title: HEK293 cells, RVFV N protein expression, day 2, replicate 3

city: Missoula

first: J Stephen

last: Lodmell

state: MT

address: 32 campus drive

department: Biological Sciences

institute: The University of Montana

description:
N3
readcount.txt
fpkm.txt
NvsMock.DEG.fasta
NvsMock.DEG.txt
NvsMP_12.DEG.fasta
NvsMP_12.DEG.txt
A3SS.miso_summary.txt
A5SS.miso_summary.txt
MXE.miso_summary.txt
RI.miso_summary.txt
SE.miso_summary.txt
N_vs_MP_12.miso_bf.filtered.xlsx
N_vs_Mock.miso_bf.filtered.xlsx

data_processing:
Indexes of the reference genome (hg19 = GRCh37 Genome Reference Consortium Human Build 37) were built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene (RPKM, Reads Per Kilobase of exon model per Million mapped reads, Mortazavi et al., 2008).
Differential expression analysis of two conditions/groups was performed using the DESeq2 R package (Anders et al., 2012)
Alternative splicing analysis. MISO v0.5.2 was used for alternative splicing event analysis, difference detection and visualization. MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples.
Assembly: HG19
Supplementary files format and content: readcount.txt: statistics list of expression level for all genes = reads count of all gene. fpkm.txt: statistics list of expression level for all genes = FPKM of all genes. *.DEG.txt: gene list of differential expression genes (three different comparisons, MP_12_vs_Mock, N_vs_Mock, and N_vs_MP_12). *.DEG.fasta: sequence information of differential expression genes.
Supplementary files format and content: MISO (Mixture of Isoforms) analysis of alternatively splicing events from the mapped Illumina reads. MISO quantitates the abundances of alternative mRNA isoforms by using PSI(percentage spliced in), PSI denotes the fraction of mRNAs that represent the inclusion isoform. There is a file for each alternative splicing event category: A3SS for Alternative 3' splice site, A5SS for Alternative 5' splice site, MXE for Mutually exclusive, RI for retention intron, SE for Skipping exon. Each file contains the PSI numbers for each of the nine samples, xls format. The MISO summary results were used to study the variation of psi among three different comparisons ( MP_12_vs_Mock, N_vs_Mock, and N_vs_MP_12) for each of the five families of alternative splicing events. The threshold values used were delta_psi>=0.2 and BF>=10. Files format is xlsx.

growth_protocol: HEK293 cells were maintained in DMEM media supplemented with 10% FBS and antibiotics in humidified 5% CO2 incubator at 37C

extract_protocol:
Total RNA was extracted from mock- and MP12-infected cells using the PureLink RNA Mini Kit (Thermo Fisher Scientific)
Poly-A mRNA was selected from total RNA using oligo-dT bound magnetic beads and strand specific NEBNext Ultra RNA libraries were synthesized for paired-end 150 bp (PE 150) on an Illumina HiSeq 2000 platform (Illumina Inc.).

treatment_protocol: 80–90% confluent HEK293 cells were washed with phosphate-buffered saline (PBS) and overlaid with either PBS (mock infection) or MP12 virus at 0.1 MOI (RVFV infection) in DMEM without serum or antibiotics and incubated for one hour at 37˚C and 5% CO2. The media was then replaced with DMEM media supplemented with 10% FBS and antibiotics in humidified 5% CO2 incubator at 37C. Three other plates with HEK293 cells were transfected with RVFV N protein expression plasmid (lipofectamine 2000, Thermo Fisher Scientific), according to the manufacturer's protocol. The transfected cells were kept for two days in DMEM media supplemented with 2% FBS and antibiotics in humidified 5% CO2 incubator at 37C.

value: Human embryonic kidney

value: wild type

value: RVFV N protein expression plasmid transfection


title: HEK293 cells, RVFV N protein expression, day 2, replicate 1

status: Public on Sep 12 2023

type: SRA

country: USA

description:
N1
readcount.txt
fpkm.txt
NvsMock.DEG.fasta
NvsMock.DEG.txt
NvsMP_12.DEG.fasta
NvsMP_12.DEG.txt
A3SS.miso_summary.txt
A5SS.miso_summary.txt
MXE.miso_summary.txt
RI.miso_summary.txt
SE.miso_summary.txt
N_vs_MP_12.miso_bf.filtered.xlsx
N_vs_Mock.miso_bf.filtered.xlsx

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: HEK293 cells, RVFV infection, day 2, replicate 2

description:
MP12_2
readcount.txt
fpkm.txt
MP_12vsMock.DEG.fasta
MP_12vsMock.DEG.txt
NvsMP_12.DEG.fasta
NvsMP_12.DEG.txt
A3SS.miso_summary.txt
A5SS.miso_summary.txt
MXE.miso_summary.txt
RI.miso_summary.txt
SE.miso_summary.txt
MP_12_vs_Mock.miso_bf.filtered.xlsx
N_vs_MP_12.miso_bf.filtered.xlsx

value: RVFV infection, MP-12 strain


title: HEK293 cells, RVFV N protein expression, day 2, replicate 2

description:
N2
readcount.txt
fpkm.txt
NvsMock.DEG.fasta
NvsMock.DEG.txt
NvsMP_12.DEG.fasta
NvsMP_12.DEG.txt
A3SS.miso_summary.txt
A5SS.miso_summary.txt
MXE.miso_summary.txt
RI.miso_summary.txt
SE.miso_summary.txt
N_vs_MP_12.miso_bf.filtered.xlsx
N_vs_Mock.miso_bf.filtered.xlsx


title: HEK293 cells, RVFV infection, day 2, replicate 3

description:
MP12_3
readcount.txt
fpkm.txt
MP_12vsMock.DEG.fasta
MP_12vsMock.DEG.txt
NvsMP_12.DEG.fasta
NvsMP_12.DEG.txt
A3SS.miso_summary.txt
A5SS.miso_summary.txt
MXE.miso_summary.txt
RI.miso_summary.txt
SE.miso_summary.txt
MP_12_vs_Mock.miso_bf.filtered.xlsx
N_vs_MP_12.miso_bf.filtered.xlsx


title: HEK293 cells, Mock infection, day 2, replicate 3

description:
Mock3
readcount.txt
fpkm.txt
MP_12vsMock.DEG.fasta
MP_12vsMock.DEG.txt
NvsMock.DEG.fasta
NvsMock.DEG.txt
A3SS.miso_summary.txt
A5SS.miso_summary.txt
MXE.miso_summary.txt
RI.miso_summary.txt
SE.miso_summary.txt
MP_12_vs_Mock.miso_bf.filtered.xlsx
N_vs_Mock.miso_bf.filtered.xlsx

value: mock infection


title: HEK293 cells, RVFV infection, day 2, replicate 1

description:
MP12_1
readcount.txt
fpkm.txt
MP_12vsMock.DEG.fasta
MP_12vsMock.DEG.txt
NvsMP_12.DEG.fasta
NvsMP_12.DEG.txt
A3SS.miso_summary.txt
A5SS.miso_summary.txt
MXE.miso_summary.txt
RI.miso_summary.txt
SE.miso_summary.txt
MP_12_vs_Mock.miso_bf.filtered.xlsx
N_vs_MP_12.miso_bf.filtered.xlsx


title: Mod1_1

city: Beijing

first: Shan

last: Jiang

address: No. 16, Nanxiao Road/Street

country: China

institute: China Academy of Chinese Medical Sciences

data_processing:
Raw reads of fastq format were firstly processed using fastp
The clean reads were mapped to the reference genome using HISAT2
FPKM3 of each gene was calculatedandthe read counts of each gene were obtained by HTSeq-count
Differential expression analysis was performed using the DESeq2
PCA analysis were performedusingR(v 3.2.0) to evaluate the biological duplication of samples
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) accordingtothemanufacturer’s protocol.
the libraries were constructedusingVAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

tag: tissue

value: Liver

value: model


title: ATRX KO2

type: RNA

city: London

first: Sarfraz

last: Shafiq

state: Ontario

address: Victoria Hospital, 800 commissioners road east

department: Anatomy and Cell Biology

country: Canada

institute: University of Western Ontario

description:
p17 all genes CTL2 vs KO2
Total forebrain RNA (10 μg) was isolated from three P17 pairs of littermate-matched AtrxFoxG1Cre and control mice using the RNeasy Mini kit (Qiagen Cat# 74104). cRNA was generated and hybridized to an Affymetrix Mouse Genome 430 2.0 Array at the London Regional Genomics Center (London, Canada).

data_processing:
Probe signal intensities were generated using GCOS1.4 (Affymetrix Inc., Santa Clara, CA) using default values for the Statistical Expression algorithm parameters and a Target Signal of 150 for all probe sets and a Normalization Value of 1.
Gene level data was generated using the RNA preprocessor in GeneSpring GX 7.3.1 (Agilent Technologies Inc., Palo Alto, CA). Data were then transformed (measurements less than 0.01 set to 0.01), normalized per chip to the 50th percentile, and per gene to control samples. Probe sets representing Atrx transcripts were removed (10 sets). The remaining probe sets were filtered by fold change ≥1.5 between control and AtrxFoxG1Cre samples, and by confidence level of P<0.05. Significantly overrepresented GO categories were determined using the Enrichr web platform

label: biotin

source_name: brain

value: brain

value: atrx ko

tag: age


title: JDH3_1

value: BBBPH


title: ATRX KO1

description:
p17 all genes CTL1 vs KO1
Total forebrain RNA (10 μg) was isolated from three P17 pairs of littermate-matched AtrxFoxG1Cre and control mice using the RNeasy Mini kit (Qiagen Cat# 74104). cRNA was generated and hybridized to an Affymetrix Mouse Genome 430 2.0 Array at the London Regional Genomics Center (London, Canada).


title: F1 generation with C. gibelio mtDNA (termed F1 C. gibelio x C. carpio), infected group, repl. 1

city: Brno

first: Jiri

last: Vorel

address: Kotlarska 267/2

department: Department of Botany and Zoology

country: Czech Republic

institute: Masaryk University

description: gibel.featureCounts.tsv

data_processing:
Quality check (FastQC v. 0.11.9)
Quality trimming (Trimmomatic v. 0.36, CROP:250 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:35)
Alignment (STAR v. 2.7.3a; employing default parameters, except for --outFilterMismatchNoverLmax 0.1 and --twopassMode Basic)
Quality control after alignment concerning the number and percentage of uniquely- and multi-mapped reads, rRNA contamination, the mapped regions, the read coverage distribution, strand specificity, gene biotypes, and PCR duplication was performed using several tools (RSeQC v. 2.6.2; Picard toolkit v. 2.18.27; Qualimap v. 2.2.2; BioBloom tools v. 2.3.4)
DGE analysis (featureCounts v. 1.6.3 with settings -s 2 -T 10 -F GTF -Q 0 -d 1 -D 25000; DESeq2 v1.20.0)
Functional annotation (KEGG pathway database; clusterProfiler v 3.12.0)
Assembly: ASM336829v1, GCA_000951615.2
Supplementary files format and content: tab-delimited text file with featureCounts for samples that originated and mapped significantly better on the C. carpio reference genome
Supplementary files format and content: tab-delimited text file with featureCounts for samples that originated and mapped significantly better on the C. gibelio reference genome

organism: Carassius gibelio x Cyprinus carpio 'xingguonensis'

source_name: Head kidney

growth_protocol: Catching and artificial breeding

extract_protocol:
NEBNext Poly(A) mRNA Magnetic Isolation Module
NEBNext Ultra Directional RNA Library Prep Kit for Illumina

value: Head kidney


title: HEK293 cells, Mock infection, day 2, replicate 1

description:
Mock1
readcount.txt
fpkm.txt
MP_12vsMock.DEG.fasta
MP_12vsMock.DEG.txt
NvsMock.DEG.fasta
NvsMock.DEG.txt
A3SS.miso_summary.txt
A5SS.miso_summary.txt
MXE.miso_summary.txt
RI.miso_summary.txt
SE.miso_summary.txt
MP_12_vs_Mock.miso_bf.filtered.xlsx
N_vs_Mock.miso_bf.filtered.xlsx


title: JDH2_2


title: F1 generation with C. gibelio mtDNA (termed F1 C. gibelio x C. carpio), control group, repl. 3

