL.txt

value: iPSCs


title: WT Week1 1

description: Coccidioides posadasii Silveira


title: msh1_16-hr_rep2


title: MUC2814

value: female


title: WT Week0 3

description: Coccidioides posadasii Silveira

value: Week0 at 4C


title: MUC2813


title: msh1_16-hr_rep1


title: WT Week0 2

description: Coccidioides posadasii Silveira


title: MUC2812


title: iPSC fAD AD24 2

description:
AD24PS3
readcount iPSC fAD Vs CTL.txt


title: MUC2811


title: iPSC fAD AD24 1

description:
AD24PS2
readcount iPSC fAD Vs CTL.txt


title: WT Week0 1

description: Coccidioides posadasii Silveira


title: cue1_16-hr_rep2


title: WT 25 2-3

description: Coccidioides posadasii Silveira


title: iPSC fAD AD21 1

description:
AD21PS1
readcount iPSC fAD Vs CTL.txt


title: MUC2810


title: cue1_16-hr_rep1


title: wildtype_16-hr_rep3

value: wild type


title: MUC2808


title: WT 25 2-2

description: Coccidioides posadasii Silveira


title: wildtype_16-hr_rep2


title: iPSC fAD AD20 3

description:
AD20PS3
readcount iPSC fAD Vs CTL.txt


title: iPSC fAD AD20 2

description:
AD20PS2
readcount iPSC fAD Vs CTL.txt


title: WT 37 2-3

description: Coccidioides posadasii Silveira


title: WT 25 2-1

description: Coccidioides posadasii Silveira


title: wildtype_16-hr_rep1


title: iPSC fAD AD20 1

description:
AD20PS1
readcount iPSC fAD Vs CTL.txt


title: iPSC fAD AD25 1

description:
AD25PS1
readcount iPSC fAD Vs CTL.txt


title: WT 37 2-2

description: Coccidioides posadasii Silveira


title: MUC2807


title: MUC2806


title: cue1_16-hr_rep3


title: sal1_12-hr_rep3


title: WT 37 2-1

description: Coccidioides posadasii Silveira


title: iPSC fAD AD7 1

description:
AD7_5_1
readcount iPSC fAD Vs CTL.txt


title: sal1_12-hr_rep2


title: MUC2805


title: iPSC CTL GB14 1

description:
GB1410_1
readcount iPSC fAD Vs CTL.txt


title: MUC2804


title: WT 25 1-2

description: Coccidioides posadasii Silveira


title: MUC2809


title: iPSC CTL GB2 2

description:
GB2_1_2
readcount iPSC fAD Vs CTL.txt


title: sal1_12-hr_rep1


title: WT 25 1-3

description: Coccidioides posadasii Silveira


title: 3-17T_R1:Escherichia coli str. BL21:AMPLICON

city: Nanjing

first: Shu

last: Xu

state: Jiangsu Province

address: China Pharmaceutical University

institute: China Pharmaceutical University

data_processing:
Illumina software used for basecalling.
Assembly: E. coli BL21 genome, NCBI assembly GCA_000001635.1.
Supplementary files format and content: The processed data files are provided in VCF format, containing variant calls for the sequenced regions.
Library strategy: Amplicon sequencing

organism: Escherichia coli BL21

source_name: Escherichia coli str. BL21

growth_protocol: E. coli BL21 cells were grown in LB medium at 37°C with shaking at 200 rpm until the OD600 reached 0.6.

extract_protocol:
Genomic DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturer's instructions.
The amplicon library was prepared by PCR amplification of the target region using specific primers. The PCR products were purified using AMPure XP beads (Beckman Coulter) and quantified using Qubit (Thermo Fisher Scientific). Libraries were constructed using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer's instructions.

