title: Tregs, Patient 3 (507) 3months post-treatment

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

data_processing:
Image analysis and base calling were done by the Real Time Analysis Software (RTA) v2.4.11. The resulting .bcl files were converted into .fastq files with the bcl2fastq v2.18 software.
Fastq files were analysed for qualtiy using FastQC 0.11.8 and FastQScreen 0.14.0
Fastq files were aligned to the GRCh38.p12 assembly using STAR 2.7.2 with the following parameters STAR --runThreadN 10 --genomeDir x --genomeLoad LoadAndKeep --limitBAMsortRAM 20000000000 --readFilesIn x --readFilesCommand zcat –outFileNamePrefix x  --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --seedSearchStartLmax 30 --outSAMtype BAM SortedByCoordinate --outBAMcompression 10
Aligned BAM files were then used to generate a counts table with featureCounts v1.6.2 with the following paramters and using the Gencode Human annotation version 30: featurecounts -a gencode.v30.annotation.gtf-G GRCh38.p12.fasta -o counts.txt -F GTF -g gene_name -t exon -T 10 --largestOverlap
Diffrential gene expression analysis was performed using limma version 3.40.6 with the limma/voomWithQualityWeights pipeline as described in the limma vignette and using some commands from the edgeR package (version 3.26.7) . In short: a counts table was read into a DGEList object using the edgeR function DGEList and filtered for all genes with a counts of atleast 5 in 2 or more samples. Normalization factors were calculated using the edgeR function calcNormFactors. The DGEList object was then voom transformed using the voomWithQualityWeights function with standard settings. Fitting and Statistics were performed using the lmFit and eBayes function, again with standard settings.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: counts.txt is a tab delimited text file including gene counts per sample.

source_name: isolated blood regulatory T cells

extract_protocol:
PBMC were isolated over density gradient centrifugation. Whole PBMC were washed two times with 50ml PBS -/- and subsequently labeld by Miltenyi MACS CD4/CD25CD127dim antibodys/microbeads and seperated by magnetic columns. Isolated Treg were counted manually and stored at 150.000 cells/ml of RNA protect reagent and immediately frozen on -80°C for RNA extraction.
Total RNA was extracted from MACS sorted Treg cells according to the “Purification of total RNA from animal and human cells” protocol of the RNeasy Plus Micro Kit (QIAGEN, Hilden, Germany). In brief, cells were stored in RNAprotect buffer and shipped on dry ice. After thawing the samples were pelleted by centrifugation for 5 minutes at 5,000 x g, the RNAlater was replaced by 350 µl buffer RLT Plus and the samples were homogenized by vortexing for 30 sec. Genomic DNA contamination was removed using gDNA Eliminator spin columns. Next one volume of 70 % ethanol was added and the samples were applied to RNeasy MinElute spin columns followed by several wash steps. Finally total RNA was eluted in 12 μl of nuclease free water. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip reagent set (Agilent, Palo Alto, CA, USA). The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from 100 pg total-RNA. Double stranded cDNA was amplified by LD PCR (13 cycles) and purified via magnetic bead clean-up. Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA). 150 pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposome. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step 1:5 dilutions of index 1 (i7) and index 2 (i5) primers were used. The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems, Inc., Woburn, MA, USA). Equimolar amounts of each library were sequenced on a NextSeq 500 instrument controlled by the NextSeq Control Software (NCS) v2.2.0, using a 75 Cycles High Output Kit with the dual index, single-read (SR) run parameters.

treatment_protocol: Three newly diagnosed RRMS patients were recruited at the St. Josef Hospital Bochum following inclusion and exclusion criteria of ethic approval from the Ruhr-University Bochum. Pre-treatment blood samples were collected from all three patients before initiation of PA supplementation. All patients recieved PA two times 500mg on a daily basis and additional blood was drawn on d14 and d90 of PA supplementation.

tag: disease state

value: relapse remitting MS

tag: patient

value: PA supplementation

tag: timepoint

value: regulatory T cells


title: HAMVEC EV PIC 4

status: Public on Aug 22 2022

type: RNA

city: Norfolk

first: Allison

middle: Heath

last: Mathiesen

state: VA

address: 700 W Olney Rd, Department of Physiology

country: USA

institute: Eastern Virginia Medical School

description: miRNA was detected using the NanoString miRNA Array according to manufactuers instructions

hyb_protocol: not provided

scan_protocol: not provided

data_processing: The NanoString RCC files were normalized in Rosalind and a threshold cutoff of 20 was applied for the normalized samples.

molecule: total RNA

organism: Homo sapiens

source_name: HAMVEC PIC Treated

label_protocol: not provided

growth_protocol: HAMVEC were cultured in endothelial cell media supplemented with growth factors and Pen/Strep until 70% confluency. Human adipose tissue was obtained from subjects undergoing bariatric surgery.

extract_protocol:
Conditioned media was collected and EV were isolated via serial ultracentrifugation and characterized using nanoparticle tracking analysis and electron microscopy.
Total RNA was collected using the GenElute single cell RNA purification kit (Sigma Life Sciences, Cat # RNB300)

treatment_protocol: HAMVEC PIC treatment was performed by supplementing media with TGF-beta, TNF-alpha, and IFN-gamma at 5ng/ml for 6 days.

tag: tissue

value: HAMVEC PIC Treated


title: CTR_rep2

type: SRA

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

library_source: transcriptomic

data_processing:
Reads quality was evaluated using FastQC (version 0.11.8, Babraham Institute Cambridge, UK) tool and was trimmed using TrimGalore software to remove adapter and low-quality bases (Q < 20).
Then reads were mapped to the human Ensembl GRCh38 build reference genome using STAR version 2.5.0a using Gene annotations corresponding to the Ensembl annotation release 96
The same gene annotations were used to quantify the gene-level read counts using HTSeq-count version 0.8.0
Data normalization and differential analysis for gene expression were performed using Bioconductor R package edgeR version 3.28
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized cpm values for each Sample

source_name: rhabdomyosarcoma alveolar cell line

extract_protocol:
Cells were harvested and centrifuged at 3000 rpm for 5 min at 4°C. Supernatant was then removed and cell pellet was resuspended in 1 ml of ice-cold PBS and centrifuged at 2000 rpm for 5 min at 4°C. After removing the supernatant, cell pellet was resuspended in 1 mL of TRIzol reagent (Invitrogen) and RNA extraction was carried out following Invitrogen protocol. RNA was then quantified using Nanodrop.
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit (Lexogen, Vienna, Austria) according to manufacturer's instructions. The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NextSeq500 (Illumina) with a read length of 75 bp.

tag: cell line

tag: gene fusion

value: pax3-foxo1 fusion positive cell line

tag: knockdown

value: control


title: gapctrl_3

city: New York City

first: Coen

last: van Solingen

state: New York

address: 435 E30th street, Science Building 723T, Science Building 723T

department: Cardiology/Medicine

institute: NYU School of Medicine

description:
gapctrl_3_57_S57
processed data file: gapmerCHROME_vs_gapCTRL.csv

data_processing:
 RNA-seq reads with aligned using the STAR, version 2.5, aligner against hg19 genome/transcriptome.
Gene counting was done using featureCounts , version 1.5.2, against hg19 annotations.
Raw counts were normalized and DE analysis was performed using DESeq2, version 3.4.
Genome_build: hg19
Supplementary_files_format_and_content: base mean data was calculated from reads of three replicate samples. Fold change was calculated as gapCHROME over gapctrl. P-values were calculated on these data. Data was used in manuscript for bioinformatics sections.

growth_protocol: THP were cultivated in RPMI (ATCC) with 10% non-heat inactivated FBS and 1% P/S.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) and Direct-zol RNA MiniPrep columns (Zymo Research).
Illumina TruSeq RNA sample preparation kit. Illumina HiSeq, 2x150bp configuration, single index, per lane

treatment_protocol: cells were tranfected with gapmers designed to target all variants of CHROME or a control gapmer and subsequent stimulated with LPS (500 ng/mL) or a control vehicle

tag: cell type

value: monocytic cell line

tag: modification

value: transfection with control gapmer


title: gapCHROME_1

value: transfection with gapmer targetting CHROME


title: ATEV SC 1

source_name: Adipose Tissue-Subcutaneous

value: Adipose Tissue-Subcutaneous


title: scATAC_PLZF_RARA_Ctrl

city: Marseille

first: Estelle

last: Duprez

address: 27 Boulevard Lei Roure

country: France

institute: CRCM

library_source: genomic

data_processing:
reads alignment, filtering, barcode counting anb unique molecular identifier (UMI) counting:
reads alignment to the mm10 genomes, filtering, barcode counting and unique molecular identifier (UMI) counting were performed with cellranger version 4.0.0 with Mouse reference dataset-2.1.0
Genome_build: mm10 (genome-build GRCm38.p4,genome-version GRCm38,genome-date 2012-01,genome-build-accession NCBI:GCA_000001635.6)
Supplementary_files_format_and_content: Filtered gene-barcode matrix in MEX format (only detected cellular barcodes) stored in the Market Exchange Format (MEX) for sparse matrices with also gzipped TSV files for genes and barcode sequences corresponding to row and column indices respectively.

molecule: genomic DNA

organism: Mus musculus

source_name: PLZF/RARA transformed progenitor cells

extract_protocol: NOT PROVIDED

value: Late promyelocytes

value: Leukemic bone marrow

tag: treatment

value: Corn Oil 10% DMSO / Intraperitoneally injected


title: HAMVEC EV PIC 1


title: Tregs, Patient 2 (502) 3months post-treatment

city: Freiburg

country: Germany


title: gapctrl_1

description:
gapctrl_1_55_S55
processed data file: gapmerCHROME_vs_gapCTRL.csv


title: Tregs, Patient 3 (507) 14days post-treatment


title: HAMVEC EV C 1

source_name: HAMVEC Control

value: HAMVEC Control


title: HAMVEC EV PIC 3


title: HAMVEC EV PIC 2


title: HAMVEC EV C 2


title: gapctrl_2

description:
gapctrl_2_56_S56
processed data file: gapmerCHROME_vs_gapCTRL.csv


title: HAMVEC EV C 5


title: Tregs, Patient 1 (499) 14days post-treatment


title: Tregs, Patient 3 (507) pre-treatment

value: baseline


title: Tregs, Patient 2 (502) pre-treatment


title: Tregs, Patient 2 (502) 14days post-treatment


title: HAMVEC EV C 4


title: HAMVEC EV C 3


title: Tregs, Patient 1 (499) pre-treatment


title: Tregs, Patient 1 (499) 3months post-treatment


title: 3seq_HeLa_TNFa-DRB_R2

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

data_processing:
Adapters were trimmed with Cutadapt v1.13
Mapping to the hg38 genome was performed with STAR v2.6.1d. For 3'seq, reads were mapped to the hg19 genome with Bowtie2.
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v1.3.1
For mNET-seq profiles, only the most 3' nucleotide of the second read was used with the strandedness of the first read
Bigwig files were generated with the Deeptools2 v2.5.0.1 bamCoverage tool
Genome_build: mNET-seq: hg38. 3'seq: hg19.
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

growth_protocol: HeLa cells were maintained in DMEM with 10% fetal bovine serum

extract_protocol:
Nascent RNAs for mNET-seq were purified from Pol II IP products of solublilized chromatin. Nuclear RNAs were purified following cellular fractionation for 3'seq.
Libraries were prepared according to the protocol of TruSeq Small RNA Library Preparation Kit (Illumina) for mNET-seq. Libraries were prepared according to the protocol of NEBNext Fast DNA Library Prep Set for Ion Torrent (NEB) for 3'seq.

treatment_protocol: Cells were treated with DMSO, DRB, or TNFα for the amount of time indicated in the sample's name.

value: HeLa

tag: agent

value: TNFa-DRB

tag: time

value: 30 min

tag: antibody

tag: molecule subtype

value: nuclear RNA


title: 3seq_HeLa_TNFa-DRB_R1


title: PGC1b_siRnu12_1_RANKL_RAW rep1

city: La Jolla

first: Christopher

last: Glass

state: CA

address: 9500 Gilman Dr

department: CMM

institute: University of California, San Diego

data_processing:
FASTQ files were processed to assess quality by determining general sequencing bias, clonality and adapter sequence contamination.  RNA sequencing reads were aligned to the mm10 mouse reference genome using STAR.  Gene expression levels were calculated using HOMER by counting all strand specific reads within exons.  Only the most abundant transcripts, including multiple alternative variants, were selected for each gene, and the genes with a length smaller than 250 bp were removed.  Transcripts per million (TPM) were used to evaluate the correlation among replicates.  Differential gene expression was calculated using DESeq2 to assess both biological and technical variability between experiments.
Assembly: mm10

source_name: RAW 264.7 cell

extract_protocol:
Total RNA was isolated from culture cells and purified using a Direct-zol RNA MicroPrep Kit (Zymo Research) as described by the manufacture.  mRNAs were enriched by incubation with Oligo d(T) Magnetic Beads (NEB).
To fragment Poly A-enriched mRNA, mRNAs were incubated in 2X Superscript III first-strand buffer (Invitrogen) with 10 mM DTT at 94°C for 9 minutes.  The 10 µ l of fragmented mRNAs were incubated with 0.5 µl of Random primers (3 µg/µl) (Invitrogen), 0.5 µl of Oligo dT primer (50 µM) (Invitrogen), 0.5 µl of SUPERase-In (Ambion), and 1 µl of dNTPs (Invitrogen) at 50°C for 1 min.  After the incubation, 5.8 µl of water, 1 µl of DTT (100 mM), 0.1 µl of Actinomycin D (2 µg/µL), 0.2 µl of 1% Tween-20 and 0.5 µl of Superscript III (Invitrogen) were added and incubated on the following conditions: 25°C for 10 min, 50°C for 50 min, and 4°C hold.  The mixture was purified with RNAClean XP beads (Beckman Coulter) as described by the manufacture and eluted with 10 µl of water.  For second-strand synthesis with dUTP, the RNA/cDNA double-stranded hybrid was then added to 1.5 µl of Blue Buffer (Enzymatics), 1.1 µl of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 µl of RNAse H (5 U/µl) (Enzymatics), 1.05 µl of water, 1 µl of DNA polymerase I (Enzymatics), and 0.15 µl of 1% Tween-20.  The mixture was incubated at 16°C for 2.5 hr.  The resulting dUTP-marked dsDNA was purified with 2 µl of SpeedBeads (GE Healthcare) in 20% PEG 8000/2.5M NaCl (final 13% PEG 8000), and eluted with 40 µl of EB (Zymo Research).  The eluted dsDNA was carried out end repair by blunting, A-tailing and adapter ligation as previously described (Heinz et al., 2010) using barcoded adapters (Bioo Scientific).  The end repaired dsDNA was amplified for 16 cycles using 0.05 U/µl KAPA High Fidelity HotStart (Kapa Biosystems) and 1 µM each of primers Solexa 1GA and Solexa 1GB.  The amplified libraries were selected using PAGE/TBE gel (Invitrogen) for 225-325 bp fragments by gel extraction.