description: gibel.featureCounts.tsv


title: JDH2_1


title: F1 generation with C. gibelio mtDNA (termed F1 C. gibelio x C. carpio), infected group, repl. 4

description: gibel.featureCounts.tsv


title: F1 generation with C. gibelio mtDNA (termed F1 C. gibelio x C. carpio), control group, repl. 2

description: gibel.featureCounts.tsv


title: F1 generation with C. gibelio mtDNA (termed F1 C. gibelio x C. carpio), control group, repl. 1

description: gibel.featureCounts.tsv


title: Con3_4

value: control


title: paternal backcrosses (backcross C. carpio x F1 hybrid), infected group, repl. 5

description: carp.featureCounts.tsv


title: Con2_2


title: ProliHH_G6PC_P3

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

data_processing:
Trimmed reads were aligned to the human genome (hg38, Genome Reference Consortium GRCh38) using Hisat2-2.0.0-beta
FPKM (fragments per kilobase of exon per million fragments mapped) values were calculated by Cufflinks using default parameters for gene expression levels
The counts expression profiles were normalized  by Deseq2 using rlog function
Assembly: hg38
Supplementary files format and content: tab-delimited text files include log2 tranformed counts for each Sample

source_name: liver

growth_protocol: Primary human hepatocytes or proliferating human hepatocytes were seeded at 2 x 104 cells/cm2 on 6-wells collagen-coated plates (Corning) in hypoxia . The medium was changed every 3 days. At day 6 of the primary culture, cells cultured in the presence of EHM or HM were harvested via trypsinization

extract_protocol:
Proliferaitng human hepatocyte or mouse liver were removed, flash frozen on dry ice, total RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: liver

value: Proliferating Human Hepatocytes

value: G6PC mutation

value: Proliferating Human Hepatocytes from patient with Glycogen storage disease type I cultured at Passage 3  in hypoxia


title: ProliHH_G6PC_P4

value: Proliferating Human Hepatocytes from patient with Glycogen storage disease type I cultured at Passage 4  in hypoxia


title: ProliHH_G6PC_P2

value: Proliferating Human Hepatocytes from patient with Glycogen storage disease type I cultured at Passage 2  in hypoxia


title: ProliHH_LDLR_P4

value: LDLR mutation

value: Proliferating Human Hepatocytes from patient with Familial hypercholesterolemia cultured at Passage 4  in hypoxia


title: HEK293 cells, Mock infection, day 2, replicate 2

description:
Mock2
readcount.txt
fpkm.txt
MP_12vsMock.DEG.fasta
MP_12vsMock.DEG.txt
NvsMock.DEG.fasta
NvsMock.DEG.txt
A3SS.miso_summary.txt
A5SS.miso_summary.txt
MXE.miso_summary.txt
RI.miso_summary.txt
SE.miso_summary.txt
MP_12_vs_Mock.miso_bf.filtered.xlsx
N_vs_Mock.miso_bf.filtered.xlsx

value: Human embryonic kidney

value: wild type


title: F1 generation with C. gibelio mtDNA (termed F1 C. gibelio x C. carpio), control group, repl. 4

description: gibel.featureCounts.tsv


title: paternal backcrosses (backcross C. carpio x F1 hybrid), infected group, repl. 4

description: carp.featureCounts.tsv


title: Con1_5

value: Liver


title: ProliHH_LDLR_P2

value: Proliferating Human Hepatocytes from patient with Familial hypercholesterolemia cultured at Passage 2  in hypoxia


title: Con1_1


title: paternal backcrosses (backcross C. carpio x F1 hybrid), infected group, repl. 2

description: carp.featureCounts.tsv


title: ProliHH_LDLR_P3

value: Proliferating Human Hepatocytes from patient with Familial hypercholesterolemia cultured at Passage 3  in hypoxia


title: paternal backcrosses (backcross C. carpio x F1 hybrid), infected group, repl. 1

description: carp.featureCounts.tsv


title: paternal backcrosses (backcross C. carpio x F1 hybrid), infected group, repl. 3

description: carp.featureCounts.tsv


title: ProliHH_OTC_P3

value: OTC mutation

value: Proliferating Human Hepatocytes from patient with Ornithine transcarbamylase cultured at Passage 3  in hypoxia


title: Ink4a_DMSO_16hr_2

city: Rochester

first: Chris

last: Harris

state: New York

address: 575 Elmwood Avenue

institute: University of Rochester Medical Center

data_processing:
Data formatting bcl2fastq version 2.20.0
Data cleaning FastP version 0.23.1 with the following parameters:  "--length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -y –r".1
Genome alignment STAR_2.7.9a with the following parameters: "—twopass Mode Basic --runMode alignReads --outSAMtype BAM Unsorted – outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical –outReadsUnmapped Fastx".2
Read quantification subread-2.0.1, featureCounts, -s 2 -t exon -g gene_name
Assembly: GRCm39 + gencode M31
Supplementary files format and content: tab-delimited text file of gene counts

source_name: pancreas

growth_protocol: Cells were subcultured into DMEM supplemented with 10% dialyzed fetal bovine serum for 16 hours, then treated for 16 hours with DMSO or with 5 nM all trans retinoic acid dissolved in DMSO.

extract_protocol:
RNA was prepared with RNAeasy columns from Qiagen, using manufacturer's recommended protocol
Libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols

treatment_protocol: Cells in DMEM/10% dialyzed FBS were treated for 16 hours with DMSO or with 5 nM all trans retinoic acid dissolved in DMSO.

value: pancreas

value: Pancreatic ductal adenocarcinoma

value: derived from KrasLSL-G12D/+; Ink4a/Arflox/lox; p48-Cre mice

value: DMSO 16 hr


title: pure line of C. carpio, infected group, repl. 6

description: carp.featureCounts.tsv

organism: Cyprinus carpio

value: Head kidney


title: Ink4a_ATRA5nm_16hr_3

value: 5 nM all trans retinoic acid 16 hr


title: ProliHH_OTC_P2

value: liver

value: Proliferating Human Hepatocytes

value: Proliferating Human Hepatocytes from patient with Ornithine transcarbamylase cultured at Passage 2  in hypoxia


title: pure line of C. carpio, infected group, repl. 5

description: carp.featureCounts.tsv


title: paternal backcrosses (backcross C. carpio x F1 hybrid), control group, repl. 3

description: carp.featureCounts.tsv


title: paternal backcrosses (backcross C. carpio x F1 hybrid), control group, repl. 2

description: carp.featureCounts.tsv


title: Con2_1

value: control


title: paternal backcrosses (backcross C. carpio x F1 hybrid), control group, repl. 1

description: carp.featureCounts.tsv


title: F1 generation with C. carpio mtDNA (termed F1 C. carpio x C. gibelio), infected group, repl. 3

description: gibel.featureCounts.tsv


title: ProliHH_OTC_P4

value: Proliferating Human Hepatocytes from patient with Ornithine transcarbamylase cultured at Passage 4  in hypoxia


title: pure line of C. carpio, infected group, repl. 3

description: carp.featureCounts.tsv


title: Ink4a_DMSO_16hr_3


title: ProliHH_P3

value: WT

value: Proliferating Human Hepatocytes cultured at Passage 3 in hypoxia


title: ProliHH_P2

value: Proliferating Human Hepatocytes cultured at Passage 2 in hypoxia


title: RNA-Seq_Saline_rep3

city: Helsinki

first: Liang

last: Wang

address: Viikinkaari 5

country: Finland

institute: University of Helsinki

data_processing:
Clean reads were aligned to a Bowtie2 2.1.0 indexed human genome (hg19 sourced from UCSC).
The mapped reads of each sample were assembled using StringTie with default settings.
StringTie and DESeq2 1.18.1 were used to estimate the expression levels of all transcripts.
StringTie was used to perform expression level for mRNAs by calculating FPKM.Differential gene expression was called using DESeq2 1.18.1
Genome_build: hg19
Supplementary_files_format_and_content: bigWig,tsv

organism: Macaca mulatta

source_name: Cortical neuron

extract_protocol:
Total RNA of each sample was extracted using AxyPrep Multisource RNA Miniprep Kit(Axygen). Polyadenylated mRNA was purified using NEBNext Poly(A) mRNA Magnetic Isolation Module
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Four male rhesus monkeys (Macaca mulatta; 3-4-year old; weighing from 3.0 to 5.0 kg),  were randomly divided into saline group (n=2) and morphine group (n=2). Morphine was subcutaneously (s.c.) injected into the back legs of monkey three times daily (at 9:00, 14:00, and 21:00 o’clock) for 90 days continuously to produce dependence. The doses of morphine were gradually elevated as following paradigm: day 1-7:3 mg/kg, day 8-14:6 mg/kg, day 15-21:9 mg/kg, day 22-28:12 mg/kg, day 29-90:15 mg/kg. Monkeys in saline group was injected subcutaneously three times daily with same volume of 0.9% saline (0.5 mL/kg) as a control.

value: Adult cortical neuron purified from the cortex regio

value: treated with saline as a control


title: Control, rep2

city: Boston

first: Alberto

middle: Marin

last: González

state: MA

address: 3 Blackfan St

department: PCMM

institute: Boston Children's Hospital

library_source: genomic

data_processing:
bcl2fastq, standard parameters
bowtie2, -q --local -X 1000
samtools fixmate, sort, markdup
samtools index
bamCoverage (deeptools), --binSize 10 --normalizeUsing RPKM
Assembly: mm9
Supplementary files format and content: bigwig files normalized by RPKM and averaged using a running window of 10 bp

molecule: genomic DNA

source_name: Spleen/lymph node

extract_protocol:
Nuclei were harvested by sequential lysis in lysis buffer one (LB1), two (LB2), and three (LB3) which were supplemented with protease inhibitor (ThermoFisher Scientfic Cat# 78429; 1X final concentration added right before use). LB1 consists of 50mM HEPES-KOH (pH 7.5, MilliporeSigma Cat# H4034 & P9333), 140mM NaCl (MilliporeSigma Cat# 7653), 1mM EDTA (pH 8.0, MilliporeSigma Cat# E6758), 10% glycerol (MilliporeSigma Cat# G5516), 0.5% Igepal CA-630 (MilliporeSigma Cat# I8896), 0.25% Triton X-100 (MilliporeSigma Cat# T8787) and KOH to adjust pH to 7.5. LB2 consists of 10mM Tri-HCl pH 8.0 (Quality Biological Cat# 351-007-101), 200 mM NaCl, 1mM EDTA pH 8.0, 0.5 mM EGTA and HCl to adjust pH to 8.0. LB3 consists of 10mM Tris-HCl (pH 8.0), 100 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 0.1% Sodium deoxycholate (MilliporeSigma Cat# 30970), 0.5% N-lauroylsarcosine (MilliporeSigma Cat# L7414) and HCl to adjust pH to 8.0. Cells were re-suspended in LB1 and rotated for 10 minutes at four degrees Celsius. Then, cells were pelleted at 2000 rpm, re-suspended in LB2 and rotated for 5 minutes at four degrees Celsius. Then, cells were pelleted at 2000 rpm and re-suspended in LB3. Nuclei were then sonicated at 4 degrees Celsius using a Fisher 150E Sonic Dismembrator with settings: 50% amplitude, 30 s ON, 30 s OFF for 12 min total time. Following sonication, samples were pelleted to remove cellular debris at 20,000g for 10 minutes at four degrees. After IP, DNA was extracted from reverse crosslinked chromatin samples by incubation with RNaseA (Thermo Fisher Scientific Cat# EN0531) for 15 min at 37C; and proteinase K (Thermo Fisher Scientific Cat# AM2546) for 1h at 65C. DNA was subsequently purified using MinElute (Qiagen Cat# 28004) purification.
DNA libraries were prepared and amplified using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs Cat# E7103L) and dual-indexed NEBNext Multiplex Oligos for Illumina (New England BioLabs Cat# E6440S). Final libraries were pooled, quantified with QuBit (Thermo), Bioanalyzer (Agilent) and qPCR (BioRad), then sequenced on a Novoseq SP 100 flow cell (Illumina) using paired-end 2x50bp

value: Spleen/lymph node

value: Primary

value: CD8+ OT-1 T cell

value: Control


title: Fresh_PHH_G6PC

value: hepatocyte

value: G6PC mutation

value: Fresh Primary Human Hepatocytes from patient with Glycogen storage disease type I