treatment_protocol: Plasmids for electro-transferring Taqtth and sgRNA expression

value: Escherichia coli str. BL21


title: iPSC CTL GB2 1

description:
GB2_1_1
readcount iPSC fAD Vs CTL.txt


title: WT 25 1-1

description: Coccidioides posadasii Silveira


title: MUC2802

first: Stefanie

last: Eyerich


title: 3-17NT_R1:Escherichia coli str. BL21:AMPLICON


title: iPSC CTL GB1 2

description:
GB1_4_2
readcount iPSC fAD Vs CTL.txt


title: WT 37 1-3

description: Coccidioides posadasii Silveira


title: MUC2801


title: MUC2803


title: WT 37 1-2

description: Coccidioides posadasii Silveira


title: iPSC fAD AD7 2

description:
AD7_5_2
readcount iPSC fAD Vs CTL.txt


title: siCTRL_input1

data_processing:
After mRNA-seq, the reads were mapped to the genome hg19 with UCSC Known Genes as reference. The TopHat version 2.1.1 with default parameter values was used to map to the human genome. mRNA half-life of the HEK293T cell and C4-2 cells was computed as described before. In short, the mRNA levels were first normalized to RPKM (Reads Per Kilobase Million). To reduce the noise due to genes that showed a higher expression levels after inhibition of transcription, we then scaled the FPKM values based on the expression levels of top 10 genes which were most stable between time points, so that these genes will have no change of expression between time points. The RNA degradation rate kdecay was defined as the mean values of ratio from RPKM at time 0 over the RPKM value at each other time point (0hour, 6hour and 12hour, 24hour). After that the pseudo-mRNA half-life t1/2 was calculated as ln2/kdecay.
After base-calling using guppy_basecaller(version 3.6.1), the direct RNA-seq of Nanopore reads with quality value more than 7 were aligned to the human genome (Hg38, GRCh38.p13 from GENCODE database) using Minimap with --secondary=no -ax splice -uf -k14 option. Tombo resquiggle was used to assigned to transcript sequence as reference from the website: https://www.gencodegenes.org/human. We extracted the median, standard deviation, mean, and dwell time from nanopore raw signal data in each direct RNA sequencing read to calculate the probability of Nm modification using the training models from rRNA. The modified base supported by at least 5 modified transcripts were identified as modified Nm sites.
After mRNA-seq, the reads were mapped to the genome hg19 with UCSC Known Genes as reference. The TopHat version 2.1.1 with default parameter values was used to map to the human genome. We used the software piranha to analyze the RIP-seq data with default parameters. The Homer annotatePeaks.pl script was used to annotate peaks from the RIP-seq data.  We used a P-value cutoff 0.01 to define FBL-binding RNAs in the C4-2 cells.
Assembly: hg19 for NGS RNA-seq
Supplementary files format and content: abundance measurements for each sample
Supplementary files format and content: bigwig for each sample

growth_protocol: The human prostate cancer cell line C4-2 was a gift from L. Chung at Cedars-Sinai Medical Center and were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS). HEK293T cells were purchased from the American Type Culture Collection (ATCC) and cultured in DMEM medium supplemented with 10% FBS. Both cell lines were maintained at 37 °C and 5% CO2 in a humidified atmosphere and were authenticated and routinely screened for Mycoplasma.

extract_protocol:
RIP-seq was used to detect the mRNA binding sites of FBL in C4-2 cells. C4-2 cells were lysed in RIP lysis buffer and incubated with FBL antibody (anti-FBL (Abcam, Cat#ab5821))-magnetic beads mixture at 4 °C overnight to enrich RNA binding protein. The RNA that bound to FBL protein were collected by Proteinase K digestion, followed by purification and precipitation.
The RIP experiment in C4-2 cells was performed using the EZ-Magna RIP kit (Millipore) with the procedure provided by the manufacturer.
For high-throughput sequencing, input and RIP-ed RNA samples were shipped to BGI for library preparation and sequencing using the DNBseq platform.

value: C4-2 Cell line

value: prostate cancer

tag: transfection

value: siCTRL

tag: antibody


title: MUC2800


title: WT 37 1-1

description: Coccidioides posadasii Silveira


title: MUC2799


title: MUC2798


title: WT 30 1-3

description: Coccidioides posadasii Silveira


title: siCTRL_RIP2

value: anti-FBL (Abcam, Cat#ab5821)


