title: RNA-SEQ, A12-14-1, PCBN1, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-14-1 from patient PCBN1
processed_counts.txt
processed_TPM.txt
A12-14-1

tag: race

tag: pathologic stage

tag: 5-year disease status

value: recurrence

tag: sample type


title: KO_BM_GFP-Tm+_2

status: Public on Apr 27 2022

type: SRA

city: Minato-ku

first: Takaharu

last: Kimura

state: Tokyo

address: 4-6-1 Shirokanedai

country: Japan

institute: The University of Tokyo

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor and low-quality sequence, then aligned to mouse reference sequence mm10 with STAR.
Aligned reads were counted with featureCounts.
Raw counts were analyzed by DESeq2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: *.txt: Tab-delimited text files with raw gene counts.

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow stromal cells

extract_protocol:
Total RNA were extracted from sorted cells with the RNeasy Plus Micro Kit (Qiagen).
Libraries were prepared with the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing and SMARTer ThruPLEX DNA-Seq Kit (Takara Bio).

tag: age

value: postnatal day 21

tag: genotype

value: Conditional PTH1R KO

tag: cell type

value: Bone marrow stromal cells


title: Brown adipose tissue, cPTU+TH_12H_B21

city: Lyon

first: Yanis

last: ZEKRI

address: 32-34 Avenue Tony Garnier

country: France

institute: IGFL-ENS

description:
TH kinetics.txt
PTU+TH_12H_B21

data_processing:
Reads were mapped on mouse mm10 genome using Bowtie Galaxy version 2.3.2.2 with default parameters
Read were counted using htseqcount Galaxy version 0.6.1galaxy3 using these parameters // Mode : Union / Stranded : Reverse / Minimul alignement quality : 10 / Feature type : exon / ID Attribute : gene name
Differential gene expression analysis was performed with DESeq2 (R package, Version 1.34.0) using the following thresholds: adjusted p-value <0.05; average expression > 10 reads per million, log2 fold-change > 0.6 or < -0.6. The effect of mutations on both cold exposure and HFD was obtained using the interaction model (Ge, 2021). Thresholds for the interaction were the following: average expression > 10 reads per million, adjusted p-value < 0.05.
Differentially expressed genes expression was visualized as clustered heatmaps using Pheatmap R package (RRID:SCR_016418)
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw counts of all samples from the same experiment (TH injection for target genes, cold exposure and HFD in 3 different tables. Each sample is preceded by a, b or c, which allows to quickly identify the 3 different experiments)

source_name: Brown adipose tissue

extract_protocol:
RNAs were extracted using Trizol. Total RNA was converted to cDNA using MMLV reverse transcriptase. 1ug of total RNA was used for the construction of sequencing libraries
cDNA libraries were prepared using the total RNA SENSE kit (Lexogen, Vienna, Austria) and analyzed on a Nextseq 500 sequencer (Illumina)

tag: tissue

value: Brown adipose tissue

value: 8-12 weeks

tag: Sex

value: Male

tag: background strain

value: Wild-type

tag: treatment

value: PTU+TH 12h


title: WT_Coil_1

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

country: USA

institute: CWRU

data_processing:
Illumina reads were mapped to reference genome using STAR Aligner program.
The expression levels of genes were determined using Cufflinks and presented as FPKM.
Differential expression analysis was done using Cuffdiff.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: genematrix.tsv: Tab-delimited text file containing FPKM for all samples and genes.

source_name: Liver

growth_protocol: Fmo3+/+ or Fmo3-/- genotype on C57Bl6/J Background.

extract_protocol:
Mice were euthanized, and perfused with saline. The liver was removed and flash frozen in liquid nitrogen. RNA was harvested using Trizol reagent/Qiagen RNeasy Kit.
RNA-Seq libraries were generated using the Illumina mRNA TruSEQ Directional library kit and sequenced using an Illumina NovaSeq 6000.

treatment_protocol: Corn oil vehicle or 25ug/kg TCDD weekly via intraperitoneal injection for 6 weeks.

tag: strain

value: Liver

value: Corn Oil Vehicle


title: RNA-SEQ, A12-14-6, PCBN3, prostate tissue

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

description:
Paired-end RNA-seq for prostate tissue sample A12-14-6 from patient PCBN3
processed_counts.txt
processed_TPM.txt
A12-14-6

data_processing:
Base-calling was performed with CASAVA 1.9
FASTQ files were pre-processed to remove sequencing adaptors with Trimmomatic v0.36.
Paired-end trimmed FASTQ files were aligned to hg19 using STAR.
RSEM was used to estimate read counts for each genomic feature.
Assembly: hg19
Supplementary files format and content: tab separated values, gene symbol, description, transcripts-per-million (TPM) or count

organism: Homo sapiens

source_name: prostate tissue

extract_protocol:
RNA was extracted from OCT prostate tissues using the Qiagen RNeasy kit or from frozen buffy coats using the Macharay-Nagel NucleoSpin RNA Blood  kit.
Libraries were prepared with the NEBNext Globin and rRNA depletiion library construction kit and the Illumina TruSeq stranded total RNA with ribo-zero globin kit.
Paired-end

treatment_protocol: Patients with prostate cancer underwent radical prostatectomy with no prior therapy. Blood was drawn into EDTA tubes prior to surgery. Prostate tissues were grossed, accessioned, embedded in OCT, and frozen.

tag: disease state

value: prostate cancer

tag: patient id

tag: gender

value: male

tag: preoperative psa

tag: sample gleason score

tag: % tumor

tag: % tumor-in-normal contamination

tag: patient gleason score

value: WHITE

value: TUMOR


title: RNA-SEQ, A12-14-2, PCBN1, prostate tissue

description:
Paired-end RNA-seq for prostate tissue sample A12-14-2 from patient PCBN1
processed_counts.txt
processed_TPM.txt
A12-14-2

tag: race

tag: pathologic stage

tag: 5-year disease status

tag: sample type


title: RNA-SEQ, A12-17-1, PCBN1, buffy coat

description:
Paired-end RNA-seq for buffy coat sample A12-17-1 from patient PCBN1
processed_counts.txt
processed_TPM.txt
A12-17-1

source_name: buffy coat

tag: age


title: KO_Bone_GFP+_2

source_name: Bone cells

tag: genotype

tag: cell type

value: Bone cells


title: 6867-NN-18

city: Nashville

first: Lance

last: Riley

state: TN

address: 9445 MRB4, 2213 Garland Ave

department: Biomedical Engineering

institute: Vanderbilt University

data_processing:
Sequenced reads were mapped and gene counts were quantified using Illumina DRAGEN RNA pipeline v. 3.6.3
Gene count data was compiled using tximport
Differential gene expression was determined using DESeq2 using Cook's outliers to filter out low expression and alpha = 0.01 to for significance.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw counts for every gene and every sample.
Supplementary_files_format_and_content: Matrix table with DEseq2 counts for every gene and every sample.

source_name: Heart

extract_protocol:
LVs were dissected from hearts and homognized in TRIzol reagent. RNA was isolated with a Zymo Direct-Zol Miniprep kit using the standard protocol.
Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kits according to standard protocols.

treatment_protocol: All mice administered tamoxifen through I.P. injections for 5 days. 2 weeks later, mice were subjected to continuous AngII through osmotic pumps for 8 weeks, and then were euthanized.

tag: tissue

value: Left ventricle tissue

value: Tln2-null; Tln1-specific CF knockout


title: KO_BM_GFP-Tm+_1

value: postnatal day 21


title: Ctrl_Bone_GFP-Tm+_2

value: Wild type


title: Brown adipose tissue, cPTU+TH_12H_B19

description:
TH kinetics.txt
PTU+TH_12H_B19

tag: Sex

tag: background strain

tag: treatment


title: Huh7.5 cells, Scramble, SADS-CoV infected, 24 hours, biol rep 3

city: Chapel Hill

first: Rita

last: Meganck

state: North Carolina

address: 135 Dauer Drive

department: Epidemiology

institute: UNC Chapel Hill

description: Sample 9

data_processing:
Fastq files were trimmed using BBDuK version 38.87 with the parameters ktrim=r k=23 hdist=1 minlen=50.
Trimmed reads were aligned to the human genome (hg19) using STAR version 2.7.7a with the parameters --peOverlapNbasesMin 30 --outSAMtype BAM SortedByCoordinate.
BAM files were indexed using Samtools version 1.12.
Features were counted using featureCounts as part of Subread version 2.0.1 with the parameters -T 4 -s 2 -d 25 -p -P -B -M -O.
Differential expression analysis was performed using DESeq2 version 1.30.1 under the Variable design.
Assembly: hg19
Supplementary files format and content: Tab-delimited text file containing feature counts for each sample

growth_protocol: Huh7.5 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested from cells using TRIzol reagent, following the manufacturer's protocol. 100ng of total RNA was used for library preparation.
Libraries for sequencing were prepared using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus following the manufacturer's protocol.

treatment_protocol: Cells were prewashed with PBS, then incubated with 300 uL of SADS-CoV-RFP inoculum (MOI=0.5) at 37C for 1 hour with rocking every 15 minutes. Viral inoculum was removed, and cells were replenished with 3 mL of DMEM supplemented with 2% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C for 24 hours before harvest

tag: cell line

value: hepatocarcinoma cells

value: WT

value: SADS-CoV infection

tag: time

value: 24 hours post infection


title: Brown adipose tissue, cPTU+TH_6H_B17

description:
TH kinetics.txt
PTU+TH_6H_B17

value: Brown adipose tissue

value: 8-12 weeks

value: Male

value: Wild-type

value: PTU+TH 6h


title: Ctrl_Bone_GFP-Tm+_1


title: KO_BM_GFP-Tm+_3

value: Conditional PTH1R KO

value: Bone marrow stromal cells


title: 6867-NN-15

tag: gender

tag: strain


title: Brown adipose tissue, cPTU+TH_12H_B20

description:
TH kinetics.txt
PTU+TH_12H_B20

value: PTU+TH 12h


title: Brown adipose tissue, cPTU+TH_6H_B15

description:
TH kinetics.txt
PTU+TH_6H_B15


title: WT_Coil_0

value: Liver

value: Corn Oil Vehicle


title: Ctrl_Bone_GFP+_3

value: Bone cells


title: Brown adipose tissue, cPTU+TH_6H_B12

description:
TH kinetics.txt
PTU+TH_6H_B12


title: 6867-NN-14

value: Left ventricle tissue

value: Female


title: Brown adipose tissue, cPTU+TH_6H_B13

description:
TH kinetics.txt
PTU+TH_6H_B13


title: Ctrl_Bone_GFP+_1

value: postnatal day 21

value: Wild type


title: Huh7.5 cells, PLAC8 KO, biol rep 2

description: Sample 5

value: hepatocarcinoma cells

value: PLAC8 knockout

value: mock

value: not applicable


title: 6867-NN-13

value: Male


title: WT_Coil_3


title: Brown adipose tissue, cPTU+TH_3H_B11

description:
TH kinetics.txt
PTU+TH_3H_B11

value: Brown adipose tissue

value: 8-12 weeks

value: Wild-type

value: PTU+TH 3h


title: Huh7.5 cells, Scramble, SADS-CoV infected, 24 hours, biol rep 1

description: Sample 7

value: WT

value: SADS-CoV infection

value: 24 hours post infection


title: Huh7.5 cells, PLAC8 KO, biol rep 1

description: Sample 4


title: Ctrl_Bone_GFP+_2

value: Bone cells


title: Huh7.5 cells, Scramble, SADS-CoV infected, 24 hours, biol rep 2

description: Sample 8


title: Brown adipose tissue, cPTU+TH_3H_B9

description:
TH kinetics.txt
PTU+TH_3H_B9


title: Ctrl_BM_GFP-Tm+_3

value: Bone marrow stromal cells


title: 6867-NN-12

value: Left ventricle tissue

value: Female

value: Tln2-null; Tln1-specific CF knockout


title: Huh7.5 cells, Scramble, biol rep 3

description: Sample 3

value: hepatocarcinoma cells


title: Ctrl_Bone_GFP-Tm+_3

value: postnatal day 21

value: Wild type


title: 6867-NN-16


title: Huh7.5 cells, Scramble, biol rep 2

description: Sample 2

value: mock

value: not applicable


title: Huh7.5 cells, PLAC8 KO, biol rep 3

description: Sample 6

value: PLAC8 knockout


title: Huh7.5 cells, Scramble, biol rep 1

description: Sample 1


title: 6867-NN-10


title: Ctrl_BM_GFP-Tm+_1


title: 6867-NN-8


title: 6867-NN-9

value: Male


title: Brown adipose tissue, cPTU+TH_3H_B8

description:
TH kinetics.txt
PTU+TH_3H_B8

value: Brown adipose tissue

value: 8-12 weeks

value: Wild-type


title: Brown adipose tissue, cPTU_B5

description:
TH kinetics.txt
PTU_B5

value: PTU


title: 6867-NN-6


title: GBM 12-0106 Vehicle

city: Durham

first: Simranjit

middle: X.