title: pure line of C. carpio, infected group, repl. 2

description: carp.featureCounts.tsv

value: Head kidney


title: pure line of C. carpio, infected group, repl. 4

description: carp.featureCounts.tsv


title: pure line of C. carpio, infected group, repl. 1

description: carp.featureCounts.tsv


title: ProliHH_P4

value: liver

value: Proliferating Human Hepatocytes

value: Proliferating Human Hepatocytes cultured at Passage 4 in hypoxia


title: F1 generation with C. carpio mtDNA (termed F1 C. carpio x C. gibelio), infected group, repl. 1

description: gibel.featureCounts.tsv


title: F1 generation with C. carpio mtDNA (termed F1 C. carpio x C. gibelio), infected group, repl. 2

description: gibel.featureCounts.tsv


title: Ink4a_ATRA5nm_16hr_2

value: pancreas

value: Pancreatic ductal adenocarcinoma

value: derived from KrasLSL-G12D/+; Ink4a/Arflox/lox; p48-Cre mice

value: 5 nM all trans retinoic acid 16 hr


title: pure line of C. carpio, control group, repl. 4

description: carp.featureCounts.tsv


title: RNA-Seq_Saline_rep1

value: Adult cortical neuron purified from the cortex regio


title: RNA-Seq_Saline_rep2

value: treated with saline as a control


title: Fresh_PHH_LDLR

value: LDLR mutation

value: Fresh Primary Human Hepatocytes from patient with Familial hypercholesterolemia


title: F1 generation with C. carpio mtDNA (termed F1 C. carpio x C. gibelio), control group, repl. 4

description: gibel.featureCounts.tsv


title: pure line of C. carpio, control group, repl. 3

description: carp.featureCounts.tsv


title: F1 generation with C. carpio mtDNA (termed F1 C. carpio x C. gibelio), control group, repl. 3

description: gibel.featureCounts.tsv


title: Fresh_PHH_OTC

value: OTC mutation

value: Fresh Primary Human Hepatocytes from patient with Ornithine transcarbamylase


title: RNA-Seq_Morphine_rep3

value: treated with Morphine


title: Fresh_PHH _Rep3

value: hepatocyte

value: WT

value: Fresh Primary Human Hepatocytes


title: Control, rep3

value: Spleen/lymph node

value: Primary

value: CD8+ OT-1 T cell

value: Control


title: pure line of C. carpio, control group, repl. 2

description: carp.featureCounts.tsv

value: Head kidney


title: F1 generation with C. carpio mtDNA (termed F1 C. carpio x C. gibelio), control group, repl. 2

description: gibel.featureCounts.tsv


title: RNA-Seq_Morphine_rep2


title: F1 generation with C. carpio mtDNA (termed F1 C. carpio x C. gibelio), control group, repl. 1

description: gibel.featureCounts.tsv


title: RNA-Seq_Morphine_rep1


title: Fresh_PHH _Rep1

value: liver


title: pure line of C. carpio, control group, repl. 1

description: carp.featureCounts.tsv


title: Fresh_PHH _Rep2


title: Retina_ID_105680

status: Public on Sep 11 2023

type: genomic

city: Bethesda

first: Jayshree

last: Advani

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description: retina sample

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

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

data_processing:
GenomeStudio Methylation Module User Guide
Average Beta or normalized (provide the normalization method) Average Beta
M values

label: Cy5 and Cy3

source_name: retina

label_protocol: Standard Illumina Protocol

extract_protocol: DNA were isolated from homogenized retina tissue in TRIzol® (Invitrogen, Carlsbad, CA) as per the previously published protocol (Chomczynski et al., 1993). DNA was quantified using the QuantiFluor® dsDNA System (Promega, Madison, WI). 500 ng of DNA from each retina sample was used for the MethylationEPIC BeadChip.

tag: gender

value: M

tag: mgs grade


title: Retina_ID_105690

description: retina sample


title: PLSCR1-TG-OD-rep1

city: GaungZhou

first: Minglei

last: Zhao

address: 7#, Jinsui Road

institute: Sun yat sen 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

extract_protocol:
retina 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

treatment_protocol: OD-AOH(acute ocular hypertension)-1h, then harvest the retinas after 5 days

tag: strain

value: TG


title: WT-OD-rep1


title: PLSCR1-TG-OD-rep2


title: WT-OD-rep2


title: Retina_ID_105629

description: retina sample

value: F


title: Retina_ID_105627

description: retina sample


title: Retina_ID_105677

description: retina sample


title: Retina_ID_105692

description: retina sample


title: Retina_ID_105686

description: retina sample


title: Retina_ID_105676

description: retina sample


title: Retina_ID_105672

description: retina sample


title: Retina_ID_105671

description: retina sample


title: Retina_ID_105668

description: retina sample


title: Retina_ID_105624

description: retina sample


title: Retina_ID_105667

description: retina sample


title: Retina_ID_105664

description: retina sample


title: Retina_ID_105665

description: retina sample


title: Retina_ID_105663

description: retina sample


title: Retina_ID_105623

description: retina sample


title: Retina_ID_105662

description: retina sample


title: Retina_ID_105685

description: retina sample


title: Retina_ID_105625

description: retina sample


title: Retina_ID_105679

description: retina sample


title: Retina_ID_105649

description: retina sample


title: Retina_ID_105660

description: retina sample


title: Retina_ID_105651

description: retina sample


title: Retina_ID_105659

description: retina sample


title: Retina_ID_105638

description: retina sample


title: Retina_ID_105643

description: retina sample


title: Retina_ID_105642

description: retina sample


title: Retina_ID_105639

description: retina sample


title: Retina_ID_105644

description: retina sample


title: Retina_ID_66691

description: retina sample


title: Retina_ID_68880

description: retina sample


title: Retina_ID_68839

description: retina sample


title: Retina_ID_68840

description: retina sample


title: Retina_ID_68838

description: retina sample


title: Retina_ID_105682

description: retina sample


title: Retina_ID_68878

description: retina sample


title: Retina_ID_68833

description: retina sample


title: Retina_ID_68821

description: retina sample


title: Retina_ID_68837

description: retina sample


title: Retina_ID_68873

description: retina sample


title: Retina_ID_68822

description: retina sample


title: Retina_ID_68811

description: retina sample


title: Retina_ID_68807

description: retina sample


title: Retina_ID_68800

description: retina sample


title: Retina_ID_68797

description: retina sample


title: Retina_ID_68791

description: retina sample


title: Retina_ID_68789

description: retina sample


title: Retina_ID_68788

description: retina sample


title: Retina_ID_68780

description: retina sample


title: Retina_ID_68781

description: retina sample


title: Retina_ID_68783

description: retina sample


title: Retina_ID_68776

description: retina sample


title: Retina_ID_68773

description: retina sample


title: Retina_ID_68768

description: retina sample


title: Retina_ID_68775

description: retina sample


title: Retina_ID_68762

description: retina sample


title: Retina_ID_66682

description: retina sample


title: Retina_ID_66683

description: retina sample


title: Retina_ID_68691

description: retina sample


title: Retina_ID_68697

description: retina sample


title: Retina_ID_68712

description: retina sample


title: Retina_ID_68664

description: retina sample


title: Retina_ID_68654

description: retina sample


title: Retina_ID_68744

description: retina sample


title: Retina_ID_68650

description: retina sample


title: Retina_ID_68645

description: retina sample


title: Retina_ID_68813

description: retina sample


title: Retina_ID_66678

description: retina sample


title: Retina_ID_68774

description: retina sample


title: Retina_ID_68640

description: retina sample


title: Retina_ID_66667

description: retina sample


title: Retina_ID_68634

description: retina sample


title: Retina_ID_68633

description: retina sample


title: Retina_ID_68796

description: retina sample


title: Retina_ID_68632

description: retina sample


title: Retina_ID_68629

description: retina sample


title: Retina_ID_68619

description: retina sample


title: Retina_ID_68616

description: retina sample


title: Retina_ID_68610

description: retina sample


title: Retina_ID_68606

description: retina sample


title: Retina_ID_68601

description: retina sample


title: Retina_ID_68587

description: retina sample


title: Retina_ID_68684

description: retina sample


title: Retina_ID_66663

description: retina sample


title: Retina_ID_68584

description: retina sample


title: Retina_ID_68557

description: retina sample


title: Retina_ID_68549

description: retina sample


title: Retina_ID_68561

description: retina sample


title: Retina_ID_66655

description: retina sample


title: Retina_ID_68560

description: retina sample


title: Retina_ID_68527

description: retina sample


title: huRetina_ID_162

description: retina sample


title: huRetina_ID_160

description: retina sample


title: huRetina_ID_154

description: retina sample


title: huRetina_ID_147

description: retina sample


title: huRetina_ID_152

description: retina sample


title: huRetina_ID_145

description: retina sample


title: huRetina_ID_158

description: retina sample


title: Retina_ID_68605

description: retina sample


title: Retina_ID_68607

description: retina sample


title: huRetina_ID_146

description: retina sample


title: huRetina_ID_139

description: retina sample


title: huRetina_ID_142

description: retina sample


title: huRetina_ID_136

description: retina sample


title: Retina_ID_68555

description: retina sample


title: Retina_ID_66660

description: retina sample


title: huRetina_ID_140

description: retina sample


title: huRetina_ID_125

description: retina sample


title: huRetina_ID_133

description: retina sample


title: huRetina_ID_135

description: retina sample


title: huRetina_ID_122

description: retina sample


title: huRetina_ID_138

description: retina sample


title: huRetina_ID_132

description: retina sample


title: huRetina_ID_124

description: retina sample


title: huRetina_ID_65R

description: retina sample


title: huRetina_ID_165

description: retina sample


title: huRetina_ID_121

description: retina sample


title: huRetina_ID_107

description: retina sample


title: huRetina_ID_109

description: retina sample


title: huRetina_ID_116

description: retina sample


title: huRetina_ID_105

description: retina sample


title: huRetina_ID_104

description: retina sample


title: huRetina_ID_106

description: retina sample


title: huRetina_ID_103

description: retina sample


title: huRetina_ID_101

description: retina sample


title: huRetina_ID_97

description: retina sample


title: huRetina_ID_96

description: retina sample


title: huRetina_ID_93

description: retina sample


title: huRetina_ID_87

description: retina sample


title: huRetina_ID_86

description: retina sample


title: huRetina_ID_127

description: retina sample


title: huRetina_ID_84

description: retina sample


title: huRetina_ID_83

description: retina sample


title: huRetina_ID_77

description: retina sample


title: huRetina_ID_78

description: retina sample


title: huRetina_ID_74

description: retina sample


title: huRetina_ID_81

description: retina sample


title: huRetina_ID_65

description: retina sample


title: huRetina_ID_67

description: retina sample


title: huRetina_ID_61

description: retina sample


title: huRetina_ID_58

description: retina sample


title: huRetina_ID_69

description: retina sample


title: huRetina_ID_63

description: retina sample


title: huRetina_ID_59

description: retina sample


title: huRetina_ID_48

description: retina sample


title: huRetina_ID_51

description: retina sample


title: huRetina_ID_55

description: retina sample


title: huRetina_ID_52

description: retina sample


title: huRetina_ID_23

description: retina sample


title: huRetina_ID_24

description: retina sample


title: huRetina_ID_44

description: retina sample


title: huRetina_ID_29

description: retina sample


title: huRetina_ID_19

description: retina sample


title: huRetina_ID_13

description: retina sample


title: huRetina_ID_14

description: retina sample


title: huRetina_ID_9

description: retina sample


title: huRetina_ID_11

description: retina sample


title: huRetina_ID_34

description: retina sample


title: huRetina_ID_20

description: retina sample


title: PFC_CON_Replicate_2

city: Beaverton

first: Lyndsey

middle: Elizabeth

last: Shorey-Kendrick

state: Oregon

address: 505 NW 185th Ave

institute: Oregon Health and Science University

hyb_protocol: Converted DNAs were applied to Illumina Infinium Methylation EPIC 8-Sample Beadchips following the Infinium HD Methylation 15019521v01 protocol.

scan_protocol: Processed BeadChips were scanned using the Illumina iScan+ with ICS v3.3.28 and intensity data was extracted with Illumina GenomeStudio software (GenomeStudio v2011.1 with Methylation Analysis Module v1.9.0).