value: RAW 264.7 cell

value: Bone marrow cell

tag: genotype

value: Wild type

value: Osteoclast differentiation


title: PGC1b_siCont_Veh_RAW rep2


title: PGC1b_siCont_RANKL_RAW rep1


title: PGC1b_siDancr_1_RANKL_RAW rep2


title: PGC1b_siRnu12_1_RANKL_RAW rep2


title: PGC1b_siDancr_1_RANKL_RAW rep1


title: PGC1b_siCont_RANKL_RAW rep2


title: N3-Non-tum-bearing-1

city: Singapore

first: Kanaga

last: Sabapathy

state: --None--

address: 11 Hospital Crescent

department: Division of Cellular & Molecular Research

country: Singapore

institute: National Cancer Centre Singapore

hyb_protocol: Hybridization was performed according to standard protocols.

scan_protocol: Scanning was performed according to standard protocols.

data_processing: The R package affy was used for data processing. The rma function (Robust Multiarray Average) was used for quantile normalization and background correction.

label: biotin

source_name: Non-tumor bearing breast

label_protocol: Labeling was performed according to standard Affymetrix protocols.

extract_protocol: Total RNA was extracted using TRIzol reagent according to manufacturer’s instructions and homogenized using QIAGEN TissueLyser II. Extracted RNA was treated with DNase and purified on a RNeasy column. RNA quality and quantity were analyzed on a ND-1000 NanoDrop spectrophotometer and reverse transcribed using Superscript II (Invitrogen), before running on the human Clariom™ S Assay (ThermoFisher Scientific).

treatment_protocol: Free-hand dissection using sterile scalpel blades was performed on mastectomy specimens to obtain five samples per tumor from different regions, as well as from non-pathological regions around the tumor to obtain peri-tumoral stromal samples. Tissues within 1 cm macroscopic distance from the visible tumor were avoided to ensure only non-pathological breast tissue is collected. Within each distance zone (Zone 1: 1-3 cm, Zone 2: 3-5 cm, Zone 3: 5-7 cm), tissue was collected in four radial directions with an approximate size of 0.5 x 0.5 x 0.5 cm.

value: Non-tumor bearing breast

tag: patient id

tag: patient age

tag: ethnicity

value: Indian

tag: region

value: NTB

tag: distance zone from tumor edge

tag: molecular subtype

tag: stromal cluster


title: N3-Non-tum-bearing-2

tag: tissue


title: N3-Non-tum-bearing-3


title: PGC1b_siCont_Veh_RAW rep1

tag: cell line


title: 3seq_HeLa_TNFa-DMSO_R2

value: TNFa-DMSO


title: N3-Non-tum-bearing-5


title: N2-Non-tum-bearing-3

value: Malay


title: N3-Non-tum-bearing-4


title: N2-Non-tum-bearing-4


title: 3seq_HeLa_TNFa-DMSO_R1


title: N2-Non-tum-bearing-5


title: N2-Non-tum-bearing-1


title: 3seq_HeLa_DRB_R2

value: DRB


title: PGC1b_siRnu12_2_Day4 rep1

source_name: Bone marrow cell

tag: cell type


title: PGC1b_siRnu12_2_Day4 rep2


title: N1-Non-tum-bearing-4


title: N1-Non-tum-bearing-3


title: N1-Non-tum-bearing-5


title: 3seq_HeLa_DRB_R1


title: N1-Non-tum-bearing-2


title: N2-Non-tum-bearing-2


title: N1-Non-tum-bearing-1


title: Cortex SCA1 KI [Atxn1 154Q/2Q] Replicate 3

city: New Haven

first: Janghoo

last: Lim

state: Connecticut

address: 295 Congress Ave, BCMM Ste 139

department: Neuroscience

institute: Yale University

data_processing:
STAR was utilized to align FASTQ reads to mouse reference genome (mm10).
FeatureCounts was used to quantify read counts per gene in Python 3.10
Read counts were used for subsequent quantification and differential expression analysis using the DESeq2 package in the R environment. Gene expression with an FDR-adjusted p-value < 0.05 was considered significant and genes with a Log2FoldChange greater than |0.25| were used in final analyses
Assembly: mm10
Supplementary files format and content: Comma-separated file file containing normalized counts for each biological sample, completed using DESeq2 package in the R environment.

source_name: Cortex

growth_protocol: Not applicable

extract_protocol:
Cerebella and cortex were macrodissected, flash frozen, and kept at -80°C until further processing. The same individual conducted all tissue extractions to eliminate variability in sample collection. RNA was extracted using a Qiagen RNeasy Mini Kit, and DNA was removed with DNase I as described in the manufacturer's protocol. Total RNA was sent to the Yale Center for Genome Analysis for library prepration and sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were maintained on a 12 hour light/dark cycle with standard chow and ad libitum access to water. SCA1 KI [Atxn1 154Q/2Q] mice were maintained on a pure C57BL/6J background (Watase et al., 2002). All procedures were approved by the Yale University Institutional Animal Care and Use Committee. For RNA-sequencing, male mice were used.

tag: strain

tag: age

value: 12 weeks

value: Cortex

value: SCA1 KI [Atxn1 154Q/2Q]


title: Cortex SCA1 KI [Atxn1 154Q/2Q] Replicate 2


title: PGC1b_siRnu12_1_Day4 rep1

tag: treatment


title: PGC1b_siDancr_2_Day4 rep2

tag: time


title: 3seq_HeLa_DMSO_R1

value: HeLa

tag: agent

value: DMSO

tag: antibody


title: PGC1b_siDancr_2_Day4 rep1

tag: genotype


title: PGC1b_siDancr_1_Day4 rep2


title: PGC1b_siDancr_1_Day4 rep1


title: Cortex Wild-type Replicate 3

value: Wild-type


title: Cortex Wild-type Replicate 2


title: Cortex SCA1 KI [Atxn1 154Q/2Q] Replicate 1


title: PGC1b_siRnu12_1_Day4 rep2


title: 3seq_HeLa_DMSO_R2

value: 30 min

tag: molecule subtype

value: nuclear RNA


title: PGC1b_siCont_Day4 rep1

value: Bone marrow cell


title: PGC1b_siCont_Day0 rep2

value: Wild type


title: Cerebellum SCA1 KI [Atxn1 154Q/2Q] Replicate 3

source_name: Cerebellum

value: Cerebellum


title: BC7-Stroma-L3

source_name: Tumor adjacent normal tissue

value: Stroma

tag: patient id

tag: patient age

value: L

value: LumA


title: PGC1b_siCont_Day4 rep2

value: Osteoclast differentiation


title: BC7-Stroma-L1

tag: ethnicity

value: Malay

tag: region

value: Normal


title: Cerebellum SCA1 KI [Atxn1 154Q/2Q] Replicate 2

value: 12 weeks


title: PGC1b_siCont_Day0 rep1


title: Pgc1b_flox_Ad_Cre_Day4 rep2

value: Pgc1b flox/flox


title: BC7-Stroma-M3

value: M

tag: distance zone from tumor edge

tag: molecular subtype


title: Cerebellum Wild-type Replicate 3

tag: tissue


title: Cerebellum SCA1 KI [Atxn1 154Q/2Q] Replicate 1

value: SCA1 KI [Atxn1 154Q/2Q]


title: BC7-Stroma-S3

value: S

tag: stromal cluster


title: Cortex Wild-type Replicate 1

value: Cortex

value: Wild-type


title: Pgc1b_flox_Ad_RFP_Day4 rep2

tag: cell line

tag: cell type


title: Cerebellum Wild-type Replicate 2

tag: strain

tag: age


title: BC7-Stroma-S2


title: Pgc1b_flox_Ad_Cre_Day4 rep1

tag: treatment

tag: time


title: BC7-Stroma-L2

value: Basal


title: BC7-Stroma-M2


title: BC7-Stroma-Inf3

value: Inf


title: BC6-Stroma-L2

value: Chinese


title: BC7-Tum-Inf

source_name: Breast Tumor

value: Tumor


title: BC7-Tum-M


title: BC7-Tum-L


title: Cerebellum Wild-type Replicate 1

value: Cerebellum


title: Pgc1b_flox_Ad_RFP_Day4 rep1

value: Bone marrow cell


title: BC7-Tum-S

value: LumA


title: Pgc1b_flox_Ad_Cre_Day0 rep2

value: Osteoclast differentiation


title: BC7-Stroma-S1

value: Stroma

value: Malay


title: BC6-Stroma-L3

value: L


title: BC7-Tum-C

value: C

value: Normal


title: BC6-Stroma-L1


title: Pgc1b_flox_Ad_Cre_Day0 rep1

value: Pgc1b flox/flox


title: SLOTim3pos-1_2

city: Minneapolis

first: David

last: Masopust

state: MN

address: 2101 6th St SE

department: Department of Microbiology and Immunology

institute: University of Minnesota

description: Tim3+ Slamf6- gp33+ CD8 T cells

data_processing:
The sequences were processed with the Collection of Hierarchical UMII-RIS Pipelines (CHURP, v 0.2.2) developed by the Research Informatics Solutions (RIS) group at the Minnesota Supercomputing Institute. The reference implementation of the CHURP package is at: https://github.com/msi-ris/CHURP.git.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes count values for each sample

source_name: spleen and lymph nodes

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
For infections, mice were intravenously (i.v.) injected with with LCMV MN-2X106 PFU.
30 days after infection, cells from spleen and lymph nodes were obtained by mechanical disruption.
Live CD8a+ H2: Db-gp33 tet+ cell populations from the spleen and lymph nodes of LCMV-MN infected mice isolated by sorting on a BD FACSAria II and were further sorted based on their surface markers into Tim3+ Slamf6- and Tim3- Slamf6+  populations.

tag: gender

value: female

tag: disease state

value: chronic infection; LCMV-MN

tag: time point

value: 30+ days after infection

value: spleen and lymph nodes

value: Live CD8a+ H2:Db-gp33 tet+ T cell

tag: cell subtype

value: Tim3+ Slamf6-

value: Tim3+ Slamf6- cells sorted from Live CD8a+ H2:Db-gp33 tet+ cells on a BD FACSAria II


title: SLOTim3pos-1_3

description: Tim3+ Slamf6- gp33+ CD8 T cells


title: Pgc1b_flox_Ad_RFP_Day0 rep2

tag: genotype


title: SLOTim3pos-1_1

description: Tim3+ Slamf6- gp33+ CD8 T cells


title: BC6-Stroma-M2

tag: patient id

tag: patient age

tag: ethnicity

value: Chinese

value: M


title: Pgc1b_flox_Ad_RFP_Day0 rep1

value: Bone marrow cell


title: SLOSlamf6pos-1_3

description: Tim3- Slamf6+ gp33+ CD8 T cells

value: Tim3- Slamf6+

value: Tim3- Slamf6+  sorted from Live CD8a+ H2:Db-gp33 tet+ cells on a BD FACSAria II


title: SLOSlamf6pos-1_1

description: Tim3- Slamf6+ gp33+ CD8 T cells


title: BC6-Stroma-Inf3

value: Stroma

tag: region

value: Inf

tag: distance zone from tumor edge

tag: molecular subtype

value: Basal


title: BC6-Stroma-Inf2

tag: tissue

value: Normal

tag: stromal cluster


title: BC6-Stroma-Inf1


title: Day4_RANKL rep2

tag: cell line

tag: cell type

value: Wild type

value: Osteoclast differentiation


title: BC6-Stroma-M1

value: LumA


title: Day4_RANKL_RGFP966 rep2

tag: treatment


title: BC6-Stroma-S3

value: S


title: BC6-Stroma-S1


title: SLOSlamf6pos-1_2

description: Tim3- Slamf6+ gp33+ CD8 T cells

tag: strain

value: female

value: chronic infection; LCMV-MN

value: 30+ days after infection

value: spleen and lymph nodes


title: BC6-Tum-S

value: Tumor

value: Chinese


title: BC6-Tum-C

value: C


title: BC6-Stroma-S2


title: BC6-Tum-Inf


title: Day4_RANKL rep1

value: Bone marrow cell

tag: time


title: Day4_RANKL_RGFP966 rep1


title: BC4-Stroma-L1

value: L


title: BC4-Stroma-L3

value: Stroma


title: BC6-Tum-M

value: M


title: mouse_hepatocytes_LDB1_ko3_H3K27ac

city: Bethesda

first: GUOYOU

last: LIU

state: Maryland

address: 50 South Dr, Building 50, Room 3150

institute: NIH/NIDDK

data_processing:
Raw sequence reads were trimmed with cutadapt v2.7(Martin, 2011) to remove any adapters while performing light quality trimming with parameters "-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -q 20 --minimum-length=25".
For ChIPseq, Reads were aligned to the human GENCODE release 25 assembly using Bowtie2 v2.3.5(Langmead and Salzberg, 2012).
For ChIPseq, Multimapping reads were removed with samtools v1.9 using the “view” subcommand and the additional argument “-q 20”, and duplicate reads were removed with the Picard v2.21.4 (Toolkit, 2019) Mark Duplicates tool.
For ChIPseq, BigWig signal tracks were created with deepTools v3.3.1 (Ramirez et al., 2016) using the bamCoverage tool with the additional arguments “–normalize Using CPM –extend Reads 300”.
For ChIPseq, peaks were called for each replicate individually using macs v2.2.7.1(Zhang et al., 2008). Pooled peaks were separately called by providing both replicates simultaneously to macs2. Final peaks for each antibody were selected as pooled peaks that also had a peak intersecting it by at least 1 bp in all replicates using BEDTools v2.29.0 (Quinlan and Hall, 2010) and pybedtools 0.8.0 (Dale et al., 2011).
Genome_build: mm10
Supplementary_files_format_and_content: Excel files.xls contain peaks coordinates. Bigwig files are created with deepTools v3.3.1 using the bamCoverage tool.

