title: Sample23

city: San Sebastian

first: Maider

last: Muñoz-Culla

address: Paseo Dr.Begiristain s/n

institute: Biodonostia Institute

data_processing:
Reads were aligned using BWA and STAR
circRNA prediction was performed by CIRCexplorer2 and CIRI2 adhering to the recommendation by the authors. Moreover, only circRNAs supported by both algorithms were considered as bona fide circRNAs
CircRNA expression was based on back-spliced junctions-spanning reads according to CIRI2 quantification
Kallisto algorithm was used for transcript pseudoalignment, identification and quantification
Genome_build: hg19
Supplementary_files_format_and_content: raw read counts

source_name: Blood

extract_protocol:
miRNeasy mini kit for total RNA isolation
rRNA was depleted from the total RNA sample using the Ribo-Zero rRNA removal kit and followed by purification and fragmentation steps. To construct the sequencing libraries, a strand-specific cDNA synthesis was performed, the 3’ ends were adenylated and adaptors were ligated.

value: PBMC

value: Multiple Sclerosis

tag: ls-ocmb characterization

value: Negative LS-OCMB status


title: Brain endothelial cell 469

status: Public on Dec 21 2020

type: SRA

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description: Brain endothelial cell 469

library_source: transcriptomic

data_processing:
The sequencing reads were first aligned to the mouse reference genome GRCm38 (mm10) with tophat (version 2.1.1). The duplicated reads were removed using samtools software (version 0.1.18). The raw read counts for each gene were then calculated using featureCounts function from the Subread package (version 1.4.6-p5)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each sample

molecule: total RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
Pdgfb ret mice were crossed with Cldn5-GFP; Cspg4-DsRed mice for endothelial cell (positive for GFP, negative for dsRed) isolation based on fluorescence-activated cell sorting (FACS),  followed by the SmartSeq2 methodology for the generation and sequencing of full length polyadenylated cDNAs
Libraries for RNA-seq were prepared by using SMART-seq2 methodology

tag: strain

tag: tissue

value: brain

tag: age

value: adult mice

tag: genotype

value: Pdgfb ret/+

tag: cell type

value: endothelial cell


title: Brain endothelial cell 468

description: Brain endothelial cell 468


title: Sample07

country: Spain

organism: Homo sapiens

tag: disease state


title: Brain endothelial cell 467

description: Brain endothelial cell 467


title: Brain endothelial cell 466

description: Brain endothelial cell 466


title: Sample19

value: Positive LS-OCMB status


title: Sample16


title: Sample14


title: Brain endothelial cell 465

description: Brain endothelial cell 465


title: Sample02


title: Brain endothelial cell 474

description: Brain endothelial cell 474


title: Brain endothelial cell 463

description: Brain endothelial cell 463


title: Brain endothelial cell 461

description: Brain endothelial cell 461


title: Sample05


title: Brain endothelial cell 464

description: Brain endothelial cell 464


title: Sample04


title: PM_7d_1dose_3 (rna-seq)

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

country: USA

institute: University of Michigan

data_processing:
Alignment with STAR
Raw counts with featureCounts
Genome_build: hg19
Supplementary_files_format_and_content: raw counts

source_name: BEAS-2B cells

growth_protocol: BEAS-2B, a bronchial epithelial cell line, were cultured on collagen-coated tissue-culture plates in serum-free Bronchial Epithelial Growth Medium (Lonza)

extract_protocol:
All RNA was isolated by Trizol and further cleaned using RNeasy. mRNA was made into libraries and sequenced on the Illumina HiSeq 4000 using single-end 50-mer sequencing reads with 12 samples multiplexed per lane.
Single end 50 TruSeq mRNA

treatment_protocol: PM2.5 was collected from a manual sampler on Emfab filters over a 24 h period from Jan-Feb 2015 in Beijing, China. PM2.5 was extracted by sonicating filters in distilled water. Cells were treated in 6-well plates with doses of 1 or 30 µg/cm2 of PM2.5 for 24 hours. For experiments involving repeated exposures, cells were treated with a dose of 1 µg/cm2 each day for a total of 7 days. Cells were washed between each treatment.

tag: cell line

tag: treatment


title: PM_24h_30dose_2 (rna-seq)


title: PM_7d_1dose_1 (rna-seq)


title: Brain endothelial cell 458

description: Brain endothelial cell 458


title: Brain endothelial cell 456

description: Brain endothelial cell 456


title: Brain endothelial cell 455

description: Brain endothelial cell 455


title: Brain endothelial cell 457

description: Brain endothelial cell 457


title: PM_24h_30dose_3 (rna-seq)


title: Brain endothelial cell 459

description: Brain endothelial cell 459


title: PM_24h_30dose_1 (rna-seq)


title: Brain endothelial cell 454

description: Brain endothelial cell 454


title: Control_7d_3 (rna-seq)


title: PM_7d_1dose_2 (rna-seq)