data_processing: All analysis was performed using R statistical software (version 4.1.1). Data normalization and QC were performed using the minfi and ChAMP packages. We examined density plots of beta values at each preprocessing and filtering step. Stratified quantile normalization preprocessing was performed using minfi to adjust for probe-type bias in beta distributions.  Probes previously determined to be functional and valid in Macaca mulatta (referred to as MM_valid) [PMID: 33471557] were retained prior to removing probes with failed detection p-value> 0.01 in >=25% of samples.

source_name: PFC

label_protocol: DNAm was assessed on the MethylationEPIC BeadChips, measuring over 850,000 CpGs at a nucleotide resolution, at the Fred Hutchinson Cancer Research Center Genomics Resource. In brief, 500ng of DNA was bisulfite converted using the EZ DNA Methylation Kit (Zymo Research) following the Illumina-specified instructions.

extract_protocol: Placental and fetal tissue DNA was extracted using the AllPrep miRNA kit (Qiagen) and the QIAcube for automated nucleic acid extraction (Qiagen, USA).

treatment_protocol: Edibles were administered prior to the animal’s daily chow to ensure consumption on an empty stomach and to confirm complete ingestion. Animals were slowly titrated up to 2.5mg/7kg/day of THC using published weight-based medical cannabis acclimation recommendations approximately 4 months prior to undergoing time-mated breeding. Each THC-exposed pregnant animal (n=5) continued to consume a daily edible of 2.5mg/7kg/day throughout pregnancy.

value: PFC

tag: Sex

tag: group

value: CON


title: PFC_THC_Replicate_3

value: THC


title: PFC_CON_Replicate_3


title: Right_CON_Replicate_4

source_name: Right

value: Right


title: Cerebellum_CON_Replicate_5

source_name: Cerebellum

value: Cerebellum


title: PFC_THC_Replicate_2


title: Right_CON_Replicate_1


title: Right_THC_Replicate_5


title: Right_CON_Replicate_5


title: Right_CON_Replicate_2


title: PFC_CON_Replicate_4


title: Right_THC_Replicate_4


title: Cerebellum_THC_Replicate_1


title: Right_THC_Replicate_1


title: PFC_CON_Replicate_5


title: Cerebellum_THC_Replicate_4


title: PFC_CON_Replicate_1


title: PFC_THC_Replicate_4


title: Cerebellum_CON_Replicate_2


title: PFC_THC_Replicate_1


title: Lung_CON_Replicate_5

source_name: Lung

value: Lung


title: Cerebellum_THC_Replicate_2


title: Cerebellum_CON_Replicate_4


title: Right_THC_Replicate_3


title: Right_CON_Replicate_3


title: PFC_THC_Replicate_5


title: Cerebellum_CON_Replicate_1


title: Placenta_CON_Replicate_5

source_name: Placenta

value: Placenta


title: Cerebellum_THC_Replicate_5


title: Placenta_CON_Replicate_4


title: Cerebellum_THC_Replicate_3


title: Lung_THC_Replicate_4


title: Lung_THC_Replicate_5


title: Lung_CON_Replicate_4


title: Placenta_THC_Replicate_5


title: F4MKO+FSTL1 liver rep1

first: Kong

last: Xingxing

address: Songhu Road 2005

department: School of Life Sciences

institute: Fudan University

data_processing:
The raw sequencing data was filtered with trim-galore (v0.6.7) by removing reads containing sequencing adapter and reads with low-quality base.
The clean reads were mapped to the reference genome (mm10) using Hisat2 (2.2.1). Quantification of gene expression was calculated using FeatureCounts (v2.0.1), converted to transcripts per million (TPM) using the R software.
Assembly: mm10
Supplementary files format and content: csv files include counts values for each samples

extract_protocol:
Three liver tissue samples of each group for RNA sequencing were collected. Total RNA was isolated using the Trizol method according to manufacturer’s instructions. RNA quality was measured using the Agilent 2100 Bioanalyzer (RNA 6000 Nano Kit; Agilent Technologies, Santa Clara, CA, USA).
cDNA libraries for each sample were constructed as reported previously (Yao et al., 2022).
Libraries were sequenced on BGIseq500 platform (BGI-Shenzhen, China), using 150 bp paired-end reads aimed at 30 million reads per sample.

value: overexpression of FSTL1 in skeletal muscle IRF4 KO

value: a high fat and high carbohydrate diet


title: F4MKO+FSTL1 liver rep3


title: F4MKO+FSTL1 liver rep2


title: Lung_THC_Replicate_3


title: F4MKO liver rep3

value: skeletal muscle IRF4 KO


title: Placenta_THC_Replicate_3


title: Lung_CON_Replicate_3


title: Placenta_THC_Replicate_4


title: F4MKO liver rep2

value: skeletal muscle IRF4KO


title: F4MKO liver rep1


title: Lung_THC_Replicate_2


title: Placenta_CON_Replicate_2


title: liver WT rep2

value: WT


title: liver WT rep3


title: Placenta_THC_Replicate_2


title: Placenta_CON_Replicate_3


title: Lung_CON_Replicate_2


title: PCd7, 221005, Input

first: Ousmane

middle: Hamadoun

last: Cisse

address: 10 Center Dr,

institute: National Institutes of Health

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Hiseq X  output.
To remove rat DNA, ChIP-seq reads were aligned to the rat genome ( GCF_000001895.5)  using Bowtie2 version 2.2.5. Only unmapped  reads were retained.
ChIP-seq reads were aligned to the Pneumocystis carinii genome using bwa mem version 0.7.17-r1188
Peaks were called uing MACS v3.0.0a5 with the significance cut-off q-value <=0.05 (narrowPeak files)
bigWig files were generated using the bamCoverage from deepTools package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate (bins per millions; bin size; 50 bp)
Assembly: GCF_001477545.1
Supplementary files format and content: bigWig, narrowPeak

organism: Pneumocystis carinii

source_name: coculture day 7

extract_protocol:
Cells were fixed with formaldehyde for 10 minutes using the active motif Low cell ChIP-seq (cat # 53084). After quenching and cell lysis, chromatin was sonicated using a Q800R3 Sonicator (Qsonica) with recirculating chiller.
ChIP-seq libraries were prepared using the active motif Low cell ChIP-seq (cat # 53084) that include the Next Gen DNA library kit and Next Gen Indexing kit. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 14 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using SPRIselect  beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: coculture day 7

value: Pneumocystis + epithelial cell lines

value: culture date:04/07/22

tag: chip antibody

value: pre immune serum


title: liver WT rep1

value: liver


title: PCd0, 221005, Input

source_name: coculture day 0

value: coculture day 0

value: culture date:03/31/22


title: Lung_CON_Replicate_1

value: M

value: CON


title: Placenta_CON_Replicate_1


title: PCd0, 221005, Pc_A_d0

value: CENP-A (Genescript #1598083)


title: Lung_THC_Replicate_1

value: Lung

value: THC


title: PCd7, 221005, Pc_A_d7


title: PC1, 201103, Pc_PC Input

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Hiseq X  output.
To remove rat DNA, ChIP-seq reads were aligned to the rat genome ( GCF_000001895.5)  using Bowtie2 version 2.2.5. Only unmapped  reads were retained.
ChIP-seq reads were aligned to the Pneumocystis carinii genome using bwa mem version 0.7.17-r1188
Peaks were called uing MACS v3.0.0a5 with the significance cut-off q-value <=0.05 (narrowPeak files)
bigWig files were generated using the bamCoverage from deepTools package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate (bins per millions; bin size; 50 bp)
Assembly: GCF_001477545.1
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: lungs

value: lungs

value: infected rat 1

value: infection level 5+

value: collect date:01/18/00


title: PC1, 201103, Pc_C

value: CENP-C (Genescript # 1525058 )


title: PC1, 201103, Pc_PA Input


title: PC1, 201103, Pc_A


title: Placenta_THC_Replicate_1

value: Placenta


title: genomic DNA from SOL08_LC_FrozenTissue

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

description: SAMPLE 14

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

data_processing:
BeadStudio software v3.2
Unmethylated and methylated signal intensities

extract_protocol: genomic DNA was extracted and purified from cell lines or clinical samples using QIAquick DNA mini kit according to standard instructions

value: Male

tag: sample type

value: clinical sample

tag: disease state

value: lung adenocarcinoma

tag: subtype

value: Solid subtype


title: genomic DNA from SOL03_LC_FrozenTissue

description: SAMPLE 12


title: genomic DNA from ACI05_LC_FrozenTissue

description: SAMPLE 6

value: Female

value: Acinar subtype


title: genomic DNA from ACI09_LC_FrozenTissue

description: SAMPLE 9


title: genomic DNA from SOL07_LC_FrozenTissue

description: SAMPLE 13


title: genomic DNA from ACI06_LC_FrozenTissue

description: SAMPLE 7


title: genomic DNA from SOL02_LC_FrozenTissue

description: SAMPLE 11


title: genomic DNA from SOL01_LC_FrozenTissue

description: SAMPLE 10


title: HN2 C24 shRunx2 2

city: Tokyo

first: Takuro

last: Nakamura

address: 3-8-31 Ariake, Koto-ku

department: The Cancer Institute

institute: Japanese Foundation for Cancer Research

description: Gene expression data from mouse mesenchymal chondrosarcoma

hyb_protocol: Following fragmentation, 7.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 PM Array. GeneChips were washed and stained in the Affymetrix GeneAtlas Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneAtlas Imaging Station.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: mesenchymal chondrosarcoma cell introduced with shRNA for Runx2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Sarcoma cells and chondrogenic progenitor cells were maintained in IMDM supplemented with 10% FBS

extract_protocol: Total RNA was purified using RNA Easy kit (QIAGEN) according to the manufacturer's protocol

treatment_protocol: Short hairpin RNA-mediated gene silencing for HEY1-NCOA2 or Runx2 was performed

value: mesenchymal chondrosarcoma cell

value: introduced with shRNA for Runx2


title: HN2 C24 shRunx2 1


title: HN2 C24 shRunx2 3


title: genomic DNA from MPP11_LC_FrozenTissue

description: SAMPLE 3

value: Micropapillary subtype


title: genomic DNA from ACI08_LC_FrozenTissue

description: SAMPLE 8


title: genomic DNA from MPP12_LC_FrozenTissue

description: SAMPLE 4


title: genomic DNA from ACI02_LC_FrozenTissue

description: SAMPLE 5


title: genomic DNA from MPP09_LC_FrozenTissue

description: SAMPLE 2


title: HN2 C24 shNTC 2

source_name: mesenchymal chondrosarcoma cell introduced with shRNA of non-target control


title: genomic DNA from MPP07_LC_FrozenTissue

description: SAMPLE 1


title: cognitively healthy control 20 [229]

last: Chao

address: Huashan Rd, No. 2018

institute: Shanghai Decoding Research Institute

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip array (850K chip) according to standard Illumina protocol.

scan_protocol: 850K arrays were scanned and imaged by BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: Data analysis was performed in R software using the ChAMP pipeline from Bioconductor at default setting.

label: Cy3, Cy5

source_name: genomic DNA extracted from cognitively healthy control 20

extract_protocol: Genomic DNA was extracted and purified from blood white cells using Blood DNA Extraction Kit (QIAGEN) according to the manufacturer's protocol.

