title: HLO_Control

city: Ann Arbor

first: Jonathan

last: Sexton

state: MI

address: 1150 W. Medical Center Dr., RM 4742F

institute: University of Michigan, Ann Arbor

data_processing:
Transcripts were mapped to the GRCh38 2020-A reference transcriptome
Genes excluded if only detected in 5 or fewer cells, cells excluded if over 30% of reads were mitochondrial or if they had fewer than 10,000 total reads
For differential expression, corrected for over-dispersion using sctransform v2 with Seurat v4 which fits a robust negative binomial model for the per-gene variance by the expression mean.
DESeq2 to compute average log fold-change and adjusted p-value for each gene between cells under different conditions.
UMAP in monocle 3 was used to visualize
Supplementary_files_format_and_content: Barcodes,features, and matrix

source_name: iPSC

extract_protocol:
Cells were removed from chips with trypsin treatment. Intact HLOs were removed from matrigel by dispase treatment followed by trypsin treatment.
Library was constructed using the 10X Genomics protocol by the University of Michigan Advanced Genomics Core.

tag: cell type

value: iPSC-derived liver organoids

value: DMSO

tag: post-differentiation


title: Abrams cells untreated control

status: Public on Jan 24 2022

type: RNA

city: Blacksburg

first: Joanne

last: Tuohy

state: Virginia

address: 205 Duck Pond Dr

department: Small Animal Clinical Sciences

country: USA

institute: Virginia Maryland College of Veterinary Medicine

description: Control

data_processing:
Arrays were analysed with an Applied Biosystems 7500 Fast Real-Time PCR System (Thermo Fisher Scientific, Massachusetts, USA). The cycle threshold (Ct) values acquired from array analysis were analysed using the GeneGlobe RT2 Profiler PCR Data Analysis tool (Qiagen, Hilden, Germany) which calculated fold change relative to untreated cells for each evaluated OS cell line, via the ∆∆Ct methodology. The house keeping gene GAPDH was selected for normalization because treatment did not seem to alter expression.
Ct values were normalized to GAPDH (matrix normalized template) and fold change was computed relative to untreated control cells (fold change template)

label: SYBR Green

molecule: total RNA

organism: Canis lupus familiaris

source_name: Canine OS cell line, untreated, naïve

label_protocol: Qiagen RT2 First Strand kit was utilized to synthesize 200ng cDNA in accordance with the manufacturer’s protocol (Qiagen, Hilden, Germany).

extract_protocol: 1mL of TRI Reagent (Zymo Research, California, USA) was added to each well of cells to harvest cells for RNA extraction. the Direct-zol RNA miniprep extraction kit (product# R2051, Zymo Research, California, USA) was utilized for RNA extraction by following the manufacturer’s protocol.

tag: cell line

value: Abrams

value: Canine OS cell line

tag: treatment

value: naïve


title: Abrams cells sham treated control

description: Sham Control, test of treatment process without delivering treatment

source_name: Canine OS cell line,Sham treated

value: Sham treated


title: PaDLOC_Tenofovir_InarigivirSoproxil

type: SRA

library_source: transcriptomic

organism: Homo sapiens

value: Tenofovir + Inarigivir Soproxil

value: Chip


title: D418 cells Histotripsy treated

description: Test of histotripsy treatment

source_name: Canine OS cell line, Histotripsy treated

value: Histotripsy treated


title: Abrams cells histotripsy treated

description: Test of histotripsy treatment


title: Control 2 years, replicate 6

city: Montreal

first: Roberta

middle: M

last: Palmour

state: Quebec

address: 1033 Pine West

department: Psychiatry

country: Canada

institute: McGill

description: miRNA expression data from the hippocampus of vervet green monkeys sacrificed at 2 years after birth

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan at the McGill Genome Center

data_processing: The data were analyzed with FlexArray software and the Bioconductor package in R. These data were normalized using the Robust Multi-Array (RMA) normalization method. Probe sets have been trimmed for present/absent calls, annotation, and where multiple probe sets were available for a single miRNA only the probe set showing the highest mean expression value was selected

label: biotin

organism: Chlorocebus aethiops

source_name: Chlorocebus aethiops hippocampus sacrificed at 2 years post sucrose exposure

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: miRNeasy Qiazol extraction performed according to manufacturers specifications

treatment_protocol: Whole hippocampus was extracted and placed in a 1 ml sterile vial containing GITC

tag: age

value: Sacrificed at 2 years

tag: ethanol exposure

value: Pre Natal sucrose exposure


title: 931 T-24 R2

city: Freiburg

first: Severin

last: Dicks

address: Breisacherstr. 153

department: Institute of Medical Bioinformatics and Systems Medicine

country: Germany

institute: University Freiburg Medical Center

data_processing:
Basecalling: bcl2fastq 2.20.0.422
Adapter trimming and low quality reads trimming: Trimmomatic 0.38; HEADCROP:3 TRAILING:10 SLIDINGWINDOW:4:15 MINLEN:18
Alignment and counting reads per gene: STAR 2.6.1b;
--outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.05 i--alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMatchNmin 16 --quantMode GeneCounts TranscriptomeSAM --outSAMtype BAM SortedByCoordinate
Genome_build: mm10
Supplementary_files_format_and_content: table with raw gene counts for every gene

organism: Mus musculus

source_name: murine small intestinal TKA organoids

growth_protocol: TKA organoids were mechanically disrupted, seeded in 3 mg/ml Matrigel, and provided with Advanced DMEM/F12 supplemented with 1% (v/v) Penicillin/Streptomycin, 10 mM HEPES, 1 x GlutaMAX™ Supplement, 1 x N-2 Supplement, 1 x B-27™ Supplement, 1 mM n-acetyl-cysteine, 50 ng/mL EGF, and 100 ng/mL Noggin. Organoids were seeded 40 h prior to the onset of the experiments to allow re-development of a cystic shape.

extract_protocol:
Total RNA was isolated using the peqGOLD MicroSpin Total RNA Kit (Peqlab/VWR Life Science, 12-6831)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: TKA organoids were treated with 5 ng/ml human TGFβ1 for 6, 24, 48, and 72 h. For control, organoids were harvested at the onset of the experiment or after cultivation for 72 h in presence of solvent.

tag: strain

tag: tissue

value: small intestinal TKA organoids

tag: organoid line

tag: genotype

value: Apcdelta/delta, KrasG12D, Trp53R172H, tgVillin-CreERT2

value: 24 h TGFBeta1


title: D418 cells sham treated control


title: Control 2 years, replicate 5


title: 931 C-72 R2

value: 72 h solvent


title: 931 T-6 R2

value: 6 h TGFBeta1


title: Control 2 years, replicate 3


title: PaDLOC_Tenofovir

value: Tenofovir


title: PaDLOC_FIAU

value: iPSC-derived liver organoids

value: FIAU


title: 931 C-72 R1


title: D17 cells histotripsy treated

description: Test of histotripsy treatment


title: Control 2 years, replicate 1


title: PaDLOC_APAP

value: APAP


title: 931 C-0 R1

value: 0 h solvent


title: D17 cells untreated control

description: Control

value: Canine OS cell line

value: naïve


title: D17 cells sham treated control

value: Sham treated


title: PaDLOC_Control

value: DMSO

value: Chip


title: 931 T-72 R1

value: 72 h TGFBeta1


title: H6

city: Tianjin

first: miaomiao

last: Jiang

address: 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin

country: China

institute: Tianjin University of Traditional Chinese Medicine

data_processing:
Library strategy: 16S rRNA-seq
Illumina MiSeq platform was used for paired-end sequencing.
A modified QIIME 2 2019.4 conda environment was used as the basic sequences process pipeline.(Diversity script version: 5.0)
Raw sequence data were demultiplexed using the demux plugin following by primers cutting with cutadapt plugin. Amplicon_type_and_reigion: 16S_V3V4. Amplicon sequences length range was limited from 292 to 480
Sequences were then quality filtered, denoised, merged and chimera removed using the DADA2 plugin.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: stool bacteria

extract_protocol:
Fresh feces from each mouse were collected and temporarily placed in sterile tubules, and then snap-frozen in liquid nitrogen.Total DNA from stool bacteria was extracted using QIAamp DNA stool mini kit from Qiagen (Germantown, MD, USA) according to the manufacturer’s instructions. Then, the target fragment was selected for PCR amplification, and the magnetic beads were purified, recycled and quantified by fluorescence. Illumina TruSeq Nano DNA LT Library Prep Kit was used  for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: group

value: hydroxytyrosol

tag: Sex

value: female


title: Cul5 cKO rep3

city: Philadelphia

first: Paula

last: Oliver

state: PA

address: 816F ARC, 3615 Civic Center Blvd.

department: Department of Pathology, Perelman School of Medicine

institute: University of Pennsylvania

data_processing:
Paired-end reads were pseudo-aligned to the GRCm38 (mm10) genome using Kallisto (V0.46.2) to give TPM values.
TMM-normalized log2CPM values were estimated using R Bioconductor package edgeR (V3.34.0) for differential expression analysis.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: TPM of each transcript mapped to ENSEMBL ID.
Supplementary_files_format_and_content: processed_counts.txt: normalized counts (log2CPM)

source_name: Spleen

growth_protocol: Isolated naïve CD4+ were activated and cultured under Th9 polarizing conditions for 48 hrs.

extract_protocol:
Total RNA was isolated using TRIzol reagent and poly-A selection was used to remove rRNA.
DNA library was quantified using Qubit and sequenced on a BGIseq500 platform.

treatment_protocol: Mice were either WT or Cul5fl/flCD4-Cre.

value: Cul5 cKO


title: H5


title: D418 cells untreated control

description: Control


title: Cul5 cKO rep2


title: 062 Coronary artery bulk ATAC

city: Charlottesville

first: Clint

middle: L

last: Miller

state: VA

department: Center for Public Health Genomics

institute: University of Virginia

library_source: genomic

data_processing:
Bulk ATAC-seq sample processing was all conducted using the PEPATAC pipeline (version 0.8.6). This includes alignment, duplicate removal, mitochondrial read removal, and peak-calling
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak (peaks from each individual sample)

molecule: genomic DNA

source_name: Coronary artery

extract_protocol:
Frozen coronary artery segments were broken down into small pieces using mortar and pestle under dry ice and liquid nitrogen. Nuclei were isolated using iodixanol/sucrose gradients following the Omni-ATAC protocol (Corces et al. Nature Methods 2017). 50,000 nuclei were washed in cold ATAC Resuspension Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) + 0.1% Tween-20 and centrifuged for 10 minutes at 500 g at 4°C. 50,000 nuclei were then resuspended in 50 µl of transposition mix (25 µl 2X TD buffer, 2.5 µl of Tn5 transposase (Illumina), 16.5 µl PBS, 0.01% digitonon, 0.1% Tween-20). Samples were subsequently transposed for 30 minutes at 37°C with shaking (1000 rpm).
Transposed DNA was first purified using the Zymo DNA Clean and Concentrator-5 Kit. Libraries were subsequently constructed and amplified according to Supplementary Protocol 1 in the Omni-ATAC protocol (Corces et al. Nature Methods 2017). Each library underwent 5 cycles of pre-amplification and then additional amplification cycles (determined by qPCR of pre-amplified mixtures)

treatment_protocol: Human hearts were obtained from heart transplant recipients or rejected donor hearts. Hearts were all placed in cardioplegic solution prior to dissection of the left anterior descending (LAD), left circumflex (LCX), and right coronary arteries (RCA). All coronary artery samples were flash frozen in liquid nitrogen in the same manner

value: Coronary artery (RCA)

value: male


title: 931 T-6 R1

value: small intestinal TKA organoids

value: Apcdelta/delta, KrasG12D, Trp53R172H, tgVillin-CreERT2

value: 6 h TGFBeta1


title: 931 T-24 R1

value: 24 h TGFBeta1


title: Cul5 cKO rep1


title: H3


title: Control 2 years, replicate 2

value: Sacrificed at 2 years

value: Pre Natal sucrose exposure


title: 054 Coronary artery bulk ATAC

value: Coronary artery (LAD)


title: 039 Coronary artery bulk ATAC


title: H2


title: WT rep2

value: WT


title: T6

value: tyrosol


title: 005 Coronary artery bulk ATAC


title: H1


title: 008 Coronary artery bulk ATAC


title: 061 Coronary artery bulk ATAC


title: JraSCR-12hpi-2

city: PUNE

first: Girish

middle: S

last: Ratnaparkhi

state: MH

address: Dr. Homi Bhabha Road Pashan Pune 411008

department: Biology

country: India

institute: Indian Institute of Science Education & Research

data_processing:
Bcl2fastq for base calling and adapter trimming
4-5 million reads per sample were mapped to Drosophila genome using Star Aligner (2.5.2.a)
Gene expression counts were generated using Htseq-count (v0.6.0) and DE analysis was performed using Deseq2
Genome_build: dm6
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample ...