title: Brain endothelial cell 462

description: Brain endothelial cell 462


title: PM_24h_1dose_2 (rna-seq)


title: PM_24h_1dose_1 (rna-seq)


title: Brain endothelial cell 451

description: Brain endothelial cell 451


title: Control_7d_2 (rna-seq)


title: Brain endothelial cell 460

description: Brain endothelial cell 460


title: Brain endothelial cell 450

description: Brain endothelial cell 450


title: Brain endothelial cell 453

description: Brain endothelial cell 453


title: Brain endothelial cell 448

description: Brain endothelial cell 448


title: PM_24h_1dose_3 (rna-seq)


title: Control_7d_1 (rna-seq)


title: Brain endothelial cell 452

description: Brain endothelial cell 452


title: Control_24h_3 (rna-seq)


title: Brain endothelial cell 445

description: Brain endothelial cell 445


title: Brain endothelial cell 446

description: Brain endothelial cell 446


title: Control_24h_1 (rna-seq)


title: Brain endothelial cell 444

description: Brain endothelial cell 444


title: PM_24h_30dose_3 (errbs)

library_source: genomic

data_processing:
Reads were trimmed with trim_galore/0.4.0
Reads were aligned with bismark/0.14.3 and bowtie/2.2.1
Methylation calls were made with bismark/0.14.3
Genome_build: hg19
Supplementary_files_format_and_content: bismark methylation calls

molecule: genomic DNA

extract_protocol:
DNA was isolated using Dneasy. DNA was bisulfite converted using Zymo EZ DNA Methylation kit.
Bisulfite-converted DNA were fragmented using MspI restriction-enzyme digestion, resolved on agarose gel, and gel-eluted fragments were made into libraries using Illumina TruSeq.


title: Brain endothelial cell 442

description: Brain endothelial cell 442


title: PM_24h_30dose_2 (errbs)


title: Brain endothelial cell 447

description: Brain endothelial cell 447


title: Control_24h_3 (errbs)


title: PM_24h_1dose_2 (errbs)


title: Brain endothelial cell 449

description: Brain endothelial cell 449


title: Control_7d_2 (errbs)


title: PM_24h_1dose_3 (errbs)


title: PM_7d_1dose_3 (errbs)


title: Brain endothelial cell 443

description: Brain endothelial cell 443


title: PM_7d_1dose_2 (errbs)


title: Control_7d_3 (errbs)


title: Brain endothelial cell 437

description: Brain endothelial cell 437


title: Brain endothelial cell 441

description: Brain endothelial cell 441


title: Brain endothelial cell 439

description: Brain endothelial cell 439


title: Brain endothelial cell 440

description: Brain endothelial cell 440


title: Control_24h_2 (rna-seq)


title: Brain endothelial cell 435

description: Brain endothelial cell 435


title: Control_7d_1 (errbs)


title: Control_24h_2 (errbs)


title: Brain endothelial cell 438

description: Brain endothelial cell 438


title: PM_24h_30dose_1 (errbs)


title: Brain endothelial cell 433

description: Brain endothelial cell 433


title: Brain endothelial cell 436

description: Brain endothelial cell 436


title: PM_24h_1dose_1 (errbs)


title: Control_24h_1 (errbs)


title: Brain endothelial cell 432

description: Brain endothelial cell 432


title: Brain endothelial cell 430

description: Brain endothelial cell 430


title: SPT6i_ATACseq_rep2

city: San Diego

first: George

last: Sen

state: CA

address: 9500 Gilman Drive

institute: UCSD

data_processing:
Illumina Hiseq 4000 reads were trimmed and filtered using Partek Flow. High quality reads were aligned using TopHat v2.1.0 for alignment into BAM files.
BAM files were imported into the RNA-seq pipeline of Partek Genomic Suite, version 6.6 (Copyright 2009, Partek Inc., St. Louis, MO, USA), and RPKM counts were calculated (RefSeq Transcripts 85 2018-05-02). Exclusions include a mininum reads of 10 in one out of 4 samples. RPKM values were log2-transformed with an offset value of 0.000001.
Genome_build: hg19
Supplementary_files_format_and_content: peaks.bed
Raw ChIP-seq reads were aligned using Bowtie v2.3.
MACS2 (version 2.2.4) was used for call peaks in individual replicates using Input ChIP-seq as the control sample.
Peaks overlapped among all replicates were obtained using bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: peaks.bed
The raw reads were trimmed with cutadapt2.5 before aligned to the GRCh37 using bowtie2.3.
The alignment files were then deduplicated using picard2.20 prior to being converted to tag files and subjected to peaking calling using macs2.2.4.
The overlapped peaks from different samples were then merged into a consensus set of peaks prior to being divided into evenly spaced 500bp chromatin regions over which the aligned reads could be recounted for differential enrichment analysis using DiffBind2.14.
Under the hood, DEseq2 was invoked to perform the differential analysis. FDR of less or equal to 0.05 was used to correct for the multiple tests.
Genome_build: hg19
Supplementary_files_format_and_content: SPT6.RNAseq.txt file:  normalized counts (log2 transformed RPKM values).