source_name: hepatocytes

growth_protocol: Mice were housed in a clean conventional vivarium at ~22 oC, with a 12:12-h dark-light cycle (lights on at 06:00).

extract_protocol: ChIP-qPCR and ChIPmentatation were performed as described previously (Krivega and Dean, 2018a; Schmidl et al., 2015).

treatment_protocol: Mice were ad libitum access to water and chow (LabDiet, Advanced Protocol 5V0T, 12.5% kcal from fat). Ldb1 flox mice (Zhao et al., 2007) and Albumin-Cre mice (003574, The Jackson Laboratory) were mated to obtain control mice (Ldb1flox/flox) and liver-specific Ldb1 knockout mice Ldb1flox/flox; Alb-Cre+/-) on a C57Bl6 background. Only male littermates were used.

value: hepatocytes

tag: chip antibody

value: H3K27ac (Abcam 4729)

value: Ldb flox/flox;Alb-Cre regular chow

tag: age

value: 7 weeks post natal


title: BC4-Stroma-L2

value: Normal


title: BC4-Stroma-S2

value: S

value: LumA


title: Day0 rep1

value: Wild type

value: Osteoclast differentiation


title: BC4-Stroma-M1

value: Basal


title: mouse_hepatocytes_LDB1_ko1_H3K27ac


title: mouse_hepatocytes_LDB1_ko3_Input


title: BC4-Stroma-Inf3

value: Inf


title: NKO_96h rep1

value: NCoR flox/flox, LysMCre


title: WT_96h rep2

value: NCoR flox/flox


title: BC4-Tum-Inf

value: Tumor

value: Chinese


title: WT_96h rep1

value: Bone marrow cell


title: NKO_96h rep2


title: BC4-Stroma-Inf1

value: Stroma


title: BC4-Tum-C

value: C


title: BC4-Stroma-Inf2


title: BC4-Stroma-S1


title: mouse_hepatocytes_LDB1_ko1_Input

value: hepatocytes


title: mouse_hepatocytes_flox3_H3K27ac

value: H3K27ac (Abcam 4729)

value: Ldb flox/flox regular chow


title: BC4-Tum-S


title: mouse_hepatocytes_flox2_Input

value: 7 weeks post natal


title: BC6-Tum-L

value: L


title: BC4-Tum-M

value: M

value: LumA


title: BC4-Tum-L


title: mouse_hepatocytes_flox2_H3K27ac


title: mouse_hepatocytes_flox3_Input


title: mouse_hepatocytes_flox1_H3K27ac


title: NKO_24h rep1

value: Osteoclast differentiation


title: BC5-Stroma-Inf3

value: Normal


title: BC5-Stroma-L1


title: NKO_24h rep2


title: BC5-Stroma-M1


title: NKO_12h rep2


title: WT_24h rep1


title: BC5-Stroma-Inf2

value: Inf


title: BC5-Stroma-S2

value: S


title: Brn3b_ATACseq_Rep3_Trial1

city: San Joan d'Alacant

first: Eloísa

last: Herrera

address: Av Ramon y Cajal s/n

department: Instituto Neurociencias Alicante

country: Spain

institute: CSIC-UMH

description:
ATC313_16640_TAAGGC
processed data file (merged):
ATAC_Contra_3_mm10_clean.rpkm.bw
ATAC_Contra_merged_mm10_clean.rpkm.bw

data_processing:
ATACseq: Paired-end reads were aligned with Bowtie2 v2.3.4.2 to mm10 mouse genome. Duplicated reads were removed with Picardtools v2.18.21. We used MAPQ > 20 to filter non-unique alignments. Only paired reads were used for posterior analysis. Peak calling was performed with MACS2 v2.1.1 as indicated in (Fernandez-Albert et al., 2019) .
RNAseq: Reads were aligned with HISAT2 v2.1.0 to the mouse genome. Mapped reads were annotated to genes from Ensemble (GRCm38.89) and quantified using Htseq v0.11.1. Differential expression analysis was performed using DESeq2 v1.26.0.
Genome_build: mm10
Supplementary_files_format_and_content: abundance measurements; bigwig

source_name: embryo

extract_protocol:
Retinas from embryos at E16.5 were dissected in HBSS buffer without Ca 2+ and Mg 2+ . In the case of retinas from Pou4f2 SunGFP embryos the ventrotemporal region was remove by dissection. Retinas were digested and disaggregated with the help of a P1000 using an enzymatic solution composed by colagenase, trypsin 23/08/2138 0,125%, BSA 0.2 mg/mL and DNAse 1μl/mL during 25’ at 37ºC. Digestion was stopped by adding DMEM with fetal bovine serum at 10% and disaggregation of the tissue was checked under microscope. The suspension was filtered and centrifugated at 1,250 rpm during 5’ at RT. The pellet was resuspended and sorted by flow cytometry to harvest our interest cells.
RNA was extracted from sorted cells using PicoPure TM RNA Isolation Kit (Arcturus) and libraries were made and sequenced in a HiSeq 2500 sequencer (Illumina, Inc).
Retinas from embryos at E16.5 were dissected in HBSS buffer without Ca 2+ and Mg 2+ . In the case of retinas from Pou4f2 SunGFP embryos the ventrotemporal region was remove by dissection. Retinas were digested and disaggregated with the help of a P1000 using an enzymatic solution composed by Colagenase, Trypsin 0,125%, BSA 0.2 mg/mL and DNAse 1μl/mL during 25 min at 37ºC. Digestion was stopped by adding DMEM with fetal bovine serum at 10% and disaggregation of the tissue was checked under microscope. The suspension was filtered and centrifuged at 1250 rpm during 5 min at RT. The pellet was resuspended and sorted by flow cytometry to harvest 50000 green fluorescent cells. Cell suspension was spin down at 500 g for 5 min at 4ºC and treated with cold lysis buffer (10mMTrisCl ph7.4, 10mM NaCl, 3mM MgCl 2 , 0.1% Igepal). The suspension was centrifuged at 500 g during 10 min at 4ºC. We discard the supernatant, and we make sure that the pellet was placed on ice. After that we continued with the transposition reaction and purification following the protocol as (Buenrostro et al., 2013, 2015) .
Libraries were purified and sequenced by an Illumina HiSeq 2500 sequencer (Illumina, Inc).

value: C57/DBA F1

value: retina

tag: gender

value: pooled male and female

value: WT


title: BC5-Tum-S

value: Tumor

value: Chinese


title: BC3-Stroma-M1

value: Stroma


title: BC3-Stroma-L1


title: BC5-Tum-L


title: mouse_hepatocytes_flox1_Input

value: hepatocytes


title: Brn3b_ATACseq_Rep3_Trial2

tag: genotype


title: BC5-Tum-Inf

tag: patient id


title: WT_24h rep2

value: Bone marrow cell

value: NCoR flox/flox


title: NKO_12h rep1

value: NCoR flox/flox, LysMCre


title: BC3-Stroma-M2

tag: patient age

value: M


title: Brn3b_ATACseq_Rep2_Trial1

description:
ATC213_16637_TAAGGC
processed data file (merged):
ATAC_Contra_2_mm10_clean.rpkm.bw
ATAC_Contra_merged_mm10_clean.rpkm.bw


title: WT_12h rep2


title: NKO_6h rep2


title: BC3-Stroma-Inf3

tag: ethnicity


title: Brn3b_ATACseq_Rep1_Trial1

description:
ATC113_16634_TAAGGC
processed data file (merged):
ATAC_Contra_1_mm10_clean.rpkm.bw
ATAC_Contra_merged_mm10_clean.rpkm.bw


title: BC5-Tum-M

tag: region

value: LumA


title: BC3-Stroma-S3

tag: distance zone from tumor edge


title: Day0 rep2

value: Wild type

value: Osteoclast differentiation


title: BC3-Stroma-L2

value: L

tag: molecular subtype


title: BC3-Tum-M

tag: tissue


title: BC5-Tum-C

value: C

value: LumB

tag: stromal cluster


title: Brn3b_ATACseq_Rep2_Trial1_re

description:
ATC213re_16637_TAAGGC
processed data file (merged):
ATAC_Contra_2_mm10_clean.rpkm.bw
ATAC_Contra_merged_mm10_clean.rpkm.bw

value: C57/DBA F1

value: retina


title: BC3-Stroma-S2

value: S

value: Normal


title: BC3-Stroma-Inf2

value: Chinese

value: Inf


title: BC3-Tum-L

value: Tumor


title: Brn3b_ATACseq_Rep2_Trial2

value: pooled male and female

value: WT


title: WT_6h rep2

tag: cell line

value: Bone marrow cell

value: NCoR flox/flox


title: Brn3b_ATACseq_Rep1_Trial2


title: WT_6h rep1

tag: cell type


title: BC5-Stroma-S1

value: Stroma


title: Sert_ATACseq_Rep2_Trial2

description:
ATC210_16638_CGTACT
processed data file (merged):
ATAC_Ipsi_2_mm10_clean.rpkm.bw
ATAC_Ipsi_merged_mm10_clean.rpkm.bw


title: Sert_ATACseq_Rep2_Trial1


title: Sert_ATACseq_Rep1_Trial2

description:
ATC110_16635_CGTACT
processed data file (merged):
ATAC_Ipsi_1_mm10_clean.rpkm.bw
ATAC_Ipsi_merged_mm10_clean.rpkm.bw


title: Sert_ATACseq_Rep3_Trial2

description:
ATC310_16641_CGTACT
processed data file (merged):
ATAC_Ipsi_3_mm10_clean.rpkm.bw
ATAC_Ipsi_merged_mm10_clean.rpkm.bw


title: NKO_1h rep1

value: NCoR flox/flox, LysMCre

tag: treatment


title: WT_12h rep1

value: Osteoclast differentiation


title: NKO_6h rep1


title: WT_1h rep2


title: Sert_ATACseq_Rep3_Trial1

tag: strain


title: Sert_ATACseq_Rep1_Trial1


title: BC3-Stroma-Inf1

value: LumA


title: NKO_1h rep2

tag: time


title: BC3-Tum-Inf


title: BC3-Tum-C

value: C


title: BC2-Stroma-L3

value: L


title: BC2-Stroma-M1

value: M


title: BC2-Stroma-Inf3


title: BC2-Stroma-M2


title: BC3-Stroma-S1


title: BC2-Stroma-S1


title: BC2-Stroma-S2


title: BC2-Stroma-L2


title: BC3-Tum-S


title: BC2-Tum-L


title: WT_1h rep1


title: NKO_0h rep2


title: BC2-Stroma-S3


title: Brn3b_RNAseq_Rep1

description:
EH13_5_21150_CGATGT
processed data file (merged):
EH13.rna.clean.rpkm.bw

molecule: polyA RNA

value: C57/DBA F1

value: retina


title: Sert_RNAseq_Rep3

description:
EH10_6_21155_GTTTCG
processed data file (merged):
EH10_56_clean.rpkm.bw


title: BC2-Stroma-L1

value: Normal


title: BC2-Stroma-Inf2

value: Chinese


title: BC2-Stroma-Inf1

value: Inf


title: BC2-Tum-M

value: Tumor


title: Sert_RNAseq_Rep2

description:
EH10_5_21154_CCGTCC
processed data file (merged):
EH10_56_clean.rpkm.bw

value: pooled male and female


title: WT_0h rep2


title: Sert_RNAseq_Rep1

description:
EH10_4_21153_ATGTCA
processed data file (merged):
EH10_56_clean.rpkm.bw

value: WT


title: BC1-Stroma-L3


title: NKO_0h rep1

value: Bone marrow cell


title: Brn3b_RNAseq_Rep3

description:
EH13_8_21152_CAGATC
processed data file (merged):
EH13.rna.clean.rpkm.bw


title: Brn3b_RNAseq_Rep2

description:
EH13_6_21151_TGACCA
processed data file (merged):
EH13.rna.clean.rpkm.bw


title: Input_FLAG_PGC1b_DRRM_Day4 rep1

data_processing:
FASTQ files were mapped to the mm10 mouse reference genome with Bowtie2.  Peaks were called with HOMER (findPeaks) using parameters “-style factor -minDist 200 -size 200”.  After merging these peaks, correlations among replicates from the same cell subset/treatment were evaluated by correlation using tag counts.  The two most highly correlated samples were used for identifying the most robust peaks using the irreproducible discovery rate (IDR) method.  For this step, peaks were called with HOMER’s findPeaks, using parameters “-L 0 -C 0 -fdr 0.9 -minDist 200 -size 200”.  IDR peaks from different conditions involved in a comparison merged with HOMER’s mergePeaks and annotated with HOMER’s annotatePeaks.pl.  The raw tags of all samples which had reasonable correlation were quantified with HOMER (annotatePeaks.pl) using parameter “-noadj”.  Peaks which contained at least 4 tags in at least 1 sample were used to identify differentially bounded peaks (DBP) by DESeq2.  Peaks were categorized as distal peaks which are 2 kb away from known TSS and promotor peaks which are located within 2 kb region of known TSS sites.
ChIP peak single was normalized to the sequence depth.
Assembly: mm10

