title: Y18M-3 [sRNA]

city: Lanzhou

first: Liyan

last: hu

address: Jiangouyan,Qilihe

department: Key Laboratory of Yak Breeding in Gansu Province

institute: Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences

data_processing:
The high-quality clean reads were obtained by using fastp v0.18.0 to remove unqualified reads including adapters reads, low-quality reads with quality score < Q20, and readings exceeding 10% of unknown
Ribo-Zero Gold rRNA Removal Kitwas was used to remove ribosomal RNA
Clean reads were mapped to GenBank database v209.0 and Rfam database v11.0 for annotation
HISAT2 ver.2.1.0 was used to compare clean reads to the yak reference
the mapping reads for each sample are assembled using Stringtie (version 1.3.4)
Assembly: Bos taurus reference genome (UMD3.1)
Supplementary files format and content: RPM,TPM and FPKM was used to standardize the raw counts of circRNA, miRNA and mRNA,respectively.

organism: Bos grunniens

source_name: testis

growth_protocol: In this study, all animal-related procedures conformed to the China Council on Animal Care and the Ministry of Agriculture of the People’s Republic of China guidelines. All yak-handling procedures were approved by The Animal Care and Use Committee of the Lanzhou Institute of Husbandry and Pharmaceutical Sciences Chinese Academy of Agricultural Sciences (Permit No: LIHPS-2022-0144).

extract_protocol:
The total RNA of yak testicular tissue was isolated and purified using a Trizol reagent kit according to the manufacturer's instructions. A 1% agarose gel was used to detect RNA degradation and contamination. The purity and concentration of total RNA were evaluated on Nanodrop 2000 and Qubit® 2.0 fluorometer, , and RNA integrity number (RIN) was monitored by Agilent 2100 Bioanalyzer.
Only high-quality RNA samples with an RNA concentration > 80 ng/μL, a purity of 1.80–2.10 and RIN > 7 were used for subsequent studies. Subsequently, ribosomal RNA (rRNA) was removed from high-quality RNA samples using a Ribo-Zero Gold rRNA Removal Kit, while the remaining RNA was generated into complementary DNA (cDNA) libraries using a NEBNext Ultra RNA Library Prep Kit (New England Biolabs, Ipswich, MA, USA). Finally, these constructed libraries were paired-end sequenced using the Illumina HiSeq2500 sequencer from Gene Denovo Biotechnology Co., Ltd.

treatment_protocol: The nine healthy 6-month-old (Y6M), 18-month-old (Y18M), and 4-year-old (Y4Y) male yaks from the same cooperative in Xiahe County (N34°51'50', E102°26'9') in Gannan Tibetan Autonomous Prefecture were selected for surgical biopsy to collect testicular tissue. Briefly, yaks were anesthetized with Jingsongling (Zhengfeng, Lanzhou, China) and then wiped with iodophor. After local anesthesia, the yaks were castrated with sterile scalpels. Subsequently, the wounds of these yaks were immediately sutured with surgical needles and penicillin and streptomycin were applied to prevent infection. The collected testicular tissue was washed with PBS (SolarBio, Beijing, China) and quickly placed into a cryotube, which was quickly frozen in liquid nitrogen.

value: testis

value: developmental stage

value: adulthood


title: Kmt2c_Kmt2d_dKO_ChIP_H3K27ac_Rep1

status: Public on Aug 09 2024

type: SRA

city: New York

first: Naitao

last: Wang

state: NY

address: 1275 York Avenue

department: HOPP

country: USA

institute: Memorial Sloan Kettering Cancer Center

library_source: genomic

data_processing:
RNAseq sequence data were processed and mapped to the mouse genome (mm10) using STAR v2.3 (Alexander Dobin, et al. Bioinformatics, 1 January, 2013)
Single cell RNAseq reads obtained from the 10x Genomics scRNAseq platform were demultiplexed and mapped to mouse genome (mm10) using the Cell Ranger package (10X Genomics).
ATACseq reads were quality and adapter trimmed using Trim Galore before aligning to mouse genome (mm10) with Bowtie2 with the default parameters.
ChIPseq and CUT_n_RUN reads were quality and adapter trimmed using Trim Galore before aligning to mouse genome assembly mm10 with Bowtie2 using the default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq: tab-delimited text files include raw gene counts. ATACseq, ChIPseq and CUT_n_RUN: bigWig files. Sinlge cell RNAseq: barcodes, features, and matrix raw files.

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse bladder urothelial cells

growth_protocol: For ChIPseq, CUT_n_RUN, RNAseq and ATACseq, urothelial organoids were cultured in advanced DMEM/F12 (#12634010, Gibco) [supplemented with B27 (2% v/v, #17504044, Gibco), Noggin conditioned medium (10% v/v), R-spondin conditioned medium (10% v/v), EGF (50ng/ml, #AF-100-15, PeproTech), Y-27632 (10µM, #S1049, Selleckchem), A83-01 (0.5µM, #S7692, Selleckchem), N-Acetyl-L-cysteine (1.25mM, #A9165, Millipore Sigma), Primocin (1% v/v, #ant-pm-2, InvivoGen), Penicillin-Streptomycin (1% v/v, #15140122, Gibco), L-Glutamine (1% v/v, 25030081, Gibco), and GlutaMAX (1% v/v, #35050061, Gibco)]. For single cell RNAseq, live urothelial cells were sorted out as DAPI-/EpCAM+/nlsEGFP+.

extract_protocol:
In RNAseq, total RNA was extracted with Trizol reagent following the manufacture's instruction. ATACseq was performed using standard protocol (Jason D Buenrostro, et al. Natur Methods, 06 October, 2013). For each control and Kmt2c/d KO group, 50K cells were proceessed for transposase treatment. ChIPseq was performed using standard ChIP protocol (Shipra Shukla, et al. Cancer Cell, 16 November, 2017). Ten million cells were used for each antibody. Cut_n_Run was performed using standard protocol (Peter J Skene, et al. Nature Protocols, 12 April, 2018). For each control and Kmt2c/d KO group, 250K cells were used. DNA fragments from ChIPseq and Cut_n_Run were extracted with cycle/gel purification kit (#740609, TAKARA). In scRNAseq, 5K live cells in each mouse were processed for encapsulation and library preparation.
RNAseq libraries were prepared using standard Illumina polyA library preparation protocol. Single cell RNAseq libraries were prepared with 10X genomics Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 according to manufacturer’s specifications. ATACseq, ChIPseq and CUT_n_RUN libraries were prepared using standard Illumina epigenetic library preparation protocol
RNAseq and scRNAseq:poly (A) capture; ATACseq, CUT_n_RUN, and ChIPseq: epigenetic library.

treatment_protocol: In CRISPR system, urothelial cells were edited with CRISPR/Cas9 (pLentiCRISPR_v2 one vector system). In Cre-Loxp system, urothelial cells from Tmprss2-CreERT2-IRES-nlsEGFP;Kmt2cf/f;Kmt2df/f mouse were infected with Adeno-mCherry (Control) and Adeno-mCherry-P2A-Cre (Kmt2c/d dKO). In scRNAseq, live urothelial cells from Tmprss2-CreERT2-IRES-nlsEGFP;Kmt2cf/f;Kmt2df/f mice with or without 3-month tamoxifen treatment (2 doses, 3mg/dose) were isolated as Kmt2c/d KO (n=3 mice) and Control group (n=4 mice), respectively.

tag: ChIP


title: HOS_sgNAT10_2

city: Guangzhou

first: Yutong

last: Zou

address: No.58, Zhongshan Rd.2

country: China

institute: The First Affiliated Hospital of Sun Yat-sen University

library_source: transcriptomic

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads with low-quality base (base quality less than or equal to 15) ratio  more than 20%; (3) Removing reads with unknown base ratio more than 5%.
Bowtie2 was applied to align the clean reads to the gene set.
Expression level of gene was calculated by RSEM.
Differential expression analysis was performed using the DESeq2.
Assembly: GRCh38
Supplementary files format and content: FPKM value of genes calculated by RSEM.

molecule: polyA RNA

organism: Homo sapiens

source_name: HOS

extract_protocol:
RNA was extracted according to TRIzol protocol.
The RNA-seq library was prepared by fragmenting the RNAs, synthesizing cDNA fragments, repairing double-stranded cDNA ends, and ligating adaptors. The final library was obtained through PCR amplification. RNA libraries were prepared for sequencing according to standard BGISeq-500 library construction protocol.

tag: cell line

value: HOS

tag: cell type

value: Osteosarcoma


title: Kmt2c_Kmt2d_dKO_scRNAseq_Rep1

molecule: total RNA

tag: rnaseq

value: Single cell RNAseq


title: Y18M-2 [sRNA]

tag: tissue

tag: treatment


title: Control_ChIP_H3K27ac_Rep1


title: L1_LSC_rep1

city: Beijing

first: Yuqing

address: NO.11 Xizhimen South St, Xicheng district, Beijing

department: Institute of Hematology

institute: Peking University People’s Hospital

description: Samples from patient #L1

data_processing:
Clean reads were obtained by removing adaptor sequence/low-quality sequence from raw reads.
Index of the reference genome was built using Bowtie v2.0.6.
Paired-end clean reads were aligned to the reference genome of Homo sapiens GRCh38 using Hisat2 v2.1.0.
FPKM values were obtained using HTSeq v0.6.0.
Assembly: GRCh38
Supplementary files format and content: Excel files include FPKM values for each sample.

source_name: Bone marrow

extract_protocol:
Total RNA was extracted using the RNeasy Mini kit (cat# 74104, Qiagen) following manufacturer’s recommendations.
RNA libraries were prepared for sequencing using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina

value: Bone marrow

value: CD34+CD38-CD58- bone marrow mononuclear cells

tag: genotype


title: HOS_sgNAT10_1


title: Kmt2c_Kmt2d_dKO_ChIP_KDM6A_Rep1


title: M3_nonLSC_rep3

description: Samples from patient #M3

value: CD34+CD38+, CD34-CD38-, and CD34-CD38+ bone marrow mononuclear cells

value: WT1/ABL=72.4%;  MLL-PTD mutation/ABL=18.6%;  FLT3-ITD=43%


title: HOS_NC_2


title: HOS_NC_1


title: Y6M-3 [sRNA]

value: adolescence


title: Control_ChIP_KDM6A_Rep1


title: M3_nonLSC_rep2

description: Samples from patient #M3


title: Y6M-2 [sRNA]


title: M3_nonLSC_rep1

description: Samples from patient #M3


title: Kmt2c_Kmt2d_dKO_ChIP_KMT2D_Rep1


title: L1_LSC_rep3

description: Samples from patient #L1


title: Y6M-1 [sRNA]


title: Control_ChIP_KMT2D_Rep1


title: 143B_sgNAT10_1


title: Y4Y-3 [sRNA]

value: infancy


title: Kmt2c_Kmt2d_dKO_scRNAseq_Rep2


title: M3_LSC_rep2

description: Samples from patient #M3

value: CD34+CD38- bone marrow mononuclear cells


title: M3_LSC_rep3

description: Samples from patient #M3


title: Kmt2c_Kmt2d_dKO_ChIP_KMT2C_Rep1


title: 143B_NC_2


title: M3_LSC_rep1

description: Samples from patient #M3


title: Control_ChIP_KMT2C_Rep1


title: Y18M-1 [sRNA]


title: Y4Y-2 [sRNA]


title: Y4Y-1 [sRNA]


title: 143B_NC_1


title: Kmt2c_Kmt2d_dKO_ChIP_Input_Rep1

value: Input


title: M2_nonLSC_rep2

description: Samples from patient #M2


title: Y18M-3


title: A7-35-23 CO2 24h 3

city: Iowa City

first: Damian

middle: J

last: Krysan

state: IA

address: 25 South Grand, 2040 ML

department: Division of Pediatrics & Infectious Disease

institute: University of Iowa Hospitals and Clinics

data_processing:
Paired-end Illumina sequence read files were evaluated for quality and the absence of adaptor sequence using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Read files were mapped to C. neoformans reference genome H99 v48 (FungiDB).
Gene transcript expression was quantified using HISAT2 and Stringtie.
Assembly: FungiDB-48_CneoformansH99
Supplementary files format and content: Normalized_counts.xlsx - normalized gene counts
Supplementary files format and content: Raw_gene_counts.xlsx - unnormalized gene counts

organism: Cryptococcus neoformans

growth_protocol: Overnight cultures of indicated strains were washed and diluted to 7.5x10^5 cells/mL, 3 mL cultured per condition in a 6-well plate in RPMI 1640 medium with 165 mM MOPS, pH 7 for 24 hours at 37°C in ambient air or 5% CO2.