title: siCTRL_RIP1


title: 50ppm NOPEO treated MDA-MB-231 for 24 hours    2

city: nanchang

first: Chao

last: Yang

state: jiangxi

address: 1688 Meiling Avenue

department: cancer center

institute: Jiangxi University of Traditional Chinese Medicine

data_processing:
IEukaryotic mRNA sequencing is based on the Illumina Novaseq 6000 sequencing platform, which sequences all the mRNAs transcribed at a certain period of time in specific tissues or cells of eukaryotic organisms. Sequencing experiments are performed using the Illumina TruseqTM RNA sample prep Kit method for library construction.
The concentration and purity of the extracted RNA were examined using Nanodrop2000, RNA integrity was detected by agarose gel electrophoresis, and RIN values were determined by Agilent2100. A single library build required total RNA ≥1ug, concentration ≥35ng/μL, OD260/280 ≥1.8, OD260/230 ≥1.0
Assembly: 1. Library enrichment, PCR amplification of 15 cycles; 2. 2% agarose gel recovery of target bands; 3. TBS380 (Picogreen) quantification, mixed on board in proportion to the data; 4. Bridge PCR amplification on cBot to generate clusters; 5. Sequencing on Illumina platform (PE library, read length 2×150bp).
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 RPKM values for each Sample

growth_protocol: The TNBC cell lines MDA-MB-231  were cultured in   Leibovits' medium (L-15) containing 10% (v/v) fetal bovine serum (FBS) and maintained at 37°C.

extract_protocol:
The samples were dissolved by Trizol and post to Shanghai Majorbio Bio-Pharm Technology Co., Ltd, China for sequencing.
RNA libraries were prepared for sequencing  using illumina protocols.

treatment_protocol: The MDA-MB-231 cells were exposed to NOPEO or DMSO for 24 h.

value: breast cancer cell

value: NOPEO


title: 50ppm NOPEO treated MDA-MB-231 for 24 hours    1

value: WT


title: MUC2797

value: male


title: WT 30 1-2

description: Coccidioides posadasii Silveira

value: liquid culture


title: siFBL_2_6h

data_processing:
mRNA half-life of the HEK293T cells and C4-2 cells was computed as described before. In short, the mRNA levels were first normalized to RPKM (Reads Per Kilobase Million). To reduce the noise due to genes that showed a higher expression levels after inhibition of transcription, we then scaled the FPKM values based on the expression levels of top 10 genes which were most stable between time points, so that these genes will have no change of expression between time points. The RNA degradation rate kdecay was defined as the mean values of ratio from RPKM at time 0 over the RPKM value at each other time point (0hour, 6hour, 12hour, 24hour). After that the pseudo-mRNA half-life t1/2 was calculated as ln2/kdecay.
After base-calling using guppy_basecaller (version 3.6.1), the direct RNA-seq of Nanopore reads with quality value more than 7 were aligned to the human genome (Hg38, GRCh38.p13 from GENCODE database) using Minimap with --secondary=no -ax splice -uf -k14 option. Tombo resquiggle was used to assigned to transcript sequence as reference from the website: https://www.gencodegenes.org/human . We extracted the median, standard deviation, mean, and dwell time from Nanopore raw signal data in each direct RNA sequencing read to calculate the probability of Nm modification using the training models from rRNA. The modified base supported by at least 5 modified transcripts were identified as modified Nm sites.
Assembly: hg19 for NGS RNA-seq. hg38 for Nanopore RNA-seq.
Supplementary files format and content: *.count.txt: Tab-delimited text files include abundance measurements.
Supplementary files format and content: *.bw: bigWig files.

extract_protocol: RNA was extracted from the HEK293T and C4-2 cells.

tag: sirna

value: siFBL

tag: time point


title: WT 30 1-1

description: Coccidioides posadasii Silveira

tag: genotype


title: MUC2796

value: psoriasis


title: DMSO treated MDA-MB-231 for 24 hours   3

tag: cell line

value: DMSO


title: siFBL_2_12h


title: MUC2795

tag: diagnosis


title: DMSO treated MDA-MB-231 for 24 hours  1


title: siFBL_2_3h


title: siCTRL_input2


title: siFBL_2_0h


title: DMSO treated MDA-MB-231 for 24 hours  2


title: iPSC CTL GB1 1

description:
GB1_4_1
readcount iPSC fAD Vs CTL.txt

value: iPSCs


title: MUC2794

tag: patient id


title: CE-30

city: Philadelphia

first: Ramkrishna

last: Mitra

state: Pennsylvania

address: 233 S 10th street

institute: Thomas Jefferson University

data_processing:
Adapter sequence trimming was performed by TrimGalore
The tools Hisat2 and StringTie were used to perform sequence mapping and transcript assembling, respectively.
For differential expression analysis, read counts were imported into the tool edgeR.
Assembly: GRCh38
Supplementary files format and content: Ensembl gene IDs and read counts are provided in tab-delimited text files as the processed data files.