organism: Drosophila melanogaster

source_name: Enterocyte specific Gal4 crossed to w1118 line-Uninfected

growth_protocol: Flies were grown on standard corn meal agar in a 12 hour light/dark cycle @ 25C

extract_protocol:
Guts were pulled out of the abdomen and homogenised in Trizol and RNA was extracted.
Lexogen (Quantseq 3'mRNA-seq library prep kit for Illumina)

treatment_protocol: Flies were starved without food and water and allowed to feed on a filter paper dipped in a concentrated culture of Pseudomonas entomophila for 2 hours

value: 12 hours post infection with Pseudomonas entomophila

value: Gut

value: 6-8 day adult female

value: JraSCR (CRISPR mutant)


title: JraSCR-12hpi-4


title: T5

value: female


title: JraSCR-12hpi-3


title: 931 T-48 R1

value: 48 h TGFBeta1


title: H4

value: hydroxytyrosol


title: T3


title: WT rep1


title: JraSCR-4hpi-2

value: 4 hours post infection with Pseudomonas entomophila


title: JraSCR-4hpi-4


title: 069 Coronary artery bulk ATAC

value: male


title: T2


title: WT rep3


title: 094 Coronary artery bulk ATAC


title: 036 Coronary artery bulk ATAC


title: 015 Coronary artery bulk ATAC

value: Coronary artery (RCA)


title: JraSCR-UC-3

value: Uninfected


title: JraSCR-UC-2


title: S6

value: salidroside


title: T1


title: JraSCR-UC-4


title: 080 Coronary artery bulk ATAC


title: S4


title: 050 Coronary artery bulk ATAC


title: 053 Coronary artery bulk ATAC


title: 112 Coronary artery bulk ATAC


title: JraSCR-4hpi-3


title: S2


title: JraWT-12hpi-4

value: JraWT (CRISPR control)


title: 058 Coronary artery bulk ATAC


title: 046 Coronary artery bulk ATAC


title: T4


title: JraWT-4hpi-3


title: S1


title: JraWT-4hpi-4


title: 030 Coronary artery bulk ATAC


title: JraWT-4hpi-2


title: 057 Coronary artery bulk ATAC


title: 040 Coronary artery bulk ATAC


title: M5

value: model


title: JraWT-UC-3


title: JraWT-UC-2


title: 020 Coronary artery bulk ATAC

value: Coronary artery (LAD)


title: JraWT-12hpi-3


title: JraWT-UC-4


title: S5


title: 014 Coronary artery bulk ATAC


title: S3


title: JraWT-12hpi-2


title: 023 Coronary artery bulk ATAC


title: M1


title: JraRNAi-24hpi-3

value: 24 hours post infection with Pseudomonas entomophila

value: NP-Gal4ts > JraRNAi


title: M2


title: C6

value: control


title: 045 Coronary artery bulk ATAC


title: JraRNAi-24hpi-1

value: Gut


title: JraRNAi-24hpi-2

value: 6-8 day adult female


title: M6


title: C5


title: 064 Coronary artery bulk ATAC


title: 027 Coronary artery bulk ATAC


title: JraRNAi-12hpi-3

value: 12 hours post infection with Pseudomonas entomophila


title: M4

value: female


title: M3


title: MA2

city: Kunming

first: Juehua

last: Yu

address: Xicang Rd

institute: Kunming Medical University

description: MA-treated mouse

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: hippocampus

extract_protocol:
Tissues were removed, flash frozen on dry ice, and RNA was harvested using Qiagen Kit. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hippocampus

tag: phenotype

value: MA


title: C3


title: MA1

description: MA-treated mouse


title: MA3

description: MA-treated mouse


title: JraRNAi-12hpi-2


title: 009 Coronary artery bulk ATAC


title: Control3

description: control mouse

value: saline


title: C2


title: 079 Coronary artery bulk ATAC

value: male


title: JraRNAi-4hpi-3

value: 4 hours post infection with Pseudomonas entomophila


title: C1


title: Control2

description: control mouse


title: JraRNAi-4hpi-2


title: Control1

description: control mouse


title: 066 Coronary artery bulk ATAC


title: JraRNAi-4hpi-1


title: SPM_3

city: Harbin

first: Can

last: Wei

address: Baojian Road

department: Department of Pathophysiology

institute: Harbin Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: spermine treated group (SPM)

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Spermine treatment accompanied diabetic model for 12 weeks

value: heart; myocardium


title: RNAseq_hPGC_wk7_M_r1

city: Cambridge

first: Walfred

last: Tang

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

description: Primary cells

data_processing:
The sequencing quality of libraries were checked by FastQC (v0.11.5). The low-quality reads and adaptor sequences were removed by Trim Galore (v0.4.1) using the default parameters.
The pre-processed reads were mapped to the human reference genome (UCSC GRCh38/hg38) using STAR (2.7.1a) (parameters: ‘--outFilterMismatchNoverLmax 0.05 --outFilterMultimapNmax 50 --outMultimapperOrder Random’) guided by the Gencode Human Release 30 comprehensive gene annotation.
Raw read counts per gene were extracted by the featureCounts function of the Subread package (1.6.2) using the default parameters. Normalized read counts and differentially expressed genes (absolute(log2(fold change)) > 2 and adjusted p-value < 0.05) were obtained using DEseq2 (1.26.0) in R (3.6.2) / Bioconductor (3.10.1).
Genome_build: hg38
Supplementary_files_format_and_content: Excel table with mRNA expression level [log2(normalised counts +1)] for all genes and differential expression [log2(fold change) and adjusted p-values] for selected contrast pairs

source_name: hPGC isolated from developmental week 7 genital ridge

extract_protocol: Total RNA was extracted with the PicoPure RNA Isolation Kit. Total RNA (0.5-2 ng) was reverse transcribed and amplified into cDNA using Ovation RNA-Seq System V2 (Nugen) according to manufacturer’s instructions.  Amplified cDNA was sonicated into 250 bp by Covaris S220 Focused-ultrasonicators. Subsequently, RNASeq library was generated with 500 ng of fragmented cDNA using Ovation Ultralow DR Multiplex System (Nugen). Library was quantified by KAPA Library Quantification Kit (Kapa Biosystems) using QuantStudio 6 Flex Real-Time PCR System (Applied Biosystems).

tag: facs

value: TNAP and cKIT+

tag: gender

value: Male


title: C4


title: 007 Coronary artery bulk ATAC

value: Coronary artery (LAD)


title: JraRNAi-UC-3

value: Uninfected


title: 068 Coronary artery bulk ATAC


title: SPM_2


title: 049 Coronary artery bulk ATAC


title: JraRNAi-UC-2

value: NP-Gal4ts > JraRNAi


title: SPM_1


title: JraRNAi-12hpi-1


title: DCM_3

source_name: diabetic cardiomyopathy model group (DCM)

value: Diabetic model for 12 weeks


title: 108 Coronary artery bulk ATAC


title: w1118-24hpi-3

value: 24 hours post infection with Pseudomonas entomophila

value: Gut

value: NP-Gal4ts > w1118


title: 067 Coronary artery bulk ATAC

value: Coronary artery (LCX)


title: DCM_2


title: 019 Coronary artery bulk ATAC


title: w1118-24hpi-2

value: 6-8 day adult female


title: DCM_1


title: 083 Coronary artery bulk ATAC


title: RNAseq_hPGC_wk7_M_r2

description: Primary cells

value: hPGC isolated from developmental week 7 genital ridge


title: w1118-24hpi-1


title: w1118-12hpi-3

value: 12 hours post infection with Pseudomonas entomophila


title: GBM14 cells, ONC206+Romidepsin 2

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from GBM14 cells treated with ONC206+Romidepsin.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 2.0 ST for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the Robust Multiarray Average (RMA), R version 3.6.0, and the Brainarray affy (version 1.62.0) and hugene20sthsentrezgcdf (version 24.0.0) R packages.

source_name: GBM14 cells

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: GBM14 cells were maintained in DMEM+10%FBS.

extract_protocol: Total RNA was isolated using the miRNAeasy Mini Kit (QIAGEN 217004).

treatment_protocol: GBM14 cells were treated with 10µM ONC206 and/or 2.5nM Romidepsin (or DMSO vehicle control) for 24h.

value: glioblastoma cell line GBM14


title: GBM14 cells, Romidepsin 2

description: Gene expression data from GBM14 cells treated with Romidepsin.

value: Romidepsin


title: CK_3

source_name: normal control group

value: Normal control


title: GBM14 cells, ONC206+Romidepsin 1


title: GBM14 cells, Romidepsin 1


title: CK_1

value: heart; myocardium


title: GBM14 cells, ONC206 2

description: Gene expression data from GBM14 cells treated with ONC206.


title: MN_CRT35_nodrug_01

first: Andrew

middle: E

last: Aplin

address: 233 South 10th St.

institute: Thomas Jefferson University

data_processing:
De-multiplexing and data aggregation was performed using the Braod Picard Pipeline
RNA sequencing fastq files were aligned to the GRCh38 human reference genome using Star aligner (v 2.6.1a), gencode v30
RSEM was used to quantify gene and transcript level expression
transcripts per million data were calculated using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file for log normalized counts per million for each sample

source_name: metastatic melanoma cells

growth_protocol: Melanoma cells were grown in DMEM medium10-013-CV from corning supplemented with 10% FBS. CRT34 and CRT35 medium was implemente with PD0325901 (35nM) and PLX4720 (1uM)

extract_protocol:
Qiagen RNeasy mini kit
TruSeq RNA Library Prep Kit v2

treatment_protocol: Melanoma cells were treated with PD0325901 (35nM) and PLX4720 (1uM) if drug is indicated.

tag: sample type

value: melanoma cell line

tag: condition

value: DMSO


title: CK_2


title: w1118-12hpi-1


title: MN_CRT35_nodrug_02


title: MN_CRT35_nodrug_03


title: JraRNAi-UC-1


title: MN_CRT35_drug_03

value: Combo


title: w1118-4hpi-3

value: 4 hours post infection with Pseudomonas entomophila


title: w1118-12hpi-2


title: OIR WT-3

city: Changsha

first: Jingling

last: Zou

state: Hunan

address: No. 139, Middle Renmin Road, furong district

department: Department of Ophthalmology

institute: The Second Xiangya Hospital of Central South University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using Hisat2 tools soft
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
GRCm38
Genome_build: tab-delimited text files include FPKM values for each Sample ...

source_name: Retina

extract_protocol:
Retinas were coleected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA)  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: retina

value: post natal day 17

value: wild type

value: oxygen-induced retinopathy (OIR)


title: MN_CRT35_drug_02


title: OIR WT-2


title: MN_CRT35_drug_01


title: w1118-4hpi-2

value: Gut

value: NP-Gal4ts > w1118


title: OIR WT-1


title: GBM14 cells, DMSO 1

description: Gene expression data from GBM14 cells treated with DMSO.


title: GBM14 cells, DMSO 2


title: GBM14 cells, ONC206 1


title: experiment2-Unfed-13dpf

city: Kumamoto

first: Asako

last: Shindo

address: 2-2-1 Honjo, Chuo-ku

country: Japan

institute: Kumamoto University

data_processing:
Quality filtering of reads was performed using Sickle v1.33, and filtered reads were mapped to the reference genes (Xenopus laevis, http://www.xenbase.org/other/static-xenbase/ftpDatafiles.jsp) using hisat2.
The mapped reads were counted using the featureCounts.
Genome_build: Xenopus laevis, http://www.xenbase.org/other/static-xenbase/ftpDatafiles.jsp
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Xenopus laevis

source_name: tadpoles

extract_protocol:
Fed and unfed tadpoles at 10 and 16 dpf were anesthetized, and the GI tubes were isolated using a thin razor and forceps. A total of 20–26 intestinal tubes from each stage were collected and homogenized in TRIzol LS reagent (#10296010; Thermo Fisher Scientific). RNA was purified using RNA Clean & Concentrator-5 (R1014; Zymo Research, Irvine, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: unfed

tag: developmental stage


title: experiment2-Unfed-16dpf


title: experiment2-Unfed-10dpf


title: MN_CRT34_nodrug_03


title: w1118-4hpi-1

value: 6-8 day adult female


title: OIR KO-3

value: IL-19 KO


title: w1118-UC-3

value: Uninfected


title: OIR KO-2


title: MN_CRT34_nodrug_02


title: MN_CRT34_nodrug_01


title: w1118-UC-2


title: experiment2-Fed-13dpf

value: Fed


title: experiment2-Fed-10dpf


title: experiment2-Fed-16dpf


title: OIR KO-1


title: RA WT-3

value: room air


title: w1118-UC-1


title: MN_CRT34_drug_03


title: RA WT-2


title: MN_CRT34_drug_01


title: experiment1-Unfed-10dpf


title: experiment1-Unfed-13dpf


title: RA WT-1


title: S2 cells, Bead_Recovery_2

city: Mandi

first: Baskar

last: Bakthavachalu

state: Himachal Pradesh

address: Kamand

department: School of Biosciences and Bioengineering

institute: Indian Institute of Technology

data_processing:
fastq files were mapped to dm6 reference genome using STAR v2.5.3 using default parameters
Read counts.txt were obtained using HTseq with “-s reverse” parameter
DESeq2 was used to perform differential expression analysis
Genome_build: dm6
Supplementary_files_format_and_content: tab-delimited text files include log2FoldChange and pvalues

source_name: S2R+ cells

growth_protocol: Drosophila S2R+ cells were obtained from DGRC and cultured in semi-adhering state in Schneider’s medium (S2 medium) with 10% FBS, penicillin and streptomycin at 250C. Cells were maintained at 50% confluency in fresh S2 media for atleast 24h before used for stress experiments.