last: Singh

state: NC

address: 203 Research Drive, MSRB1 Room 143

department: Pathology

institute: Duke University

data_processing:
Paired-end 150 bp sequencing was performed by Novogene on an Illumina NovaSeq 6000 machine, with data quality control performed by Novogene.
Bowtie 2 was used for alignment and Cufflinks 2.2.2 was used for gene expression profiling. HTSeq and edgeR were used for differential count analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Excel matrix with abundance measurements for every gene with FPKM > 10; all four samples included.

source_name: Primary brain tumor tissue

growth_protocol: Patient-derived GBM cells (GBM 12-0160 and GBM 12-0106) were maintained in human neural stem cell (NSC) medium (STEMCELL, cat# 05751) supplemented with EGF 20 ng/mL, FGF 10 ng/mL, and heparin 2 µg/mL. These cells were plated and passaged on laminin-coated tissue culture plates.

extract_protocol:
Total RNA was extracted using the Quick-RNA Miniprep kit (Zymo Research, cat# R1054).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: GBM 12-0160 and GBM 12-0106 cells were treated with vehicle or ALA (0.25 µM) for 2 weeks in NSC medium.

tag: disease state

value: Glioblastoma (GBM)

value: Primary brain tumor tissue

value: Patient-derived GBM cells (GBM 12-0106)

value: Vehicle


title: Brown adipose tissue, cPTU_B3

description:
TH kinetics.txt
PTU_B3


title: AML Gab2 HET mouse 1

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

data_processing:
Basecalls performed using RTA 2.7.7
Bad quality reads were filtered out using Trimmomatic (v 0.36) with the following paramters: HEADCROP:3 TRAILING:10 MINLEN:25
paired-end reads were aligned to the mm10 genome assembly using STAR (v2.5.2b), and read count per gene was subsequently estimated with the following parameters: --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999  --outFilterMismatchNoverLmax 0.05 i--alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMatchNmin 16  --quantMode GeneCounts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt file including read count per gene for each sample

source_name: Whole murine bone marrow

extract_protocol:
RNA was purified according to manufacturer's protocol (Roboklon, Cat#E3598)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow

value: Mx1-Cre; Dnmt3a+/-; Flt3ITD/ITD; Gab2+/-


title: Brown adipose tissue, cPTU_B2

description:
TH kinetics.txt
PTU_B2


title: AML Gab2 KO mouse 3

value: Mx1-Cre; Dnmt3a+/-; Flt3ITD/ITD; Gab2-/-


title: Brown adipose tissue, cPTU+TH_3H_B7

description:
TH kinetics.txt
PTU+TH_3H_B7

value: PTU+TH 3h


title: AML Gab2 HET mouse 2


title: 6867-NN-5

value: Left ventricle tissue


title: Brown adipose tissue, cPTU_B4

description:
TH kinetics.txt
PTU_B4


title: GBM 12-0160 ALA

value: Patient-derived GBM cells (GBM 12-0160)

value: L-Alanosine (ALA)


title: GBM 12-0160 Vehicle


title: AML Gab2 KO mouse 2


title: AML Gab2 KO mouse 1


title: 6867-NN-11

value: Tln2-null; Tln1-specific CF knockout


title: Ctrl_BM_GFP-Tm+_2

value: postnatal day 21

value: Wild type

value: Bone marrow stromal cells


title: Brown adipose tissue, bBATKO Chow-6

description:
HFD BATKO 3.5d.txt
BATKO_Chow_6

value: Brown adipose tissue

value: 8-12 weeks

value: Male

value: BATKO

value: Chow


title: 6867-NN-3


title: GBM 12-0106 ALA

value: Glioblastoma (GBM)

value: Primary brain tumor tissue

value: Patient-derived GBM cells (GBM 12-0106)


title: AML Gab2 WT mouse 3

value: Bone marrow

value: Mx1-Cre; Dnmt3a+/-; Flt3ITD/ITD; Gab2+/+


title: Brown adipose tissue, bBATKO Chow-5

description:
HFD BATKO 3.5d.txt
BATKO_Chow_5


title: AML Gab2 WT mouse 2


title: Brown adipose tissue, bBATKO HFD-14

description:
HFD BATKO 3.5d.txt
BATKO_HFD_14

value: HFD


title: 6867-NN-4

value: Left ventricle tissue

value: Female


title: AML Gab2 WT mouse 1


title: Brown adipose tissue, bBATKO HFD-15

description:
HFD BATKO 3.5d.txt
BATKO_HFD_15


title: 6867-NN-2


title: THP-1 macrophages IL-26-treated-rep 1

city: Shanghai

first: zhihua

last: Ran

address: 160 pujian road

department: Division of Gastroenterology and Hepatology

country: China

institute: Renji Hospital, School of Medicine, Shanghai Jiao Tong 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 (FPKM) 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.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Ensembl V101 GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: THP-1 macropahges

growth_protocol: THP-1 monocytes (ATCC, Manassas, VA, USA) were cultured in RPMI 1640 medium (Gibco, USA) containing 10% fetal bovine serum (FBS).

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: THP-1 derived macrophages were generated by incubating THP-1 cells with PMA (50 ng/ml) for 24h.Then THP-1 macrophages were treated with IL-26 (0.28 μM) for 24h

value: treated with IL-26 for 24h


title: THP-1 macrophages IL-26-treated-rep 3


title: THP-1 macrophages untreated-rep 3

value: untreated


title: GMP-21dL/14dR [ATAC-seq]

city: Philadelphia

first: George

last: Hajishengallis

state: PA

address: School of Dental Medicine

institute: University of Pennsylvania

library_source: genomic

data_processing:
Cell Ranger ATAC's pipelines was used to align reads, generate peak matrix with single-cell accessibility counts and fragment file with all unique fragments across all single cells, using ‘refdata-cellranger-atac-mm10-1.2.0’.
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: peak matrix with single-cell accessibility counts and fragment file

molecule: genomic DNA

growth_protocol: C57BL/6 mice were trained by subjecting them to LIP for 21 days followed by ligature removal (to enable inflammation resolution) for 14 days (‘21dL/14dR’ mice) or were not ligated during the entire period (‘NL’ controls). Hematopoietic progenitors (LSKs; Lin-cKit+Sca1+) and granulocyte-macrophage progenitors (GMP; Lin-cKit+Sca1-CD16/32+CD34+) in mice bone marrow were sorted by FACS for single cell ATAC-seq analysis of epigenomic profile.

extract_protocol:
LSK and GMP cells from the BM of LIP-subjected mice or unligated control mice were sorted by flow cytometry. Nuclei isolation for single-cell ATAC sequencing was performed according to the “Nuclei Isolation for Single Cell ATAC Sequencing demonstrated protocol” (10x Genomics).
Nuclei suspension was mixed with the tagmentation mix and incubated for 1 hr at 37°C. After mixing with a barcoding mix, the nuclei were loaded into a 10x chip H together with barcoded beads and partitioning oil (Chromium Next GEM Chip H Single Cell Kit v1.1, Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1, 10x Genomics) and encapsulated using the Chromium controller (10x Genomics). The Gel Bead-In EMulsions (GEMs) was transferred into a PCR tube and amplified for 12 cycles in a thermocycler. The barcoded DNA was purified and subjected to an index PCR for 11 cycles.

value: LIP for 21 days followed by ligature removal for 14 days

value: Mouse GMP cells


title: THP-1 macrophages untreated-rep 2


title: LSK-21dL/14dR [ATAC-seq]

value: Mouse LSK cells


title: THP-1 macrophages untreated-rep 1


title: GMP-NL [ATAC-seq]

value: not ligated


title: 6867-NN-1

value: Male


title: Brown adipose tissue, bCTRL Chow-4

description:
HFD BATKO 3.5d.txt
CTRL_Chow_4

value: Brown adipose tissue

value: 8-12 weeks

value: CTRL


title: 190628_CIRM_Mouse__liver_RNAseq_Hep_4F_Day2_2

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

description:
liver4F_RNA_exons.raw.xlsx
190628_CIRM_Mouse__liver_Hep_4F_Day2_2_T6__rna-seq_4000_pe_150_Paloma_S6_L002_R1_001

data_processing:
Sequenced reads were quality tested using FASTQC v0.11.2 using the default parameters.
RNA-Seq: Alignment to the hg19 genome (from illumina iGenome) was performed using the STAR aligner version 2.5.3a using the --outFilterIntronMotifs RemoveNoncanonical parameter. Gene expression was quantified using the HOMER analysis suite version 4.9.1, makeTagDirectory, analyzeRepeats.pl across exons of RefSeq genes.
ATAC-Seq: Adapter sequences were trimmed using TrimGalore v0.4.5 then aligned using bwa mem v0.7.12. Bam files were sorted, fixmated, marked duplicates, indexed, filtered low quality reads by samtools v1.9. For each sample, peaks were called by macs2 v2.1.2 by using command "callpeak --slocal 1000 --qvalue 0.05 -g mm -f BAMPE". The the called narrow peaks from each sample were merged to get a union peak file. Homer v4.9.1 was used to quantify the read counts in each of the union peak by commands makeTagDirectory and analyzeRepeats.
Single-Cell RNA-Seq: Reads were processed using 10X Genomics Cell Ranger pipeline v3.1.0 aligned to Cell Ranger mm10 v1.2.0 reference with default settings
Genome_build: mm10 (illumina iGenome) for RNA-Seq and ATAC-Seq, Cell Ranger mm10 v1.2.0 for Single-Cell RNA-Seq.
Supplementary_files_format_and_content: liver4F_RNA_exons.raw.xlsx contains the raw read count quantified for each gene for the RNA-Seq data. liver4F_ATAC_peakunion.raw.txt contains the raw read count quantified for each peak for the ATAC-Seq data. liver4F_SC_minusDox_filtered_feature_bc_matrix.h5 and liver4F_SC_plusDox_filtered_feature_bc_matrix.h5 are the two compressed filtered cell X gene count table generated for Single-Cell RNA-Seq.