growth_protocol: DLBCL parental cell lines were purchased from and cultured as described by ATCC

extract_protocol:
TRIzol Reagent from Invitrogen Cat # 15596026
NEBNext Ultra II RNA Library Preparation Kit for SUDHL6 and Illumina Stranded Total RNA Prep, ligation with RiboZero Plus for SUDHL16.
RNA-sequencing for SUDHL6 and SUDHL16 parental and ABT-199/venetoclax-resistant cell lines were done using Illumina HiSeq 4000 and NovaSeq 6000 platforms, respectively.

treatment_protocol: Parental DLBCL ABT-199/venetoclax-resistant DLBCL cell lines were generated by chronic exposure to gradually increasing concentrations of ABT-199/venetoclax and could grow at a concentration of 10x the original IC50.

value: DLBCL


title: 50ppm NOPEO treated MDA-MB-231 for 24 hours   3


title: siFBL_1_6h


title: MUC2793

growth_protocol: RNA analysis of skin biopsies, skin biopsies were stored at -80°C in RNAlater solution until RNA preparation

tag: age


title: CE-29


title: siFBL_1_3h


title: Responders 9

city: Trento

first: Simone

last: Detassis

address: Via Sommarive 9

department: CIBIO

country: Italy

institute: University of Trento

description: Responder to abiraterone acetate. The patients were considered responders to AA if they either achieved a radiological response without PSA progression and performance status deterioration, or in the presence of PSA reduction ≥ 50% compared to the baseline values without radiological progression and performance status deterioration.

data_processing: Matrix non-normalized represents non-normalized Ct values. miRNAs non-detected in at least 20% of the samples were removed and Ct equal or higher than 40 were considered non-detected. Matrix normalized template represents Ct values of panels normalised on miR-425-5p. Fold change template represents responders (R) evaluated relative to non-responders (NR) [2^-(ΔCt NR – ΔCt R)]

label: SYBR

source_name: blood

label_protocol: 80 ng of extracted RNA were retro-transcribed using a Universal cDNA Synthesis kit (Exiqon – Qiagen) together with 4 uL of 5X Reaction buffer, 2 uL of enzyme and DNase and RNase free water up to 20 uL of total reaction volume. The reaction was performed in a T100 Thermal Cycler (BioRad) as follows: 42°C for 60 minutes and 95°C for 5 minutes. Exiqon microRNA Ready-to-Use PCR (miRCURY LNA Universal RT mi-croRNA PCR Human panel I+II, V4.M – Qiagen) was used for miRNA profiling. cDNA template was diluted 1:50 in nuclease-free water and mixed 1:1 with 2X SYBR Green Universal PCR Master Mix (Exiqon – Qiagen) for a 10 uL of total reaction volume. The reaction was performed on a CFX384 Real-Time PCR Detection System (BioRad) as fol-lows: 95°C for 10 minutes, 40 amplification cycles at 95°C for 10 seconds and 60°C for 1 minute.

extract_protocol: 5-mL blood sample was obtained from each patient at the baseline (before starting AA administration). Each blood sample was collected in EDTA-treated tubes and immediately centrifuged for 15 minutes at 2500 rpm at 4°C. The plasma layer was carefully collected without disturbing the buffy coat, and stored at -80°C in 250-500 µL aliquots. Total RNA from 250 uL of plasma samples was extracted using miRNeasy® Se-rum/Plasma Kit (Qiagen) according to the manufacturer's instructions and eluted in 40 uL of DNase- and RNase-free water. Briefly, plasma samples were lysed by adding 5 volumes of QIAzol Lysis Reagent containing 1ug of MS2 phage RNA. After chloroform addition, the aqueous phase was loaded onto RNeasy Mini Spin Columns, and washing steps were performed according to manufacturer’s protocol. Qubit RNA HS Assay Kit (Thermo Fisher) was used with the Qubit Fluorometer, to provide an accurate method for the quantification of the 18 samples used for Exiqon miRNome RT-qPCR panels (Qiagen).