extract_protocol:
After stress and recovery, RNA was isolated using TRIzol reagent (Invitrogen, USA) as per the manufacturer’s protocol. RNA concentration was measured using Qubit RNA assay kit in Qubit 2.0 Flurometer (Life Technologies, USA). RNA integrity was confirmed using the RNA Nano 6000 assay kit of the Bioanalyzer 2100 system (Agilent Technologies, USA).
Poly(A) enriched mRNA library was made using TruSeq RNA Library Preparation Kit V2 (RS-122-2001) and sequenced using HiSeq SR Rapid Cluster Kit v2 (GD-402-4002) to generate 1X50 single end reads on Illumina HiSeq 2500 sequencing platform.

treatment_protocol: To induce stress, cells were subjected to 0.5mM sodium arsenite in S2 media for 3 hours at room temperature on a rocking shaker. After 3 hours, arsenite containing S2 media was removed by centrifugation at 1000 rpm for 2’ and the cells were washed three times with fresh media and kept for recovery in fresh complete S2 media. Recovering cells were placed on the rocking shaker for additional 3h at room temperature.

value: S2R+ cells

value: treated with 0.5mM sodium arsenite for 3h and then recovered for 3h

value: Click-iT


title: experiment1-Fed-13dpf


title: S2 cells, Bead_Recovery_1


title: KPL Com TCR

city: Dallas

first: Huiyu

last: Li

state: Texas

address: 6000 Harry Hines Blvd

institute: UT Southwestern Medical Center

data_processing:
Library strategy: TCR-seq
Sequenced scRNA-seq samples were processed through Cellranger pipelines (v3.1.0).
Cellranger count was used to align reads to mouse reference genome (mm10, 2020-A, from 10x Genomics) and generate single cell feature counts for single library.
For scTCR-seq data, TCR reads were aligned to reference genome and TCR annotation was performed using the 10x cellranger vdj pipeline with provided reference (cellranger-vdj-GRCm38-alts-ensembl-4.0.0).
Cellranger aggr were applied next to aggregate each sample library for grouped analysis with same effective sequencing depth.
Seurat (3.2.1) package was used for multiple library data integration and downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix, mtx

source_name: Immune cells sorted from allografts

growth_protocol: KP (n=10) and KPL (n=10) allografts were harvested 14 days after subcutaneous implantation (average tumor size ~200 mm3). For each sample, individual tumors harvested from different mice were pooled with live CD45+ CD3- : CD45+ CD3+ cells sorted and mixed back as 1:1 ratio.

extract_protocol:
Cells were sorted, counted, and loaded onto scRNAseq chips following manufacturer's instruction.
Single cell libraries and TCR libraries were generated with Chromium Single Cell V(D)J Reagent Kit (10x Genomics, PN-10000006, PN-10000009, PN-1000071) following per manufacturer’s instruction.

value: tumor

value: KPL


title: MN_4.11_02

value: melanoma cell line

value: gSOX10 #4


title: MN_4.11_03


title: S2 cells, Bead_Stress_3

value: treated with 0.5mM sodium arsenite


title: KPL Com GEX

data_processing:
Sequenced scRNA-seq samples were processed through Cellranger pipelines (v3.1.0).
Cellranger count was used to align reads to mouse reference genome (mm10, 2020-A, from 10x Genomics) and generate single cell feature counts for single library.
For scTCR-seq data, TCR reads were aligned to reference genome and TCR annotation was performed using the 10x cellranger vdj pipeline with provided reference (cellranger-vdj-GRCm38-alts-ensembl-4.0.0).
Cellranger aggr were applied next to aggregate each sample library for grouped analysis with same effective sequencing depth.
Seurat (3.2.1) package was used for multiple library data integration and downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix, mtx


title: Progenitors rep5

city: Dresden

first: Caren

last: Norden

state: Sachsen

address: Pfotenhauerstr. 108

institute: Max Planck Institute of Molecular Cell Biology and Genetics

data_processing:
Basecalling performed using bcl2fastq version 2.19.1
Read alignment performed using GSNAP version 2018-07-04
gsnap -d GRCz11 --gunzip -A sam -t 6 --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000 -B 5 -N 0 -n 1 -s EnsemblGene-95.ss.GRCz11.iit --read-group-platform=illumina
Read counting performed using featureCounts version 1.6.3
featureCounts -a annotation/danio_rerio/GRCz11/EnsemblGene-95.GRCz11.TR.gtf -s 0 -Q 1 -T 8
Genome_build: Danio rerio GRCz10
Supplementary_files_format_and_content: Matrix table (.xlsx) with normalised gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table (.txt) with raw gene counts for every gene and every sample

molecule: polyA RNA

organism: Danio rerio

growth_protocol: Embryos were incubated at 28ºC until 24 hpf, then at 21ºC until 30 hpf and finally at 28ºC until 42 hpf.

extract_protocol:
Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tg(ath5:gap-RFP), Tg(crx:gap-CFP), Tg(ptf1a:gal4,UAS:gap-YFP). For each of the 5 replicates, 25 retinas were pooled.   During dissection, retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation, the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA-coated glass pipettes.   500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix (Peqlab). Purification of the amplified cDNA was performed using Ampure XP Beads (Beckman Coulter).
Libraries were prepared accoridng to SmartSeq-2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads.

treatment_protocol: MS-222 (0.01%) prior to dissection of the retinas.

value: 42 hpf

tag: expression of reporter genes


title: Amacrine cells/Horizontal cells rep5


title: KPL PD1 TCR

tag: cell line


title: Retinal ganglion cells rep5


title: S2 cells, Bead_Stress_1

tag: treatment


title: MN_4.11_01


title: MN_2.18_01_2

value: gSOX10 #2


title: MN_CRT34_drug_02

value: Combo


title: KPL BGB TCR


title: S2 cells, Bead_Recovery_3


title: S2 cells, Bead_Control_2

value: untreated


title: S2 cells, Bead_Control_3


title: KPL PD1 GEX


title: MN_A375_03


title: KPL BGB GEX


title: Photoreceptors rep5

tag: age


title: MN_2.18_01_0


title: Progenitors rep4


title: KPL CTR TCR

value: vehicle+IgG


title: Amacrine cells/Horizontal cells rep4


title: S2 cells, Bead_Control_1


title: MN_A375_02


title: experiment1-Fed-10dpf


title: S2 cells, Rin_RNAi_Recovery_3

value: Rin RNAi


title: KPL CTR GEX


title: Retinal ganglion cells rep4


title: MN_A375_01


title: S2 cells, Rin_RNAi_Recovery_2


title: S2 cells, Bead_Stress_2


title: KP TCR

value: KP


title: Photoreceptors rep4


title: EH003-4: PBRT16_PB_2

data_processing:
De-multiplexing and data aggregation was performed using the Braod Picard Pipeline
RNA sequencing fastq files were aligned to the GRCh38 human reference genome using Star aligner (v 2.6.1a), gencode v33
RSEM was used to quantify gene and transcript level expression
transcripts per million data were calculated using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file for log normalized counts per million for each sample

source_name: melanoma cells

growth_protocol: 1205Lu and paradox breaker resistant tumor (PBRT) #15 and #16 cells were cultured in MCDB153 with 2% FBS, 20% Leibowitz L-15 medium, and 5 μg/ml insulin.

extract_protocol:
Qiagen RNeasy mini kit
Tru-Seq paired-end Strand Specific

treatment_protocol: 1205Lu and 1205Lu-PBRT #15 and #16 cells were treated with DMSO or 0.5 μmol/L PLX8394

value: 1205 Lu TR PBRT 16

value: PB

tag: drug sensitivity

value: Resistant


title: S2 cells, Rin_RNAi_Recovery_1

value: S2R+ cells

value: treated with 0.5mM sodium arsenite for 3h and then recovered for 3h


title: S2 cells, Rin_RNAi_Stress_3


title: Amacrine cells/Horizontal cells rep3


title: EH003-3: PBRT16_PB_1


title: EH002-4: PBRT15_PB_2

value: 1205 Lu TR PBRT 15


title: S2 cells, Rin_RNAi_Stress_2


title: EH002-3: PBRT15_PB_1


title: Retinal ganglion cells rep3


title: mRNA-Seq P14 ko testicular replicate 2

city: beijing

first: shuntai

last: yu

state: beijing

address: 7 Science Park Road ZGC Life Science Park, Beijing

department: transgenic animal center

institute: NIBS

data_processing:
Basecalls performed using CASAVA version 1.9
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using STAR v2.6.1a with default parameters
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using featureCounts function from Rsubread (v2.0.1) and fpkm function of edgeR. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: testicular cells

growth_protocol: Mice were bred and maintained under a controlled temperature (22-25ºC) with a 12 h-light/12 h-dark cycle (light on from 7 am to 7 pm)

extract_protocol:
Total RNA of testes was extracted using Trizol reagent (15596026; Invitrogen). Poly(A) mRNA was isolated from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB,E7490L).
Libraries for mRNA abundance examination was prepared by using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). Libraries for ribosome footprints examination was prepared by linker ligation, reverse transcription, circularization as described previously (Ingolia et al., 2012).

tag: strain

tag: growth phase


title: mRNA-Seq P14 ko testicular replicate 1


title: KP GEX

tag: tissue

value: tumor


title: S2 cells, Rin_RNAi_Stress_1


title: mRNA-Seq P14 het testicularreplicate 2

tag: genotype


title: Progenitors rep2


title: EH001-2: 1205Par_DMSO_2

value: melanoma cell line

value: 1205 Lu TR Parental

value: DMSO

value: Sensitive


title: Photoreceptors rep3

value: 42 hpf


title: S2 cells, Rin_RNAi_Control_2


title: mRNA-Seq P14 het testicular replicate 1


title: S2 cells, Rin_RNAi_Control_3


title: EH001-1: 1205Par_DMSO_1


title: Amacrine cells/Horizontal cells rep2


title: K27AC_Dex1hr_GBS4eKO_ChIPseq [GBS4eKO_Dex_K27ac.rep2.1]

city: Research Triangle Park

first: Jackson

middle: Andrew

last: Hoffman

state: North Carolina

address: 111 TW Alexander Dr, Building 101 Room C432

department: DIR

institute: NIEHS

data_processing:
Adapter sequences were trimmed from ChIP-seq reads using Cutadapt (Martin, 2011) and low quality reads were removed from analysis using Sickle (Joshi NA et al., 2011). Alignment was performed with Bowtie2 (Langmead and Salzberg, 2012). Aligned reads were sorted and processed with Samtools (Li et al., 2009) and de-duplicated using Picard Tools (http://broadinstitute.github.io/picard). Peaks were called using MACS2 (Zhang et al., 2008) and Homer (Heinz et al., 2010) using a false discovery rate cutoff of 0.001, and regions of high depth or with high signal in untreated or input samples were used to filter out false positive peak calls. Peak overlaps and distance analyses were performed using Bedtools (Quinlan and Hall, 2010). Coverage files and heatmaps were generated using Deeptools (Ramírez et al., 2016).
For 4C-seq, data was processed using Pipe4C (Krijger et al., 2020) and run via Rscript for R version 3.6.1 with the following parameters: trimLength=0, mismatchMax=0, and minAmountReads=10. Data QC involved reviewing output reports to verify that the overall alignment rate was typically >85% and resulted in at least 1 million reads aligned to the fragment index. Results were visualized using ggplot2 (Wickham, 2016).
Genome_build: hg19
Supplementary_files_format_and_content: bw

growth_protocol: Cells were cultured in modified Eagle medium (MEM) containing 10% fetal bovine serum, 1X Penicillin/Streptomycin (Sigma P0781), 1% HEPES (Sigma H0887), 1X Glutamax (Gibco 35050), and 250 ug/ml G418 (Gibco 10131).