molecule: polyA RNA

source_name: Hep-4F mouse liver tissue

extract_protocol:
RNA-Seq: Isolated livers were homogenized with a polytrone in Trizol immediately after collecting tissues. The extracted RNA was purified with RNeasy Mini Kit (QIAGEN) from the homogenates with DNaseI tretment (RNase-Free DNase Set, QIAGEN) to get rid of genomic DNA.
ATAC-Seq: Frozen liver samples were processed for ATAC-seq using the Omni-ATAC seq protocol [PMID: 28846090]. Briefly, around 20 mg of frozen tissue was used to isolate nuclei via Dounce homogenization followed by density gradient centrifugation. After isolation of nuclei, transposition mixture was added for transposition reaction.
SIngle-cell RNA-Seq: Liver cells were isolated after collagenase perfusion as described before [PMID: 29553556] to get single cell suspension. Briefly, hepatocytes and other cells were isolated separately with different gravity of centrifuge and both fractions were mixed at the same number of cells. Then, the mixture was subjected to scRNA-Seq using Next GEM Single Cell 3’ kit v3.1 (10x Genomics).
RNA-Seq: RNA quality was assessed and all samples had a minimum RNA integrity number (RIN) of 8.6. RNA library preps were prepared using the Illumina TruSeq Stranded Total RNA Sample Prep kit with Ribo-zero Gold (cat. no. RS-122-2301). ATAC-Seq: All ATAC-seq analysis was performed on two biological replicates. Frozen liver samples were processed for ATAC-seq using the omni-ATAC seq protocol (Corces et al, 2017, Nature Methods). Libraries were constructed using published Nextera PCR primers (Buenrostro et al 2013, Nature methods) and checked for quantity on a TapeStation 2200 (Agilent). Single-Cell RNA-Seq: Liver cells were isolated after collagenase perfusion as described before. Briefly, hepatocytes and other cells were isolated separately with different gravity of centrifuge and both fractions were mixed at the same number of cells. Then, these fractions were subjected to scRNA-Seq using Next GEM Single Cell 3’ kit v3.1.
ATAC-Seq: Libraries were constructed using published Nextera PCR primers [PMID: 24097267] followed by checking the quality on a TapeStation2200 (Agilent).
Single-Cell RNA-Seq: Libraries were prepared using Next GEM Single Cell 3’ kit v3.1 (10x Genomics).
stranded paired-end mRNA-seq; paired-end ATAC-Seq; 10X Genomics Chromium v3 3' Single-Cell RNA-Seq

treatment_protocol: Hep4F mice were treated with Dox in drinking water (0.1 mg/ml) and liver samples were collected at the indicated time-points. For carbon tetrachloride (CCl4) treatment, the mice were intraperitoneally injected with CCl4 (Sigma) (5 ul/g mouse of 10% CCl4 in corn oil) once and the livers were collected 3 days after the injection. For Single-Cell-RNA-Seq, Hep4F mice were treated with or without Dox (0.1 mg/ml) in drinking water for 1 day and then Dox water was replaced by normal water. Liver samples were collected 1 day after Dox withdrawal (1d-on_1d-off) and subjected to liver cell isolation.

value: 2 days

value: liver


title: Brown adipose tissue, bCTRL Chow-3

description:
HFD BATKO 3.5d.txt
CTRL_Chow_3

value: Chow


title: 190628_CIRM_Mouse__liver_RNAseq_Hep_4F_Day2_1

description:
liver4F_RNA_exons.raw.xlsx
190628_CIRM_Mouse__liver_Hep_4F_Day2_1_T5__rna-seq_4000_pe_150_Paloma_S5_L001_R1_001


title: Brown adipose tissue, bCTRL Chow-2

description:
HFD BATKO 3.5d.txt
CTRL_Chow_2


title: 229E | A549 + Cas13d+N20 2

city: Stanford

first: Augustine

last: Chemparathy

state: CA

address: 290 Jane Stanford Way

department: Bioengineering

institute: Stanford University

data_processing:
STAR 2.5.4b was used to generate a genome index with hg19 and GFP. Command: STAR --runMode genomeGenerate --runThreadN 10 --genomeDir {dirname_here} --genomeFastaFiles {fname_here} --sjdbGTFfile {fname_here} --sjdbOverhang 100
STAR 2.5.4b was used to align paired reads to the genome index. Command: STAR --genomeDir {dirname_here} --readFilesIn {fname_here} {fname_here} --runThreadN 10 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix {user_option}  --readFilesCommand gunzip -c
Htseq-count was used to calculate read counts. Command: htseq-count -i gene_id {bam_fname_here} {gtf_fname_here} -r pos -s no -f bam > {output_fname_here}
Fragments per kilobase transcript per million mapped reads (FPKM) were quantified by the following method: for each sample, for each gene HTseq-count values were divided by gene length in kilobases (quantified by GTFtools; Command: python2.7 GTFtools_0.6.9/gtftools.py -l {output_fname} {gtf_fname}) and divided the total sample count in millions.
Genome_build: hg19
Supplementary_files_format_and_content: TXT FPKM files are tab-delimited with gene in the first column and FPKM in the second
Supplementary_files_format_and_content: TXT non-FPKM files are tab-delimited with gene in the first column and read count in the second

source_name: human A549 lung carcinoma cells

growth_protocol: A549 cells were cultured in 10% fetal bovine serum (Thermo Fisher Scientific) in DMEM (Thermo Fisher Scientific) and were incubated at 37°C in a 5% CO2 atmosphere.

extract_protocol:
Total RNA was prepared from transfection experiments after 48 h using a Qiagen RNeasy Plus Mini kit. mRNA was then extracted using a NEBNext Poly(A) mRNA Magnetic Isolation Module and RNAseq libraries were prepared using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina sequencing. RNA-seq libraries were sequenced on an Illumina NextSeq instrument with at least 30 million reads per library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: we used a type LNP, termed a lipitoid, to transiently transfect human A549 lung carcinoma cells with the Cas13d mRNA and in vitro synthesized crRNA(s). At 48 hpi, we isolated cellular RNA and performed whole-cell RNA sequencing (RNA-seq).

value: lung carcinoma

tag: time point

value: 15 days after transfection


title: 190628_CIRM_Mouse__liver_RNAseq_Hep_4F_Day1_1

description:
liver4F_RNA_exons.raw.xlsx
190628_CIRM_Mouse__liver_Hep_4F_Day1_1_T3__rna-seq_4000_pe_150_Paloma_S3_L001_R1_001

value: 1 day


title: CT(S+/-) [CT-8]

city: Lexington

first: Erhard

last: Bieberich

state: KY

address: 800 Rose Str

department: Physiology

institute: University of Kentucky

data_processing:
Illumina RTA3
Sequence reads were trimmed of adaptor sequences, and mapped to the mm10 genome build using STAR.
FeatureCounts was used to generate the reads per gene, and these were normalized as FPKM (Reads per Kilobase of transcript per Million mapped reads)
DESeq2 was used to identify differentially abundant transcripts, with criterion being adjusted (Benjamini-Hochberg) p<0.05
Genome_build: mm10
Supplementary_files_format_and_content: Results of DESeq2 analysis for all transcripts

source_name: Cortex

extract_protocol:
RNA was extracted from the fresh brain cortex using the miniRNeasy extraction kit (Qiagen,#74134).
A total amount of 0.4 ug of RNA was used for cDNA library construction at Novogene using an NEBNext® Ultra 2 RNA Library Prep Kit for Illumina® (cat NEB #E7775, New England Biolabs, Ipswich, MA, USA) according to the manufacturer’s protocol.

value: Mixed background (C3H and C57BL/6)

value: Cortex

value: 10 months old

value: heterozygous (fro/+)


title: 190628_CIRM_Mouse__liver_RNAseq_Hep_4F_Day1_2

description:
liver4F_RNA_exons.raw.xlsx
190628_CIRM_Mouse__liver_Hep_4F_Day1_2_T4__rna-seq_4000_pe_150_Paloma_S4_L001_R1_001


title: Brown adipose tissue, bBATKO HFD-12

description:
HFD BATKO 3.5d.txt
BATKO_HFD_12

value: BATKO

value: HFD


title: 190628_CIRM_Mouse__liver_RNAseq_Hep_4F_Day0_2

description:
liver4F_RNA_exons.raw.xlsx
190628_CIRM_Mouse__liver_Hep_4F_Day0_2_T2__rna-seq_4000_pe_150_Paloma_S2_L001_R1_001

value: 0 day


title: Brown adipose tissue, bCTRL Chow-1

description:
HFD BATKO 3.5d.txt
CTRL_Chow_1

value: Male


title: CT(S-/-) [CT-7]

value: homozygous (fro/fro)


title: THP-1 macrophages IL-26-treated-rep 2

value: treated with IL-26 for 24h


title: 229E | A549 + Cas13d+N20 1

value: 14 days after transfection


title: 190628_CIRM_Mouse__liver_RNAseq_Hep_4F_Day0_1

description:
liver4F_RNA_exons.raw.xlsx
190628_CIRM_Mouse__liver_Hep_4F_Day0_1_T1__rna-seq_4000_pe_150_Paloma_S1_L001_R1_001


title: 229E | A549 + Cas13d+R19 2

value: 13 days after transfection


title: CT(S-/-) [CT-6]


title: LSK-NL [ATAC-seq]

value: not ligated

value: Mouse LSK cells


title: Brown adipose tissue, bCTRL HFD-11

description:
HFD BATKO 3.5d.txt
CTRL_HFD_11

value: Brown adipose tissue

value: 8-12 weeks

value: CTRL


title: 229E | A549 + Cas13d+R19 1

value: lung carcinoma

value: 12 days after transfection


title: Brown adipose tissue, bCTRL HFD-10

description:
HFD BATKO 3.5d.txt
CTRL_HFD_10


title: SARS-CoV-2 | A549 + Cas13d+SN1+SN4 2

value: 11 days after transfection


title: SARS-CoV-2 | A549 + Cas13d+SN1+SN4 1

value: 10 days after transfection


title: 190628_CIRM_Mouse__liver_RNAseq_Hep_4F_1d_on_2d0ff_1

description:
liver4F_RNA_exons.raw.xlsx
190628_CIRM_Mouse__liver_Hep_4F_1d_on_2d0ff_1_T9__rna-seq_4000_pe_150_Paloma_S9_L002_R1_001

value: 1 day on 2 days off

value: liver


title: 190628_CIRM_Mouse__liver_RNAseq_Hep_4F_1d_on_2d0ff_2

description:
liver4F_RNA_exons.raw.xlsx
190628_CIRM_Mouse__liver_Hep_4F_1d_on_2d0ff_2_T10__rna-seq_4000_pe_150_Paloma_S10_L002_R1_001


title: Female KO4

city: Los Angeles

first: Karen

last: Reue

address: 695 Charles E Young Dr South

institute: University of California, Los Angeles

data_processing:
Reads were aligned using STAR 2.6.1 to the mouse genome mm10
The read-count per gene was quantified with featureCounts and mm10 GTF file
Differential gene expression analysis was performed with EdgeR 3.26.8 and limma 3.40.6 with trimmed mean of M values (TMM) normalization.
Genome_build: mm10
Supplementary_files_format_and_content: raw count and cpm

source_name: Primary proximal tubule cells

extract_protocol:
Primary proximal tubule cells from 3-4 mice were pooled and separated into 4 technical replicates. RNA was isolated with Trizol, and then cleaned using Qiagen RNeasy kit
Strand-specific RNA-seq libraries were constructed with the Universal plus mRNA-Seq Kit (NuGEN Technologies).

value: Diet1 KO

value: kidney

value: primary proximal tubule cell

value: Female


title: Female KO3


title: 190628_CIRM_Mouse__liver_RNAseq_Hep_4F_1d_on_1d0ff_2

description:
liver4F_RNA_exons.raw.xlsx
190628_CIRM_Mouse__liver_Hep_4F_1d_on_1d0ff_2_T8__rna-seq_4000_pe_150_Paloma_S8_L002_R1_001

value: 1 day on 1 day off


title: 190628_CIRM_Mouse__liver_RNAseq_Hep_4F_1d_on_1d0ff_1

description:
liver4F_RNA_exons.raw.xlsx
190628_CIRM_Mouse__liver_Hep_4F_1d_on_1d0ff_1_T7__rna-seq_4000_pe_150_Paloma_S7_L002_R1_001


title: Brown adipose tissue, bCTRL HFD-9

description:
HFD BATKO 3.5d.txt
CTRL_HFD_9

value: Male

value: HFD


title: SARS-CoV-2 | A549 + Cas13d+SN4 2

value: 9 days after transfection


title: Female KO2


title: 190628_CIRM_Mouse__liver_RNAseq_Control_2

description:
liver4F_RNA_exons.raw.xlsx
190628_CIRM_Mouse__liver_Control_2_T12__rna-seq_4000_pe_150_Paloma_S12_L003_R1_001

value: 3 days


title: SARS-CoV-2 | A549 + Cas13d+SN4 1

value: 8 days after transfection


title: 190628_CIRM_Mouse__liver_RNAseq_Control_1

description:
liver4F_RNA_exons.raw.xlsx
190628_CIRM_Mouse__liver_Control_1_T11__rna-seq_4000_pe_150_Paloma_S11_L003_R1_001