treatment_protocol: Abiraterone acetate after docetaxel failure. The treatment consisted of daily oral administration of AA (1000 mg) plus prednisone 5 mg twice a day.

tag: gender

value: Male


title: CE-28


title: MUC2791

value: female

tag: batch id


title: Responders 7


title: Responders 8


title: CE-27


title: siFBL_1_12h


title: MUC2790

source_name: non-lesional skin


title: CE-26


title: Responders 4


title: siCTRL_2_6h


title: MUC2788


title: CE-25


title: MUC2789


title: siCTRL_2_3h


title: Responders 3


title: WR2

city: La Jolla

first: Nathan

last: Lewis

address: 9500 Gilman Dr

institute: UCSD

description: control/WT

data_processing:
Sequence data for RNA-Seq were quality controlled using FastQC and summarized with multiQC (Ewels et al., 2016). Low-quality bases were trimmed from the reads with Trimmomatic (Bolger et al., 2014). Reads were then mapped to the human GRCh38.p12 genome and quantified with Salmon (Patro et al., 2017).
Assembly: human GRCh38.p12 genome
Supplementary files format and content: CSV file containing TPMs

source_name: liver

extract_protocol:
Total RNA were extracted using Direct-zol™ RNA Microprep (Zymo Research) according to the manufacture instructions
Total RNA was assessed for quality using an Agilent Tapestation 4200, and samples with an RNA Integrity Number (RIN) greater than 8.0 were used to generate RNA sequencing libraries using the TruSeq Stranded mRNA Sample Prep Kit with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, starting with 1 ug of RNA and modifying RNA shear time to five minutes.

tag: tissue

value: liver

value: hepatocyte

value: control


title: Responders 2


title: siFBL_1_0h


title: MUC2786


title: MUC2792


title: MUC2787


title: Responders 1


title: Responders 6


title: siCTRL_2_0h

value: siCTRL


title: siCTRL_2_12h


title: WR3

description: control/WT


title: WR1

description: control/WT


title: TR3

description: NAFLD model

value: palmitic acid


title: siCTRL_1_6h


title: MUC2784


title: Non-responders 9

description: Non-responder to abiraterone acetate. The patients were considered responders to AA if they either achieved a radiological response without PSA progression and performance status deterioration, or in the presence of PSA reduction ≥ 50% compared to the baseline values without radiological progression and performance status deterioration


title: Non-responders 8


title: siCTRL_1_3h


title: Responders 5


title: Non-responders 7


title: Non-responders 6


title: MUC2783


title: siCTRL_1_12h


title: TR1

description: NAFLD model


title: MUC2782


title: siCTRL_1_0h


title: Non-responders 5


title: siNOP56_rep2_6h

source_name: HEK293T cell line


title: hipsc-cm, DOX1

city: Zhengzhou

first: Ying

last: Peng

address: No.1 Jianshe East Road, Erqi District, Zhengzhou City, Henan Province

institute: ；The First Affiliated Hospital of Zhengzhou University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by  Removing reads containing sequencing adapter, Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%;  Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes row counts for each sample

source_name: heart

extract_protocol:
Total RNA was extracted through trizol reagent
polyA probes were used to retrieve mRNA from total RNA, then fragment and add adaptor to build a library

value: heart

value: hiPSC-CM

value: DOX


title: MUC2781


title: MUC2780

value: male


title: hipsc-cm, DOX2


title: Non-responders 3


title: siNOP56_rep2_12h


title: MUC2779


title: MUC2785


title: hipsc-cm, PBS1

value: PBS


title: siNOP56_rep2_24h


title: Non-responders 2


title: hipsc-cm, DOX3


title: mouse DRG, culture d7, rep6

city: Würzburg

first: Robert

last: Blum

address: Josef-Schneider-Str. 11

department: Department of Neurology

institute: University Hospital Würzburg

data_processing:
Base calling with Illumina NextSeq RTA v2.11.3
FASTQ conversion with bcl2fastq v2.20.0.422
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) v2.5 (parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
Alignment of trimmed reads to mouse genome using STAR (Dobin et al., 2013)  v2.7.2b with default parameters except for including transcript annotations from RefSeq annotation version 108.20200622
Calculation of read counts on exon level summarized for each gene (RefSeq annotation version 108.20200622 for GRCm38.p6) using featureCounts v1.6.4 from Subread package (Liao et al., 2014) (parameters: -s 2 -t exon -M -O --fraction).
Assembly: GRCm38.p6
Supplementary files format and content: Character (TAB) separated value file containing raw read counts