extract_protocol:
For ChIPseq, cells were fixed in PBS with 1% methanol-free formaldehyde (Thermoscientific 28906) at 37C for 10 min and quenched with glycine. Cell pellets were resuspended in MNase swelling buffer (25 mM HEPES pH 7.9, 1.5 mM MgCl2, 10 mM KCl, 0.1% NP-40, 5 mM Sodium Butyrate, 0.5 mM PMSF, and protease inhibitor cocktail (PIC) (ThermoFisher Scientific, 78429)) for enzymatic fragmentation or into hypotonic buffer (10 mM HEPES-NaOH pH 7.9, 10 mM KCl, 1.5 mM MgCl2, 340 mM sucrose, 10% glycerol, 0.1% Triton X-100, 5 mM Sodium Butyrate, 0.5 mM PMSF, and PIC) for mechanical sonication. Cells were incubated on ice for 10 min then subjected to Dounce homogenization using 20-strokes (Duran Wheaton Kimble, 357542). For enzymatic fragmentation with MNase, nuclei were sedimented through digestion buffer (15mM Hepes pH 7.9, 60mM KCl, 15mM NaCl, 0.32M Sucrose, 5 mM Sodium Butyrate, 0.5 mM PMSF, and PIC) by centrifugation for 7 min at 930g (4C). Nuclei pellets were fully resuspended in digestion buffer containing 3.3 mM CaCl2 and digested with MNase (0.7U/1x10^6 cells, Worthington, cat#) at 37C for 15min. MNase fragmentation was stopped by addition of 10 mM EGTA and incubation for 5 min on ice. Digested nuclei were lysed in LB3 buffer (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N- Lauroylsarcosine, 1% Triton X-100, 5 mM Sodium Butyrate, 0.5 mM PMSF, and PIC) using 5-passages through a 25g ( 0.508 mm x 1.6 cm) needle and brief sonication using 4 cycles (30 sec on/off, power high, 4C) with a Bioruptor sonicator (source). MNase digested chromatin lysate was recovered after 15 min centrifugation at 13,000g (4C).  For mechanical sonication, nuclei pellets were resuspended in Shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 0.5 mM PMSF, 5 mM Sodium Butyrate, 0.1% SDS, and PIC) and chromatin was fragmented by sonication using the Covaris S220 (Peak Power, 175; Duty Factor, 10; Cycles/Burst, 200; Total Time, 600 sec). Sonicated chromatin was recovered by centrifugation at 20,000g (4C) for 10 min.
4C-seq was performed according to the published protocol (Krijger et al., 2020). Briefly, batches of 5-10 million cells were fixed in 2% Formaldehyde solution and flash frozen in liquid nitrogen. A single pellet of 5-10 million cells was used for each 4C replicate. Chromatin was first digested with NlaIII, ligated with T4 DNA Ligase to generate the 3C template, and purified with NucleoMag PCR beads. The purified 3C template was subsequently digested with DpnII, ligated with T4 DNA Ligase to generate the 4C template, and again purified with NucleoMag PCR beads.
ChIP-seq libraries were generated using the ACCEL-NGS® 2S PLUS DNA library kit according to manufacturer’s protocol and sequenced on the Illumina NextSeq platform.
4C-seq libraries were generated by two-step PCR using Expand Long Template PCR kit. The first step PCR reaction used reading and non-reading primers to amplify 4C fragments and was purified with a 0.8X AMPure XP purification. The second step PCR reaction added sequencing adapters and indexes and was purified using Qiagen PCR purification kits. Libraries were sequenced on an Illumina MiSeq with a target of 1-2 million single-end, 100bp reads per library.

treatment_protocol: For Dexamethasone treatments, cells were initially cultured for 24 hours in reduced-serum, hormone-stripped media (Phenol-red free MEM (Gibco 51200) with 5% Charcoal/Dextran treated FBS (R&D Systems S11650), 1X Penicillin/Streptomycin (Sigma P0781), 1% HEPES (Sigma H0887), 1X Glutamax (Gibco 35050), and 250 ug/ml G418 (Gibco 10131)). Subsequently, Dexamethasone (Sigma D4902) was added to the media at 100 nM for all treatments timepoints and 9.5 x 10-4% ethanol was used as vehicle control.

tag: cell line/type

value: A1-2 GBS4eKO breast cancer cells

value: 1hr Dex

tag: antibody

value: Abcam ab4729


title: S2 cells, Rin_RNAi_Control_1

value: untreated

value: Rin RNAi


title: K27AC_EtOH_GBS4eKO_ChIPseq [GBS4eKO_EtOH_K27ac.rep2.1]

value: EtOH


title: S2 cells, Mock_RNAi_Recovery_3

value: Mock RNAi


title: Photoreceptors rep2


title: Progenitors rep3


title: K27AC_Dex1hr_GBS3eKO_ChIPseq [GBS3eKO_Dex_K27ac.rep2.1]

value: A1-2 GBS3eKO breast cancer cells


title: S2 cells, Mock_RNAi_Recovery_2

value: S2R+ cells


title: Progenitors rep1


title: Amacrine cells/Horizontal cells rep1


title: S2 cells, Mock_RNAi_Recovery_1

value: treated with 0.5mM sodium arsenite for 3h and then recovered for 3h


title: K27AC_Dex1hr_GBS2eKO_ChIPseq [GBS2eKO_Dex_K27ac.rep2.1]

value: A1-2 GBS2eKO breast cancer cells


title: S2 cells, Mock_RNAi_Stress_3

value: treated with 0.5mM sodium arsenite


title: K27AC_EtOH_GBS3eKO_ChIPseq [GBS3eKO_EtOH_K27ac.rep2.1]


title: Retinal ganglion cells rep1


title: S2 cells, Mock_RNAi_Stress_2


title: S2 cells, Mock_RNAi_Stress_1


title: K27AC_EtOH_GBS2eKO_ChIPseq [GBS2eKO_EtOH_K27ac.rep2.1]


title: Photoreceptors rep1


title: MN_2.18_01_1

value: melanoma cell line

value: gSOX10 #2


title: K27AC_EtOH_GBS1eKO_ChIPseq [GBS1eKO_EtOH_K27ac.rep2.1]

value: A1-2 GBS1eKO breast cancer cells


title: S2 cells, Mock_RNAi_Control_3


title: S2 cells, Mock_RNAi_Control_2


title: K27AC_Dex1hr_A12_ChIPseq [A12_Dex_K27ac.rep2.1]

value: A1-2 breast cancer cells


title: K27AC_Dex1hr_GBS1eKO_ChIPseq [GBS1eKO_Dex_K27ac.rep2.1]


title: S2 cells, Mock_RNAi_Control_1


title: U2932-DMSO-rep3

city: Zürich

first: Peter

last: Leary

address: Winterthurerstrasse 190

department: Functional Genomics Center Zürich

country: Switzerland

institute: ETH Zürich

data_processing:
raw counts
Supplementary_files_format_and_content: raw counts

growth_protocol: RIVA and OCI-LY3 were cultured in IMDM supplemented with 10% FBS, 100 U/ml penicillin and 100 µg/ml streptomycin. U-2932 were cultured in RPMI1640 supplemneted with 20% FBS, 100 U/ml penicillin and 100 µg/ml streptomycin.

extract_protocol:
RNA was isolated using NucleoSpin RNA kit (Macherey-Nagel).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In vitro: RIVA, U-2932 and OCI-LY3 were treated for 6 hours with 1 µM ibrutinib or dimethyl sulfoxide DMSO. In vivo: RIVA and U-2932 were orthotopically transplanted into MISTRG mice and mice were treated for two weeks with Ibru (in 5% DMSO, 30% PEG300, 5% Tween80, 60% ddH2O; 25 mg/kg/day; 5 treatments per week) or vehicle starting from day 14 post transplantation.

tag: disease subtype

value: Diffuse large B-cell lymphoma

tag: agent

value: DMSO


title: Retinal ganglion cells rep2

value: 42 hpf


title: S2 cells, stress_3h_rec_3h_3

value: WT


title: U2932-DMSO-rep1


title: WT (MeCP2 KO) rep5

city: Houston

first: Jian

last: Zhou

address: 1250 Moursund St

institute: BCM

description: Litter 3

data_processing:
First 10 nucleotides of each read are trimmed using fastp v0.20.0
Trimmed reads are aligned to the mouse reference genome GRCm38v23 using STAR v2.7.2c
Gene read counts are computed by setting --quantMode to GeneCounts in STAR

source_name: prefrontal cortex

extract_protocol:
Total RNA was isolated from dissected tissue using the RNeasy Mini Kit (Qiagen, 74104)
A double-stranded DNA library was created using 250ng of total RNA. First, cDNA was created using the fragmented 3’ poly (A) selected portion of total RNA and random primers. Libraries were created from the cDNA by first blunt ending the fragments, attaching an adenosine to the 3’ end and finally ligating unique adapters to the ends. The ligated products were then amplified using 15 cycles of PCR.

value: N129/FVB hybrid


title: S2 cells, stress_3h_rec_3h_2


title: RIVA-ibrutinib 6h-rep3

source_name: RIVA

value: RIVA

value: ibrutinib


title: WT (MeCP2 KO) rep4

description: Litter 3


title: U2932-DMSO-rep2


title: RIVA-ibrutinib 6h-rep2


title: S2 cells, stress_3h_rec_3h_1


title: S2 cells, stress_3h_3


title: S2 cells, stress_3h_2


title: RIVA-ibrutinib 6h-rep1


title: WT (MeCP2 KO) rep3

description: Litter 3


title: In vivo-RIVA-ibrutinib-M10


title: Maternal LT-GE 3_RNA-Seq

city: Columbia

first: Yuanyuan

middle: R

state: MO

address: University of Missouri School of Medicine, One Hospital Dr., Medical Sciences Building, NW508, Medical Sciences Building, NW508, Medical Sciences Building, M659

department: Ob&Gyn

institute: University of Missouri

data_processing:
RNA_Seq_step 1: Approximately 25- to 30-million sequencing reads were generated for each mRNA preparation. Quality control assessments were performed on RNA-Seq raw files by FASTQC.
RNA_Seq_step 2: Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to UCSC Genome Browser mouse GRCm38/mm10 reference sequence using RNA-STAR.
RNA_Seq__step 3: Readings were quantified and normalized by the fraction of reads assigned to each gene relative to the total number of reads to uniformly compare gene expression.
RNA_Seq_step 4: The number of fragments in each gene annotated in the RefSeq database was calculated using htseq-count from the HTSeq package. The DESeq platformwas utilized to evaluate DEGs by estimation of fold change and dispersion of sequence.
RRBS_step 1: Bisulfite-converted DNA libraries were produced and amplified, and single-end reads were sequenced on an Illumina HiSeq-2500 following library quality control.
RRBS_step 2: Quality control of RRBS raw reads was assessed by FastQC. Adaptor trimming and removal of trimmed reads shorter than 20 bp at the end of sequences were used by Trim Galore
RRBS_step 3: Bismark aligner was used to map trimmed bisulfite reads to UCSC Genome Browser mouse GRCm38/mm10 reference sequence.
RRBS_step 4: Post alignment and Bismark supplementary methylation extractor script that operates on Bismark result files were used to extract the methylation call for every single methylation locus analysis. Reads were filtered based on coverage, with a cutoff of at least three reads per site, and normalized for coverage before analysis.
RRBS_step 5: Statistical tests were conducted at each CpG site to determine differentially methylated loci (DML) followed by differentially methylated regions (DMRs). Because of our high average CpG coverage in a relatively small window size, we performed smoothing to quantify DMRs on a set of specified thresholds like minimum difference in the methylation levels between the groups of samples including minimum number CpG sites required (3 CpGs) and minimum length (30 bps) required for DMR determination.
Genome_build: UCSC Genome Browser mouse GRCm38/mm10 reference sequence
Supplementary_files_format_and_content: Statistical analysis summary of normalized abundance measurements for Differentially expressed gene (DEGs), Differentially methylated loci (DML), Differentially methylated regions (DMRs) and Integrative analysis by R (version 3.6.1).

source_name: Mammary tumor

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Genomic DNAs were extracted from the mammary tumors of mice offspring using DNeasy Blood and Tissue Kit (Qiagen). Quality control was performed with Agilent Bioanalyser.
RNA libraries or bisulfite-converted DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Dams were treated with either control or 250mg/kg GE diets from 4 weeks of age in mothers until weaning, all offspring remained control diet throughout the experiment.

