title: RNA-seq of LHCN-M2 cells with inducible sDUX treated with doxycycline for 6 hrs replicate 3

city: Minneapolis

first: Micah

last: Gearhart

address: 6-160 Jackson Hall, 321 Church St.

institute: University of Minnesota

description: sDUX 6hr rep3

data_processing:
Paired-end Illumina sequencing reads were trimmed with TrimGalore (0.6.0).
Transcript abundance was quantified using the human Gencode annotations (v38) using Salmon (v 1.9) with the GC-bias correction option.
Counts were imported into R (4.2.1) using tximport (v 1.24.0). Differentially expressed genes were identified with DESeq2 (v1.36.0).
Assembly: GRCh38
Supplementary files format and content: Excel table of normalized FPKMs and Raw Counts and rdata object containing annotated DESeq2 dataset.
Supplementary files format and content: NarrowPeak format for called peaks and bigWig files of merged coverage.

source_name: cell line

extract_protocol:
Swift rapid RNA library kit
RNA-seq samples were extracted with Zymo RNA extraction kit.

value: cell line

tag: cell line

value: immortalized human myoblast

tag: lentiviral _transduction

value: FUGW-rtTA and pSAM2-sDUX

value: 200 ng/mL doxycycline for 6 hrs


title: Total epidermal cells from SCD1-/-  mice (Male) at P1

status: Public on Feb 08 2023

type: SRA

city: Shanghai

first: Yueqing

last: Xue

state: 上海市

address: 319 Yueyang Road

country: China

institute: Shanghai Institute of Nutrition and Health

library_source: transcriptomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and  paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: raw counts and fpkm

molecule: total RNA

organism: Mus musculus

source_name: skin

extract_protocol:
Digest the skin samples to get the epidermal cells and RNA was harvested using Trizol reagent.
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: strain

tag: tissue

value: skin

tag: cell type

value: epidermal cells

tag: Sex

value: Male

tag: age

value: post natal day 1

tag: genotype


title: Total epidermal cells from SCD1-/-  mice (Female) at P1

value: Female


title: RNA-seq of LHCN-M2 cells with inducible sDUX treated with doxycycline for 6 hrs replicate 2

state: MN

department: Genetics, Cell Biology and Development

country: USA

description: sDUX 6hr rep2

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: LHCN-M2 immortalized human myoblasts were cultured in F10 medium (HyClone) with 20% FBS (Peak Serum), 2-mercaptoethanol 1x (Gibco), 10-9 M dexamethasone (Sigma), 10 ng/mL bFGF (Peprotech), Glutamax (Gibco), and Penicillin/Streptomycin (P/S, Gibco) at 37°C and 5% CO2

treatment_protocol: Cells were mock treated or treated with doxycycline as indicated.

tag: treatment


title: 204339300117_R06C01

type: genomic

city: Heidelberg

first: Daniel

last: Schrimpf

address: Im Neuenheimer Feld 224

department: Neuropathology

country: Germany

institute: University Hospital Heidelberg, Intitute of Pathology

description:
Methylation data from tumor sample
Sample 18

hyb_protocol: Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing:
Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'  Average beta
processed data file includes: Average Beta

molecule: genomic DNA

source_name: ERMS

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

treatment_protocol: An automated extraction was done with a Maxwell system (Promega, Fitchburg, WI, USA) and the Maxwell 16 FFPE Plus LEV DNA Purification Kit according to the manufacturer’s instructions.

value: tumor

tag: tissue preparation

value: FFPE


title: ADCC.80

type: RNA

city: Brescia

first: Stefano

last: Calza

state: Brescia

address: Viale Europa 11

department: DMMT

country: Italy

institute: University of Brescia

description: gene expression

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Data were processed using R version 4.2.1 and Bioconductor, with package oligo

label: biotin

source_name: FFPE tissue

label_protocol: not provided

extract_protocol: not provided

value: Adenoid cystic carcinoma (ACC)

tag: subject id

value: Patient 80


title: ADCC.15

description: gene expression

value: Patient 15


title: 204339300117_R04C01

description:
Methylation data from tumor sample
Sample 17


title: ADCC.83

description: gene expression

value: Patient 83


title: 203989100105_R06C01

description:
Methylation data from tumor sample
Sample 16


title: Total epidermal cells from WT mice (Male) at P1

value: WT


title: RNA-seq of LHCN-M2 cells with inducible sDUX treated with doxycycline for 6 hrs replicate 1

description: sDUX 6hr rep1


title: ADCC.78

description: gene expression

value: Patient 78


title: 203989100005_R03C01

description:
Methylation data from tumor sample
Sample 15


title: RNA-seq of LHCN-M2 cells with inducible DUXB-VP64 treated with doxycycline for 6 hrs replicate 3

description: DUXB-VP64 6hr rep3

value: cell line

value: FUGW-rtTA and pSAM2-DUXB-VP64


title: RNA-seq of LHCN-M2 cells with inducible DUXB-VP64 treated with doxycycline for 6 hrs replicate 2

description: DUXB-VP64 6hr rep2

value: immortalized human myoblast


title: Total epidermal cells from WT mice (Female) at P1


title: ADCC.77

description: gene expression

value: Patient 77


title: Adult Small intestinal  Myh11Cre+;PdgfraEGFP- single cell RNA seq

city: Boston

first: Ramesh

last: Shivdasani

state: MA

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

description: Myh11CreERT2;Rosa26tDt+;PdgfraEGFP- mesenchymal cells from small intestine. Animal was injected 2X with 10 mg TAM on two consecutive days and harvested 5 days later.

data_processing:
Aligned to mm10 using cellranger v3.0.2
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger filtered matrix and corresponding barcodes and features

source_name: Whole Small Intestine Mesenchyme

extract_protocol:
Cells were isolated from entire small intestinal tissues, epithelium denuded via 20 minutes in warm 10mM EDTA/HBSS (at 37 degress C), and tissue further minced by fine scalpels. Digestion of tissue was performed using 3 mg/ml collagenase II (Worthington) in 5%FBS/HBSS at 37 degrees C. Supernatants were collected 40 minutes after digestion, washed to remove debris, treated with ACK lysis buffer to remove RCBs, and strained through a 40 uM filter. Lysates were washed in PBS/0.1%BSA and antibody-labelling was performed prior to FACS. FACS-sorted cells were spun at 300 rcf for 10 minutes, and loaded on a 10X Chromium Controller (10X Genomics) for targeting 5-10,000 cells using the single cell 3' V3.1 assay. Reverse transcription, cDNA amplification and library prep were completed according to manufacturer's protocol. Sequencing of library was performed using a HiSeq4000 Illumina System.
Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10X Genomics)

value: Whole Small Intestine Mesenchyme

tag: sort strategy

value: Adult


title: ADCC.24

description: gene expression

value: Patient 24


title: Adult colonic  Myh11Cre+;PdgfraEGFP- single cell RNA seq

description: Myh11CreERT2;Rosa26tDt+;PdgfraEGFP- mesenchymal cells from colon. Animal was injected 2X with 10 mg TAM on two consecutive days and harvested 5 days later.

source_name: Whole Colon Mesenchyme

value: Whole Colon Mesenchyme


title: RNA-seq of LHCN-M2 cells with inducible DUXB-VP64 treated with doxycycline for 6 hrs replicate 1

description: DUXB-VP64 6hr rep1

value: 200 ng/mL doxycycline for 6 hrs


title: 205624630150_R06C01

description:
Methylation data from tumor sample
Sample 13

value: tumor


title: ADCC.5

description: gene expression

value: Patient 5


title: ADCC.76

description: gene expression

value: Adenoid cystic carcinoma (ACC)

value: Patient 76


title: P14-stage PdgfraEGFP Single Cell RNA-seq rep2

description: Small intestinal PEGFP+ mesenchyme from P14 pups (roughly 5 combined). Stripped as much muscle/serosa as possible.

source_name: Proximal Small Intestinal Cells

value: Proximal Small Intestinal Cells


title: 205624630150_R05C01

description:
Methylation data from tumor sample
Sample 12

value: FFPE


title: RNA-seq of LHCN-M2 cells with inducible DUXB treated with doxycycline for 6 hrs replicate 3

description: DUXB 6hr rep3

value: FUGW-rtTA and pSAM2-DUXB


title: 205624630146_R05C01

description:
Methylation data from tumor sample
Sample 11


title: RNA-seq of LHCN-M2 cells with inducible DUXB treated with doxycycline for 6 hrs replicate 2

description: DUXB 6hr rep2


title: 203989100005_R01C01

description:
Methylation data from tumor sample
Sample 14


title: P14-stage PdgfraEGFP Single Cell RNA-seq rep1

description: Small intestinal PEGFP+ mesenchyme from P14 pups (roughly 5 combined).


title: ADCC.75

description: gene expression

value: Patient 75


title: RNA-seq of LHCN-M2 cells with inducible DUXB treated with doxycycline for 6 hrs replicate 1

description: DUXB 6hr rep1

value: cell line


title: 205624630146_R04C01

description:
Methylation data from tumor sample
Sample 10


title: P14-stage Whole Mesenchyme Single Cell RNA seq

description: Proximal small intestinal mesenchyme from P14 pups (roughly 9 combined).

source_name: Proximal Small Intestine Mesenchyme

value: Proximal Small Intestine Mesenchyme

value: Wild-Type


title: P9-stage Whole Mesenchyme Single Cell RNA seq rep3

description: Proximal small intestinal mesenchyme from P9 pups (roughly 9 combined).

value: EPCAM-


title: ADCC.73

description: gene expression

value: Patient 73


title: ADCC.72

description: gene expression

value: Patient 72


title: 205624630146_R03C01

description:
Methylation data from tumor sample
Sample 9


title: RNA-seq of LHCN-M2 cells with inducible DUXA-VP64 treated with doxycycline for 6 hrs replicate 3

description: DUXA-VP64 6hr rep3

value: immortalized human myoblast

value: FUGW-rtTA and pSAM2-DUXA-VP64


title: RNA-seq of LHCN-M2 cells with inducible DUXA-VP64 treated with doxycycline for 6 hrs replicate 2

description: DUXA-VP64 6hr rep2

value: 200 ng/mL doxycycline for 6 hrs


title: P9-stage Whole Mesenchyme Single Cell RNA seq rep1


title: ADCC.71

description: gene expression

value: Patient 71


title: 203989100006_R03C01

description:
Methylation data from tumor sample
Sample 7

value: tumor


title: P5-stage Whole Mesenchyme Single Cell RNA seq rep2

description: Proximal small intestinal mesenchyme from P5 pups (roughly 9 combined).


title: 203989100005_R05C01

description:
Methylation data from tumor sample
Sample 6


title: RNA-seq of LHCN-M2 cells with inducible DUXA treated with doxycycline for 6 hrs replicate 3

description: DUXA 6hr rep3

value: FUGW-rtTA and pSAM2-DUXA


title: P5-stage Whole Mesenchyme Single Cell RNA seq rep1


title: RNA-seq of LHCN-M2 cells with inducible DUXA treated with doxycycline for 6 hrs replicate 2

description: DUXA 6hr rep2


title: ADCC.70

description: gene expression

value: Adenoid cystic carcinoma (ACC)

value: Patient 70


title: P5-stage PdgfraEGFP Single Cell RNA-seq

description: Small intestinal PEGFP+ mesenchyme from P5 pups (roughly 5 combined). Stripped as much muscle/serosa as possible.

value: Proximal Small Intestinal Cells


title: RNA-seq of LHCN-M2 cells with inducible DUXA treated with doxycycline for 6 hrs replicate 1

description: DUXA 6hr rep1


title: ADCC.13

description: gene expression

value: Patient 13


title: 204339300117_R08C01

description:
Methylation data from tumor sample
Sample 8

value: FFPE


title: ADCC.45

description: gene expression

value: Patient 45


title: 205624640018_R02C01

description:
Methylation data from tumor sample
Sample 4

source_name: AS


title: P9-stage Whole Mesenchyme Single Cell RNA seq rep2

value: Proximal Small Intestine Mesenchyme


title: P4-stage Whole Mesenchyme Single Cell RNA seq

description: Small intestinal mesenchyme from P4 pups (roughly 9 combined).

value: Wild-Type


title: RNA-seq of LHCN-M2 cells with inducible DUXA-VP64 treated with doxycycline for 6 hrs replicate 1

description: DUXA-VP64 6hr rep1

value: cell line


title: RNA-seq of LHCN-M2 cells treated with doxycycline for 6 hrs replicate 3

description: Control 6hr rep3

value: wild type


title: 205624630180_R08C01

description:
Methylation data from tumor sample
Sample 3


title: ADCC.69

description: gene expression

value: Patient 69


title: ADCC.63

description: gene expression

value: Patient 63


title: P2-stage PdgfraEGFP Single Cell RNA-seq

description: Proximal small intestinal hi and lo PEGFP+ mesenchyme from P2 pups (roughly 5 combined).