extract_protocol:
Cells were collected via centrifugation from growth medium, lyophilized overnight and RNA harvested according to manufacturer protocol for Invitrogen PureLink RNA Mini Kit.
Total RNA (>2 ug per sample) was submitted to Azenta Life Sciences for standard RNA-Seq next-generation sequencing. The RNA samples were quantified using Qubit 2.0 Fluorometer (ThermoFisher) and RNA integrity was checked using TapeStation (Agilent Technologies). The RNA sequencing libraries were prepared using the NEB Next Ultra II RNA Library Prep Kit for Illumina using manufacturer instructions (New England Biolabs). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 min at 94°C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3' ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies) and quantified by using Qubit 2.0 Fluorometer (ThermoFisher) as well as by quantitative PCR (KAPA Biosystems). The sequencing libraries were multiplexed and clustered onto a flowcell. After clustering, the flowcell was loaded onto the Illumina HiSeq instrument according to manufacturer instructions. The samples were sequenced using a 2x150 bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mismatch was allowed for index sequence identification.

tag: strain

value: wild-type

tag: time


title: 143B_sgNAT10_2


title: Control_ChIP_Input_Rep1


title: Y18M-2


title: Y18M-1


title: Kmt2c_Kmt2d_dKO_ATACseq_Rep2

tag: atacseq

value: ATACseq


title: A7-35-23 CO2 24h 2


title: M2_nonLSC_rep3

description: Samples from patient #M2


title: M2_nonLSC_rep1

description: Samples from patient #M2


title: A7-35-23 CO2 24h 1


title: Y6M-3


title: A1-84-14 CO2 24h 3


title: Kmt2c_Kmt2d_dKO_ATACseq_Rep1


title: M2_LSC_rep2

description: Samples from patient #M2


title: M2_LSC_rep1

description: Samples from patient #M2


title: A1-84-14 CO2 24h 2


title: Control_ATACseq_Rep2


title: Y6M-2


title: Y6M-1


title: A1-84-14 CO2 24h 1


title: M1_nonLSC_rep4

description: Samples from patient #M1


title: Kmt2c_Kmt2d_dKO_RNAseq_Rep2

value: RNAseq


title: H99 CO2 24h 3


title: Control_ATACseq_Rep1


title: M1_nonLSC_rep3

description: Samples from patient #M1


title: Kmt2c_Kmt2d_dKO_RNAseq_Rep1


title: H99 CO2 24h 2


title: Y4Y-2

value: testis


title: Control_RNAseq_Rep2


title: M2_LSC_rep3

description: Samples from patient #M2


title: Y4Y-1

value: developmental stage


title: M1_nonLSC_rep1

description: Samples from patient #M1


title: Control_RNAseq_Rep1


title: M1_nonLSC_rep2

description: Samples from patient #M1


title: Heart_LPS_rep5

city: Changsha

first: Weizhi

last: Zhang

state: Hunan

address: Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, No. 139 Middle Renmin Road, Changsha, Hunan, 410011, China.

department: Department of Cardiovascular Surgery

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) 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.
Assembly: GRCm39
Supplementary files format and content: Spreadsheet file includes FPKM value, TPM value, read count and average FPKM value for each Sample

source_name: heart

growth_protocol: 10-week-old healthy, specific pathogen-free, and wild-type C57BL/6 male mice were provided by Hunan SJA Laboratory Animal Co., Ltd. (Changsha, China) and raised at the Laboratory Animal Center of the Second Xiangya Hospital, Central South University (Changsha, China). All mice were placed in 12-hour light/dark cycle surroundings with standard ambient temperature, humidity, and oxygen concentrations and were provided with freely available food and water.

extract_protocol:
After 12 hours of treatment, heart tissues were collected from the mice. Total RNA was extracted from myocardial tissue samples using TRIzol reagent and purified with chloroform, isopropyl alcohol, and ethanol. The quality of RNA samples was evaluated by concentration, 28S/18S ratio, and RNA quality number (RQN) measured by a fragment analyzer with the Standard Sensitivity RNA Analysis Kit (15 nt) (DNF-471).
mRNAs were enriched from high-quality RNA samples (RQN＞7.0, 28S/18S＞1.0), fragmented and used as templates for synthesizing cDNAs. cDNAs were subjected to end-repair, add a single ‘A’ nucleotide to the 3’ ends, set up to ligate adaptors with the cDNAs, and finally be amplified to construct libraries. After quality control, cDNAs were circularized to generate DNA nanoballs via rolling cycle amplification, which were then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis.

treatment_protocol: 10-week-old healthy, specific pathogen-free, and wild-type C57BL/6 male mice were randomly assigned to the PBS group and the LPS group (n=5/group). In order to construct mouse models of sepsis-induced myocardial dysfunction, the LPS group were given a single intraperitoneal injection of 10 mg/kg LPS, while the PBS group were given an equal volume of PBS as controls.

value: heart

tag: Sex

value: male

value: wild type


title: A7-35-23 Amb 24h 3

value: Ambient Air


title: sgKmt2c+sgKmt2d_RNAseq_Rep2


title: Heart_LPS_rep4

institute: The Second Xiangya Hospital of Central South University

value: a single intraperitoneal injection of 10 mg/kg LPS


title: M1_LSC_rep3

description: Samples from patient #M1

value: Bone marrow


title: Y4Y-3


title: Heart_LPS_rep3


title: A7-35-23 Amb 24h 1


title: A7-35-23 Amb 24h 2


title: M1_LSC_rep2

description: Samples from patient #M1


title: A1-84-14 Amb 24h 3


title: sgKmt2c+sgKmt2d_RNAseq_Rep1


title: Heart_LPS_rep2


title: M1_LSC_rep1

description: Samples from patient #M1


title: sgKmt2d_RNAseq_Rep1


title: A1-84-14 Amb 24h 2


title: sgKmt2c_RNAseq_Rep2


title: Heart_LPS_rep1


title: Heart_PBS_rep5

value: an equal volume of PBS


title: A1-84-14 Amb 24h 1


title: H99 Amb 24h 3


title: Heart_PBS_rep4


title: sgControl_RNAseq_Rep2


title: Heart_PBS_rep3


title: M1_LSC_rep4

description: Samples from patient #M1


title: iPSC-CM DMSO 1

city: Cambridge

first: Jessica

last: Garbern

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing:
Raw Illumina NovaSeq sequence data (.bcl) files were de-multiplexed and converted into fastq.gz files using the -mkfastq command in cellranger v6.1.1 from 10X Genomics.
Fastq.gz files were processed using 10X Genomics cellranger v6.1.1 to produce UMI matrix (matrix.mtx.gz) and cell (barcode.tsv.gz) and gene (features.tsv.gz) files.
Processed files were converted into Seurat objects using Seurat v4.0.5, then data were filtered and normalized using SCTransform in Seurat.
Normalized data were used to perform principal component analysis and gene expression analysis.
Note that names of cellranger output files have been changed for clarity. Prior to input into Seurat, organize files into sample-specific folders then change names of processed files to “matrix.mtx.gz”, “barcodes.tsv.gz” and “features.tsv.gz” to allow Seurat to read files.
Genome_build: GRCH38 (hg38)
Supplementary_files_format_and_content: matrix table with raw gene counts for every gene and every cell

source_name: iPSC-derived cardiomyocytes

growth_protocol: Human iPSCs were seeded at 150,000 cells/ml (20 ml) into a 125 ml Erlenmeyer flask on a shaker platform at 70 rpm. Cardiomyocyte differentiation was performed starting 4 days after cell seeding (day 0 of differentiation) by treating cells with CHIR99021 (6 µM) for 48 hours, then treating cells with IWP4 (5 µM) for 48 hours. Cardiomyocytes were beating by day 7 of differentiation.

extract_protocol:
iPSC-CM spheroids were dissociated using the STEMDiff Cardiomyocyte Dissociation Kit (Stem Cell Technologies) then filtered through a 70 µm strainer. Single cells were washed then resuspended in phosphate buffered saline (PBS) containing 0.04% bovine serum albumin (BSA) at a concentration of 1000 cells/µL. Single cells were prepared with the 10X Genomics Chromium Single Cell 3’ v3 Reagent Kit according to the 10X Genomics Single Cell Protocols Cell Preparation Guide. 10,000 cells per sample were used for loading into a single lane of a NovaSeq S4 flow cell.
Library construction was performed using the 10x Chromium single cell 3' v3 kit according to the manufacturer's instructions.

treatment_protocol: Human iPSC-CM spheroids at day 9 of differentiation (2 days after onset of beating) were transferred to a low adhesion 6 well plate and treated for 2 days with LOM612 (5 µM) or DMSO (0.2%). Samples were harvested at 48 hours for scRNAseq processing.