title: Female KO1


title: Brown adipose tissue, aBATKO 30°C-16

description:
BATKO 4C 24h.txt
BATKO30-16

value: Brown adipose tissue

value: 8-12 weeks

value: BATKO


title: Brown adipose tissue, aBATKO 30°C-15

description:
BATKO 4C 24h.txt
BATKO30-15


title: Female WT4

value: WT


title: SARS-CoV-2 | A549 + Cas13d+SN1 2

value: lung carcinoma

value: 7 days after transfection


title: CT(S+/-) [CT-5]

value: Mixed background (C3H and C57BL/6)

value: Cortex

value: 10 months old

value: heterozygous (fro/+)


title: 190628_CIRM_Mouse__liver_RNAseq_CCl4_3

description:
liver4F_RNA_exons.raw.xlsx
190628_CIRM_Mouse__liver_CCl4_3_T15__rna-seq_4000_pe_150_Paloma_S15_L003_R1_001

value: liver


title: Brown adipose tissue, bCTRL HFD-7

description:
HFD BATKO 3.5d.txt
CTRL_HFD_7

value: CTRL


title: Female WT3

value: kidney

value: primary proximal tubule cell

value: Female


title: 190628_CIRM_Mouse__liver_RNAseq_CCl4_2

description:
liver4F_RNA_exons.raw.xlsx
190628_CIRM_Mouse__liver_CCl4_2_T14__rna-seq_4000_pe_150_Paloma_S14_L003_R1_001

value: 3 days


title: Brown adipose tissue, aBATKO 30°C-14

description:
BATKO 4C 24h.txt
BATKO30-14

value: Male


title: Female WT2


title: Brown adipose tissue, aBATKO 30°C-13

description:
BATKO 4C 24h.txt
BATKO30-13

value: Brown adipose tissue


title: A549 + Cas13d+NT5 2

value: 5 days after transfection


title: Brown adipose tissue, aBATKO 30°C-17

description:
BATKO 4C 24h.txt
BATKO30-17

value: 8-12 weeks

value: BATKO


title: A549 + Cas13d+NT5 1

value: lung carcinoma

value: 4 days after transfection


title: Female WT1

value: WT


title: Male KO3

value: Diet1 KO


title: Plasma cfDNA BC11

city: Ein Kerem

first: Benjamin

middle: P

last: Berman

address: Hadassah University Medical Center, Bldg 3 rm 30

country: Israel

institute: Hebrew University of Jerusalem

description: circulating DNA

data_processing:
Base calling and alignment: Fast5 files were taken from previous publication (EGAD00001006888), which were generated using real-time high-accuracy basecalling during GridION run. Fast5 files were demultiplexed with guppy_barcoder (Version 5.0.16+b9fcd7b5b) using “--trim_barcodes --barcode_kits EXP-NBD104”. Individual barcode Fast5 files were processed into fastq and bam files using Megalodon v. 2.4.2 with the following command-line parameters “--edge-buffer 0 --mod-min-prob 0 --guppy-params ‘-d /usr/local/hurcs/guppy/6.0.1/data --barcode_kits EXP-NBD104 --trim_barcodes’ --remora-modified-bases dna_r9.4.1_e8 hac 0.0.0 5mc CG 0 --guppy-config dna_r9.4.1_450bps_hac.cfg”. Internally, Megalodon used Guppy server version 6.0.1+652ffd1, and basecalling model r9.4.1_450bps_hac. By default, Megalodon filters out multi-mapping (supplementary) reads and uses the minimap2 “map-ont” mode to filter low quality mappings.
Anonymized BAM files: Individual tile Fast5 files were run individually, and mod_mapping.bam files were merged using samtools merge (v1.14). Samtools/HTSlib versions before v.1.14 do not handle the Mm/Ml modification tages. Because Megalodon reports only the reference sequence in the BAM records, and does not report any base substitutions, these are anonymous BAM files which do not contain any SNP information, and thus contain no personally identifiable information. These are the primary files used for both fragmentomic and methylation analysis. These are the "meg242.remora1.edgefix.mod_mappings.sorted.hg38.bam" files deposited here.
Megalodon methyl bed file extraction: To extract (stranded) methylation information from the mod_mapping.bam files, we used modbam2bed (https://github.com/epi2me-labs/modbam2bed) v.0.4.5, specifying a minimum probability threshold of 0.667, and filtering out positions with 0 confident reads using awk. The full command line was “modbam2bed --cpg -t 4 -a 0.333 -b 0.667 | awk ‘($5>0){print} > out.bed”. All coordinates are in GRCh38 and are 0-based. These files are named “*.meg242.remora1.edgefix.modbam2bed.5mC.cut0.667.hg38.bed”. Column 11 corresponds to the percent of reads methylated. Modbam2bed does not provide a column for the actual number of reads that this percentage is based on, but it can be calculated from the other columns. readCount=(col5*col10)/1000. We also processed this into a simple bedgrpah with just the methylation fraction (beta) values in files named "meg242.remora1.edgefix.modbam2bed.5mC.cut0.667.hg38.sorted.bedgraph". These can be loaded into any genome browser.
DeepSignal methylation calling and processing.  Raw Fast5 files were processed with DeepSignal Version 0.1.8 (4), with model “model.CpG.R9.4_1D.human_hx1.bn17.sn360.v0.1.7+/bn_17.sn_360.epoch_9.ckpt”, which was downloaded from the DeepSignal Google Drive (https://drive.google.com/open?id=1zkK8Q1gyfviWWnXUBMcIwEDw3SocJg7P). We used the DeepSignal call_mods (modification_call) output tsv file, extracting the (strand-specific) methylation calls for each CpG from column 9 (called_label field), and calculated a methylation beta value by taking the number of methylated reads (value 1) divided by the total number of reads (value 0 or value 1). These were collapsed into a bedgraph file with a value between 0-1 for every CpG covered. These are the "sorted.grouped.0based.bedgraph.gz" deposited here.
Assembly: GRCh38
Library strategy: WGS

source_name: Plasma

extract_protocol:
Blood collected in EDTA tubes, centrifuged 1500g for 10 minutes. cfDNA extracted from 4mL of plasma using QIAamp Circulating Nucleic Acid Kit (QIAGEN, 55114), and stored at -80C before library construction.
Oxford Nanopore SQK-LSK109 (all samples except for 19_326 also used the multiplex protocol NBD-EXP104)

value: Lung adenocarcinoma


title: Brown adipose tissue, aBATKO 4°C-12

description:
BATKO 4C 24h.txt
BATKO4-12


title: A549 + Cas13d only 2

value: 3 days after transfection


title: Brown adipose tissue, aBATKO 4°C-8

description:
BATKO 4C 24h.txt
BATKO4-8


title: Plasma cfDNA BC10

description: circulating DNA


title: A549 + Cas13d only 1

value: 2 days after transfection


title: Brown adipose tissue, aBATKO 4°C-11

description:
BATKO 4C 24h.txt
BATKO4-11


title: 190628_CIRM_Mouse__liver_RNAseq_CCl4_1

description:
liver4F_RNA_exons.raw.xlsx
190628_CIRM_Mouse__liver_CCl4_1_T13__rna-seq_4000_pe_150_Paloma_S13_L003_R1_001

value: liver


title: UNSTIM_C

first: Michelle

last: Yen

address: 279 Campus Dr. West, Beckman Center, room B-173

department: Molecular and Cellular Physiology

data_processing:
reads were mapped to reference using STAR v2.5, mismatch = 2
quantification was performed with HTseq v0.6.1, -m union
differentially expressed genes were identified using DESeq2, v2_1.6.3, with padj < 0.05
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: CSV format with two columns: ensembl gene ID and counts normalized by DESeq2

source_name: CD8+ T cells

growth_protocol: Human T cells (from PBMCs) were pre-activated with plate-bound anti-CD3 and soluble anti-CD28 for 4d, washed, then rested overnight without stimulation.

extract_protocol:
Total RNA from 1-2 million cells per condition was extracted using an RNeasy micro kit (Qiagen)
0.2 μg input RNA was used for each sample, and libraries were constructed using the NEBnext Ultra II RNA Library Prep Kit for Illumina using mRNA enrichment

treatment_protocol: Pre-activated, rested CD8+ T cells were isolated via MACS, then stimulated with 100nM cytokine/surrogate ligand or left unstimulated for 24hr. at 37C.

value: UNSTIM

value: CD8+ T cells from PBMC

tag: donor

value: C


title: Brown adipose tissue, aBATKO 4°C-7

description:
BATKO 4C 24h.txt
BATKO4-7


title: Male KO1

value: kidney

value: primary proximal tubule cell


title: Male KO2

value: Male


title: SARS-CoV-2 | A549 + Cas13d+SN1 1

value: 6 days after transfection


title: UNSTIM_B

value: B


title: Brown adipose tissue, aCTRL 30°C-22

description:
BATKO 4C 24h.txt
CTRL30-22

value: Brown adipose tissue

value: 8-12 weeks

value: CTRL


title: Male WT4

value: WT


title: Male WT3


title: Plasma cfDNA BC08

description: circulating DNA


title: Plasma cfDNA BC05

description: circulating DNA

value: Healthy control


title: Brown adipose tissue, aCTRL 30°C-21

description:
BATKO 4C 24h.txt
CTRL30-21


title: UNSTIM_A

value: A


title: Plasma cfDNA BC04

description: circulating DNA


title: MY193R_C


title: Brown adipose tissue, aCTRL 30°C-20

description:
BATKO 4C 24h.txt
CTRL30-20


title: Male WT2


title: Plasma cfDNA BC03

description: circulating DNA


title: Brown adipose tissue, aCTRL 4°C-2

description:
BATKO 4C 24h.txt
CTRL4-2


title: MY193R_B


title: Male WT1


title: Plasma cfDNA BC01

description: circulating DNA

value: Lung adenocarcinoma


title: MY193R_A


title: Brown adipose tissue, aCTRL 30°C-19

description:
BATKO 4C 24h.txt
CTRL30-19


title: Brown adipose tissue, aCTRL 4°C-5

description:
BATKO 4C 24h.txt
CTRL4-5


title: Plasma cfDNA BC09

description: circulating DNA


title: MY190R_B


title: Brown adipose tissue, aCTRL 4°C-1

description:
BATKO 4C 24h.txt
CTRL4-1


title: MY190R_A


title: Plasma cfDNA S1 (19_326)

description: circulating DNA


title: AOM/DSS-5FU/I-d3

first: Ken

last: Lau

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

description:
single index
282_d3

data_processing:
After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using DROPEST pipeline (https://github.com/hms-dbmi/dropEst). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods
Barcodes were filtered (Chen et al., 2021), resulting in the processed data table.
MGI-Seq: Biological read: read1 - 3' end.  Technical read: read2 -UMI/cell barcode - the oligo barcodes are inDrop which is positioned exactly as in (Klein et al., 2015)
NovaSeq:Technical read: read1 - UMI/cell barcode - the oligo barcodes are TruDrop which is positioned exactly as in (Southard-Smith et al., 2020). Biological read: read2 - 3' end
Assembly: Mouse: GRCm38.85
Supplementary files format and content: Delimited tables, with cells and genes, as columns and rows, filtered

source_name: colon

growth_protocol: primary cells

extract_protocol:
Mouse pithelial cell suspensions were generated accroding to protocol in (Vega et al., 2022). Cells were encapsulated using the inDrop platform (1CellBio), and RNA was extracted according to the protocol of Klein et al., 2015. Chen et al., 2021.
CEL-Seq linear amplification of using standard structure (single index) (Klein et al., 2015) or TruDrop library structure (dual index) (Southard-Smith et al., 2020)
RNA-Seq was performed on Novaseq6000 with a 2 x 150 paired-end kit standard run (for dual index)
RNA-Seq was performed on BGI MGI-Seq (for single index) 100 read 1, 50 read2

tag: prep

value: inDrop scRNA-seq

value: AOM/DSS tumors - normal dissociation


title: Ppz1-overexpressing at 2% Galactose

city: CERDANYOLA DEL VALLES

first: JOAQUIN

last: ARINO

state: Barcelona

address: ED. IBB

department: Biochemistry & Mol. Biol.