title: RNA-seq of LHCN-M2 cells treated with doxycycline for 6 hrs replicate 2

description: Control 6hr rep2

value: immortalized human myoblast


title: ADCC.68

description: gene expression

value: Patient 68


title: 202259350188_R03C01

description:
Methylation data from tumor sample
Sample 2

source_name: HGESS


title: 205624630180_R07C01

description:
Methylation data from tumor sample
Sample 5


title: P1-stage Whole Mesenchyme Single cell RNA-seq rep2

description: proximal small intestinal mesenchyme from P1 pups (roughly 9 combined).

value: EPCAM-


title: ADCC.62

description: gene expression

value: Patient 62


title: ADCC.64

description: gene expression

value: Patient 64


title: ADCC.66

description: gene expression

value: Adenoid cystic carcinoma (ACC)

value: Patient 66


title: JZ12

status: Public on Feb 07 2023

city: Cambridge

first: Jorge

last: Lopez-Tello

state: Please Select

address: Centre for trophoblast research, Dept Physiology, Development and  Neuroscience, DOWNING ST

country: United Kingdom

institute: University of Cambridge

description: Placenta JZ

data_processing: gene expression  normalized to Actb/Gapdh/ Ywhaz as reference genes. Target gene signals normalized to housekeeping genes; 2^-deltaCt

label: SYBR Green

source_name: Placenta

extract_protocol: Total RNA was extracted with RNeasy Plus Mini Kit (Qiagen) RNA was reverse transcribed using a high-capacity cDNA reverse transcription kit (Applied Biosystems) according to manufacturer’s instructions. Samples were analysed with a StepOne real-time PCR machine (Thermo Fisher Scientific) in duplicate using SYBR Green qPCR master mix (Applied Biosystems, Thermo Fisher Scientific)

tag: condition

value: Control

value: mouse dissected placenta GD16


title: JZ16

description: Placenta JZ

value: SGA


title: JZ15

description: Placenta JZ


title: JZ17

description: Placenta JZ


title: JZ9

description: Placenta JZ


title: JZ10

description: Placenta JZ


title: JZ11

description: Placenta JZ


title: RNA-seq of LHCN-M2 cells treated with doxycycline for 6 hrs replicate 1

description: Control 6hr rep1

value: 200 ng/mL doxycycline for 6 hrs


title: JZ13

description: Placenta JZ


title: JZ8

description: Placenta JZ


title: JZ7

description: Placenta JZ


title: P1-stage Whole Mesenchyme Single cell RNA-seq rep1

value: Proximal Small Intestine Mesenchyme


title: JZ3

description: Placenta JZ


title: JZ4

description: Placenta JZ


title: JZ5

description: Placenta JZ


title: 202163110068_R08C01

description:
Methylation data from tumor sample
Sample 1

value: tumor

value: FFPE


title: JZ18

description: Placenta JZ


title: JZ2

description: Placenta JZ


title: JZ1

description: Placenta JZ


title: Brain 17

description: fetal brains

source_name: brain tissue

value: mouse fetal brain GD16


title: Brain 16

description: fetal brains


title: JZ6

description: Placenta JZ


title: Brain 15

description: fetal brains


title: Brain 14

description: fetal brains


title: Brain 13

description: fetal brains


title: Brain 12

description: fetal brains


title: Brain 10

description: fetal brains


title: Brain 8

description: fetal brains


title: Brain 5

description: fetal brains


title: Brain 1

description: fetal brains


title: Brain 3

description: fetal brains


title: Brain 2

description: fetal brains


title: Brain 4

description: fetal brains


title: Brain 7

description: fetal brains


title: Tongue 2

city: Pullman

first: Michael

middle: Paul

last: Phelps

state: WA

address: 100 Dairy Rd

department: Animal Sciences

institute: Washington State University

hyb_protocol: Standard NanoString nCounter hybridization conditions were used for the analysis of gene expression

data_processing: Data processing was performed with nSolver software version 4.0 using default normalization conditions

organism: Oncorhynchus mykiss

source_name: Tongue 2

growth_protocol: Clonal rainbow trout from the Swanson and Oregon State University lines were grown to adulthood (2-3 years old) in recirculating systems

extract_protocol: The extraction protocol varied by tissue type from Tri-Reagent extractions (e.g., muscle), to commercial RNA extraction kits (e.g., Zymo)

treatment_protocol: No treatments were performed on the rainbow trout.

value: Male


title: Tongue 3

source_name: Tongue 3


title: Brain 11

description: fetal brains


title: Extraocular Muscle 2

source_name: Extraocular Muscle 2


title: Extraocular Muscle 3

source_name: Extraocular Muscle 3


title: Brain 6

description: fetal brains


title: Extraocular Muscle 1

source_name: Extraocular Muscle 1


title: Brain 9

description: fetal brains


title: Bulbus Arteriosus 2

source_name: Bulbus Arteriosus 2


title: Bulbus Arteriosus 3

source_name: Bulbus Arteriosus 3


title: Bulbus Arteriosus 1

source_name: Bulbus Arteriosus 1


title: Tongue 1

source_name: Tongue 1


title: Pyloric Caeca 3

source_name: Pyloric Caeca 3


title: Pyloric Caeca 1

source_name: Pyloric Caeca 1


title: Distal Intestine 1

source_name: Distal Intestine 1


title: Distal Intestine 3

source_name: Distal Intestine 3


title: Pelvic Fin 3

source_name: Pelvic Fin 3


title: Pyloric Caeca 2

source_name: Pyloric Caeca 2


title: Pelvic Fin 1

source_name: Pelvic Fin 1


title: Retina 3

source_name: Retina 3


title: Retina 2

source_name: Retina 2


title: Retina 1

source_name: Retina 1


title: Testes 3

source_name: Testes 3


title: Cardiac Stomach 1

source_name: Cardiac Stomach 1


title: Cardiac Stomach 2

source_name: Cardiac Stomach 2


title: WT-Day5.CMSIP2

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Removed the low quality reads; Bsmap was used to map the CMS-IP sequences to mm10.
Macs2 was used to call CMS-IP peaks; 10x single cell data was analyzed using Seurat v3.
DESeq2 was used to call differential 5hmC peaks.
Genome_build: mm10
Supplementary_files_format_and_content: csv and bigwig

source_name: mESC day5

growth_protocol: E14-NKX2-5-EmGFP mESC (18) was purchased from Mutant Mouse Resource & Research Centers (MMRRC). Cells were cultured on mitomycin C treated mouse embryonic fibroblasts (MEF) as feeder cells. The culture medium includes Knock-out Dulbecco's Modified Eagle's Medium (Gibco), 15% fetal bovine serum (Omega), 0.5% penicillin-streptomycin (Gibco), 0.1 mM non-essential amino acids (Gibco), 0.1mM 2-mercaptoetanol (Sigma), and 103 U/mL of leukemia inhibitory factor (Millipore).The handing drop differentiation in mESCs was conducted according to the previous protocol (20). Briefly, mESCs were suspended in differentiation culture medium without leukemia inhibitory factor (LIF). Embryonic bodies (EBs) were formed by culturing cells within drops on the up-turned inner surface of the lid of the dishes for 2 days. EBs then were collected from the lids and cultured in the non-adhesive dishes to expand for additional 3 days. The expanded EBs were then cultured in the cell culture dishes to allow them attach for next 5 days.

extract_protocol:
Genomic DNA was isolated using Qiagen DNeasy Blood and Tissue kit. RNA was isolated using Qiagen RNeasy mini kit.
CMS-IP library construction: DNA was sheared using Covaris Adaptive Focused Acoustic to the center at 200 bp. DNA fragments were size selected and ligated with methylated adaptors and treated with sodium bisulfite (invitrogen). The extra adapters were removed by AmpurXP (Beckman). The DNA was then denatured for 10 minutes at 95 °C (0.4 M NaOH, 10 mM EDTA), neutralized by the addition of cold 2M ammonium acetate (pH 7.0) for 10 min on ice. Then denatured DNA fragments were incubated with 1 μl anti-CMS antiserum in 1x IP buffer (10 mM sodium phosphate pH 7.0, 140 mM NaCl, 0.05% Triton X-100) for 2 h at 4 °C, and then precipitated with protein A/G beads. Precipitated DNA was eluted with proteinase K, purified with phenol chloroform, amplified and enriched by 10-12 cycles PCR using Kapa HiFi uracil polymerase. RNA-seq library construction is followed standard illumina library construction protocols. MethylC-seq: DNA was sheared using Covaris Adaptive Focused Acoustic to the center at 300 bp. DNA fragments were size selected and ligated with methylated adaptors and treated with sodium bisulfite (invitrogen). Libraries were enriched by 4-6 cycles PCR using Kapa HiFi uracil polymerase.

treatment_protocol: No treatment

value: embryonic stem cell (ESC)

tag: genotype/variation

value: wild type


title: WT-Day2.CMSIP1

source_name: mESC day2


title: Total epidermal cells from SCD1-/-  mice at P21

source_name: skin

value: skin

value: epidermal cells

value: Female

value: post natal day 21


title: Pelvic Fin 2

source_name: Pelvic Fin 2


title: snRNA-seq_ALIOS_3mo

city: Philadelphia

first: Yang

last: Xiao

state: PA

address: 12-193 Smilow Translational Research Center, 3400 Civic Center Boulevard

institute: UNIVERSITY OF PENNSYLVANIA

data_processing:
The raw fastq files of snRNA-seq were mapped to Mus musculus assembly GRCm38 (mm10) using CellRanger (3.0.2). Unique molecular identifiers (UMI) count matrices were imported into Seurat (3.2.0) (Stuart et al., 2019) to generate Seurat object to each experiment.
The raw fastq files of mouse livers and human livers were mapped to Mus musculus genome assembly GRCm38 (mm10) and Homo sapiens genome assembly GRCh38 (hg38) respectively using Cellranger-atac (1.2.0). The fragment count matrix was imported into ArchR
The raw fastq files of RNA-seq were mapped to Mus musculus assembly GRCm38 (mm10) using STAR (2.5.4) with --quantMode GeneCounts to generate gene count matrix. The matrix was imported into R package DEseq2 to quantify gene expression
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: raw counts files and metadata of cell identity with assigned cluster identity for snRNA-seq; fragment counts files and metadata with assigned cluster identity for snATAC-seq; raw counts files and Deseq2 output for RNA-seq

source_name: whole liver

growth_protocol: C57BL/6J mice were housed in the animal facility with 12h dark/light cycle (7:00am to 7:00pm) and ad libitum access to food and water

extract_protocol:
For snRNA-seq and snATAC-seq, liver nuclei were isolated and loaded to 10X Genomics Chromium controller
For liver RNA-seq, RNA were extracted from whole liver using Trizol and Qiagen RNeasey Mini kit.
For Stellate Cell RNA-seq, RNA were extracted from stellate cells isolated from livers injected with AAV-TBG-GFP and AAV-TBG-Ephb2.
snRNAseq libraries were prepared according to manufacturer’s instructions of Chromium Next GEM Single Cell 3′ Kit
snATACseq libraries were prepared according to manufacturer’s instructions of Chromium Next GEM Single Cell ATAC kit
liver RNA-seq were submitted to Novogene for library preparation
Stellate Cell RNA-seq were prepared according to  manufacturer’s instructions of KAPA RNA HyperPrep with RiboErase
snRNA-seq, snATAC-seq, bulk RNA-seq

treatment_protocol:
C57BL/6J  were fed normal chow or modified ALIOS diet for 3 months or 9 months
C57BL/6J  were injected with AAV8-TBG-GFP or AAV-TBG-Ephb2 and fed normal chow for a week

value: whole liver

value: modified ALIOS diet for 3 months


title: Cardiac Stomach 3

source_name: Cardiac Stomach 3


title: Distal Intestine 2

source_name: Distal Intestine 2


title: Testes 1

source_name: Testes 1


title: Testes 2

source_name: Testes 2


title: 205624630146_R08C01

description:
Methylation data from tumor sample
Sample 22

source_name: ERMS


title: WT-Day5.CMSIP1


title: Ovaries 2

source_name: Ovaries 2


title: Ovaries 3

source_name: Ovaries 3


title: JZ14

description: Placenta JZ

source_name: Placenta

value: Control


title: Head Kidney 3

source_name: Head Kidney 3


title: Visceral Fat 3

source_name: Visceral Fat 3


title: Head Kidney 2

source_name: Head Kidney 2


title: ADCC.81

description: gene expression

source_name: FFPE tissue

value: Adenoid cystic carcinoma (ACC)