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed in biological replicates as previously described (Heinz et al., 2018: Sakai et al., 2019) with modifications as follows.  For H3K27ac ChIP assays, cells were cross-linked with 1% (vol/vol) formaldehyde (Thermo Fisher Scientific) in PBS for 10 min at room temperature.  For NCoR1, HDAC3, PU.1, p65, Jdp2, Fosl2, PGC1b and FLAG-tag ChIP assays, cells were cross-linked with 2 mM disuccinimidyl glutarate (DSG) (ProteoChem) in PBS for 30 min at room temperature, and then directly a second crosslinking was performed by the addition of 1% (vol/vol) formaldehyde in PBS for 10 min.  The crosslinking reaction was quenched by 0.125 M glycine (Thermo Fisher Scientific).  Cells were washed once with cold PBS and pelleted at 1,000 g for 5 min at 4°C.  Crosslinked cells were resuspended in ice-cold hypotonic buffer (10 mM HEPES-KOH (pH 7.9), 85 mM KCl, 1 mM EDTA, 1% NP-40, 1 mM PMSF (Sigma), 0.5 mM sodium butyrate (Sigma), 1X protease inhibitor cocktail (Sigma)), and centrifuged at 1,000 g for 5 min at 4°C to obtain a nuclear fraction.  Nuclear pellets were resuspended in 100 ml of either LB3 buffer (10 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-laurosylsarcosine, 1 mM PMSF, 0.5 mM sodium butyrate, 1X protease inhibitor cocktail for H3K27ac ChIP) or PIPA-NR buffer (20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.4% sodium deoxycholate, 0.1% SDS, 1% NP-40, 0.5 mM DTT, 1 mM PMSF, 0.5 mM sodium butyrate, 1X protease inhibitor cocktail, for NCoR, HDAC3, PU.1, p65, Fosl2, PGC1b and FLAG-tag ChIP).  Chromatin DNA was sonicated in a 96 Place microTUBE Rack (Covaris) using a Covaris E220 for 12-18 cycles with the following setting: time, 60 seconds; duty, 5.0; PIP, 140; cycles, 200; amplitude, 0.0; velocity, 0.0; dwell, 0.0. Samples were centrifuged at 15,000 rpm for 10 min at 4°C, and the supernatant was used for immunoprecipitation.  LB3 lysate was diluted 1.1-fold with 10% Triton X-100.  1% of the lysate was kept as ChIP input.  The lysates were rotated with each antibody pre-bound to 20 ml of beads (10 ml of Dynabeads protein A (Invitrogen) + 10 ml of Dynabeads protein G (Invitrogen)) overnight at 4°C.  After the immunoprecipitation, beads were collected on a magnet and washed three times each with wash buffer I (20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA, 1 mM PMSF, 0.5 mM sodium butyrate, 1X protease inhibitor cocktail), wash buffer III (10 mM Tris-HCl (pH 7.5), 250 mM LiCl, 1% Triton X-100, 0.7% sodium deoxycholate, 1 mM EDTA, 1 mM PMSF, 0.5 mM sodium butyrate, 1X protease inhibitor cocktail) and twice with TET (10 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.2% Tween-20, 1 mM PMSF, 0.5 mM sodium butyrate, 1X protease inhibitor cocktail), and then resuspended in 25 ml of TT (10mM Tris-HCl (pH 7.5), 0.05% Tween-20).
The immunoprecipitated chromatin samples were used for library preparation with NEBNext Ultra II Library kit (NEB) according to the manufacturer’s instructions.  DNA in 46.5 ml of NEB reactions was crosslinks reversed by adding 4 ml of 10% SDS, 4.5 ml of 5 M NaCl, 3 ml of 500 mM EDTA, 1 ml of 20 mg/ml proteinase K (NEB) and 20 ml of water by incubation for 1 hr at 55°C, and then 30 min at 65°C.  DNA was purified with 2 ml of SpeedBeads (GE Healthcare) in 20% PEG 8000/1.5 M NaCl (Final 12% PEG 8000), and eluted with 25 ml of TT.  The eluted DNA was amplified for 14 cycles in 50 ml of PCR reactions using NEBNext High-Fidelity 2X PCR Master Mix and 0.5 mM each of primers Solexa 1GA and Solexa 1GB.  The amplified libraries were purified with 2 ml of SpeedBeads in 20% PEG 8000/2.5 M NaCl (Final 13% PEG 8000), eluted with 20 ml of TT, size selected using PAGE/TBE gel (Invitrogen) for 225-325 bp fragments by gel extraction, and single-end sequenced on HiSeq 4000.  ChIP input material (1% of sheared DNA) in 46.5 ml of TE was crosslinks reversed by adding 4 ml of 10% SDS, 4.5 ml of 5 M NaCl, 3 ml of 500 mM EDTA, 1 ml of 20 mg/ml proteinase K and 20 ml of water by incubation for 1 hr at 55°C, and then 30 min at 65°C.  The input DNA was purified with SpeedBeads as described above, and eluted with 25 ml of TT.  The eluted input DNA was prepared for libraries and amplified as described for ChIP samples.

value: RAW 264.7 cell

tag: chip antibody


title: BC2-Tum-C


title: BC2-Tum-S

value: S


title: BC1-Stroma-M3

value: Stroma


title: Input_FLAG_PGC1b_WT_Day4 rep1


title: BC1-Stroma-M2

value: LumB


title: BC1-Stroma-Inf2


title: FLAG_PGC1b_DRRM_Day4 rep2

value: FLAG


title: BC1-Stroma-L2

value: LumA


title: BC1-Stroma-M1


title: BC1-Stroma-Inf3


title: HFD_mouse_hepatocytes_Ldb1ko-3

data_processing:
Raw sequence reads were trimmed with cutadapt v2.7(Martin, 2011) to remove any adapters while performing light quality trimming with parameters "-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -q 20 --minimum-length=25".
For RNAseq, Trimmed reads were mapped to the Homo sapiens hg38 or mouse mm10 reference genome  using hisat2 v2.1.0 (Kim et al., 2015) with default parameters. For ChIPseq, Reads were aligned to the human GENCODE release 25 assembly using Bowtie2 v2.3.5(Langmead and Salzberg, 2012).
For RNAseq, multimapping reads were filtered using samtools 1.9 (Li et al., 2009). For ChIPseq, Multimapping reads were removed with samtools v1.9 using the “view” subcommand and the additional argument “-q 20”, and duplicate reads were removed with the Picard v2.21.4 (Toolkit, 2019) Mark Duplicates tool.
For RNAseq, uniquely aligned reads were counted using subread featureCounts v1.6.4 with default parameters (Liao et al., 2014) except that “-s1” option for this sense-stranded library. For ChIPseq, BigWig signal tracks were created with deepTools v3.3.1 (Ramirez et al., 2016) using the bamCoverage tool with the additional arguments “–normalize Using CPM –extend Reads 300”.
For RNAseq, Differential expression between groups of samples was tested using R version 3.5.1 (R Core Team, 2018) (R Core Team) with DESeq2 1.22.1 (Love et al., 2014). For ChIPseq, peaks were called for each replicate individually using macs v2.2.7.1(Zhang et al., 2008). Pooled peaks were separately called by providing both replicates simultaneously to macs2. Final peaks for each antibody were selected as pooled peaks that also had a peak intersecting it by at least 1 bp in at least one of the replicates using BEDTools v2.29.0 (Quinlan and Hall, 2010) and pybedtools 0.8.0 (Dale et al., 2011).
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: Excel files.xlsx contain all gene TPM counts from RNAseq results. Excel files.xls contain peaks coordinates. Bigwig files are created with deepTools v3.3.1 using the bamCoverage tool.

growth_protocol: Mice were housed in a clean conventional vivarium at ~22 oC, with a 12:12-h dark-light cycle (lights on at 06:00). HepG2 cells (HB-8065, ATCC) were cultured in MEM medium (Corning, MT10010CV) with 10% FBS (ATLANTA Biologicals, s12450) and 1 ×Penicillin-Streptomycin (Gibco, 15140-122).

extract_protocol:
RNA was extracted by PureLink RNA mini kit (Invitrogen, 12183020), and DNA was removed by DNase digestion (Invitrogen, 12185-010).
For RNA sequencing, libraries were constructed from 1 mg total RNA by using the Truseq Stranded mRNA sample preparation kit (Illumina 20020493). ChIP-qPCR and ChIPmentatation were performed as described previously (Krivega and Dean, 2018a; Schmidl et al., 2015).

treatment_protocol: Mice were ad libitum access to water and chow (LabDiet, Advanced Protocol 5V0T, 12.5% kcal from fat) or high fat diet (HFD, 89067-469, 60% kcal fat, VWR). Ldb1 flox mice (Zhao et al., 2007) and Albumin-Cre mice (003574, The Jackson Laboratory) were mated to obtain control mice (Ldb1flox/flox) and liver-specific Ldb1 knockout mice Ldb1flox/flox; Alb-Cre+/-) on a C57Bl6 background. Only male littermates were used. To generate LDB1 knockout HepG2 clones, pSpCas9-2A-GFP plasmid (Addgene, Plasmid #4813) containing a guide RNA targeting the first exon of the LDB1 gene was electroporated into HepG2 cells by using Lonza nucleofector with kit V (VCA-1003).

value: hepatocytes

value: Ldb flox/flox;Alb-Cre high fat diet for 15 weeks

tag: age

value: 23 weeks post natal


title: BC1-Stroma-S1


title: BC1-Stroma-L1

value: L


title: Input_FLAG_PGC1b_DRRM_Day4 rep2


title: HFD_mouse_hepatocytes_Ldb1ko-4


title: BC2-Tum-Inf


title: Input_FLAG_PGC1b_WT_Day4 rep2


title: NCI-H446 ERY974+cisplatin-9

city: Kajiwara

first: YUJI

last: SANO

state: Kamakura

country: Japan

institute: Chugai Pharmaceutical Co., Ltd

data_processing:
The RNAseq reads were mapped to human (GRCh38) and mouse (GRCm38) RefSeq transcripts  using  bowtie 1.1.2
Reads mapped to the transcripts of both organisms were excluded
The calculation of fragments per kilobase of transcript per million reads mapped (FPKM) using RSEM v1.2.31
Assembly: GRCh38 + CRCm38 with RefSeq annotations
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism:
Homo sapiens
Mus musculus

growth_protocol: NCI-H446 were expanded in vitro, and inoculated into the huNOG mice.

extract_protocol:
RNA was harvested from the tumors using RNeasy mini kit (Qiagen). Total RNA was used for RNAseq.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: When tumor was established, 7.5 mg/kg cisplatin was administered one day before the administration of 5 mg/kg ERY974 in the combination group. In the monotherapy group, each agent was administered as described above. Then, tumours were collected on day 6 after ERY974 administration and used for RNA analysis.