source_name: Human epidermal keratinocyte

growth_protocol: Primary keratinocytes were grown on culture dishes in keratinocyte EPILIFE medium (Life technologies).

extract_protocol:
Cells were washed briefly with phosphate-buffered saline (PBS) two times. Permeabilized nuclei were obtained by resuspending cells in 250µL Nuclear Permeabilization Buffer [(10 mM Tris-HCl (pH 7.4) (BP-152, Thermo Fisher Scientific), 10 mM NaCl (S271-3, Thermo Fisher Scientific), 3 mM MgCl2 (194698, MP Biomedicals), 0.1% Tween-20 (P7949, Sigma), 0.1% IGEPAL-CA630 (I8896, Sigma), 0.01% digitonin (G9441, Promega) in Molecular biology water (46000-CM, Corning)], and incubating for 5 min on a rotator at 4°C. Nuclei were then pelleted by centrifugation for 5 min at 500 x g at 4°C. The pellet was resuspended in 25µL ice-cold Tagmentation Buffer [33 mM Tris-acetate (pH = 7.8) (BP-152, Thermo Fisher Scientific), 66 mM K-acetate (P5708, Sigma), 11 mM Mg-acetate (M2545, Sigma), 16 % DMF (DX1730, EMD Millipore) in Molecular biology water (46000-CM, Corning)]. An aliquot was then taken and counted by hemocytometer to determine nuclei concentration. Approximately 50,000 nuclei were resuspended in 10 µL ice-cold Tagmentation Buffer, and incubated with 1µL Tagmentation enzyme (FC-121-1030; Illumina) at 37 °C for 30 min with shaking 500 rpm. The tagmentated DNA was purified using MinElute PCR purification kit (28004, Qiagen).
The libraries were amplified using NEBNext High-Fidelity 2X PCR Master Mix (M0541, NEB) with primer extension at 72°C for 5 min, denaturation at 98°C for 30s, followed by 8 cycles of denaturation at 98°C for 10 s, annealing at 63°C for 30 s and extension at 72°C for 60 s. Amplified libraries were then purified using MinElute PCR purification kit (28004, Qiagen), and two size selection steps were performed using SPRIselect bead (B23317, Beckman Coulter) at 0.55X and 1.5X bead-to-sample volume rations, respectively. Sequencing was performed at the UC San Diego IGM Genomics Center on an Illumina NovaSeq 6000 using the 100 bp paired-end protocol.
The ATAC-seq was performed in CTLi and SPT6i cells in duplicates.

treatment_protocol: SPT6 siRNA knockdown and induced to differentiation by 1.2mM calcium

value: keratinocyte

value: transfect with SPT6i and undergo Ca2+ induced differentiation for 3 days

tag: time point

value: 3 days


title: CTLi_ATACseq_rep2

description: CTLi.ATACseq.peaks.bed

value: transfect with Control siRNA and undergo Ca2+ induced differentiation for 3 days


title: Brain endothelial cell 429

description: Brain endothelial cell 429


title: Input_Diff_CHIP

extract_protocol:
10 million cells were crosslinked with 2mM DSG and 1% formaldehyde in the experiment. The ChIP experiment was done using the Lab ChIP-seq protocol, DNA was isolated with Thermo Scientific's GeneJET Gel Extraction kit
ChIP-seq libraries were prepared with TruSeq RNA Library Prep Kit (Illumina) then multiplexed

value: Ca2+ induced differentiation for 3 days


title: PM_7d_1dose_1 (errbs)