value: Patient 81


title: Spleen 3

source_name: Spleen 3


title: Head Kidney 1

source_name: Head Kidney 1


title: Spleen 1

source_name: Spleen 1


title: Ovaries 1

source_name: Ovaries 1


title: Liver 3

source_name: Liver 3


title: Liver 2

source_name: Liver 2


title: Spleen 2

source_name: Spleen 2


title: Liver 1

source_name: Liver 1


title: Visceral Fat 2

source_name: Visceral Fat 2


title: Visceral Fat 1

source_name: Visceral Fat 1


title: Gill 3

source_name: Gill 3


title: Brain 2

source_name: Brain 2


title: Brain 1

source_name: Brain 1


title: Gill 1

source_name: Gill 1


title: Gill 2

source_name: Gill 2


title: Heart 2

source_name: Heart 2


title: Heart 3

source_name: Heart 3


title: Heart 1

source_name: Heart 1


title: Red Skeletal Muscle 1

source_name: Red Skeletal Muscle 1


title: Red Skeletal Muscle 3

source_name: Red Skeletal Muscle 3


title: Red Skeletal Muscle 2

source_name: Red Skeletal Muscle 2


title: Adductor Skeletal Muscle 3

source_name: Adductor Skeletal Muscle 3


title: Adductor Skeletal Muscle 4

source_name: Adductor Skeletal Muscle 4


title: Caudal Skeletal Muscle 1

source_name: Caudal Skeletal Muscle 1


title: Caudal Skeletal Muscle 2

source_name: Caudal Skeletal Muscle 2


title: Adductor Skeletal Muscle 2

source_name: Adductor Skeletal Muscle 2


title: Hypaxial Skeletal Muscle 3

source_name: Hypaxial Skeletal Muscle 3


title: Adductor Skeletal Muscle 1

source_name: Adductor Skeletal Muscle 1


title: Hypaxial Skeletal Muscle 2

source_name: Hypaxial Skeletal Muscle 2


title: Brain 3

source_name: Brain 3


title: Epaxial Skeletal Muscle 1

source_name: Epaxial Skeletal Muscle 1


title: Pelvic Fin Skeletal Muscle 2

source_name: Pelvic Fin Skeletal Muscle 2


title: Pelvic Fin Skeletal Muscle 4

source_name: Pelvic Fin Skeletal Muscle 4


title: Hypaxial Skeletal Muscle 1

source_name: Hypaxial Skeletal Muscle 1


title: Pelvic Fin Skeletal Muscle 3

source_name: Pelvic Fin Skeletal Muscle 3


title: Pelvic Fin Skeletal Muscle 1

source_name: Pelvic Fin Skeletal Muscle 1


title: Epaxial Skeletal Muscle 2

source_name: Epaxial Skeletal Muscle 2


title: Epaxial Skeletal Muscle 3

source_name: Epaxial Skeletal Muscle 3


title: RW2

city: Hangzhou

first: Xiaoyu

last: Wang

state: Zhejiang

address: Yuhangtang Road

department: College of Life Sciences

institute: Zhejiang University

data_processing:
Raw data were firstly processed through in-house perl scripts as a quality control. Demultiplexed and quality filtered reads were then aligned to S. melonis TY genome sequence using Bowtie2-2.2.3. HTSeq 0.6.1 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions was performed using the DESeq Rpackage (1.18.0).
The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.
Assembly: ASM176134v1
Supplementary files format and content: fpkm

organism: Sphingomonas melonis TY

source_name: wild type

growth_protocol: shake-flask culture, LB culture, 30℃, 200 rpm

extract_protocol:
Total bacterial samples were collected (A600 = 0.6 at the time of collected), mixed with 0.2 volumes of stop-mix (95% ethanol and 5% phenol, v/v) and snap-frozen in liquid nitrogen. Pellets were resuspended in 100 μl lysozyme solution (15 mg/ml lysozyme in TE buffer, pH = 8.0). Total RNA was isolated with Omega-E.Z.N.A.® Bacterial RNA Kit.
Briefly, RNA degradation and contamination were monitored on 1% agarose gels. The integrity of RNA sample was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, USA). Sequencing libraries were generated from rRNA-depleted RNA using the RiboMinus Bacteria 2.0 Transcriptome Isolation Kit (Thermo Scientific, USA) following the manufacturer’s recommendations.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol: The wild type (WT) of S. melonis TY and snc251 deleted cells carrying either a plasmid overexpressing SNC251 (Δsnc251 comp.), or an empty control vector (Δsnc251) were grown in Luria-Bertani (LB) culture to an OD600 of 0.6.

value: TY


title: RSNC251C-1

source_name: Δsnc251 comp.

value: {delta}snc251 comp.


title: RW3


title: RSNC251C-3


title: RSNC251C-2


title: RSNC251-1


title: GD125 spleen from pups with no E.coli infection and with IL27RA KO, r1 [ATAC-seq]

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

data_processing:
Reads were aligned to mouse genome (mm10) with bowtie2 (PMID: 19261174). Reads mapped to multiple positions of the genome were excluded and only one read was kept if multiple reads mapped to the same position.
Read enriched regions (peaks) were predicted by MACS3 (PMID: 18798982).
Assembly: mm10
Supplementary files format and content: txt file; columns from left to right: chromosome, start, end, name, int(-10*log10qvalue), reserved column, fold-change at peak summit, -log10pvalue at peak summit, -log10qvalue at peak summit, relative summit position to peak start

extract_protocol:
Cells were washed with cold PBS and pelleted by centrifugation (500g, 5min, 4°C). Nuclei were isolated by subjecting cells to 100uL of RSB-lysis buffer (10mM Tris-HCl ph 7.4, 10mM NaCl, 3mM MgCl2, 1uL/mL of Digitonin, 1uL/mL of Tween20, and 1uL/mL of NP40) for 3-5 min on ice.
Libraries were prepared with approximately 50 to 75 thousand cells using a Tagment DNA Enzyme and Buffer Large Kit (Illumina, 20034198) and following the Omni-ATAC protocol (PMID: 28846090).

value: no E. coli infection

value: IL-27R KO

tag: tissue/cell type

value: Macrophages (myeloid cells) from spleen


title: GD249 spleen from pups with no E.coli infection and with intact IL27RA, r1 [ATAC-seq]

value: IL-27R WT


title: GD127 spleen from pups with no E.coli infection and with IL27RA KO, r3 [ATAC-seq]


title: GD131 spleen from pups with E.coli infection and with IL27RA KO, r3 [ATAC-seq]

value: E. coli infection


title: GD250 spleen from pups with no E.coli infection and with intact IL27RA, r2 [ATAC-seq]


title: GD130 spleen from pups with E.coli infection and with IL27RA KO, r2 [ATAC-seq]


title: GD254 spleen from pups with E.coli infection and intact IL27RA, r3 [ATAC-seq]


title: GD251 spleen from pups with no E.coli infection and with intact IL27RA, r3 [ATAC-seq]


title: GD126 spleen from pups with no E.coli infection and with IL27RA KO, r2 [ATAC-seq]


title: GD129 spleen from pups with E.coli infection and with IL27RA KO, r1 [ATAC-seq]


title: GD165 macrophages from pups with E.coli infection and with IL27RA KO, r2

data_processing:
Reads were aligned to mouse genome (mm10) with subread-align version 2.0.1 (PMID: 23558742)
Read counts were calculated with the featureCounts function from Rsubread version 2.0.1 (PMID: 24227677) against RefSeq gene annotation
Gene expression level from RNA-Seq is measured by rpkm (PMID: 18516045) with an in-house script.
Assembly: mm10
Supplementary files format and content: txt file; columns from left to right: gene symbol , log2(RPKM+1)+0.0001 for each sample

source_name: Macrophages (myeloid cells) from spleen

extract_protocol:
Spleens were homogenized in TRI Reagent® (Molecular Research Center, Cincinnati, OH). Using the commercial product protocol, the upper aqueous layer following phase separation was mixed with an equal volume of 75% ethanol and transferred to EZNA RNA isolation columns (Omega Biotek, Norcross, GA). The manufacturer’s instructions were followed to complete the tissue RNA isolation. RNA isolation from approximately 7.5x104 splenic myeloid cells was conducted with the RNeasy Plus Mini Kit (Qiagen, cat#74134) according to the manufacturer’s instructions.
RNA-Seq libraries were built using KAPA mRNA HyperPrep Kit (KAPA Biosystems,Wilmington MA) with 100-500 ng of total RNA according to manufacturer’s recommendation.


title: RSNC251-3


title: GD253 spleen from pups with E.coli infection and intact IL27RA, r2 [ATAC-seq]


title: RW1

value: wild type


title: RSNC251-2


title: GD164 macrophages from pups with E.coli infection and with IL27RA KO, r1


title: GD163 macrophages from pups with no E.coli infection and with IL27RA KO, r1


title: GD368 macrophages from pups with E.coli infection and with intact IL27RA, r1


title: GD369 macrophages from pups with E.coli infection and with intact IL27RA, r2


title: GD370 macrophages from pups with E.coli infection and with intact IL27RA, r3


title: GD365 macrophages from pups with no E.coli infection and with intact IL27RA, r1


title: GD367 macrophages from pups with no E.coli infection and with intact IL27RA, r3


title: GD366 macrophages from pups with no E.coli infection and with intact IL27RA, r2


title: GD597 spleen from pups with E.coli infection and with IL27RA KO, r3

source_name: Spleen

value: Spleen


title: GD252 spleen from pups with E.coli infection and intact IL27RA, r1 [ATAC-seq]


title: GD596 spleen from pups with E.coli infection and with IL27RA KO, r2


title: GD594 spleen from pups with no E.coli infection and with IL27RA KO, r3


title: GD595 spleen from pups with E.coli infection and with IL27RA KO, r1


title: GD593 spleen from pups with no E.coli infection and with IL27RA KO, r2


title: GD592 spleen from pups with no E.coli infection and with IL27RA KO, r1


title: GD599 spleen from pups with no E.coli infection and with intact IL27RA, r2


title: GD602 spleen from pups with E.coli infection and with intact IL27RA, r2


title: GD600 spleen from pups with no E.coli infection and with intact IL27RA, r3


title: GD603 spleen from pups with E.coli infection and with intact IL27RA, r3


title: GD598 spleen from pups with no E.coli infection and with intact IL27RA, r1


title: Fissure margin cells, HHst.34, Replicate 3

city: Midlothian

first: Joe

last: Rainger

state: Scotland

address: Easter Bush Campus

department: The Division of Functional Genetics and Development

institute: The Roslin Institute

data_processing:
Sequencing quality was evaluated using FASTQC (version 0.11.4). Sequencing adaptors were trimmed using Cutadapt[19] (version 1.16) and Trimmgalore (version 0.4.1).
Trimmed sequences were aligned to the chicken genome (galgal6) using STAR aligner to generate bam files, which were then coordinate sorted and indexed using Samtools (version 1.6).
A count matrix of transcripts annotated in Ensembl (version 103) was subsequently generated from bam files using featureCounts part of the Subread package(version 2.0.1).
Assembly: galgal6
Supplementary files format and content: tab-delimited text files of per-gene read counts determined by Featurecounts

organism: Gallus gallus

source_name: Fissure margin cells

growth_protocol: Fertilised Hyline eggs were incubated at 37oC from day 0

extract_protocol:
RNA was extracted using Trizol reagent (Ambion) and treated with Turbo DNaseI (Thermo #AM2238).
Libraries were prepared from 500ng of the total-RNA sample using the NEBNEXT Ultra II Directional RNA Library Prep kit (NEB #7760) with Poly-A mRNA magnetic isolation (NEB #E7490) according to the manufacturer’s protocol.