value: iPSC-derived cardiomyocytes

value: DMSO (0.2%) (control)


title: sgKmt2c_RNAseq_Rep1


title: H99 CO2 24h 1


title: iPSC-CM LOM 2


title: sgKmt2d_RNAseq_Rep2


title: iPSC-CM LOM 1


title: H99 Amb 24h 2


title: iPSC-CM DMSO 2


title: U2OS, Input, ChIP

status: Public on Aug 08 2024

city: Suzhou

first: Zimu

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

data_processing:
Raw Data of ChIP-Seq was aligned to the reference genome (UCSC hg38) using BWA-MEM (v0.7.17)
Peaks were identified using MACS2 (v2.2.7)
Assembly: hg38
Supplementary files format and content: bigwig files
Supplementary files format and content: peak text files

source_name: cell line

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared for sequencing using standard MGI protocols

value: cell line

value: osteosarcoma

tag: chip antibody


title: sgControl_RNAseq_Rep1


title: H99 Amb 24h 1


title: MG63, H3K27ac, ChIP


title: Heart_PBS_rep2


title: HOS-GNE, H3K27ac, ChIP

value: HOS


title: HOS, H3K27ac, ChIP


title: HOS, Input, ChIP


title: U2OS, H3K27ac, ChIP


title: 143B, H3K27ac, ChIP


title: Tale3_rep2

city: Valencia

first: Jose

last: Gadea

address: Ingeniero Fausto Elio

department: Stress

country: Spain

institute: IBMCP

description:
TALE50_vsTALE3.processed.tsv
TALE55_vs_TALE3.processed.tsv

data_processing:
quality trimming of raw reads and adapter removal with cutadapt (http://journal.embnet.org/index.php/embnetjournal/article/view/200), and quality analysis of clean reads with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Clean read pairs longer than 20nt were  mapped to the Nicotiana benthamiana NbV1 genome using HISAT2 (https://www.nature.com/articles/s41587-019-0201-4).
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Number of read counts mapped to one and only one gene (uniquely mapped) were obtained with htseq-count (https://www.biorxiv.org/content/10.1101/002824v2)
Differential expression analysis was done with DESeq2 (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8).
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Nicotiana benthamiana

source_name: leaves

growth_protocol: Nicotiana benthamiana plants were grown under growth chamber conditions at 23 °C and photoperiod of 16 h light/8 h dark.

extract_protocol: Leaf samples (100 mg) from three independent inoculated N. benthamiana plants were randomly harvested at 36 hpi and pooled as a single replicate. Total RNA was extracted using E.Z.N.A® Plant RNA kit following RNase-free DNase (Omega Bio-Tek®, GA, USA) treatment.

treatment_protocol: Leaves of 6-week-old plants were by pressure infiltration

value: leaves

value: infiltrated with TALE3


title: 143B, Input, ChIP


title: MG63, Input, ChIP


title: Tale55_rep3

value: infiltrated with TALE55


title: Tale55_rep2


title: Tale55_rep1


title: Tale3_rep1


title: Tale3_rep3


title: Tale26_rep3

value: infiltated with TALE26


title: Tale26_rep1


title: Tale9_rep2

value: infiltrated with TALE9


title: Tale9_rep3


title: Tale9_rep1


title: piloting Y-seq , CMC 2 hr; OH-_RT1306

city: Chestnut Hill

first: Huiqing

last: Zhou

state: Massachusetts

address: 2609 Beacon St.

department: Chemistry

institute: Boston College

data_processing:
Remove PCR duplication upon deduplication by "BBMap" tools "clumpify.sh" as the library carries the UMI sequence.
Adaptors were trimmed by the “cutadapt” program.
Reads were aligned to the rRNA or the Refseq genome using bowtie2 aligner
Single base reads counting were performed with bam-readcount.
Stop counts and total count coverage were performed with bedtools genomecov.
Assembly: hg38
Supplementary files format and content: For piloting Y-seq libariescsv.gz files for lib1-lib6 were outputs of bam-readcount,  3p.txt and totalcov.txt were the reads counts stop at the postion and total read for the position. For mut-Y-seq libaraies processed  data, the processed.csv files are files containg mutation rate, deletion rate, and insertion rate at single base position; 3p.csv and total.csv files are generated by bedtools genomecov and are used to calculate the stop rate.

source_name: HEK-293T cells

extract_protocol:
RNA samples were extracted from HEK-293T cells using the TRIzol reagent and standard protocol; poly-A RNA was purified by oligo(dT)25 Dynabeads.
Libraries were constructed using ligation-based library construction approach reported in Methods session in the current work.

value: HEK-293T cells


title: Tale50_rep1

value: infiltated with TALE50


title: Tale26_rep4


title: 22hr_FCM_TGFB_STB-009, bio rep 2

city: Boston

first: Heather

last: Faust

address: 60 Fenwood Road

institute: Brigham and Women's Hopsital

description:
Illumina SmartSeq 2
Sample_96
Bulk_RNA_seq_raw_counts_genenames
cell lysate

data_processing:
Reads were mapped to the GRCh38.93 transcriptome using kallisto 0.42.4 and transcriptional levels of genes were quantified with the log2(TPM + 1) (transcripts per kilobase million) metric.
Aligned reads were imported into Deseq2 using tximport
Removed outlier samples based on total reads mapped per sample and heatmap of count matrix.
Deseq2 was used to quantify differentially expressed genes
Assembly: GRCh38.93
Supplementary files format and content: .xls file of raw count matrix

source_name: Primary cultured fibroblasts

growth_protocol: Primary human synovial fibroblasts were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 10% CO2 at 37C

extract_protocol:
10K were lysed in 25uL  pf TCL buffer with 1% BME and submitted for sequencing.
Full-length cDNA and sequencing libraries were performed using Illumina Smart-seq2 protocol. Libraries were sequenced on MiSeq from Illumina to generate 35 base paired-end reads

value: Primary cultured fibroblasts

value: Synovial tissue fibroblasts

value: Fat conditioned media+ TGFB (10ng/mL)

value: 22 hours


title: 22hr_FCM_TGFB_STB-009, bio rep 1

description:
Illumina SmartSeq 2
Sample_95
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_FCM_TGFB_AMP005, bio rep 1

description:
Illumina SmartSeq 2
Sample_91
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_FCM_TGFB_STB-002, bio rep 1

description:
Illumina SmartSeq 2
Sample_93
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: piloting Y-seq , CMC 20 min; OH-_RT1306


title: 22hr_TGFB_STB-009, bio rep 2

description:
Illumina SmartSeq 2
Sample_90
Bulk_RNA_seq_raw_counts_genenames
cell lysate

value: TGFB (10ng/mL)


title: piloting Y-seq , CMC 2 hr; OH-_wtRT


title: piloting Y-seq , None_RT1306


title: Tale50_rep2


title: Tale50_rep3


title: 22hr_TGFB_STB-009, bio rep 1

description:
Illumina SmartSeq 2
Sample_89
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_TGFB_STB-002, bio rep 2

description:
Illumina SmartSeq 2
Sample_88
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_FCM_TGFB_STB-009, bio rep 1

description:
Illumina SmartSeq 2
Sample_83
Bulk_RNA_seq_raw_counts_genenames
cell lysate

value: 4 hours


title: 22hr_TGFB_AMP005, bio rep 1

description:
Illumina SmartSeq 2
Sample_85
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_TGFB_STB-002, bio rep 1

description:
Illumina SmartSeq 2
Sample_87
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_TGFB_AMP005, bio rep 2

description:
Illumina SmartSeq 2
Sample_86
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_FCM_TGFB_AMP005, bio rep 1

description:
Illumina SmartSeq 2
Sample_79
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_FCM_TGFB_STB-002, bio rep 1

description:
Illumina SmartSeq 2
Sample_81
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_TGFB_STB-009, bio rep 2

description:
Illumina SmartSeq 2
Sample_78
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_FCM_TGFB_AMP005, bio rep 2

description:
Illumina SmartSeq 2
Sample_80
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_TGFB_STB-009, bio rep 1

description:
Illumina SmartSeq 2
Sample_77
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_FCM_TGFB_STB-002, bio rep 2

description:
Illumina SmartSeq 2
Sample_94
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_TGFB_STB-002, bio rep 2

description:
Illumina SmartSeq 2
Sample_76
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_TGFB_STB-002, bio rep 1

description:
Illumina SmartSeq 2
Sample_75
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_TGFB_AMP005, bio rep 2

description:
Illumina SmartSeq 2
Sample_74
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_TGFB_AMP005, bio rep 1

description:
Illumina SmartSeq 2
Sample_73
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_FCM_GCR_ant_STB-009, bio rep 2

description:
Illumina SmartSeq 2
Sample_72
Bulk_RNA_seq_raw_counts_genenames
cell lysate

value: Fat conditioned media+Mifepristone (10uM)


title: 22hr_TNF_STB-009, bio rep 2

description:
Illumina SmartSeq 2
Sample_70
Bulk_RNA_seq_raw_counts_genenames
cell lysate

value: TNFa (5ng/mL)


title: 22hr_FCM_GCR_ant_STB-009, bio rep 1

description:
Illumina SmartSeq 2
Sample_71
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_Basal_STB-009, bio rep 2

description:
Illumina SmartSeq 2
Sample_68
Bulk_RNA_seq_raw_counts_genenames
cell lysate

value: No stimulation


title: 22hr_TNF_STB-009, bio rep 1

description:
Illumina SmartSeq 2
Sample_69
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_Basal_STB-009, bio rep 1

description:
Illumina SmartSeq 2
Sample_67
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_FCM_STB-009, bio rep 1

description:
Illumina SmartSeq 2
Sample_65
Bulk_RNA_seq_raw_counts_genenames
cell lysate

value: Fat conditioned media


title: 22hr_FCM_STB-009, bio rep 2

description:
Illumina SmartSeq 2
Sample_66
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_FCM_TGFB_STB-009, bio rep 2

description:
Illumina SmartSeq 2
Sample_84
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_FCM_TNF_STB-009, bio rep 1

description:
Illumina SmartSeq 2
Sample_63
Bulk_RNA_seq_raw_counts_genenames
cell lysate

value: Fat conditioned media+TNFa (5ng/mL)


title: 22hr_FCM_TNF_STB-009, bio rep 2

description:
Illumina SmartSeq 2
Sample_64
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_FCM_TGFB_STB-002, bio rep 2

description:
Illumina SmartSeq 2
Sample_82
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_Cortisol_STB-009, bio rep 2

description:
Illumina SmartSeq 2
Sample_62
Bulk_RNA_seq_raw_counts_genenames
cell lysate

value: Cortisol (100nM)


title: 22hr_TNF_STB-002, bio rep 2

description:
Illumina SmartSeq 2
Sample_58
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_Cortisol_STB-009, bio rep 1

description:
Illumina SmartSeq 2
Sample_61
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_FCM_GCR_ant_STB-002, bio rep 1

description:
Illumina SmartSeq 2
Sample_59
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_FCM_GCR_ant_STB-002, bio rep 2

description:
Illumina SmartSeq 2
Sample_60
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_Basal_STB-002, bio rep 2

description:
Illumina SmartSeq 2
Sample_56
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_FCM_STB-002, bio rep 2

description:
Illumina SmartSeq 2
Sample_54
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_Basal_STB-002, bio rep 1

description:
Illumina SmartSeq 2
Sample_55
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_FCM_STB-002, bio rep 1

description:
Illumina SmartSeq 2
Sample_53
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_FCM_TNF_STB-002, bio rep 2

description:
Illumina SmartSeq 2
Sample_52
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_FCM_GCR_ant_AMP005, bio rep 2

description:
Illumina SmartSeq 2
Sample_48
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_Cortisol_STB-002, bio rep 1

description:
Illumina SmartSeq 2
Sample_49
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_TNF_AMP005, bio rep 1

description:
Illumina SmartSeq 2
Sample_45
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_TNF_STB-002, bio rep 1

description:
Illumina SmartSeq 2
Sample_57
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_Basal_AMP005, bio rep 1