value: female

value: blood leukocytes

value: cognitively healthy status

value: cognitively normal


title: cognitively healthy control 8 [211]

source_name: genomic DNA extracted from cognitively healthy control 8


title: cognitively healthy control 17 [224]

source_name: genomic DNA extracted from cognitively healthy control 17


title: cognitively healthy control 19 [227]

source_name: genomic DNA extracted from cognitively healthy control 19


title: HN2 C24 shHEY1 2

source_name: mesenchymal chondrosarcoma cell introduced with shRNA for HEY1

value: introduced with shRNA for HEY1


title: HN2 C24 shHEY1 3


title: HN2 C24 shNTC 1

value: introduced with shRNA of non-target control


title: cognitively healthy control 16 [223]

source_name: genomic DNA extracted from cognitively healthy control 16


title: cognitively healthy control 9 [212]

source_name: genomic DNA extracted from cognitively healthy control 9


title: cognitively healthy control 15 [222]

source_name: genomic DNA extracted from cognitively healthy control 15


title: HN2 C24 shHEY1 1


title: cognitively healthy control 6 [209]

source_name: genomic DNA extracted from cognitively healthy control 6

value: male


title: HN2 C24 shNTC 3


title: cognitively healthy control 18 [226]

source_name: genomic DNA extracted from cognitively healthy control 18


title: cognitively healthy control 14 [221]

source_name: genomic DNA extracted from cognitively healthy control 14


title: cognitively healthy control 13 [218]

source_name: genomic DNA extracted from cognitively healthy control 13


title: HN2 C5 shRunx2 1


title: HN2 C5 shRunx2 3


title: HN2 C5 shRunx2 2


title: HN2 C5 shHEY1 2


title: HN2 C5 shNTC 3


title: HN2 C5 shHEY1 3


title: cognitively healthy control 5 [208]

source_name: genomic DNA extracted from cognitively healthy control 5


title: HN2 C5 shNTC 2


title: cognitively healthy control 12 [217]

source_name: genomic DNA extracted from cognitively healthy control 12


title: cognitively healthy control 10 [213]

source_name: genomic DNA extracted from cognitively healthy control 10


title: cognitively healthy control 11 [215]

source_name: genomic DNA extracted from cognitively healthy control 11


title: HN2 C5 shNTC 1

source_name: mesenchymal chondrosarcoma cell introduced with shRNA of non-target control


title: HN2 C34

source_name: mesenchymal chondrosarcoma cell


title: HN2 C26


title: HN2 C35


title: HN2 C5 shHEY1 1


title: HN2 C33


title: HN2 C24


title: cognitively healthy control 7 [210]

source_name: genomic DNA extracted from cognitively healthy control 7


title: HN2 C20


title: HN2 C18


title: cognitively healthy control 2 [204]

source_name: genomic DNA extracted from cognitively healthy control 2


title: HN2 C7


title: HN2 C5


title: AD patient 20 [718]

source_name: genomic DNA extracted from AD-affeced patient 20

value: late status of cognitive decline

value: severe dementia - Alzheimer's Disease


title: cognitively healthy control 3 [205]

source_name: genomic DNA extracted from cognitively healthy control 3


title: cognitively healthy control 1 [203]

source_name: genomic DNA extracted from cognitively healthy control 1


title: cognitively healthy control 4 [206]

source_name: genomic DNA extracted from cognitively healthy control 4


title: HN2 C15


title: AD patient 14 [728]

source_name: genomic DNA extracted from AD-affeced patient 14


title: AD patient 19 [740]

source_name: genomic DNA extracted from AD-affeced patient 19


title: AD patient 17 [737]

source_name: genomic DNA extracted from AD-affeced patient 17


title: AD patient 10 [720]

source_name: genomic DNA extracted from AD-affeced patient 10


title: eSZ HN2 3

description: Gene expression data from mouse embryonic chondrogenic progenitor

source_name: chondrogenic progenitor cell expressing HEY1-NCOA2

value: chondrogenic progenitor cell

value: expressing HEY1-NCOA2


title: eSZ HN2 2


title: HN2 C1


title: AD patient 16 [736]

source_name: genomic DNA extracted from AD-affeced patient 16


title: AD patient 18 [738]

source_name: genomic DNA extracted from AD-affeced patient 18


title: AD patient 13 [727]

source_name: genomic DNA extracted from AD-affeced patient 13


title: AD patient 11 [721]

source_name: genomic DNA extracted from AD-affeced patient 11


title: AD patient 15 [735]

source_name: genomic DNA extracted from AD-affeced patient 15


title: eSZ vector 3

source_name: chondrogenic progenitor cell with empty vector

value: with empty vector


title: AD patient 9 [715]

source_name: genomic DNA extracted from AD-affeced patient 9


title: eSZ vector 1


title: eSZ HN2 1


title: AD patient 5 [711]

source_name: genomic DNA extracted from AD-affeced patient 5


title: AD patient 12 [724]

source_name: genomic DNA extracted from AD-affeced patient 12


title: eSZ vector 2


title: AD patient 7 [713]

source_name: genomic DNA extracted from AD-affeced patient 7


title: AD patient 3 [708]

source_name: genomic DNA extracted from AD-affeced patient 3


title: AD patient 8 [714]

source_name: genomic DNA extracted from AD-affeced patient 8


title: genomic DNA from NOR03_LC_FrozenTissue

description: SAMPLE 19

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

data_processing: BeadStudio software v3.2

value: FEMALE

value: clinical sample

value: normal lung tissue


title: AD patient 6 [712]

source_name: genomic DNA extracted from AD-affeced patient 6


title: AD patient 4 [709]

source_name: genomic DNA extracted from AD-affeced patient 4


title: AD patient 2 [707]

source_name: genomic DNA extracted from AD-affeced patient 2


title: MCI subject 20 [54]

source_name: genomic DNA extracted from MCI-affeced patient 20

value: early status of cognitive decline

value: early phase of dementia


title: MCI subject 19 [51]

source_name: genomic DNA extracted from MCI-affeced patient 19

value: female


title: AD patient 1 [705]

source_name: genomic DNA extracted from AD-affeced patient 1

value: blood leukocytes


title: genomic DNA from NOR01_LC_FrozenTissue

description: SAMPLE 17


title: genomic DNA from NOR02_LC_FrozenTissue

description: SAMPLE 18


title: genomic DNA from LEP04_LC_FrozenTissue

description: SAMPLE 15

value: lung adenocarcinoma

value: Lepidic subtype


title: MCI subject 17 [47]

source_name: genomic DNA extracted from MCI-affeced patient 17


title: genomic DNA from LEP03_LC_FrozenTissue

description: SAMPLE 14


title: genomic DNA from LEP02_LC_FrozenTissue

description: SAMPLE 13


title: MCI subject 16 [46]

source_name: genomic DNA extracted from MCI-affeced patient 16


title: MCI subject 15 [38]

source_name: genomic DNA extracted from MCI-affeced patient 15


title: MCI subject 13 [35]

source_name: genomic DNA extracted from MCI-affeced patient 13


title: genomic DNA from LEP05_LC_FrozenTissue

description: SAMPLE 16


title: MCI subject 14 [36]

source_name: genomic DNA extracted from MCI-affeced patient 14


title: C4-6 [ACC29C4D1-10-0]

city: Copenhagen

first: William

middle: Winston

last: Agace

address: Blegdamsvej 3B

department: Skin Immunology Research Center

country: Denmark

institute: Copenhagen University

description:
TIGL-EP-230 c4-6 Alpha Clonotypes.xlsx
TIGL-EP-230 c4-6 Beta Clonotypes.xlsx

data_processing:
Demultiplexing of raw sequencing data Separation of TCR alpha and beta reads using BLAST Assembly and annotation of reads using MiXCR Quality control and error correction Quantification of T cell clonotypes
Assembly: GRCh38
Supplementary files format and content: Excel files in supplementary tables of publication include T cell clonotype count values for each Sample
Library strategy: rhTCRseq

source_name: T cell

extract_protocol:
Qiagen Rneasy
rhTCRseq

value: T cell

tag: library

value: TCR


title: C4-6 [ACC32pre-10-0]


title: C4-6 [ACC32C4D1-10-0]


title: C4-6 [ACC22pre-10-0]


title: C4-6 [ACC17EOC6-10-0]


title: genomic DNA from LEP01_LC_FrozenTissue

description: SAMPLE 12

value: MALE


title: C4-6 [ACC17C4D1-10-0]


title: genomic DNA from PAP01_LC_FrozenTissue

description: SAMPLE 7

value: Papillary subtype


title: MCI subject 8 [22]

source_name: genomic DNA extracted from MCI-affeced patient 8

value: male


title: C4-6 [ACC31pre-10-0]


title: MCI subject 12 [31]

source_name: genomic DNA extracted from MCI-affeced patient 12


title: genomic DNA from PAP05_LC_FrozenTissue

description: SAMPLE 11


title: C4-6 [ACC16C4D1-10-0]


title: genomic DNA from PAP03_LC_FrozenTissue

description: SAMPLE 9


title: MCI subject 7 [20]

source_name: genomic DNA extracted from MCI-affeced patient 7


title: genomic DNA from MPP04_LC_FrozenTissue

description: SAMPLE 4

value: Micropapillary subtype


title: P6

city: Krakow

first: Tomasz

last: Szmatoła

state: Małopolskie

address: Mickiewicza 21

department: OMEI

country: Poland

institute: University of Agriculture in Krakow

data_processing:
The raw sequences were quality controlled using FastQC.
Flexbar software was used to remove Illumina adapters and poly-A sequences, and also reads that did not pass quality filteration criteria (phred quality <20)
The raw reads were aligned to the reference, while the whole procedure was followed by alignment parameters from ENCODE3's STAR-RSEM pipeline
The quality control metrics across aligned reads per sample were obtained using RNA-SeQC software
The differential expression estimation was proceed with utilization of DeSeq2 Bioconductor R-project package.
Assembly: ARS-UCD1.2
Supplementary files format and content: Files containing gene counts for every gene and every sample created with htseq-count software

organism: Bos taurus

source_name: blastocysts

extract_protocol:
RNA was extracted from blastocysts from prepubertal and blastocysts from pubertal heifers with an Arcturus PicoPure RNA Isolation Kit (#KIT0204, Applied Biosystems, USA) in accordance with the manufacturer’s instructions.
The cDNA libraries were prepared according to the SMARTer Stranded Total RNA Seq Kit v3- Pico Input Mammalian (Takara Bio, USA, Inc). The quality and quantity of the obtained libraries were measured with Qubit (Invitrogen, ThermoFisher Scientific), TapeStation2200 (Agilent, Santa Clara, CA, USA) and High Sensitivity D1000 ScreenTape RNA ScreenTape (Agilent, Santa Clara, CA, USA) according to the manufacturer’s instructions.

value: blastocysts

tag: development stage

value: pubertal


title: MCI subject 18 [48]

source_name: genomic DNA extracted from MCI-affeced patient 18


title: genomic DNA from MPP06_LC_FrozenTissue

description: SAMPLE 6

value: FEMALE


title: C1-3 [ACC31C4D1-10-0]

description:
TIGL-EP-230 c1-3 Alpha Clonotypes.xlsx
TIGL-EP-230 c1-3 Beta Clonotypes.xlsx


title: P5


title: P4

value: prepubertal


title: MCI subject 9 [25]

source_name: genomic DNA extracted from MCI-affeced patient 9


title: P7


title: MCI subject 11 [29]

source_name: genomic DNA extracted from MCI-affeced patient 11


title: MCI subject 10 [27]

source_name: genomic DNA extracted from MCI-affeced patient 10


title: MCI subject 5 [17]

source_name: genomic DNA extracted from MCI-affeced patient 5


title: C1-3 [ACC27C4D1-10-0]


title: genomic DNA from MPP03_LC_FrozenTissue

description: SAMPLE 3

value: clinical sample


title: P2


title: genomic DNA from PAP02_LC_FrozenTissue

description: SAMPLE 8


title: C1-3 [ACC22C4D1-10-0]


title: C1-3 [ACC23pre-10-0]


title: genomic DNA from PAP04_LC_FrozenTissue

description: SAMPLE 10


title: C1-3 [ACC16pre-10-0]


title: P1


title: P3


title: C1-3 [ACC23C4D1-10-0]


title: genomic DNA from MPP01_LC_FrozenTissue

description: SAMPLE 1


title: genomic DNA from MPP05_LC_FrozenTissue

description: SAMPLE 5


title: replicate 2 fixed pupal hemocytes, 3 chips

city: Marburg

first: Katja

last: Rust

address: Emil-Mannkopff-Str. 2

country: Germany

institute: Phillips-University Marburg

description: Takara ICELL8

library_source: transcriptomic single cell

data_processing:
Raw sequencing files (bcl) were converted into a single fastq file using Illumina bcl2fastq software (v2.20.0.422) for each method.
Each fastq file was de-multiplexed and analyzed using Cogent NGS analysis pipeline (CogentAP) from Takara Bio (v1.0).
“cogent demux” wrapper function was used to allocate the reads to the cells based on the cell barcodes provided in the well-list files.
“cogent analyze” wrapper function performed a preliminary analysis
read trimming with cutadapt (version 3.2)
genome alignment to Drosophila M. Version 103 using STAR (version 2.7.2a)
read counting for exonic, genomic and mitochondrial regions in Drosophila M. genes from ENSEMBL gene annotation version 103 using featureCounts (version 2.0.1); and summarizing the gene counts into gene matrices  with number of reads expressed for each cell in each gene
Subsequent analyses were performed using Seurat v4.1.1 in Rstudio 2022.02.2
Assembly: dmel ENSEMBL gene annotation version 103
Supplementary files format and content: Tab-separated metadata files and genematrix files