source_name: dorsal root ganglia

growth_protocol: Primary DRG cell cultures were prepared from adult 4 to 6 weeks old wild-type mice. Mice were sacrificed by CO2 asphyxiation and cervical dislocation. DRG were collected in ice-cold HBSS. Isolated DRG were treated with 0.6 U/ml Liberase TH (Sigma-Aldrich) and 0.6 U/ml Liberase TM (Sigma-Aldrich) in EDTA (3,3 mM) buffered DMEM. DRG were plated on poly-L-lysine (PLL)-coated 3.5 cm culture dishes. Cells were cultivated in DMEM/F12, GlutaMAX™ supplement (Gibco), 10% fetal calf serum (FCS, Sigma-Aldrich), and 1% penicillin/streptomycin supplemented with 10ng/ml EGF and FGF (Sigma-Aldrich) at 37°C, 5% CO2 atmosphere. After 7 d in culture, total RNA was prepared from 2 culture dishes with the Qiagen RNA Mini kit.

extract_protocol:
Total RNA was extracted from cell cultures using the Qiagen RNA Mini Kit.
RNA quality was checked using a 2100 Bioanalyzer with the RNA 6000 Nano kit (Agilent Technologies). The RIN for all samples was ≥8.7. DNA libraries suitable for sequencing were prepared from 500 ng of total RNA with oligo-dT capture beads for poly-A-mRNA enrichment using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to manufacturer’s instructions (½ volume). After 15 cycles of PCR amplification, the size distribution of the barcoded DNA libraries was estimated ~325 bp by electrophoresis on Agilent DNA 1000 Bioanalyzer microfluidic chips.

value: dorsal root ganglia

tag: developmental stage

value: adult (4-6 weeks)

tag: time

value: 7 days in vitro

value: wild type


title: siNOP56_rep2_0h


title: TR2

description: NAFLD model

tag: cell type

tag: treatment


title: siNOP56_rep1_6h


title: MUC2778

value: Atopic eczema


title: Non-responders 1

value: Male


title: MUC2777


title: hipsc-cm, PBS2


title: hipsc-cm, PBS3


title: MUC2774

value: psoriasis

value: female


title: mouse DRG, culture d7, rep5

tag: strain


title: siNOP56_rep1_24h


title: mouse DRG, culture d7, rep4


title: phyllode tumor cells, si ZFPM2-AS1, rep3 [LJSI2]

city: Guangzhou

first: Shishi

last: He

address: 107 Yanjiang West Road

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

data_processing:
Use bcl-convert software to convert BCL files to FASTQ files, high quality Clean Reads were obtained by filtering the raw sequences. (parameter: quality limit: 0.05)
High-quality reads were mapped to hg38 using STAR_2.6.1a
FPKM counts were calculated using RSEM v1.2.28
Data integration using Perl v5
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes FPKMs for each sample

source_name: Tumor

growth_protocol: Malignant phyllode tumor cells were grown in DMEM/F-12 medium containing 15% FBS, and supplemented with penicillin (50 units/ml), streptomycin (100 mg/ml), insulin (10 μg/ml), EGF (20 ng/ml), and hydrocortisone (0.5 mg/ml). All cells were incubated at 37°C in 5% CO2.

extract_protocol:
Total RNA extracted using Trizol following manufacturer's instructions.
3 μg of total RNA was subjected to library synthesis using the NEBNext® Ultra™ RNA Library Prep Kit.

treatment_protocol: Lipo3000 was used to transfect siRNA of NC or ZFPM2-AS1 (100 nM) into phyllode tumor cells for 6 hours.

