title: F2_D1 individual, grown at 4C [T4_P4.B11_F2_D1]


title: Control [DK852]

status: Public on Dec 31 2022

type: SRA

city: Cincinnati

first: Scott

middle: M

last: Langevin

state: OH

address: 160 Panzeca Way, ML0056

department: Department of Environmental Health

country: USA

institute: University of Cincinnati College of Medicine

library_source: transcriptomic

data_processing:
Base calling software: Casava 1.8
Preprocessing: Sequence reads were pre-processed to remove adapters and retain only 16-30 base pair- length reads
Alignment: Reads were aligned to the reference human genome (hg19) using the Bowtie aligner
Counts: The reads aligning to each known miRNA were counted using Bioconductor packages for next-generation sequencing data analysis based on miRNA definitions in miRBase database
Normalized abundance measures: RPKM
Assembly: hg19
Supplementary files format and content: The processed data file is in .csv format and contains a table of miRNA transcripts (rows) and normalized abundance (RPKM) data for each sample (columns)

molecule: total RNA

organism: Homo sapiens

source_name: serum small extracellular vesicles

growth_protocol: Cells were cultivated in supplier-recommended media with 10% fetal bovine serum (FBS) that was super-depleted of exosomes via 18 hour ultracentrifugation at 100,000g (verified via nanoparticle tracking analysis) and 1% penicillin/streptomycin at 37°C with 5% CO2 in 150 cm2 flasks with 25mL media. To achieve adequate volume for exosome isolation, cells were cultured in 2-pair sets of flasks in triplicate (6 flasks total per cell-line). Culture media were replaced approximately 48 hours prior to cells reaching 80-90% confluence; media and cells were respectively collected after 48 hours. The media from each 2-flask pair were combined (50mLtotal). After media was harvested, cells were detached from each flask and pooled for each cell-line.

extract_protocol:
Total RNA was extracted from each exosome pellet using the miRNeasy Micro kit (Qiagen, Valencia, CA) according to the manufacturer’s suggested protocol.
The NEBNext small RNA sample library preparation kit (New England BioLabs, Ipswich, MA) was used with 20 ng to 1 µg of total RNA in a 6-µL solution as input, following the manufacturer’s protocol with modification of library size selection

tag: age

tag: Sex

value: Male

tag: source

value: small extracellular vesicles

tag: tissue type

value: Benign - pituitary adenoma

tag: molecule type

value: microRNA


title: Control [DK854]

value: Female

value: Benign - ovarian fibrothecoma


title: F2_D2 individual, grown at 4C [T4_P4.B1_F2_D2]

city: Vienna

first: Rahul

last: Pisupati

address: Dr. Bohrgasse 3

country: Austria

institute: Gregor Mendel Institute

library_source: genomic

data_processing:
Raw sequencing reads were trimmed using cutadapt
Trimmed reads were mapped to reference TAIR10 genome using Bismark
Assembly: TAIR10
Supplementary files format and content: Files are in bedgraph format with "chromosome position strand context mc_score total_reads methylated"

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: leaf

extract_protocol:
DNA was extracted from leaf tissue and performed bisulfite treatment
Libraries were constructed and sequenced through Illumina HiSeq

tag: tissue

value: leaf

tag: developmental stage

value: 7-10 leave rosette

tag: cell type

tag: genotype

tag: treatment


title: young  mouse 3 ( 8 weeks) [Sequel II]

city: NORWICH

first: Laura

last: mincarelli

state: County (optional)

address: Norwich Research Park, Colney Lane, Colney

country: United Kingdom

institute: Earlham Institute

description: single cell fulllenght cDNA (10x Genomics)

data_processing:
Illumina data
Raw Illumina sequencing data were analysed with the 10X Genomics CellRanger pipeline (version 3.0.2) to obtain a single-cell expression matrix object.
Using Seurat v3 in R data were normalised using NormalizeData
data from multiple samples were merged using the FindIntegrationAnchors and IntegrateData commands
count matrices produced by short-read sequencing for individual libraries were combined in Seurat using FindIntegrationAnchors and IntegrateData functions
Illumina and PacBio reads were integrated in Seurat using the CreateAssayObject command to add the long-read data to an existing Seurat object already containing the short-read data
Pacbio data
Circular Consensus reads (CCS) were generated using smrtlink-6.0.0.47841 amnd the command "ccs --numThreads=24 --noPolish --minLength=50 --maxLength=15000 --minPasses=1 --minPredictedAccuracy=0.8"
Reads with identified polydA or polydT were demultiplexed using bbduk and the 10X genomics barcodes identified from the short-read analysis
Long-reads were mapped to the mouse genome (mm10) using Minimap 2 (v2.17), and to the gencode (vM19) transcriptome. De novo transcript annotation was performed with TALON  v.5 was used to generate custom transcriptome using gencode v.M24 and GRCm38.p6. Minimum identity threshold 0.9, coverage 0.8. Novel features filtered with N=5 reads in K=3 samples. Transcriptome then filtered for mis-called antisense transcripts. Novel features were merged with v.M24 reference to make custom annotation. Count matrices were generated using HTSeq, the alignments to the genome (GRCm38.p6, Minimap2) and the TALON annotation
Novel exons were identified by investigating the alignment of the reads to the transcriptome
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: gene level counts
Supplementary_files_format_and_content: de novo annotation
Supplementary_files_format_and_content: gene levels counts

organism: Mus musculus

source_name: bone marrow cells

extract_protocol:
Bone marrow was isolated from spine, femora, tibiae, and ilia,blood cell depletion was performed with ammonium chloride lysis  and lineage negative cells were isolated using the EasySep Mouse Hematopoietic Progenitor Cell Isolation Kit
3’ end single cell RNA-Seq using the 10X Genomics Chromium (V2 Kit) according to manufacturer’s protocol
Libraries compatible for Illumina platform and for Pacific Biosciences Sequel/Sequel II systems were prepared from input cDNA

value: Lineage negative, cKit (Cd117) positive (LK) cell fraction

tag: strain

value: female

value: 8 weeks


title: Control [DK853]

value: Benign - acoustic neuroma


title: HFDS_SO-03-67_Lu

city: Morgantown

first: Christina

last: Umbright

state: WV

address: 1095 Willowdale Road

department: HELD

institute: DHHS/PHS/CDC/NIOSH

description:
total RNA including small RNAs
HighFatDietSilica_03months
SO03Lu_tophat_counts.csv

data_processing:
Basecalls were performed using bcl2fastq/2.19.
Sequence reads were trimmed for adaptor sequence low-quality using Trimmomatic/0.35 with the following parameters ILLUMINACLIP:adapters/TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 (for SL03Lu) or 60 (SL09Lu)
Sequences were mapped with the Rattus norvegicus Rnor 6.0 genome from NCBI downloaded July 31st, 2015 using Tophat/2.0.9 (Trapnell, C. et al., 2012) and Bowtie2/2.2.9 (Langmead B. and Salzberg S., 2012)
Aligned sequences were identified, sorted, and counted using Samtools/0.1.19 (Li, H. et al. 2009), Python/2.7.3 and HTSeq/0.6.1
Genome_build: Rnor6.0
Supplementary_files_format_and_content: tab-delimted text file including raw counts in a matrix containing all samples

organism: Rattus norvegicus

source_name: lung

growth_protocol: This experiment was conducted in an animal facility (NIOSH, Morgantown, WV) accredited by AAALAC International following a protocol approved by the Institutional Animal Care and Use Committee (IACUC). Male Fischer (CDF®) rats (F344/DuCrl) 3 months of age were purchased from Charles River Laboratories (Wilmington, MA). Rats were housed 3 per cage in a temperature (22-25C) and humidity (30-70%) controlled environment following a 12hr light-dark schedule with free access to Harlan Teklad Global 18% Protein Rodent Diet, 2918 irradiated rodent chow, (Harlan Laboratories, Frederick, MD, USA) and tap water.

extract_protocol:
Total RNA, including miRNA and other small RNA molecules, was isolated from a piece of the lung tissue using the miRNeasy Mini Kit (Qiagen, Inc.; Valencia, CA) following the procedure provided by the manufacturer, including optional DNase treatment with RNase-Free DNase (Qiagen, Inc.; Valencia, CA).
One microgram total RNA/sample was used to create sequencing libraries using the Illumina TruSeq® Stranded Total RNA Library Prep with Ribo-Zero Gold  (Illumina, Inc., San Diego, CA) following the  manufacturer's protocol with the exception of only 12 PCR cycles used to enrich the DNA fragments.

treatment_protocol: Acclimated rats were fed either a regular-fat diet (RFD; 18% kcal as fat) (Envigo, Indianapolis, IN) or a high-fat diet (HFD; 60% kcal as fat) (Envigo, Indianapolis, IN) for two weeks and then exposed by whole-body inhalation to either air or crystalline silica (15 mg/m3, 6 hours/day, 5 days). The respective diets were continued throughout the experiment, and at designated post-exposure time intervals (1, 3, 6, and 9 months) rats were euthanized and tissues collected.

value: Fischer 344

value: lung

value: male

tag: diet

value: high 60% kcal as fat diet

value: silica, 15 mg/m3, 6 hours/day, 5 days

tag: post-exposure timepoint

value: 03 months


title: young  mouse 1 ( 8 weeks) [Sequel II]


title: Control [DK851]

value: Male

value: small extracellular vesicles

value: Benign - Schwannoma


title: F2_D1 individual, grown at 4C [T4_P4.B10_F2_D1]


title: HFDS_SO-03-66_Lu


title: F2_D2 individual, grown at 4C [T4_P4.A9_F2_D2]


title: RDA_SO_09_109_Lu

description:
total RNA including small RNAs
RegularDietAir_09months
SO09Lu_tophat_counts.csv

value: regular 18% kcal as fat diet

value: air

value: 09 months


title: Control [DK850]

value: Benign - meningioma

value: microRNA


title: HFDS_SO-03-63_Lu


title: HNSCC Case [DK263]

tag: ajcc stage

value: II

value: HNSCC


title: RDA_SO_09_111_Lu


title: aged mouse 2 (72 weeks) [Sequel II]

value: Lineage negative, cKit (Cd117) positive (LK) cell fraction

value: female

value: 72 weeks


title: F2_D1 individual, grown at 4C [T4_P4.A8_F2_D1]

value: leaf

value: 7-10 leave rosette


title: F2_D1 individual, grown at 4C [T4_P4.A7_F2_D1]


title: HFDS_SO-03-64_Lu

value: Fischer 344

value: lung

value: male

value: high 60% kcal as fat diet

value: silica, 15 mg/m3, 6 hours/day, 5 days


title: HNSCC Case [DK262]

value: Male

value: I

value: small extracellular vesicles


title: HFDS_SO-03-62_Lu

value: 03 months


title: F2_D1 individual, grown at 4C [T4_P4.A6_F2_D1]


title: HNSCC Case [DK261]

value: microRNA


title: HFDA_SO-03-57_Lu

description:
total RNA including small RNAs
HighFatDietAir_03months
SO03Lu_tophat_counts.csv

value: air


title: F2_D1 individual, grown at 4C [T4_P4.A5_F2_D1]


title: F2_D2 individual, grown at 4C [T4_P4.A4_F2_D2]


title: HNSCC Case [DK259]

value: II

value: HNSCC


title: HFDA_SO-03-52_Lu


title: HFDA_SO-03-51_Lu


title: F2_D2 individual, grown at 4C [T4_P4.A3_F2_D2]


title: HNSCC Case [DK257]


title: F2_D1 individual, grown at 4C [T4_P4.A2_F2_D1]


title: HFDA_SO-03-50_Lu


title: HFDA_SO-03-58_Lu


title: HNSCC Case [DK256]


title: FXS_8

type: RNA

city: Helsinki

first: Maija

last: Castrén

address: P.O.BOX 63

department: Faculty of Medicine/Physiology

country: Finland

institute: University of Helsinki

description:
SST-RMA expression value derived from Transcriptome Analysis Console
HEL69_5_1day

hyb_protocol: Following fragmentation, 5.2 ug of cRNA was hybridized for 16 hr at 45oC on Affymetrix Human Clariom D arrays. The Clariom D arrays were washed and stained in the Affymetrix Fluidics Station 450 (GeneChip Expression Wash, Stain and Scan User Manual for Cartridge Arrays, P/N 702731 Rev. 4, Affymetrix).