country: Spain

institute: UNIVERSITAT AUTONOMA BARCELONA

data_processing:
Sequencing in a MiSeq apparatus, application RNA-Seq, GenerateFASTQ workflow, 120 bases single end, 94.5% reads > Q30
mapping with Bowtie2  V.:2.1.0 on S. cerevisiae EF4 assembly. Mapping % 96,75 +/- 1.25)
Quantified with SeqMonk v0.32.1
Feature generator using CDS. Duplicates removed. Over feature from 50-50. Quantitated with Read Count. Quantitation using Opposite Strand to Probe, correcting for total count only in probes to largest store
data imported into Excel
Assembly: S. cerevisiae EF4 assembly
Supplementary files format and content: AnnotProbeReport_GEO.xlsx, excel file containing the output of the SeqMonk analysis (Annotate Probe Report)

organism: Saccharomyces cerevisiae

source_name: whole cell

growth_protocol: Yeast cell cultures were normally grown in SC medium minus uracil, to maintain the plasmid, and in the presence of 100 μg/ml of doxycycline, to avoid overexpression of the PPZ1 cloned in the pCM190 plasmid.

extract_protocol:
Total RNA purification was performed by using the Ambion RiboPure™-Yeast Total RNA Isolation Kit.
TruSeq LT (Illumina)

treatment_protocol: Cells containing either the empty pCM190 or the pCM190-PPZ1 plasmid grown o/n in SC-uracil medium in the presence of 100 μg/ml of doxycycline, were washed twice with SC-Ura medium to completely remove doxycycline, and resuspended in 200 ml of the same medium (in the absence of doxycycline) to reach OD600=0.2. Cultures were grown for 3.5h, reaching OD600=0.55.  At this point 50 ml of each culture were rapiddly filtrated, cells washed with SC-Ura without glucose and resuspended in 50 ml of fresh SC-Ura medium containing either, 2% glucose, 0.25% glucose or 2% galactose.    After 1h of growth cells from 20 ml of each culture were collected by centrifugation at 4⁰C, washed with cold water and kept at -80⁰C up to RNA purification.

tag: transformed

value: pCM190 vector bearing PPZ1 ORF

value: 2% Galactose


title: Ppz1-overexpressing at 0.25 % glucose

value: 0.25 % glucose


title: control at 2% Galactose

value: empty pCM190 vector


title: MY188R_C

value: CD8+ T cells from PBMC

value: C


title: Ppz1-overexpressing at 2% glucose

value: 2% glucose


title: AOM/DSS-5FU/I-d1_1

description:
single index
281_d1_1


title: control at 0.25 % glucose


title: Brown adipocytes, Input-Tra

first: Yanis

last: ZEKRI

address: 32-34 Avenue Tony Garnier

description: ChIP TRa+TH  Paired-end (narrow_Peaks).bed

data_processing:
Reads were mapped on mouse mm10 genome using Bowtie Galaxy version 2.3.2.2 with default parameters
Peaks were called using MACS2 Callpeak version 2.1.1.20160309.6 using input files as control files. Peaks with a score inferior at 60 were filetered out
De novo motif search was performed using Cistrome SeqPos motif tool (version 1.0.0). Genes within 30kb of peaks were chosen using GREAT (great stanford)
Distance distribution of binding sites around transcription starting sites and functional distribution of binding sites in the genome were assessed using PAVIS (manticore)
Assembly: mm10
Supplementary files format and content: Narrow peaks table of TRa1 ChIP (which was made using the input files as a control files. Thus, this table is relative to the input files)

source_name: Brown adipose tissue

growth_protocol: Adult male mice expressing a GS-tagged version of TRa1 specifically in brown adipocytes. Animals were made hypothyroid using propylthiouracil containing food during two weeks and were injected with thyroid hormones during 24h. After this treatment, brown adipose tissue was collected

extract_protocol:
Freshly dissected small pieces of brown adipose tissue were crosslinked during 25min at room temperature under agitation in the crosslink solution (250mM disuccinimidyl glutarate, 50mM HEPES, 100mM NaCl, 1mM EDTA, 0.5mM EGTA). Then, 1% formaldehyde was added for 20 further minutes followed by 50mM glycine addition. The tissue was rinsed several times with PBS. Chromatin immunoprecipitation was then performed as previously described (Chatonnet et al., 2013).
Sequencing libraries were prepared from the immunoprecipitated fraction and the input fraction as control, using the Accel-NGS 2S Plus DNA library kits with single indexing (Swift Biosciences).

value: Male

value: TRa1 GS-tagged

value: Thyroid hormone

tag: chip antibody


title: control at 2% glucose


title: Brown adipocytes, ChIP-Tra

value: Brown adipose tissue

tag: age

value: 8-12 weeks

value: antibody to immunoprecipitate Tra


title: MY188R_B

value: B


title: Plasma cfDNA BC02

description: circulating DNA

value: Healthy control


title: MY188R_A

value: A


title: MY190R_C


title: 5XFAD 9 month old retina (pooled from 5-6 mice), treated with efavirenz 2

first: David

last: Buchner

address: 10900 Euclid Ave

department: Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
Reads were mapped to the mm10 version of the mouse genome using HISAT2 (v2.0.4)
After novel transcript detection, we merge novel coding transcripts with reference transcripts to get complete reference, then we map clean reads to it using Bowtie2(v2.2.5), then calculate gene expression level for each sample with RSEM (v1.2.12)
Assembly: mm10
Supplementary files format and content: tab-delimited .txt file of FKPMs

source_name: Retina

extract_protocol:
Trizol
Library construction was performed by BGI. The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process.

treatment_protocol: Efavirenz treatment (0.08 mg/kg body weight) in drinking water, starting at 3 months of age until 9 months of age

value: Retina

value: mouse model of Alzheimer's disease

value: efavirenz


title: 5XFAD 9 month old retina (pooled from 5-6 mice), treated with efavirenz 3


title: 5XFAD 9 month old retina (pooled from 5-6 mice), treated with efavirenz 1


title: Normal_thyroid_from_patient_I12

type: RNA

city: Milan

first: Emanuela

last: Minna

state: Select...

address: via Amadeo 42

country: Italy

institute: Istituto Nazionale dei Tumori

description:
This sample was not analyzed in GSE97070
9534190022_F

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol using a iScan microarray reader (Illumina)

data_processing:
Raw data were log2 transformed and normalized with robust spline normalization using the lumi package from Bioconductor.
The processed data file includes log2-normalized intensities
The file Normalized_data_matrix_gene_symbols.xlsx provides the key for  gene symbols used in the normalized data matrix, non-normalized data matrix and associated Entrez_Gene_ID.

source_name: Non-neoplastic thyroid

label_protocol: According to Illumina whole genome DASL assay

extract_protocol: Total RNA was extracted from the FFPE sections by miRNeasy FFPE kit (Qiagen) and RNA quality was assessed  by 2100 Bioanalyzer (Agilent Technologies).

value: thyroid

value: normal

tag: sampleID


title: 5XFAD 9 month old retina (pooled from 5-6 mice), untreated 2

value: control


title: MY189F_B

tag: cell type

value: CD8+ T cells from PBMC


title: WT_Male_Uninfected

city: Livermore

first: Stephen

middle: Patrick

last: Wilson

address: 7000 East Ave

department: BBTD

institute: LLNL

data_processing:
Cellranger mkfastq to generate FASTQ
Cellranger count to generate count matrix
Assembly: mm10
Supplementary files format and content: gene list (features.tsv) and cell barcodes (barcodes.tsv) as well as gene/barcode matrices (matrix.mtx) are provided for each experimental group.

source_name: Immune cells from the knee joints

extract_protocol:
Single-cell preparation of brain-derived cells were obtained from freshly dissected brain cells from infected and uninfected mice. Brain cortices were dissected in cold Hibernate A medium (BrainBits LLC) and sliced to approximately 0.5 mm before transferred to a 15 mL falcon tube with Hibernate A and B27 medium (HABG) (Thermo Fischer Scientific). Collected tissue samples in 15 mL conical tubes were warmed up to 30°C in a shaking water bath for 8 minutes, before the HABG supernatant replaced with activated papain (34 U/mL, Worthington Biochemical Corporation) and the tubes placed back into the shaking water bath for tissue digestion (30°C, 150 rpm) for 30 minutes. Cells were released from the digested tissues by trituration using a fire-polished Pasteur pipette. Released cells were collected in the supernatant and filtered through a 70 mm MACS Smart Strainer (Miltenyi Biotec) into a new 15 mL conical tube. The single cell suspension was layered onto a Optiprep density gradient to separate cells from debris, after centrifugation (800 x g, 15 min, 22°C). The debris fraction was collected, and the gradient material diluted with HAGB before tubes were centrifuged (200 x g, 5 min, 22°C). The supernatant was aspirated, and ACK lysis buffer (Thermo Fisher Scientific) was added to the cell suspension remove any remaining red blood cells (5 min, RT). Hank’s balanced salt solution (Thermo Fisher) was added to the cell suspension containing the lysis buffer and tubes were centrifuged (200 x g, 5 min, 22°C). To remove dead cells from the single cell suspension, a Dead cell removal kit (Miltenyi Biotec) was used as directed by the vendor.
Cells were resuspended in PBS with 0.04% non-acetylated BSA prior to the single-cell sequencing step using Chromium Single-cell 3ʹ GEM, Library & Gel Bead Kit v3 (10× Genomics) on a 10x Genomics Chromium Controller following manufacturers protocol. Single-cell library preparation was performed using Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v3 (10x Genomics, Pleasanton, CA, USA; Catalog no. 1000075) following the manufacturer’s protocol.

treatment_protocol: Route of infection: C57BL/6J as well as mice genetically deficient in MAVS (B6;129-Mavstm1Zjc/J; Jax stock No: 008634) were obtained from Jackson Laboratory. Mavs-/- animals were crossed to WT C57BL/6 mice to generate a heterozygous F1 generation. F1 littermates were crossed to generate homozygous WT and KO F2 progeny. Matched WT and KO animals from the same generation were were inoculated intranasally with 5x105 PFU RVFV MP-12.

tag: infection status

value: uninfected brain

value: whole brain


title: WT_Female_Infected

source_name: brain cells from infected wild type female mouse

value: infected brain


title: KO_Female_Infected

source_name: brain cells from infected Mavs-/- female mouse


title: KO_Male_Uninfected

source_name: brain cells from uninfected Mavs-/- male mouse


title: WT_Male_Infected

source_name: brain cells from infected wild type male mouse


title: 5XFAD 9 month old retina (pooled from 5-6 mice), untreated 3

tag: tissue


title: MY189F_A


title: Normal_thyroid_from_patient_I9

description:
This sample used the same tissue analyzed in:
GSM2550972
9534190022_C


title: MY179F_C

value: C


title: 5XFAD 9 month old retina (pooled from 5-6 mice), untreated 1


title: Thyroid_primary_tumor_from_patient_I8

description:
This sample used the same tissue analyzed in:
GSM2550982
9534190047_J

source_name: MTC

value: medullary thyroid cancer (MTC)

value: P 8


title: Thyroid_primary_tumor_from_patient_I6

description:
This sample used the same tissue analyzed in:
GSM2550980
9534190047_D

value: P 6


title: RNA-seq 240 h (kd) rep 3

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

data_processing:
mRNA-Seq reads were aligned to the mouse reference sequence mm10 (NCBI GRCm38.p6) using STAR version 2.7.0c.
Differential gene expression was calculated using DESeq2 version 1.30.0. Normalised fragments per kilobase per million (FPKM) were calculated using R version 4.0.3.
Differential gene lists were filtered with R to only include genes with an adjusted p-value < 0.05 and an absolute log fold change > 0.58.
Genome_build: mm10
Supplementary_files_format_and_content: bed files include FPKM values per gene for each sample

source_name: Embryonic Stem Cells

growth_protocol: mESC were cultured on gelatine-coated plates and re-plated every other day. DMEM Glutamax-based medium was supplemented with 10% FBS superior, 1% MEM non-essential amino acids, 1% beta-Mercaptoethanol and 5µg LIF (per 500ml medium).

extract_protocol:
For RNA-seq, cells were cultured and treated as described above. For RNA isolation, the RNeasy Mini Kit was used according to the manufacturer’s instructions. Quality and quantity of isolated RNA were evaluated using the NanoDrop 2000.
Libraries were prepared and sequenced (~20M single reads per sample) using the Next-Seq 500 sequencing platform (high-output Kit, 75 Cycles v2 Chemie) at the Genomics Core Facility (University Hospital Münster, Münster).