description:
Illumina SmartSeq 2
Sample_43
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_FCM_AMP005, bio rep 2

description:
Illumina SmartSeq 2
Sample_42
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_FCM_TNF_AMP005, bio rep 2

description:
Illumina SmartSeq 2
Sample_40
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_FCM_TNF_AMP005, bio rep 1

description:
Illumina SmartSeq 2
Sample_39
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_FCM_AMP005, bio rep 1

description:
Illumina SmartSeq 2
Sample_41
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_Cortisol_AMP005, bio rep 2

description:
Illumina SmartSeq 2
Sample_38
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_Cortisol_AMP005, bio rep 1

description:
Illumina SmartSeq 2
Sample_37
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_FCM_GCR_ant_STB-009, bio rep 2

description:
Illumina SmartSeq 2
Sample_36
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_TNF_STB-009, bio rep 1

description:
Illumina SmartSeq 2
Sample_33
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_TNF_STB-009, bio rep 2

description:
Illumina SmartSeq 2
Sample_34
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_FCM_GCR_ant_STB-009, bio rep 1

description:
Illumina SmartSeq 2
Sample_35
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_Basal_STB-009, bio rep 2

description:
Illumina SmartSeq 2
Sample_32
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_FCM_STB-009, bio rep 2

description:
Illumina SmartSeq 2
Sample_30
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_Cortisol_STB-002, bio rep 2

description:
Illumina SmartSeq 2
Sample_50
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: piloting Y-seq , CMC 2 hr; OH-_SS III


title: 4hr_FCM_STB-009, bio rep 1

description:
Illumina SmartSeq 2
Sample_29
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_FCM_TNF_STB-002, bio rep 1

description:
Illumina SmartSeq 2
Sample_51
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_Cortisol_STB-009, bio rep 1

description:
Illumina SmartSeq 2
Sample_25
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_FCM_TNF_STB-009, bio rep 1

description:
Illumina SmartSeq 2
Sample_27
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_Cortisol_STB-009, bio rep 2

description:
Illumina SmartSeq 2
Sample_26
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_Basal_AMP005, bio rep 2

description:
Illumina SmartSeq 2
Sample_44
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_FCM_GCR_ant_AMP005, bio rep 1

description:
Illumina SmartSeq 2
Sample_47
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_TNF_AMP005, bio rep 2

description:
Illumina SmartSeq 2
Sample_46
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_FCM_TNF_STB-009, bio rep 2

description:
Illumina SmartSeq 2
Sample_28
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_TNF_STB-002, bio rep 1

description:
Illumina SmartSeq 2
Sample_21
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_TNF_STB-002, bio rep 2

description:
Illumina SmartSeq 2
Sample_22
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_Basal_STB-002, bio rep 2

description:
Illumina SmartSeq 2
Sample_20
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_FCM_STB-002, bio rep 1

description:
Illumina SmartSeq 2
Sample_17
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_FCM_TNF_STB-002, bio rep 1

description:
Illumina SmartSeq 2
Sample_15
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_FCM_TNF_STB-002, bio rep 2

description:
Illumina SmartSeq 2
Sample_16
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_FCM_STB-002, bio rep 2

description:
Illumina SmartSeq 2
Sample_18
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_Basal_STB-002, bio rep 1

description:
Illumina SmartSeq 2
Sample_19
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_FCM_GCR_ant_AMP005, bio rep 1

description:
Illumina SmartSeq 2
Sample_11
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_TNF_AMP005, bio rep 2

description:
Illumina SmartSeq 2
Sample_10
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_Cortisol_STB-002, bio rep 2

description:
Illumina SmartSeq 2
Sample_14
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_Cortisol_STB-002, bio rep 1

description:
Illumina SmartSeq 2
Sample_13
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_Basal_STB-009, bio rep 1

description:
Illumina SmartSeq 2
Sample_31
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_Basal_AMP005, bio rep 2

description:
Illumina SmartSeq 2
Sample_8
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_TNF_AMP005, bio rep 1

description:
Illumina SmartSeq 2
Sample_9
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_FCM_TNF_AMP005, bio rep 1

description:
Illumina SmartSeq 2
Sample_3
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: piloting Y-seq , OH-_RT1306


title: 4hr_FCM_AMP005, bio rep 1

description:
Illumina SmartSeq 2
Sample_5
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_FCM_AMP005, bio rep 2

description:
Illumina SmartSeq 2
Sample_6
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_Cortisol_AMP005, bio rep 1

description:
Illumina SmartSeq 2
Sample_1
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_FCM_TNF_AMP005, bio rep 2

description:
Illumina SmartSeq 2
Sample_4
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_Basal_AMP005, bio rep 1

description:
Illumina SmartSeq 2
Sample_7
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_FCM_GCR_ant_STB-002, bio rep 1

description:
Illumina SmartSeq 2
Sample_23
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 4hr_Cortisol_AMP005, bio rep 2

description:
Illumina SmartSeq 2
Sample_2
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: 22hr_FCM_TGFB_AMP005, bio rep 2

description:
Illumina SmartSeq 2
Sample_92
Bulk_RNA_seq_raw_counts_genenames
cell lysate


title: [DNAm]Sarcoidosis (Progressive) 26

type: genomic

city: Aurora

first: Ivana

last: Yang

state: CO

institute: University of Colorado - Anschutz Medical Campus

hyb_protocol: per Manufacturer Instructions

scan_protocol: per Manufacturer Instructions

data_processing: IDAT files were processed using the sesame R package with default parameters. Known problematic probes and probes with > 25% missingess were removed. Remaining missing values were imputed using mean M value for non-missing values for that probe.

label: Cy5 and Cy3

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Progressive) 26

label_protocol: per Manufacturer Instructions

growth_protocol: Cells were stored in RLT buffer at –80°C

extract_protocol: DNA and RNA were extracted using the Qiagen AllPrep DNA/RNA extraction mini kit. Purified genomic DNA was bisulfite-converted with the Zymo EZ-96 DNA Methylation bisulfite conversion kit, followed by whole-genome amplification and enzymatic fragmentation.

tag: diagnosis

value: sarcoidosis (progressive)

tag: age

value: m

tag: race

value: black

tag: ethnicity

value: not Hispanic or Latino

tag: smoking status

value: never

tag: scadding stage

tag: acute disease

value: n

tag: multiorgan involvement

tag: fvc (% predicted)

tag: fev1 (% predicted)

tag: dlco (% predicted)

tag: ever treated for sarcoidosis

value: y

tag: array

tag: position

tag: pc1 (methylation)

tag: pc2 (methylation)

tag: pc3 (methylation)

tag: pc4 (methylation)

tag: pc5 (methylation)


title: [DNAm]Sarcoidosis (Progressive) 7

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Progressive) 7

tag: diagnosis

tag: age

tag: Sex

tag: race

value: white


title: [DNAm]Sarcoidosis (Progressive) 5

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Progressive) 5

value: f

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: acute disease


title: [DNAm]Sarcoidosis (Progressive) 9

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Progressive) 9

tag: multiorgan involvement

tag: fvc (% predicted)

tag: fev1 (% predicted)

tag: dlco (% predicted)


title: [DNAm]Sarcoidosis (Progressive) 24

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Progressive) 24

tag: ever treated for sarcoidosis

tag: array

tag: position

tag: pc1 (methylation)


title: [DNAm]Sarcoidosis (Progressive) 11

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Progressive) 11

tag: pc2 (methylation)

tag: pc3 (methylation)

tag: pc4 (methylation)

tag: pc5 (methylation)


title: [DNAm]Sarcoidosis (Progressive) 16

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Progressive) 16

tag: diagnosis

tag: age

tag: Sex

tag: race

value: former


title: [DNAm]Sarcoidosis (Progressive) 21

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Progressive) 21

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: acute disease


title: [DNAm]Sarcoidosis (Progressive) 18

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Progressive) 18

tag: multiorgan involvement

tag: fvc (% predicted)

tag: fev1 (% predicted)

tag: dlco (% predicted)


title: [DNAm]Sarcoidosis (Progressive) 14

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Progressive) 14

tag: ever treated for sarcoidosis

tag: array

tag: position

tag: pc1 (methylation)


title: [DNAm]Sarcoidosis (Progressive) 19

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Progressive) 19

tag: pc2 (methylation)

tag: pc3 (methylation)

tag: pc4 (methylation)

tag: pc5 (methylation)


title: [DNAm]Sarcoidosis (Progressive) 8

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Progressive) 8

tag: diagnosis

tag: age

tag: Sex

tag: race


title: [DNAm]Sarcoidosis (Non-Progressive) 5

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 5

value: sarcoidosis (non-progressive)

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: acute disease


title: [DNAm]Sarcoidosis (Progressive) 10

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Progressive) 10

tag: multiorgan involvement

tag: fvc (% predicted)

tag: fev1 (% predicted)

tag: dlco (% predicted)


title: [DNAm]Sarcoidosis (Progressive) 17

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Progressive) 17

tag: ever treated for sarcoidosis

tag: array

tag: position

tag: pc1 (methylation)


title: [DNAm]Sarcoidosis (Progressive) 4

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Progressive) 4

tag: pc2 (methylation)

tag: pc3 (methylation)

tag: pc4 (methylation)

tag: pc5 (methylation)


title: [DNAm]Sarcoidosis (Progressive) 22

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Progressive) 22

tag: diagnosis

tag: age

tag: Sex

tag: race


title: [DNAm]Sarcoidosis (Progressive) 6

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Progressive) 6

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: acute disease


title: [DNAm]Sarcoidosis (Non-Progressive) 9

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 9

tag: multiorgan involvement

tag: fvc (% predicted)

tag: fev1 (% predicted)

tag: dlco (% predicted)


title: [DNAm]Sarcoidosis (Progressive) 25

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Progressive) 25

tag: ever treated for sarcoidosis

tag: array

tag: position

tag: pc1 (methylation)


title: [DNAm]Sarcoidosis (Progressive) 12

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Progressive) 12

tag: pc2 (methylation)

tag: pc3 (methylation)

tag: pc4 (methylation)

tag: pc5 (methylation)


title: [DNAm]Sarcoidosis (Progressive) 15

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Progressive) 15

tag: diagnosis

tag: age

tag: Sex

tag: race


title: [DNAm]Sarcoidosis (Progressive) 3

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Progressive) 3

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: acute disease


title: [DNAm]Sarcoidosis (Progressive) 13

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Progressive) 13

tag: multiorgan involvement

tag: fvc (% predicted)

tag: fev1 (% predicted)

tag: dlco (% predicted)


title: [DNAm]Sarcoidosis (Non-Progressive) 7

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 7

tag: ever treated for sarcoidosis

tag: array

tag: position

tag: pc1 (methylation)


title: [DNAm]Sarcoidosis (Progressive) 1

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Progressive) 1

tag: pc2 (methylation)

tag: pc3 (methylation)

tag: pc4 (methylation)

tag: pc5 (methylation)


title: [DNAm]Sarcoidosis (Progressive) 2

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Progressive) 2

tag: diagnosis

tag: age

tag: Sex

tag: race


title: [DNAm]Sarcoidosis (Progressive) 23

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Progressive) 23

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: acute disease


title: [DNAm]Sarcoidosis (Non-Progressive) 6

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 6

tag: multiorgan involvement

tag: fvc (% predicted)