scan_protocol: Clariom D arrays were scanned using the Hewlett-Packard GeneChip Scanner 3000 (GCS3000)

data_processing: The CEL files were processed and normalized using Transcriptome Console Software default analysis settings to perform Gene Level Analysis (Gene Level-SST-RMA)

label: biotin

source_name: FXS patient

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip WT Plus reagent Kit, Manual Target Preparation for GeneChip Whole Transcript Expression Arrays, P/N 703174 Rev.5, Affymetrix)

growth_protocol: Human iPS cell clusters were grown as neurospheres in neuronal differentiation medium. After 6 weeks, neurospheres were plated on poly-D-lysin/laminin coated plates and allowed to differentiate for 7 days

extract_protocol: Total RNA was extracted using RNA Purification Kit (Norgen Biotek Corp.) according to the manufacturer’s instructions.

value: iPS cell-derived neural progenitors

tag: disease state

value: fragile X syndrome


title: F2_D1 individual, grown at 4C [T4_P4.A1_F2_D1]

value: leaf


title: RDS_SO-03-47_Lu

description:
total RNA including small RNAs
RegularDietSilica_03months
SO03Lu_tophat_counts.csv

value: regular 18% kcal as fat diet


title: FXS_6

description:
SST-RMA expression value derived from Transcriptome Analysis Console
HEL70_3_7days


title: HNSCC Case [DK255]


title: HNSCC Case [DK253]

value: Female


title: RDS_SO-03-46_Lu

value: Fischer 344

value: lung


title: F2_D2 individual, grown at 4C [T4_P4.A11_F2_D2]

value: 7-10 leave rosette


title: FXS_3

description:
SST-RMA expression value derived from Transcriptome Analysis Console
HEL100_2_7days


title: HNSCC Case [DK252]


title: FXS_4

description:
SST-RMA expression value derived from Transcriptome Analysis Console
HEL70_3_Neuro


title: F2_D2 individual, grown at 4C [T4_P3.H9_F2_D2]


title: HNSCC Case [DK251]


title: RDS_SO-03-44_Lu

value: male

value: silica, 15 mg/m3, 6 hours/day, 5 days


title: F2_D2 individual, grown at 4C [T4_P3.H8_F2_D2]


title: FXS_2

description:
SST-RMA expression value derived from Transcriptome Analysis Console
HEL100_2_1day


title: HNSCC Case [DK250]

value: Male

value: I


title: RDS_SO-03-43_Lu

value: 03 months


title: F2_D2 individual, grown at 4C [T4_P3.H7_F2_D2]


title: FXS_9

description:
SST-RMA expression value derived from Transcriptome Analysis Console
HEL69_5_7days


title: FXS_7

description:
SST-RMA expression value derived from Transcriptome Analysis Console
HEL69_5_Neuro


title: FXS_1

description:
SST-RMA expression value derived from Transcriptome Analysis Console
HEL100_2_Neuro


title: FXS_5

description:
SST-RMA expression value derived from Transcriptome Analysis Console
HEL70_3_1day


title: RDS_SO-03-45_Lu


title: F2_D1 individual, grown at 4C [T4_P3.H6_F2_D1]


title: HNSCC Case [DK249]

value: small extracellular vesicles

value: microRNA


title: CTRL_6

description:
SST-RMA expression value derived from Transcriptome Analysis Console
HEL11_4_7days

source_name: Healthy subject

value: healthy


title: F2_D2 individual, grown at 4C [T4_P3.H5_F2_D2]


title: F2_D2 individual, grown at 4C [T4_P3.H4_F2_D2]


title: RDA_SO-03-41_Lu

description:
total RNA including small RNAs
RegularDietAir_03months
SO03Lu_tophat_counts.csv

value: air


title: CTRL_7

description:
SST-RMA expression value derived from Transcriptome Analysis Console
HEL23_3_Neuro

value: iPS cell-derived neural progenitors


title: HNSCC Case [DK247]

value: II

value: HNSCC


title: RDA_SO-03-42_Lu

value: regular 18% kcal as fat diet


title: HNSCC Case [DK248]


title: CTRL_8

description:
SST-RMA expression value derived from Transcriptome Analysis Console
HEL23_3_1day


title: CTRL_9

description:
SST-RMA expression value derived from Transcriptome Analysis Console
HEL23_3_7days


title: RDA_SO-03-40_Lu


title: F2_D2 individual, grown at 4C [T4_P3.H3_F2_D2]

value: leaf


title: RDA_SO-03-38_Lu

value: Fischer 344


title: beas_before_3

city: Wuhan

first: Xiaoshu

last: Zhou

address: Xinhua Road

country: China

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) 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 (v1.2.12).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
The cells were lysed with TRIzol reagents and the total RNA was extracted. Oligo(dT)-attached magnetic beads were used to purified mRNA.
Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library.

value: lung

tag: cell line

value: Lung epithelial cell line

value: Wild type

value: control


title: F2_D2 individual, grown at 4C [T4_P3.H2_F2_D2]

value: 7-10 leave rosette


title: beas_before_2


title: P_6046 individual, grown at 4C [T4_P4.A10_P_6046]


title: HNSCC Case [DK245]

value: Male

value: I


title: HNSCC Case [DK243]

value: small extracellular vesicles


title: Hypodermal SLAM-ITseq rep3

city: Seville

first: Peter

last: Askjaer

address: UPO Carretera de Utrera km 1

country: Spain

institute: Centro Andaluz de Biología del Desarrollo

data_processing:
Bioinformatics analysis was performed using SLAM-DUNK (http://t-neumann.github.io/slamdunk/) with default parameters.
The tcount output file was then loaded into R and Spearman correlation coefficients between genotypes and replicas were calculated for the cumulative coverage on all Ts in the 3’-UTR (coverageOnTs; an indicator for transcript abundance in the sample).
The DESeq2 package was used to test if coverageOnTs were different between BN1158 (- FLP) and BN1190 (+ FLP) samples. Next, the countdata package was used to perform a beta-binomial test on conversionsOnTs (number of T>C conversions) and coverageOnTs values to calculate p values for conversion rates (conversionsOnTs/coverageOnTs) of individual transcripts comparing BN1158 (- FLP) and BN1190 (+ FLP) samples.
To increase stringency, transcripts with <18 T>C reads (conversionsOnTs) were excluded and for genes represented by several transcripts, only the transcript with the lowest p value was retained. Finally, p values were adjusted for multiple comparison (Benjamini & Hochberg method).
Genome_build: ce10
Supplementary_files_format_and_content: fastq_slamdunk_mapped_filtered_tcount.tsv files from SLAM-DUNK pipeline; contain conversionsOnTs and coverageOnTs values.
Supplementary_files_format_and_content: Epidermis_BN1190_min17TtoC_FDR_10pct.txt containing information on 197 genes significantly labelled in strain BN1190.

organism: Caenorhabditis elegans

source_name: L4 larvae

growth_protocol: Eggs were obtained by sodium hypochlorite treatment and incubated in M9 containing 0.01% Tween-20 (M9-T) overnight at 18°C without food. For each strain and replica, three 60 mm NGM plates with a lawn of OP50 E. coli were seeded each with approximately 350 synchronized L1 larvae and incubated at 20°C for 28 h until reaching L3 stage.

extract_protocol:
Samples were lysed in 5 freeze/thaw cycles (1 min in liquid nitrogen; 3 min in 37°C shaker) and left for 3 min at RT. Then, 100 µl chloroform was added, tubes were shaken vigorously for 15 seconds and left for 3 min at RT. After centrifugation at 12000 g, 4ºC for 15 min, the aqueous phases (~300 µl) were transferred to new tubes containing 0.5 µl 0.1 M DTT and 0.5 µl 20 mg/ml glycogen. RNA was precipitated by adding 250 µl isopropanol and centrifugation at 12000 g, 4ºC for 10 min. Supernatants were removed and pellets were washed in 500 µl EtOH 75%. After centrifugation and removal of the supernatants, the pellets were left to dry for 5 min and resuspended in 20 µl 1 mM DTT. After incubation at 55ºC for 10 min, residual DNA was digested by treatment with DNase I (New England Biolabs) in a total volume of 50 µl at 37ºC for 10 min. DNase I was inactivated by addition of 0.5 µl 0.5 M EDTA. RNA was purified with Monach spin columns (New England Biolabs), eluted in 20 µl 1 mM DTT and evaluated on a Nanodrop. Alkylation of RNA was performed by incubating 1.5 µg RNA with 25 µl DMSO, 5 µl 0.1 M iodoacetamide (Sigma-Aldrich) and 5 µl 0.5 M sodium phosphate (pH 8.0) in a total volume of 50 µl at 50ºC for 15 min. The reaction was stopped by adding 1 µl 1M DTT. RNA was precipitated by adding 0.5 µl 20 mg/ml glycogen, 5 µl 3 M sodium acetate (pH 5.2) and 180 µl 96% ethanol followed by incubation at -20ºC for 20 min and centrifugation at 15000 g, 4ºC for 20 min. The supernatants were removed and the pellets were washed in 180 µl 75% ethanol followed by centrifugation at 15000 g, 4ºC for 5 min. Again, supernatants were removed and pellets were left to dry for 5 min. RNA was resuspended in 15 µl H2O, incubated at 55ºC for 8 min and evaluated on a Nanodrop.
NGS libraries were prepared at EMBL GeneCore using a QuantSeq 3′ mRNA-Seq Library Prep Kit for Illumina (Lexogen).

treatment_protocol: At this point, 4-thiouracil (Sigma-Aldrich) dissolved at 200 mg/ml in DMSO was diluted 1:100 in H2O and 1 ml was added on top of each NGM plate. Plates were left to dry in a laminar flow hood (~1 h) and incubated at 20°C for a total of 17 h. L4 larvae were washed off the plates with M9-T, collected in 15 ml tubes and washed three times in M9-T. Finally, worms were pelleted in 1.5 ml tubes (~1000 L4s per tube). The supernatant was aspired to leave ~50 µl and 500 µl Trizol was added. Tubes were snap frozen in liquid nitrogen and stored at -80°C until used.

value: L4 larvae

tag: flp recombinase

value: Hypodermis (dpy-7p::FLP)


title: CTRL_5

description:
SST-RMA expression value derived from Transcriptome Analysis Console
HEL11_4_1day

value: healthy


title: F2_D2 individual, grown at 4C [T4_P3.H1_F2_D2]


title: HNSCC Case [DK246]

tag: age

value: microRNA


title: Hypodermal SLAM-ITseq rep2


title: Hypodermal SLAM-ITseq rep1


title: HNSCC Case [DK244]

tag: Sex

value: II


title: beas_before_1


title: Control strain rep4


title: CTRL_4

description:
SST-RMA expression value derived from Transcriptome Analysis Console
HEL11_4_Neuro

value: iPS cell-derived neural progenitors


title: F2_D2 individual, grown at 4C [T4_P3.H11_F2_D2]


title: HNSCC Case [DK241]

value: Female

tag: source

value: HNSCC


title: HNSCC Case [DK242]

tag: tissue type


title: beas_after_2

value: 10 Gy X-ray radiation


title: F2_D1 individual, grown at 4C [T4_P3.H10_F2_D1]

value: leaf


title: HNSCC Case [DK240]

tag: molecule type


title: Control strain rep2

tag: tissue


title: CTRL_2

description:
SST-RMA expression value derived from Transcriptome Analysis Console
HEL46_11_1day


title: F2_D2 individual, grown at 4C [T4_P3.G9_F2_D2]

tag: developmental stage


title: HNSCC Case [DK258]


title: beas_after_1

value: lung

tag: cell type

value: Lung epithelial cell line


title: H446_before_3

value: Small cell lung cancer cell line

tag: genotype

value: Wild type

value: control


title: CTRL_1

description:
SST-RMA expression value derived from Transcriptome Analysis Console
HEL46_11_Neuro


title: MCF-7 cells, siZ5, rep2

city: hefei

first: li

last: yong

state: anhui province

address: 安徽省合肥市经开区九龙路111号安大新区

institute: anhui university

data_processing:
Illumina HiSeq 1000 platform used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using HISAT2 software
Exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by Cufflinks
Genome_build: mm9
Supplementary_files_format_and_content: Excel file includes the expression values of transcripts for each Sample

source_name: MCF-7 cells

growth_protocol: MCF-7 cells were grown in DMEM medium supplemented with 10% fetal bovine serum and antibiotics. Cell cultures were maintained at 37℃ with 5% CO2.