value: Fissure margin cells

tag: developmental stage

tag: time

value: Day 7

value: WT


title: Dorsal retina cells, HHst.34, Replicate 1

source_name: Dorsal retina cells

value: Dorsal retina cells

value: Day 9


title: Fissure margin cells, HHst.34, Replicate 2


title: Dorsal retina cells, HHst.34, Replicate 2


title: Fissure margin cells, HHst.34, Replicate 1


title: Dorsal retina cells, HHst.34, Replicate 3


title: Dorsal retina cells, HHst.30, Replicate 3


title: Dorsal retina cells, HHst.30, Replicate 2


title: Dorsal retina cells, HHst.30, Replicate 1


title: Fissure margin cells, HHst.30, Replicate 3


title: Fissure margin cells, HHst.30, Replicate 2


title: Fissure margin cells, HHst.30, Replicate 1


title: nonInfected_HBEday7_m6A

city: Gothenburg

first: Tanmoy

last: Mondal

state: Västra Götaland

address: Bruna Stråket 16

department: Department of Clinical Chemistry and Transfusion Medicine

country: Sweden

institute: University of Gothenburg

data_processing:
RNA-Seq: Single-end sequencing reads from SMARTer-Stranded Total RNA-Seq Kit v2 were analyzed with FastQC for quality control (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and adapters were removed using Trim Galore v0.6.6 with a minimal length threshold of 20bp. Trimmed reads from Vero infected and non-infected cells were aligned to the concatenated chlSab2 (Chlorosebus sabeus) , wuhCor1 (SARS-CoV-2) reference genomes plus Escherichia coli str. K-12 substr. MG1655 (Spike-in) or the SARS-CoV-2 + E. coli genome, obtained from the UCSC Genome Browser (http://hgdownload.soe.ucsc.edu/goldenPath/) using HISAT2 v2.2.1 with parameters (-U --rna-strandness R). Sequencing data from human bronchial epithelial non-infected infected cells was mapped to the concatenated human (hg38) + SARS-CoV-2 (wuhCor1) + E.coli (bacterial Spike-in) reference genomes. Duplicate alignments were labeled using markDuplicates from Picard v2.23.4 and marked alignment files were further processed using Sambamba v0.7.1 keeping uniquely mapping reads separated by strand after duplicate removal.
RIP-Seq: Uniquely mapping reads were quantified using featureCounts from the Rsubread package, following by differential expression analysis with DESeq2 using two replicates per condition. Genes were considered differentially expressed with an absolute log2 fold change value > 1 and an adjusted p-value of < 0.01 (Vero cells) and absolute log2 fold change value > 0.5 and adjusted p-value of < 0.1 (Human epithelium cells)
Assembly: Homo sapiens: hg38
Assembly: Chlorocebus sabaeus: chlSab2
Assembly: SARS-CoV-2: wuhCor1
Assembly: Escherichia coli K-12, substr. MG1655: U00096.2
Supplementary files format and content: bigwig files for coverage
Supplementary files format and content: narrowPeak files for called peaks

source_name: Human bronchial epithelium

growth_protocol: Vero CCL-81 cells were cultured in DMEM, 1% penicillin-streptomycin and 10% fetal calf serum at 37°C at 5% CO2. MucilAirTM, corresponding to reconstructed human bronchial epithelium cultures differentiated at the air/liquid interface (ALI), were purchased from Epithelix (Saint-Julien-en-Genevois, France). Cultures were maintained in ALI conditions in transwells with 700 µL of MucilAirTM medium (Epithelix) in the basal compartment, and kept at 37°C under a 5% CO2 atmosphere.

extract_protocol:
RNA was isolated from Vero CCL-81 cells (non-infected and post 48h infection) using TRIZOL reagent (Invitrogen). RNA fragmentation followed by m6A RIP was performed with 15ug of RNA spiked-in with 9 ng of Bacterial RNA. Epithelial cultures were washed in cold PBS and then lyzed in 150 µL of Trizol reagent (Thermofisher Scientific) added to the apical side of the insert. RNA was purified using the Direct-zol miniprep kit (ZR2080, Zymo Research), according to the manufacturer's specifications.
Sequencing libraries were prepared using SMARTer Stranded Total RNA-Seq Kit v2 (Pico Input Mammalian) from Takara and single-end sequenced (1X 88 bp) on Illumina NextSeq 2000 and 550 platforms.

treatment_protocol: T25 flasks with Vero CCL-81 (ATCC) were infected with the three different SARS-CoV-2 variants and medium or infected cells were harvested in trizol post 48 hours infection for RNA-sequencing studies. SARS-CoV-2 infection was performed as previously described (Robinot et al., Nat Comm. 2021). Briefly, the apical side of ALI cultures was washed once, and cells were then incubated with 106 plaque-forming units (pfu) of the isolate BetaCoV/France/IDF00372/2020 (EVAg collection, Ref-SKU: 014V-03890) diluted in 150 µl of DMEM medium. The viral input was left on the apical side for 4 h at 37 °C, and then removed by 3 apical washes. The basal medium was replaced every 2-3 days. Apical supernatants were harvested every 2-3 days by adding 200 µL of MucilairTM medium on the apical side, with an incubation of 20 min at 37°C prior to collection.

value: Human bronchial epithelium

tag: antibody

value: m6A (Synaptic Systems, Cat# 202003)

value: Non-infected Human Bronchial Epithelium Cells (7 dpi)

tag: spike-in organism

value: Escherichia coli K-12


title: nonInfected_HBEday7_totalRNA


title: SARS-CoV-2_HNE_infected_m6A

data_processing:
RIP-seq: Single-end sequencing reads from SMARTer-Stranded Total RNA-Seq Kit v2 were analyzed with FastQC for quality control (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and adapters were removed using Trim Galore v0.6.6 with a minimal length threshold of 20bp. Trimmed reads from Vero infected and non-infected cells were aligned to the concatenated chlSab2 (Chlorosebus sabeus) , wuhCor1 (SARS-CoV-2) reference genomes plus Escherichia coli str. K-12 substr. MG1655 (Spike-in) or the SARS-CoV-2 + E. coli genome, obtained from the UCSC Genome Browser (http://hgdownload.soe.ucsc.edu/goldenPath/) using HISAT2 v2.2.1 with parameters (-U --rna-strandness R). Sequencing data from human bronchial epithelial non-infected infected cells was mapped to the concatenated human (hg38) + SARS-CoV-2 (wuhCor1) + E.coli (bacterial Spike-in) reference genomes. Duplicate alignments were labeled using markDuplicates from Picard v2.23.4 and marked alignment files were further processed using Sambamba v0.7.1 keeping uniquely mapping reads separated by strand after duplicate removal.
RNA-seq: Uniquely mapping reads were quantified using featureCounts from the Rsubread package, following by differential expression analysis with DESeq2 using two replicates per condition. Genes were considered differentially expressed with an absolute log2 fold change value > 1 and an adjusted p-value of < 0.01 (Vero cells) and absolute log2 fold change value > 0.5 and adjusted p-value of < 0.1 (Human epithelium cells)
Assembly: hg38
Assembly: chlSab2
Assembly: wuhCor1
Assembly: U00096.2
Supplementary files format and content: bigwig files for coverage
Supplementary files format and content: narrowPeak files for called peaks

source_name: Human nasal epithelium

value: Human nasal epithelium

value: SARS-CoV-2-infected Human Nasal Epithelium Cells


title: SARS-CoV-2_HNE_infected_totalRNA


title: nonInfected_HNE_totalRNA

value: Non-infected Human Nasal Epithelium Cells


title: nonInfected_HBEday7_input


title: nonInfected_HBEday4_totalRNA

value: Non-infected Human Bronchial Epithelium Cells (4 dpi)


title: GD601 spleen from pups with E.coli infection and with intact IL27RA, r1

value: IL-27R WT

tag: strain


title: SARS-CoV-2_HBEday7_infected_totalRNA

value: SARS-CoV-2 infected Human Bronchial Epithelium Cells (7 dpi)


title: nonInfected_HBEday4_input


title: nonInfected_HBEday4_m6A


title: nonInfected_HNE_m6A


title: SARS-CoV-2_HBEday7_infected_m6A


title: SARS-CoV-2_HBEday7_infected_input


title: SARS-CoV-2_HBEday4_infected_input

value: SARS-CoV-2 infected Human Bronchial Epithelium Cells (4 dpi)


title: SARS-CoV-2_HBEday4_infected_m6A


title: SARS-CoV-2_HBEday4_infected_totalRNA


title: P6_SC_DAPT_48h_TDT_WGBS_rep1

city: Los Angeles

first: John

middle: Duc

last: Nguyen

state: CA

address: 3711 Baldwin Street, Unit 602

department: Stem Cell

institute: USC

data_processing:
WGBS: libraries were sequenced at 150 base pairs paired-end. Reads were trimmed with a hard clip of 20bp at both the 5’ and 3’ ends using Trim Galore (20) and aligned as paired end reads to a bisulfite-converted GRCm38/mm10 genome assembly using Bismark with the options --bowtie2 -N 1 -L 20 --non_directional --unmapped -X 800 --dovetail. Spiked-in lambda DNA was aligned to a bisulfite-converted J02459.1 lambda genome to assess bisulfite conversion percentage. Only libraries with >98% bisulfite conversion rate were kept. Unmapped paired end reads were mapped separately as single end read1 and read2 using Bismark with the options --bowtie2 --non_directional. Paired end and single end mapped reads were individually deduplicated using deduplicate_bismark, and then merged using samtools (htslib v1.7). The methylation status of individual cytosine in the genome was called using Bismark Methylation Extractor (21). The cytosine methylation and coverage data was used to call differentially methylated regions (DMR) between samples using methylKit (22) with the following parameters: only cytosine sites with at least a coverage of 2 were kept, tiling window of 1000 bp, step size of 1000 bp, percent methylation difference of at least 10 (sensitivity), and a false discovery rate (FDR) of < 0.05. Differential analysis was iteratively called between two samples from all possible combinations C(4,2) of the following cell types and stages: E13.5 PG, P1 HC, P1 SC, P21 SC. Bedtools intersect was used to identify the 4 sets of mutually exclusive DMRs capturing distinct DNA methylation signatures. DMRs were centered on Atoh1 peaks to be used in downstream analyses.
CUT&Tag: libraries were sequenced at 37 base pairs paired-end. We processed CUT&Tag data using the CUT&Tag Data Processing and Analysis pipeline from the Henikoff lab (15). Briefly, reads were hard-trimmed to 25bp and aligned to the GRCm38/mm10 genome assembly using bowtie2 (16) using parameters --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Duplicates were removed using Picard (17). Next, we applied a normalization factor to each sample based on the signal over the common peak regions. Briefly, for histones with narrow peak distributions such as H3K4me1 and CUTAC (H3K4me2), SEACR (18) was used to call peaks with non-normalized IgG control track and stringent threshold, and taking only the top 1% of regions by AUC. For histones with broad peak distributions such as H3K27me3, MACS2 (11, 19) was used to call peaks with the --broad and --q 0.1 options set against an IgG control. Bedtools intersect was used to filter for only common overlapping peaks between all samples and replicates. 4,718 shared peaks were called for H3K27me3; 4,869 shared peaks were called for CUTAC; 4,620 shared peaks were called for H3K4me1. Alignment count data was quantified over shared peaks using summarizedOverlaps (GenomicAlignments_1.30.0). calcNormFactors (edgeR v3.36.0) was used to calculate normalization factors for each sample and scaled to total library size. Samples were scaled to the normalization factor for visualization in IGV or heatmaps.
scMultiome: Raw sequencing data from multiple flow cells for both RNA and ATAC libraries in fastq format were used as input into cellranger-arc count (10x Genomics, v2.0.0) for simultaneous alignment against the mouse mm10 genome.
The cellranger- arc output files ‘filtered_feature_bc_matrix.h5’ and ‘atac_fragments.tsv.gz’ were used as input into Seurat v4.1.0 for standard quality control pre-processing, resulting in 4,882 nuclei post-filtering for the P1 dataset, and 7,049 nuclei post-filtering for the P8 dataset. ATAC peaks were called using macs2 v2.1.2. Multiome datasets were clustered based on RNA, ATAC, and weighted-nearest neighbor (Hao et al, 2021) to generate UMAPs. This resulted in 20 clusters for the P1 dataset, and 19 clusters for the P8 dataset. Clusters were assigned cell types based on known cell markers.
Representative signal tracks were visualized in IGV v2.4.14. ATAC peaks were filtered by hair cell enhancers previously identified (Tao et al., 2021), and intersected to find common, P1-specific, and P8-specific regions. Heatmaps were generated using deepTools v3.2.0 computeMatrix and plotHeatmap.
Cell barcodes from clusters of interest (P1 GER, P8 GER, P1 IPh/BC, P8 IPh, and P8 BC) were used to extract ATAC reads belonging to each respective cell type and generate a pseudobulk ATAC dataset.
Peaks were called on the pseudobulk ATAC datasets and common peaks were used as input into DESeq2 v1.34.0 to scale the signal between P1 and P8 datasets.
Assembly: mm10
Supplementary files format and content: DMR.bed regions were generated as follows: The cytosine methylation and coverage data was used to call differentially methylated regions (DMR) between samples using methylKit (22) with the following parameters: only cytosine sites with at least a coverage of 2 were kept, tiling window of 1000 bp, step size of 1000 bp, percent methylation difference of at least 10 (sensitivity), and a false discovery rate (FDR) of < 0.05. Differential analysis was iteratively called between two samples from all possible combinations C(4,2) of the following cell types and stages: E13.5 PG, P1 HC, P1 SC, P21 SC. Bedtools intersect was used to identify the 4 sets of mutually exclusive DMRs capturing distinct DNA methylation signatures. DMRs were centered on Atoh1 peaks to be used in downstream analyses.
Supplementary files format and content: WGBS.cov replicates were generated as follows: libraries were sequenced at 150 base pairs paired-end. Reads were trimmed with a hard clip of 20bp at both the 5’ and 3’ ends using Trim Galore (20) and aligned as paired end reads to a bisulfite-converted GRCm38/mm10 genome assembly using Bismark (21) with the options --bowtie2 -N 1 -L 20 --non_directional --unmapped -X 800 --dovetail. Spiked-in lambda DNA was aligned to a bisulfite-converted J02459.1 lambda genome to assess bisulfite conversion percentage. Only libraries with >98% bisulfite conversion rate were kept. Unmapped paired end reads were mapped separately as single end read1 and read2 using Bismark with the options --bowtie2 --non_directional. Paired end and single end mapped reads were individually deduplicated using deduplicate_bismark, and then merged using samtools (htslib v1.7). The methylation status of individual cytosine in the genome was called using Bismark Methylation Extractor (21).
Supplementary files format and content: WGBS.bw are converted from WGBS.cov files.
Supplementary files format and content: 10x.h5seurat files were generated as follows: The cellranger-arc output files ‘filtered_feature_bc_matrix.h5’ and ‘atac_fragments.tsv.gz’ were used as input into Seurat v4.1.0 for standard quality control pre-processing and filtering out poor-quality nuclei.scMultiome datasets were clustered using ‘uniform manifold approximation and projection’ (UMAP) and ‘weighted-nearest neighbor’ (WNN) from Seurat, which integrates both the gene expression and the accessibility information to define a “joint” cellular state. Datasets were also clustered based on RNA and ATAC for comparison. Clusters were assigned cell type identities based on known cell markers. For the P8 dataset, clusters identified as spiral ganglia neurons, roof cells, and spiral prominence cells were removed because they were driving the majority of the differences between the clusters. Afterwards, P8 cells were re-clustered and re-assigned cell type identity. The P70_integrate_wildtype_deaf_10x_scRNA_scATAC.h5seurat file is an integration of the P70_wildtype and P70_deafened cochlea datasets.