treatment_protocol: Smarcb1 kd cells were treated with 1µg doxycycline per ml medium every day. RNA-seq experiments were performed 48 h, 72 h and 240 h after knockdown induction

value: mESC with conditional Smarcb1 knockdown

value: treated with doxycycline

tag: smarcb1 expression

value: knockdown

value: 81K1 (based on OG2)


title: MY179F_B

tag: treatment

value: B


title: MY189F_C


title: RNA-seq 240 h (kd) rep 2

tag: cell line


title: MY179F_A

value: A


title: KO_Male_Infected

source_name: brain cells from infected Mavs-/- male mouse


title: Normal_thyroid_from_patient_I11

description:
This sample used the same tissue analyzed in:
GSM2550974
9534190047_I

value: thyroid


title: MY173R_C


title: Thyroid_primary_tumor_from_patient_I5

description:
This sample used the same tissue analyzed in:
GSM2550979
9534190047_A

value: P 5


title: RNA-seq 240 h (kd) rep 1


title: Thyroid_primary_tumor_from_patient_I4

description:
This sample used the same tissue analyzed in:
GSM2550978
9534190022_J

value: P 4


title: Thyroid_primary_tumor_from_patient_I3

description:
This sample used the same tissue analyzed in:
GSM2550977
9534190022_G

value: P 3


title: RNA-seq 240 h (ctrl) rep 3

value: untreated

value: unchanged


title: MY173R_B

value: CD8+ T cells from PBMC


title: Thyroid_primary_tumor_from_patient_I2

description:
This sample used the same tissue analyzed in:
GSM2550976
9534190022_D

value: P 2


title: RNA-seq 240 h (ctrl) rep 1


title: Thyroid_primary_tumor_from_patient_I1

description:
This sample used the same tissue analyzed in:
GSM2550975
9534190022_A

value: medullary thyroid cancer (MTC)

value: P 1


title: RNA-seq 240 h (ctrl) rep 2


title: Thyroid_primary_tumor_from_patient_I7

description:
This sample used the same tissue analyzed in:
GSM2550981
9534190047_G

value: P 7


title: MY141F_C

value: C


title: MY141F_B


title: Thyroid_lymph_node_metastasis_from_patient_I8

description:
This sample used the same tissue analyzed in:
GSM2550971
9534190047_L

value: M 8


title: Thyroid_lymph_node_metastasis_from_patient_I7

description:
This sample used the same tissue analyzed in:
GSM2550970
9534190047_K

value: M 7


title: RNA-seq 72 h (kd) rep 2

value: mESC with conditional Smarcb1 knockdown

value: treated with doxycycline

value: knockdown

value: 81K1 (based on OG2)


title: MY172F_C


title: MY141F_A

value: A


title: RNA-seq 48 h (ctrl) rep 3


title: MY173R_A


title: MY172F_B

value: B


title: Thyroid_lymph_node_metastasis_from_patient_I6

description:
This sample used the same tissue analyzed in:
GSM2550969
9534190047_H

value: thyroid

value: M 6


title: IDMF_3

city: Ann Arbor

first: William

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

description: Gene expression data from IDMF-treated astrocyte cultures

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol.

scan_protocol: The standard Affymetrix protocol was following using the GeneChip™ Scanner.

data_processing: Robust multichip average (RMA) was used to generate expression intensity estimates (R package: oligo; function: rma).

label: biotin

source_name: Fetal astrocytes

label_protocol: Biotinylated cDNA was prepared following the standard Affymetrix protocol using the GeneChip WT labeling kit.

growth_protocol: Experiments were performed using human fetal astrocytes derived from cerebral cortex (cat. no. 882A-05f; Cell Applications, San Diego, CA). Cells were grown to sub-confluence in human astrocyte growth medium (cat. no. 820-500, Cell Applications).

extract_protocol: RNA was extracted following the incubation period using the RNAeasy Mini Plus kit (Qiagen, Hilden, Germany) and robotic Qiacube Connect station (Qiagen).

treatment_protocol: Stock solutions of MMF, DRF and IDMF were prepared in DMSO (50 mM) and subse-quent dilutions were made using distilled water. The experiment was performed using 12 replicate cultures, each of which was assigned to one of 4 experimental treatments (CTL, n = 3; MMF, n = 3, DRF, n = 3; IDMF, n = 3). CTL cells were treated with sterile distilled water. Test materials were added to subconfluent cultures at a concentration of 2.5 µM and cells were incubated for 24 hours.

value: IDMF

tag: replicate

value: replicate 3


title: MMF_2

description: Gene expression data from MMF-treated astrocyte cultures

value: MMF

value: replicate 2


title: DRF_1

description: Gene expression data from DRF-treated astrocyte cultures

value: DRF

value: replicate 1


title: MY172F_A

value: CD8+ T cells from PBMC


title: MMF_1


title: Thyroid_lymph_node_metastasis_from_patient_I5

description:
This sample used the same tissue analyzed in:
GSM2550968
9534190047_E

value: medullary thyroid cancer (MTC)

value: M 5


title: RNA-seq 72 h (kd) rep 3

value: mESC with conditional Smarcb1 knockdown


title: DRF_2


title: MMF_3


title: DRF_3


title: IDMF_2


title: IDMF_1


title: CTL_3

description: Gene expression data from CTL-treated astrocyte cultures

value: CTL


title: RNA-seq 48 h (ctrl) rep 2

value: untreated

value: unchanged


title: Thyroid_lymph_node_metastasis_from_patient_I4

description:
This sample used the same tissue analyzed in:
GSM2550967
9534190047_B

value: M 4


title: RNA-seq 72 h (kd) rep 1

value: treated with doxycycline

value: knockdown

value: 81K1 (based on OG2)


title: Thyroid_lymph_node_metastasis_from_patient_I3_2

description:
This sample used the same tissue analyzed in:
GSM2550966
9534190022_K

value: thyroid


title: MY145F_B

value: B


title: RNA-seq 48 h (kd) rep 3


title: MY145F_A

value: A


title: CTL_2

value: replicate 2


title: MY145F_C

value: C


title: RNA-seq 48 h (kd) rep 2


title: Thyroid_lymph_node_metastasis_from_patient_I2

description:
This sample used the same tissue analyzed in:
GSM2550964
9534190022_E

value: M 2


title: Thyroid_lymph_node_metastasis_from_patient_I3_1

description:
This sample used the same tissue analyzed in:
GSM2550965
9534190022_H


title: Thyroid_lymph_node_metastasis_from_patient_I1

description:
This sample used the same tissue analyzed in:
GSM2550963
9534190022_B

value: M 1


title: CTL_1

value: replicate 1


title: RNA-seq 48 h (ctrl) rep 1


title: MY143R_C

value: CD8+ T cells from PBMC


title: RNA-seq 48 h (kd) rep 1

value: mESC with conditional Smarcb1 knockdown


title: IL7_C


title: MY143R_B


title: ChIP-seq Smarca4 (kd)

data_processing:
Fastq files were trimmed and prepared for further processes using TrimGalore! with automatic detection for adapter sequences, and Galaxy's default settings (Trim low-quality ends from reads in addition to adapter removal: quality score threshold 20; overlap with adapter sequence required to trim a sequence: 1; maximum allowed error rate: 0.1; discard reads that became shorter than length 20).
The resulting alignment was filtered with samtools 1.9 to include only uniquely mapped reads with less than two mismatches.
Alignement was performed using Bowtie2 using mm10 as reference genome and Galaxy's default settings.
ChIP-seq peaks were called with the algorithm MACS2 and default parameters for single samples (Histone / TF against input).
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files were created with MACS2 and represent ChIP-seq peaks, including the MACS-specific score per identified peak region.

extract_protocol:
Ezh2, H3K4me3, H3K27ac: Cells were fixed in 1 % formaldehyde, quenched with 0.125 M Glycine, extraction was performed with ice-cold lysis buffer according to our laboratory standards. Samples were sonified, ChIP was performed with the indicated antibodies and afterwards samples were treated with elution buffer, Proteinase K and RNase A. All samples were purified using the QIAquick PCR Purification Kit. H3K27me3, Smarca4: fixation according to Active Motif proticol (formaldehyde, Glycine), snap-frozen and shipped to Active Motif.
Libraries were prepared and sequenced (~20M single read per sample) using the Next-Seq 500 sequencing platform (high-output Kit, 75 Cycles v2 Chemie) at the Genomics Core Facility (University Hospital Münster, Münster).

treatment_protocol: Smarcb1 kd cells were treated with 1µg doxycycline per ml medium every day. ChIP-seq experiments were performed 72h after knockdown induction

tag: cell type/genotype

tag: chip-seq antibody

value: Smarca4:Abcam, #ab110641


title: MY143R_A


title: ChIP-seq H3K4me3 (ctrl)

data_processing:
Fastq files were trimmed and prepared for further processes using TrimGalore! with automatic detection for adapter sequences, and Galaxy's default settings (Trim low-quality ends from reads in addition to adapter removal: quality score threshold 20; overlap with adapter sequence required to trim a sequence: 1; maximum allowed error rate: 0.1; discard reads that became shorter than length 20).
The resulting alignment was filtered with samtools 1.9 to include only uniquely mapped reads with less than two mismatches.
Alignement was performed using Bowtie2 using mm10 as reference genome and Galaxy's default settings.
ChIP-seq peaks were called with the algorithm MACS2 (TFs) and SICER (histones) and default parameters for single samples (histone / TF against input).
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files were created with MACS2 (TFs Smarca4 and Ezh2) and SICER (H3K27me3, H3K27ac, H3K4me3) and represent ChIP-seq peaks, including the MACS-specific score per identified peak region (TFs) or SICER's p-value (histones).

value: untreated

value: H3K4me3:Diagenode, # pAB-003-050


title: CTR3_176

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

institute: università di padova

description: Gene expression data from primary GBM cells treated with DMSO at 24h

hyb_protocol: 5.5ug of sscDNA were fragmentated and 5.2 uf were hybridized for 16 hr at 45°C on GeneChip Human Clariom S Array (GPL23159 Platform). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized using TAC software using RMA and Repated Measure for patients were applied

source_name: primary GBM cells

label_protocol: Biotinylated cRNA were prepared according to the standardThermoFisher protocol starting  from 100ng of Total RNA using the ThermoFisher WTA Kit

growth_protocol: Primary GBM cells were cultured DMEM/F12 supplemented with 10% BIT9500 , 20 ng/ml basic Fibroblast Growth Factor (bFGF) and 20 ng/ml Epidermal Growth Factor (EGF) and maintained in an atmosphere of 2% oxygen, 5% carbon dioxide and balanced nitrogen in a H35 hypoxic cabinet.

extract_protocol: RNA was extracted using Trizol

treatment_protocol: Treatment with DMSO or 5uM Trichostatin A or Vorinostat for 24h

value: DMSO

tag: sample


title: ChIP-seq Smarca4 (ctrl)

value: unchanged


title: SAHA3_176

description: Gene expression data from primary GBM cells treated with 5uM Vorinostat at 24h

value: Vorinostat Treatment


title: ChIP-seq H3K27me3 (kd)

value: treated with doxycycline

value: knockdown

value: H3K27me3:Active Motif, # 39155

value: 81K1 (based on OG2)


title: IL7_B

value: B


title: IL7_A

value: A


title: ChIP-seq H3K4me3 (kd)


title: ChIP-seq H3K27me3 (ctrl)


title: SAHA4_176


title: PBMC of DVT patients,replicate 5

city: Jinan

first: Chu

last: Chu

address: 18877 Jingshi Road

institute: Shandong First Medical University & Shandong Academy of Medical Sciences

description: miRNA expression of DVT patients

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse miRNA Microarray (8*60K) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: PBMC

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-ColorLow RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN,Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/nAM1556 ) following the manufacturer's instructions.

treatment_protocol: Venous blood samples were obtained after overnight fasting at study inclusion. Samples were processed within 4 h of collection.  PBMCs were isolated by Ficoll density-gradient centrifugation.