value: Tumor

value: Breast phyllode tumor cells

value: ZFPM2-AS3 knockdown

value: si ZFPM2-AS3


title: Non-responders 4


title: mouse DRG, culture d7, rep3


title: phyllode tumor cells, si ZFPM2-AS1, rep2 [JWYSI2]

value: ZFPM2-AS2 knockdown

value: si ZFPM2-AS2


title: MUC2772


title: mouse DRG, culture d7, rep2


title: siNOP56_rep1_0h


title: siNOP56_rep1_12h


title: MUC2771


title: phyllode tumor cells, si ZFPM2-AS1, rep1 [GXSI]

value: ZFPM2-AS1 knockdown

value: si ZFPM2-AS1


title: mouse DRG, culture d7, rep1


title: phyllode tumor cells, si NC, rep3 [LJNC]

value: WT

value: si NC


title: MUC2770

value: male


title: Mouse_spleen_KAS-seq_Input, rep2

city: Chicago

first: Ruitu

last: Lyu

state: IL

address: 929 E 57th Street

department: Chemistry

institute: The University of Chicago

data_processing:
To align Opti-KAS-seq and KAS-seq data to the reference genome of interest, we utilized the trim_galore package to trim off low-quality sequence, adaptor sequence and primer sequence from single-end or paired-end raw fastq files
Subsequently, we employed bowtie2 to perform the read alignment of Opti-KAS-seq and KAS-seq data. Mapped reads in sam files from the aligners are sorted and converted to bam files using ‘samtools sort’, which are subsequently deduplicated using ‘picard MarkDuplicates’ (pair-end data) or ‘samtools rmdup’ (single-end data).
For single-end Opti-KAS-seq or KAS-seq data, mapped reads were extended to 150bp as default, irrespective of the initial sequencing data's read length. For paired-end KAS-seq data, the KAS-Analyzer incorporates a Python script, facilitating the merging of "properly paired" mapped reads into a singular interval
Peak calling for broad KAS-seq was executed using epic2, which identified broad peaks maintaining a false discovery rate (FDR) of 0.05 and a 1.5-fold change relative to the Input. Comprehensive quality control measures, such as library complexity metrics, inter-replicate correlation analyses, fingerprint plots, saturation analyses, genomic distribution of KAS-seq peaks, enrichment within gene-coding regions, and the Fraction of Reads in Peaks (FRiP) metric, were executed with the KAS-Analyzer package.
Deduplicated mapped KAS-seq reads were converted to bedGraph and bigWig using deeptools bamCoverage and UCSC tools.
Assembly: mm10
Supplementary files format and content: bed, peaks list.
Supplementary files format and content: bigWig, read density.
Library strategy: KAS-seq

source_name: Spleen

growth_protocol: Murine embryonic stem (ES) cells were purchased from ATCC (CRL-1821) and were cultured in DMEM (Gibco 11995) supplemented with 10% (v/v) fetal bovine serum (Gibco), 1 mM L-glutamine (Gibco), 0.1 mM β-mercaptoethanol (Gibco), 1% (v/v) nonessential amino acid stock (100x, Gibco), 1% penicillin/streptomycin stock (100x, Gibco), and 1,000 U/mL LIF (Millipore)

extract_protocol:
Then, 1 µg genomic DNA was suspended in 95 µL DNA elution buffer supplemented with 5 µL 20 mM DBCO-PEG4-biotin (DMSO solution, Sigma, 760749), 25 mM K3BO3, and incubated at 37 °C for 1.5 h while being gently shaken. Next, 5 µL RNase A (Thermo, 12091039) was added into the reaction mixture followed by incubation at 37 °C for 5 min. Biotinylated gDNA was then recovered by DNA Clean & Concentrator-5 kit (Zymo, D4013).
gDNA was suspended into 100 µL water and was fragmented to 150–350 bp size by using Bioruptor Pico at 30s-on/30s-off setting for 30 cycles; 5% of the fragmented DNA was saved as input, and the remaining 95% was used to enrich biotin-tagged DNA by incubation with 10 µL pre-washed Dynabeads MyOne Streptavidin C1 (Thermo, 65001) at room temperature for 15 min. The beads were washed, and DNA was eluted by heating the beads in 15 µL H2O at 95 °C for 10 min. Eluted DNA and its corresponding input were used for library construction by using Accel-NGS Methyl-seq DNA library kit (Swift, 30024).

treatment_protocol: Cells harvested from the culture dish or Fluorescence-activated cell sorting (FACS) cells were washed with DPBS and subsequently resuspended in 50 µL of ATAC-Resuspension Buffer (RSB) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin. After gentle pipetting, the suspension was incubated on ice for 3 minutes. The cells were then treated with 1 mL of cold ATAC-RSB containing 0.1% Tween-20 and centrifuged at 500 RCF for 5 minutes at 4ºC. Following a wash with 1 mL DPBS, the cells underwent N3-kethoxal labeling at 37 ºC with continuous agitation. The labeling process involved a 15-minute incubation in 5mM N3-kethoxal in PBS.