title: SPT6i_ATACseq_rep1


title: Brain endothelial cell 428

description: Brain endothelial cell 428


title: Brain endothelial cell 426

description: Brain endothelial cell 426


title: Brain endothelial cell 425

description: Brain endothelial cell 425


title: Brain endothelial cell 427

description: Brain endothelial cell 427


title: SPT6i_Pol2_CHIPseq_rep1

tag: antibody


title: Input_Pro_CHIP

value: undifferentiated keratinocytes


title: Brain endothelial cell 434

description: Brain endothelial cell 434


title: SPT6i_Pol2_CHIPseq_rep2


title: Input_SPT6Pol2CHIP


title: Differentiation_Pol2_CHIPseq_rep3


title: Brain endothelial cell 424

description: Brain endothelial cell 424


title: Differentiation_Pol2_CHIPseq_rep2


title: CTLi_ATACseq_rep1

description: CTLi.ATACseq.peaks.bed


title: Proliferation_Pol2_CHIPseq_rep3


title: Brain endothelial cell 422

description: Brain endothelial cell 422


title: Brain endothelial cell 423

description: Brain endothelial cell 423


title: Brain endothelial cell 431

description: Brain endothelial cell 431


title: Differentiation_Pol2_CHIPseq_rep1


title: Brain endothelial cell 421

description: Brain endothelial cell 421


title: Brain endothelial cell 420

description: Brain endothelial cell 420


title: Proliferation_Pol2_CHIPseq_rep2


title: Brain endothelial cell 419

description: Brain endothelial cell 419


title: Proliferation_Pol2_CHIPseq_rep1


title: Input_for_SPT6_CHIPseq

value: calcium induced differentiation


title: Brain endothelial cell 418

description: Brain endothelial cell 418


title: SPT6_CHIPseq_rep2


title: Brain endothelial cell 416

description: Brain endothelial cell 416


title: SPT6_CHIPseq_rep1


title: Brain endothelial cell 415

description: Brain endothelial cell 415


title: Brain endothelial cell 414

description: Brain endothelial cell 414


title: CTLi_RNAseq_rep2

growth_protocol: Primary keratinocytes were grown on culture dishes  in keratinocyte EPILIFE medium (Life technologies).

extract_protocol:
RNA was isolated using GeneJET RNA purification kit (Thermo Scientific).
RNA-seq libraries were prepared with TruSeq RNA Library Prep Kit (Illumina) then multiplexed

treatment_protocol: SPT6 siRNA knockdown and placed on dermis for organotypic culture

value: transfect with SPT6i and undergo organotypic culture

value: 6 days


title: CTLi_RNAseq_rep1


title: Brain endothelial cell 413

description: Brain endothelial cell 413


title: CTLi_RNAseq_rep3


title: SPT6i_RNAseq_rep3


title: Brain endothelial cell 411

description: Brain endothelial cell 411


title: SPT6i_RNAseq_rep1


title: SPT6i_RNAseq_rep2


title: Brain endothelial cell 412

description: Brain endothelial cell 412


title: SiHa cells, sinc2

city: Hangzhou

first: Yanan

last: Zhang

state: Zhejiang

address: No. 1 Xueshi Road - Shangcheng

country: China

institute: Women’s Hospital, School of Medicine, Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Supplementary_files_format_and_content: gene_expression.txt is a tab-delimited text file including FPKM values for each Sample
Trinity.gene.fasta is the sequence of the mRNA expression spectrum changed after we passed the circrna known as the circcdkn2b-as1

source_name: cervix

growth_protocol: SiHa cells were cultured in DEME medium containing 10% FBS

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: with or without circCDKN2B-AS1 konckdown

value: cervix

value: SiHa

tag: control


title: Brain endothelial cell 417

description: Brain endothelial cell 417


title: Brain endothelial cell 409

description: Brain endothelial cell 409


title: Brain endothelial cell 410

description: Brain endothelial cell 410


title: Brain endothelial cell 406

description: Brain endothelial cell 406


title: Brain endothelial cell 405

description: Brain endothelial cell 405


title: Brain endothelial cell 407

description: Brain endothelial cell 407


title: H16_5_SCC

data_processing:
Illumina Casava1.8 software used for basecalling.
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the reference genome using Tophat2 package.
The mapped reads of each sample were assembled using StringTie, all transcriptomes were merged to reconstruct a comprehensive transcriptome.
Unmapped reads were still mapped to genome using tophat-fusion. CIRCExplorer2 was used to denovo assemble the mapped reads to circular RNAs at first; Then, back splicing reads were identified in unmapped reads by tophat-fusion and CIRCExplorer2. All samples were generated unique circular RNAs.
Supplementary_files_format_and_content: circ_expression.txt is a tab-delimited text file including FPKM values for each Sample
0_circRNA.fasta is the sequence information of the circrna identified in our article.

source_name: cervical tissues

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.  Ribosomal RNA was deleted.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HPV16 positive Cervical squamous cell carcinoma