extract_protocol:
The total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: MCF-7 breast cancer cell line

value: breast

value: CircFAT1(e2) was knocked down in siZ5 group


title: F2_D1 individual, grown at 4C [T4_P3.G7_F2_D1]

value: 7-10 leave rosette

tag: treatment


title: Control strain rep1

value: L4 larvae

tag: strain


title: H446_before_1


title: CTRL_3

description:
SST-RMA expression value derived from Transcriptome Analysis Console
HEL46_11_7days

value: healthy


title: MCF-7 cells, siZ5, rep3

address: 安徽省合肥市经开区九龙路111号安大新区


title: P_6046 individual, grown at 4C [T4_P3.G6_P_6046]


title: Control strain rep3


title: MCF-7 cells, siZ5, rep1

address: 安徽省合肥市经开区九龙路111号安大新区


title: control rep2

city: Jena

first: Kathrin

last: Fröhlich

state: Thuringia

address: Winzerlaer Straße 2

department: Fakultät für Biowissenschaften, Bacterial RNA Biology

country: Germany

institute: Friedrich-Schiller-Universität Jena

data_processing:
Sequencing of the cDNA libraries was performed by Dr. Andreas Brachmann (LMU, munich, Parniske group)
cDNA reads were imported into CLC Genomics Workbench v11.0 and analysed using mostly standard parameters.
Adaptor- and quality trimming was performed using the trim reads command with the following settings: Sequence = GATCGTCGGACTGTAGAACTCTGAACGTGTAGA, Strand = Minus, Action = Remove adapter, Scores = Mismatch: 2, Gapcost: 3, Cutoff: 10, Cutoff at end: 4
The trimmed reads were checked for quality and mapped to the C.crescentus reference genome: NCBI Acc.number: NC_011916 using the following settings: Mismatch cost =  2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8, Global alignment = Yes, Strand specific = Reverse, Maximum number of hits for a read = 10
Reads mapping in CDS were counted, and genes with a total count cutoff of >10 in all samples were considered for analysis. Read counts were normalized (CPM), and transformed (log2). Differential expression was tested using the built in tool corresponding to edgeR in exact mode with tagwise dispersions. Genes with a fold-change of > 3.0 in either condition and a FDR adjusted p-value < 0.01 were considered to be differentially expressed.
Genome_build: NC_011916
Supplementary_files_format_and_content: Read count table and edgeR (exact mode) analysis

organism: Caulobacter vibrioides

source_name: whole bacterial cells

growth_protocol: C. crescentus NA1000 wild-type and 3xFLAG::hfq strains were cultivated in PYE medium to OD660 of 1.0

extract_protocol:
RNA was isolated by phenol-chloroform extraction using standard protocols. Prepared RNA was digested with DNaseI. Integrity of the prepared RNA was tested using a Bioanalyzer.
cDNA libraries were prepared using the NEBNext Small RNA Library Prep Set for Illumina (NEB E7300), according to the manufacturer's instructions. Quality of the prepared libraries was tested using a Bioanalyzer.

treatment_protocol: Cells equivalent to 50 OD660 units were collected and subjected to RNA co-immunoprecipitation.

value: wild-type

tag: growth phase

value: RNA coIP


title: MCF-7 cells, siNC, rep3

address: 安徽省合肥市经开区九龙路111号安大新区


title: CoIP rep1


title: CoIP rep2


title: control rep1


title: H446_after_3


title: F2_D1 individual, grown at 4C [T4_P3.G5_F2_D1]


title: MCF-7 cells, siNC, rep2

address: 安徽省合肥市经开区九龙路111号安大新区


title: H446_after_2


title: H446_before_2


title: F2_D1 individual, grown at 4C [T4_P3.H12_F2_D1]


title: MCF-7 cells, siNC, rep1

address: 安徽省合肥市经开区九龙路111号安大新区


title: H446_after_1


title: F2_D1 individual, grown at 4C [T4_P3.G3_F2_D1]


title: A549_before_3

value: Lung adenocarcinoma cell line


title: A549_before_2


title: F2_D2 individual, grown at 4C [T4_P3.G2_F2_D2]


title: F2_D2 individual, grown at 4C [T4_P3.G11_F2_D2]


title: A549_before_1


title: F2_D1 individual, grown at 4C [T4_P3.G12_F2_D1]


title: A549_after_2


title: A549_after_3


title: P_6191 individual, grown at 4C [T4_P3.G10_P_6191]


title: F2_D1 individual, grown at 4C [T4_P3.G4_F2_D1]


title: A549_after_1


title: F2_D1 individual, grown at 4C [T4_P3.F9_F2_D1]


title: F2_D2 individual, grown at 4C [T4_P3.G1_F2_D2]


title: F2_D2 individual, grown at 4C [T4_P3.G8_F2_D2]


title: Kidney_APL_rep4

city: Tonomachi, Kawasaki-ku, Kawasaki City, Kanagawa, JAPAN

first: Kohei

last: Matsushita

country: Japan

institute: National Institute of Health Sciences

hyb_protocol: We followed protocol of Gene Expression Hybridazation Kit (Agilent)

scan_protocol: We followed protocol of G2565BA microarray scanner (Agilent)

data_processing: Data acquisition and normalization were used Feature Extraction Software

source_name: 150 mg/kg of APL, 4 weeks

label_protocol: We followed protocol of SureTag DNA labeling Kit

extract_protocol: We followed protocol of RNeasy Mini Kit (Qiagen)

value: 150 mg/kg of APL

tag: treatment-time

value: 4 weeks

value: SD rat

tag: gender

value: male

value: 10 weeks-old

value: kidney


title: F2_D1 individual, grown at 4C [T4_P3.F7_F2_D1]

value: leaf


title: F2_D1 individual, grown at 4C [T4_P3.F6_F2_D1]


title: F2_D2 individual, grown at 4C [T4_P3.F5_F2_D2]


title: Kidney_Control_rep4

source_name: 0.5% methylcellulose, 4 weeks

value: 0.5% methylcellulose


title: Kidney_APL_rep1


title: Kidney_APL_rep2


title: Kidney_Control_rep3


title: Kidney_APL_rep3


title: Kidney_Control_rep2


title: F2_D1 individual, grown at 4C [T4_P3.F8_F2_D1]


title: F2_D2 individual, grown at 4C [T4_P3.F3_F2_D2]


title: F2_D2 individual, grown at 4C [T4_P3.F2_F2_D2]


title: F2_D1 individual, grown at 4C [T4_P3.F12_F2_D1]


title: F2_D1 individual, grown at 4C [T4_P3.F1_F2_D1]


title: F2_D1 individual, grown at 4C [T4_P3.F11_F2_D1]


title: F2_D2 individual, grown at 4C [T4_P3.E9_F2_D2]


title: F2_D2 individual, grown at 4C [T4_P3.F10_F2_D2]


title: Kidney_Control_rep1


title: F2_D1 individual, grown at 4C [T4_P3.E7_F2_D1]


title: F2_D1 individual, grown at 4C [T4_P3.E6_F2_D1]


title: beas_after_3

value: lung

value: Lung epithelial cell line

value: Wild type

value: 10 Gy X-ray radiation


title: F2_D1 individual, grown at 4C [T4_P3.E8_F2_D1]

value: 7-10 leave rosette


title: Liver_FGF21_low_07

city: Giessen

first: Denise

last: Gessner

address: Heinrich-Buff-Ring

department: Animal Physiology and animal nutrition

institute: JLU Giessen

hyb_protocol: 3.8 µg fragmented and labeled ss cDNA were hybridized to Affymetrix Bovine Gene 1.0 arrays for 16 h at 45° C and 60 rpm in a GeneChip hybridization oven 640.

scan_protocol: Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G. Fluidics and scan functions were controlled by the Affymetrix GeneChip Command Console v4.3.3 software.

data_processing: Summarized probe set signals in log2 scale were calculated by using the GCCN-SST-RMA algorithm with the Applied Biosystems GeneChip Expression Console v1.4 Software. After exporting into Microsoft Excel, average signal values, comparison fold changes (FC) and significance P-values were calculated.

label: Biotin

organism: Bos taurus

source_name: Liver FGF21 low group

label_protocol: 200 ng of total RNA was used to generate double-stranded cDNA. 12 µg of subsequently synthesized cRNA were purified and reverse transcribed into single-stranded (ss) cDNA, whereby unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin.

growth_protocol: The experiment with multiparous Holstein cows was carried out at the Educational and Research Centre for Animal Husbandry Hofgut Neumühle (Münchweiler an der Alsenz, Rhineland-Palatinate, Germany). All procedures described in this study were performed according to the German Animal Welfare Act. The animal experiment was approved by the local Animal Care and Use Committee (Provincial Government of Coblenz, Germany, 23 177–07/ G15–20–040725_M).

extract_protocol: Total RNA from frozen liver aliquots (15-20 mg) was isolated using TRIzol reagent (Invitrogen, Karlsruhe, Germany) according to the manufacturer’s protocol. RNA quality was checked with an Agilent 2100 Bioanalyzer using the RNA 6000 Nano Kit (Agilent Technologies Inc., CA, USA). Samples were processed at an Affymetrix Service Provider and Core Facility, “KFB-Center of Excellence for Fluorescent Bioanalytics” (Regensburg, Germany; www.kfb-regensburg.de) as previously described. The RNA integrity number (RIN) value for all liver biopsy samples was 6.02 ± 0.54 (mean ± SD).

treatment_protocol: All animals received the same TMR, which was sufficient to meet requirements of the cows during dry period and lactation, respectively.

tag: breed

value: Holstein

value: female

tag: condition

value: FGF21 low

value: liver


title: Liver_FGF21_low_06


title: Liver_FGF21_low_08


title: F2_D1 individual, grown at 4C [T4_P3.E5_F2_D1]


title: F2_D1 individual, grown at 4C [T4_P3.E4_F2_D1]


title: Liver_FGF21_low_04


title: PER910, Zebularine-treated

type: genomic

city: perth

first: Carlos

middle: A

last: Aya-bonilla

state: WA

address: 32 kinship street

country: Australia

institute: Telethon Kids Institute

hyb_protocol: 750ng of DNA was treated with sodium bisulfite using the Zymo EZ DNA Methylation kit (Irvine). DNA was then hybridized to the Infinium MethylationEPIC BeadChip (Illumina). After washing off unhybridized DNA, a single base extension was recorded to calculate the methylation level at the CpG probe site.

scan_protocol: The BeadChips were scanned using an Illumina iScan

data_processing: Quality control (QC) checks were performed using Bioconductor pachages, lumi and minfi in  R version 3.4.0.1.  No samples were excluded based on mean detection p-values across the probes or due to gender discrepancies.

label: Cy3, Cy5

label_protocol: DNA methylation assays were performed as per standard manufacturer’s instructions by the Australian Genome Research Facility.

growth_protocol: One million cells per millilitre were seeded into each well of a 24-well cell culture plate containing RPMI 1640 supplemented with 20% heat inactivated foetal calf serum (FCS), L-glutamine (2mM final concentration), 2-mercaptoethanol (50uM final concentration), 1% non-essential amino acid mix (100x) and 1% 100mM sodium pyruvate solution. Cell cultures were incubated in a humidified 37 oC atmosphere conatining 5% CO2 in air.

extract_protocol: Genomic DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen) according to manufacturer’s instructions. DNA was quantified using a NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific).

treatment_protocol: For each cell line, demethylating drugs were added at a final concentration of 1.5µM azacitidine, 1.5µM decitabine, 6µM zebularine in comparison to vehicle control and cells were incubated for 72 hours at 37°C.

tag: disease state

value: KMT2A-rearranged infant Acute Lymphoblastic Leukemia (ALL)

value: Male

tag: cell line

value: Zebularine

tag: chromosome abnormality


title: Liver_FGF21_low_05


title: F2_D1 individual, grown at 4C [T4_P3.F4_F2_D1]


title: PER826, Zebularine-treated

tag: Sex

value: Female


title: P_6191 individual, grown at 4C [T4_P3.E3_P_6191]


title: PER785, Zebularine-treated


title: K1_male with konzo [202259340124_R03C01]

city: Washington,DC

first: Nino

last: Gustavo

state: Washington,DC,

address: Sheikh Zayed Campus,111 Michigan Avenue,

department: Center for Precision Medicine and Genomics Research

institute: Childrens National Hospital

hyb_protocol: DNA methylation array (850k/EPIC)

scan_protocol: Raw intensity values (idat files) were generated from each EPIC BeadChip row using the iScan system.