value: Lung tumor

value: Day 6


title: FLAG_PGC1b_WT_Day4 rep2


title: WT_0h rep1

value: NCoR flox/flox

value: Osteoclast differentiation


title: BC1-Tum-S

value: Tumor

value: Chinese


title: BC1-Tum-L


title: FLAG_PGC1b_DRRM_Day4 rep1

value: Bone marrow cell


title: BC1-Stroma-S3


title: BC1-Stroma-S2


title: NCI-H446 ERY974+cisplatin-8


title: BC1-Stroma-Inf1

value: Inf


title: HFD_mouse_hepatocytes_Ldb1ko-1


title: FLAG_PGC1b_WT_Day4 rep1

value: RAW 264.7 cell


title: NCI-H446 ERY974+cisplatin-7


title: NCI-H446 ERY974+cisplatin-4


title: BC1-Tum-M

value: M


title: HFD_mouse_hepatocytes_control-4

value: Ldb flox/flox high fat diet for 15 weeks


title: Input_PGC1b_siRnu12_Day4 rep2


title: Input_PGC1b_siRnu12_Day4 rep1


title: NCI-H446 ERY974+cisplatin-5


title: NCI-H446 ERY974+cisplatin-3


title: NCI-H446 ERY974+cisplatin-2


title: BC1-Tum-Inf


title: BC1-Tum-C

value: C


title: HFD_mouse_hepatocytes_control-3


title: Input_PGC1b_siDancr_Day4 rep2


title: NCI-H446 ERY974+cisplatin-6


title: HFD_mouse_hepatocytes_Ldb1ko-2


title: HFD_mouse_hepatocytes_control-2


title: NCI-H446 ERY974+cisplatin-1


title: Input_PGC1b_siDancr_Day4 rep1


title: NCI-H446 Cisplatin-9

value: Cisplatin


title: NCI-H446 Cisplatin-6


title: RC_mouse_hepatocytes_Ldb1ko-3

value: hepatocytes

value: Ldb flox/flox;Alb-Cre regular chow

value: 7 weeks post natal


title: NCI-H446 Cisplatin-8


title: HFD_mouse_hepatocytes_control-1

value: 23 weeks post natal


title: RC_mouse_hepatocytes_Ldb1ko-2


title: NCI-H446 Cisplatin-7

value: Lung tumor


title: NCI-H446 Cisplatin-3

value: Day 6


title: RC_mouse_hepatocytes_Ldb1ko-1


title: NCI-H446 Cisplatin-2


title: NCI-H446 ERY974-9


title: RC_mouse_hepatocytes_control-3

value: Ldb flox/flox regular chow


title: Input_PGC1b_siCont_Day0 rep2


title: RC_mouse_hepatocytes_control-2


title: NCI-H446 ERY974-8


title: NCI-H446 ERY974-6


title: NCI-H446 ERY974-7


title: Input_PGC1b_siCont_Day0 rep1


title: NCI-H446 ERY974-5


title: Input_PGC1b_siCont_Day4 rep2


title: PGC1b_siRnu12_Day4 rep2


title: NCI-H446 ERY974-4


title: NCI-H446 ERY974-3


title: NCI-H446 Cisplatin-5


title: PGC1b_siRnu12_Day4 rep1


title: CBs

city: Cold Spring Harbor

first: Gayan

middle: Indhu

last: Balasooriya

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were maped to mm10 whole genome using STAR 2.7 aligner
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts (FPKM) for every gene and every cell in every sample.

source_name: Cardiac Body Cells

growth_protocol: In vitro cultures

extract_protocol:
Samples were processed in Fluidigm C1™ Single-Cell Auto Prep System
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mature Cardiac Cells

value: C57BL/6 x CAST/EiJ

tag: Sex

value: male


title: RC_mouse_hepatocytes_control-1

tag: genotype


title: PGC1b_siDancr_Day4 rep2

value: Bone marrow cell


title: Input_PGC1b_siCont_Day4 rep1


title: NCI-H446 ERY974-2


title: NCI-H446 ERY974-1


title: mESCs (triplicate)

source_name: Embryonic Stem Cells

value: mESC


title: NCI-H446 vehicle-7

value: Vehicle


title: NCI-H446 vehicle-6


title: NCI-H446 vehicle-9


title: CPCC-rep#3

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were maped to mm10 whole genome using STAR 2.7 aligner
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts (FPKM) for every gene and every replicate. Counts from biological triplicates are in one file

source_name: Cardiac Precursor Cells

growth_protocol: In vitro

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen). ). 0.5 ug  of total RNA was used to construct the sequencing libraries. Libraries were generated using Clontech SMART-Seq® v4 Ultra® Low Input RNA Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cardiac Precursor Cells


title: PGC1b_siCont_Day4 rep2


title: PGC1b_siCont_Day4 rep1


title: NCI-H446 vehicle-2


title: PGC1b_siCont_Day0 rep2


title: PGC1b_siDancr_Day4 rep1


title: NCI-H446 Cisplatin-1


title: NCI-H446 vehicle-1


title: CPCC-rep#2


title: NCI-H446 vehicle-4


title: CPCC


title: NCI-H446 vehicle-5


title: H3K27ac_Pgc1b_flox_Ad_Cre_Day4 rep2


title: mESCs-rep#3


title: NCI-H446 vehicle-8


title: MKN45 Vehicle 3

growth_protocol: PC10, NCI-H446, MKN74, and MKN45 were expanded in vitro, and inoculated into the humanized mice.

extract_protocol: RNA was harvested from the tumors using RNeasy mini kit (Qiagen). Total RNA was used for RNAseq.

treatment_protocol: When tumor was established, 1mg/kg ERY974 was administered (day 0), and tumor was collected on day 3.

value: Gastric tumor

value: Day 3


title: mESCs-rep#2


title: H3K27ac_Pgc1b_flox_Ad_Cre_Day4 rep1


title: NCI-H446 vehicle-3


title: PGC1b_siCont_Day0 rep1


title: CPCC-rep#1


title: H3K27ac_Pgc1b_flox_Ad_RFP_Day4 rep2


title: MKN45 ERY974 3


title: MKN45 ERY974 2


title: MKN45 Vehicle 2


title: MKN45 Vehicle 1


title: MKN45 ERY974 1


title: MKN74 ERY974 3


title: E8.5 WT

city: Mishima

first: Yumiko

last: Saga

state: Shizuoka

address: 1111 Yata

department: Department of Gene Function and Phenomics

institute: National Institute of Genetics

data_processing:
For all libraries, Low-quality sequences, adapters and polyA or T were trimmed or removed using Cutadapt(version 2.8) with the following options: "-e 0.1 -q 20 -m 20 -O 3 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a A{100} -a T{100}". The raw reads and processed reads in each step were checked using FastQC (version 0.11.7, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
To map reads to the mouse reference genome, the mouse reference genome and gene annotation GTF (UCSC mm10 downloaded from Illumina iGenomes;https://support.illumina.com/sequencing/sequencing_software/igenome.html) were used. Splicing-site and exon information were extracted from the gene annotation GTF file using the Python scripts hisat2_extract_splice_sites.py and hisat2_extract_exons.py, respectively, from the HISAT2 (version 2.1.0) package. The index of the reference genome and annotated transcripts was built using hisat2-build. Clean reads were then mapped to the indexed reference genome using HISAT2 (version 2.1.0) with default option.
The obtained BAM files were sorted by genomic coordinates using the SAMtools(version 1.9) "sort" command.
Raw read counts per gene were calculated using featureCounts(version 2.0.0) with options: "-s 2 -t exon -g gene_id -a iGenomes/mm10/Annotation/Genes/genes.gtf".
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

source_name: Embryonic tissue

extract_protocol:
Whole embryos were dissolved in Trizol reagent then RNA was extracted.
We used KAPA-Stranded mRNA-seq kit (Illumina Platforms. KR0960-v5.17) and followed the accompanied protocol.

value: ICR

value: embryo

value: wild-type


title: H3K27ac_Pgc1b_flox_Ad_Cre_Day0 rep1


title: H3K27ac_Pgc1b_flox_Ad_RFP_Day4 rep1


title: H3K27ac_Pgc1b_flox_Ad_Cre_Day0 rep2


title: mESCs-rep#1


title: NCI-H446 ERY974 3


title: E8.5 Ddx6 KO rep2


title: H3K27ac_Pgc1b_flox_Ad_RFP_Day0 rep2


title: MKN74 ERY974 2


title: E8.5 Ddx6 KO rep1


title: MKN74 Vehicle 3


title: MKN74 ERY974 1


title: MKN74 Vehicle 1


title: NCI-H446 ERY974 1


title: H3K27ac_WT_Day4_RGFP966 rep2


title: NCI-H446 Vehicle 2


title: H3K27ac_Pgc1b_flox_Ad_RFP_Day0 rep1


title: RT112, IgG, rep3

city: Birmingham

first: Ryan

last: Miller

state: AL

address: 1824 Sixth Ave S

department: Pathology

institute: UAB

data_processing:
Base calls were performed using bcl2fastq2 for NextSeq output
ChIP-seq reads were trimmed from 3' end to remove Illumina adapters using CutAdapt
ChIP-seq reads were aligned to the UCSC hg38 genome using Bwa-mem2. Only uniquely mapping reads were retained.
PCR duplicates were removed using Picard MarkDuplicates
Spike-in normalized BigWig files were produced using deepTools bamCoverage with a scaling factor derived by dividing E. coli read counts by total read counts and normalizing to the smallest number for each CUT&RUN mark
Alignment files were converted to BEDPE format using bedtools bamtobed and extended to the full fragment length. Scaled bedgraphs were generated using bedtools genomecoverage and the E. coli spike in normalization factor. Peaks were called with SEACR in stringent mode using these bedgraphs as input. Peaks were merged and reported in BED file format.
Assembly: hg38
Supplementary files format and content: BigWig, SEACR called peak BED files (replicates merged)

growth_protocol: DMEM, 10% FBS, 37C with 5% CO2

extract_protocol:
Adherent cells were detached with Accutase and processed using the EpiCypher CUTANA CUT&RUN kit according to manufacturer instructions. 0.5 ng E. coli spike-in DNA was added for normalization.
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs). Libraries were size selected using Ampure XP bead from Beckman Coulter to retain fragments >150 bp. Libraries were amplified using 14 cycles on the thermocycler and validated using the Agilent High Sensitivity D1000 Tapestation Kit. All libraries were pooled and sequenced on a 150 cycle Mid Output v2.5 Illumina kit.
CUT&RUN

value: Human bladder transitional cell carcinoma

tag: cut&run antibody

value: IgG (EpiCypher, 13-0042)


title: NCI-H446 ERY974 2

value: Lung tumor


title: NCI-H446 Vehicle 1


title: PC10 ERY974 2


title: H3K27ac_WT_Day4_Veh rep2


title: RT112, H3K4me3, rep3

value: H3K4me3 (EpiCypher, 13-0041)


title: PC10 ERY974 1


title: PC10 vehicle 3


title: PC10 ERY974 3


title: H3K27ac_WT_Day0_Veh rep2


title: RT112, H3K4me3, rep1


title: PC10 vehicle 2


title: NCI-H446 Vehicle 3


title: RT112, H3K4me3, rep2


title: E7.5 WT


title: RT112, IgG, rep2


title: RT112, ARID1ACST, rep3

value: ARID1A (Cell Signaling Technology, 12354)


title: RT112, ARID1ACST, rep2


title: PC10 vehicle 1


title: H3K27ac_WT_Day4_Veh rep1


title: Dentate Gyrus Differentiation CHIR99021+DAPT - DIV30 - 48h on Msl - Rep 2

city: Genova

first: Luca

last: Pandolfini

state: Genova

address: Via Enrico Melen 83, Building B

department: Center for Human Technologies

institute: Istituto Italiano di Tecnologia - I

data_processing:
Transcripts were pseudoaligned using Salmon in mapping-based mode (with its default "--validateMappings" flag). A decoy-aware version of the Ensembl mouse transcriptome (mm10; refgenomes.databio.org) was used as a reference.
Assembly: mm10 (refgenomes.databio.org)
Supplementary files format and content: Salmon counts

source_name: Human induced pluripotent stem cells

growth_protocol: Starting from hiPSCs (ATCC DYS0100) cells were seeded onto Geltrex™ LDEV-Free Reduced Growth Factor Basement Membrane Matrix (ThermoFisher, A1413202) in Essential 8™ Medium (ThermoFisher A1517001) containing Essential 8™ Medium Supplement(ThermoFisher A1517-01), 100 U/ml Penicillin-streptomycin, and 2 μM Y-27632 (Cell Guidance Systems SM02-5). Less than 24 hours later, E8 containing Y-27632 was aspirated and fresh E8 media without Y-27632 was added. E8 media was changed daily for another 2 days. Cells were then subjected to neural induction (DIV 0) and incubated in WiBiTi media based in DMEM/F-12 containing containing 2mM Glutamine, 1 mM Sodium Pyruvate, 100 U/ml Penicillin-streptomycin, 1mM Non-essential amino acids, 0.05mM β-mercaptoethanol, 10 μM 53AH, 10 μM LDN193189 hydrochloride, 1 μM RepSox (SigmaAldrich R0158-5MG), N-2 Supplement 100X, and B-27 Supplement minus Vitamin A 50X. WiBiTi was changed daily until DIV 10 where cells were passaged and reseeded in N2B27 media containing Y-27632 at a density of 200,000 cells/cm2 on poly-l-ornithine and Laminin iMatrix-511silk E8 (511 human laminin, Amsbio AMS.892 021) coated plastic. Less than 24 hours later, N2B27 containing Y-27632 was aspirated and fresh WiBiTi media without Y-27632 was added. Cells were maintained in WiBiTi for another 4 days until DIV 15, where the media was changed to N2B27. The following day, DIV 16, cells were then cultured for an additional 6 days (DIV 21) in CH27 media, N2B27 media supplemented with 3 μM CHIR99021 (SigmaAldrich SML1046-5MG). At DIV 21 cells reach confluency and required another passage in CH27 media supplemented with Y-27632 and onto poly-l-ornithine/511 human laminin coated plastic at a density of 200,000 cells/cm2. Less than 24 hours later, CH27 containing Y-27632 was aspirated and fresh CH27 media without Y-27632 was added. Media was changed daily with fresh CH27 until DIV 28 wherein cells were passaged for longitudinally maintaining the huDG NSC niche, their final reseeding, frozen in N2B27 containing Y-27632 and 10% DMSO, fixed for immunocytodetection, or allowed to grow another 6 days in N2B27 media for qRT-PCR harvesting.     Starting from DIV 28, huDG NSCs were passaged and reseeded in N2B27 media containing Y-27632 at a density of 100,000 cells/cm2 on poly-l-ornithine/511 human laminin coated plastic. Less than 24 hours later, CH27 containing Y-27632 was aspirated and fresh CH27 media without Y-27632 was added. CH27 media was changed daily for 2 weeks from the reseeding date (DIV 42) whereupon cells were passaged again in an identical manner until DIV 200.