source_name: Inner ear cochlea

growth_protocol: Wildtype mice in a mixed background of CD1 and FVB/NJ, and C57BL/6 were bred

extract_protocol:
Isolate cochlear sensory epithelium: For E13.5, the inner ear was dissected from the mouse head, followed by incubation in PBS containing 0.5 U/ml of Dispase II (Sigma D4693) and 275 U/ml of Collagenase Type 1 (Worthington LS004196) at room temperature for 10 minutes. The Dispase II and Collagenase were removed and quenched with PBS + 5% Fetal Bovine Serum (FBS) (Genclone 25-514).  The cochlear epithelium was separated from the mesenchyme and dissociated into single cells. For P1, P6, P8, and P21 cochleas, the inner ear was extracted and placed in a dish containing ice-cold modified artificial cerebrospinal fluid solution (ACSF) [119 mM NaCl, 2.5 mM KCl, 2.5 mM CaCl2, 1.3 mM MgCl2, 1 mM NaH2PO4, 26.2 mM NaHCO3, 10mM HEPES, 11mM D-Glucose] on top of an ice block. Cartilage and bone were removed to expose the cochlear epithelium. Finally, the cochlear epithelium was separated from the spiral ganglion and modiolus, and then placed into a separate dish containing ACSF on ice until all ears were processed.    Obtain single cell/nuclei: For E13.5 and P1, cochleas were enzymatically dissociated with a cocktail of 400µl of 0.25% Trypsin, 50µl of 1 mg/ml Dispase, and 50µl of 1 mg/ml collagenase for 20 minutes at 37°C. After incubation, the digested tissue was titurated 100 times using a small-bore 200µl pipette and centrifuged at 500x g for 5 minutes at 4°C. For P6, P8, and P21, the sensory epithelium and stria were placed into a 1ml Dounce tissue grinder (Wheaton 357538) on ice with 1 ml of chilled homogenization buffer (250mM sucrose, 25mM KCl, 5mM MgCl2, 20 mM HEPES-KOH pH 7.9, 20% glycerol). Before use, the following components were added at their respective concentrations: 1mM DTT (Thermo Scientific R0861), 0.5mM Spermidine (Sigma S0266), 1% BSA (Sigma A4503), and 1x cOmplete EDTA-free protease inhibitor cocktail (Roche 11836170001). NP-40 (Calbiochem 492015) was spiked into the Dounce tissue grinder at a final concentration of 0.3%. The tissue was homogenized with a chilled loose pestle by first pressing the pestle down and turning to grind the tissue, followed by quick upstrokes 10 to 15 times to create cavitation. It was critical to not lift the Dounce pestle above the liquid layer to reduce bubbles. This process was repeated with a chilled tight pestle. Although some epithelial tissue was sometimes still visible, no further homogenization was performed as this may jeopardize the integrity of the already-released nuclei. The homogenate was filtered using a Falcon 5ml round bottom polystyrene test tube with a 40 µm cell strainer snap cap and spun down at 1000 x g and 4°C for 10 minutes. The supernatant was decanted, and the pellet was resuspended in 1ml of nuclei wash buffer (NWB) (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.1% NP-40). Before use, the following components were added at the respective concentrations: 1mM DTT, 0.5mM Spermidine, 2% BSA, and 1x cOmplete EDTA-free protease inhibitor cocktail.     Purifying celltypes: Fluorescence-activated cell sorting (FACS) of cells or nuclei was performed on either an Aria I, Aria II, or FACSymphony (BD Biosciences). For CUT&RUN and CUT&Tag, cells or nuclei were sorted into NWB. For WGBS, cells or nuclei were sorted into lysis buffer (10 mM Tris pH 7.5, 100 mM NaCl, 1 mM EDTA, and 0.01% Triton X-100). For Single Cell Multiome ATAC + Gene expression (10x Genomics), cells or nuclei were sorted into PBS and 0.1% BSA. Cells/nuclei were used for downstream NGS experiments (WGBS, CUT&Tag, 10x Genomics scMultiome).
WGBS: Cells/nuclei were lysed in lysis buffer (10mM Tris pH 7.5, 100mM NaCl, 1mM EDTA, and 0.01% Triton X-100) and digested with Proteinase K at 3mAU/ml at 65C for at least 1 hour. gDNA was purified using Genomic DNA Clean & Concentrator-10 (Zymo Research). Unmethylated Lambda DNA was spiked in at 0.5% of input gDNA. Libraries were prepared using the Pico Methyl-Seq Library Prep Kit (Zymo Research)  CUT&Tag: The following antibodies were used: Rabbit anti-H3K4me1 antibody (Active Motif 61633), rabbit anti-H3K4me2 antibody (Epicypher 13-0027), rabbit anti-H3K4me3 antibody (Active Motif 39159), rabbit anti-H3K27me3 antibody (Active Motif 39155). The guinea pig anti-Rabbit IgG antibody (Antibodies-online.com ABIN101961) was used as the secondary antibody. Tn5-tagmented DNA fragments were amplified using NEBNext HiFi 2x PCR Master Mix, a universal i5 primer and a uniquely barcoded i7 primer for 14 cycles. Library concentration and fragment distribution were measured on the Agilent Tapestation using a High Sensitivity D5000 ScreenTape (Agilent 5067-5592). Libraries were size-selected for DNA fragments greater than 150 bp using SPRISelect beads (Beckman Coulter B23318).    scMultiome  ATAC + Gene Expression protocol (10x Genomics)

treatment_protocol: For transdifferentiation experiments, the cochlear sensory epithelium cultured on SPI black filter membranes. To initiate Lfng-CreER-mediated lineage tracing of supporting cells, (Z)-4-Hydroxytamoxifen (Sigma H7904) was added to the culture media. For transdifferentiation experiments, DAPT was added to the culture media.    To generate P70 long-term deafened mice, we used a Lfng-CreERT2; NuTRAP; Pou4f3DTR mouse to lineage trace SCs and specifically kill hair cells after diphtheria toxin treatment. Lfng-CreERT2;NuTRAP mice were used as wildtype controls. Mice received tamoxifen at P21, diphtheria toxin (Sigma-Aldrich D0564) at P28, and allowed to mature to P70, at which point cochlear tissues were harvested for input into a scMultiome reaction.

tag: tissue

value: Inner ear cochlea

value: mixed (CD1,FVB/NJ, C57BL/6)

value: Lfng-creERT2, Atoh1-GFP

value: primary tissue explant culture, 0.02mg/ml (Z)-4-Hydroxytamoxifen, 10µM DAPT


title: P0_SC_DAPT_48h_TDT_WGBS_rep1


title: P21_SC_CUTAC_H3K4me2_CutnTag_rep1

data_processing:
WGBS: libraries were sequenced at 150 base pairs paired-end. Reads were trimmed with a hard clip of 20bp at both the 5’ and 3’ ends using Trim Galore (20) and aligned as paired end reads to a bisulfite-converted GRCm38/mm10 genome assembly using Bismark with the options --bowtie2 -N 1 -L 20 --non_directional --unmapped -X 800 --dovetail. Spiked-in lambda DNA was aligned to a bisulfite-converted J02459.1 lambda genome to assess bisulfite conversion percentage. Only libraries with >98% bisulfite conversion rate were kept. Unmapped paired end reads were mapped separately as single end read1 and read2 using Bismark with the options --bowtie2 --non_directional. Paired end and single end mapped reads were individually deduplicated using deduplicate_bismark, and then merged using samtools (htslib v1.7). The methylation status of individual cytosine in the genome was called using Bismark Methylation Extractor (21). The cytosine methylation and coverage data was used to call differentially methylated regions (DMR) between samples using methylKit (22) with the following parameters: only cytosine sites with at least a coverage of 2 were kept, tiling window of 1000 bp, step size of 1000 bp, percent methylation difference of at least 10 (sensitivity), and a false discovery rate (FDR) of < 0.05. Differential analysis was iteratively called between two samples from all possible combinations C(4,2) of the following cell types and stages: E13.5 PG, P1 HC, P1 SC, P21 SC. Bedtools intersect was used to identify the 4 sets of mutually exclusive DMRs capturing distinct DNA methylation signatures. DMRs were centered on Atoh1 peaks to be used in downstream analyses.
CUT&Tag: libraries were sequenced at 37 base pairs paired-end. We processed CUT&Tag data using the CUT&Tag Data Processing and Analysis pipeline from the Henikoff lab (15). Briefly, reads were hard-trimmed to 25bp and aligned to the GRCm38/mm10 genome assembly using bowtie2 (16) using parameters --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Duplicates were removed using Picard (17). Next, we applied a normalization factor to each sample based on the signal over the common peak regions. Briefly, for histones with narrow peak distributions such as H3K4me1 and CUTAC (H3K4me2), SEACR (18) was used to call peaks with non-normalized IgG control track and stringent threshold, and taking only the top 1% of regions by AUC. For histones with broad peak distributions such as H3K27me3, MACS2 (11, 19) was used to call peaks with the --broad and --q 0.1 options set against an IgG control. Bedtools intersect was used to filter for only common overlapping peaks between all samples and replicates. 4,718 shared peaks were called for H3K27me3; 4,869 shared peaks were called for CUTAC; 4,620 shared peaks were called for H3K4me1. Alignment count data was quantified over shared peaks using summarizedOverlaps (GenomicAlignments_1.30.0). calcNormFactors (edgeR v3.36.0) was used to calculate normalization factors for each sample and scaled to total library size. Samples were scaled to the normalization factor for visualization in IGV or heatmaps.
scMultiome: Raw sequencing data from multiple flow cells for both RNA and ATAC libraries in fastq format were used as input into cellranger-arc count (10x Genomics, v2.0.0) for simultaneous alignment against the mouse mm10 genome.
The cellranger- arc output files ‘filtered_feature_bc_matrix.h5’ and ‘atac_fragments.tsv.gz’ were used as input into Seurat v4.1.0 for standard quality control pre-processing, resulting in 4,882 nuclei post-filtering for the P1 dataset, and 7,049 nuclei post-filtering for the P8 dataset. ATAC peaks were called using macs2 v2.1.2. Multiome datasets were clustered based on RNA, ATAC, and weighted-nearest neighbor (Hao et al, 2021) to generate UMAPs. This resulted in 20 clusters for the P1 dataset, and 19 clusters for the P8 dataset. Clusters were assigned cell types based on known cell markers.
Representative signal tracks were visualized in IGV v2.4.14. ATAC peaks were filtered by hair cell enhancers previously identified (Tao et al., 2021), and intersected to find common, P1-specific, and P8-specific regions. Heatmaps were generated using deepTools v3.2.0 computeMatrix and plotHeatmap.
Cell barcodes from clusters of interest (P1 GER, P8 GER, P1 IPh/BC, P8 IPh, and P8 BC) were used to extract ATAC reads belonging to each respective cell type and generate a pseudobulk ATAC dataset.
Peaks were called on the pseudobulk ATAC datasets and common peaks were used as input into DESeq2 v1.34.0 to scale the signal between P1 and P8 datasets.
Assembly: mm10
Supplementary files format and content: DMR.bed regions were generated as follows: The cytosine methylation and coverage data was used to call differentially methylated regions (DMR) between samples using methylKit (22) with the following parameters: only cytosine sites with at least a coverage of 2 were kept, tiling window of 1000 bp, step size of 1000 bp, percent methylation difference of at least 10 (sensitivity), and a false discovery rate (FDR) of < 0.05. Differential analysis was iteratively called between two samples from all possible combinations C(4,2) of the following cell types and stages: E13.5 PG, P1 HC, P1 SC, P21 SC. Bedtools intersect was used to identify the 4 sets of mutually exclusive DMRs capturing distinct DNA methylation signatures. DMRs were centered on Atoh1 peaks to be used in downstream analyses.
Supplementary files format and content: WGBS.cov replicates were generated as follows: libraries were sequenced at 150 base pairs paired-end. Reads were trimmed with a hard clip of 20bp at both the 5’ and 3’ ends using Trim Galore (20) and aligned as paired end reads to a bisulfite-converted GRCm38/mm10 genome assembly using Bismark (21) with the options --bowtie2 -N 1 -L 20 --non_directional --unmapped -X 800 --dovetail. Spiked-in lambda DNA was aligned to a bisulfite-converted J02459.1 lambda genome to assess bisulfite conversion percentage. Only libraries with >98% bisulfite conversion rate were kept. Unmapped paired end reads were mapped separately as single end read1 and read2 using Bismark with the options --bowtie2 --non_directional. Paired end and single end mapped reads were individually deduplicated using deduplicate_bismark, and then merged using samtools (htslib v1.7). The methylation status of individual cytosine in the genome was called using Bismark Methylation Extractor (21).
Supplementary files format and content: WGBS.bw are converted from WGBS.cov files.
Supplementary files format and content: 10x.h5seurat files were generated as follows: The cellranger-arc output files ‘filtered_feature_bc_matrix.h5’ and ‘atac_fragments.tsv.gz’ were used as input into Seurat v4.1.0 for standard quality control pre-processing and filtering out poor-quality nuclei.scMultiome datasets were clustered using ‘uniform manifold approximation and projection’ (UMAP) and ‘weighted-nearest neighbor’ (WNN) from Seurat, which integrates both the gene expression and the accessibility information to define a “joint” cellular state. Datasets were also clustered based on RNA and ATAC for comparison. Clusters were assigned cell type identities based on known cell markers. For the P8 dataset, clusters identified as spiral ganglia neurons, roof cells, and spiral prominence cells were removed because they were driving the majority of the differences between the clusters. Afterwards, P8 cells were re-clustered and re-assigned cell type identity. The P70_integrate_wildtype_deaf_10x_scRNA_scATAC.h5seurat file is an integration of the P70_wildtype and P70_deafened cochlea datasets.
Library strategy: Cut&Tag