data_processing: Intensity values were converted to beta (β) and m-values using the Bioconductor minfi package. β-values (β=M/(M+U+100), where M is methylated intensity and U is unmethylated intensity for the same position) are used for visualization and m-value (M=log2(M/U)) for statistical analyses. Quality filtration parameters, used to filter out low quality probes were: probes that are represented by less than 3 beads for greater than 5% of the samples (49,632 probes), probes having quality p-value less than 0.05 (15,032 probes), probes having SNP (9,956 probes), and probes mapping to multiple sites in the genome (“cross-reactive probes”; 41,482 probes). Probes filtered for quality p-values and SNP probes were determined by detectionP and dropLociWithSnps functions of the minfi package, cross-reactive probes by dropXreactiveLoci function of the maxprobes package and bead related filtration by beadcount function of the wateRmelon package 9. The probe intensity was normalized by Subset-quantile Within Array Normalization (SWAN). A total of 795,169 quality filtered normalized probes were used for subsequent differential methylation analysis using limma package in R.  Quality visualization was done using champ.QC function of ChAMP package in R, and PCA plots were done using base R package.

label: cy3, cy5

source_name: male with konzo

label_protocol: Illumina Infinium MethylationEPIC Beadchip kit (32 samples, 4 beadchip arrays) was used in accordance with manufacturer's instructions.

extract_protocol: Genomic DNA was isolated from whole blood by the Tshala-Katumbay lab at two sites in DRC  and sent to the Center for Genetic Medicine Research at Children's National Hospital. DNA concentration was determined by the Qubit fluorometer Broad Range dsDNA kit. DNA was bisulfite converted using Zymo Methylation Lightning Kit.

tag: clincal phenotype

value: konzo case

value: M

tag: age

value: whole blood


title: PER490, Zebularine-treated


title: PER785, Decitabine-treated

value: Decitabine


title: Liver_FGF21_low_03

tag: tissue


title: K2_male with konzo [202259340124_R04C01]


title: PER784, Zebularine-treated


title: F1_D2 individual, grown at 4C [T4_P3.E2_F1_D2]

value: leaf

tag: developmental stage


title: F2_D1 individual, grown at 4C [T4_P3.E1_F2_D1]

tag: cell type


title: K4_male with konzo [202259350142_R02C01]


title: Liver_FGF21_low_01


title: PER490, Decitabine-treated


title: P_6046 individual, grown at 4C [T4_P3.E12_P_6046]

tag: genotype


title: F2_D1 individual, grown at 4C [T4_P3.E11_F2_D1]

tag: treatment


title: Liver_FGF21_high_07

source_name: Liver FGF21 high group

value: FGF21 high


title: Liver_FGF21_high_08


title: F2_D2 individual, grown at 4C [T4_P3.E10_F2_D2]


title: K7_male with konzo [202259340124_R01C01]


title: PER910, Decitabine-treated


title: PER490, Azacitidine-treated

value: Azacitidine


title: Liver_FGF21_low_02


title: K8_male with konzo [202259340124_R02C01]


title: PER910, Azacitidine-treated


title: PER785, Azacitidine-treated


title: PER826, Azacitidine-treated


title: PER703, Decitabine-treated


title: Liver_FGF21_high_05


title: Liver_FGF21_high_06


title: K5_male with konzo [202259350142_R03C01]


title: K6_male with konzo [202259350142_R04C01]


title: PER785, Control

value: Control


title: PER784, Decitabine-treated


title: Liver_FGF21_high_04


title: PER910, Control


title: K3_female with konzo [202259350144_R01C01]

source_name: female with konzo

value: F


title: Liver_FGF21_high_03

value: Holstein


title: PER784, Azacitidine-treated


title: PER703, Zebularine-treated


title: F2_D2 individual, grown at 4C [T4_P3.D6_F2_D2]

value: 7-10 leave rosette


title: F2_D2 individual, grown at 4C [T4_P3.D9_F2_D2]


title: K9_female with konzo [202259350144_R04C01]


title: PER490, Control


title: Liver_FGF21_high_02

value: female


title: F2_D1 individual, grown at 4C [T4_P3.D5_F2_D1]


title: K10_female with konzo [202250800011_R01C01]


title: K11_female with konzo [202250800011_R02C01]


title: F2_D1 individual, grown at 4C [T4_P3.D4_F2_D1]


title: F2_D1 individual, grown at 4C [T4_P3.D3_F2_D1]


title: PER826, Control


title: K3_male with konzo [202259350142_R01C01]


title: Liver_FGF21_high_01

value: liver


title: K15_female with konzo [202259350144_R02C01]


title: PER703, Azacitidine-treated

value: KMT2A-rearranged infant Acute Lymphoblastic Leukemia (ALL)


title: F2_D2 individual, grown at 4C [T4_P3.D2_F2_D2]


title: PER826, Decitabine-treated


title: PER703, Control


title: F2_D2 individual, grown at 4C [T4_P3.D1_F2_D2]


title: PER784, Control


title: K13_female with konzo [202250800011_R04C01]


title: SK-MEL-197

city: Badalona

first: IJC

last: Bioinformatics

state: Catalonia

address: Josep Carreras Building, Ctra de Can Ruti, Camí de les Escoles, s/n

institute: Josep Carreras Leukemia Research Institute

description: Melanoma cell line

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Genome Studio V2011.2

label_protocol: Standard Illumina labelling protocol

extract_protocol: DNA was quantified by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel. Bisulfite conversion of 600 ng of each sample was perform according to the manufacturer's recommendation for Illumina Infinium Assay. Effective bisulphite conversion was checked for three controls that were converted simultaneously with the samples. 4 ul of bisulfite converted DNA were used to hybridize on Infinium Human Methylation EPIC BeadChip, following Illumina Infinium HD Methylation protocol. Chip analysis was performed using Illumina HiScan SQ fluorescent scanner.


title: F2_D2 individual, grown at 4C [T4_P3.D7_F2_D2]


title: K16_female with konzo [202259350144_R03C01]


title: F2_D1 individual, grown at 4C [T4_P3.D11_F2_D1]


title: KO/ERRb-wt_12-1, biological rep2

city: Koto-ku

first: Tomoyoshi

last: Nakadai

state: Tokyo

institute: Cancer Institute of JFCR

description: 10_Tomo_MGA 2.0ST_012420170__(MoGene-2_0-st)

hyb_protocol: Hybridization was performed at 45 degrees celcius for 17 hours. The arrays were washed and stained in the GeneChip Fluidic Station 450 (Affymetrix) by using Hybridization, Wash and Stain kit (Affymetrix).

scan_protocol: The arrays were scanned by the GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
The data expressed as CEL files were normalized by the robust multiarray average (RMA) method with the Expression Console software (Affymetrix).
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: KO/ERRb-wt, clone 12-1

label_protocol: cDNA synthesis and labeling was performed by using the GeneChip WT plus reagent kit (Affimetrix) with standard method.

growth_protocol: N2B27 medium supplemented with 2 inhibitor (CH99021 and PD0325901) and LIF

extract_protocol: RNeasy (Qiagen)

treatment_protocol: N2B27 medium supplemented with 2 inhibitor (CH99021 and PD0325901) and doxycycline for 3 days

value: embryonic stem (ES) cells

tag: genotype/variation

value: KO/ERRb-wt

tag: clone id

value: clone 12-1


title: KO/ERRb-wt_12-3 biological rep2

description: 12_Tomo_MGA 2.0ST_01242017_(MoGene-2_0-st)

source_name: KO/ERRb-wt, clone 12-3

value: clone 12-3


title: F2_D2 individual, grown at 4C [T4_P3.D10_F2_D2]


title: KO/ERRb-wt_12-3 biological rep1

description: 11_Tomo_MGA 2.0ST_01242017_(MoGene-2_0-st)


title: KO/ERRb-wt_12-1, biological rep1

description: 9_Tomo_MGA 2.0ST_01242017_(MoGene-2_0-st)


title: KO/mock_8-4, biological rep2

description: 8_Tomo_MGA 2.0ST_01242017_(MoGene-2_0-st)

source_name: KO/mock, clone 8-4

value: KO/mock

value: clone 8-4


title: C2_healthy male control [202259340124_R07C01]

source_name: healthy male control

value: healthy control

value: M

value: whole blood


title: C1_healthy male control [202259340124_R06C01]


title: F2_D2 individual, grown at 4C [T4_P3.C9_F2_D2]

source_name: leaf

value: leaf


title: C3_healthy male control [202259340124_R08C01]


title: C8_healthy male control [202259340124_R05C01]


title: KO/mock_8-3, biological rep2

description: 6_Tomo_MGA 2.0ST_01242017_(MoGene-2_0-st)

source_name: KO/mock, clone 8-3

value: clone 8-3


title: F2_D1 individual, grown at 4C [T4_P3.C7_F2_D1]


title: C6_healthy male control [202259350142_R07C01]


title: F2_D2 individual, grown at 4C [T4_P3.D12_F2_D2]


title: KO/mock_8-4, biological rep1

description: 7_Tomo_MGA 2.0ST_01242017_(MoGene-2_0-st)


title: F2_D2 individual, grown at 4C [T4_P3.C6_F2_D2]


title: KO/mock_8-3, biological rep1

description: 5_Tomo_MGA 2.0ST_01242017_(MoGene-2_0-st)


title: F2_D2 individual, grown at 4C [T4_P3.C4_F2_D2]


title: C5_healthy male control [202259350142_R06C01]


title: F2_D1 individual, grown at 4C [T4_P3.C5_F2_D1]


title: WT/mock_5-5, biological rep2

description: 4_Tomo_MGA 2.0ST_01242017__(MoGene-2_0-st)

source_name: WT/mock, clone 5-5

value: WT/mock

value: clone 5-5


title: C13_healthy female control [202259350144_R05C01]

source_name: healthy female control

value: F


title: CD21-Cre AtrC/KD_1459

city: New York

first: Shan

last: Zha

state: NY

address: 1130 Saint Nicholas Ave.

institute: Columbia University

data_processing:
library strategy: high-throughput genome translocation sequencing (HTGTS)
Basecalls performed using Illumina RTA version 1.18.54
Miseq reads was first de-multiplexed by fastq-multx tool from ea-util, then adaptor sequence was further trimmed with SeqPrep utility.
Pre-processed reads were then mapped to customized mm9 genome using Bowtie2. The best-path searching algorithm (related to YAHA; ref. 50) was used to identify optimal sequence alignments from Bowtie2-reported top alignments (alignment score > 50).
The reads are then filtered to exclude mispriming events, germ-line (unmodified) sequence, sequential joints, and duplicated reads. A “duplicate read” is defined by bait and prey alignment coordinates within 2 nt of another read’s bait and prey alignments. To plot all of the S-region junctions, including those in the repeats but unequivocally mapped to an individual switch region, we combined the ones filtered by a mappability filter but unequivocally mapped to S regions with “good” reads passing both the mappability (both deduplicated) filters (please see ref. 28 for simulation and details on plotting). MHs are defined as regions of 100% homology between the bait and prey-break site. Insertions are defined as regions containing nucleotides that map to neither the bait and prey-break site. Blunt junctions are considered to have no MHs or insertions.
Assembly: mm9
Supplementary files format and content: .xlsx files generated from tab-delimited text files after analysis for reads distribution

source_name: B cells

growth_protocol: Purified splenic B (CD43-) cells from mice were cultured in RPMI mediume with cytokines (anti-CD40 (1 ng/mL; BD Pharmingen) and IL-4 (20 ng/mL; R&D)).

extract_protocol:
Genomic DNA was extracted from day 4 cultured B cells.
Libraries were prepared according to protocol in (Hu J, et al. Nat Protoc 11:853–871.(2016)) Linear amplifications were performed using Sμ-specific biotin primer  5′/5BiosG/CAGACCTGGGAATGTATGGT3′) and followed by nesting PCR with (5′CACACAAAGACTCTGGACCTC3′)  AflII is used to remove germ-line sequence.
high-throughput genome translocation sequencing (HTGTS). Sequenced with MiSeq 500v

treatment_protocol: Cells were cultured for 4 days and analyzed via flow cytometry before DNA extraction.