extract_protocol:
All in vitro samples used for transcriptomic assays were harvested by 5’, 37oC trypsinization after which was inactivated with inactivated Fetal Bovine Serum (Euroclone ECS0180L). Detached cells were homogeneously suspended in solution, collected in microcentrifuge tubes and pelleted at 200 g for 5’. After centrifugation, the supernatant was aspirated, and the cell pellet was disrupted and processed using NucleoSpin® RNA kit (Machery-Nagel, 740955.250). RNA concentration was measured using a NanoDrop™ Lite Spectrophotometer (ThermoFisher ND-LITE).
RNA-seq libraries were prepared with the Stranded Total RNA Prep with Ribo-Zero Plus Kit (Illumina) as described in manufacturer's instructions

treatment_protocol: When ready to differentiate, either endogenously or by NOTCH inhibitor, DAPT, huDG NSCs were seeded onto poly-l-ornithine/purified mouse laminin coated plates. For immuncytodetection purposes, cells were seeded onto Eppendorf biofilm-bottom plates as they did not survive differentiation on Eppendorf glass-bottom plates without a layer of mESC-derived hippocampus neurons, derived using the protocol from Terrigno et al, 2018. Cells were also seeded in a density corresponding to their age and purpose i.e. for RNAseq, DIV 28 cells were plated at 200,000 cells/cm2 and DIV160 cells were plated at 400,000 cells/cm2. After passaging/thawing, cell suspensions were centrifuged at 200 g for 4 minutes and the cell pellet resuspended in CH27 supplemented with Y-27632. Less than 24 hours later, CH27 containing Y-27632 was aspirated and fresh CH27 media without Y-27632 was added. Media was changed daily with fresh CH27 until cells reached 90% confluency (after ~10 days) whereupon media was changed to Dentate Gyrus Differentiation (DGD) media, containing DMEM/F-12 2mM Glutamine, 1 mM Sodium Pyruvate, 100 U/ml Penicillin-streptomycin, 0.05mM β-mercaptoethanol, N-2 Supplement (100X) B-27 Supplement (50X) (with Vitamin A, ThermoFisher 125870-01), 20 ng/ml Recombinant human BDNF (NBP2-52006, Novus Biologicals), and 0.5 mM Ascorbate (A92902, Sigma Aldrich). Experimental differentiation media included +3 μM CHIR99021 (DGDC), +12.5 μM DAPT (DGDD, Sigma Aldrich D5942-5MG), or both (DGDCD).

value: ATCC- DYS0100

value: CHIR99021+DAPT on Msl

tag: replicate


title: Dentate Gyrus Differentiation CHIR99021+DAPT - DIV30 - 48h on Lam511 - Rep 3

value: CHIR99021+DAPT on Lam511


title: Input_PGC1b_WT_Day4 rep2

value: Bone marrow cell


title: Dentate Gyrus Differentiation CHIR99021+DAPT - DIV30 - 48h on Msl - Rep 1


title: RT112, IgG, rep1


title: Dentate Gyrus Differentiation CHIR99021+DAPT - DIV30 - 48h on Lam511 - Rep 1


title: H3K27ac_WT_Day4_RGFP966 rep1


title: Dentate Gyrus Differentiation CHIR99021+DAPT - DIV30 - 48h on Lam511 - Rep 2


title: Input_PGC1b_WT_Day4 rep1


title: Dentate Gyrus Differentiation CHIR99021 - DIV30 - 48h on Msl - Rep 3

value: CHIR99021 on Msl


title: Dentate Gyrus Differentiation CHIR99021+DAPT - DIV30 - 48h on Msl - Rep 3


title: Dentate Gyrus Differentiation CHIR99021 - DIV30 - 48h on Msl - Rep 2


title: RT112, ARID1AAbcam, rep3

value: ARID1A (Abcam, ab182560)


title: Input_PGC1b_WT_Day0 rep2


title: Input_PGC1b_WT_Day0 rep1


title: H3K27ac_WT_Day0_Veh rep1


title: RT112, ARID1ACST, rep1


title: Dentate Gyrus Differentiation CHIR99021 - DIV30 - 48h on Msl - Rep 1


title: Dentate Gyrus Differentiation CHIR99021 - DIV30 - 48h on Lam511 - Rep 2

value: CHIR99021 on Lam511


title: RT112, ARID1AAbcam, rep2


title: PGC1b_WT_Day4 rep2


title: RT112 cells, ARID1A kd, GSK126 treatment rep 3

data_processing:
Basecall to fastq file generation (bcl2fastq2/2.20.0-foss-2016b-Python-2.7.12)
Fragments aligned to the human genome using Star (STAR/2.7.3a-GCC-6.4.0-2.28)
Aligned fragments counted using Salmon (Salmon/0.14.1-foss-2018b)
DESeq2 analysis performed (variables for modeling: replicate, genotype, treatment) to obtain differential gene expression data, raw counts, and normalized counts (DESeq2_1.28.1)
Data was filtered to exclude genes where there were less than 3 samples with normalized read counts less than or equal to 5
Genome_build: GENCODE v32 (GRCh38.p13)
Supplementary_files_format_and_content: raw_counts.csv file is a matrix of raw read counts (every gene for every sample) obtained from R package DESeq2

source_name: bladder cancer

growth_protocol: RT112 cells grown in DMEM with pen/strep and 10% FBS in a 5% CO2 cell culture incubator

extract_protocol:
RNA from cultured cells was extracted with Direct-zol RNA miniprep kit (Zymo research)
Library prep was performed using a KAPA Stranded mRNA-seq kit (KK8421) and prepared for sequencing using standard Illumina protocol (final loading concentration 1.65pM)

value: Human bladder carcinoma

value: ARID1A knockdown


title: Dentate Gyrus Differentiation CHIR99021 - DIV30 - 48h on Lam511 - Rep 1


title: Dentate Gyrus Differentiation CHIR99021 - DIV30 - 48h on Lam511 - Rep 3


title: COV434 cells, 3np, rep1

city: Wuhan

first: Wenpei

last: Xiang

address: Institute of Reproductive Health, Tongji Medical College, No.13 Hangkong Road

country: China

institute: Huazhong University of Science and Technology

data_processing:
Basecalls were performed using bcl2fastq2 v2.17.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic v0.39
Trimmed sequence reads were mapped to GRCh38/hg38 using HISAT2 v2.1
Assembly: hg38
Supplementary files format and content: text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using TRIzol RNA Isolation Reagents (Invitrogen) according to the manufacturers' instruction.
RNA libraries for RNA-seq were prepared using VAHTS Stranded mRNA-seq Library Prep Kit for Illumina

value: Human ovarian granulosa tumour cell

value: 3-nitropropanoic acid


title: COV434 cells, control, rep2

value: control


title: PGC1b_WT_Day0 rep2


title: COV434 cells, 3np, rep3


title: RT112, ARID1AAbcam, rep1

value: Human bladder transitional cell carcinoma


title: COV434 cells, 3np, rep2


title: COV434 cells, control, rep1


title: RT112 cells, ARID1A kd, GSK126 treatment rep 2


title: PU.1_WT_Day4 rep2


title: hiBMEC Control 3

city: College Park

first: Alisa

last: Morss Clyne

state: MD

address: 8278 Paint Branch Dr.

institute: University of Maryland

data_processing:
usegalaxy.org version 22.05.rc1
Quality assessment using FASTQC (all passed)
Trimmomatic on paired-end reads to remove low-quality bases and adaptor sequences
HISAT2 on paired-end reads to align them
FeatureCounts to align HISAT2 data to human (hg38) genome
FPKMCount to convert data to FPKM
Assembly: hg38
Supplementary files format and content: tab-deliminated text files containing FPKM for each sample

extract_protocol:
RNA was extracted using a phenol/chloroform extraction.
Library was constructed by Novogene USA (Sacremento, CA)

value: iPSC

value: WT

value: BMEC differentiation


title: PGC1b_WT_Day0 rep1


title: hiBMEC Control 2


title: A549NB, scRNAseq

city: Beijing

first: Xiaofei

last: Zheng

state: Beijing

address: No.27, Taiping Road

institute: Beijing Institute of Radiation Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sample demultiplexing, barcode processing, and unique molecular identifers (UMI) counting were performed by using the 10x Genomics pipeline CellRanger v.2.1.0 with default parameters. Specifcally, for each library, raw reads were demultiplexed using the pipeline command ‘cellranger mkfastq’ in conjunction with ‘bcl2fastq’ (v2.17.1.14, Illumina) to produce two fastq fles: the read 1 fle contains 26-bp reads, each consists of a cell barcode and a unique molecule identifer (UMI), and the read 2 file contains 96-bp reads including cDNA sequences. Reads then were aligned to the human reference genome (GRCh38), fltered, and counted using ‘cellranger count’ to generate the gene-barcode matrix.
For scRNA-seq data, expression matrices were processed using scCANCER (v2.2.1) . Briefly, the droplets having low transcripts diversity, capturing lysed cells or doublets were filtered based on five matrices: the number of total unique molecular identifiers (UMIs), the number of expressed genes and the percentages of UMIs from mitochondrial, ribosomal and  dissociation-associated genes per cell. Doublet score was performed by scCANCER using binary classification-based and co-expression-based algorithm, scds (v.1.2.0). After quality control, downstream analyses were performed based on Seurat (v4.1.0) in which canonical correlation analysis (CCA) was applied to integrate scRNA-seq data and remove the batch effect between different samples.
For scATAC-seq data, we computed per-cell quality control metrics using the DNA accessibility assay, including the strength of the nucleosome banding pattern and transcriptional start site (TSS) enrichment score and removed low-quality cells based on these metrics.
Assembly: GRCh38
Supplementary files format and content: .gz files including filtered tab-separated values files and matrix files

growth_protocol:
Purified A549 cells were monoclonally cultured in DMEM medium.
Irradiated A549 cells for scRNA-seq were harvested after continued culturing for 2 h and 6 h after irradiation; irradiated A549 cells for scATAC-seq were harvested at immediate and after continued culturing for 2 h after irradiation; A549 cells in control group for scRNA-seq and scATAC-seq were all harvest at the same time with 2h post-irradiation goups.

extract_protocol:
Irradiated A549 cells were harvested after continued culturing for 2 h and 6 h after irradiation. For scATAC-seq, irradiated A549 cells were harvested immediately and after continued culturing for 2 h after γ-ray treatment. Non-irradiated A549 cells for scRNA-seq and scATAC-seq were both harvested at 2 h after radiation. Single-cell sample preparation was conducted according to Sample Preparation Demonstrated Protocol provided by 10x Genomics as follows: 1mL of cell suspensions from each sample was pelleted in Eppendorf tubes by centrifugation (400 g, 5min). The supernatant was discarded, and the cells pellet was then resuspended in 1x PBS with 0.04% BSA, followed by two washing procedures by centrifugation (150 g, 3min). After the second wash, cells were resuspended in ~500 uL 1x PBS with 0.04% BSA followed by gently pipetting mix 10-15 times. Cells were counted using an Invitrogen Countess automated cell counter (LUNAⅡ) and the viability of cells was assessed by Trypan Blue staining (0.4%). After cell harvest, library and sequencing were completed by JingNeng company.
Libraries were prepared using the 10x Genomics Chromium Controller in conjunction with the single-cell 3′ v2 kit.

treatment_protocol: Purified A549 cells used in experimental groups were treated with Gy γ-ray.

value: lung cancer

value: Ctrl (purified)


title: RT112 cells, ARID1A kd, DMSO treatment rep 3

value: DMSO


title: NCI-H446 Cisplatin-4

value: Lung tumor

value: Cisplatin

value: Day 6


title: RT112 cells, ARID1A kd, GSK126 treatment rep 1


title: PU.1_WT_Day4 rep1

value: Bone marrow cell


title: PGC1b_WT_Day4 rep1


title: RT112 cells, ARID1A wt, GSK126 treatment rep 3

value: ARID1A wildtype


title: A549CD, scRNAseq

description: 10x Genomics

value: IR 6h (purified)


title: Experiment 2

city: Groningen

first: Reinoud

last: Gosens

address: Antonius Deusinglaan 1

department: Molecular Pharmacology

country: Netherlands

institute: University of Groningen

data_processing:
Library preparation was checked by calculating ribosomal (and globin) content.
Checks for possible sample and barcode contamination were performed and a set of standard quality metrics for the raw dataset was determined using quality control tools (FstQC v0.34 and FastQA).
Prior to alignment, the reads were trimmed for adapter sequences using Trimmomatic v0.30.
Assembly: To align the reads of each sample, the  human reference GRCh37.75 was used. Data was analyzed with DESEQ2 in R studio v1.4.1106
Supplementary files format and content: Count files

source_name: H9 derived cholinergic neurons

growth_protocol: For differentiation of H9WA09 cells into airway cholinergic neurons, several stages were passed (Supplementary Table 1). Vagal NCC induction was started when pluripotent stem cells were 40-60% confluent. Pluripotent stem cells were first differentiated into vagal NCCs in 12 days. Two types of media were used: KSR medium (KnockOut DMEM (Thermo Fisher, 10829018) and 15% KnockOut Serum Replacement (Thermo Fisher, 10828028)) and N2 medium (DMEM HEPES (Thermo Fisher, 12320032), 1% Penicillin-Streptomycin (Thermo Fisher , 15070063), and 10 µg/ml N2 supplement (Thermo Fisher, A1370701)). The manufacturer supplies N2 supplement as 100x, but double the amount was used in this protocol. KSR and N2 medium were freshly supplemented with 10 µM SB431542 (STEMCELL Technologies, Vancouver, Canada, 72234), 1 µM LDN193189 (STEMCELL Technologies, Vancouver, Canada, 72147), 3 µM CHIR99021 (STEMCELL Technologies, Vancouver, Canada, 72054), and 1 µM retinoic acid. The medium was changed every other day, medium composition according to Supplementary Table 2.