value: Lfng-creER, NuTRAP

value: 100 mg/kg tamoxifen

value: rabbit anti-H3K4me2 (Epicypher 13-0027),


title: P0_SC_DAPT_48h_TDT_GFP_WGBS_rep2


title: P0_SC_DAPT_48h_TDT_GFP_WGBS_rep1


title: P21_SC_CUTAC_H3K4me2_CutnTag_rep2


title: P6_SC_DAPT_48h_TDT_WGBS_rep2


title: P8_SC_CUTAC_H3K4me2_CutnTag_rep1


title: P8_SC_CUTAC_H3K4me2_CutnTag_rep2


title: P0_SC_DAPT_48h_TDT_WGBS_rep2


title: P1_SC_CUTAC_H3K4me2_CutnTag_rep1

value: Lfng-GFP

value: no treatment


title: P1_SC_CUTAC_H3K4me2_CutnTag_rep2


title: P1_HC_CUTAC_H3K4me2_CutnTag_rep1


title: P1_HC_CUTAC_H3K4me2_CutnTag_rep2


title: P8_SC_H3K4me1_CutnTag_rep2

value: rabbit anti-H3K4me1 (Active Motif 61633)


title: P8_SC_H3K4me1_CutnTag_rep1


title: P21_SC_H3K4me1_CutnTag_rep2


title: P21_SC_H3K27me3_CutnTag_rep1

value: rabbit anti-H3K27me3 (Active Motif 39155)


title: P1_SC_H3K27me3_CutnTag_rep1


title: P1_SC_H3K27me3_CutnTag_rep2


title: P1_HC_H3K27me3_CutnTag_rep2


title: P8_SC_H3K27me3_CutnTag_rep1


title: P1_HC_H3K27me3_CutnTag_rep1


title: P21_SC_H3K4me1_CutnTag_rep1


title: P21_SC_H3K27me3_CutnTag_rep2


title: P1_SC_H3K4me1_CutnTag_rep2


title: P1_HC_H3K4me1_CutnTag_rep2


title: P8_SC_H3K27me3_CutnTag_rep2


title: P1_HC_H3K4me1_CutnTag_rep1


title: P1_SC_H3K4me3_CutnTag_rep1

value: rabbit anti-H3K4me3 (Active Motif 39159)


title: P1_HC_H3K4me3_CutnTag_rep1


title: P21_SC_WGBS_rep1

description:
DMR_pre-established.bed
DMR_de_novo_HC-specific.bed
DMR_de_novo_SC-specific.bed
DMR_de_novo_common.bed


title: P6_SC_WGBS_rep2


title: P1_HC_WGBS_rep2


title: P21_SC_WGBS_rep2


title: P1_SC_WGBS_rep2


title: P6_SC_WGBS_rep1


title: P1_SC_H3K4me3_CutnTag_rep2


title: P1_HC_WGBS_rep1


title: E13_5_PG_WGBS_rep2


title: Neutrophils Lung Sick 1

city: Parkville

first: Nishika

last: Ranathunga

state: VIC

address: 1G Royal Parade

country: Australia

data_processing:
The base calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6, while the FASTQ file generation and de-multiplexing utilised bcl2fastq conversion software v2.15.0.4.
Reads were aligned to the mouse genome mm39 using Rsubread version 2.4.3.
Read counts were summarized using the Rsubread featureCounts function and GENCODE annotation version M27.
Assembly: mm39
Supplementary files format and content: tab-delimited text files; columns represent Ensembl ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

source_name: Lung

extract_protocol:
RNA from FACS sorted neutrophils and macrophages was extracted with a RNeasy Plus Micro Kit (QIAGEN) according to the manufacturer’s protocol.
Next-generation sequencing libraries were created with 10 ng of RNA from samples with distinct 18S and 28S peaks and RNA integrity number values greater than 7, using an NEBNext Ultra II Directional RNA Library Prep Kit from Ilumina (New England Biolabs) according to the manufacturer’s protocol. RNA libraries were pooled and sent for singleend 75 bp sequencing at the Genomics Laboratory (The Walter and Eliza Hall Institute of Medical Research) on a NextSeq 500 next-generation sequencer (Illumina) to obtain ∼20 million reads per sample.

value: Lung

tag: cell type

value: Neutrophils

value: APLAID mutant

value: 23 days

tag: animal line

value: APLAID/FLP


title: Neutrophils Lung Sick 2

institute: Walter and Eliza Hall Institute of Medical Research

tag: age

value: 34 days


title: E13_5_PG_WGBS_rep1

value: Inner ear cochlea

value: mixed (CD1,FVB/NJ, C57BL/6)

tag: genotype


title: Neutrophils Lung HC 2

value: Control


title: P1_SC_H3K4me1_CutnTag_rep1

tag: treatment


title: Neutrophils Skin Sick 2

source_name: Skin

value: Skin


title: Neutrophils Lung HC 1


title: Neutrophils Skin HC 1


title: Macrophages Lung HC 2

value: Macrophages


title: Macrophages Lung HC 1


title: Macrophages Lung Sick 2


title: P1_HC_H3K4me3_CutnTag_rep2


title: Macrophages Lung Sick 1


title: Macrophages Skin HC 2


title: P1_SC_WGBS_rep1


title: Macrophages Skin HC 1


title: c-Kit+/Sca-1+/Lin- bone marrow progenitors, NUP98-NSD1, sh#1 [NUPwt_sh_69_3]

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

institute: OSR - San Raffaele Scientific Institute

data_processing:
Reads were trimmed using the JAVA tool trimmomatic (V 0.32)
Trimmed reads were alignmed using STAR aligner V 2.5.3a
Read counts per gene calculated using the featureCounts function from the Rsubread package (V 1.32.4), based on GENCODE gene annotation M22
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: Bone marrow

growth_protocol: c-Kit+/Sca-1+/Lin- bone marrow progenitors were grown in RPMI medium containing IL-3 (20 ng/ml), IL-6 (20 ng/ml), and SCF (100 ng/ml)

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
Processing of 12 samples with the "mRNA Stranded TruSeq" library protocol in order to obtain 10.0M clusters of fragments of  - 1x75nt of length through NextSeq 500 High 75

treatment_protocol: Cells were incubated with the supernatant from Phoenix packaging cells transfected with the retroviral constructs expressing NUP98-NSD1 and MSCV. After geneticin selection, constitutive knockdown of Nizp1 expression was achieved in NUP98-NSD1 expressing cells using Nizp1-specific pLKO.1-puro based shRNA constructs

value: Bone marrow

tag: cell line

value: Bone marrow progenitors


title: c-Kit+/Sca-1+/Lin- bone marrow progenitors, NUP98-NSD1, sh#1 [NUPwt_sh_69_1]


title: Macrophages Skin Sick 2


title: c-Kit+/Sca-1+/Lin- bone marrow progenitors, NUP98-NSD1, sh#1 [NUPwt_sh_69_2]


title: c-Kit+/Sca-1+/Lin- bone marrow progenitors, NUP98-NSD1, sh#2 [NUPwt_sh_70_3]


title: c-Kit+/Sca-1+/Lin- bone marrow progenitors, NUP98-NSD1, sh#2 [NUPwt_sh_70_2]


title: Neutrophils Skin HC 2


title: c-Kit+/Sca-1+/Lin- bone marrow progenitors, NUP98-NSD1, sh#2 [NUPwt_sh_70_1]


title: Neutrophils Skin Sick 1


title: c-Kit+/Sca-1+/Lin- bone marrow progenitors, NUP98-NSD1, sh#ctrl [NUPwt_plko_2]

value: sh#ctrl


title: c-Kit+/Sca-1+/Lin- bone marrow progenitors, NUP98-NSD1, sh#ctrl [NUPwt_plko_1]


title: Macrophages Skin Sick 1


title: c-Kit+/Sca-1+/Lin- bone marrow progenitors, NUP98-NSD1, sh#ctrl [NUPwt_plko_3]


title: c-Kit+/Sca-1+/Lin- bone marrow progenitors, MSCV, sh#ctrl [MSCV_plko_2]

value: MSCV


title: c-Kit+/Sca-1+/Lin- bone marrow progenitors, MSCV, sh#ctrl [MSCV_plko_3]


title: c-Kit+/Sca-1+/Lin- bone marrow progenitors, MSCV, sh#ctrl [MSCV_plko_1]


title: LSC_H3K27ac

city: Stanford

first: Feng

last: Pan

address: 265 Campus Drive

department: Pathology

institute: Stanford University School of Medicine

data_processing:
The sequencing reads were mapped to the mouse genome (mm9) using BWA. Duplicated reads were removed using Picard.
MACS2 was used for peak calling with default parameters.
Enhancer states were extracted from ChromHMM segmentation states and annotated by GREAT.
Enhancers were ranked from H3K27ac ChIP-seq using ROSE with default parameters.
Enrichment of known and de novo motifs were found using HOMER.
Assembly: mm9
Supplementary files format and content: bed files were generated by ChromHMM
Supplementary files format and content: bigwig files were generated by deeptools

source_name: bone marrow

growth_protocol: Murine MLL-AF10 leukemia cells were grown in RPMI 1640 supplemented with 20% fetal bovine serum (FBS), 20% WEHI-conditioned medium, and 1% penicillin-streptomycin.