tag: fev1 (% predicted)

tag: dlco (% predicted)


title: [DNAm]Sarcoidosis (Non-Progressive) 4

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 4

tag: ever treated for sarcoidosis

tag: array

tag: position

tag: pc1 (methylation)


title: [DNAm]Sarcoidosis (Non-Progressive) 25

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 25

tag: pc2 (methylation)

tag: pc3 (methylation)

tag: pc4 (methylation)

tag: pc5 (methylation)


title: [DNAm]Sarcoidosis (Non-Progressive) 33

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 33

tag: diagnosis

tag: age

tag: Sex

tag: race


title: [DNAm]Sarcoidosis (Non-Progressive) 3

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 3

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: acute disease


title: [DNAm]Sarcoidosis (Non-Progressive) 38

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 38

tag: multiorgan involvement

tag: fvc (% predicted)

tag: fev1 (% predicted)

tag: dlco (% predicted)


title: [DNAm]Sarcoidosis (Non-Progressive) 36

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 36

tag: ever treated for sarcoidosis

tag: array

tag: position

tag: pc1 (methylation)


title: [DNAm]Sarcoidosis (Non-Progressive) 34

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 34

tag: pc2 (methylation)

tag: pc3 (methylation)

tag: pc4 (methylation)

tag: pc5 (methylation)


title: [DNAm]Sarcoidosis (Non-Progressive) 27

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 27

tag: diagnosis

tag: age

tag: Sex

tag: race


title: [DNAm]Sarcoidosis (Non-Progressive) 32

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 32

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: acute disease


title: [DNAm]Sarcoidosis (Non-Progressive) 35

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 35

tag: multiorgan involvement

tag: fvc (% predicted)

tag: fev1 (% predicted)

tag: dlco (% predicted)


title: [DNAm]Sarcoidosis (Non-Progressive) 21

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 21

tag: ever treated for sarcoidosis

tag: array

tag: position

tag: pc1 (methylation)


title: [DNAm]Sarcoidosis (Non-Progressive) 37

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 37

tag: pc2 (methylation)

tag: pc3 (methylation)

tag: pc4 (methylation)

tag: pc5 (methylation)


title: [DNAm]Sarcoidosis (Non-Progressive) 31

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 31

tag: diagnosis

tag: age

tag: Sex

tag: race


title: [DNAm]Sarcoidosis (Non-Progressive) 26

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 26

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: acute disease


title: [DNAm]Sarcoidosis (Non-Progressive) 23

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 23

tag: multiorgan involvement

tag: fvc (% predicted)

tag: fev1 (% predicted)

tag: dlco (% predicted)


title: [DNAm]Sarcoidosis (Non-Progressive) 22

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 22

tag: ever treated for sarcoidosis

tag: array

tag: position

tag: pc1 (methylation)


title: [DNAm]Sarcoidosis (Non-Progressive) 28

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 28

tag: pc2 (methylation)

tag: pc3 (methylation)

tag: pc4 (methylation)

tag: pc5 (methylation)


title: [DNAm]Sarcoidosis (Non-Progressive) 2

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 2

tag: diagnosis

tag: age

tag: Sex

tag: race


title: [DNAm]Sarcoidosis (Non-Progressive) 19

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 19

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: acute disease


title: [DNAm]Sarcoidosis (Non-Progressive) 14

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 14

tag: multiorgan involvement

tag: fvc (% predicted)

tag: fev1 (% predicted)

tag: dlco (% predicted)


title: [DNAm]Sarcoidosis (Non-Progressive) 29

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 29

tag: ever treated for sarcoidosis

tag: array

tag: position

tag: pc1 (methylation)


title: [DNAm]Sarcoidosis (Non-Progressive) 16

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 16

value: Hispanic or Latino

tag: pc2 (methylation)

tag: pc3 (methylation)

tag: pc4 (methylation)

tag: pc5 (methylation)


title: [DNAm]Sarcoidosis (Non-Progressive) 18

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 18

tag: diagnosis

tag: age

tag: Sex

tag: race


title: [DNAm]Sarcoidosis (Non-Progressive) 11

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 11

value: asian

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: acute disease


title: [DNAm]Sarcoidosis (Non-Progressive) 13

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 13

tag: multiorgan involvement

tag: fvc (% predicted)

tag: fev1 (% predicted)

tag: dlco (% predicted)


title: [DNAm]Sarcoidosis (Non-Progressive) 24

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 24

tag: ever treated for sarcoidosis

tag: array

tag: position

tag: pc1 (methylation)


title: [DNAm]Sarcoidosis (Non-Progressive) 15

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 15

tag: pc2 (methylation)

tag: pc3 (methylation)

tag: pc4 (methylation)

tag: pc5 (methylation)


title: [DNAm]Sarcoidosis (Non-Progressive) 30

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 30

tag: diagnosis

tag: age

tag: Sex

tag: race


title: [DNAm]Sarcoidosis (Non-Progressive) 20

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 20

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: acute disease


title: [DNAm]Sarcoidosis (Non-Progressive) 12

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 12

tag: multiorgan involvement

tag: fvc (% predicted)

tag: fev1 (% predicted)

tag: dlco (% predicted)


title: Mycorrhizal, 11 weeks-post-inoculation, biol rep 4

first: Uta

last: Paszkowski

address: 93 Lawrence Weaver Rd

department: Plant Sciences

country: United Kingdom

institute: University of Cambridge

data_processing:
Raw RNAseq reads were quality-filtered to remove low quality reads using FastQC v0.12. Illumina adaptor sequences were trimmed with Trim Galore v0.6.7.
Sample libraries were mapped to the M. paleacea reference genome (GCA_014180765.2) with STAR 2.7.11a.
Mapped reads were counted with Subread (v2.0.6) using the featureCounts function. Only genes with a minimum total of fifty reads across all timepoints/conditions were considered for downstream analysis.
Differential expression analysis was performed with the DESeq2 v1.22.2 R package. Differentially expressed genes were identified by pairwise comparison of mock-inoculated vs. mycorrhizal samples at the same time-point, with a significance threshold of log2 fold-change > |1| and adjusted p-value < 0.05.
Assembly: ASM1418076v2
Supplementary files format and content: tab-delimited text file that includes raw counts for each Sample

organism: Marchantia paleacea

source_name: Thallus midrib

growth_protocol: Four-week-old M. paleacea thalli were transferred to sand pots (5 × 5 × 6 cm, W × L × H). The AMS pots were inoculated with 4% R. irregularis crude inoculum, the mock-inoculated control treatment pots were inoculated with twice-autoclaved 4% (v/v) R. irregularis crude inoculum. Crude inoculum was produced by prolonged co-culture of Tagetes multiflora and R. irregularis (DAOM197198) spores in sand. Inoculated and mock-inoculated plant pots were placed in trays fitted with a closed plastic dome. Plants were grown at 22 °C, 16h day/night cycle with a light intensity of 200 μmol m−2 s−1 PAR. M. paleacea plants were watered three times per week with “artificial rainwater solution” (pH 5.8) until harvesting.

extract_protocol:
Samples were harvested after 5, 8 and 11 WPI, washed in distilled water and fixed in ice-cold 100% methanol. For each biological replicate, four thalli were collected and pooled together for subsequent analysis. The midribs of collected thalli were excised to remove apical notches, lateral margins and gemma cups. After sectioning, midribs were washed 3x in ice cold phosphate-buffered saline (pH 7.4) and snap frozen in liquid nitrogen. The excised midribs were ground in liquid nitrogen with mortar and pestle and total RNA was extracted using PureLinkTM Plant RNA Reagent (Thermo Fisher Scientific, Waltham, USA), following manufacturer’s instructions. 2% (w/v) polyvinylpyrrolidone (PVP40) was added to the Plant RNA Reagent mixture before extraction to improve RNA purity.
cDNA library preparation was performed using 1.1μg of total RNA with a TruSeq Stranded mRNA Library High Throughput Kit (Illumina, San Diego, USA) according to manufacturer’s instructions (Catalog #RS-122-9004, DOC, Part #15031047 Rev.E). Library quality was assessed using a DNA1000 chip on a Bioanalyzer 1200 (Agilent Technologies, Santa Clara, USA) and library quantities were measured with a Qubit dsDNA BR Assay Kit (Thermo Fisher Scientific, Waltham, USA).

tag: tissue

value: Thallus midrib

tag: genotype

value: WT

tag: treatment

value: inoculated with R. irregularis

tag: time

value: 11 weeks post-inoculation


title: Mycorrhizal, 11 weeks-post-inoculation, biol rep 3


title: AAV-Null_rep1

type: RNA

city: Cork

first: Gerard

last: O'Keeffe

address: Western Gateway Building, Western Road

department: Anatomy and Neuorscience

country: Ireland

institute: University College Cork

description:
Gene expression 20 weeks after AAV-Null injection
O2

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µL containing 1x Fragmentation Buffer (Agilent) and 2x Gene Expression Blocking Agent (Agilent) following the manufacturer’s instructions. On completion of the fragmentation reaction, 55 µL of 2x Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Rat Gene Expression Microarray v2 G4858A-074036 8x60K for 17 hours at 65°C in a rotating Agilent G2545A hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 1 minute with 37°C Gene Expression Wash Buffer 2 (Agilent), then dried in an ozone-free atmosphere.

scan_protocol: Microarray slides were scanned with an Agilent Microarray Scanner (Agilent G2565C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Image analysis and quantification of fluorescence data were carried out with Agilent Feature Extraction Software 11.5.1.1 using the Agilent protocol GE1_1105_Oct12, grid template 074809_D_F_20150624 and the QC Metric Set GE1_QCMT_Oct12, default parameters.

organism: Rattus norvegicus

source_name: Brain, SN, 20 weeks

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 2000 ng RNA using the Agilent Low-Input QuickAmp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated using the RNeasy Plus Universal Tissue Kit (QIAGEN) following the manufacturer's recommendations. The protocol includes an on-column DNase digestion. Total RNA was quantified in a NanoDrop Spectrophotometer and quality was confirmed using a 4200 TapeStation (Agilent Technologies, Inc.).