value: Mammary tumor

value: FVB

value: ~25 weeks

value: SV40 Tag transgenic mice

value: Maternal LT-GE


title: Maternal LT-GE 2_RNA-Seq


title: S2 cells, stress_3h_1

value: S2R+ cells

value: treated with 0.5mM sodium arsenite


title: RIVA-DMSO-rep3


title: WT (MeCP2 KO) rep1

description: Litter 3


title: S2 cells, control_3h_3

value: untreated


title: MeCP2 KO rep 5

description: Litter 3


title: MeCP2 KO rep 4

description: Litter 3


title: Control 3_RNA-Seq

value: Control


title: In vivo-RIVA-ibrutinib-M9


title: Control 2_RNA-Seq


title: Maternal LT-GE 4_RNA-Seq


title: In vivo-RIVA-ibrutinib-M7


title: C20: transcription inactivity sample3

city: Jilin city

first: Bing

last: Shao

state: Jilin province

address: Jilin street 5

institute: Jilin Medical University

hyb_protocol: Each slide of microarray was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit in Hybridization Oven (Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions.

scan_protocol: After 65℃,10rpm, 17 hours hybridization, slides were washed in staining dishes (Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions.Slides were scanned by Agilent Microarray Scanner (Agilent technologies, Santa Clara, CA, US).

data_processing:
Data were extracted with Feature Extraction software 12.0.Background correction and quantile normalization was applied in order to make the 6 arrays comparable which performed in the RStudio software. The statistical method of paired T test was utilized for screening the differentially expressed LncRNAs and mRNAs(Fold change >=2.0 and P-value <0.05) was considered statistically significance.
After normalization, the distributions of log2-ratios among all tested samples were nearly the same. Control probes and low expressed probes were filtered out. Probes were considered expressed when the ﬂuorescent signal is “P” in all the three samples in any groups.If one gene corresponds to multiple detection probes, the maximum value of the probes was taken as the expression signal value.

source_name: PBMCs

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using Trizol reagent (Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN value to inspect RNA integrity

tag: diagnosis

value: HIV infected

tag: gender

value: Male

value: whole blood

tag: cell type

value: PBMCs


title: S2 cells, control_3h_2

tag: condition

value: WT


title: C12: transcription active sample3


title: S2 cells, control_3h_1


title: C13: transcription inactivity sample1


title: MeCP2 KO rep 3

description: Litter 3

value: N129/FVB hybrid


title: C2: transcription active sample1


title: C5: transcription active sample2


title: C14: transcription inactivity sample2


title: MeCP2 KO rep 2

description: Litter 3


title: Maternal LT-GE 1_RNA-Seq


title: In vivo-RIVA-vehicle-M4

value: Diffuse large B-cell lymphoma

value: RIVA

value: vehicle


title: WT (MeCP2 KO) rep2

description: Litter 3


title: In vivo-RIVA-vehicle-M2


title: Control 1_RNA-Seq

value: Mammary tumor

value: FVB


title: In vivo-RIVA-vehicle-M3


title: MeCP2 KO rep 1

description: Litter 3


title: T-30V Mouse POD 30 samples, hashed and pooled

city: Stanford

first: Michael

last: Januszyk

state: CA

address: 257 Campus Dr

department: Surgery

institute: Stanford University

data_processing:
Base calls were converted to reads with the software Cell Ranger (10X Genomics; version 3.1)'s implementation mkfastq. These were then aligned against either the  mm10 v3.0.0 genome using Cell Ranger’s count function (an implementation of STAR v2.7.0) with SC3Pv3 chemistry and 5,000 expected cells per sample.
Cell barcodes representative of quality cells were delineated from barcodes of apoptotic cells or background RNA based on a threshold of having at least 1000 transcripts profiled and less than 10% of their transcriptome of mitochondrial origin.
UMIs from each cell barcode were retained for all downstream analysis. Raw UMI counts were normalized with a scale factor of 10,000 UMIs per cell and subsequently natural log transformed with a pseudocount of 1 using the R package Seurat (version 3.1.1).
Since samples were hashtagged and pooled, the cell barcodes for each mouse are kept in a separate assay embedded within the standard three 10X output files, which is the recommended storage format for HTO-indexed 10X data. Each of the nine samples contained pooled data from five separate mice based on two separate FACS gates (Lin- or Lin+). These samples are represented by the following HTO antibodies (near the bottom of features.tsv):  Unwounded Lin+ Mouse 1: T1 TotalSeq-B-0301,MouseHashTag1--M1-42_30-F11-TSB  Unwounded Lin- Mouse 1: T1 TotalSeq-B-0302,MouseHashTag2--M1-42_30-F11-TSB  Unwounded Lin+ Mouse 2: T1 TotalSeq-B-0303,MouseHashTag3--M1-42_30-F11-TSB  Unwounded Lin- Mouse 2: T1 TotalSeq-B-0304,MouseHashTag4--M1-42_30-F11-TSB  Unwounded Lin+ Mouse 3: T1 TotalSeq-B-0305,MouseHashTag5--M1-42_30-F11-TSB  Unwounded Lin- Mouse 3: T1 TotalSeq-B-0306,MouseHashTag6--M1-42_30-F11-TSB  Unwounded Lin+ Mouse 4: T3 TotalSeq-B-0307,MouseHashTag7--M1-42_30-F11-TSB  Unwounded Lin- Mouse 4: T3 TotalSeq-B-0308,MouseHashTag8--M1-42_30-F11-TSB  Unwounded Lin+ Mouse 5: T2 TotalSeq-B-0309,MouseHashTag9--M1-42_30-F11-TSB  Unwounded Lin+ Mouse 5: T2 TotalSeq-B-0310,MouseHashTag10--M1-42_30-F11-TSB    POD2 PBS-treated Lin+ Mouse 1: T2 TotalSeq-B-0301,MouseHashTag1--M1-42_30-F11-TSB  POD2 PBS-treated Lin- Mouse 1: T2 TotalSeq-B-0302,MouseHashTag2--M1-42_30-F11-TSB  POD2 PBS-treated Lin+ Mouse 2: T2 TotalSeq-B-0303,MouseHashTag3--M1-42_30-F11-TSB  POD2 PBS-treated Lin- Mouse 2: T2 TotalSeq-B-0304,MouseHashTag4--M1-42_30-F11-TSB  POD2 PBS-treated Lin+ Mouse 3: T2 TotalSeq-B-0305,MouseHashTag5--M1-42_30-F11-TSB  POD2 PBS-treated Lin- Mouse 3: T2 TotalSeq-B-0306,MouseHashTag6--M1-42_30-F11-TSB  POD2 PBS-treated Lin+ Mouse 4: T1 TotalSeq-B-0307,MouseHashTag7--M1-42_30-F11-TSB  POD2 PBS-treated Lin- Mouse 4: T1 TotalSeq-B-0308,MouseHashTag8--M1-42_30-F11-TSB  POD2 PBS-treated Lin+ Mouse 5: T3 TotalSeq-B-0309,MouseHashTag9--M1-42_30-F11-TSB  POD2 PBS-treated Lin+ Mouse 5: T3 TotalSeq-B-0310,MouseHashTag10--M1-42_30-F11-TSB    POD2 Verteporfin-treated Lin+ Mouse 1: T3 TotalSeq-B-0301,MouseHashTag1--M1-42_30-F11-TSB  POD2 Verteporfin-treated Lin- Mouse 1: T3 TotalSeq-B-0302,MouseHashTag2--M1-42_30-F11-TSB  POD2 Verteporfin-treated Lin+ Mouse 2: T3 TotalSeq-B-0303,MouseHashTag3--M1-42_30-F11-TSB  POD2 Verteporfin-treated Lin- Mouse 2: T3 TotalSeq-B-0304,MouseHashTag4--M1-42_30-F11-TSB  POD2 Verteporfin-treated Lin+ Mouse 3: T3 TotalSeq-B-0305,MouseHashTag5--M1-42_30-F11-TSB  POD2 Verteporfin-treated Lin- Mouse 3: T3 TotalSeq-B-0306,MouseHashTag6--M1-42_30-F11-TSB  POD2 Verteporfin-treated Lin+ Mouse 4: T2 TotalSeq-B-0307,MouseHashTag7--M1-42_30-F11-TSB  POD2 Verteporfin-treated Lin- Mouse 4: T2 TotalSeq-B-0308,MouseHashTag8--M1-42_30-F11-TSB  POD2 Verteporfin-treated Lin+ Mouse 5: T1 TotalSeq-B-0309,MouseHashTag9--M1-42_30-F11-TSB  POD2 Verteporfin-treated Lin+ Mouse 5: T1 TotalSeq-B-0310,MouseHashTag10--M1-42_30-F11-TSB      POD7 PBS-treated Lin+ Mouse 1: T-7P TotalSeq-B-0301,MouseHashTag1--M1-42_30-F11-TSB  POD7 PBS-treated Lin- Mouse 1: T-7P TotalSeq-B-0302,MouseHashTag2--M1-42_30-F11-TSB  POD7 PBS-treated Lin+ Mouse 2: T-7P TotalSeq-B-0303,MouseHashTag3--M1-42_30-F11-TSB  POD7 PBS-treated Lin- Mouse 2: T-7P TotalSeq-B-0304,MouseHashTag4--M1-42_30-F11-TSB  POD7 PBS-treated Lin+ Mouse 3: T-7P TotalSeq-B-0305,MouseHashTag5--M1-42_30-F11-TSB  POD7 PBS-treated Lin- Mouse 3: T-7P TotalSeq-B-0306,MouseHashTag6--M1-42_30-F11-TSB  POD7 PBS-treated Lin+ Mouse 4: T-7P TotalSeq-B-0307,MouseHashTag7--M1-42_30-F11-TSB  POD7 PBS-treated Lin- Mouse 4: T-7P TotalSeq-B-0308,MouseHashTag8--M1-42_30-F11-TSB  POD7 PBS-treated Lin+ Mouse 5: T-7P TotalSeq-B-0309,MouseHashTag9--M1-42_30-F11-TSB  POD7 PBS-treated Lin+ Mouse 5: T-7P TotalSeq-B-0310,MouseHashTag10--M1-42_30-F11-TSB    POD7 Verteporfin-treated Lin+ Mouse 1: T-7V TotalSeq-B-0301,MouseHashTag1--M1-42_30-F11-TSB  POD7 Verteporfin-treated Lin- Mouse 1: T-7V TotalSeq-B-0302,MouseHashTag2--M1-42_30-F11-TSB  POD7 Verteporfin-treated Lin+ Mouse 2: T-7V TotalSeq-B-0303,MouseHashTag3--M1-42_30-F11-TSB  POD7 Verteporfin-treated Lin- Mouse 2: T-7V TotalSeq-B-0304,MouseHashTag4--M1-42_30-F11-TSB  POD7 Verteporfin-treated Lin+ Mouse 3: T-7V TotalSeq-B-0305,MouseHashTag5--M1-42_30-F11-TSB  POD7 Verteporfin-treated Lin- Mouse 3: T-7V TotalSeq-B-0306,MouseHashTag6--M1-42_30-F11-TSB  POD7 Verteporfin-treated Lin+ Mouse 4: T-7V TotalSeq-B-0307,MouseHashTag7--M1-42_30-F11-TSB  POD7 Verteporfin-treated Lin- Mouse 4: T-7V TotalSeq-B-0308,MouseHashTag8--M1-42_30-F11-TSB  POD7 Verteporfin-treated Lin+ Mouse 5: T-7V TotalSeq-B-0309,MouseHashTag9--M1-42_30-F11-TSB  POD7 Verteporfin-treated Lin+ Mouse 5: T-7V TotalSeq-B-0310,MouseHashTag10--M1-42_30-F11-TSB    POD14 PBS-treated Lin+ Mouse 1: T-14P TotalSeq-B-0301,MouseHashTag1--M1-42_30-F11-TSB  POD14 PBS-treated Lin- Mouse 1: T-14P TotalSeq-B-0302,MouseHashTag2--M1-42_30-F11-TSB  POD14 PBS-treated Lin+ Mouse 2: T-14P TotalSeq-B-0303,MouseHashTag3--M1-42_30-F11-TSB  POD14 PBS-treated Lin- Mouse 2: T-14P TotalSeq-B-0304,MouseHashTag4--M1-42_30-F11-TSB  POD14 PBS-treated Lin+ Mouse 3: T-14P TotalSeq-B-0305,MouseHashTag5--M1-42_30-F11-TSB  POD14 PBS-treated Lin- Mouse 3: T-14P TotalSeq-B-0306,MouseHashTag6--M1-42_30-F11-TSB  POD14 PBS-treated Lin+ Mouse 4: T-14P TotalSeq-B-0307,MouseHashTag7--M1-42_30-F11-TSB  POD14 PBS-treated Lin- Mouse 4: T-14P TotalSeq-B-0308,MouseHashTag8--M1-42_30-F11-TSB  POD14 PBS-treated Lin+ Mouse 5: T-14P TotalSeq-B-0309,MouseHashTag9--M1-42_30-F11-TSB  POD14 PBS-treated Lin+ Mouse 5: T-14P TotalSeq-B-0310,MouseHashTag10--M1-42_30-F11-TSB    POD14 Verteporfin-treated Lin+ Mouse 1: T-14V TotalSeq-B-0301,MouseHashTag1--M1-42_30-F11-TSB  POD14 Verteporfin-treated Lin- Mouse 1: T-14V TotalSeq-B-0302,MouseHashTag2--M1-42_30-F11-TSB  POD14 Verteporfin-treated Lin+ Mouse 2: T-14V TotalSeq-B-0303,MouseHashTag3--M1-42_30-F11-TSB  POD14 Verteporfin-treated Lin- Mouse 2: T-14V TotalSeq-B-0304,MouseHashTag4--M1-42_30-F11-TSB  POD14 Verteporfin-treated Lin+ Mouse 3: T-14V TotalSeq-B-0305,MouseHashTag5--M1-42_30-F11-TSB  POD14 Verteporfin-treated Lin- Mouse 3: T-14V TotalSeq-B-0306,MouseHashTag6--M1-42_30-F11-TSB  POD14 Verteporfin-treated Lin+ Mouse 4: T-14V TotalSeq-B-0307,MouseHashTag7--M1-42_30-F11-TSB  POD14 Verteporfin-treated Lin- Mouse 4: T-14V TotalSeq-B-0308,MouseHashTag8--M1-42_30-F11-TSB  POD14 Verteporfin-treated Lin+ Mouse 5: T-14V TotalSeq-B-0309,MouseHashTag9--M1-42_30-F11-TSB  POD14 Verteporfin-treated Lin+ Mouse 5: T-14V TotalSeq-B-0310,MouseHashTag10--M1-42_30-F11-TSB    POD30 PBS-treated Lin+ Mouse 1: T-30P TotalSeq-B-0301,MouseHashTag1--M1-42_30-F11-TSB  POD30 PBS-treated Lin- Mouse 1: T-30P TotalSeq-B-0302,MouseHashTag2--M1-42_30-F11-TSB  POD30 PBS-treated Lin+ Mouse 2: T-30P TotalSeq-B-0303,MouseHashTag3--M1-42_30-F11-TSB  POD30 PBS-treated Lin- Mouse 2: T-30P TotalSeq-B-0304,MouseHashTag4--M1-42_30-F11-TSB  POD30 PBS-treated Lin+ Mouse 3: T-30P TotalSeq-B-0305,MouseHashTag5--M1-42_30-F11-TSB  POD30 PBS-treated Lin- Mouse 3: T-30P TotalSeq-B-0306,MouseHashTag6--M1-42_30-F11-TSB  POD30 PBS-treated Lin+ Mouse 4: T-30P TotalSeq-B-0307,MouseHashTag7--M1-42_30-F11-TSB  POD30 PBS-treated Lin- Mouse 4: T-30P TotalSeq-B-0308,MouseHashTag8--M1-42_30-F11-TSB  POD30 PBS-treated Lin+ Mouse 5: T-30P TotalSeq-B-0309,MouseHashTag9--M1-42_30-F11-TSB  POD30 PBS-treated Lin+ Mouse 5: T-30P TotalSeq-B-0310,MouseHashTag10--M1-42_30-F11-TSB    POD30 Verteporfin-treated Lin+ Mouse 1: T-30V TotalSeq-B-0301,MouseHashTag1--M1-42_30-F11-TSB  POD30 Verteporfin-treated Lin- Mouse 1: T-30V TotalSeq-B-0302,MouseHashTag2--M1-42_30-F11-TSB  POD30 Verteporfin-treated Lin+ Mouse 2: T-30V TotalSeq-B-0303,MouseHashTag3--M1-42_30-F11-TSB  POD30 Verteporfin-treated Lin- Mouse 2: T-30V TotalSeq-B-0304,MouseHashTag4--M1-42_30-F11-TSB  POD30 Verteporfin-treated Lin+ Mouse 3: T-30V TotalSeq-B-0305,MouseHashTag5--M1-42_30-F11-TSB  POD30 Verteporfin-treated Lin- Mouse 3: T-30V TotalSeq-B-0306,MouseHashTag6--M1-42_30-F11-TSB  POD30 Verteporfin-treated Lin+ Mouse 4: T-30V TotalSeq-B-0307,MouseHashTag7--M1-42_30-F11-TSB  POD30 Verteporfin-treated Lin- Mouse 4: T-30V TotalSeq-B-0308,MouseHashTag8--M1-42_30-F11-TSB  POD30 Verteporfin-treated Lin+ Mouse 5: T-30V TotalSeq-B-0309,MouseHashTag9--M1-42_30-F11-TSB  POD30 Verteporfin-treated Lin+ Mouse 5: T-30V TotalSeq-B-0310,MouseHashTag10--M1-42_30-F11-TSB    Values for each barcode for each cell can be found with the lookup indices of 33540, 33541, 33542, and 33533, respectively, in the matrix.mtx file.  Please see the associated Seurat vignette for additional details: https://satijalab.org/seurat/v3.1/hashing_vignette.html
Hashtag oligos (HTOs) for samples were demultiplexed using Seurat’s implementation HTODemux. Briefly, k-medoid clustering is performed on the normalized HTO values, after which a ‘negative’ HTO distribution is calculated. For each HTO,  the cluster with the lowest average value is treated as the negative group and a negative binomial distribution is fit to this cluster. Using the 0.99 quantile of this distribution as a threshold, each cell is classified as positive or negative for each HTO. Cells that are positive for more than one HTOs are annotated as doublets and removed. Cells that are not positive for any HTO are also removed. This is accomplished using Seurat's workflow as described in this Vignette: https://satijalab.org/seurat/v3.1/hashing_vignette.html
As recommended, a threshold of P-adjusted < 0.1 was used to define significance for differentially expressed genes
Genome_build: mm10 v3.0.0
Supplementary_files_format_and_content: Filtered 10X matrix counts