extract_protocol:
GMP, LSCs, and mAML cells were harvested, fixed, and sheared using an E220 focused-ultrasonicator (Covaris)
After H3 antibody immobilization, sheared chromatin was indexed and pooled for IP against histone marks and transcription factors. ChIPed DNA was amplified, size-selected, and subject to sequencing on an Illumina NextSeq 500 or HiSeq2500 platform.

treatment_protocol: LSCs were treated with A-485 for 0h, 24h, 48h, and 72h.

value: leukemia stem cell

tag: chip antibody

value: H3K27ac (abcam, ab4729)


title: LSC_input


title: LSC_H3K4me1

value: H3K4me1 (abcam, ab8895)


title: LSC_H3K4me3


title: GMP_H3K4me1

value: granulocyte-monocyte progenitors


title: mAML_input

value: mature AML cells


title: mAML_H3K4me1


title: GMP_H3K27ac


title: mAML_H3K27ac


title: mAML_H3K4me3


title: GMP_H3K4me3


title: F1-21

city: La Jolla

first: Yuta

last: Takahashi

address: 10010 N Tottey Pines Rd

institute: Salk Institute

data_processing:
Bisulfite sequencing reads were checked for read quality using FastQC
aligned to the mm10 genome with Bismark (PMID: 21493656)
Bismark uses a C to T converted version of the genome and Bowtie (PMID: 19261174) alignment (we allowed maximum 1 seed mismatch) to identify base-specific methylation percentages.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph

source_name: F1-21 from Ldlrc1

growth_protocol: Mice were bred in the animal facility of the Salk Institute

extract_protocol:
Genomic DNA was isolated from mice tails, sperms or ESCs using a proteinase K digestion-phenol/chloroform extraction based method.
Target enrichment-genome methyl sequencing was performed as described previously using the SureSelectXT Methyl-Seq Target Enrichment System for Illumina Multiplexed Sequencing (Agilent Technologies) with a customized capture library following manufacturer's protocol. The biotinylated RNA capture probe library to capture specific genomic loci was designed to include three loci on mouse genome; mm10, chr6:118556982-118565982, chr9:111265293-111280293, and chr9:21720056-21729056. Three μg of genomic DNA was sheared to 150-180 bp fragments using Covaris M220. Following hybridization between sheared DNA and the capture library, captured genome DNA was purified using streptavidin beads. Bisulfite conversion of the captured DNA was performed using the EZ DNA Methylation-Gold Kit (Zymo Research). Following indexing and sample pooling with 10% PhiX, sequencing was conducted using Illumina NextSeq500, at PE150.

value: Tail

value: F1 offspring from Ldlrc1

tag: targeted cgi

value: Ldlr CGI


title: F1-13

source_name: F1-13 from Ldlrc1


title: WT ICR

source_name: mouse WT

value: ICR


title: LSC_A485_8h_rep1

data_processing:
RNA-seq reads were mapped with STAR against the mouse genome (mm9).
Differential expression analysis were carried out with raw counts using RSEM/EBseq
Assembly: mm9
Supplementary files format and content: raw gene counts for every gene and every sample

extract_protocol:
RNA was extracted using RNeasy Plus Kits from Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: LSCs were treated with A-485 for 0h, 8h, 24h, 48h, and 72h.

tag: disease state

value: Tumor

value: treated with A485 for 8 hours


title: LSC_A485_72h_rep1

value: treated with A485 for 72 hours


title: LSC_A485_72h_rep2


title: LSC_A485_48h_rep2

value: treated with A485 for 48 hours


title: LSC_A485_0h_rep1

value: untreated


title: LSC_A485_0h_rep2


title: GMP_input


title: LSC_24h_P300

value: treated with A485 for 24 hours


title: LSC_A485_24h_rep2


title: LSC_A485_24h_rep1


title: LSC_72h_P300


title: LSC_0h_P300


title: LSC_48h_P300


title: LSC_72h_H2K27ac


title: LSC_72h_input


title: LSC_0h_H2K27ac


title: LSC_0h_input


title: LSC_48h_input


title: LSC_A485_8h_rep2


title: LSC_A485_48h_rep1


title: Stage E7.5 embryo 2 section 9 region C

city: Guangzhou

first: Guangdun

last: Peng

address: 190 Kaiyuan Road

department: Guangzhou Institutes of Biomedicine and Health

institute: Chinese Academy of Sciences

data_processing:
The reads for all samples are mapped to the mm10 using Tophat v2.0.8b with parameter: -p 20 -g 1 -N 4 --read-edit-dist 4 --microexon-search
The mapped reads were used to estimate transcriptomic alignment rates, and were also used as input in Cufflinks v2.1.1 (Trapnell et al., 2013) to quantify gene expression levels (fragment per kilobase per million, FPKM) with the default parameters
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each embryo

source_name: Mouse embryonic cells

growth_protocol: Embryos from pre-gastrulation to late-gastrulation mouse were embedded with OCT and subjected to cryosection.

extract_protocol:
According to Geo-seq (Chen et al., 2017), RNA from LCM samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier.
Libraries were constructed using illumina Nextera XT DNA sample preparation kit

treatment_protocol: Sample from sections were laser-microdissected and collected for single-cell based RNA sequencing.

value: Late-gastrulation embryo (E7.5)

tag: tag


title: Stage E7.5 embryo 2 section 9 region D


title: Stage E7.5 embryo 2 section 9 region A


title: Stage E7.5 embryo 2 section 9 region B


title: Stage E7.5 embryo 2 section 8 region D1


title: Stage E7.5 embryo 2 section 8 region C1


title: Stage E7.5 embryo 2 section 8 region C2


title: Stage E7.5 embryo 2 section 8 region D2


title: LSC_24h_H2K27ac


title: Stage E7.5 embryo 2 section 8 region A


title: LSC_48h_H2K27ac


title: LSC_24h_input


title: Stage E7.5 embryo 2 section 7 region D2


title: Stage E7.5 embryo 2 section 6 region C2


title: Stage E7.5 embryo 2 section 6 region D2


title: Stage E7.5 embryo 2 section 7 region B


title: Stage E7.5 embryo 2 section 7 region A


title: Stage E7.5 embryo 2 section 7 region C2


title: Stage E7.5 embryo 2 section 7 region D1


title: Stage E7.5 embryo 2 section 6 region B


title: Stage E7.5 embryo 2 section 6 region C1


title: Stage E7.5 embryo 2 section 6 region D1


title: Stage E7.5 embryo 2 section 5 region D2


title: Stage E7.5 embryo 2 section 8 region B


title: Stage E7.5 embryo 2 section 5 region C2


title: Stage E7.5 embryo 2 section 5 region B


title: Stage E7.5 embryo 2 section 5 region C1


title: Stage E7.5 embryo 2 section 5 region A


title: Stage E7.5 embryo 2 section 4 region C2


title: Stage E7.5 embryo 2 section 4 region D2


title: Stage E7.5 embryo 2 section 4 region B


title: Stage E7.5 embryo 2 section 4 region D1


title: Stage E7.5 embryo 2 section 4 region A


title: Stage E7.5 embryo 2 section 7 region C1


title: Stage E7.5 embryo 2 section 3 region D2


title: Stage E7.5 embryo 2 section 3 region D1


title: Stage E7.5 embryo 2 section 3 region C1


title: Stage E7.5 embryo 2 section 3 region C2


title: Stage E7.5 embryo 2 section 3 region B


title: Stage E7.5 embryo 2 section 6 region A


title: Stage E7.5 embryo 2 section 3 region A


title: Stage E7.5 embryo 2 section 5 region D1


title: Stage E7.5 embryo 2 section 1 region A


title: Stage E7.5 embryo 2 section 2 region D


title: Stage E7.5 embryo 2 section 2 region A


title: Stage E7.5 embryo 2 section 2 region C


title: Stage E7.5 embryo 2 section 2 region B


title: Stage E7.5 embryo 1 section 9 region A


title: Stage E7.5 embryo 1 section 9 region B


title: Stage E7.5 embryo 1 section 9 region C


title: Stage E7.5 embryo 2 section 4 region C1


title: Stage E7.5 embryo 1 section 8 region D2


title: Stage E7.5 embryo 1 section 8 region D1


title: Stage E7.5 embryo 1 section 8 region C2


title: Stage E7.5 embryo 2 section 1 region B


title: Stage E7.5 embryo 1 section 9 region D


title: Stage E7.5 embryo 1 section 8 region B


title: Stage E7.5 embryo 1 section 8 region C1


title: Stage E7.5 embryo 1 section 8 region A


title: Stage E7.5 embryo 1 section 7 region D2


title: Stage E7.5 embryo 1 section 7 region D1


title: Stage E7.5 embryo 1 section 7 region C1


title: Stage E7.5 embryo 1 section 7 region B


title: Stage E7.5 embryo 1 section 7 region A


title: Stage E7.5 embryo 1 section 6 region D2


title: Stage E7.5 embryo 1 section 6 region D1


title: Stage E7.5 embryo 1 section 7 region C2


title: Ldlr c1

source_name: chimera Ldlrc1

value: Chimera generated from Ldlr HR1ex ESC


title: Stage E7.5 embryo 1 section 6 region C1


title: Stage E7.5 embryo 1 section 6 region B


title: Stage E7.5 embryo 1 section 6 region C2


title: Stage E7.5 embryo 1 section 6 region A


title: Stage E7.5 embryo 1 section 5 region D2


title: Stage E7.5 embryo 1 section 5 region D1


title: Stage E7.5 embryo 1 section 5 region B


title: Stage E7.5 embryo 1 section 5 region C2


title: Stage E7.5 embryo 1 section 5 region A


title: Stage E7.5 embryo 1 section 4 region D2


title: F04, 144

city: Chicago

last: Carrithers

state: IL

address: 912 S Wood

department: Neurology

institute: University of Illinois

hyb_protocol: bisulfite converted genomic DNA was fragmented and hybridized to the Illumina Infinium MethylationEpic Bead Arrays

scan_protocol: Illumina iScan

data_processing: R software version 4.03. Data were normalized using the preprocessQuantile function from the minfi R package (Aryee et al. 2014), using the method of Touleimat and Tost (2012).

label: cy3, cy5

source_name: whole blood

label_protocol: per standard Illumina protocol

extract_protocol: Advanced XL automated instrument (Qiagen Cat. No. 9001875) using EZ1&2 DNA blood 350 ul kit (Qiagen Cat. No.951054)

value: whole blood

value: MS

tag: race

value: Black or African American

tag: ethnicity

value: NOT Hispanic or Latino

tag: gender

value: Male

tag: medication

value: Ambulate

value: Relapsing Remtting Multiple Sclerosis


title: B02, 51

value: CONTROL

value: White

value: Female

value: Other neurological disorders

value: Posttraumatic migraine after car accident


title: F02, 149

value: Migraine


title: Stage E7.5 embryo 1 section 4 region D1

tag: developmental stage


title: H04, 79

value: Hispanic or Latino

value: Copaxone/Glatiramer

value: Cane

value: Relapsing Remitting Multiple Sclerosis


title: B02, 89

value: whole blood

value: Headache


title: Stage E7.5 embryo 1 section 4 region C2

value: Late-gastrulation embryo (E7.5)


title: Stage E7.5 embryo 1 section 4 region C1


title: D01, 47

value: MS

value: NOT Hispanic or Latino

value: Tecfidera


title: C03, 106

value: Male

value: Ambulate


title: F01, 54

value: Black or African American


title: E03, 114

value: CONTROL

value: Tinnitus


title: Stage E7.5 embryo 1 section 4 region B


title: H03, 62

value: Female

value: Wheelchair


title: D03, 52


title: G01, 41

value: White

value: Hispanic or Latino


title: Stage E7.5 embryo 1 section 4 region A


title: C01, 36

value: Other neurological disorders


title: C04, 73

value: Betaseron/Extavia

value: Relapsing Remitting Multiple Sclerosis


title: F03, 61

value: whole blood

value: Copaxone/Glatiramer


title: G02, 44

value: Migraine and small aneurysm


title: E01, 30

value: NOT Hispanic or Latino

value: Headache tensional


title: H02, 57

value: MS

value: Tecfidera


title: D04, 87

value: Black or African American

value: Ambulate

value: Idiopathic Intracranial pressure


title: H01, 29

value: CONTROL

value: Female

value: Headache


title: E04, 111

value: White

value: Hispanic or Latino

value: shoulder pain


title: D02, 53

value: Male

value: Ocrevus

value: Wheelchair

value: Relapsing Remitting Multiple Sclerosis


title: G03, 123

value: whole blood

value: Other neurological disorders

value: Epilepsy


title: H01, 103

value: MS

value: NOT Hispanic or Latino

value: Tysabri

value: Cane


title: G04, 74

value: Black or African American

value: Ambulate


title: G02, 56

value: Female

value: Copaxone/Glatiramer


title: D01, 46


title: A02, 40

value: CONTROL

value: Migraines


title: Stage E7.5 embryo 1 section 3 region B

value: Late-gastrulation embryo (E7.5)