tag: strain

value: Sprague Dawley

value: Female

value: brain

tag: group

value: AAV-Null


title: AAV-aSyn_rep4

description:
Gene expression 20 weeks after AAV-aSynuclein injection
M5

value: AAV-aSyn


title: AAV-aSyn_rep3

description:
Gene expression 20 weeks after AAV-aSynuclein injection
M4


title: AAV-aSyn_rep2

description:
Gene expression 20 weeks after AAV-aSynuclein injection
M3


title: AAV-Null_rep2

description:
Gene expression 20 weeks after AAV-Null injection
O3


title: AAV-Null_rep4

description:
Gene expression 20 weeks after AAV-Null injection
O5


title: AAV-aSyn_rep1

description:
Gene expression 20 weeks after AAV-aSynuclein injection
M2


title: Mycorrhizal, 11 weeks-post-inoculation, biol rep 2


title: Mycorrhizal, 11 weeks-post-inoculation, biol rep 1


title: Mycorrhizal, 8 weeks-post-inoculation, biol rep 3

value: 8 weeks post-inoculation


title: Mycorrhizal, 5 weeks-post-inoculation, biol rep 4

value: 5 weeks post-inoculation


title: Mycorrhizal, 8 weeks-post-inoculation, biol rep 4


title: [DNAm]Sarcoidosis (Non-Progressive) 17

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 17

tag: diagnosis

tag: age

value: white

value: not Hispanic or Latino

value: never

value: y

value: n

tag: ever treated for sarcoidosis

tag: array

tag: position

tag: pc1 (methylation)

tag: pc2 (methylation)

tag: pc3 (methylation)

tag: pc4 (methylation)

tag: pc5 (methylation)


title: Mycorrhizal, 8 weeks-post-inoculation, biol rep 2


title: Mycorrhizal, 8 weeks-post-inoculation, biol rep 1


title: Control, 11 weeks-post-inoculation, biol rep 4

value: Control


title: Control, 11 weeks-post-inoculation, biol rep 2

value: Thallus midrib


title: Mycorrhizal, 5 weeks-post-inoculation, biol rep 1

value: WT


title: Control, 11 weeks-post-inoculation, biol rep 3


title: Control, 8 weeks-post-inoculation, biol rep 1


title: [DNAm]Healthy Control 9

source_name: Bronchoalveolar lavage cells from: Healthy Control 9

value: control

tag: Sex

value: m

tag: race

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: acute disease

tag: multiorgan involvement

tag: fvc (% predicted)

tag: fev1 (% predicted)

tag: dlco (% predicted)


title: Control, 5 weeks-post-inoculation, biol rep 2

tag: tissue

tag: genotype

tag: treatment

tag: time


title: Control, 5 weeks-post-inoculation, biol rep 3


title: [DNAm]Healthy Control 4

source_name: Bronchoalveolar lavage cells from: Healthy Control 4

tag: diagnosis

tag: age

tag: array

tag: position

tag: pc1 (methylation)

tag: pc2 (methylation)

tag: pc3 (methylation)


title: Control, 8 weeks-post-inoculation, biol rep 2


title: Mycorrhizal, 5 weeks-post-inoculation, biol rep 2

value: inoculated with R. irregularis


title: [DNAm]Healthy Control 5

source_name: Bronchoalveolar lavage cells from: Healthy Control 5

tag: Sex

value: f

tag: race

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: pc4 (methylation)

tag: pc5 (methylation)


title: Stage6_rep2

city: Seoul

first: Do Young

last: Hyeon

state: Select State

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
Adapter sequences (TruSeq universal and indexed adapters) were removed using Trimmomatic software (v0.39).
The adapter-trimmed reads were then aligned to the Spirodela polyrhiza reference genome (Spolyrhiza_290) using HISAT2 aligner (v2.2.1) with default options.
After filtering out duplicated reads using Picard tools (v2.25.5), the number of reads mapped to gene features were counted using HTSeq (v0.11.3).
Fragments per kilobase of transcript per million fragments mapped (FPKM) was estimated by dividing the mapped read counts by gene length and total number of reads mapped onto protein-coding genes.
Assembly: Spolyrhiza_290
Supplementary files format and content: A tab-delimited text file including FPKM values for each sample

organism: Spirodela polyrhiza

source_name: frond tissues

growth_protocol: Duckweeds were regularly transferred to fresh SH medium once every 7 days. Plants were cultivated in a climate chamber with 60 % relative humidity under long-day conditions (16-h-light/8-h-dark cycles, 23 °C day / 20 °C night regime, 70 μmol m–2 s–1 photon flux density).

extract_protocol:
Total RNA was extracted from frond tissues of S. polyrhiza plants at development stages 2 - 6 (n = 3 for stages 2 - 4 and n = 2 for stages 5 - 6), using the Qiagen RNeasy mini kit (Qiagen, Germany) according to the manufacturer's instructions.
Samples that met the quality control criterion (RNA integrity number > 0.8) were used for library construction. After quality assessment and RNA quantification, mRNA sequencing libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, USA), following the manufacturer’s instructions.

tag: tissue

value: frond tissues

tag: genotype

value: wild-type

tag: developmental stage

value: Stage 6


title: Control, 5 weeks-post-inoculation, biol rep 1

tag: treatment

tag: time


title: [DNAm]Healthy Control 8

source_name: Bronchoalveolar lavage cells from: Healthy Control 8

tag: diagnosis

tag: age

value: Hispanic or Latino

tag: acute disease

tag: multiorgan involvement

tag: fvc (% predicted)

tag: fev1 (% predicted)

tag: dlco (% predicted)

tag: array


title: Stage6_rep1


title: AAV-Null_rep3

description:
Gene expression 20 weeks after AAV-Null injection
O4

tag: strain

value: Sprague Dawley

tag: Sex

value: Female

value: brain

tag: group

value: AAV-Null


title: [DNAm]Healthy Control 16

source_name: Bronchoalveolar lavage cells from: Healthy Control 16

tag: race

value: white

tag: ethnicity

value: not Hispanic or Latino

tag: smoking status

value: never

tag: scadding stage

tag: position

tag: pc1 (methylation)

tag: pc2 (methylation)

tag: pc3 (methylation)

tag: pc4 (methylation)

tag: pc5 (methylation)


title: Stage5_rep2

tag: tissue

tag: genotype

tag: developmental stage

value: Stage 5


title: Stage4_rep3

value: Stage 4


title: Stage5_rep1


title: [DNAm]Sarcoidosis (Non-Progressive) 1

source_name: Bronchoalveolar lavage cells from: Sarcoidosis (Non-Progressive) 1

tag: diagnosis

value: sarcoidosis (non-progressive)

tag: age

tag: acute disease

value: n

tag: multiorgan involvement

tag: fvc (% predicted)

tag: fev1 (% predicted)

tag: dlco (% predicted)

tag: ever treated for sarcoidosis

value: y

tag: array


title: Stage4_rep2


title: Stage3_rep3

value: Stage 3


title: [DNAm]Healthy Control 15

source_name: Bronchoalveolar lavage cells from: Healthy Control 15

value: control

tag: Sex

value: m

tag: race

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: position

tag: pc1 (methylation)


title: Stage3_rep2

tag: tissue

value: frond tissues

tag: genotype

value: wild-type

tag: developmental stage


title: Stage3_rep1


title: Mycorrhizal, 5 weeks-post-inoculation, biol rep 3

value: Thallus midrib

value: WT

tag: treatment

value: inoculated with R. irregularis

tag: time

value: 5 weeks post-inoculation


title: Stage4_rep1


title: Stage2_rep3

value: Stage 2


title: Control, 8 weeks-post-inoculation, biol rep 3

value: Control

value: 8 weeks post-inoculation


title: Stage2_rep2


title: [DNAm]Healthy Control 7

source_name: Bronchoalveolar lavage cells from: Healthy Control 7

tag: diagnosis

tag: age

value: f

value: white

value: not Hispanic or Latino

value: never

tag: acute disease

tag: multiorgan involvement

tag: fvc (% predicted)

tag: pc2 (methylation)

tag: pc3 (methylation)

tag: pc4 (methylation)

tag: pc5 (methylation)


title: BglaT2

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

department: Microbiology

institute: Pusan National University

description: B. gladioli treated with 200 mM NaCl

data_processing:
Raw FASTQ reads were refined by eliminating sequences with suboptimal quality scores, using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). A in-house Python script ensured the alignment of the forward and reverse reads.
Filtered clean reads were mapped to reference genome of each bacteria using the Burrows-Wheeler Aligner (BWA), employing the maximal exact match approach.
Generated SAM ﬁles were subsequently sorted by genomic coordinates using the SAMtools program.
The Subread package and featureCounts tool tallied the reads for each coding sequence.
Gene transcript levels were assessed using the RPKM metric.
Assembly: Burkholderia gladioli BSR3 GCF_000194745.1
Assembly: Pectobacterium carotovorum subsp. carotovorum PCC21 GCF_000294535.1
Assembly: Ralstonia solanacearum GMI1000 GCF_000009125.1
Supplementary files format and content: txt: tab-delimited text files include RPKM values for each sample

organism: Burkholderia gladioli

growth_protocol: Burkholderia gladioli BSR3 and Pectobacterium carotovorum subsp. carotovorum PCC21 were cultured in LB broth at 28°C. Ralstonia solanacearum GMI1000 were cultured at 28°C in casamino acid peptone glucose (CPG) medium (1 g/L casamino acids, 10 g/L peptone, 5 g/L glucose). All liquid cultures were incubated in a shaker-incubator at 200 rpm. Bacterial cultures in the early exponential phase were prepared for both salt-susceptible and salt-tolerant pathogens. To induce a salt stress response, these cultures were exposed to 200 mM NaCl for 2 hours. Cultures without NaCl addition were used as negative controls.

extract_protocol:
For sequencing library preparation, 4 ml of bacterial cultures were harvested by centrifugation at 5000 × g for 10 minutes and then stabilized using the RNAprotect Bacteria Reagent (Qiagen, CA, USA). Total RNA was extracted using the RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. RNA quality and quantity were measured with an Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA). Ribosomal RNA was depleted using the NEBNext rRNA Depletion Kit (New England Biolabs, MA, USA).
The enriched RNA was then used to construct cDNA libraries with the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, CA, USA) according to the manufacturer’s protocol. Paired-end NGS sequencing was performed on the Illumina NovaSeq 6000 platform (Macrogen, Seoul, Korea).

tag: strain

value: 200 mM NaCl

value: wild type

value: 2 hours


title: BglaT1

description: B. gladioli treated with 200 mM NaCl


title: BglaC3

description: B. gladioli

value: sterile water


title: [DNAm]Healthy Control 2

source_name: Bronchoalveolar lavage cells from: Healthy Control 2

value: control

tag: Sex

value: m

tag: race

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: fev1 (% predicted)

tag: dlco (% predicted)

tag: array

tag: position


title: Stage2_rep1

tag: tissue

value: frond tissues

tag: genotype

value: wild-type

tag: developmental stage


title: HUVECs, exposed to a binary suspension of 5% pharmacologically-dehydrated RBCs (pdRBCs) in hRBCs

city: Cartersville

first: Marina

last: Michaud

state: GA

address: 28 Cass Station Dr NW

department: School of Medicine

institute: Emory University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
For snRNA-seq samples, demultiplexing, barcoded processing, gene counting, and aggregation were performed using the 10x CellRanger software (v.7.0.0).
Assembly: Human GRCh38 (GENCODE v32/Ensembl98)
Supplementary files format and content: Tab-separated value (tsv) files for barcodes and genes with matrix files from output of CellRanger processing.

source_name: Vascular

growth_protocol: After introduction of approximately 1,000,000 cells/mL of human umbilical vein endothelial cells (HUVECs) in endothelial growth media (EGM-2, Lonza) with 8% dextran, the microfluidic device was connected to a syringe and tubing filled with EGM-2 and infused at a volumetric flow rate of 1.25 mL/min at 37 ºC and 5% CO2 until a confluent monolayer of endothelial cells is present (approximately 48 hours).