organism: Drosophila melanogaster

source_name: pupal hemocyte

extract_protocol:
50-60 2-10h APF pupae were collected and washed in 1 x PBS. The pupae were then transferred to 1 x Schneider´s Drosophila medium (Gibco) supplemented with 10% FBS, 50 units/mL penicillin, and 50 µg/mL streptomycin and opened using forks to rinse out the hemolymph. Cells were filtered through a 50-µm cell strainer and collected in a total volume of 500 µL. Subsequently, centrifugation at 500 x g and 4°C for 20 minutes was performed. The supernatant was discarded, and the pellet was resuspended with 500 µL PBS + 0.01 % BSA for single-cell sequencing of live cells. For fixed samples, the previous pellet was resuspended with 100 µL 1 x PBS and subsequently fixed by adding 4 volumes of ice-cold 100% methanol (final concentration of 80% methanol in PBS) and thoroughly mixed with a pipette. Cells were stored at - 20°C until use (1-3 days). For single-cell sequencing, cells were moved to 4°C and kept on ice throughout the procedure. Fixed cells were pelleted at 500 x g for 15 minutes and rehydrated in 500 µL PBS + 0.01 % BSA. For datasets 1 and 2 we used fixed samples, while we used live cells for dataset 3.
The Takara ICELL8 5,184 nano-well chip was used with the full-length SMART-Seq ICELL8 Reagent Kit. Cell suspensions were fluorescent-labelled with live/dead stain, Hoechst and propidium iodide (NucBlue Cell Stain Reagent, Thermo Fisher Scientific) for 15 min prior to their dispensing into the Takara ICELL8 5,184 nano-well chip. CellSelect Software (Takara Bio) was used to visualize and select wells containing single and live cells. Next, cDNA was synthesized via oligo-dT priming in a one-step RT-PCR reaction. P5 indexing primers for subsequent library preparation were dispensed into all wells receiving a different index, in addition to Terra polymerase and reaction buffer. Transposase enzyme and reaction buffer (Tn5 mixture) were dispensed to selected wells. P7 indexing primers were dispensed to wells. Final Illumina libraries were amplified and pooled as they were extracted from the chip. Pooled libraries were purified and size selected using Agencourt AMPure XP magnetic beads (Beckman Coulter) to obtain an average library size of 500 bp. A typical yield for a library comprised of ~ 1,300 cells was ~ 15 nM. Libraries were sequenced on the HiSeq 4000 (Illumina) to obtain on average ~ 0.3 Mio reads per cell (SE; 50 bp).

value: pupal hemocyte

value: hml[delta]-Gal4, UAS-eGFP

value: 2-10h APF, untreated


title: MCI subject 4 [14]

first: Shan

source_name: genomic DNA extracted from MCI-affeced patient 4

value: female

value: blood leukocytes

value: early status of cognitive decline

value: early phase of dementia


title: replicate 1 and 3, fixed pupal hemocytes

description: Takara ICELL8


title: C1-3 [ACC14C4D1-10-0]

value: T cell

value: TCR


title: MCI subject 2 [12]

source_name: genomic DNA extracted from MCI-affeced patient 2


title: C4-6 [ACC09EOC12-10-0]


title: C1-3 [ACC14pre-10-0]


title: P8


title: C1-3 [AC29pre-10-0]


title: MV411,FHT-1015, 4h,ATACseq, biol rep 2

city: Cambridge

first: Salih

last: Topal

address: 500 Technology Square Suite 700

institute: Foghorn Therapeutics

data_processing:
Reads were trimmed for adapter sequences using  cutdapt3 and aligned to version hg38 of the human genome using bowtie2 (parameters -k 4, -X2000, --local ,--mm)
Multimapping alignments were removed and only the the alignment with the highest score for each read pair was kept
Duplicate reads were removed using Picard Tookit and alignments mapping to mitochondrial genome were excluded
Alignments were filtered for size smaller than 120 bp and read ends shifted +4 or -5 nucleotides depending on the direction of the read
Peak calling was performed using MACS2.0 with a shift parameter of -75 and an extension size of 150 without modelling
Signal tracks were created using the fold enrichment option
Consistent peaks among replicates were obtained using IDR using a soft idr threshold of 0.1
Differential genome accessibility calculation was performed using limma package
Motif enrichment was performed using Meme suite tools (MEME-chip)7 and CISBP transcription motif data from MEME motif database version 12.19
Ridge regression analysis was performed using glmnet R package with coefficients calculated using the minimum estimated lambda
Genomic context annotation was performed using the annotatePeaks function of HOMER package using hg38 version of the human genome
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
DNA extraction was performed as described in Buenrostro et al., 2013
ATAC-seq library was generated as described in Buenrostro et al., 2013. Following library generation, left- and right- size selection was performed with SPRIselect beads (Beckman Coulter) according to the manufacturer’s recommendations.

tag: cell line

value: acute myeloid leukemia

value: WT

value: dual SMARCA4/SMARCA2 inhibition

tag: time


title: MCI subject 6 [18]

source_name: genomic DNA extracted from MCI-affeced patient 6

value: male


title: MV411,FHT-1015, 4h,ATACseq, biol rep 3

tag: cell type

tag: genotype


title: MV411,FHT-1015, 4h,ATACseq, biol rep 1

tag: treatment


title: MV411,DMSO,4h,ATACseq,biol rep3

value: negative control


title: MV411,DMSO,4h,ATACseq,biol rep2


title: MCI subject 3 [13]

source_name: genomic DNA extracted from MCI-affeced patient 3


title: genomic DNA from MPP02_LC_FrozenTissue

description: SAMPLE 2

value: MALE

value: lung adenocarcinoma

value: Micropapillary subtype


title: C1-3 [ACC09C4-10-0]


title: MV411,DMSO,4h,ATACseq,biol rep1


title: C4-6 [ACC27pre-10-0]


title: HCT116,FHT-1015, 4h,ATACseq, biol rep 3

value: colorectal adenocarcinoma


title: HCT116,FHT-1015, 4h,ATACseq, biol rep 2


title: HCT116,FHT-1015, 4h,ATACseq, biol rep 1


title: HCT116,DMSO,4h,ATACseq,biol rep3


title: HCT116,DMSO,4h,ATACseq,biol rep2


title: DU4475,FHT-1015, 4h,ATACseq, biol rep 3

value: invasive breast carcinoma


title: HCT116,DMSO,4h,ATACseq,biol rep1


title: MCI subject 1 [10]

source_name: genomic DNA extracted from MCI-affeced patient 1


title: Spl_ 46

city: Montpellier

first: Sandrine

last: Ruffel

address: 2 Place Viala

department: Montpellier University

country: France

institute: INRA

description: Gene expression data from 16 days Arabidopsis roots on hydoponic solution supplemented with EG 100 mM

hyb_protocol: Following fragmentation, 5.5ug of cDNA were hybridized for 16 hr at 48C on GeneChip 1.1ST Array Strip. GeneChips were washed and stained in the Affymetrix GeneAtlas Fluidics Station.

scan_protocol: Array strips were scanned using the Affymetrix GeneAtlas Imaging Station.

data_processing: The data quality analysis was done with the Affymetrix Expression Console software. The normalization of the raw data was done with the Affymetrix Transcriptome Analysis Console software using the GCRMA method.

organism: Arabidopsis thaliana

source_name: EG 100mM

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip® WT PLUS Reagent Kit Manual Target Preparation for GeneChip® Whole Transcript (WT) Expression Arrays).

growth_protocol: Seeds were surface sterilized and kept at 4°C in dark until sowing on 1/2 Murashige and Skoog basal salt medium agar plates [2.2 g L-1 MS (Sigma), 1% sucrose (Euromedex), 0.05% MES (Euromedex), and 0.7% agar (Sigma), pH 5.7 adjusted using KOH]. For pre-germination, plates were incubated vertically in growth chamber under long-day conditions (16h/8h, 21℃, 60% humidity). After 10 days, seedlings were transferred to a hydroponic medium [1.25 mM KNO3, 0.75 mM MgSO4, 1.5 mM Ca(NO3)2, 0.5 mM KH2PO4, 50 μM Fe-EDTA, 50 μM H3BO3, 12 μM MnSO4, 0.70 μM CuSO4, 1 μM ZnSO4, 0.24 μM MoO4Na2, 100 μM Na2SiO3] and further grown under the same culture conditions

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Plants were grown in the hydroponic solution for 6 more days and treated for 15min. One part of the plants was transferred to the same hydroponic solution as a control for the osmotic pressure. The other part of the plants was transferred to the same hydroponic solution supplemented with various concentrations of various solutes : Sodium chloride at 25, 50, 75 or 100mM or Sorbitol at 50, 100 or 150mM or Polyethylene glycol 8000 at 75, 100, 125 or 150mM or Ethylene glycol at 50, 100, 150 or 200mM. Root collection was done 15 minutes after application of the osmotic treatments.

tag: tissue

value: Roots

tag: cultivar

tag: age

value: 16 days


title: Spl_ 48

description: Gene expression data from 16 days Arabidopsis roots on hydoponic solution supplemented with EG 200 mM

source_name: EG 200mM


title: DU4475,FHT-1015, 4h,ATACseq, biol rep 2


title: Spl_ 45

description: Gene expression data from 16 days Arabidopsis roots on hydoponic solution supplemented with EG 50 mM

source_name: EG 50mM


title: DU4475,DMSO,4h,ATACseq,biol rep3


title: DU4475,FHT-1015, 4h,ATACseq, biol rep 1


title: Spl_ 47

description: Gene expression data from 16 days Arabidopsis roots on hydoponic solution supplemented with EG 150 mM

source_name: EG 150mM


title: DU4475,DMSO,4h,ATACseq,biol rep2


title: Spl_ 41

description: Gene expression data from 16 days Arabidopsis roots on hydoponic solution supplemented with PEG 75 mM

source_name: PEG 75mM


title: Spl_ 44

description: Gene expression data from 16 days Arabidopsis roots on hydoponic solution supplemented with PEG 150 mM

source_name: PEG 150mM


title: DU4475,DMSO,4h,ATACseq,biol rep1


title: Spl_ 40

description: Gene expression data from 16 days Arabidopsis roots on hydoponic solution supplemented with sorbitol 150 mM

source_name: Sorbitol 150mM


title: Spl_ 42

description: Gene expression data from 16 days Arabidopsis roots on hydoponic solution supplemented with PEG 100 mM

source_name: PEG 100mM


title: A375,FHT-1015, 4h,ATACseq, biol rep 3

value: melanoma


title: Spl_ 43

description: Gene expression data from 16 days Arabidopsis roots on hydoponic solution supplemented with PEG 125 mM

source_name: PEG 125mM


title: Spl_ 37

description: Gene expression data from 16 days Arabidopsis roots on hydoponic solution supplemented with NaCl 100mM

source_name: NaCl 100mM


title: Spl_ 38

description: Gene expression data from 16 days Arabidopsis roots on hydoponic solution supplemented with sorbitol 50 mM

source_name: Sorbitol 50mM


title: A375,FHT-1015, 4h,ATACseq, biol rep 1


title: Spl_ 34

description: Gene expression data from 16 days Arabidopsis roots on hydoponic solution supplemented with NaCl 25mM

source_name: NaCl 25mM


title: Spl_ 36

description: Gene expression data from 16 days Arabidopsis roots on hydoponic solution supplemented with NaCl 75mM

source_name: NaCl 75mM


title: Spl_ 35

description: Gene expression data from 16 days Arabidopsis roots on hydoponic solution supplemented with NaCl 50mM

source_name: NaCl 50mM


title: Spl_ 32

value: hydoponic solution supplemented with EG 200 mM


title: A375,DMSO,4h,ATACseq,biol rep3


title: Spl_ 31

value: hydoponic solution supplemented with EG 150 mM


title: Spl_ 33

description: Gene expression data from 16 days Arabidopsis roots on hydoponic solution