value: anti-CD40 and Il4 activated B cells

value: CD21-Cre AtrC/KD

tag: strain


title: CD21-Cre AtrC/-_1878

value: CD21-Cre AtrC/-


title: C4_healthy male control [202259350142_R05C01]


title: F2_D2 individual, grown at 4C [T4_P3.C3_F2_D2]

value: 7-10 leave rosette


title: WT/mock_5-2, biological rep2

description: 2_Tomo_MGA 2.0ST_01242017_(MoGene-2_0-st)

source_name: WT/mock, clone 5-2

value: embryonic stem (ES) cells

value: clone 5-2


title: C7_healthy male control [202259350142_R08C01]


title: F2_D1 individual, grown at 4C [T4_P3.C8_F2_D1]


title: C14_healthy female control [202259350144_R06C01]


title: C15_healthy female control [202259350144_R07C01]


title: CD21-Cre AtrC/-_1703


title: WT/mock_5-5, biological rep1

description: 3_Tomo_MGA 2.0ST_01242017_(MoGene-2_0-st)


title: WT/mock_5-2, biological rep1

description: 1_Tomo_MGA 2.0ST_01242017_(MoGene-2_0-st)


title: F2_D2 individual, grown at 4C [T4_P3.C2_F2_D2]


title: F2_D2 individual, grown at 4C [T4_P3.C12_F2_D2]


title: C16_healthy female control [202259350144_R08C01]


title: F2_D1 individual, grown at 4C [T4_P3.C1_F2_D1]


title: CD21-Cre AtrC/KD_1460


title: C9_healthy female control [202250800011_R05C01]


title: F2_D1 individual, grown at 4C [T4_P3.C11_F2_D1]


title: C10_healthy female control [202250800011_R06C01]


title: F2_D2 individual, grown at 4C [T4_P3.B9_F2_D2]


title: C12_healthy female control [202250800011_R08C01]


title: F2_D1 individual, grown at 4C [T4_P3.B8_F2_D1]


title: F2_D1 individual, grown at 4C [T4_P3.B7_F2_D1]


title: F1_D1 individual, grown at 4C [T4_P3.B6_F1_D1]


title: F2_D2 individual, grown at 4C [T4_P3.B5_F2_D2]


title: WGBS h1 double rep1

city: Taipei

first: Paoyang

last: Chen

state: Taiwan

address: 128 Sec. 2, Academia Rd, Nankang, Taipei 11529 Taiwan, R.O.C.

country: Taiwan

institute: Academia Sinica

data_processing:
Bisulfite-seq reads were aligned using BS Seeker2
Generate a CG methylation level track from methylation level files (CGmap)
Genome_build: TAIR10
Supplementary_files_format_and_content: CGmap files

source_name: WGBS h1 double

extract_protocol:
DNA was isolated using Qiagen kit
Genomic DNA was randomly fragmented to 100 ~ 700 bp by sonication. Then library preparation included end-repair, A-tailing, methylated adaptor ligation and bisulfite conversion. Finally, the library was amplified to enrichment ideal libary for sequencing.

value: Seedlings

value: h1 double mutant


title: WGBS nrpd2a rep1

source_name: WGBS nrpd2a

value: nrpd2a mutant


title: WGBS h2aw/h1 quadruple rep2

source_name: WGBS h2aw/h1 quadruple

value: h2aw/h1 quadruple mutant


title: WGBS h2aw/h1 quadruple rep1


title: WGBS h2aw_drm2-2 rep2

source_name: WGBS h2aw_drm2-2

value: h2aw_drm2-2 mutant


title: F2_D1 individual, grown at 4C [T4_P3.B4_F2_D1]


title: WGBS nrpd2a rep2


title: WGBS h2aw_drm2-2 rep1


title: F2_D2 individual, grown at 4C [T4_P3.D8_F2_D2]


title: WGBS h2aw/nrpd2a rep2

source_name: WGBS h2aw/nrpd2a

value: h2aw/nrpd2a mutant


title: F2_D1 individual, grown at 4C [T4_P3.B3_F2_D1]

value: leaf


title: F2_D2 individual, grown at 4C [T4_P3.B2_F2_D2]


title: WGBS h2aw/nrpd2a rep1


title: F2_D2 individual, grown at 4C [T4_P3.C10_F2_D2]


title: C11_healthy female control [202250800011_R07C01]

value: healthy control

value: whole blood


title: WGBS drm2-2 rep2

source_name: WGBS drm2-2

value: drm2-2 mutant


title: WGBS h1 double Rep2


title: F2_D1 individual, grown at 4C [T4_P3.B1_F2_D1]


title: F2_D2 individual, grown at 4C [T4_P3.B12_F2_D2]


title: F2_D1 individual, grown at 4C [T4_P3.B10_F2_D1]


title: WGBS h2aw/cmt2-3 rep2

source_name: WGBS h2aw/cmt2-3

value: h2aw/cmt2-3 mutant


title: F1_D2 individual, grown at 4C [T4_P3.B11_F1_D2]


title: WGBS cmt2-3 rep2

source_name: WGBS cmt2-3

value: cmt2-3 mutant


title: F2_D1 individual, grown at 4C [T4_P3.A9_F2_D1]


title: WGBS cmt2-3 rep1


title: F2_D1 individual, grown at 4C [T4_P3.A7_F2_D1]


title: F2_D2 individual, grown at 4C [T4_P3.A8_F2_D2]


title: WGBS h2aw/kyp6 rep2

source_name: WGBS h2aw/kyp6

value: h2aw/kyp6 mutant


title: WGBS h2aw/kyp6 rep1


title: WGBS drm2-2 rep1


title: F2_D2 individual, grown at 4C [T4_P3.A6_F2_D2]


title: WGBS h2aw/cmt2-3 rep1


title: WGBS kyp6 rep2

source_name: WGBS kyp6

value: kyp6 mutant


title: WGBS kyp6 rep1


title: F2_D1 individual, grown at 4C [T4_P3.A4_F2_D1]

value: 7-10 leave rosette


title: WGBS h2aw rep2

source_name: WGBS h2aw

value: h2aw mutant


title: F2_D2 individual, grown at 4C [T4_P3.A3_F2_D2]

source_name: leaf


title: WGBS h2aw rep1


title: F2_D2 individual, grown at 4C [T4_P3.A5_F2_D2]


title: F2_D1 individual, grown at 4C [T4_P3.A2_F2_D1]


title: WGBS col-wt rep2

source_name: WGBS col-wt

value: wild type


title: F2_D1 individual, grown at 4C [T4_P3.A1_F2_D1]


title: WGBS col-wt rep1

value: Seedlings


title: F2_D2 individual, grown at 4C [T4_P3.A12_F2_D2]


title: F2_D2 individual, grown at 4C [T4_P3.A11_F2_D2]


title: RNA h2aw/cmt2-3 rep2

data_processing:
RNA-seq alignment using Tophat 2.1.0 with default parameters
Calculate RPKM of genes by using cuffdiff (cufflinks-2.2.1) with default parameters
Genome_build: TAIR10
Supplementary_files_format_and_content: RPKM values for WT and mutant samples

source_name: RNA h2aw/cmt2-3

growth_protocol: Long day conditions

extract_protocol:
RNA was isolated using Qiagen kit
RNA-seq libraries are made after Ribo-Zero depletion of rRNA


title: RNA h2aw/cmt2-3 rep1


title: F2_D1 individual, grown at 4C [T4_P3.A10_F2_D1]

data_processing:
Raw sequencing reads were trimmed using cutadapt
Trimmed reads were mapped to reference TAIR10 genome using Bismark
Assembly: TAIR10
Supplementary files format and content: Files are in bedgraph format with "chromosome position strand context mc_score total_reads methylated"

extract_protocol:
DNA was extracted from leaf tissue and performed bisulfite treatment
Libraries were constructed and sequenced through Illumina HiSeq


title: K12_female with konzo [202250800011_R03C01]

source_name: female with konzo

value: konzo case

value: F


title: wildtype_1772

source_name: B cells

value: anti-CD40 and Il4 activated B cells


title: P_6046 individual, grown at 4C [T4_P2.H9_P_6046]


title: RNA cmt2-3 rep1

source_name: RNA cmt2-3


title: F2_D2 individual, grown at 4C [T4_P2.H7_F2_D2]


title: RNA h2aw_drm2-2-55105_6 rep2


title: RNA h2aw_drm2-2-55105_6 rep1


title: RNA cmt2-3 rep2


title: F2_D1 individual, grown at 4C [T4_P2.H6_F2_D1]


title: F2_D1 individual, grown at 4C [T4_P2.H8_F2_D1]


title: RNA drm2-2-55103_4 rep2


title: F2_D2 individual, grown at 4C [T4_P2.H5_F2_D2]


title: GAS_141

city: Aurora

first: Ivana

last: Yang

state: CO

address: 1635 Aurora Ct

institute: University of Colorado

hyb_protocol: Illumina protcol

scan_protocol: Illumina protcol

data_processing:
R package minfi was used to transform the raw data
normalized and generate M value
hg19

source_name: PBMC

label_protocol: Illumina protcol

extract_protocol:
High-quality DNA from PBMCs was extracted
prepared using standard protocols (Bisulfite conversion Qiagen, hybridization, and Infinium Methylation Assay Illumina)

tag: alive


title: GAS_149


title: RNA drm2-2-55103_4 rep1


title: F2_D2 individual, grown at 4C [T4_P2.H4_F2_D2]

city: Vienna

first: Rahul

last: Pisupati

institute: Gregor Mendel Institute


title: GAS_137


title: GAS_103


title: RNA col-wt-55101_2 rep2


title: F2_D2 individual, grown at 4C [T4_P2.H3_F2_D2]


title: GAS_139


title: GAS_140


title: RNA col-wt-55101_2 rep1


title: GAS_132


title: RNA h2aw/nrpd2a rep2

source_name: RNA h2aw/nrpd2a


title: GAS_126


title: GAS_118


title: CIICUG_464


title: F1_D1 individual, grown at 4C [T4_P2.H1_F1_D1]


title: RNA h2aw/nrpd2a rep1


title: F2_D1 individual, grown at 4C [T4_P2.H12_F2_D1]


title: RNA nrpd2a rep2

source_name: RNA nrpd2a

value: nrpd2a mutant


title: CIICUG_239


title: GAS_104


title: CIICUG_375


title: GAS_116


title: RNA h2aw/kyp6 rep2

source_name: RNA h2aw/kyp6


title: CIICUG_369


title: CIICUG_449


title: RNA nrpd2a rep1


title: F2_D2 individual, grown at 4C [T4_P2.H10_F2_D2]


title: F2_D2 individual, grown at 4C [T4_P2.G9_F2_D2]


title: CIICUG_257


title: CIICUG_272


title: GAS_123


title: RNA h2aw/kyp6 rep1


title: F2_D1 individual, grown at 4C [T4_P2.G8_F2_D1]


title: CIICUG_331


title: F2_D1 individual, grown at 4C [T4_P2.G7_F2_D1]


title: GAS_143


title: F2_D2 individual, grown at 4C [T4_P2.H11_F2_D2]


title: RNA kyp6 rep2

source_name: RNA kyp6


title: F2_D2 individual, grown at 4C [T4_P2.H2_F2_D2]


title: RNA kyp6 rep1


title: RNA h2aw/h1 quadruple rep2

source_name: RNA h2aw/h1 quadruple

value: h2aw/h1 quadruple mutant


title: F2_D1 individual, grown at 4C [T4_P2.G5_F2_D1]

value: leaf


title: RNA h2aw/h1 quadruple rep1


title: F2_D1 individual, grown at 4C [T4_P2.G4_F2_D1]


title: RNA h1 double Rep2

source_name: RNA h1 double

value: h1 double mutant


title: F2_D2 individual, grown at 4C [T4_P2.G3_F2_D2]


title: CIICUG_414


title: F2_D2 individual, grown at 4C [T4_P2.G2_F2_D2]


title: GAS_136


title: F2_D1 individual, grown at 4C [T4_P2.G6_F2_D1]


title: RNA h1 double rep1


title: CIICUG_458


title: F2_D2 individual, grown at 4C [T4_P2.G1_F2_D2]


title: RNA h2aw rep1

source_name: RNA h2aw


title: GAS_114


title: P_6046 individual, grown at 4C [T4_P2.G11_P_6046]


title: GAS_131


title: anti-PD-1 rep3

city: Washington

first: Lu

last: Jin

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University

data_processing:
Raw data quality was checked using FastQC (v0.11.9), and adapter trimming on raw data was performed using Cutadapt (v3.5)
The reference genome was downloaded from Ensembl mm10 release 99, and the reference genome index was built using Bowtie2 (v2.4.1) software.
Paired-end trimmed reads alignment and raw read count calculation were performed using RSEM software (v1.3.1).  Statistical analysis was performed using the DESeq2 package (v1.36.0) in R (v4.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: tumor

growth_protocol: MMTV-NeuT mice were obtained from Jackson Labs (FVB-Tg(MMTV-Erbb2)NK1Mul/J) and FAT-ATTAC mice on a C57BL/6 background were kindly provided by Dr. Philipp Scherer, University of Texas Southwestern, which were crossed into the FVB strain and crossed with MMTV-NeuT mice to produce NeuT/ATTAC mice

extract_protocol:
Total RNA was extracted using Qiagen's miRNeasy extraction kit according to manufacturer's instructions.
RNA libraries were prepared for sequencing using standard illumina protocols.