source_name: POD30 mice

extract_protocol:
Samples were isolated using FACS as either lineage negative or lineage positive. RNA extraction was performed using Qiagen miRNeasy kit (cat. 1071023) with on column DAnase treatment per the manufacturer’s recommendations. The Clontech Smarter Ultra Low Input RNA kit (Takara Bio, Cat. 634848) was used to generate cDNA from 150 pg total RNA following the manufacturer’s recommendations.  Amplified cDNA was purified using SPRI Ampure Beads (Beckman Coulter, Cat. A63880) and the quality and quantity was measured using a High Sensitivity DNA chip on the Agilent 2100 Bioanalyzer (Agilent Technologies).
cDNA was sheared to an average length of 300 basepairs using a Covaris S2 ultrasonicator (Covaris) and libraries were generated with the Clontech Low Input Library Prep kit (Takara Bio, Cat. 634947).
The samples were uniquely barcoded, pooled, and sequenced on a single lane of the NextSeq 500 (Illumina).

treatment_protocol: Fresh mouse tissue specimens wereminced on ice. The tissue was then digested for 60 minutes in a 37 deg C water bath agitator in 2 mg/mL collagenase (collagenase type IV, ThermoFisher) digest buffer in Medium 199 (HyClone, GE Healthcare) consisting of 5% fetal bovine serum (Gibco FBS, ThermoFisher), DNase I (Worthington), Poloxamer 188 (Cat. P5556-100ML, Sigma), HEPES, and CaCl2. The digest was quenched with quench media (DMEM (Gibco DMEM, ThermoFisher) with 15% FBS), then centrifuged at 300 x G for 5 minutes at 4 deg C, resuspended in quench media, and filtered through 100, 70, and 40um cell strainers (Falcon cell strainer, ThermoFisher). Red blood cell lysis was performed using Hybri-Max (Sigma) per the manufacturers protocol. Histopaque was performed using Histopaque-1119 (Sigma Aldrich), per the manufacturers protocol.   Cells were counted and re-suspended in FACS buffer. Primary antibodies were applied, and cells were stained in the dark with gentle agitation for 30 minutes. Cells were then washed thoroughly in FACS buffer. Staining with secondary antibodies was conducted in the same manner. Propidium iodine (PI, Thermofisher, Cat. P3566, lot: 1755970, 3 ug/mL) or DAPI (Thermofisher, Cat. 3571) were used as a viability marker. Fibroblasts were isolated using the FACS Aria II system. For RNA sequencing, cells were sorted into chilled lysing reagent under RNA/DNAse-free conditions (Trizol LS, ThermoFisher).

value: Mouse dorsal wound tissue

tag: days after wounding

value: 30 days


title: stk-17com-K rep2

city: Beijing

first: Chengcheng

last: Hu

address: NO.1 Beichen West Road

institute: Institute of Microbiology, Chinese Academy of Sciences

data_processing:
Basecalling was performed using a software developed for BGISEQ-500.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke v1.5.2, then mapped to Neurospora crassa whole genome (GCA_000182925.2) using HISAT v2.0.4 with parameters -p 8 --phred64 --sensitive -I 1 -X 10000
After analyzing the efficiency of aligned clean reads to reference genome by Bowtie2 v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200, gene expression were calculated as Fragments Per Kilobase of exon per Megabase of library size (FPKM) using RSME v1.2.12 with default parameters.
Differential expressed genes were caracterized using a protocol from Audic S. et al.,  Genome Research, 1997.
Genome_build: GCA_000182925.2
Supplementary_files_format_and_content: excel file include FPKM values for all Samples and data for differential expressed genes between each two Samples, as well as the annotation of each genes.

organism: Neurospora crassa

source_name: mycelium

growth_protocol: Briefly, 15 small pieces of mycelial mats (1-2 mm2) were grown in liquid Vogel’s medium for 13 h and then treated with or without ketoconazole for 12 h.

extract_protocol:
Harvested samples were immediately frozen, and then ground into fine powder in liquid nitrogen. Total RNA extraction was performed according to the standard TRIzol protocol (Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Ketoconazole were added to a final concentration of 1 μg/mL

value: ketoconazole


title: stk-17com-K rep1


title: stk-17com-K rep3


title: stk-17ko-K rep3


title: T-30P Mouse POD 30 samples, hashed and pooled


title: T-14V Mouse POD 14 samples, hashed and pooled

source_name: POD14 mice

value: 14 days


title: In vivo-U2932-ibrutinib-M9

tag: cell line

value: ibrutinib


title: WT (Phf14+/-) rep2

description: Litter 2


title: WT (Phf14+/-) rep3

description: Litter 2


title: stk-17ko-K rep2

tag: treatment


title: In vivo-U2932-ibrutinib-M6


title: T-14P Mouse POD 14 samples, hashed and pooled


title: WT (Phf14+/-) rep1

description: Litter 2


title: T7-V Mouse POD 7 samples, hashed and pooled

source_name: POD7 mice

value: 7 days


title: In vivo-U2932-ibrutinib-M5


title: Phf14+/- rep2

description: Litter 2


title: WT-K rep3

value: wild type


title: Phf14+/- rep3

description: Litter 2


title: stk-17ko-K rep1


title: In vivo-U2932-vehicle-M4


title: In vivo-U2932-vehicle-M3


title: T3 Mouse unwounded + POD 2 samples, hashed and pooled

source_name: POD0/2 mice

value: 4 days or immediate


title: Phf14+/- rep1

description: Litter 2


title: WT-K rep1


title: WT (Tcf20+/-) rep3

description: Litter 1


title: T2 Mouse unwounded + POD 2 samples, hashed and pooled

value: 3 days or immediate


title: stk-17com rep3

value: control (no treatment)


title: OTII mTEClo/int replicate

city: Nantes

first: Matthieu

last: Giraud

address: 30 bd Jean Monnet

department: CRTI

country: France

institute: INSERM _ Université de Nantes

data_processing:
Illumina NextSeq 500 machine
single-end 75bp reads
Alignment to the mm10 genome was done using Tophat 2
Read count and normalization was performed using Cuffdiff 2 between two conditions of two biological replicates each
Genome_build: mm10
Supplementary_files_format_and_content: xlsx text files include normalized FPKM and stats for each sample pair

source_name: medullary thymic epithelial cells

extract_protocol:
Total RNA was extracted with miRNeasy Micro Kit (Qiagen)
SMART-Seq-v4-Ultra Low Input RNA Kit (Clontech) combined to the Nextera library preparation kit (Illumina)

treatment_protocol: mTEClo/int were isolated from individual mice using a BD FACS Aria III cell sorter, following the typical isolation procedure