title: SiHa cells, sinc1


title: Brain endothelial cell 408

description: Brain endothelial cell 408

value: brain


title: Brain endothelial cell 403

description: Brain endothelial cell 403

value: adult mice


title: H16_4_SCC


title: SiHa cells, sicirc2

tag: circCDKN2B-AS1 knockdown


title: Brain endothelial cell 400

description: Brain endothelial cell 400

value: Pdgfb ret/+


title: Brain endothelial cell 399

description: Brain endothelial cell 399

value: endothelial cell


title: SiHa cells, sicirc1


title: H16_1_SCC


title: Brain endothelial cell 397

description: Brain endothelial cell 397


title: Brain endothelial cell 396

description: Brain endothelial cell 396


title: Brain endothelial cell 404

description: Brain endothelial cell 404


title: H16_2_Hs

value: HPV16 positive HSIL tissues


title: H16_4_Hs


title: H16_6_SCC


title: H16_3_SCC


title: Brain endothelial cell 402

description: Brain endothelial cell 402


title: H16_2_SCC


title: H16_3_Hs


title: H16_1_Hs


title: Brain endothelial cell 401

description: Brain endothelial cell 401


title: H16_5_Hs


title: H16_6_Hs


title: Brain endothelial cell 390

description: Brain endothelial cell 390


title: Brain endothelial cell 395

description: Brain endothelial cell 395


title: Brain endothelial cell 394

description: Brain endothelial cell 394


title: Brain endothelial cell 393

description: Brain endothelial cell 393


title: Brain endothelial cell 391

description: Brain endothelial cell 391


title: Brain endothelial cell 398

description: Brain endothelial cell 398


title: H16_4_In

value: HPV16 positive cervical epithelium tissues


title: H16_1_In


title: H16_6_In


title: Brain endothelial cell 392

description: Brain endothelial cell 392


title: H16_5_In


title: Brain endothelial cell 388

description: Brain endothelial cell 388


title: H16_2_In


title: Brain endothelial cell 386

description: Brain endothelial cell 386


title: N_5_cv

value: HPV negative cervical epithelium tissues


title: N_1_cv


title: Control (Tn5 5x)

city: St Louis

first: Ricardo

last: D'Oliveira Albanus

state: MO

address: 4370 Duncan Avenue, Suite 6306D, Jeffrey T. Fort Neuroscience Bdg.

department: Neurology

institute: Washington University School of Medicine

data_processing:
Reads were trimmed for barcodes and aligned to the hg19 reference human genome using BWA (v. 0.7.15) similarly to our previous study (Scott et al., Nat Comm 2016), with additional parameters -I 200,200,5000 to avoid larger ATAC-seq fragments being discarded.
We removed duplicate alignments using Picard and retained properly paired and uniquely mapped alignments with high mapping quality (MAPQ ≥ 30). We called broad and narrow peaks using MACS2 (v. 2.1.1.20160309) with flags -g hs --nomodel --shift -100 --extsize 200 -B [--broad] --keep-dup all and kept peaks that were both outside blacklisted regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) and reached 5% FDR.
Sample QC was determined using ataqv (https://github.com/ParkerLab/ataqv).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: BedGraph files from MACS2.

source_name: GM12878 lymphoblastoid cell line

growth_protocol: We cultured GM12878 cells following the ENCODE GM12878 cell culture protocol (https://www.encodeproject.org/documents/1bb75b62-ac29-4368-9855-68d410e1963a/), except that we added plasmocin (Invivogen, San Diego, CA; 50 ug/mL) to the growth media to prevent mycoplasma contamination.

extract_protocol: We conducted ATAC-seq as described in Buenrostro et al. (Curr. Protoc. Mol. Biol. 2015) using a home-made Tn5 that we synthesized as described in Picelli et al. (Genome Res. 2014). For each replicate we incubated 250,000 cells with 12.5 uL of 1:1 mix of Tn5 that carry 5-methylC-MEDS-A oligos and MEDS-B oligos at 37℃ for 30 minutes in a 50 uL reaction. We column-purified the tagmented DNA using the Zymo DNA Clean & Concentrator-5 kit (Zymo Research, Irvine, CA). We constructed Illumina sequencing library using the Kitzman lab custom index primers. We PCR-amplified a total of 11 cycles (5 initial + 6 additional) until amplification curve reached its mid-log phase (⅓ to ½ of max signal), and then purified the products using SPRI beads prepared as in (Rohland and Reich, Genome Res. 2012) and eluted in 22 uL of TTE8 buffer.

value: Lymphoblastoid cell line

value: Control

tag: tn5 concentration


title: Brain endothelial cell 389

description: Brain endothelial cell 389


title: Brain endothelial cell 387

description: Brain endothelial cell 387


title: N_4_cv


title: Brain endothelial cell 385

description: Brain endothelial cell 385


title: H16_3_In


title: N_3_cv


title: Brain endothelial cell 384

description: Brain endothelial cell 384


title: Brain endothelial cell 382

description: Brain endothelial cell 382


title: Brain endothelial cell 383

description: Brain endothelial cell 383


title: Brain endothelial cell 381

description: Brain endothelial cell 381


title: iHER2-HLO(Dox+)_rep2

city: okayama

first: Takeshi

last: Takarada

state: okayama

address: 2-5-1 Shikata-cho

department: Graduate School of Medicine, Dentistry and Pharmaceutical Sciences

country: Japan

institute: Okayama university

data_processing:
All sequence reads were extracted in FASTQ format using the CASAVA 1.8.4 pipeline.
Genome_build: Filtered reads were mapped to hg19 using HISAT2 (v2.1.0).