extract_protocol:
Endothelial cells were removed from the microfluidic devices and resuspended in media. The suspension was passed through 70 and 40 μm cell strainers and centrifuged at 500xg at 4°C for 10 minutes. For RBC lysis, ACK buffer was added. For immediate single-cell capture, the cells were pelleted at 400xg at 4°C for 5 minutes and resuspended in PBS containing 1.0% BSA to get a concentration of 500 cells/μl.
For single-cell RNA sequencing (scRNA-seq), barcoded gel bead-in-emulsions (GEMs) were generated from single-cell suspensions with gel beads and reverse transcription (RT) mix on the Chromium Controller, following the 10x Genomics workflow. Following RT and cDNA amplification, the Chromium Next GEM 5’reagent kit v2 (10x Genomics) was used to generate 5’ gene expression libraries. Gene expression libraries were prepared using the Chromium Next GEM 5’reagent kits v2 (10x Genomics). GEMs were generated and barcoded by loading single-cell suspensions along with gel beads and reverse transcription master mix onto Chromium Next GEM Chip K and running on the 10x Genomics chromium controller. Following reverse transcription, the cDNA was amplified and used to generate 5’ gene expression libraries. The cDNA and gene expression libraries were quantified using a Qubit 3.0 fluorometer, and quality was assessed using HS DNA chips and 2100 Bioanalyzer (Agilent Technologies). Sequencing was performed using massively parallel sequencing on the Illumina Novaseq S4 platform, targeting ~50,000 reads/cell to capture the expression of ~1000–2000 transcripts/cell.

treatment_protocol: Human umbilical vein endothelial cells (HUVECs) were exposed to healthy red blood cells (hRBCs) or a binary suspension of 5% pharmacologically-dehydrated RBCs (pdRBCs) in hRBCs, using a four-channel 50 µm microfluidic device. To generate pdRBCs that mimic the decreased deformability of sickle RBCs, hRBCs were pharmacologically-dehydrated with nystatin and high sucrose washes according to established practices to create RBCs with an increased mean corpuscular hemoglobin concentration of 40-42 g/dL.  Following endothelialization of the microfluidic channels, the hRBC or 5% pdRBCs were perfused for 4 hours.

value: Vascular

tag: cell line

value: Human umbilical vein endothelium cells (HUVECs)

tag: cell type

value: Endothelial cells

tag: treatment

value: 5% pdRBCs in hRBCs


title: BglaT3

description: B. gladioli treated with 200 mM NaCl

tag: time


title: HUVECs, exposed to healthy RBC (hRBC) flow

description: 10x Genomics

value: hRBCs


title: Control, 11 weeks-post-inoculation, biol rep 1

value: Thallus midrib

value: WT

value: Control

value: 11 weeks post-inoculation


title: [DNAm]Healthy Control 12

source_name: Bronchoalveolar lavage cells from: Healthy Control 12

tag: diagnosis

tag: age

value: white

value: not Hispanic or Latino

value: never

tag: acute disease

tag: multiorgan involvement

tag: fvc (% predicted)

tag: pc1 (methylation)

tag: pc2 (methylation)

tag: pc3 (methylation)

tag: pc4 (methylation)

tag: pc5 (methylation)


title: [DNAm]Healthy Control 11

source_name: Bronchoalveolar lavage cells from: Healthy Control 11

tag: Sex

tag: race

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: fev1 (% predicted)

tag: dlco (% predicted)

tag: array

tag: position


title: SAM24425533 HCM-CSHL-0459-C17 DMSO

city: South San Francisco

first: Matt

last: Grimmer

state: CA

address: 455 E Grand Ave.

department: Oncology Bioinformatics

institute: Genentech

description: Illumina NovaSeq 6000 LIB5464134_SAM24425533_S7_L002_R1_001.fastq.gz  LIB5464134_SAM24425533_S7_L002_I1_001.fastq.gz

data_processing:
Preprocessing and quality control Single Nucleus RNA-seq (snRNA-seq) data were processed using the Cell Ranger pipeline v3.0.246 with default parameters. Quality control (QC) metrics were calculated for each cell using the `SingleCellExperiment` package. A threshold of 10% for the percentage of reads mapped to mitochondrial genes and ensured a minimum percentage of ribosomal RNA reads were applied to filter out low-quality cells. Only cells passing these criteria were included for downstream analysis. Normalization and feature selection Cell count data were normalized by a size factor based on the total counts for each cell and then log-transformed using the `scran` package to control for sequencing depth and RNA composition bias, along with variance stabilization.
Assembly: hg38
Supplementary files format and content: rds file containing single cell experiment object from R

source_name: Small Intestine

growth_protocol: PDM-272 (HCM-CSHL-0459-C17) were initially obtained from ATCC and maintained in Organoid Media Formulation #1 (ATCC). Specifically, the formulation using Advanced DMEM:F12 is supplemented with 10 mM HEPES, 2mM L-Glutamine, 1x B27 supplement (Thermo), 100 ng/ml Noggin, 50 ng/ml EGF, 10 nM Gastrin (Tocris), 10 uM SB202190 (Selleckchem), 500 nM A83-01 (Tocris), 10 mM Nicotinamide (Sigma) and 1.25 mM N-acetyl cysteine. This formulation does not contain supplemented Wnt ligands.

extract_protocol:
Treated PMD-272 organoid plugs were placed on ice to allow for plug softening and then resuspended in ice cold PBS, pelleted, dissociated using Accutase and gently pipetted to dissociate. Quality of dissociation, viability, and cell amount determined by Vi-CELL BLU instrument (Beckman Coulter). Dissociated cells were then lysed, nuclei isolated and determined for quality isolation.
snRNAseq libraries was generated using Chromium Single Cell Next GEM Reagent Kit (10X Genomics) and sequenced in HiSeq6000 (Illumina) per manufacturer’s instructions.

treatment_protocol: PDM-272 (HCM-CSHL-0459-C17) were treated in biologic duplicate with DMSO or Ceapin-A7 (3 μM) for 48 hours and processed following the Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequence (Demonstrated Protocol CG000365, Rev C, 10X Genomics) protocol.

tag: tissue

value: Small Intestine

tag: cell line

tag: cell type

value: Adenocarcinoma

tag: treatment

value: DMSO


title: SAM24425531 HCM-CSHL-0459-C17 Ceapin-A7

description: Illumina NovaSeq 6000 LIB5464133_SAM24425531_S8_L002_R1_001.fastq.gz  LIB5464133_SAM24425531_S8_L002_I1_001.fastq.gz


title: SAM24425530 HCM-CSHL-0459-C17 Ceapin-A7

description: Illumina NovaSeq 6000 LIB5464132_SAM24425530_S9_L002_R1_001.fastq.gz  LIB5464132_SAM24425530_S9_L002_I1_001.fastq.gz


title: SAM24425534 HCM-CSHL-0459-C17 DMSO

description: Illumina NovaSeq 6000 LIB5464135_SAM24425534_S12_L002_R1_001.fastq.gz  LIB5464135_SAM24425534_S12_L002_I1_001.fastq.gz


title: BglaC1

description: B. gladioli

tag: strain

value: sterile water

tag: genotype

value: wild type

tag: time

value: 2 hours


title: RC4-2B, biol rep 3

city: Gainesville

first: Alexander

last: Ishov

address: 2033 Mowry Rd

institute: University of Florida

data_processing:
Short reads were mapped to the GRCh38 reference transcriptome using STAR
Assembly: Short reads were mapped to the GRCh38
Supplementary files format and content: tab-delimited text file includes the readcount list with the annotation of each gene
Supplementary files format and content: tab-delimited text file includes the FPKM list with the annotation of each gene

source_name: prostate

growth_protocol: Cells were propogated in RPMI-1640 medium suplemented with 10% FBS, 1X penicillin/streptomycin at 5% CO2, 37C .

extract_protocol:
total RNA was isolated using RNeasy Plus Kit (QIAGENE) according to the manual
unknown

value: prostate

value: human prostate cell line


title: [DNAm]Healthy Control 13

source_name: Bronchoalveolar lavage cells from: Healthy Control 13

tag: diagnosis

value: control

tag: age

value: f

tag: acute disease

tag: multiorgan involvement

tag: fvc (% predicted)

tag: pc1 (methylation)

tag: pc2 (methylation)

tag: pc3 (methylation)

tag: pc4 (methylation)

tag: pc5 (methylation)


title: RC4-2B, biol rep 2

tag: tissue


title: RC4-2B, biol rep 1

tag: cell line


title: C4-2B, biol rep 3

tag: cell type


title: [DNAm]Healthy Control 14

source_name: Bronchoalveolar lavage cells from: Healthy Control 14

tag: Sex

tag: race

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: fev1 (% predicted)

tag: dlco (% predicted)

tag: array

tag: position


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 207

city: Utrecht

first: Joost

last: Koedijk

address: Heidelberglaan 25

country: Netherlands

institute: Princess Máxima Center for Pediatric Oncology

data_processing:
After pre-processing, reads were aligned to GRCh38 and gencode version 31. Pre-processing of RNA-seq data was done with the institute's standardized pipelines implementing GATK 4.0 best practices for variant calling using a wdl and cromwell-based workflow (PMID: 25431634 by Van der Auwera et al. & van Belzen et al. PMID 37400763).
Assembly: GRCh38
Supplementary files format and content: Raw counts

source_name: bone marrow

extract_protocol:
Total RNA was isolated from tumor samples using the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to standard protocol on the QiaCube (Qiagen).
RNA-sequencing libraries were generated from 300 ng RNA using the KAPA RNA HyperPrep Kit with RiboErase (Roche). Sequencing was performed using the NovaSeq 6000 (2 x 150 bp) (Illumina).

value: bone marrow

tag: cytogenetics

tag: relevant mutations

tag: treatment

value: treatment-naïve


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 208


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 204

value: No relevant fusions

value: NRAS, MTOR


title: C4-2B, biol rep 2


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 203

value: KMT2A-MLLT3 + PAX5-ZCCHC7


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 205


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 206


title: [DNAm]Healthy Control 3

source_name: Bronchoalveolar lavage cells from: Healthy Control 3

tag: diagnosis

tag: age

value: asian

value: not Hispanic or Latino

tag: acute disease

tag: multiorgan involvement

tag: fvc (% predicted)

tag: pc1 (methylation)

tag: pc2 (methylation)

tag: pc3 (methylation)

tag: pc4 (methylation)


title: [DNAm]Healthy Control 1

source_name: Bronchoalveolar lavage cells from: Healthy Control 1

tag: Sex

value: m

tag: race

value: white

tag: ethnicity

tag: smoking status

value: never

tag: scadding stage

tag: pc5 (methylation)


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 200

tag: tissue

tag: cytogenetics

tag: relevant mutations


title: C4-2B, biol rep 1

tag: cell line

tag: cell type


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 198

tag: treatment


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 199


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 197


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 209


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 202


title: [DNAm]Healthy Control 10

source_name: Bronchoalveolar lavage cells from: Healthy Control 10

tag: diagnosis

tag: age

tag: acute disease

tag: multiorgan involvement

tag: fvc (% predicted)

tag: fev1 (% predicted)

tag: dlco (% predicted)

tag: array

tag: position


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 196

value: PAX5-KDM4C + PAX5-ZCCHC7


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 194


title: [DNAm]Healthy Control 6

source_name: Bronchoalveolar lavage cells from: Healthy Control 6

tag: Sex

tag: race

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: pc1 (methylation)

tag: pc2 (methylation)

tag: pc3 (methylation)

tag: pc4 (methylation)