treatment_protocol: Fibrosis was induced in mice at 6 weeks of age by biweekly i.p. injection of 0.4 mg/kg AP20187 dissolved in vehicle (4% ethanol, 10% PEG-400, and 1.75% Tween-20 in water). Animals at 8 weeks of age were injected i.p. twice weekly with 100 μg of the anti-PD-1 or a matching isotype-specific IgG mAb.  This dose achieved a plasma level of 36 µg/ml, suggesting even distribution in total blood volume.

value: NeuT/ATTAC

value: conditional model of mammary fibrosis

value: tumor


title: GAS_121


title: F2_D1 individual, grown at 4C [T4_P2.F9_F2_D1]


title: F2_D1 individual, grown at 4C [T4_P2.G10_F2_D1]


title: RNA h2aw rep2


title: GAS_125


title: F2_D1 individual, grown at 4C [T4_P2.F8_F2_D1]


title: anti-PD-1 rep2


title: CIICUG_225


title: RNA col-wt rep2

source_name: RNA col-wt


title: F2_D2 individual, grown at 4C [T4_P2.F7_F2_D2]


title: anti-PD-1 rep1


title: GAS_107


title: F2_D1 individual, grown at 4C [T4_P2.F6_F2_D1]


title: IgG rep3

value: IgG


title: F2_D1 individual, grown at 4C [T4_P2.G12_F2_D1]


title: CIICUG_602


title: ΔH, H2/CO2, biol rep 1

city: Tübingen

first: Bastian

last: Molitor

state: Baden Württemberg

address: Schnarrenbergstr. 94-96

department: Center for Applied Geosciences

institute: University of Tübingen

data_processing:
Sequencing reads were quality filtered and trimmed with BBMap version 38.93 and FastX Toolkit version 0.0.14 with specific parameters for paired-end reads.
Reads from each bioreactor culture were mapped to the reference genomes of M. thermautotrophicus ΔH (CP064324), M. thermautotrophicus Z-245 (CP064336 and CP064337) and M. marburgensis Marburg (CP069376 and CP069377) using BWA-MEM version 0.7.17.
Mapped reads were assigned to genomic features using the FeatureCounts program from the Subread package version 2.0.1. Additionally, an alignment-free quantification of gene features was performed using Salmon version 1.5.2.
Pairwise differential expression analysis was performed on the Salmon counts using DESeq2 version 1.32.0 with the homologous genes present in the pan-genome database (see manuscript) and ConsensusDE version 1.10.0.
The adjusted P-value cut-off threshold was set to 0.05
Assembly: Reference genomes of M. thermautotrophicus ΔH (CP064324), M. thermautotrophicus Z-245 (CP064336 and CP064337) and M. marburgensis Marburg (CP069376 and CP069377)
Supplementary files format and content: quant.sf = Salmon's quantification file, plain-text, tab-separated file, with the headers: Name, Length, EffectiveLength, TPM, NumReads

organism: Methanothermobacter thermautotrophicus

source_name: prokaryotic

growth_protocol: Briefly: The three microbes were culivated continuously in bioreactors with minimal salts media and fed and 80/20 v/v % gas mixture of H2/CO2. Details on cultivation can be found in manuscript.

extract_protocol:
A hot phenol method was used for RNA extraction. The samples were thawed on ice and centrifuged at 4°C and 4100 × g for 10 min, the supernatant discarded, and the samples resuspended in 800 µL of RNase free water.
The 800 µL were mixed with 950 µL of saturated phenol (Sigma-Aldrich, Merck, Germany) and 115 μL of a lysis solution in Lysing Matrix B (MP Biomedicals Germany GmbH, Eschwege, Germany). The lysis solution contained sodium acetate (20 mM pH 5.2), sodium dodecyl sulfate (SDS; 0.5 % v/v), ethylenediaminetetraacetic acid (EDTA; 1 mM), and DNase/RNase-free distilled water (DI; Invitrogen, Thermo Fischer Scientific, Germany).
The cells were homogenized for one cycle (5 x 40 s at 6 m/s and 20 s off) in a FastPrep-24TM 5G bead-beater (MP Biomedicals Germany GmbH, Eschwege, Germany) and then centrifuged at room temperature and 21130 × g for 10 min (5424 Eppendorf, Hamburg, Germany). The top layer was placed into 600 µL of phenol-chloroform-isoamyl alcohol (ROTI® Aqua-P/C/I, Carl Roth, Karlsruhe, Germany) and centrifuged as in the previous step. This step was repeated twice.
The top layer was added to 1.2 mL of ethanol (undenatured absolute, SERVA Electrophoresis GmbH, Heidelberg, Germany) and left overnight at -80 °C to precipitate the RNA. The following day, the tubes were centrifuged at 4°C and 21130 × g for 10 min, and then the supernatant was removed. The RNA pellet was washed with 1 mL of 75% v/v ethanol solution and centrifuged as in the previous step. The supernatant was pipetted off, and the pellet was resuspended with 53 µL of DNase/RNase-free distilled water.
The RNA was cleaned (which included DNA depletion) and concentrated using the RNA Clean & Concentrator kit (Zymo Research, Irvine, CA, United States), according to the manufacturer’s instructions. The cleaning and concentrating protocols were repeated four times.
RNA libraries for RNA-seq were prepared using 100 ng of RNA and the TruSeq™ Stranded Total RNA Kit with Ribo-Zero™ Plus following manufacturer's protocols.

treatment_protocol: After 7 days of which 2.7 days were at steady state, four-times 9 ml of bioreactor sample was placed in 5 mL of prechilled RNAlater (overnight at 4°C). The samples were stored overnight at 4°C and then frozen at -20°C until RNA isolation.

value: prokaryotic

value: [delta]H

value: WT

value: exponential growth (continous bioreactors) day 7

tag: reactor id


title: IgG rep2


title: F2_D1 individual, grown at 4C [T4_P2.F5_F2_D1]

source_name: leaf

value: 7-10 leave rosette


title: F2_D2 individual, grown at 4C [T4_P2.F4_F2_D2]


title: GAS_105


title: Z-245, H2/CO2, biol rep 4


title: RNA col-wt rep1

value: Seedlings

value: wild type


title: GAS_120


title: F2_D2 individual, grown at 4C [T4_P2.F3_F2_D2]


title: Z-245, H2/CO2, biol rep 3


title: Aortas, ang II treated mice 6 months, rep3

city: Nashville

first: Wei

state: TN

address: 2213 Garland Ave

department: Medicine

institute: VUMC

data_processing:
Quality control (QC) was performed on all sequencing reads using FastQC and reads were trimmed by cutadapt.
Reads were then be aligned to mouse genome (mm10) using STAR and quantified by featureCounts.
Differential expression detection was performed by R package DESeq2.
Assembly: mm10
Supplementary files format and content: txt, gene expression count table

source_name: Aortic homogenates

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: ang II or vehicle was infused subcuteneously for 2 weeks by osmotic minipump. Samples were harvested 2, 4 and 6 months later.

value: Aortic homogenates

value: Ang II infusion

tag: time

value: 6 months


title: Aortas, ang II treated mice 6 months, rep4


title: F2_D1 individual, grown at 4C [T4_P2.F1_F2_D1]

address: Dr. Bohrgasse 3


title: Z-245, H2/CO2, biol rep 1


title: Aortas, ang II treated mice 6 months, rep1


title: CIICUG_447


title: F2_D1 individual, grown at 4C [T4_P2.F12_F2_D1]


title: IgG rep1

tag: disease state


title: CIICUG_386


title: F2_D2 individual, grown at 4C [T4_P2.F2_F2_D2]


title: Aortas, sham treated mice 6 months, rep4

value: Sham infusion


title: F2_D1 individual, grown at 4C [T4_P2.F11_F2_D1]

value: leaf


title: CIICUG_110


title: ameloblastoma5

city: Bangkok

first: Nakarin

last: Kitkumthorn

address: Yothi

country: Thailand

institute: Mahidol University

description: Tumor

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

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

data_processing: RnBeads version 2.0.0

source_name: ameloblastoma

label_protocol: Standard Illumina Protocol

extract_protocol: Phenol-chloroform

value: Tumor

value: ameloblastoma

tag: gender

value: Female


title: Dental follicle1

description: Normal

source_name: Dental follicle

value: Normal

value: Dental follicle


title: ΔH, H2/CO2, biol rep 3

value: prokaryotic


title: Aortas, sham treated mice 6 months, rep3


title: Aortas, sham treated mice 6 months, rep2


title: F2_D2 individual, grown at 4C [T4_P2.E9_F2_D2]


title: CIICUG_258


title: CIICUG_266


title: F2_D2 individual, grown at 4C [T4_P2.E8_F2_D2]


title: shPRMT1+SMARCA4-WT

city: Nanjing

first: Xiangwei

last: Zeng

state: Jiangsu

address: Xianlin avenue

institute: Nanjing university

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Sequencing reads were aligned to the mm10 reference genome with Bowtie2
CUT&Tag libraries were sequenced with the Illumina Nova6000 sequencer.
MACS2 (version 2.2.7.1) was used to call peaks
Peak annotation was performed by R package ChIPseeker
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: colon

growth_protocol: McCoy's 5 A,10% fetal bovine serum. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Approximately 10,000 cell nuclei were prepared and treated with concanavalin A-coated magnetic beads.
After combining the primary and secondary antibodies, the pA-Tn5 transposome was used to bind and label DNA. Then, the library was established by purifying and amplifying DNA.

value: colon

tag: cell line

value: Human eukaryotic cells

tag: chip antibody


title: Aortas, sham treated mice 6 months, rep1

value: WT


title: F2_D2 individual, grown at 4C [T4_P2.F10_F2_D2]

value: 7-10 leave rosette


title: shPRMT1+SMARCA4-R1157W

value: SMARCA4-R1157W mutant


title: F2_D1 individual, grown at 4C [T4_P2.E7_F2_D1]


title: Aortas, ang II treated mice 6 months, rep2


title: Z-245, H2/CO2, biol rep 2

value: exponential growth (continous bioreactors) day 7


title: CIICUG_139


title: Aortas, ang II treated mice 4 months, rep4

value: Aortic homogenates

value: 4 months


title: ameloblastoma2

description: Tumor


title: CIICUG_430


title: CIICUG_138


title: Aortas, ang II treated mice 4 months, rep3

value: Ang II infusion


title: Aortas, ang II treated mice 4 months, rep1


title: CIICUG_374


title: ameloblastoma4

description: Tumor


title: Aortas, ang II treated mice 4 months, rep2


title: F2_D2 individual, grown at 4C [T4_P2.E4_F2_D2]


title: ameloblastoma1

description: Tumor

value: Male


title: Dental follicle2

description: Normal


title: Aortas, sham treated mice 4 months, rep4

value: Sham infusion


title: Aortas, sham treated mice 4 months, rep3


title: F2_D1 individual, grown at 4C [T4_P2.E3_F2_D1]

value: leaf


title: ameloblastoma3

description: Tumor

value: Tumor

value: ameloblastoma


title: Aortas, sham treated mice 4 months, rep2


title: Dental follicle3

description: Normal

value: Normal


title: Physiological Flow Biol Rep 3

city: Los Angeles

first: Megan

middle: L

last: McCain

state: CA

address: 1024 Downey Way

institute: USC

description: p5.CCTAGTGGAC-TGGCTCATGT.HHYHLDSX2_CCTAGTGGAC-TGGCTCATGT

data_processing:
Partek Flow Genomic Analysis software
Sequence reads were trimmed for Phred quality score of 20 and minimum read length of 25
Trimmed sequence reads were mapped to hg38 using STAR (2.7.8a) and quantified using Gencode 38 (V2) annotation in Partek Flow Genomic Analysis Software.
Read counts per gene were normalized to fragments per kilobase of transcript per million mapped reads (FPKM)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Proximal Tubule

growth_protocol: RPTEC/TERT1 (CRL-4031, ATCC) cells were cultured in DMEM:F12 medium supplemented with the hTERT Immortalized RPTEC Growth Kit (ATCC) and 1% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were lysed with 1% beta mercaptoethanol in Buffer RLT lysis buffer (Qiagen) and RNA was isolated using the Rneasy Micro kit (Qiagen). RNA with RINe above 8.0 were submitted for sequencing at the Genome Technology Access Center at Washington University in St. Louis.
Paired-end libraries were prepared using Clontech SMARTer Illumina Kit and sequenced on a NovoSeq 6000 (Illumina).