source_name: iHER2-iPSC (iHER2-1383D2)

growth_protocol:
Differentiation protocol. The hiPSCs (1 × 104) were suspended in 1 ml of freshly prepared StemFit containing 10 µM Y27632, and 4 µl of iMatrix511 was added to a 3.5-cm culture dish. The culture medium was replaced the next day with fresh StemFit without Y27632. After culturing for 2–3 days, cells were washed with PBS, and differentiation was induced by changing the culture medium at each time point. Chemically-defined CDM2 medium  36 was used as the basal culture medium 15, 16, 37, and cytokines or other chemicals were added to prepare each differentiation medium. The composition of CDM2 basal medium is described in Supplementary Table 5. The composition of chemicals or cytokines used in this study and incubation times were as follows: anterior primitive streak (CDM2 basal medium + 100 ng/ml activin A, 3 µM CHIR99021) for 1 day, definitive endoderm (CDM2 basal medium + 100 ng/ml activin A, 250 nM LDN193189) for 2 days, anterior foregut endoderm (CDM2 basal medium + 100 ng/ml noggin, 10 µM SB431542, 50 µg/ml L-ascorbic acid) for 4 days, ventralized anterior foregut endoderm (CDM2 basal medium + 20 ng/ml BMP4, 3 µM CHIR99021, 1 µM ATRA, 50 µg/ml L-ascorbic acid) for 4 days, and lung progenitor (CDM2 basal medium + 20 µM DAPT, 3µM CHIR99021, 10 ng/ml KGF, 10 ng/ml FGF10) for 7 days. Culture dishes were washed using CDM2 medium when the composition of chemicals or cytokines was changed.
HLO culture protocol. Alveolization (AL) medium (1 ml) (Supplementary Table 5), which was freshly prepared before use, was supplemented with 10 μM Y27632 and added to each well of a plate with 12-well inserts. Fetal lung fibroblasts (5 × 105) (MRC5, RIKEN BRC, Japan) and CPMhigh lung progenitor cells (1 × 104) were suspended in 100 µl of AL medium containing 10µM Y27632 and mixed with an equal volume of Matrigel (Corning, NY). AL medium without Y27632 was changed every 2–3 days for 2–3 weeks. Doxycycline (1 μg/ml) (Takara, Shiga) treatment was started on day 3 after initiating HLO 3D-cultures. Neratinib (HKI-272, 100 nM) (Chemscene, Monmouth Junction, NJ) with doxycycline treatment was also started on day 3 after initiating HLO 3D-cultures. To measure the morphological complexity index of HLOs, the outer area of the HLO from the inner circular area was divided by the inner area. Areas >200 μm were evaluated using ImageJ software.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN).
Sequencing libraries were KAPA RNA HyperPrep Kit with RiboErase (HMR) (Kapa Biosystems) and SeqCap Adapter Kit (Set A or Set B, Roche) following manufacture`s instruction. The initial amount of total RNA was 1000 ng.

value: lung

value: human lung organoid


title: N_2_cv


title: Parental-HLO(Dox+)_rep1

source_name: human iPSC (1383D2)

value: Parental-HLODOX+


title: PAWUUS-R-IgG control

city: New York

first: Shella

last: Saint Fleur-Lominy

state: New York

address: 550 First Avenue, Smilow Building 1207

department: Medicine

institute: NYU Langone Health

data_processing:
Align to reference genome (hg19) using Bowtie2
Remove duplicate reads using Sambamba
Peaks calling with MACS2
Genome_build: hg19
Supplementary_files_format_and_content: bigwig contains peak information

source_name: B-ALL patient sample

growth_protocol: The paired patient samples were thawed at 37 degrees, spun down and resuspended in RPMI. After counting cells were immediately used for downstream analysis.

extract_protocol:
Cells were cross-linked in 1% formaldehyde, lysed and then sheared chromatin was immunoprecipitated with antibodies targeting various histone marks (H3K4me3, H3K27me3, H3K27ac,  H3K9ac, and H3K9me3). A small aliquot was set aside prior to immunoprecipitation as input DNA. Quality control was performed using an Agilent Technologies 2100 Bioanalyzer prior to library preparation.
Libraries were prepared according to Illumina's instructions.