extract_protocol:
After spheroid formation, the vagal cells undergo airway cholinergic neuron induction and airway cholinergic neuron maturation. On day 16 of the protocol, the VP spheroid medium was aspirated, and the spheroids were dissociated using EDTA (0.5 mM; wash twice, followed by 10 min incubation, 37°C). The cell suspension was carefully transferred to a tube and centrifuged (290 g, 1 min, RT). The supernatant was aspirated, and the cell pellet was resuspended in airway neuron (AN) medium (Neurobasal medium supplemented with 10 µg/ml N2 supplement, 20 µl/ml B27 supplement, 10 µg/ml Glutamax, and 10 µg/ml MEM Nonessential Amino Acids). 10 ng/ml BDNF (Peprotech, 450-02) and 100 µM freshly prepared L-Ascorbic Acid (Sigma-Aldrich, A5960) were added before medium change. Dissociated spheroids were plated onto culture plates pre-coated with 15 µg/mL Poly-L-Ornithine (PLO, Sigma-Aldrich, P4538), 2 µg/mL fibronectin (FB, Thermo Fisher, 33016015), and 2 µg/mL laminin (LM, R&D systems, 3400-010-02).
In the first stage of airway cholinergic neuron induction (day 16-30), the medium was changed three times per week, changing ¾ of the total volume. In the second stage (day 30-40), the medium was changed twice per week the medium volume was 1.5 times increased. In addition, from day 35 onwards, AN medium was supplemented with 2 µg/ml FB and 2 µg/ml LM. In the final stage of airway cholinergic neuron maturation (day 40-50), the medium was changed once per week. Cells were stimulated with 10 nM dexamethasone, or with the cytokines IL-4 (10 ng/mL, Peprotech, 200-04), IL-13 (3 ng/mL, Peprotech, 200-13), and IL-33 (10ng/mL, Peprotech, 200-33). PCR analysis and immunofluorescence (IF) staining were performed on different time points: day 25, 35, and day 50. Additionally, fluorescence-activated cell sorting (FACS) was performed on day 50.

treatment_protocol: Next, the vagal NCCs were cultured in the form of floating spheroids for four days. The cells were washed with EDTA (0.5 mM) twice, followed by 10 min incubation at 37°C. After aspirating the EDTA, vagal precursor (VP) spheroid medium was added, consisting of Neurobasal Medium (Thermo Fisher, 21103049) supplemented with 10 µl/ml N2 supplement, 20 µl/ml B27 supplement (Thermo Fisher, 17504044), 10 µl/ml Glutamax (Thermo Fisher, 35050061), and 10 µl/ml MEM Nonessential Amino Acids). Prior to medium change, 10 ng/ml FGF2 (Thermo Fisher, PHG6015) and 3 µM CHIR99021 (STEMCELL Technologies, 72054) was freshly added. The cells were mechanically detached in VP spheroid medium using a serological pipette before transfer to a 6-well plate pre-coated with anti-adherence solution (STEMCELL Technologies, 07010). Detached cells from five wells of a 6-well plate were added divided over six wells of a 6-well plate. On day 14, the medium was refreshed.

tag: donor id


title: Input_p65_PU.1_WT_Day4 rep2


title: PU.1_WT_Day0 rep1


title: PU.1_WT_Day0 rep2


title: Patient R3532 treated with placebo [R3532_prot]

city: Paris

last: Michonneau

address: 1 avenue Claude Vellefaux

department: Hematology and transplantation

institute: Assistance Publique des Hôpitaux de Paris

description:
10X Genomics Feature Barcode technology and Single Cell Targeted Gene Expression.
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
filteredinbarcodes.csv.gz

library_source: other

data_processing:
library strategy: CITE-seq
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger v6.0 pipeline where ADT and mRNA sequences were concatenated and aligned using GRCh38 genome assembly as reference data. Individual outputs were concatenated without normalization with CellRanger aggr v6.0
Cell surface proteins were identified with specific oligonucleotide sequence (Format TotalSeqB, Biolegend): CD3_TotalSeqB, CD45RA_TotalSeqB, CCR4_TotalSeqB, CD4_TotalSeqB_SK3, CD4_TotalSeqB_RPAT4, CD8_TotalSeqB_SK1, CD8_TotalSeqB_RPAT8, CD25_TotalSeqB, PD1_TotalSeqB, CXCR3_TotalSeqB, CCR6_TotalSeqB, CXCR5_TotalSeqB, CCR7_TotalSeqB, CD161_TotalSeqB, CTLA4_TotalSeqB, CD95_TotalSeqB, HLA-DR_TotalSeqB, ICOS_TotalSeqB, CD39_TotalSeqB, CD27_TotalSeqB, KLRG1_TotalSeqB, CD28_TotalSeqB, CD38_TotalSeqB_HB7, CD38_TotalSeqB_HIT2, CD127_TotalSeqB, CD73_TotalSeqB, TCRVa72_TotalSeqB, CD56_TotalSeqB, CD19_TotalSeqB, CD11c_TotalSeqB, CD123_TotalSeqB, CD14_TotalSeqB, IgD_TotalSeqB, CD36_TotalSeqB, KID2DL1_TotalSeqB, NKp30_TotalSeqB, CD16_TotalSeqB, CD20_TotalSeqB, NKp46_TotalSeqB, IgM_TotalSeqB, CCR5_TotalSeqB, CD11b_TotalSeqB, NKG2D_TotalSeqB, CD24_TotalSeqB_ref1, CD24_TotalSeqB_ref2, 2B4_TotalSeqB. All sequences are available on https://www.biolegend.com/en-us/totalseq/barcode-lookup
Further processing was done with Seurat v4.0.0 (cell and gene filtering, normalization, clustering, differential gene expression analysis).
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: protein

source_name: Peripheric blood

extract_protocol:
Library was prepared using Chromium Single Cell 3ʹ version CG000317 rev B protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell 3’ version CG000317 rev B protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA and the antibody-derived tagged cDNAs. For the mRNA derived cDNA library preparation, we further proceeded according to the manufacturer’s instructions for Single Cell 3’ version CG000317 rev B protocol (10x Genomics).
Libraries were equimolar pooled to obtain at least 20,000 read pairs per cell and 5,000 read pairs for feature barcode part after sequencing on Illumina Novaseq 6000 (100 cycles cartridge).

value: Peripheric blood

value: PBMC

tag: library type

value: ADT

value: placebo


title: Patient R3733 treated with placebo [R3733_geneexp]

value: mRNA


title: Experiment 1


title: A549CC, scRNAseq

description: 10x Genomics

value: IR 2h (purified)


title: RT112 cells, ARID1A kd, DMSO treatment rep 1

value: Human bladder carcinoma

value: ARID1A knockdown


title: Patient R3733 treated with placebo [R3733_prot]


title: RT112 cells, ARID1A wt, GSK126 treatment rep 1


title: RT112 cells, ARID1A wt, GSK126 treatment rep 2


title: Input_p65_PU.1_WT_Day0 rep2


title: Patient R3532 treated with placebo [R3532_geneexp]


title: Patient R3008 treated with placebo [R3008_geneexp]


title: RT112 cells, ARID1A wt, DMSO treatment rep 3


title: hiBMEC Control 1

value: iPSC

value: WT

value: BMEC differentiation


title: Input_p65_PU.1_WT_Day4 rep1


title: Patient R2412 treated with placebo [R2412_geneexp]


title: Patient R2091 treated with azithromycine [R2091_prot]

value: azithromycine


title: A549NA, scRNAseq

description: 10x Genomics

value: lung cancer

value: Ctrl (mix)


title: RT112 cells, ARID1A kd, DMSO treatment rep 2

value: DMSO


title: Patient R2412 treated with placebo [R2412_prot]


title: Patient R3008 treated with placebo [R3008_prot]


title: Patient R2091 treated with azithromycine [R2091_geneexp]


title: RT112 cells, ARID1A wt, DMSO treatment rep 2

value: ARID1A wildtype


title: Patient R2571 treated with azithromycine [R2571_geneexp]


title: P6 Fucci Retinal Endothelial Cells - Green 3 [REC_SG2M-3]

city: Charlottesville

first: Nicholas

middle: W

last: Chavkin

address: 415 Lane Road

institute: University of Virginia

data_processing:
Raw read data was quality-control checked using FastQC v0.11.9.
Raw read data was aligned to either human genome hg38 or mouse genome GRCm38 using Kallisto v0.46.2.
Aligned data was normalized using Sleuth v0.30.0.
Assembly: hg38 or m38
Supplementary files format and content: TPM

source_name: Retina

extract_protocol:
QIAGEN RNeasy MinElute Kit was used to purify RNA.
Low cell isolation numbers required cDNA amplification for RNA sequencing. RNA preparation and cDNA amplification for Illumina next-generation sequencing was performed with the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio USA, Inc.). Retinal endothelial cell samples were transferred to the University of Virginia Genome Analysis and Technology Core, which performed cDNA library preparation with the DNA Prep, (M) Tagmentation kit (Illumina Cat #20018704). HUVEC-FUCCI samples were transferred to the Yale Center for Genomic Analysis, which performed cDNA library preparation and amplification.

value: Retina

value: Endothelial Cell


title: Input_p65_PU.1_WT_Day0 rep1

city: La Jolla

last: Glass

institute: University of California, San Diego

source_name: Bone marrow cell

value: Bone marrow cell


title: Patient R1862 treated with azithromycine [R1862_prot]

value: Peripheric blood

value: PBMC

value: ADT


title: p65_WT_Day4 rep2


title: P6 Fucci Retinal Endothelial Cells - Green 1 [REC_SG2M-1]


title: MKN74 Vehicle 2

value: Gastric tumor

value: Vehicle

value: Day 3


title: Patient R3358 treated with placebo [R3358_prot]

value: placebo


title: P6 Fucci Retinal Endothelial Cells - Green 2 [REC_SG2M-2]


title: RT112 cells, ARID1A wt, DMSO treatment rep 1

value: Human bladder carcinoma


title: Patient R4337 treated with azithromycine [R4337_geneexp]

value: mRNA


title: p65_WT_Day0 rep2


title: Patient R3358 treated with placebo [R3358_geneexp]


title: p65_WT_Day0 rep1


title: Patient R4151 treated with placebo [R4151_prot]


title: P6 Fucci Retinal Endothelial Cells - Red 3 [REC_LG1-3]


title: Patient R4151 treated with placebo [R4151_geneexp]


title: Input_Fosl2_WT_Day4 rep1


title: Patient R4124 treated with placebo [R4124_prot]


title: Patient R4090 treated with azithromycine [R4090_prot]

value: azithromycine


title: P6 Fucci Retinal Endothelial Cells - Red 2 [REC_LG1-2]


title: p65_WT_Day4 rep1


title: Patient R4090 treated with azithromycine [R4090_geneexp]


title: Input_Fosl2_WT_Day0 rep2


title: Patient R4124 treated with placebo [R4124_geneexp]


title: P6 Fucci Retinal Endothelial Cells - Red 1 [REC_LG1-1]


title: Patient R4077 treated with placebo [R4077_prot]


title: Patient R2571 treated with azithromycine [R2571_prot]


title: Patient R4337 treated with azithromycine [R4337_prot]


title: Patient R3574 treated with azithromycine [R3574_geneexp]


title: Input_Fosl2_WT_Day0 rep1


title: Patient R3574 treated with azithromycine [R3574_prot]


title: Fosl2_WT_Day4 rep1


title: P6 Fucci Retinal Endothelial Cells - Blank 1 [REC_EG1-1]


title: P6 Fucci Retinal Endothelial Cells - Blank 3 [REC_EG1-3]


title: Fosl2_WT_Day4 rep2


title: Input_Fosl2_WT_Day4 rep2


title: Fosl2_WT_Day0 rep1


title: Secondary_RA_Day7_H3K27ac_ChIPseq

city: Marseille

first: Estelle

last: Duprez

address: 27 Boulevard Lei Roure

institute: CRCM

description: Spiked-ChIPseq with S2 drosophila chromatin

data_processing:
quality control 1 before mapping
Sequencing quality control was determined using the FastQC tool
quality control 2 before mapping
Reads with a Phred quality score less than 30 were filtered out
mapping
Reads were mapped to an "hybrid genome" combining Mus musculus (GRCm38/mm10) and Drosophila melanogaster (dm6) genomes using default parameters of Bowtie2 (v2.3.4.1) . Tags were sorted according to their genome of origin (mm10 or dm6).
quality after mapping
Duplicate tags were removed by samtools rmdup function and mapped tags were filtered using samtools view -F 4 for further analysis
down-sampling through spike-in correction
A scaling factor was calculated using dm6 mapped tags (Spike-in antibody-bound regions) and mm10 mapped tags were normalized according to this scaling factor (Spike-in correction)
Genome_build: mm10 + dm6
Supplementary_files_format_and_content: Normalized-mapped reads were converted into BigWig using the deepTools suite (v2.2.4)

source_name: PLZF/RARA transformed progenitor cells

extract_protocol:
PLZF/RARA transformed progenitors (late promyelocytes: Cd45.2+, C-Kit+, Gr1+, Cd34-, FcγR+) were purified using the FACS Aria III cell sorter (Beckman Dickinson). Cell lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Genomic DNA was purified using the i-Pure kit (Diagenode)
Libraries were generated using the MicroPlex Library Preparation Kit (Diagenode) following the manufacturer's instructions and analyzed on a 2100 Bioanalyzer system (Agilent) prior sequencing.