source_name: Control hydroponic solution

value: hydoponic solution


title: Spl_ 39

description: Gene expression data from 16 days Arabidopsis roots on hydoponic solution supplemented with sorbitol 100 mM

source_name: Sorbitol 100mM


title: A375,DMSO,4h,ATACseq,biol rep1


title: A375,DMSO,4h,ATACseq,biol rep2


title: RD,FHT-1015, 4h,ATACseq, biol rep 1

source_name: RD

value: RD

value: rhabdomyosarcoma


title: A375,FHT-1015, 4h,ATACseq, biol rep 2

value: WT


title: Spl_ 29

value: hydoponic solution supplemented with EG 50 mM


title: Spl_ 30

source_name: EG 100mM

value: hydoponic solution supplemented with EG 100 mM


title: RD,DMSO,4h,ATACseq,biol rep3

value: negative control


title: RD,DMSO,4h,ATACseq,biol rep1


title: RD,DMSO,4h,ATACseq,biol rep2


title: 22RV1,FHT-1015, 4h,ATACseq, biol rep 3

value: prostate adenocarcinoma

value: dual SMARCA4/SMARCA2 inhibition


title: 22RV1,FHT-1015, 4h,ATACseq, biol rep 2


title: Spl_ 27

value: hydoponic solution supplemented with PEG 125 mM


title: 22RV1,FHT-1015, 4h,ATACseq, biol rep 1


title: Spl_ 26

value: hydoponic solution supplemented with PEG 100 mM


title: Spl_ 25

value: hydoponic solution supplemented with PEG 75 mM


title: RD,FHT-1015, 4h,ATACseq, biol rep 3


title: 22RV1,DMSO,4h,ATACseq,biol rep3


title: RD,FHT-1015, 4h,ATACseq, biol rep 2


title: Spl_ 24

value: Roots

value: hydoponic solution supplemented with sorbitol 150 mM


title: 22RV1,DMSO,4h,ATACseq,biol rep1


title: RNA-Seq K562 RED rep2

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

description:
Replicate 2 hemin
RNAseq.RED.forward.bw
RNAseq.RED.reverse.bw
K562.RED.TPM.txt
K562.RED.FPKM.txt

data_processing:
Base calling and quality control were performed in real time with standard Illumina analysis pipeline using a phiX control.
Sequenced reads were trimmed from low quality and/or short sequences and/or Illumina 3' adapters by trimmomatic v. 0.39 using the following options: LEADING:18 TRAILING:18 SLIDINGWINDOW:4:22 MINLEN:20 ILLUMINACLIP:TruSeq3-SE:2:30:10
Trimmed reads were quantified to H. sapiens hg38 GRCh38 Ensembl v.106 genome with Ensembl genome map v.106 by RSEM 1.3.1 using the following options: --fragment-length-mean 255 --star --calc-ci --ci-memory 30720. This operation was performed for both replicates separately. The results were averaged by an in-house R script.
Trimmed reads were mapped to H.sapiens genome (hg38/GRCh38 Ensembl v.106) by STAR aligner 2.7.5c with hg38 Ensembl genome map v.106 http://ftp.ensembl.org/pub/release-106/gtf/homo_sapiens/Homo_sapiens.GRCh38.106.gtf.gz. Alignment options were the following:  --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --quantMode TranscriptomeSAM
Alignment files were separated by samtools 1.15 view -F 0x10 to get forward strand alignments and by samtools 1.15 view -f 0x10 to get reverse strand alignments. Then bamCoverage (deepTools 3.5.1) tool was applied to obtain normalized expression profiles: --binSize 10 --effectiveGenomeSize 2913022398 --skipNAs --normalizeUsing RPKM --exactScaling. The obtained profiles were averaged between replicates by WiggleTools v1.2.11 and converted to bigWig format by bedGraphToBigWig tool from UCSC genome tools.
Assembly: Homo sapiens hg38/GRCh38 Ensembl release 106 genome build. Homo sapiens hg38/GRCh38 Ensembl annotation v106 in GTF format.
Supplementary files format and content: bigWig files contain normalized (RPKM, reads per kilobase million) expression signal genomewide for each strand.
Supplementary files format and content: Results files contain quantified expression values in TPM (Transcripts Per Million) and FPKM (Fragments Per Kilobase Million) for each gene per replicate and averaged between replicates.

source_name: blood

growth_protocol: The cells were drown in RPMI 1640 media (PanEco, Russia) supplemented with heat-inactivated fetal calf serum (HyClone, USA), 2 mM glutamine, 250 u/ml penicillin and 250 μg/ml streptomycin (PanEco, Russia) at 37 °C in a humidified atmosphere containing 5% CO2. For a treated samples, hemin (50 μM, neoFroxx, Germany) was added to induce the erythroid differentiation and cells were incubated further for 108 h. At this concentration, the drug did not affect cell proliferation.

extract_protocol:
Total RNA was extracted from cell lysed with Trisol reagent and PureLink RNA Micro Kit (Invitrogen) according to manufacture instruction. RNA Quality was checked with  BioAnalyser and  RNA 6000 Nano Kit(Agilent). Poly(A)+ RNA was isolated with Dynabeads® mRNA Purification Kit (Ambion).
Poly(A)+ RNA was isolated with Dynabeads® mRNA Purification Kit (Ambion). Illumina library was prepared from poly(A)+RNA with NEBNext® Ultra™II RNA Library Prep Kit for Illumina® (NEB) according to manual. Sequencing was performed on Illumina HiSeq1500 with 50 bp read length.

treatment_protocol: K562 cells incubated in the presence of 50 μM hemin (neoFroxx, Germany) for 108 h. At this concentration, the drug did not affect cell proliferation.

value: blood

value: erythroleukemia

value: erythroid differentiation

tag: agent

value: hemin


title: Spl_ 20

value: 16 days

value: hydoponic solution supplemented with NaCl 75mM


title: Spl_ 28

value: hydoponic solution supplemented with PEG 150 mM


title: 22RV1,DMSO,4h,ATACseq,biol rep2

value: WT


title: 92-1,FHT-1015, 4h,ATACseq, biol rep 3

value: uveal melanoma


title: RNA-Seq K562 RED rep1

description:
Replicate 1 hemin
RNAseq.RED.forward.bw
RNAseq.RED.reverse.bw
K562.RED.TPM.txt
K562.RED.FPKM.txt


title: Spl_ 22

value: hydoponic solution supplemented with sorbitol 50 mM


title: RNA-Seq K562 WHITE rep2

description:
Replicate 2 untreated
RNAseq.WHITE.forward.bw
RNAseq.WHITE.reverse.bw
K562.WHITE.TPM.txt
K562.WHITE.FPKM.txt

value: untreated


title: Spl_ 19

value: hydoponic solution supplemented with NaCl 50mM


title: RNA-Seq K562 WHITE rep1

description:
Replicate 1 untreated
RNAseq.WHITE.forward.bw
RNAseq.WHITE.reverse.bw
K562.WHITE.TPM.txt
K562.WHITE.FPKM.txt


title: 92-1,DMSO,4h,ATACseq,biol rep2

value: negative control


title: 92-1,FHT-1015, 4h,ATACseq, biol rep 1

value: dual SMARCA4/SMARCA2 inhibition


title: 92-1,DMSO,4h,ATACseq,biol rep3


title: Spl_ 21

value: hydoponic solution supplemented with NaCl 100mM


title: 92-1,DMSO,4h,ATACseq,biol rep1


title: LA_1

city: Shizuoka

first: Tetsuya

last: Hosooka

state: Shizuoka

address: 52-1 Yada

institute: University of shizuoka

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: GRCm38
Supplementary files format and content: Text files include FPKM values for each Sample

source_name: Liver

growth_protocol: Mice were housed at 21°C-25°C on a 12-hr light/dark cycle in the animal facility at University of Shizuoka.

extract_protocol:
Total RNA was extracted from tissues with RNeasy minikit (QIAGEN). 6.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Nextera XT DNA Library Prep kits following manufacturer's protocols.

treatment_protocol: Male 5-week-old C57BL/6J mice  fed ND, HFD, HYD supplemented with 1% HYA, or HFD supplemented with 1% LA for 26 weeks from 5-week-old.

value: Liver

tag: diet

value: HFD supplemented with 1% LA


title: Spl_ 17

value: Roots

value: hydoponic solution


title: LA_3


title: LA_2


title: HYA_3

value: HFD supplemented with 1% HYA


title: HYA_1


title: HYA_2


title: ND_2

value: normal


title: CT_3

value: high fat diet


title: ND_3


title: ND_1


title: CT_1


title: Spl_ 18

value: 16 days

value: hydoponic solution supplemented with NaCl 25mM


title: ID8_p53_BRCA2.3 [MK-15]

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

institute: Ottawa Hospital Research Institute

description:
mouse_sample_annotation.csv
txi_mouse.rds
tpm_matrix._mouse.csv

data_processing:
Pseudoalignment and transcript quantification for each sample was performed using Kallisto (v0.45.0) with the GRCm38 build of the mouse genome. The R package tximport (v1.24.0) was used to load transcript quantifications, converting to gene-level transcript estimates.
Assembly: GRCm38
Supplementary files format and content: mouse_sample_annotation.csv - Annotation table providing metadata for each sample
Supplementary files format and content: txi_mouse.rds - R object containing raw counts and tpm matrices for each sample following import with tximport
Supplementary files format and content: tpm_matrix._mouse.csv - Transcripts per million (TPM) count matrix for all genes and samples

source_name: IP tumour

extract_protocol:
Total RNA was extracted according to the manufacturer’s instructions with the RNeasy Plus Mini Kit (Qiagen) for the majority of samples. IP tumours collected from mice injected with ID8-Trp53-/-, ID8-Trp53-/-; Brca1-/-, ID8-Trp53-/-; Brca2-/-, ID8-Trp53-/-; Nf1-/-, and ID8-Trp53-/-; Pten-/- cells were isolated at endpoint using the total RNA Purification Kit (Norgen Biotek Corporation, ON, Canada) as per the manufacturer’s instructions.
RNA-Seq libraries were generated from 250 ng of total RNA as following: mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs). cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps of library preparation were done using and the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). Adapters and PCR primers were purchased from New England BioLabs.
The pool was loaded at 200pM on a Illumina NovaSeq S4 lane using Xp protocol as per the manufacturer’s recommendations. The run was performed for 2x100 cycles (paired-end mode). A phiX library was used as a control and mixed with libraries at 1% level. Base calling was performed with RTA v3. Program bcl2fastq2 v2.20 was then used to demultiplex samples and generate fastq reads

value: IP tumour

tag: model


title: ID8_p53_PTEN.4 [MK-20]


title: ID8_p53_PTEN.1 [MK-17]


title: ID8_p53_BRCA2.4 [MK-16]


title: ID8_p53_BRCA2.2 [MK-14]


title: ID8_p53_PTEN.3 [MK-19]


title: ID8_p53_BRCA2.1 [MK-13]


title: Spl_ 23

value: hydoponic solution supplemented with sorbitol 100 mM


title: ID8_p53_Nf1.4 [MK-12]


title: ID8_p53_BRCA1.4 [MK-8]


title: ID8_p53_Nf1.3 [MK-11]


title: ID8_p53_Nf1.2 [MK-10]


title: ID8_p53_BRCA1.3 [MK-7]


title: CT_2


title: VSG2_67 - E0771 tumor excised from C57BL6Ncrl mouse_DIO-CCR

city: chapel hill

first: michael

middle: francis

last: coleman

state: North Carolina

address: 235 dauer drive

institute: UNC

hyb_protocol: Labeled cDNA was hybridized to the plate using GeneTitan Hybridization Wash and Stain Kit for WT Arrays (Affymetrix)

scan_protocol: arrays were scanned using GeneTitan

data_processing: Quality control and differential gene expression was conducted using TAC4 software (Affymetrix)

source_name: Obese - chronic calorie restriction

label_protocol: The GeneChip® WT PLUS Reagent Kit (Affymetrix, Santa Clara, CA) was used to prepare the samples

growth_protocol: C57BL/6N mice were randomized to receive a control diet D12450J, or a 60% high fat diet (D12492) to promote diet induced obesity. Once obese, mice were randomized to either remain obese or undergo weight loss via 1) vertical sleeve gastrectomy with low-fat diet, 2) intermittent calorie restriction, or 3) chronic calorie restriction.

extract_protocol: RNA was isolated by bead beating in TRIzol reagent, followed by isolation with EZNA HP Total RNA kit (omega bio-tek)

treatment_protocol: All mice received either sham surgery or vertical sleeve gastrectomy. 25 weeks after initial randomization mice were orthotopically injected with E0771 cells into the 4th mammary fat pad and tumors were allowed to grow till endpoint. At endpoint the tumor was removed and used for nucleic acid extraction.

value: tumor

tag: group

value: DIO-CCR


title: ID8_p53_BRCA1.2 [MK-6]


title: ID8_p53_BRCA1.1 [MK-5]


title: VSG2_11 - E0771 tumor excised from C57BL6Ncrl mouse_DIO-CCR


title: VSG2_38 - E0771 tumor excised from C57BL6Ncrl mouse_DIO-CCR


title: CAFs from PDX treated with Fn1 SiRNA

city: SANTIAGO DE COMPOSTELA

first: Jorge

last: Barbazan

state: A Coruña

address: Trav Choupana s/n

country: Spain

institute: Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS)

data_processing:
Data processing was performed by Novogene Co Ltd
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts for each sample

source_name: Subcutaneous rectal tumor

growth_protocol: Primary CAFs were obtained from the indicated mouse strains and generated through the outgrowth protocol, and immortalized using SV40 infection. Primary CAFs were routinely culture in DMEM Glutamax Medium, Supplemented with 10% FBS and 1X ITS.