value: bone marrow

tag: patient id

value: PAWUUS

tag: diagnosis/relapse

value: relapse

tag: cohort

value: cohort B

tag: ip antibody

value: IgG Abcam #ab37415


title: PAWUUS-R-H3K9ac

value: H3K9ac Millipore #Mi 06-942


title: Brain endothelial cell 377

description: Brain endothelial cell 377

tag: strain

value: brain

value: adult mice


title: Brain endothelial cell 379

description: Brain endothelial cell 379

tag: tissue

value: Pdgfb ret/+

value: endothelial cell


title: Brain endothelial cell 378

description: Brain endothelial cell 378

tag: age


title: iHER2-HLO(Dox+)_rep1

tag: genotype


title: Brain endothelial cell 376

description: Brain endothelial cell 376

tag: cell type


title: Parental-HLO(Dox+)_rep2


title: N_6_cv


title: Brain endothelial cell 375

description: Brain endothelial cell 375


title: Brain endothelial cell 374

description: Brain endothelial cell 374


title: PAWUUS-R-H3K27me3

value: H3K27me3 Abcam #ab6002


title: Brain endothelial cell 373

description: Brain endothelial cell 373


title: PAWUUS-R-H3K27ac

value: H3K27ac Abcam #ab4729


title: Brain endothelial cell 380

description: Brain endothelial cell 380


title: Brain endothelial cell 372

description: Brain endothelial cell 372


title: Brain endothelial cell 367

description: Brain endothelial cell 367


title: Workers/Queens pharate-adults 6 ug

type: RNA

city: Alfenas

first: Angel

middle: Roberto

last: Barchuk

state: Minas Gerais

address: Rua Gabriel Monteiro Silva 700, Campus Unifal

department: Cell and Developmental Biology

country: Brazil

institute: Federal University of Alfenas

hyb_protocol: The RNA was dye-coupled and combined with hybridization buffer (49% Formamide, 49% SSC 20x and 0.2% SDS), pre-heated at 55° C for 3 min, applied to arrays, and hybridized for 17 h at 42 °C in single slide hybridization chambers placed in a water bath. A series of 30s shaking washes in 2× SSC plus 0.1% SDS; 2× SSC; 0.1× SSC and Milli-Q water at room temperature removed excess probe.

scan_protocol: The hybridized slides were scanned using an Axon Genepix 4000B scanner (Molecular Devices, Sunnyvale, CA) with GENEPIX software (Agilent Technologies, Santa Clara, CA), 10-micron resolution, Cy3 with Green Laser (532 nm), and Cy5 with Red Laser (635 nm). GenePix Pro 6.0 software was used for quantification of the spots and image analysis with default parameters.  The hybridized slides were scanned using an Axon Genepix 4000B scanner (Molecular Devices, Sunnyvale, CA) with GENEPIX software (Agilent Technologies, Santa Clara, CA), 10-micron resolution, Cy3 with Green Laser (532 nm), and Cy5 with Red Laser (635 nm). GenePix Pro 6.0 software was used for quantification of the spots and image analysis with default parameters.

data_processing: The scan results of the slides read in an Axon Genepix 4000B scanner (Molecular Devices) with GenePix® Pro 6.0 software (Agilent Technologies, Santa Clara, CA) were analyzed using the Limma package of Bioconductor software implemented in R The background was corrected by adding to the background intensities a positive constant (offset correction = 50), which restrains spurious variation in log-ratios, particularly at low intensity spots. The “print-tip loess” normalization was used to correct for within-array dye, and spatial effects and single channel normalization was used to facilitate comparison between arrays. (Queen’s sample intensity/Worker’s sample intensity) was determined for each probe in each array. After applying Bayesian statistics to shrink estimated standard errors, we used the moderated t-statistic test for each gene.

label: Cy3, Cy5

organism: Apis mellifera

label_protocol: RNA amplification was done with and according to Amino Allyl MessageAmpTM II aRNA Amplification Kit (Ambion). The amplified RNA samples (10 or 20 µg) were used for dual channel microarray hibridization with Cy3 and Cy5 dyes (with dye swaps). Dye swaps were done for each comparison and two slides were used to evaluate the differential expression.

growth_protocol: Bees were obtained from hives of Africanized hybrid Apis mellifera kept in the Experimental Apiary of the University of São Paulo in Ribeirão Preto, Brazil.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Pharate-adult (Pp) queens and workers of the same age were obtained as in Barchuk et al 2001, J Insect Science.  obtained as in Barchuk et al.

tag: sample type

value: Pool of 15 pharate-adult (Pp) workers brain. 6 microgram aRNA

value: Pool of 10 pharate-adult (Pp) queens brain. 6 microgram aRNA.


title: Brain endothelial cell 371

description: Brain endothelial cell 371


title: Brain endothelial cell 370

description: Brain endothelial cell 370


title: Brain endothelial cell 369

description: Brain endothelial cell 369


title: Workers/Queens pharate-adults 20 ug

value: Pool of 15 pharate-adult (Pp) workers brain. 20 microgram aRNA.

value: Pool of 10 pharate-adult (Pp) queens brain. 20 microgram aRNA.