value: thymus

value: CD80 lo/int medullary epithelial cells

value: OTII


title: T7-P Mouse POD 7 samples, hashed and pooled


title: OTII mTEClo/int


title: OCI-LY3-ibrutinib 6h-rep3

value: Diffuse large B-cell lymphoma


title: WT (Tcf20+/-) rep1

description: Litter 1


title: WT-K rep2


title: stk-17com rep2


title: OCI-LY3-ibrutinib 6h-rep2


title: WT (Tcf20+/-) rep2

description: Litter 1


title: stk-17com rep1


title: Tcf20+/- rep3

description: Litter 1


title: stk-17ko rep3


title: Tcf20+/- rep2

description: Litter 1


title: RipmOVA mTEClo/int

value: RipmOVAxOTII


title: OCI-LY3-DMSO-rep3

value: DMSO


title: stk-17ko rep2


title: Tcf20+/- rep1

description: Litter 1


title: K14 mTEClo/int replicate

value: K14xCIITA KO


title: stk-17ko rep1


title: OCI-LY3-DMSO-rep2


title: In vivo-U2932-vehicle-M2

value: vehicle


title: T1 Mouse unwounded + POD 2 samples, hashed and pooled

value: Mouse dorsal wound tissue

value: 2 days or immediate


title: Zdbf2-KO_3dpp_rep3

city: paris

first: teissandier

last: aurelie

address: 26 rue d'Ulm

institute: institut curie

description: Whole hypothalamus RNA from Zdbf2-KO at 3dpp

data_processing:
Adapters sequences were trimmed using TrimGalore v0.6.2 (https://github.com/FelixKrueger/TrimGalore).
Paired-end reads were mapped using STAR_2.6.1a (citation) allowing 4% of mismatches. Gencode vM13 annotation was used to quantify gene expression using quantification mode from STAR. Normalization and differential gene expression was performed using EdgeR R package (v3.22.3) (citation). Genes were called as differentially expression if the fold discovery rate (FDR) is lower than 10%.
Genome_build: mm10
Supplementary_files_format_and_content: File text with gene count

source_name: 3dpp hypothalamus

extract_protocol:
Whole hypothalamus RNA was extracted using Trizol, Dnase-treated using QIAGEN Rnase-Free Dnase Set, and quality-controlled for integrity using Tapstation.
RNA-seq libraries were prepared from 500ng of DNase-treated RNA with the TruSeq Stranded mRNA Library Prep Kit (Illumina). Sequencing was performed in 100pb paired-end reads using Novaseq 6000 (for 3dpp samples) and HiSeq2500 (for 10dpp samples).

tag: genetic background

value: C57BL/6J background

value: male

value: Heterozygous mutant (paternal transmission)


title: WT rep3

value: wild type


title: CIITAKO mTEClo/int replicate

value: CIITA KO:[CIIta(III+IV)-/-]


title: Zdbf2-KO_3dpp_rep1


title: WT rep2


title: U2932-ibrutinib 6h-rep2

value: ibrutinib


title: U2932-ibrutinib 6h-rep3


title: WT rep1

value: control (no treatment)


title: Control_3dpp_rep3

description: Whole hypothalamus RNA from WT at 3dpp

value: Wild-type


title: RipmOVA mTEClo/int replicate

value: thymus

value: CD80 lo/int medullary epithelial cells


title: mTEClo/int replicate

value: WT


title: DruB_experiments

city: Copenhagen

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

data_processing:
Library strategy: RiboMeth-seq
Barcode separation using python script
Adaptor trimming using Cutadapt v. 2.0
Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1
Counting read ends and calculating RiboMeth-seq scores using python scripts
Genome_build: Sequence reads were mapped to ribosomal sequences: 17S:FR733593.1, 26S:FR733594.1, 5S:FR733597.1, 5.8S:FR733595.1, and to predicted snoRNAs from the following chromosome annotations: chr.1:DDB0232428, chr.2:DDB0232429, chr.3:DDB0232430, chr.4:DDB0232431, chr.5:DDB0232432, chr.6:DDB0232433 from dictybase.org
Supplementary_files_format_and_content: MS Excel file contains 5' and 3' read count and calculated RiboMeth-seq score at all positions in the rRNA sequence.

organism: Dictyostelium discoideum

source_name: Cell line

growth_protocol: The D. discoideum strains AX2 and ∆drnB were cultivated in HL5 medium containing 50 μg/mL ampicillin, 250 ng/mL amphotericin, 500 U/mL penicillin/streptomycin at 22°C in shaking suspension

extract_protocol:
Cells were pelleted and resuspended in TRIzol reagent (Invitrogen) containing 10 mM EDTA (pH 8.0). RNA was extracted according to the manufacturer’s instructions
RiboMeth-seq: 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20-40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2',3' cyclic phosphate and 5' phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U, Christensen-Dalsgaard M, Krogh N, Sabarinathan R, Gorodkin J, Nielsen H. Profiling of ribose methylations in RNA by high-throughput sequencing. Angewandte Chemie. 2015;54(2):451-5 for detailed description

treatment_protocol: Filter development was performed using 5 × 108 of axenically grown D. discoideum cells pelleted for 5 min at 500 x g and washed three times with Sørensen buffer (2 mM Na2HPO4, 15 mM KH2PO4, (pH 6.7)). The pellet was resuspended in Sørensen buffer and transferred in a 6-cm dish containing two layers of Whatman® paper topped off with a nitrocellulose membrane. After 16 hours, the slugs were harvested by washing the nitrocellulose membrane with Sørensen buffer and spun down by centrifugation at 500 x g for 5 min

value: [delta]drnB


title: OCI-LY3-ibrutinib 6h-rep1

value: Diffuse large B-cell lymphoma


title: Control_3dpp_rep2

description: Whole hypothalamus RNA from WT at 3dpp


title: mTEClo/int


title: K14 mTEClo/int

value: K14xCIITA KO


title: Control_3dpp_rep1

description: Whole hypothalamus RNA from WT at 3dpp


title: OCI-LY3-DMSO-rep1

value: DMSO


title: CIITAKO mTEClo/int


title: texAM 3 [ATAC-seq]

status: Public on Jan 23 2022

city: Marseille

first: Julien

last: Maurizio

address: Centre d’Immunologie de Marseille-Luminy

institute: INSERM

description:
Pool of 3 mice
Replicate 3

data_processing:
fastq files quality control were done by fastqc (v 0.11.6) tool.
Adapter trimming was done using cutadapt (v 2.6). Bowtie2 (v 2.3.5.1) was used to align and index sequences on the mm10 mouse genome and thus generate bam files.
Then, peaks detection was made on these bam files by Genrich (v 0.6.1).
Then, all peaks detected from exAM, texAM, Host, BAL samples were pooled and merged together with bedtools (v 2.26.0).
Then a table of counts was generated from these peaks by computing signal given by filtered bam files (mitochondrial DNA removed, PCR duplicates removed, non unique alignments removed).
Then peaks with more than 10 counts in at least one condition were kept giving 48 100 peaks.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Finally, .bed file containing these 48 100 peaks is created (filtered_peaks_BAL_exAM_texAM_host.bed).
Supplementary_files_format_and_content: *_peaks.bed: Peak files for individual samples.

source_name: Live, SiglecF+, CD11c+, CD45.2+

growth_protocol: 8 weeks old WT C57BL/6 mice for isolation and expansion of AM and 8 weeks old WT C57Bl/6-Ly5.1 mice were used for transplantation of AM.

extract_protocol:
5000 from 3 mice each of BAL AM, exAM, texAM or Host AM were lyzed in lysis buffer. After centrifugation, nuclei were resuspend in reaction buffer containing Tn5 transposase. Tagmented DNA was purified using SPRI beads.
Library amplification using nextera kit has been done as described in Lara-Astiaso et al., 2014.

treatment_protocol: Mice were injected I.T with 80-100 µl PBS or 0.8 - 1.0 x 10ˆ6 exAM. At the indicated time after injection, lungs were harvested and Live, SiglecF+, CD11c+, CD45.1+ or CD45.2+ AM were FACS-sorted. Samples are from pool of 2-3 mice.

value: Whole lung sorted AM

value: Transplanted expanded AM 4 months in vivo experimental


title: Host AM 3 [ATAC-seq]

description:
Pool of 3 mice
Replicate 3

source_name: Live, SiglecF+, CD11c+, CD45.1+

value: Host AM experimental


title: texAM 1 [ATAC-seq]

description:
Pool of 3 mice
Replicate 1


title: Zdbf2-KO_3dpp_rep2

value: C57BL/6J background

value: male


title: exAM 3 [ATAC-seq]

description:
Pool of 3 mice
Replicate 3

source_name: Unsorted culture expanded AM

value: AM ex vivo 2 months culture experimental


title: texAM 2 [ATAC-seq]

description:
Pool of 3 mice
Replicate 2


title: Host AM 2 [ATAC-seq]

description:
Pool of 3 mice
Replicate 2


title: RIVA-DMSO-rep2

value: RIVA


title: Host AM 1 [ATAC-seq]

description:
Pool of 3 mice
Replicate 1


title: U2932-ibrutinib 6h-rep1

value: ibrutinib


title: BAL AM 2 [ATAC-seq]

description:
Pool of 3 mice
Replicate 2

source_name: Unsorted BAL

value: Unsorted BAL AM experimental


title: BAL AM 3 [ATAC-seq]

description:
Pool of 3 mice
Replicate 3


title: RIVA-DMSO-rep 1


title: 48h post-PHx liver treated with GSK2801 - rep1

first: Hao

last: Zhu

state: TX

institute: UT Southwestern Medical Cetern

data_processing:
Reads were mapped to the mouse reference genome GRCm38 (mm10) using HISAT (version 2.1.0) aligner with --rna-strandness F.
Mapped reads were counted using HTSeq (version 0.6.1) to obtain raw read counts for each gene.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Raw read number txt files

source_name: 48h post-PHx mouse liver

extract_protocol:
Tissues were homogenized in TRIzol with tissue homogenizer machine, followed by choloroform extraction. Total RNAs were extracted fromcholoroform layers using Rneasy RNA purification column as described in manufacturer's protocol.
Libraries were constructed using Nugen Ovation RNA-seq preparation kit.

treatment_protocol: Wild-typed B6 mice were subjected to 70% PHx. Treatment of 30 mg/kg/day of either GSK2801 or GSK8573 started two days before surgery until the liver tissues were collected

value: 48h post-PHx mouse liver

value: BAZ2 inhibitor


title: 48h post-PHx liver treated with GSK2801 - rep2


title: 48h post-PHx liver treated with GSK8573 - rep2

value: control


title: 48h post-PHx liver treated with GSK8573 - rep4


title: 48h post-PHx liver treated with GSK2801 - rep3


title: 48h post-PHx liver treated with GSK8573 - rep3


title: 48h post-PHx liver treated with GSK2801 - rep4


title: Ax_experiments


title: H2.35  input

data_processing:
Reads were mapped to the mouse reference genome GRCm38 (mm10) using BWA aligner (version 0.7.5) with default parameters
Peak calling was performed using MACS (version 1.4.2) with options -c --nomodel --p 1e-5.
BigWig files were generated usning bamCoverage command from deeptools (version 3.5.0) with --smoothLength 50 --binSize 5 and --scaleFactor.  The scaleFactors were normalization factors calculated from DiffBind based on the number of reads in peaks.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: BigWig files

source_name: H2.35 cells

growth_protocol: H2.35 (ATCC, source: BALB/c female mouse) immortalized hepatocytes were cultured in DMEM (Life Technologies) supplemented with 4% (vol/vol) FBS, 1× Pen/Strep solution (Thermo Scientific HyClone) and 200nM Dexamethasone (Sigma). Cells were cultured at 37°C and 5% CO2 in a humidified incubator.