treatment_protocol: Cells were seeded onto ibidi channel slides (ibiTreat, µ-Slide I Luer, 0.4 mm height) at a density of 200,000 cells/cm2, incubated for 5.5 hours until adherent, inserted into the flow system and exposed to 1 mL/day until confluent. Then, confluent slides were exposed to physiological (300 uL/min) or nutritive (1 mL/day) flow rates for 3 days

value: Proximal Tubule

value: RPTEC/TERT1 (CRL-4031)

value: Epithelial Cell

value: Physiological Flow


title: Nutritive Flow Biol Rep 1

description: s1.AATACACGGA-TAGGTGATCT.HNJJ3DSXY_AATACACGGA-TAGGTGATCT

value: Nutritive Flow


title: Nutritive Flow Biol Rep 2

description: s2.TCCGTTCCAC-ATGAGCTACA.HNJJ3DSXY_TCCGTTCCAC-ATGAGCTACA


title: Physiological Flow Biol Rep 4

description: p6.CACTATTCCA-TATAGGCCGA.HHYHLDSX2_CACTATTCCA-TATAGGCCGA


title: Nutritive Flow Biol Rep 3

description: s5.TCGTTAGATC-ACCAATTCGG.HHYHLDSX2_TCGTTAGATC-ACCAATTCGG


title: Physiological Flow Biol Rep 1

description: p1.CCATCAAGGA-CTGCCTCATC.HNJJ3DSXY_CCATCAAGGA-CTGCCTCATC


title: F2_D2 individual, grown at 4C [T4_P2.E1_F2_D2]

value: 7-10 leave rosette


title: F2_D2 individual, grown at 4C [T4_P2.E12_F2_D2]


title: Aortas, sham treated mice 4 months, rep1

value: WT


title: Aortas, ang II treated mice 2 months, rep4

value: 2 months


title: F2_D1 individual, grown at 4C [T4_P2.E11_F2_D1]


title: Aortas, ang II treated mice 2 months, rep2

value: Aortic homogenates


title: Aortas, ang II treated mice 2 months, rep3


title: F2_D2 individual, grown at 4C [T4_P2.E2_F2_D2]


title: F2_D1 individual, grown at 4C [T4_P2.E10_F2_D1]


title: nephrectomy 5 ATAC

city: Saint Louis

first: Nicolas

last: Ledru

state: MO

address: 660. S Euclid Ave., CB 8118

institute: Washington University in St. Louis

description:
Sample name: A3A
snATAC library portion of multiomic joint snRNA-seq and snATAC-seq dataset using 10X Chromium
A3_filtered_feature_bc_matrix.h5 (gene-by-cell and peak-by-cell count)

library_source: genomic single cell

data_processing:
Fastq files were processed with 10X Genomics' Cell Ranger software. For snRNA-seq libraries, Cell Ranger 6.0 was used. For snATAC-seq libraries, Cell Ranger ATAC 2.0 was used. For multiome libraries, Cell Ranger ARC 2.0 was used. Cell Ranger's aggr function was used for samples for which multiple lanes/libraries were prepared and sequenced.
We performed ambient RNA removal with CellBender for snRNA-seq and multiome libraries. The resulting hdf5 files are the "cellbender_filtered" files in this submission.
Assembly: hg38
Supplementary files format and content: Processed data files include fragment files for ATAC and multiome libraries. These files list unique ATAC-seq fragments sequenced in BED format with additional columns containing barcode and total number of read pairs associated with each fragment. Cell Ranger output matrices are in hdf5 format. They contain gene-by-cell and peak-by-cell count matrices. For samples B3-B5, "filtered_feature" files are snRNA-seq libraries and "filtered_peak" files are snATAC-seq libraries. For multiome libraries, the "filtered_feature" files contain both gene-by-cell and peak-by-cell count matrices. CellBender outputs are also included as "cellbender_matrix" hdf5 files, and contain gene-by-cell count matrices post-ambient RNA removal.

source_name: Adult human kidney

extract_protocol:
[Single nucleus isolation for multiomic libraries]  For single nucleus multiomic libraries, samples were cut into <2 mm pieces and homogenized using Dounce loose head homogenizers. Samples were then filtered through a 200µm cell strainer and homogenized in the Dounce tight head homogenizers. Samples were incubated on ice for 5 minutes, then filtered through a 40µm cell strainer, centrifuged at 500g for 5 minutes at 4°C. The resuspended pellet was then washed with 4ml of lysis buffer and incubated for 5 minutes at 4°C. Then the sample was centrifuged again and resuspended, then filtered through a 5µm cell strainer. After counting, nuclei suspensions were diluted if needed to target 10,000 nuclei per lane and loaded into a thermal cycler to begin the transposition reaction, following 10X Genomics’ protocol. The manufacturer protocol was followed for the completion of library preparation.
[Single nucleus isolation for snRNA-seq or snATAC-seq libraries from human adult kidney biopsy samples]  For split single nucleus snRNA-seq and snATAC-seq from biopsies, the second spin step was omitted from the nucleus isolation protocol in order to preserve nuclei.
Single nucleus suspensions were loaded into the Chromium Controller following manufacturer instructions in order to target 10,000 nuclei per lane. Lanes that were resequenced were combined with cellranger count into a single output for the entire lane. For kidney samples with enough nuclei, we prepared additional lanes, then combined lanes into a single output for the original kidney with cellranger aggr.
10x chromium 3' RNA v3, ATAC v1.1, and multiome kits used for preparation

value: adult human kidney

tag: tissue source

value: nephrectomy

tag: Sex

value: Female

tag: race

value: African-American


title: nephrectomy 4 ATAC

description:
Sample name: A2A
snATAC library portion of multiomic joint snRNA-seq and snATAC-seq dataset using 10X Chromium
A2_filtered_feature_bc_matrix.h5 (gene-by-cell and peak-by-cell count)

tag: tissue

value: Male

tag: age


title: F2_D1 individual, grown at 4C [T4_P2.E5_F2_D1]

value: leaf

tag: developmental stage

tag: cell type

tag: genotype


title: Aortas, ang II treated mice 2 months, rep1

tag: treatment

value: Ang II infusion


title: F2_D2 individual, grown at 4C [T4_P2.D8_F2_D2]


title: Aortas, sham treated mice 2 months, rep4

value: Sham infusion


title: Physiological Flow Biol Rep 2

description: p2.AGACGCTGTG-ACCGTGCTTC.HNJJ3DSXY_AGACGCTGTG-ACCGTGCTTC

value: Proximal Tubule


title: F2_D1 individual, grown at 4C [T4_P2.D7_F2_D1]


title: nephrectomy 3 ATAC

description:
Sample name: A1A
snATAC library portion of multiomic joint snRNA-seq and snATAC-seq dataset using 10X Chromium
A1_filtered_feature_bc_matrix.h5 (gene-by-cell and peak-by-cell count)


title: Aortas, sham treated mice 2 months, rep2


title: nephrectomy 3 RNA

description:
Sample name: A1R
snRNA library portion of multiomic joint snRNA-seq and snATAC-seq dataset using 10X Chromium
A1_filtered_feature_bc_matrix.h5 (gene-by-cell and peak-by-cell count)

library_source: transcriptomic single cell


title: Aortas, sham treated mice 2 months, rep1


title: F2_D1 individual, grown at 4C [T4_P2.D5_F2_D1]


title: F2_D1 individual, grown at 4C [T4_P2.D4_F2_D1]


title: nephrectomy 2 RNA

description:
Sample name: N2R
snRNA library portion of multiomic joint snRNA-seq and snATAC-seq dataset using 10X Chromium
N2_filtered_feature_bc_matrix.h5 (gene-by-cell and peak-by-cell count)

value: White


title: nephrectomy 2 ATAC

description:
Sample name: N2A
snATAC library portion of multiomic joint snRNA-seq and snATAC-seq dataset using 10X Chromium
N2_filtered_feature_bc_matrix.h5 (gene-by-cell and peak-by-cell count)


title: F2_D1 individual, grown at 4C [T4_P2.D9_F2_D1]


title: ΔH, H2/CO2, biol rep 4

value: prokaryotic

tag: strain

value: [delta]H

value: exponential growth (continous bioreactors) day 7


title: Aortas, sham treated mice 2 months, rep3


title: nephrectomy 4 RNA

description:
Sample name: A2R
snRNA library portion of multiomic joint snRNA-seq and snATAC-seq dataset using 10X Chromium
A2_filtered_feature_bc_matrix.h5 (gene-by-cell and peak-by-cell count)


title: F2_D2 individual, grown at 4C [T4_P2.D3_F2_D2]

value: 7-10 leave rosette


title: A103C_37

city: Amsterdam

first: Daan

middle: Juri

last: Kloosterman

address: Plesmanlaan 121

department: Tumor Biology & Immunology

country: Netherlands

institute: The Netherlands Cancer

description: based on mechanism of sequencing by synthesis

data_processing:
Data processed by Novogene
The Sequenced Reads/raw reads often contain low quality reads or reads with adapters, which will affect the analysis quality and reliability. To avoid this, it's necessary to filter the raw reads and get the clean reads. The procedure of raw reads filtering is as follows: (1) Remove reads containing adapters; (2) Remove reads containing N > 10% (N represents base that could not be determined); (3) Remove low quality reads: The Qscore (Quality value) of over 50% bases of the read is <= 5.
STAR software is used to accomplish the mapping. The alignment by STAR precisely and effectively performs positioning junction reads for RNA sequencing data analysis.
The abundance of transcript reflects the gene expression level directly. In RNA-seq experiment, we estimate gene expression level by the abundance of transcripts(count of sequencing) that mapped to genome or exon. Reads count is proportional to gene expression level, gene length and sequencing depth. FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments.
Assembly: mm10
Supplementary files format and content: csv file include count data for each Sample

extract_protocol:
FACS isolated cell samples were sorted directly into RLT buffer (Qiagen) and preparation of RNA library and transcriptome sequencing was conducted by Novogene Co., LTD (Beijing, China).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Nestin-Tv-a;Ink4a/Arf-/- mice (BL/6 background) and Nestin-Tv-a mice (BL/6 background) have been previously described and were bred within the Netherlands Cancer Institute (NKI) animal facility.The RCAS-PDGFB-driven mouse models of gliomagenesis (PDG) have been previously described. Briefly, glioblastomas were induced in 5- to 6-week-old animals by intracranial injection of DF-1 cells expressing an RCAS vector encoding PDGF-B HA in Nestin-Tv-a;Ink4a/Arf-/- mice (PDG-Ink4a model), or DF-1 cells expressing PDGF-B HA and a short hairpin RNA targeting TP53 in Nestin-Tv-a mice (PDG-p53). rIgG2a (for anti-PD1) was administered as isotype controls in equivalent timing and dosage as the treatment antibodies. Animals were euthanized at specified time points or upon recurrence of the tumor as monitored by regular MRI imaging, or by neurological symptoms, as approved by the Institutional Animal Care and Use Committee of the NKI.
All mouse procedures were approved by the animal ethics committee of the Netherlands Cancer Institute and performed in accordance with institutional, national and European guidelines for animal care and use. MRI scans were performed weekly to monitor tumor development. At a tumor volume >20mm3 and <90mm3, mice were distributed into treatment groups by block randomization. Radiotherapy was performed after sedation by isoflurane and irradiation of the tumor-containing quadrant was performed using a X-RAD 320 or X-RAD SmART (Precision X-Ray) 5 times daily at 2Gy doses each. Anti-PD1 (BioXcell) was administered every third day until endpoint at 200ug per dose. Anti-PD1 treatment was initiated before the first dose of radiotherapy for the concurrent treatment schedule and one day after the last dose of radiotherapy for the adjuvant treatment schedule.