treatment_protocol: A cohort of 3-5 mice was treated with retinoic acid or corn oil supplemented with 10% of DMSO for 3 or 7 days.

value: Late promyelocytes

value: Leukemic bone marrow

value: 0.8-1mg Retinoic Acid / Intraperitoneally injected

tag: chip antibodies

value: H3K27ac (Active Motif, 39133) + Spike-in antibody (Active Motif, 61686)


title: Patient R4291 treated with placebo [R4291_prot]


title: Patient R3071 treated with azithromycine [R3071_prot]


title: Patient R3071 treated with azithromycine [R3071_geneexp]


title: Fosl2_WT_Day0 rep2

first: Christopher

address: 9500 Gilman Dr

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed in biological replicates as previously described (Heinz et al., 2018: Sakai et al., 2019) with modifications as follows.  For H3K27ac ChIP assays, cells were cross-linked with 1% (vol/vol) formaldehyde (Thermo Fisher Scientific) in PBS for 10 min at room temperature.  For NCoR1, HDAC3, PU.1, p65, Jdp2, Fosl2, PGC1b and FLAG-tag ChIP assays, cells were cross-linked with 2 mM disuccinimidyl glutarate (DSG) (ProteoChem) in PBS for 30 min at room temperature, and then directly a second crosslinking was performed by the addition of 1% (vol/vol) formaldehyde in PBS for 10 min.  The crosslinking reaction was quenched by 0.125 M glycine (Thermo Fisher Scientific).  Cells were washed once with cold PBS and pelleted at 1,000 g for 5 min at 4°C.  Crosslinked cells were resuspended in ice-cold hypotonic buffer (10 mM HEPES-KOH (pH 7.9), 85 mM KCl, 1 mM EDTA, 1% NP-40, 1 mM PMSF (Sigma), 0.5 mM sodium butyrate (Sigma), 1X protease inhibitor cocktail (Sigma)), and centrifuged at 1,000 g for 5 min at 4°C to obtain a nuclear fraction.  Nuclear pellets were resuspended in 100 ml of either LB3 buffer (10 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-laurosylsarcosine, 1 mM PMSF, 0.5 mM sodium butyrate, 1X protease inhibitor cocktail for H3K27ac ChIP) or PIPA-NR buffer (20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.4% sodium deoxycholate, 0.1% SDS, 1% NP-40, 0.5 mM DTT, 1 mM PMSF, 0.5 mM sodium butyrate, 1X protease inhibitor cocktail, for NCoR, HDAC3, PU.1, p65, Fosl2, PGC1b and FLAG-tag ChIP).  Chromatin DNA was sonicated in a 96 Place microTUBE Rack (Covaris) using a Covaris E220 for 12-18 cycles with the following setting: time, 60 seconds; duty, 5.0; PIP, 140; cycles, 200; amplitude, 0.0; velocity, 0.0; dwell, 0.0. Samples were centrifuged at 15,000 rpm for 10 min at 4°C, and the supernatant was used for immunoprecipitation.  LB3 lysate was diluted 1.1-fold with 10% Triton X-100.  1% of the lysate was kept as ChIP input.  The lysates were rotated with each antibody pre-bound to 20 ml of beads (10 ml of Dynabeads protein A (Invitrogen) + 10 ml of Dynabeads protein G (Invitrogen)) overnight at 4°C.  After the immunoprecipitation, beads were collected on a magnet and washed three times each with wash buffer I (20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA, 1 mM PMSF, 0.5 mM sodium butyrate, 1X protease inhibitor cocktail), wash buffer III (10 mM Tris-HCl (pH 7.5), 250 mM LiCl, 1% Triton X-100, 0.7% sodium deoxycholate, 1 mM EDTA, 1 mM PMSF, 0.5 mM sodium butyrate, 1X protease inhibitor cocktail) and twice with TET (10 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.2% Tween-20, 1 mM PMSF, 0.5 mM sodium butyrate, 1X protease inhibitor cocktail), and then resuspended in 25 ml of TT (10mM Tris-HCl (pH 7.5), 0.05% Tween-20).
The immunoprecipitated chromatin samples were used for library preparation with NEBNext Ultra II Library kit (NEB) according to the manufacturer’s instructions.  DNA in 46.5 ml of NEB reactions was crosslinks reversed by adding 4 ml of 10% SDS, 4.5 ml of 5 M NaCl, 3 ml of 500 mM EDTA, 1 ml of 20 mg/ml proteinase K (NEB) and 20 ml of water by incubation for 1 hr at 55°C, and then 30 min at 65°C.  DNA was purified with 2 ml of SpeedBeads (GE Healthcare) in 20% PEG 8000/1.5 M NaCl (Final 12% PEG 8000), and eluted with 25 ml of TT.  The eluted DNA was amplified for 14 cycles in 50 ml of PCR reactions using NEBNext High-Fidelity 2X PCR Master Mix and 0.5 mM each of primers Solexa 1GA and Solexa 1GB.  The amplified libraries were purified with 2 ml of SpeedBeads in 20% PEG 8000/2.5 M NaCl (Final 13% PEG 8000), eluted with 20 ml of TT, size selected using PAGE/TBE gel (Invitrogen) for 225-325 bp fragments by gel extraction, and single-end sequenced on HiSeq 4000.  ChIP input material (1% of sheared DNA) in 46.5 ml of TE was crosslinks reversed by adding 4 ml of 10% SDS, 4.5 ml of 5 M NaCl, 3 ml of 500 mM EDTA, 1 ml of 20 mg/ml proteinase K and 20 ml of water by incubation for 1 hr at 55°C, and then 30 min at 65°C.  The input DNA was purified with SpeedBeads as described above, and eluted with 25 ml of TT.  The eluted input DNA was prepared for libraries and amplified as described for ChIP samples.


title: Patient R2856 treated with azithromycine [R2856_prot]


title: P6 Fucci Retinal Endothelial Cells - Blank 2 [REC_EG1-2]

value: Retina


title: Secondary_RA_Day7_Input_ChIPseq


title: Input_HDAC3_WT_Day4 rep2


title: Patient R4077 treated with placebo [R4077_geneexp]


title: Patient R2856 treated with azithromycine [R2856_geneexp]


title: Secondary_RA_Day7_H3K27me3_ChIPseq

value: H3K27me3 (Cell Signalling, C36B11) + Spike-in antibody (Active Motif, 61686)


title: Patient R3692 treated with placebo [R3692_prot]


title: Input_HDAC3_WT_Day4 rep1

value: Bone marrow cell


title: Secondary_RA_Day3_H3K27me3_ChIPseq


title: Input_HDAC3_WT_Day0 rep2


title: Patient R3692 treated with placebo [R3692_geneexp]

value: Peripheric blood


title: Patient R2315 treated with placebo [R2315_prot]

value: PBMC


title: Patient R4291 treated with placebo [R4291_geneexp]


title: PC3ML + ATEV 3

city: Norfolk

first: Allison

last: Mathiesen

address: 700 W Olney Rd, Department of Physiology

institute: Eastern Virginia Medical School

description: mRNA was detected using the NanoString PanCancer Progression Panel according to manufacturer instructions

data_processing: The NanoString RCC files were normalized in Rosalind and a threshold cutoff of 20 was applied for the normalized samples.

source_name: PC3ML prostate cancer cell

growth_protocol: PC3ML were cultured in DMEM/F12 supplemented with 10% FBS and Pen/Strep until 70% confluent

extract_protocol: Following overnight incubation cells were collected and RNA isolated using the Direct-Zol miniprep kit (Zymo research corporation cat# R2072

treatment_protocol: Once cells reached 70% confluency they were treated with EV at 100,000 EV/cell and incubated overnight

value: PC3ML prostate cancer cell

value: SC ATEV


title: Patient R2315 treated with placebo [R2315_geneexp]


title: Secondary_RA_Day3_Input_ChIPseq


title: Secondary_RA_Day3_H3K27ac_ChIPseq


title: HDAC3_WT_Day4 rep2

data_processing:
FASTQ files were mapped to the mm10 mouse reference genome with Bowtie2.  Peaks were called with HOMER (findPeaks) using parameters “-style factor -minDist 200 -size 200”.  After merging these peaks, correlations among replicates from the same cell subset/treatment were evaluated by correlation using tag counts.  The two most highly correlated samples were used for identifying the most robust peaks using the irreproducible discovery rate (IDR) method.  For this step, peaks were called with HOMER’s findPeaks, using parameters “-L 0 -C 0 -fdr 0.9 -minDist 200 -size 200”.  IDR peaks from different conditions involved in a comparison merged with HOMER’s mergePeaks and annotated with HOMER’s annotatePeaks.pl.  The raw tags of all samples which had reasonable correlation were quantified with HOMER (annotatePeaks.pl) using parameter “-noadj”.  Peaks which contained at least 4 tags in at least 1 sample were used to identify differentially bounded peaks (DBP) by DESeq2.  Peaks were categorized as distal peaks which are 2 kb away from known TSS and promotor peaks which are located within 2 kb region of known TSS sites.
ChIP peak single was normalized to the sequence depth.
Assembly: mm10


title: Patient R3950 treated with azithromycine [R3950_prot]

value: ADT


title: Input_HDAC3_WT_Day0 rep1


title: Patient R3950 treated with azithromycine [R3950_geneexp]


title: Secondary_Ctrl_Day3_H3K27me3_ChIPseq

value: Corn Oil 10% DMSO / Intraperitoneally injected


title: HDAC3_WT_Day4 rep1


title: PC3ML + ATEV 1


title: Toe PC3ML + EV PIC 2

value: HAMVEC EV PIC


title: Patient R2857 treated with azithromycine [R2857_geneexp]


title: Toe PC3ML + EV PIC 3


title: Secondary_Ctrl_Day3_Input_ChIPseq


title: HDAC3_WT_Day0 rep2


title: Patient R2488 treated with azithromycine [R2488_prot]


title: Secondary_Ctrl_Day3_H3K27ac_ChIPseq


title: Primary_RA_Day7_H3K27ac_ChIPseq


title: Patient R2226 treated with azithromycine [R2226_prot]


title: Patient R2857 treated with azithromycine [R2857_prot]


title: Input_NCoR_WT_Day4 rep2


title: Toe PC3ML + EV C 2

value: HAMVEC EV C


title: Patient R2226 treated with azithromycine [R2226_geneexp]

value: mRNA


title: Primary_RA_Day7_H3K27me3_ChIPseq


title: Patient R2488 treated with azithromycine [R2488_geneexp]

value: azithromycine


title: PC3ML + ATEV 2


title: HDAC3_WT_Day0 rep1


title: Toe PC3ML + EV C 1


title: Primary_RA_Day3_H3K27me3_ChIPseq

value: Late promyelocytes


title: Toe PC3ML + EV PIC 1


title: Toe PC3ML No EV 3

value: No Treatment


title: Primary_RA_Day3_H3K27ac_ChIPseq

value: Leukemic bone marrow

value: 0.8-1mg Retinoic Acid / Intraperitoneally injected


title: Toe PC3ML No EV 2


title: Patient R1799 treated with azithromycine [R1799_geneexp]


title: Toe PC3ML + EV C 3


title: Patient R3753 treated with placebo [R3753_prot]

value: placebo


title: Input_NCoR_WT_Day4 rep1


title: Primary_RA_Day3_Input_ChIPseq


title: Input_NCoR_WT_Day0 rep2


title: Primary_RA_Day7_Input_ChIPseq


title: NCoR_WT_Day4 rep2

value: NCoR


title: NCoR_WT_Day4 rep1

value: Bone marrow cell


title: Patient R1799 treated with azithromycine [R1799_prot]

value: Peripheric blood


title: △T PC3ML + EV PIC 3


title: NCoR_WT_Day0 rep2


title: Primary_Ctrl_Day3_H3K27ac_ChIPseq

value: H3K27ac (Active Motif, 39133) + Spike-in antibody (Active Motif, 61686)


title: Input_NCoR_WT_Day0 rep1


title: △T PC3ML + EV PIC 2

value: PC3ML prostate cancer cell


title: H3K27ac_NKO_Day4 rep2


title: NoTreatment_Replicat2_H3K4me3_ChIPseq

value: no treatment

value: H3K4me3 (Diagenode, 15410003) + Spike-in antibody (Active Motif, 61686)


title: Patient R2122 treated with placebo [R2122_prot]

value: PBMC

value: ADT


title: △T PC3ML + EV C 2

value: HAMVEC EV C


title: Toe PC3ML No EV 1


title: NoTreatment_Replicat2_H3K27me3_ChIPseq

value: H3K27me3 (Cell Signalling, C36B11) + Spike-in antibody (Active Motif, 61686)


title: Patient R3732 treated with azithromycine [R3732_prot]

value: azithromycine


title: H3K27ac_WT_Day4 rep2


title: Primary_Ctrl_Day3_H3K27me3_ChIPseq

value: Late promyelocytes

value: Corn Oil 10% DMSO / Intraperitoneally injected