title: Stage E7.5 embryo 1 section 3 region A


title: G01, 35

value: White

value: Hispanic or Latino

value: Headache, complex partial seizures


title: Stage E7.5 embryo 1 section 2 region D


title: Stage E7.5 embryo 1 section 3 region D2


title: Stage E7.5 embryo 1 section 2 region C


title: Stage E7.5 embryo 1 section 3 region C2


title: Stage E7.5 embryo 1 section 2 region B


title: Stage E7.5 embryo 1 section 2 region A


title: Stage E7.5 embryo 1 section 1 region B


title: Stage E7.5 embryo 1 section 3 region C1


title: B04, 27

value: whole blood

value: Tecfidera

value: Relapsing Remitting Multiple Sclerosis


title: Stage E7.5 embryo 1 section 1 region A


title: Stage E6.5 embryo 3 section 6 region P

value: Early-gastrulation embryo (E6.5)


title: Stage E6.5 embryo 3 section 6 region A


title: Stage E6.5 embryo 3 section 5 region P


title: Stage E6.5 embryo 3 section 4 region P


title: Stage E6.5 embryo 3 section 4 region A


title: Stage E6.5 embryo 3 section 3 region P


title: Stage E6.5 embryo 3 section 5 region A


title: Stage E6.5 embryo 3 section 3 region A


title: Stage E6.5 embryo 3 section 2 region P


title: E02, 21

value: Other neurological disorders

value: Headache


title: Stage E6.5 embryo 3 section 1 region A/P


title: Stage E6.5 embryo 3 section 2 region A


title: Stage E6.5 embryo 2 section 7 region A


title: E02, 26


title: C01, 25

value: Male


title: F01, 15

value: MS

value: Black or African American

value: NOT Hispanic or Latino


title: Stage E6.5 embryo 2 section 6 region A


title: B01, 11

value: Female

value: Cane


title: E01, 20

value: Ambulate


title: Stage E6.5 embryo 2 section 5 region P


title: Stage E6.5 embryo 2 section 7 region P


title: Stage E6.5 embryo 2 section 6 region P


title: Nalm6_apo_L

city: Hall in Tirol

first: Charlotte

middle: Dafni

last: Vavourakis

state: Tirol

address: Milser Str. 10

department: Research Institute for Biomedical Aging Research

country: Austria

institute: University of Innsbruck

description: Nalm6 late apoptosis

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to  Illumina Human MethylationEPIC methylation Beadchips using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan using standard recommended Illumina scanner setting

data_processing: minfi, ChAMP, impute

label: Cy5 and Cy3

source_name: Nalm6, 4h

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from cell pellets using the Allprep DNA/RNA/protein mini kit (Qiagen) and Genomic DNA Clean & Concentrator-10 kit (Zymo) according to standard instructions

value: Nalm6 (CVCL_0092; DSMZ ACC 128)

tag: growth medium

value: RPMI-1640 with 10% FCS, 1% L-Glutamin, 100 U/ml Penicillin, and 100 μg/ml Streptomycin

value: BH3 mimetics S63845 and ABT-737


title: H02, 6

tag: tissue


title: A04, 19

value: Ocrevus

value: Wheelchair


title: F02, 14

value: whole blood

value: White

value: Hispanic or Latino


title: Stage E6.5 embryo 2 section 4 region P

value: Early-gastrulation embryo (E6.5)


title: Stage E6.5 embryo 2 section 4 region A


title: A01, 5

value: Copaxone/Glatiramer

value: Relapsing Remitting Multiple Sclerosis


title: C02, 3

value: MS

value: Tecfidera


title: RNA_pat1dhh1_Replicate_3

city: Bethesda

first: Alan

middle: G

last: Hinnebusch

state: Maryland

address: 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institutes of Health

data_processing:
For RNA-Seq: As described earlier (Martin-Marcos et al. 2017), Illumina sequencing reads were trimmed to remove the constant adapter sequence, mixed sample sequences were separated by the sample barcodes followed by removal of PCR duplicates using a custom Python (3.7) script. The sequences aligned to yeast non-coding RNAs were removed using bowtie (Langmead et al., 2009) and non-rRNA reads (unaligned reads) were then mapped to the S. cerevisiae genome (R64-1-1 S288C Saccer3 Genome Assembly) using TopHat (Trapnell et al., 2009). Only uniquely mapped reads from the final genomic alignment were used for subsequent analyses. Normalized wiggle files and reads counts are generated with RiboSeq tools (https://github.com/hzhanghenry/RiboProR). For RNA-seq, the same protocol mentioned above for ribo-seq analysis was followed.
For ChIP-Seq: Sequence data were aligned to the SacCer3 version of the genome sequence using Bowtie2 with parameters -X 1000 -very-sensitive, to map sequences up to 1 kb with maximum accuracy. PCR duplicates from ChIP-seq data were removed using the samtools rmdup package.
Assembly: sacCer3
Supplementary files format and content: Processed data (csv) files contain raw reads for each file. For RNA-Sequencing, each file contains five columns providing: systemmatic gene name (Gene_ID), total reads (trx), reads in CDS, reads in 5' UTR and reads in 3' UTR. Foe CAGE-sequencing and parallel RNA-Sequencing, each file contains two columns providing: systemmatic gene name (Gene_ID), total reads. For Rpb1 ChIP-Seq, average occupancy  file contains five columns providing: systemmatic gene name (ORF), avg occupancy at -1, NDR, +1 and average of -1, NDR, +1

organism: Saccharomyces cerevisiae

source_name: Whole cells

extract_protocol:
For RNA-seq library preparation, total RNA was extracted and purified from aliquots of the same snapped-frozen cells described above using Zymo RNA Clean and Concentrator kit. Five µg of total RNA was randomly fragmented by mixing with 2× alkaline fragmentation solution (2 mM EDTA, 10 mM Na2CO3, 90 mM NaHCO3, pH ≈ 9.3). After incubation for 20 min at 95ºC, fragmentation reactions were mixed with ice-cold stop solution (300 mM NaOAc pH 5.5, 30 µg GlycoBlue (Invitrogen; AM9516)). RNA was precipitated by adding one part of isopropanol followed by the standard protocol of precipitation. Fragment size selection, library generation, and sequencing were carried out using the same protocol described above for RPF library preparation, except the Ribo-Zero Gold rRNA Removal Kit (Illumina; MRZ11124C) was employed to remove rRNA after linker-ligation.
In additional columns of the SAMPLES section
In additional columns of the SAMPLES section

value: W303 F2182 (MATa ura3-1 trp1-1 ade2-1 leu2-3,112 his3-11,15 delta-pat1::HIS3 delta-dhh1::KanR)


title: B01, 4

value: Black or African American

value: NOT Hispanic or Latino

value: Female


title: C02, 2

value: Male

value: Cane


title: Stage E6.5 embryo 2 section 3 region P


title: D02, 13


title: Nalm6_apo_E

description: Nalm6 early apoptosis

source_name: Nalm6, 2h

value: Nalm6 (CVCL_0092; DSMZ ACC 128)

value: RPMI-1640 with 10% FCS, 1% L-Glutamin, 100 U/ml Penicillin, and 100 μg/ml Streptomycin

value: BH3 mimetics S63845 and ABT-737


title: RNA_pat1dhh1_Replicate_1

growth_protocol: In additional columns of the SAMPLES section


title: RNA_pat1_Replicate_3


title: A01, 17

value: whole blood

value: CONTROL

value: Ambulate

value: Other neurological disorders

value: Cluster Headache


title: Nalm6_ctrl

description: Nalm6 control

source_name: Nalm6, control

value: DMSO


title: Stage E6.5 embryo 2 section 2 region P

value: Early-gastrulation embryo (E6.5)


title: RNA_pat1_Replicate_2


title: Stage E6.5 embryo 2 section 2 region A


title: Stage E6.5 embryo 2 section 1 region A/P


title: RNA_pat1_Replicate_1


title: RNA_pat1dhh1_Replicate_2


title: A02, 8

value: MS

value: Ocrevus

value: Relapsing Remitting Multiple Sclerosis


title: T_RNA_xrn1D_Replicate_2

data_processing:
As described earlier (Martin-Marcos et al. 2017), Illumina sequencing reads were trimmed to remove the constant adapter sequence, mixed sample sequences were separated by the sample barcodes followed by removal of PCR duplicates using a custom Python (3.7) script. The sequences aligned to yeast non-coding RNAs were removed using bowtie (Langmead et al., 2009) and non-rRNA reads (unaligned reads) were then mapped to the S. cerevisiae genome (R64-1-1 S288C Saccer3 Genome Assembly) using TopHat (Trapnell et al., 2009). Only uniquely mapped reads from the final genomic alignment were used for subsequent analyses. Normalized wiggle files and reads counts are generated with RiboSeq tools (https://github.com/hzhanghenry/RiboProR). For RNA-seq, the same protocol mentioned above for ribo-seq analysis was followed.
The sequenced CAGE reads of each sample were aligned to the reference genome of S. cerevisiae S288c (Assembly version: sacCer3) using HISAT2. CAGE reads mapped to rRNA genes were identified using rRNAdust (http://fantom.gsc.riken.jp/5/sstar/Protocols:rRNAdust), and were excluded from subsequent TSS analyses. CAGE reads with a mapping quality score (MAPQ) > 20 were considered uniquely mapped reads and were used for subsequent analyses. CAGE signals of biological replicates were then merged as a single sample. The transcription abundance of each TSS was quantified as the numbers of CAGE tags/reads supporting the TSS per million mapped reads (TPM). For RNA-Seq samples in parallel with CAGE-Seq, Fastq files after passing the QC and the adapter content check they were mapped to yeast genome (sacCer3) with STAR aligner, then PCR duplicates were removed by samtools.
Assembly: sacCer3
Supplementary files format and content: Processed data (csv) files contain raw reads for each file. For ribosome profiling and parallel RNA-Sequencing, Raw_counts_Ribo (Ribo-sequencing) and Raw_counts_RNA (RNA-sequencing), each file contains five columns providing: systemmatic gene name (Gene_ID), total reads (trx), reads in CDS, reads in 5' UTR and reads in 3' UTR. Foe CAGE-sequencing and parallel RNA-Sequencing, each file contains two columns providing: systemmatic gene name (Gene_ID), total reads.

extract_protocol: For RNA-seq, total RNA was extracted using hot-phenol method and the library was prepared by NHLBI Sequencing and Genomics Core at NIH (Bethesda, MD) using TruSeq Stranded mRNA Library Prep Kit (Illumina)


title: HeLa_ctrl

description: HeLa control

source_name: HeLa, control

value: HelaS3 (CVCL_0058; DSMZ ACC 161)

value: DMEM with 10% FCS, 1% L-Glutamin,100 U/ml Penicillin, 100 μg/ml Streptomycin


title: Nalm6_apo_E_extra_2

description: extra sample

source_name: Nalm6, extra


title: Stage E6.5 embryo 1 section 6 region A


title: T_RNA_dcp2D_Replicate_2


title: T_RNA_dcp2D_Replicate_1


title: B03, 16

value: Black or African American

value: NOT Hispanic or Latino

value: Female

value: Tecfidera


title: HT1080_apo_L

description: HT1080 late apoptosis

source_name: HT1080, BH3 mims, 20h

value: MEM (9.6 g/l) and Sodium Bicarbonate (1.5g/l) solved in A.d., with 10% FCS, 100 U/ml Penicillin, and 100 μg/ml Streptomycin

value: BH3 mimetics S63845 and ABT-737


title: T_RNA_WT_Replicate_2


title: Stage E6.5 embryo 1 section 5 region A


title: HeLa_apo_L

description: HeLa late apoptosis

source_name: HeLa, BH3 mims, 12h


title: Stage E6.5 embryo 1 section 7 region A


title: Stage E6.5 embryo 1 section 4 region A


title: Stage E6.5 embryo 1 section 4 region P


title: HT1080_apo_E

description: HT1080 early apoptosis

source_name: HT1080, BH3 mims, 10h


title: Nalm6_apo_L_extra_1

description: extra sample

value: Nalm6 (CVCL_0092; DSMZ ACC 128)

value: RPMI-1640 with 10% FCS, 1% L-Glutamin, 100 U/ml Penicillin, and 100 μg/ml Streptomycin


title: Stage E6.5 embryo 1 section 3 region A