value: Brain

value: CD103+ regulatory T cells

value: 5 x 2 Gy Radiotherapy + Concurrent aPD1


title: nephrectomy 1 ATAC

description:
Sample name: N1A
snATAC library portion of multiomic joint snRNA-seq and snATAC-seq dataset using 10X Chromium
N1_filtered_feature_bc_matrix.h5 (gene-by-cell and peak-by-cell count)

value: adult human kidney


title: F1_D2 individual, grown at 4C [T4_P2.D2_F1_D2]


title: A103C_36

value: Nestin-Tv-a;Ink4a/Arf-/- mice (BL/6 background)


title: nephrectomy 5 RNA

description:
Sample name: A3R
snRNA library portion of multiomic joint snRNA-seq and snATAC-seq dataset using 10X Chromium
A3_filtered_feature_bc_matrix.h5 (gene-by-cell and peak-by-cell count)

value: nephrectomy

value: Female


title: F2_D2 individual, grown at 4C [T4_P2.D1_F2_D2]


title: nephrectomy 1 RNA

description:
Sample name: N1R
snRNA library portion of multiomic joint snRNA-seq and snATAC-seq dataset using 10X Chromium
N1_filtered_feature_bc_matrix.h5 (gene-by-cell and peak-by-cell count)

value: Male


title: biopsy 6 ATAC, kidney 2

description:
Sample name: B8A
snATAC library portion of multiomic joint snRNA-seq and snATAC-seq dataset using 10X Chromium
B8_filtered_feature_bc_matrix.h5 (gene-by-cell and peak-by-cell count)

value: biopsy


title: F2_D2 individual, grown at 4C [T4_P2.D6_F2_D2]

value: leaf


title: A103C_35

value: Regulatory T cells


title: F2_D1 individual, grown at 4C [T4_P2.D12_F2_D1]


title: Tre_C_34


title: P0626,HCC Peritumor tissue,Pe_F replicate 11

city: Guangzhou

first: Shi-Ting

last: Feng

state: Guangdong

address: The Second Zhongshan Road

institute: The first affiliated hospital of Sun Yat-sen University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) 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).
Ericscript (v0.5.5) [4] and rMATS (V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively.
Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI (Beijing Genomic Institute in ShenZhen), which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12).
The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression in different samples.
Differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test . The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni.
Assembly: GCF_000001635.26
Supplementary files format and content: core_table_gene xls file includes fpkm, tpm, read count values and analysis for each sample.

source_name: HCC Peritumor tissue

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and productswere purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

value: HCC Peritumor tissue

value: c-Myc/Alb-cre transgenic


title: F2_D1 individual, grown at 4C [T4_P2.D11_F2_D1]


title: biopsy 7 ATAC

description:
Sample name: B7A
snATAC library portion of multiomic joint snRNA-seq and snATAC-seq dataset using 10X Chromium
B7_filtered_feature_bc_matrix.h5 (gene-by-cell and peak-by-cell count)

value: White


title: biopsy 6 RNA, kidney 2

description:
Sample name: B8R
snRNA library portion of multiomic joint snRNA-seq and snATAC-seq dataset using 10X Chromium
B8_filtered_feature_bc_matrix.h5 (gene-by-cell and peak-by-cell count)


title: P_6191 individual, grown at 4C [T4_P2.D10_P_6191]


title: Tre_C_33


title: F2_D2 individual, grown at 4C [T4_P2.C9_F2_D2]


title: biopsy 7 RNA

description:
Sample name: B7R
snRNA library portion of multiomic joint snRNA-seq and snATAC-seq dataset using 10X Chromium
B7_filtered_feature_bc_matrix.h5 (gene-by-cell and peak-by-cell count)


title: T0626,HCC Tumor tissue,Tu_F replicate 11

source_name: HCC Tumor tissue

value: HCC Tumor tissue


title: Tre_C_22


title: biopsy 6 RNA, kidney 1

description:
Sample name: B6R
snRNA library portion of multiomic joint snRNA-seq and snATAC-seq dataset using 10X Chromium
B6_filtered_feature_bc_matrix.h5 (gene-by-cell and peak-by-cell count)


title: F2_D2 individual, grown at 4C [T4_P2.C8_F2_D2]


title: Tre_R_20

value: 5 x 2 Gy Radiotherapy


title: Tre_R_21


title: T0619,HCC Tumor tissue,Tu_F replicate 10


title: Tre_A_26

value: 5 x 2 Gy Radiotherapy + Adjuvant aPD1


title: biopsy 6 ATAC, kidney 1

description:
Sample name: B6A
snATAC library portion of multiomic joint snRNA-seq and snATAC-seq dataset using 10X Chromium
B6_filtered_feature_bc_matrix.h5 (gene-by-cell and peak-by-cell count)


title: P0618,HCC Peritumor tissue,Pe_F replicate 9


title: F2_D2 individual, grown at 4C [T4_P2.C7_F2_D2]

value: 7-10 leave rosette


title: biopsy 5 ATAC

description:
Sample name: B5A
snATAC-seq using 10X Chromium

value: African-American


title: P0619,HCC Peritumor tissue,Pe_F replicate 10


title: Nutritive Flow Biol Rep 4

description: s6.CACTCGCATA-GATACGACTT.HHYHLDSX2_CACTCGCATA-GATACGACTT

value: Proximal Tubule

value: RPTEC/TERT1 (CRL-4031)

value: Epithelial Cell

value: Nutritive Flow


title: Tre_R_19

value: Brain

value: Nestin-Tv-a;Ink4a/Arf-/- mice (BL/6 background)


title: biopsy 5 RNA

description:
Sample name: B5R
snRNA-seq using 10X Chromium

value: adult human kidney

value: biopsy

value: Male


title: T0618,HCC Tumor tissue,Tu_F replicate 9


title: F2_D1 individual, grown at 4C [T4_P2.C5_F2_D1]

value: leaf


title: P0612,HCC Peritumor tissue,Pe_F replicate 8

value: HCC Peritumor tissue

value: c-Myc/Alb-cre transgenic


title: T0612,HCC Tumor tissue,Tu_F replicate 8

value: HCC Tumor tissue


title: F2_D2 individual, grown at 4C [T4_P2.C4_F2_D2]


title: biopsy 4 RNA

description:
Sample name: B4R
snRNA-seq using 10X Chromium

value: Female

value: White


title: biopsy 4 ATAC

description:
Sample name: B4A
snATAC-seq using 10X Chromium


title: P0608,HCC Peritumor tissue,Pe_F replicate 7


title: F2_D2 individual, grown at 4C [T4_P2.C3_F2_D2]

value: 7-10 leave rosette


title: biopsy 3 RNA, kidney 2 (B2R is from contralateral kidney to one used for B3R and B3A)

description:
Sample name: B3R
snRNA-seq using 10X Chromium


title: T0608,HCC Tumor tissue,Tu_F replicate 7


title: F2_D1 individual, grown at 4C [T4_P2.C1_F2_D1]


title: F2_D1 individual, grown at 4C [T4_P2.C2_F2_D1]


title: P0510,HCC Peritumor tissue,Pe_F replicate 6


title: biopsy 3 RNA, kidney 1 (B2R is from contralateral kidney to one used for B3R and B3A)

description:
Sample name: B2R
snRNA-seq using 10X Chromium


title: CD4_A_32

description: based on mechanism of sequencing by synthesis

value: CD4 T cell

value: 5 x 2 Gy Radiotherapy + Adjuvant aPD1


title: CD4_C_15

value: 5 x 2 Gy Radiotherapy + Concurrent aPD1


title: F2_D1 individual, grown at 4C [T4_P2.C6_F2_D1]


title: P_6191 individual, grown at 4C [T4_P2.C12_P_6191]


title: CD4_A_17


title: T0510,HCC Tumor tissue,Tu_F replicate 6


title: CD4_A_18


title: CD4_R_12

value: 5 x 2 Gy Radiotherapy


title: F2_D1 individual, grown at 4C [T4_P2.C11_F2_D1]


title: CUT&RUN H3K27ac primary RPTEC, rep 3

description:
CUT&RUN sequencing using CUTANA (Epicypher, 14-1048)
Prim_H3K27ac_peaks.broadPeak

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

source_name: primary renal proximal epithelial cells

extract_protocol:
CUT&RUN was performed with the CUTANA kit (Epicyper, 14-1048). Cell cultures were fixed with 0.5% formaldehyde for 1 minute at room temperature, then quenched with glycine to a final concentration of 125mM. Cells were scraped from dishes then spun down at 500g for 5 minutes. Cell pellets were resuspended in PBS with 1% BSA, counted, spun down again, and resuspended again. 500,000 cells in 100 ul wash buffer were incubated with Concanavalin A-conjugated paramagnetic beads, then antibodies (1:50) were added to each sample. Remaining steps were manufacturer instructions for cross-linked samples.
Library preparation was performed with NEBNext ULTRA II DNA Library Prep Kit for Illumina (New England BioLabs, E7645S)

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

tag: cut&run antibody

value: H3K27ac (Epicypher, 13-0045)

value: untreated


title: T0507,HCC Tumor tissue,Tu_F replicate 5


title: CD4_R_11

value: Brain

value: Nestin-Tv-a;Ink4a/Arf-/- mice (BL/6 background)


title: F2_D1 individual, grown at 4C [T4_P2.C10_F2_D1]


title: CUT&RUN H3K27ac primary RPTEC, rep 1


title: CD4_R_10


title: biopsy 3 ATAC, kidney 2 (B2R is from contralateral kidney to one used for B3R and B3A)

description:
Sample name: B3A
snATAC-seq using 10X Chromium

value: adult human kidney

value: biopsy


title: P0201,HCC Peritumor tissue,Pe_F replicate 4

value: HCC Peritumor tissue


title: F2_D2 individual, grown at 4C [T4_P2.B9_F2_D2]

value: leaf


title: CD8_A_30

value: CD8 T cell


title: CUT&RUN H3K4me3 primary RPTEC, rep 3

description:
CUT&RUN sequencing using CUTANA (Epicypher, 14-1048)
Prim_H3K4me3_peaks.broadPeak

value: H3K4me3 (Epicypher, 13-0041)


title: F2_D2 individual, grown at 4C [T4_P2.B8_F2_D2]


title: CD8_A_9


title: F2_D2 individual, grown at 4C [T4_P2.B7_F2_D2]


title: F2_D1 individual, grown at 4C [T4_P2.B6_F2_D1]


title: CUT&RUN H3K4me3 primary RPTEC, rep 1


title: CD8_A_8


title: CUT&RUN IgG primary RPTEC, rep 3

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

value: IgG (Epicypher, 13-0042)


title: CUT&RUN H3K4me3 primary RPTEC, rep 2


title: CD8_C_29


title: CUT&RUN H3K27ac primary RPTEC, rep 2


title: CUT&RUN IgG primary RPTEC, rep 2


title: 11-1A,HCC Tumor tissue,Tu_M replicate 2

value: HCC Tumor tissue

value: c-Myc/Alb-cre transgenic


title: F2_D2 individual, grown at 4C [T4_P2.B4_F2_D2]

value: 7-10 leave rosette


title: 11-2A,HCC Peritumor tissue,Pe_M replicate 2


title: F2_D1 individual, grown at 4C [T4_P2.E6_F2_D1]


title: T0201,HCC Tumor tissue,Tu_F replicate 4


title: CD8_C_4

value: 5 x 2 Gy Radiotherapy + Concurrent aPD1


title: 19-2A,HCC Peritumor tissue,Pe_F replicate 3


title: F2_D1 individual, grown at 4C [T4_P2.B3_F2_D1]


title: RNA-seq of NFAT5 siRNA-treated primary RPTEC, rep 3

data_processing:
Illumina bcl files were demultiplexed and processed to generate fastq files.
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read. Reads were aligned to the Ensembl release 101 assembly with STAR v2.7.9a. Sequencing performance was assessed for the total number of aligned reads and uniquely aligned reads, as well as features detected. Gene counts were calculated from uniquely aligned unambiguous reads by Subread:featureCount v2.0.3. Gene counts were then adjusted for differences in library size with TMM normalization size factors.
Assembly: hg38
Supplementary files format and content: The rnaseq_gene_counts.tsv file contains gene counts for each of the 6 samples sequenced.

source_name: primary human renal proximal epithelial cells

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

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

value: NFAT5 siRNA (Horizon Discovery, L-009618-00)


title: CD8_R_28

value: 5 x 2 Gy Radiotherapy


title: 19-1A,HCC Tumor tissue,Tu_F replicate 3


title: 12-1A,HCC Tumor tissue,Tu_M replicate 3


title: CD4_C_31

value: CD4 T cell


title: RNA-seq of NFAT5 siRNA-treated primary RPTEC, rep 2

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


title: F2_D1 individual, grown at 4C [T4_P2.B5_F2_D1]


title: F2_D1 individual, grown at 4C [T4_P2.B1_F2_D1]


title: RNA-seq of NFAT5 siRNA-treated primary RPTEC, rep 1


title: 5-2A,HCC Peritumor tissue,Pe_F replicate 2


title: CD4_C_13

value: Brain


title: CD8_R_3

value: Nestin-Tv-a;Ink4a/Arf-/- mice (BL/6 background)


title: CD8_C_6


title: 5-1A,HCC Tumor tissue,Tu_F replicate 2


title: F2_D2 individual, grown at 4C [T4_P2.B12_F2_D2]


title: CUT&RUN IgG primary RPTEC, rep 1

value: untreated


title: CD8_R_2


title: P0507,HCC Peritumor tissue,Pe_F replicate 5


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

value: Non-targeting siRNA (Horizon Discovery, D-001810-10)


title: F2_D2 individual, grown at 4C [T4_P2.B11_F2_D2]