value: PBMC

tag: disease

value: DVT


title: PBMC of DVT patients,replicate 3

description: miRNA expression of DVT patients


title: PBMC of DVT patients,replicate 4

description: miRNA expression of DVT patients


title: PBMC of DVT patients,replicate 6

description: miRNA expression of DVT patients


title: IL2_C

source_name: CD8+ T cells

tag: donor

value: C


title: PBMC of DVT patients,replicate 1

description: miRNA expression of DVT patients


title: TSA4_176

description: Gene expression data from primary GBM cells treated with 5uM Trichostatin A at 24h

value: Trichostatin A Treatment


title: SAHA2_176


title: IL2_B

value: CD8+ T cells from PBMC


title: ChIP-seq Ezh2 (kd)

value: mESC with conditional Smarcb1 knockdown

value: Ezh2:Cell Signalling, #5246S


title: CTR4_176


title: ChIP-seq H3K27ac (kd)

value: H3K27ac:abcam, #ab4729


title: PBMC of control subjects,replicate 6

description: miRNA expression of control subjects

value: control


title: IL15_B


title: ChIP-seq H3K27ac (ctrl)

value: untreated

value: unchanged


title: ChIP-seq Ezh2 (ctrl)


title: IL15_C


title: IL2_A


title: TSA2_176


title: PBMC of DVT patients,replicate 2

description: miRNA expression of DVT patients


title: Patient19

city: Southampton

first: JAYA

last: THOMAS

address: MP824 Somers Building, Southampton General Hospital, Tremona Road,

department: Cancer Science

country: United Kingdom

institute: University of Southampton

description: Transcriptome primary lung cancer at diagnosis

data_processing:
Illumina HiSeq2500 platform
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using the STAR aligner
FeatureCount was used to get the gene counts from the output bam files

extract_protocol:
Total RNA was extracted from snap-frozen tissue (n=17) or tissue stored in RNALater solution (n=2) or cell pellets (n=1). RNA extraction was using the Qiagen RNeasy (n=4) or Allprep DNA/RNA (n=2) kits or the Promega Maxwell® RSC simplyRNA Tissue (n=13) or simply RNA cells (n=1) kits. RNA concentration and quality were assessed by Thermofisher Scientific Qubit Fluorometric quantification and Agilent RNA 6000 Nano Kit for the 2100 Bioanalyzer System.
RNA-Sequencing was undertaken by Edinburgh Genomics, University of Edinburgh, Edinburgh, UK. An automated TruSeq stranded mRNA-seq library was prepared from total RNA and sequencing was by  Illumina NovaSeq system (100bp paired-end; 40million reads/sample).

tag: diagnosis

value: Non small cell lung cancer

tag: histology

value: Adenocarcinoma

value: Primary lung tumor

tag: sampling time-point

value: Baseline (at diagnosis)


title: PBMC of control subjects,replicate 4

description: miRNA expression of control subjects


title: TSA3_176


title: PBMC of control subjects,replicate 5

description: miRNA expression of control subjects


title: SAHA1_176

value: Vorinostat Treatment


title: CTR2_176

value: DMSO


title: IL15_A

value: A


title: ChIP-seq Input (Smarca4, H3K27me3) (kd)

value: treated with doxycycline

value: knockdown

value: IgG:Novusbio, #NBP2-24891

value: 81K1 (based on OG2)


title: Patient18

description: Transcriptome primary lung cancer post-treatment

value: Squamous cell carcinoma

value: Post-treatment; 1st line chemotherapy, 2nd line TKI, 3rd line EGFRi, 4/5th line TKI, 6th line Radiotherapy, 7th line aPD1 immunotherapy, 8th line TKI


title: ChIP-seq Input (Smarca4, H3K27me3) (ctrl)

value: mESC with conditional Smarcb1 knockdown


title: ChIP-seq Input (Ezh2, H3K4me3, H3K27ac) (kd)


title: TSA1_176

value: Trichostatin A Treatment


title: Patient17

source_name: Transcriptome primary lung cancer at diagnosis


title: ChIP-seq Input (Ezh2, H3K4me3, H3K27ac) (ctrl)

value: untreated


title: TSA4_61


title: Patient16


title: MycCaP_Myc_Y69_Rep1

city: Chicago

first: Debu

last: Chakravarti

state: IL

address: 303 E Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

data_processing:
For single-end reads (ChIP-seq) raw fastq files were aligned with bowtie (v1.2.2, settings: -t --best -m 1) using pre-built genome indexes for both hg38 and mm10, downloaded from source (http://bowtie-bio.sourceforge.net/manual.shtml, NCBI). For paired-end ATAC-seq, reads were aligned with bowtie2 (v2.2.6, settings: --very-sensitive -X 800). For paired-end RNA-seq, reads were aligned to the hg38 reference genome (NCBI, GRCh38.p12) using STAR (43) (v2.7.5, settings: --alignIntronMin 20 --alignIntronMax 500000).
ChIP- and ATAC-seq sequence alignment files were converted to binary format using samtools (version 1.9) and used as input for peaks calling (HOMER, v4.11.1) (settings: -tbp 1, style = factor/histone/dnase).
Using diffBind (v3.12, settings: minMembers = 4 score=DBA_SCORE_TMM_MINUS_FULL) for differential binding analysis, each timepoint (1-, 4-, 8-, 24- and 48-hr) was compared to DMSO and peaks called by HOMER were used to define a consensus peak list
Visualization for ChIP-seq data including bigwigs, heatmaps and read coverage histograms were generated with deeptools bamCoverage (settings: --binSize 1 --normalizeUsing RPGC –effectiveGenomeSize mouse/human --extendReads    120 –ignoreDuplicates), plotHeatmap and plotProfile function (deepTools v3.3.0)
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: ChIP-seq: peak .txt files from HOMER, differential binding table is output from diffBind; RNA-seq: count matrix from featureCounts; ATAC-seq: peak .xls files from macs2

source_name: MycCap

growth_protocol: All cell lines in this study were maintained in RPMI (ThermoFisher, Cat#: 11875093) supplemented with 10% Gibco FBS (REF:26140-079) in a humidified incubator at 37°C with 5% CO2

extract_protocol:
For ChIP-seq, the cell nuclear fraction was clarified from sonicated and histone-DNA complexes were isolated with antibodies. For RNA-seq, total RNA extracts were isolated from MYCi and vehicle control treated cells. For ATAC-seq, nuclei were isolated and inspected before Tn5 tagmentation.
As input for library preparation, < 1 ng – 5 ng of immunoprecipitated DNA was used. ChIPseq library preparation was carried out with KAPA Hyper Prep Kit (Cat#: KK8502). For RNAseq, 500 ng of RNA was used as input with a ribosome depletion library kit (KAPA Biosystems, Cat#: KK8560).
multiplex

treatment_protocol: Cells were isolated 72 hours after plating with a fresh media change 48-hours after plating. Each treatment was given such that isolation 72-hours after plating represents each timepoint.

value: cancer cell line

tag: antibody

value: c-MYC (abcam, ab56-9E11),


title: SAHA3_61


title: CTR1_176


title: PBMC of control subjects,replicate 1

description: miRNA expression of control subjects

value: PBMC

value: control


title: SAHA4_61


title: COCULTURE_1

city: Nanjing

first: Ziyang

last: Zheng

address: Longmian Avenue NO.101

institute: The first affiliated hospital of nanjing medaical university

data_processing:
fastp version 0.17.1
HISAT2 version 2.1.0
String Tie v1.3.4d
DESEQ2 v1.18.1
R version 3.4.3
Genome_build: gencode v27
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: COCULTURE

growth_protocol: To obtain primary chondrocytes, the cartilage of femoral condyles and tibial plateau of 5-day-old mice  was cut into pieces after washing with PBS . Next, cartilage chips were sequentially incubated with trypsin–EDTA solution and 3 mg/mL collagenase II and the digests were filtered through a 70μm cell strainer. Cells were plated in DMEM/F12  supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) .  RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer (Life Technologies, CA, USA).
Quality RNA samples were converted into cDNA libraries using VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (NR601, Vazyme, NanJing, China). VAHTSTM DNA Clean Beads (Vazyme #N411) in this study was used to purify the fragments during the process of library constructing. The purified products were enriched with 12-15 cycles of PCR to create the final cDNA library. Finally, libraries were sequenced on the Illumina Hiseq X Ten according the manufacturer's protocols.

treatment_protocol: Chondrocytes were cocultured with BMSCs and cultured alone.

tag: strain

value: Chondrocytes

value: cocultured with BMSCs


title: CONTROL_3

source_name: CONTROL

tag: cell type

value: cultured alone (control)


title: PBMC of control subjects,replicate 3

description: miRNA expression of control subjects


title: COCULTURE_2


title: Patient15

value: Non small cell lung cancer

value: Adenocarcinoma

value: Primary lung tumor

value: Baseline (at diagnosis)


title: COCULTURE_3


title: PBMC of control subjects,replicate 2

description: miRNA expression of control subjects


title: Patient14


title: LiverATAC_oil_1_S9

first: April

last: Williams

address: 10010 N Torrey Pines Rd

description:
liver4F_ATAC_peakunion.raw.txt
LiverATAC_oil_1_S9

data_processing:
Sequenced reads were quality tested using FASTQC v0.11.2 using the default parameters.
RNA-Seq: Alignment to the hg19 genome (from illumina iGenome) was performed using the STAR aligner version 2.5.3a using the --outFilterIntronMotifs RemoveNoncanonical parameter. Gene expression was quantified using the HOMER analysis suite version 4.9.1, makeTagDirectory, analyzeRepeats.pl across exons of RefSeq genes.
ATAC-Seq: Adapter sequences were trimmed using TrimGalore v0.4.5 then aligned using bwa mem v0.7.12. Bam files were sorted, fixmated, marked duplicates, indexed, filtered low quality reads by samtools v1.9. For each sample, peaks were called by macs2 v2.1.2 by using command "callpeak --slocal 1000 --qvalue 0.05 -g mm -f BAMPE". The the called narrow peaks from each sample were merged to get a union peak file. Homer v4.9.1 was used to quantify the read counts in each of the union peak by commands makeTagDirectory and analyzeRepeats.
Single-Cell RNA-Seq: Reads were processed using 10X Genomics Cell Ranger pipeline v3.1.0 aligned to Cell Ranger mm10 v1.2.0 reference with default settings
Genome_build: mm10 (illumina iGenome) for RNA-Seq and ATAC-Seq, Cell Ranger mm10 v1.2.0 for Single-Cell RNA-Seq.
Supplementary_files_format_and_content: liver4F_RNA_exons.raw.xlsx contains the raw read count quantified for each gene for the RNA-Seq data. liver4F_ATAC_peakunion.raw.txt contains the raw read count quantified for each peak for the ATAC-Seq data. liver4F_SC_minusDox_filtered_feature_bc_matrix.h5 and liver4F_SC_plusDox_filtered_feature_bc_matrix.h5 are the two compressed filtered cell X gene count table generated for Single-Cell RNA-Seq.