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 195

tag: tissue

tag: cytogenetics

tag: relevant mutations

tag: treatment


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 193


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 192


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 190

value: NRAS, KRAS


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 188

value: ETV6-RUNX1 + PAX5-EZR

value: KRAS, NUP93


title: BglaC2

description: B. gladioli

tag: strain

value: sterile water

tag: genotype

value: wild type

tag: time

value: 2 hours


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 189

value: bone marrow

value: TCF3-PBX1 + PAX5-ZCCHC7


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 201

value: No relevant fusions

value: treatment-naïve


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 191


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 187


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 186


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 184

value: PAX5-ASXL1 + PAX5-COMMD7

value: NRAS


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 182


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 185


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 183

value: FLT3, NRAS


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 181


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 179


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 177


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 178

value: MEF2D-PLEKHO1 + MEF2D-RPL22

value: PTPN11, NUP93


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 176


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 175


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 174


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 173


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 171


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 172


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 170


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 169


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 168


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 166


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 167


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 160


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 162


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 163


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 161


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 159


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 158

value: IDH2, FLT3


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 156


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 180


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 155


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 152

value: KMT2A-AFF1 + PAX5-ZCCHC7


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 151

value: NRAS, KRAS


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 154

value: ETV6-RUNX1 + PAX5-ZCCHC7


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 157


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 148

value: KRAS, RUNX1


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 147

value: AOC1, ETV6


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 153


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 146


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 150

value: CREBBP


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 144


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 145


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 143


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 142

value: PAX5-TOMM5 + PAX5-FBXO10

value: CRLF2, PAX5


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 141

value: bone marrow

value: NRAS, PTPN11


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 165

value: No relevant fusions

value: treatment-naïve


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 140

value: PAX5-RHOA + PAX5-ZCCHC7

value: KRAS


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 138


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 164


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 139


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 136


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 137

value: NRAS, PTPN14


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 135


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 133

value: PTPN11, GAS2L3


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 132


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 134


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 131


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 130

value: NRAS


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 129

value: KRAS, PAX5


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 128


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 149


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 125


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 127


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 121


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 123


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 119


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 122


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 117

value: KRAS, NRAS


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 124


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 126


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 116


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 120


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 114


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 115


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 113


title: LNT2

city: La Jolla

first: Aleksandr

last: Arzamasov

address: 10901 N Torrey Pines Rd

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Raw reads were demultiplexed and quality checked via FastQC (v0.11.9). Illumina sequencing adapters and short reads (< 20 bp) were trimmed by Cutadapt (v4.11) with parameters: --nextseq-trim=20 -m 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC
Reads were aligned to rRNA gene sequences extracted from the B. kashiwanohense Bg42221_1E1 genome using Bowtie2 (v2.4.5) to filter out rRNA reads. Unmapped (filtered) reads were pseudoaligned to the B. kashiwanohense Bg42221_1E1 transcriptome via Kallisto (v0.48) with parameters: --single -l 150 -s 20 --rf-stranded
Kallisto transcript quantification data were imported into R using the TxImport package and normalized by the TMM method in the edgeR package. Genes with < 1 count per million (CPM) in ≤ 3 samples were filtered out
Normalized, filtered data were variance-stabilized using the VOOM function in the Limma package in R
Differentially expressed genes were identified by linear modeling and Bayesian statistics using the Limma package
Assembly: Bifidobacterium catenulatum subsp. kashiwanohense Bg42221_1E1
Supplementary files format and content: tab-delimited txt file that includes a matrix with raw gene counts for every gene and every sample

source_name: cell culture

growth_protocol: Overnight culture of Bifidobacterium catenulatum subsp. kashiwanohense Bg42221_1E1 grown in MRS-AC-Glc was harvested at 5,000 × g for 5 min, washed with sugar-free MRS-AC, and used to inoculate MRS-AC medium supplemented with either Glc, Lac, LNT (10 mg/mL) or tamarind xyloglucan (XGL) (5 mg/mL) at OD600=0.01. Samples (2 mL, biological triplicates) were collected at the early exponential phase (OD600=0.35) and immediately pelleted in a prechilled centrifuge at 4,800 × g for 5 min. Cell pellets were snap-frozen in liquid nitrogen and stored at −80°C until further use.

extract_protocol:
Frozen cell pellets obtained from 2 ml of early exponential phase cultures (OD600=0.35) were resuspended in a solution containing 710 µL of the extraction mixture (200 mM NaCl, 20 mM EDTA, 20% SDS), 500 µL of phenol:chloroform:isoamyl alcohol (125:24:1, pH 4.5), and 250 µL of acid-washed glass beads (212-300 µm). Cells were disrupted using Bead Ruptor 12 (Omni International) by alternating 2 min of homogenizing at 6 m/s and 2 min of cooling on ice. Cellular debris was removed by centrifugation (16,000 × g for 10 min), and the aqueous phase was collected. RNA was precipitated with isopropanol and sodium acetate (pH 5.5) at −20 °C overnight, washed twice in ice-cold 70% ethanol, and resuspended in 100 µL of nuclease-free water. Total RNA was subjected to two consecutive DNase treatments (30 min each) with Turbo DNase (Ambion) and Baseline-ZERO DNase (Lucigen), respectively. Each treatment was followed by cleanup using MEGAclear Transcription Clean-Up Kit (Ambion). RNA was quantified via Qubit Broad Range RNA Assay Kit (Invitrogen), and RNA integrity was confirmed by gel electrophoresis in 1 % agarose and 4200 TapeStation System (Agilent). All samples had RIN > 8.0
Ribosomal RNA was depleted with the NEBNext rRNA depletion kit for bacteria (New England Biolabs) and a set of 20 pooled sequence-specific probes for B. kashiwanohense Bg42221_1E1 designed with NEBNext Custom RNA Depletion Design Tool v1.0. Barcoded libraries were made with NEBNext Ultra II directional RNA library prep kit for Illumina (New England Biolabs). Libraries were pooled and sequenced (single-end 75-bp reads) on Illumina NextSeq 500 using the High Output V2 kit (Illumina).

tag: cell type

value: cell culture

value: WT

tag: carbon source

value: Lacto-N-tetraose


title: LNT3

organism: Bifidobacterium catenulatum subsp. kashiwanohense


title: LNT1


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 118


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 112

value: HLA-A


title: XGL3

value: Xyloglucan


title: XGL2


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 111


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 110

value: PAX5-ZCCHC7 + PAX5-ETV6 + PAX5-RNF38


title: Lac2

value: Lactose


title: Lac3


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 108

value: bone marrow

value: KRAS, FLT3


title: Lac1


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 107

value: treatment-naïve


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 109


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 105

value: No relevant fusions


title: Glc2

value: Glucose


title: Glc1


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 106


title: Nasal swab cells, K9_HC_9656

city: Fort Collins

first: Steven

last: Dow

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

data_processing:
Partek Flow software, version 10.0
filtered by removing reads containing adapters and reads containing N > 10% and for Phred scores >30
Filtered reads were aligned with STAR 2.7.3a, using CanFam3.1 genome
Aligned reads were annotated and counted using HT-seq
differentially expressed genes were identified using DEseq2
Assembly: CanFam3.1
Supplementary files format and content: txt file with median ratio normalized counts

organism: Canis lupus familiaris

source_name: nasal swab cells

growth_protocol: Nasal swabs

extract_protocol:
Rneasy Mini
Takara Bio SMARTseq

treatment_protocol: RNA Later preservation, PBS wash

value: nasal swab cells

tag: disease

value: healthy control


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 102


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 103

value: NRAS


title: Nasal swab cells, K9_HC_9644


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 101


title: Nasal swab cells, K9_HC_7769


title: Nasal swab cells, K9_HC_4394


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 99


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 100


title: Nasal swab cells, K9_HC_0442


title: XGL1


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 98


title: Nasal swab cells, K9_HC_2480


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 96

value: ETV6-RUNX1 + PAX5-UBB


title: Nasal swab cells, K9_CR_8552

value: rhinitis


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 97


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 95


title: Nasal swab cells, K9_CR_5225


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 94


title: Glc3

value: cell culture


title: Nasal swab cells, K9_CR_5176


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 93


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 104


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 92


title: Liver, Exercise 5(E5)

city: Wuhan

first: Yan

last: Wang

state: China

address: Luojiashan, wuchang, wuhan

institute: College of Life Sciences, Wuhan University

data_processing:
ThesequencingdatawasfilteredwithSOAPnuke( v 1.6.5)by(1)Removingreadscontainingsequencingadapter;(2)Removingreadswhoselow-qualitybaseratio(basequalitylessthanorequalto15)ismorethan20%;(3)Removingreadswhoseunknownbase('N'base)ratioismorethan5%,afterwardscleanreadswereobtainedandstoredinFASTQformat.
ThecleandataweremappedtothereferencegenomebyHISAT(v2.1.0)
The clean data were mapped to the assembled unique gene by Bowtie2 (v2.3.4.3). The expression level of genes was calculated by RSEM (v1.3.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM for each Sample

source_name: Liver

extract_protocol:
Total RNA was extracted from tissues or cells with TRI Reagent (Sigma-Aldrich).1ug of total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using BGI Optimal Dual-mode mRNA-Seq Library Prep Kit following manufactuer's protocols.

value: Liver

value: WT

value: Exercise


title: Nasal swab cells, K9_CR_3251


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 91


title: Liver, Exercise 6(E6)


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 90


title: Liver, Exercise 4(E4)


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 88


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 89


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 86


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 87


title: Liver, Exercise 1(E1)


title: Liver, Sedentary 6(S6)

value: Sedentary


title: Nasal swab cells, K9_CR_8372


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 85


title: Liver, Exercise 2(E2)


title: Nasal swab cells, K9_CR_5392


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 84

value: KRAS


title: Liver, Sedentary 4(S4)


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 83


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 81

value: ETV6-RUNX1 (like)


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 82

value: bone marrow


title: Liver, Sedentary 2(S2)


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 79


title: Liver, Sedentary 1(S1)


title: RsolT2

description: R. solanacearum treated with 200 mM NaCl

organism: Ralstonia solanacearum

value: 200 mM NaCl

value: wild type

value: 2 hours


title: RsolT3


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 78

value: No relevant fusions

value: treatment-naïve


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 77


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 76


title: RsolC3

description: R. solanacearum

value: sterile water


title: RsolT1


title: RsolC2

description: R. solanacearum


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 74

value: TCF3-PBX1 + PAX5-IRX2 + PAX5-LINC01400


title: Liver, Exercise 3(E3)


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 71


title: RsolC1

description: R. solanacearum


title: Bulk RNA-seq of BMMCs from pediatric BCP-ALL patient 73


title: Liver, Sedentary 5(S5)