extract_protocol:
Cells were fixed with 37% formaldehyde for 5 minutes at RT with shaking, followed by glycine to a final concentration of 125 mM for 5 minutes to stop fixation. Cell were sonicated with a probe sonicator to produce 250-500 bp long DNA fragment. Sonicated lysates were incubated with corresponding antibodies overnight at 4C: anti-H3K27ac (Abcam #4729); anti-H3K4me3 (Abcam #8580); anti-H3K4me1 (Abcam #8895) and anti-Flag (Sigma F1804), followed by incubation of ChIP-grade Pierce™ magnetic protein A/G beads (Thermo Scientific) for 3 hours at 4C. DNA was purified with QIAquick PCR purification kit (Qiagen).
Library were constructed with NEBNext Ultra DNA Library Prep Kit (NEB)

treatment_protocol: Cell were treated with 500 nM of GSK8573 or GSK2801 for 3 days before collection

value: H2.35 cells

value: hepatocytes

tag: chip antibody


title: H2.35 cells overexpressed Flag-BAZ2B and treated with GSK2801

value: overexpressed Flag-BAZ2B

value: anti-Flag (Sigma F1804)


title: H2.35 cells overexpressed Flag-BAZ2A and treated with GSK2801

value: overexpressed Flag-BAZ2A


title: H2.35 cells with Flag-BAZ2B overexpression


title: exAM 2 [ATAC-seq]

description:
Pool of 3 mice
Replicate 2

tag: strain


title: exAM 1 [ATAC-seq]

description:
Pool of 3 mice
Replicate 1


title: H2.35 cells with Flag-BAZ2A overexpression


title: BAL AM 1 [ATAC-seq]

description:
Pool of 3 mice
Replicate 1


title: H2.35 cell treated with GSK2801 - H3K4me1 rep2

value: anti-H3K4me1 (Abcam #8895)


title: H2.35 cell treated with GSK2801 - H3K4me1 rep3


title: H2.35 cell treated with GSK2801 - H3K4me1 rep1


title: H2.35 cell treated with GSK2801 - H3K4me3 rep3

value: anti-H3K4me3 (Abcam #8580)


title: H2.35 cell treated with GSK8573 - H3K4me1 rep2


title: H2.35 cell treated with GSK8573 - H3K4me1 rep1


title: H2.35 cell treated with GSK8573 - H3K4me1 rep3


title: H2.35 cell treated with GSK2801 - H3K4me3 rep1


title: H2.35 cell treated with GSK8573 - H3K4me3 rep3


title: H2.35 cell treated with GSK8573 - H3K4me3 rep2


title: H2.35 cell treated with GSK2801 - H3K27ac rep3

value: anti-H3K27ac (Abcam #4729)


title: H2.35 cell treated with GSK2801 - H3K27ac rep1


title: H2.35 cell treated with GSK8573 - H3K27ac rep3


title: H2.35 cell treated with GSK2801 - H3K27ac rep2


title: 48h post-PHx liver treated with GSK2801 - input rep3

data_processing:
Reads were mapped to the mouse reference genome GRCm38 (mm10) using BWA aligner (version 0.7.5) with default parameters
Peak calling was performed using MACS (version 1.4.2) with options -c  --nomodel --p 1e-5.
BigWig files were generated usning bamCoverage command from deeptools (version 3.5.0) with --smoothLength 50 --binSize 5 and --scaleFactor.  The scaleFactors were normalization factors calculated from DiffBind based on the number of reads in peaks.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: BigWig files

extract_protocol:
Liver tissues were minced into small pieces, and were fixed with 37% formaldehyde for 15 minutes at RT with shaking, followed by glycine to a final concentration of 125 mM for 5 minutes to stop fixation. Tissues were sonicated with a probe sonicator to produce 250-500 bp long DNA fragment. Sonicated lysates were incubated with corresponding anti-H3K27ac antibodies (Abcam #4729) overnight at 4C, followed by incubation of ChIP-grade Pierce™ magnetic protein A/G beads (Thermo Scientific) for 3 hours at 4C. DNA was purified with QIAquick PCR purification kit (Qiagen).
Libraries were amplied using NEBNext Ultra II Q5 Master Mix (NEB) with primers described in https://www.encodeproject.org/documents/860c95a8-fdc4-46bd-b9b5-d44242ff20ef/@@download/attachment/ATAC_garberlab_protocol.pdf.

treatment_protocol: Wild-type B6 mice were subjected to 70% PHx. Treatment of 30 mg/kg/day of either GSK2801 or GSK8573 started two days before surgery until the liver tissues were collected


title: 48h post-PHx liver treated with GSK8573 - rep1


title: H2.35 cell treated with GSK8573 - H3K27ac rep1


title: 48h post-PHx liver treated with GSK2801 - input rep4


title: 48h post-PHx liver treated with GSK2801 - input rep1


title: 48h post-PHx liver treated with GSK8573 - input rep4


title: 48h post-PHx liver treated with GSK8573 - input rep3


title: 48h post-PHx liver treated with GSK2801 - input rep2


title: 48h post-PHx liver treated with GSK8573 - input rep2


title: 48h post-PHx liver treated with GSK8573 - input rep1


title: 48h post-PHx liver treated with GSK2801 - H3K27ac rep3


title: 48h post-PHx liver treated with GSK2801 - H3K27ac rep4


title: 48h post-PHx liver treated with GSK2801 - H3K27ac rep2


title: 48h post-PHx liver treated with GSK8573 - H3K27c rep3


title: 48h post-PHx liver treated with GSK8573 - H3K27c rep2


title: H2.35 cell treated with GSK2801 - H3K4me3 rep2


title: 48h post-PHx liver treated with GSK8573 - H3K27c rep1


title: 48h post-PHx liver treated with GSK2801 - H3K27ac rep1


title: 48h post-PHx liver treated with GSK8573 - H3K27c rep4


title: H2.35 cells treated with GSK2801  - rep2

data_processing:
Reads were mapped to the mouse reference genome GRCm38 (mm10) using BWA aligner (version 0.7.5) with default parameters
Peak calling was performed using MACS (version 1.4.2) with options  --nomodel --p 1e-5.
BigWig files were generated usning bamCoverage command from deeptools (version 3.5.0) with --smoothLength 50 --binSize 5 and --scaleFactor.  The scaleFactors were normalization factors calculated from DiffBind based on the number of reads in peaks.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: BigWig files

extract_protocol:
Nuclei were isolated with lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Transposition reactions was performed in 50,000 cells with llumina Tagment DNA Enzyme and Buffer kit (Illumina 20034197) as described in manufacture's protocol. Transposed DNA was purified with AIQuick PCR purification kit (Qiagen).
Libraries were amplied using NEBNext Ultra II Q5 Master Mix (NEB) with primers described in https://www.encodeproject.org/documents/860c95a8-fdc4-46bd-b9b5-d44242ff20ef/@@download/attachment/ATAC_garberlab_protocol.pdf.


title: H2.35 cells treated with GSK2801  - rep3


title: H2.35 cells treated with GSK8573  - rep2


title: H2.35 cell treated with GSK8573 - H3K4me3 rep1


title: H2.35 cells treated with GSK8573  - rep3


title: H2.35 cells treated with GSK8573  - rep1


title: Bone marrow stroma Dll4(E12)

city: Münster

first: Kai

last: Kruse

state: North Rhine-Westphalia

address: Roentgenstr. 20

department: Bioinformatics Core Facility

institute: Max Planck Institute for Molecular Biomedicine

description: single cell transcriptome

data_processing:
Reads were trimmed using TrimGalore (0.6.4) with the parameter --length 66
Barcodes and UMIs were extracted from the index read as specified in the BD Rhapsody Handbook
Reads were mapped to the mm10 genome using Salmon Alevin (1.1.0)
Empty wells were filtered using DropletUtils (1.6.1) using an FDR cutoff of 0.001
Doublets were filtered using sclDblFinder (1.0.0)
Cells with high mitochondrial gene expression were removed using Seurat (3.1.3) using a 20% cutoff
Counts were normalised using scran (1.14.6)
Batch correction/integration, feature selection, scaling, clustering, and marker gene identification was performed using Seurat (3.1.3)
Genome_build: mm10
Supplementary_files_format_and_content: Barcodes, features, and matrix (mtx) files were generated using write10xCounts from DropletUtils
Supplementary_files_format_and_content: Sample-specific files contain uncorrected counts after the Salmon Alevin step
Supplementary_files_format_and_content: The top-level matrix file contains fully normalised counts according to the preprocessing pipeline
Supplementary_files_format_and_content: The meta annotation file contains results from the preprocessing steps and cluster annotations for each barcode

source_name: Femur and tibia

extract_protocol:
Femurs and tibiae were harvested 3 weeks post-injection from adult mice at the age of 11 weeks. Bones were crushed by pestle and mortar with ice-cold 2% FCS/PBS and followed by 30 min digestion at 37 °C with collagenase cocktail by mixing with 2 mg/ml of collagenase IV (17104-019, Gibco), 2 mg/ml collagenase I (17100-017, Gibco), and 10 U/ml of Dispase (17105-041) in a 1:1:1 ratio. The resulting single cell suspension was subjected to depletion of lineage-positive hematopoietic cells with following reagents from Miltenyi Biotec: Lineage Cell Depletion Kit (130-090-858), CD45 Microbeads (130-052-301), CD117 Microbeads (130-091-224), and Ter-119 Microbeads (130-049-901). Lineage-depleted stromal cells were loaded into a BD Rhapsody™ Cartridge for capturing single cells for whole transcriptome according to the manufacturer’s instructions.
scRNA libraries were prepared with The BD Rhapsody Whole Transcriptome Analysis (WTA) Amplification kit.

treatment_protocol: WT mice at age of 8-week were inject with injection vehicle or pLIVE-Dll4(E12), respectively, via hydrodynamic tail vein injection. Femur and tibia were collected from mice at 3 week post injection.

value: Femur and tibia

tag: age

value: post natal week 11

value: wild type

value: pLIVE-Dll4(E12) via hydrodynamic tail vein injection


title: H2.35 cell treated with GSK8573 - H3K27ac rep2


title: Bone marrow stroma WT

description: single cell transcriptome

tag: tissue

value: injection vehicle


title: Young ILC2- Rep 2

city: New Brunswick

first: Qi

last: Yang

state: NJ

address: 89 French St

institute: Rutgers RWJMS

description: Yang 3

data_processing:
Single-end 75 bp high throughout sequencing was performed using a NextSeq 500 (Illumina)
Raw data was converted to fastq files using bcl2fastq v2.20.0.422 and quality checked using fastqc v 1.0.0.
RNA-seq reads were aligned to mm10 genome by the STAR  aligner V2.5.3a
Reads Per Kilobase of exon per Megabase  (RPKM) estimation of reference genes and transcripts using Cufflinks V2.0
Differential expression was calculated using DEseq2 (v1.1)
Genome_build: mm10
Supplementary_files_format_and_content: Text file for processed data file, and Fastq files for each sample

source_name: Lung ILC2

extract_protocol:
Lungs were removed, ILC2 cells were FACS sorted based on the following surface expression: CD45.2+ CD3- CD5- TCRβ- TCRδ- B220- CD11b- NK1.1- CD90.2+ IL33R+. Cells from 2 mice were pooled per sample and were sorted into Trizol LS
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lung ILC2

value: 8 weeks


title: Young ILC2- Rep 1

description: Yang 2


title: Old ILC2- Rep 3

description: Yang 6

value: 20 months


title: Old ILC2- Rep 2

description: Yang 5


title: Old ILC2- Rep 1

description: Yang 4


title: H2.35 cells treated with GSK2801  - rep1

value: BAZ2 inhibitor


title: minimally cystic tissue_5

city: Toronto

first: York

middle: PC

last: Pei

state: Ontario

address: 8N838, 585 University Avenue

department: Department of Medicine

institute: University of Toronto

description:
PKD1 control tissue
MCT5

hyb_protocol: Standard Illumina DASL hybridisation protocol

scan_protocol: Standard Illumina DASL scanning protocol

data_processing: The raw data were normalized using quantile normalization with BeadStudio 3.4 (Illumina). The normalized intensities and detection p-values were exported and further adjusted for batch effect with the R package ComBat.

source_name: Minimally cystic tissue from PKD1 patient, batch1

label_protocol: Standard Illumina DASL label protocol

growth_protocol: The nephrectomized kidneys were kept cooled on ice immediately after their removal in the operating room and through out the tissue retrieval procedure in the surgical pathology suite, where the renal capsule was striped and individual cysts identified.

extract_protocol: Total RNA containing miRNA was extracted from each sample using miRNeasy Mini Kit (Qiagen) with an on-column DNA digestion step to minimize genomic DNA contamination

treatment_protocol: All tissues were dissected within 30 minutes of nephrectomy, washed in cold phosphate-buffered saline, snapped frozen in liquid nitrogen, and stored in a -80°C freezer

value: PKD1 patient

value: Minimally cystic renal tissue


title: minimally cystic tissue_4

description:
PKD1 control tissue
MCT4


title: normal renal cortical tissue_1

description:
normal control tissue
KIDNEY1

source_name: Non-cancerous renal cortical tissue from nephrectomized kidney with isolated renal cell carcinoma of patient 1, batch1

value: control tissue from renal cell carcinoma

value: Non-cancerous renal cortical tissue


title: normal renal cortical tissue_2

description:
normal control tissue
KIDNEY2

source_name: Non-cancerous renal cortical tissue from nephrectomized kidney with isolated renal cell carcinoma of patient 2, batch2


title: minimally cystic tissue_6

description:
PKD1 control tissue
MCT6


title: normal renal cortical tissue_3

description:
normal control tissue
KIDNEY3

source_name: Non-cancerous renal cortical tissue from nephrectomized kidney with isolated renal cell carcinoma of patient 3, batch1


title: normal renal cortical tissue_4

description:
normal control tissue
KIDNEY4

source_name: Non-cancerous renal cortical tissue from nephrectomized kidney with isolated renal cell carcinoma of patient 4, batch1