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen), with a DNAse treatment.
Libraries were constructed by Novogene Co. Ltd

treatment_protocol: WT or MyoKO CAFs were generated by in vitro treatment with 2µM Tamoxifen. Fn1 knockdown or SiRNA control CAFs were generated using standard SiRNA protocols, as indicated in the linked publication (Barbazan et al, Nat Comms, 2023).

value: Subcutaneous rectal tumor

value: primary murine CAFs

value: WT

value: SiRNA Fn1


title: VSG2_58 - E0771 tumor excised from C57BL6Ncrl mouse_DIO-CCR


title: VSG2_23 - E0771 tumor excised from C57BL6Ncrl mouse_DIO-CCR


title: VSG2_128 - E0771 tumor excised from C57BL6Ncrl mouse_DIO-ICR

source_name: Obese - intermittent calorie restriction

value: DIO-ICR


title: ID8_p53.4 [MK-4]


title: VSG2_65 - E0771 tumor excised from C57BL6Ncrl mouse_DIO-ICR


title: VSG2_82 - E0771 tumor excised from C57BL6Ncrl mouse_DIO-ICR


title: CAFs from MyoKO mouse Cre+

value: MyosinIIA KO Cre+


title: VSG2_99 - E0771 tumor excised from C57BL6Ncrl mouse_DIO-CCR


title: VSG2_29 - E0771 tumor excised from C57BL6Ncrl mouse_DIO-ICR


title: VSG2_143 - E0771 tumor excised from C57BL6Ncrl mouse_DIO-ICR


title: VSG2_72 - E0771 tumor excised from C57BL6Ncrl mouse_DIO-ICR


title: ID8_p53.3 [MK-3]


title: CAFs from MyoKO mouse Cre-

value: MyosinIIA KO Cre-


title: CAFs non treated from PDX


title: VSG2_129 - E0771 tumor excised from C57BL6Ncrl mouse_DIO-VSG

source_name: Obese - vertical sleeve gastrectomy

value: DIO-VSG


title: VSG2_74 - E0771 tumor excised from C57BL6Ncrl mouse_DIO-VSG


title: Mouse_Face_E15_5_rep1

city: Berkeley

first: Laura

middle: E

state: California

address: 1 Cyclotron Road

department: Biosciences

institute: Lawrence Berkeley National Laboratory

data_processing:
Reads were aligned to mm10 reference genome using bowtie2 with default parameters and cell barcodes were added as a BX tag in the bam file. Only primary alignments were kept. Duplicated read pairs were removed with Picard, and proper read pairs with insert size less than 2000 were kept for further analysis.
snapATAC package was used for read counting and clustering, as well as for label transfer to integrate single-cell gene expression data.
Assembly: mm10
Supplementary files format and content: snap files

source_name: face

extract_protocol:
Face tissue was dissected from mouse embryos for each of the developmental stages e10.5-15.5, and flash frozen. Nulcei were isolated, permeabilized, suspended in tragmentation buffer, and distributed in a 96-well plate. TnT transposomes were added and upon termination of the TnT reaction, the nuclei were re-sorted in the 96-well plate.
A Biomek i7 Automated Workstation (Beckman Coulter) was used for performing downstream steps. Libraries were sequenced on a NextSeq500 or HiSeq4000 (Illumina) using custom sequencing primers.

value: face

value: mixed

tag: developmental stage


title: ID8_p53_PTEN.2 [MK-18]


title: Mouse_Face_E14_5_rep1


title: CAFs from PDX treated with control SiRNA

value: SiRNA Scramble


title: OVE16_p53_KO.3 [JP-24]

source_name: cell line

value: cell line


title: Mouse_Face_E13_5_rep1-001


title: Mouse_Face_E11_5_rep1


title: VSG2_50 - E0771 tumor excised from C57BL6Ncrl mouse_DIO-VSG


title: OVE16_p53_KO.1 [JP-22]


title: VSG2_48 - E0771 tumor excised from C57BL6Ncrl mouse_DIO-VSG


title: Mouse_Face_E10_5_rep1-003


title: Mouse_Face_E12_5_rep1


title: OVE16_p53_mut.3 [JP-21]


title: ID8_p53.1 [MK-1]


title: OVE16_p53_mut.2 [JP-20]


title: NR2F1 BG E13.5 Input 1

city: Davis

first: Alex

middle: S.

last: Nord

state: CA

address: 1544 Newton Court

department: Center for Neuroscience

institute: University of California Davis

data_processing:
We applied the MAPS pipeline to detect statistically significant H3K4me3-centric long-range chromatin interactions from PLAC-seq data. We only analyzed intra-chromosomal interactions for autosomal chromosomes, and identified chromatin interactions at 10-kb bin resolution between 20 kb and 1 Mb. We first mapped the raw paired-end reads (i.e. FASTQ file) to the mm10 reference genome using BWA mem. Next, we applied filtering steps to remove PCR duplicates, low-quality reads (MAPQ <= 30) and chimeric reads. We then split the remaining mapped reads into short-range (distance between pair ends within 1 kb) and long-range reads (distance between pair ends between 1 kb and 1 Mb). We used the short-range and long-range reads to measure protein immunoprecipitation (IP) efficiency and detect long-range chromatin interactions, respectively.
For ChIP-seq, quality-controlled FASTQ files containing the reads were further cleaned-up from the remaining adapter sequences using Trim Galore version 0.4.5. The resulting reads were aligned to the mouse (mm10) genome using BWA version 0.7.9a, and duplicates removed with Samtools version 1.8. Peaks of enriched binding regions against both negative binding and input DNA control were called using MACS version 2.1 with p-value cutoffs of 10E-4.
Assembly: mm10
Supplementary files format and content: PLAC-seq: interaction bed files
Supplementary files format and content: ChIP-seq: narrow peaks

source_name: brain

extract_protocol:
ChIP was performed using antibodies against SP9, ARX, ASCL1, GSX2, and NR2F1. Basal ganglia were dissected in cold PBS from CD1 embryos (2 L/Ab for NR2F1; 3 L/Ab for ARX, ASCL1, and GSX2). The basal ganglia consisted of the LGE, MGE and CGE progenitor and mantle zones. The dissected basal ganglia were either fixed in 1% formaldehyde at RT for 10 min (SP9, ASCL1, GSX2, NR2F1) or fixed in 1.5% formaldehyde at RT for 20 min (ARX), neutralized with glycine, and washed gently in PBS. The fixed cells were lysed with a hypotonic buffer (50 mM Tris pH 7.5 / 0.5% NP40 / 0.25% sodium deoxycholate / 0.1% SDS / 150 mM NaCl) to obtain the nuclei; these were then lysed in 1% SDS buffer and the chromatin was sheared into 300-1000 bp fragments by sonicating for 40 cycles (30 sec on and 45 sec off) using a bioruptor (Diagenode). Immunoprecipitation (IP) reactions were performed with the sheared chromatin diluted 1/10 times with “dilution buffer” (0.01% SDS, 1.1% Triton X- 100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.1, 167mM NaCl, usually in 6 ml. Antibody was then added to either 5 µg (ARX, SP9, NR2F1) or 8 µg (ACSL1, GSX2) specific antibodies. Negative control ChIP reactions used either IgG (5µg) or blocking peptide (ARX, 400x molar excess). Antibody/chromatin complexes were purified using Dynabeads (Invitrogen) and washed extensively in “wash buffer” (low salt, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 150 mM NaCl; high salt, 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 500 mM NaCl; LiCl, 0.25 M LiCl, 1% IGEPAL CA630, 1% deoxycholic acid (sodium salt), 1mM EDTA, 10mM Tris, pH 8.1 and TE). Complexes were eluted with 1% SDS, 10 mM sodium bicarbonate buffer at 65 ºC for 10 min. Eluted chromatin was reverse-crosslinked overnight at 65 ºC in the presence of 500 mM NaCl, then subsequently treated with RNase (10 µg/200 µL reaction, 15 min at 37 ºC) and Proteinase K (10 µg/200 µL reaction, 60 min at 55 ºC) and cleaned using a ChIP DNA Clean & Concentrator kit (Zymo Research). The chromatin was quality-controlled (QC) using qPCR to check for enrichment of genomic DNA fragments that were expected, and not expected, to have the different TF binding.
For ChIP-seq, libraries were prepared using an Ovation Ultralow DR Multiplex System (Nugen), size- selected in the range of 300 bp on a chip from BluePippin (Sage Science) and lastly QC tested on a Bioanalyzer (Agilent). The libraries were sequenced as single-end 50-bp reads on a HiSeq 4000 (Illumina) at the Center for Advanced Technology (UCSF). PLAC-seq libraries for E13.5 basal ganglia were prepared similar to a previously published protocol61. 3 to 7 million cells were used for each library. If the cells appeared aggregated, they were dissociated with gentle MACS dissociator or Dounce homogenizer. Each PLAC-seq library was prepared using DpnII as the restriction enzyme and Dynabeads M-280 sheep anti-rabbit IgG (Invitrogen #11203D) mixed with 5 µg of H3K4me3 (04-745, Millipore) for the chromatin immunoprecipitation step. Finally, libraries were prepared with the Illumina TruSeq adaptors and the final libraries were sent for paired-end sequencing on the HiSeq X Ten (150-bp reads) equipment.
ChIP-seq, PLAC-seq

value: brain

value: basal ganglia

value: wild-type


title: ASCL1 BG E13.5 Input 2


title: GSX2 BG E13.5 Input 1


title: SP9 ChIP E13.5 BG WT 1


title: OVE16_p53_mut.1 [JP-19]


title: ARX BG E13.5 Input 3


title: VSG2_148 - E0771 tumor excised from C57BL6Ncrl mouse_DIO-HFD

source_name: Obese - no weight loss

value: tumor

value: DIO-HFD


title: VSG2_79 - E0771 tumor excised from C57BL6Ncrl mouse_DIO-HFD


title: VSG2_52 - E0771 tumor excised from C57BL6Ncrl mouse_DIO-VSG


title: VSG2_100 - E0771 tumor excised from C57BL6Ncrl mouse_DIO-HFD


title: NR2F1 ChIP E13.5 BG WT 1


title: VSG2_36 - E0771 tumor excised from C57BL6Ncrl mouse_DIO-VSG


title: GSX2 ChIP E13.5 BG WT 1


title: SP9 BG E13.5 Input 1


title: ARX ChIP E13.5 BG WT 3

tag: chip antibody

value: Santa Cruz, cat# sc-48843


title: OVE16_p53_KO.2 [JP-23]


title: OVE16.2 [JP-17]


title: OVE16.1 [JP-16]


title: VSG2_13 - E0771 tumor excised from C57BL6Ncrl mouse_DIO-HFD