source_name: Hep-4F mouse liver tissue

extract_protocol:
RNA-Seq: Isolated livers were homogenized with a polytrone in Trizol immediately after collecting tissues. The extracted RNA was purified with RNeasy Mini Kit (QIAGEN) from the homogenates with DNaseI tretment (RNase-Free DNase Set, QIAGEN) to get rid of genomic DNA.
ATAC-Seq: Frozen liver samples were processed for ATAC-seq using the Omni-ATAC seq protocol [PMID: 28846090]. Briefly, around 20 mg of frozen tissue was used to isolate nuclei via Dounce homogenization followed by density gradient centrifugation. After isolation of nuclei, transposition mixture was added for transposition reaction.
SIngle-cell RNA-Seq: Liver cells were isolated after collagenase perfusion as described before [PMID: 29553556] to get single cell suspension. Briefly, hepatocytes and other cells were isolated separately with different gravity of centrifuge and both fractions were mixed at the same number of cells. Then, the mixture was subjected to scRNA-Seq using Next GEM Single Cell 3’ kit v3.1 (10x Genomics).
RNA-Seq: RNA quality was assessed and all samples had a minimum RNA integrity number (RIN) of 8.6. RNA library preps were prepared using the Illumina TruSeq Stranded Total RNA Sample Prep kit with Ribo-zero Gold (cat. no. RS-122-2301). ATAC-Seq: All ATAC-seq analysis was performed on two biological replicates. Frozen liver samples were processed for ATAC-seq using the omni-ATAC seq protocol (Corces et al, 2017, Nature Methods). Libraries were constructed using published Nextera PCR primers (Buenrostro et al 2013, Nature methods) and checked for quantity on a TapeStation 2200 (Agilent). Single-Cell RNA-Seq: Liver cells were isolated after collagenase perfusion as described before. Briefly, hepatocytes and other cells were isolated separately with different gravity of centrifuge and both fractions were mixed at the same number of cells. Then, these fractions were subjected to scRNA-Seq using Next GEM Single Cell 3’ kit v3.1.
ATAC-Seq: Libraries were constructed using published Nextera PCR primers [PMID: 24097267] followed by checking the quality on a TapeStation2200 (Agilent).
Single-Cell RNA-Seq: Libraries were prepared using Next GEM Single Cell 3’ kit v3.1 (10x Genomics).
stranded paired-end mRNA-seq; paired-end ATAC-Seq; 10X Genomics Chromium v3 3' Single-Cell RNA-Seq

tag: time

value: 3 days

value: liver


title: LiverATAC_oil_2_S10

description:
liver4F_ATAC_peakunion.raw.txt
LiverATAC_oil_2_S10

tag: tissue


title: CONTROL_2


title: LiverATAC_ccl4_2_S12

description:
liver4F_ATAC_peakunion.raw.txt
LiverATAC_ccl4_2_S12


title: Patient13


title: LiverATAC_ccl4_1_S11

description:
liver4F_ATAC_peakunion.raw.txt
LiverATAC_ccl4_1_S11


title: CONTROL_1


title: SAHA2_61

value: Vorinostat Treatment


title: Patient12


title: TSC_Repliseq_early_rep2

city: Tsukuba

first: Masashi

last: Hada

state: Ibaraki

address: Koyadai 3-1-1

department: Bioresource Research Center

institute: RIKEN

description:
Biological replicate 2 of 2.
TSC_Repliseq_w200ks40k_Percent_q0.05_rep2.bedGraph

data_processing:
Library strategy: Repli-seq
For Repli-seq data processing, scRepli-seq pipeline (v1.3) was used (Miura et al., 2020). Only one side of the paired-end reads (i.e., ‘XXX_R1.fastq.gz’) was used for the data analysis. The 1.3 version of this pipeline is applicable to the population-based BrdU-IP repli-seq data processing which includes adapter trimming, alignment (using mm10), normalization, and computing early/late replication timing scores as described previously (Takahashi et al., 2019). Briefly, the mapped reads of early- and late-S-phase BrdU-IP samples were counted in sliding windows of 200 kb at 40-kb followed by reads per million (rpm) normalization. Then the ratio of early-S-phase to total read counts ((early-S reads)/(early-S reads + late-S reads)) was calculated for each bin and total read counts within the bottom 5% of all bins were filtered out. The value of the ratio was converted to fit within a ±1 scale and this scaled value was defined as the early/late replication timing score of each bin.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

source_name: Trophoblast stem cell

growth_protocol: ESC and TSC lines were established from blastocysts generated by IVF. IVF was undertaken using oocytes from C57BL/6NCrSlc female mice and spermatozoa from DBA/2 male mice or JF1/Ms male mice. For establishment of ESCs, developing blastocysts were dropped onto Acidic Tyrode (Millipore #MR-004-D) to remove zona pellucida, then transferred to ESC medium containing KnockOut DMEM (Gibco # 10829018), 15% KnockOut serum replacement (KSR, Thermo #10828028), MEM Non-Essential Amino Acids Solution (Gibco #1140050), GlutaMAX supplement (Gibco #35050061), 100 µM 2-mercaptoethanol (2-ME, Sigma-Aldrich #M-7522), ESGRO Recombinant Mouse LIF Protein (Millipore #ESG1107), 1 µM PD0325901 (Stem gent #04-0006), and 1 µM CHIR99021 (Stem gent #04-0004). These blastocysts were putted onto layers of primary mouse embryonic fibroblasts treated with mitomycin-C (MMC-MEFs). After several passages, cell lines with typical ESC colonies were picked up and used for further analysis. In the case of TSCs, developing blastocysts were directory transferred to TSC medium containing the same amount of neurobasal medium (Gibco #21103049) and Dulbecco’s modified Eagle’s medium/F12 (Ham’s) (1:1) (Gibco #11320033), N2 supplement (Gibco #17502048), B27 supplement (Gibco #17504044), GlutaMAX supplement, 150 µM 2-ME, 1 µg/ml heparin (Sigma #H3149), 0.05% bovine serum albumin (Millipore #12657), 1% KSR, 50 ng/ml recombinant mouse basic FGF (Wako #062-05181), 20 ng/ml recombinant human activin A (R&D systems #338-AC), 10 µM XAV939 (Calbiochem #575545), and 5 µM Y27632 (Wako #036-24023) onto MMC-MEFs (Hirose et al., 2018; Ohinata and Tsukiyama, 2014). After several passages, cell lines with typical TSC colonies were used for further experiment.  Established ESC and TSC lines were adapted for feeder-free conditions. Briefly, ESCs were placed onto gelatin coated dish with ESC medium in which PD0325901 and CHIR99021 were removed and 1 µM GSK-3 Inhibitor IX (Millipore #361550) was added. TSCs were placed onto the dishes coated with 15 mg/ml human plasma fibronectin (Millipore #FC010) with TSC medium (Hirose et al., 2018; Ohinata and Tsukiyama, 2014). Medium was replaced every day and cells were passaged every 2 days

extract_protocol:
We followed the BrdU-immunoprecipitation (IP)-based protocol, as described previously (Ryba et al., 2011). Cells were labeled by BrdU (Sigma #B5002) for 2 hours then collected by trypsinization. Cell pellets were resuspended by 5% FBS/PBS and EtOH was added to 75% final concentration for fixation. The ethanol fixed cells were sorted into early- and late-S-phase fractions (20,000 cells per each fraction) by FACS using Sony SH800 cell sorter as described previously (Takahashi et al., 2019). Genomic DNA was extracted from each fraction and fragmented by sonication. Then immunoprecipitation with anti-BrdU mouse monoclonal antibody (BD Biosciences #555627) was performed to enrich BrdU-labeled replicating DNA.
After BrdU-IP, immunoprecipitated DNA samples were subjected to whole-genome amplification (WGA) followed by library preparation according to the previous study (Miura et al., 2020)

tag: cell state

value: early replication timing


title: Patient11


title: TSC_Repliseq_late_rep2

value: late replication timing


title: LiverATAC_2d_1_S5

description:
liver4F_ATAC_peakunion.raw.txt
LiverATAC_2d_1_S5

tag: treatment

value: 2 days


title: Patient10


title: TSC_Repliseq_late_rep1

description:
Biological replicate 1 of 2.
TSC_Repliseq_w200ks40k_Percent_q0.05_rep1.bedGraph


title: LiverATAC_2d_2_S6

description:
liver4F_ATAC_peakunion.raw.txt
LiverATAC_2d_2_S6


title: Patient9

value: Squamous cell carcinoma


title: CTR4_61

value: DMSO


title: LiverATAC_1d2d_2_S8

description:
liver4F_ATAC_peakunion.raw.txt
LiverATAC_1d2d_2_S8

value: 1 day on 2 days off


title: TSC_Repliseq_early_rep1


title: TSC_HiC_rep2

description: Biological replicate 2 of 2.

data_processing:
Hi-C data processing was done by using Docker for 4DN Hi-C pipeline (v43). The pipeline includes alignment (using mm10) and filtering steps. After filtering valid Hi-C alignments with MAPQ > 10 (.pair format file), .cool format Hi-C matrix files were generated by cooler (v0.8.7) (Abdennur and Mirny, 2020). To correct the bias of Hi-C matrices, “cooler balance” command with “—ignore-diags 1” option was applied to each .cool file. The A/B compartment (Hi-C PC1) profiles (in 200-kb bins) in each chromosome were calculated from each .cool file by “cooltools call-compartments” command of cooltools (v0.3.0) with slight modifications to perform the original A/B compartment analysis (Lieberman-Aiden et al., 2009) including the computation of Pearson correlation and covariance matrix followed by the eigen vector decomposition. The sign of Hi-C PC1 in each chromosome was corrected by gene density tracks (the sign of PC1 with higher gene density assigned as A compartment showing positive PC1 values, and the other assigned as B compartment showing negative PC1 values).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig
Supplementary_files_format_and_content: mcool

extract_protocol:
Libraries for Hi-C were generated as previously described (Kadota et al., 2020). Detailed protocol for Hi-C library preparation is available at Protocols.io (https://www.protocols.io/view/iconhi-c-protocol-ver-1-0-4mjgu4n). Briefly, collected cells were washed by 5% FBS/PBS, then fixed by 1% formaldehyde (Polyscience #18814-10) in 5% FBS/PBS for 10 min. To stop fixation, 2.5 M Glycine was added then incubated for 5 min. Fixed cells were washed and stored at -80 °C. Totally 2x106 fixed cells were lysed, permeabilized, and then digested with DpnII enzyme (4-bps cutter). Digested fragment ends were next filled with biotinylated nucleotides and the resulting blunt-end fragments were ligated.
After reverse cross-linking, ligation products were purified to obtain Hi-C DNA. 1 µg of Hi-C DNA was fragmented by sonication and the biotinylated ligation junctions were pulled down with streptavidin beads. Then, library preparation was performed on beads.


title: LiverATAC_1d2d_1_S7

description:
liver4F_ATAC_peakunion.raw.txt
LiverATAC_1d2d_1_S7


title: SAHA1_61


title: Patient8

source_name: Transcriptome primary lung cancer post-treatment

value: Pleural fluid cell block

value: Post-treatment; 1st line aPD1 immunotherapy


title: TSA1_61

value: Trichostatin A Treatment


title: Patient7


title: TSA2_61


title: TSA3_61


title: LiverATAC_1d_1_S3

description:
liver4F_ATAC_peakunion.raw.txt
LiverATAC_1d_1_S3

value: 1 day


title: Patient6

value: Non small cell lung cancer


title: CTR3_61


title: Patient5


title: CTR2_61


title: CTR1_61


title: LiverATAC_0d_2_S2

description:
liver4F_ATAC_peakunion.raw.txt
LiverATAC_0d_2_S2

value: 0 day


title: LiverATAC_0d_1_S1

description:
liver4F_ATAC_peakunion.raw.txt
LiverATAC_0d_1_S1


title: Patient4

value: Adenocarcinoma

value: Primary lung tumor


title: SUIT2, P-bi-TAT (30 µM) Rep. 2

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

hyb_protocol: 16 h to Affymetrix Clariom S Human arrays

scan_protocol: Affymetrix Scanner 3000 7G using AGCC software.

data_processing: CEL files were summarized using the Gene Level-SST RMA algorithm in Transcriptome Analysis Console v4.0.1.36 (Affymetrix) and the normalized data were subjected to one-way ANOVA with a p-value less than 0.05 . A 2-fold change was used to select entities that were statistically and differentially expressed between any two conditions.

source_name: SUIT2 cells, P-bi-TAT (30 µM)

label_protocol: Affymetrix Whole Transcript Sense Target labeling protocol

growth_protocol: Human glioblastoma multiforme SUT2 cells (ATCC, Manassas, VA) were cultured in RPMI medium containing 10% FBS at 37°C and 5% CO2/95% O2.

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

treatment_protocol: Cells were treated with P-bi-TAT (30 µM) for 24 h. Control cells were exposed to PBS, pH 7.4, for the same period of time.

tag: cell line

value: Human glioblastoma multiforme cells

value: P-bi-TAT


title: SUIT2, P-bi-TAT (30 µM) Rep. 1


title: Patient3

value: Baseline (at diagnosis)


title: LiverATAC_1d_2_S4

city: San Diego

institute: Salk Institute for Biological Studies

description:
liver4F_ATAC_peakunion.raw.txt
LiverATAC_1d_2_S4

value: liver


title: SUIT2, P-bi-TAT (30 µM) Rep. 3