value: Spleen

value: Mouse spleen

value: No treatment


title: siFBL_rep2_24h

value: siFBL


title: MUC2769

value: psoriasis


title: siFBL_rep2_6h


title: MUC2768

value: female


title: phyllode tumor cells, si NC, rep2 [JWYNC]

value: Tumor


title: siFBL_rep2_0h


title: Mouse_spleen_KAS-seq_Input, rep1


title: siFBL_rep2_12h


title: MUC2767


title: phyllode tumor cells, si NC, rep1 [GXNC]

value: Breast phyllode tumor cells


title: HEK293T cells, ZNF655 siPOOL repllicate 4

city: Zürich

address: Otto-Stern-Weg 5

institute: ETH Zurich

data_processing:
in-house snakemake RNAseq analysis pipeline
FastQC quality control
Cutadapt adapter timming
STAR alignment usiing the parameters: -outFilterMulitmapNmax 20 -quantMode GeneCounts
Assembly: hg38
Supplementary files format and content: bam files include aligned reads for each sample
Supplementary files format and content: Tab-separated value file includes raw read counts for each

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% fetal calf serum (FCS) and antibiotics in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted by Phenol/Chloroform extraction. 1ug of RNA was used for library preparation.
Ribosomal RNAs were depleted and sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA kit.

treatment_protocol: Depletions were performed for 72 hours. siPOOLs were transfected to a final concentration of 5nM with RNAiMax

value: Human embryonic kidney

value: znf655 siPOOL


title: siFBL_rep1_6h


title: Mouse_spleen_opti-KAS-seq, rep1

data_processing:
To align Opti-KAS-seq and KAS-seq data to the reference genome of interest, we utilized the trim_galore package to trim off low-quality sequence, adaptor sequence and primer sequence from single-end or paired-end raw fastq files
Subsequently, we employed bowtie2 to perform the read alignment of Opti-KAS-seq and KAS-seq data. Mapped reads in sam files from the aligners are sorted and converted to bam files using ‘samtools sort’, which are subsequently deduplicated using ‘picard MarkDuplicates’ (pair-end data) or ‘samtools rmdup’ (single-end data).
For single-end Opti-KAS-seq or KAS-seq data, mapped reads were extended to 150bp as default, irrespective of the initial sequencing data's read length. For paired-end KAS-seq data, the KAS-Analyzer incorporates a Python script, facilitating the merging of "properly paired" mapped reads into a singular interval
Peak calling for broad KAS-seq was executed using epic2, which identified broad peaks maintaining a false discovery rate (FDR) of 0.05 and a 1.5-fold change relative to the Input. Comprehensive quality control measures, such as library complexity metrics, inter-replicate correlation analyses, fingerprint plots, saturation analyses, genomic distribution of KAS-seq peaks, enrichment within gene-coding regions, and the Fraction of Reads in Peaks (FRiP) metric, were executed with the KAS-Analyzer package.
Deduplicated mapped KAS-seq reads were converted to bedGraph and bigWig using deeptools bamCoverage and UCSC tools.
Assembly: mm10
Supplementary files format and content: bed, peaks list.
Supplementary files format and content: bigWig, read density.
Library strategy: Opti-KAS-seq


title: Mouse_spleen_opti-KAS-seq, rep2


title: MUC2773

data_processing:
STAR aligner with human genome reference hg38
Bioconductor package DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: .txt

treatment_protocol: no treatment


title: MUC2766


title: HEK293T cells, ZNF655 siPOOL repllicate 3


title: siFBL_rep1_24h


title: siFBL_rep1_12h


title: Mouse_spleen_KAS-seq, rep1


title: MUC2765


title: Mouse_spleen_KAS-seq, rep2


title: HEK293T cells, ZMYND8 siPOOL repllicate 3

value: zmynd8 siPOOL


title: HEK293T cells, ZMYND8 siPOOL repllicate 4


title: MUC2764


title: HEK293T cells, control siPOOL (for ZMYND8 depletion) repllicate 4

value: ctrl siPOOL


title: MUC2763