title: Brain endothelial cell 368

description: Brain endothelial cell 368


title: PAWUUS-D-H3K9ac

value: diagnosis


title: PAWUUS-D-IgG control

value: bone marrow


title: PAWLKK-R-IgG control

value: PAWLKK


title: PAWUUS-D-H3K27ac

value: PAWUUS


title: PAWUUS-D-H3K27me3

value: cohort B


title: Brain endothelial cell 366

description: Brain endothelial cell 366


title: Brain endothelial cell 364

description: Brain endothelial cell 364


title: PAWLKK-R-H3K27me3

value: relapse


title: Brain endothelial cell 365

description: Brain endothelial cell 365


title: Brain endothelial cell 360

description: Brain endothelial cell 360


title: Brain endothelial cell 361

description: Brain endothelial cell 361


title: PAWLKK-D-IgG control

value: IgG Abcam #ab37415


title: PAWLKK-D-H3K9ac

value: H3K9ac Millipore #Mi 06-942


title: PAWLKK-D-H3K27ac


title: Brain endothelial cell 359

description: Brain endothelial cell 359

value: brain

value: adult mice


title: PAWISV-R-H3K9ac

value: PAWISV


title: PAWLKK-R-H3K27ac


title: PAWISV-R-IgG control


title: Brain endothelial cell 357

description: Brain endothelial cell 357

value: Pdgfb ret/+

value: endothelial cell


title: PAWLKK-D-H3K27me3

value: H3K27me3 Abcam #ab6002


title: PAWISV-R-H3K27ac

value: H3K27ac Abcam #ab4729


title: PAWISV-D-IgG control


title: PAWLKK-R-H3K9ac


title: Brain endothelial cell 356

description: Brain endothelial cell 356


title: Brain endothelial cell 355

description: Brain endothelial cell 355


title: Brain endothelial cell 354

description: Brain endothelial cell 354


title: Brain endothelial cell 353

description: Brain endothelial cell 353


title: Brain endothelial cell 351

description: Brain endothelial cell 351


title: Brain endothelial cell 363

description: Brain endothelial cell 363


title: Brain endothelial cell 350

description: Brain endothelial cell 350


title: Brain endothelial cell 362

description: Brain endothelial cell 362


title: Brain endothelial cell 352

description: Brain endothelial cell 352


title: PAWISV-D-H3K9ac


title: PAWISV-D-H3K27ac


title: Brain endothelial cell 349

description: Brain endothelial cell 349


title: Brain endothelial cell 358

description: Brain endothelial cell 358


title: PAWISV-D-H3K27me3


title: PAWGDA-R-H3K9ac

value: PAWGDA


title: PAWGDA-R-H3K27ac


title: Brain endothelial cell 348

description: Brain endothelial cell 348


title: PAWGDA-D-IgG control


title: Brain endothelial cell 347

description: Brain endothelial cell 347


title: Brain endothelial cell 344

description: Brain endothelial cell 344


title: Brain endothelial cell 345

description: Brain endothelial cell 345


title: PAWGDA-D-H3K9ac


title: Brain endothelial cell 346

description: Brain endothelial cell 346


title: Brain endothelial cell 342

description: Brain endothelial cell 342


title: Brain endothelial cell 341

description: Brain endothelial cell 341


title: PAWGDA-D-H3K27me3


title: Brain endothelial cell 339

description: Brain endothelial cell 339


title: Brain endothelial cell 343

description: Brain endothelial cell 343


title: PAVVBJ-R-H3K27ac

value: PAVVBJ


title: PAVVBJ-D-IgG control

value: diagnosis


title: PAWGDA-D-H3K27ac

value: bone marrow


title: PAVVBJ-R-IgG control


title: PAWGDA-R-IgG control


title: Brain endothelial cell 338

description: Brain endothelial cell 338


title: PAVVBJ-D-H3K27me3


title: PAVUJE-R-H3K9ac

value: PAVUJE


title: Brain endothelial cell 337

description: Brain endothelial cell 337


title: Brain endothelial cell 335

description: Brain endothelial cell 335


title: PAVUJE-R-IgG control


title: PAWGDA-R-H3K27me3


title: PAVVBJ-D-H3K27ac


title: PAVVBJ-R-H3K27me3


title: PAVUJE-R-H3K27ac


title: PAVUJE-D-H3K9ac


title: PAVUJE-D-IgG control


title: Brain endothelial cell 340

description: Brain endothelial cell 340


title: Brain endothelial cell 330

description: Brain endothelial cell 330


title: PAVUJE-R-H3K27me3


title: Brain endothelial cell 333

description: Brain endothelial cell 333


title: Brain endothelial cell 331

description: Brain endothelial cell 331


title: PAVUJE-D-H3K27ac


title: Brain endothelial cell 332

description: Brain endothelial cell 332


title: Brain endothelial cell 336

description: Brain endothelial cell 336


title: Brain endothelial cell 328

description: Brain endothelial cell 328


title: Brain endothelial cell 334

description: Brain endothelial cell 334


title: Brain endothelial cell 325

description: Brain endothelial cell 325


title: Brain endothelial cell 327

description: Brain endothelial cell 327


title: PAVUGI-R-H3K9ac

value: PAVUGI


title: PAVUGI-R-H3K27me3

value: cohort B


title: PAVUGI-R-H3K27ac

value: relapse


title: PAVUGI-D-IgG control

value: IgG Abcam #ab37415


title: Brain endothelial cell 323

description: Brain endothelial cell 323


title: PAVUGI-D-H3K9ac

value: H3K9ac Millipore #Mi 06-942


title: Brain endothelial cell 322

description: Brain endothelial cell 322

value: brain


title: Brain endothelial cell 321

description: Brain endothelial cell 321

value: adult mice


title: PAVUJE-D-H3K27me3


title: Brain endothelial cell 329

description: Brain endothelial cell 329


title: Brain endothelial cell 320

description: Brain endothelial cell 320


title: PAVUGI-D-H3K27ac


title: PAVSYL-R-IgG control

value: PAVSYL


title: Brain endothelial cell 318

description: Brain endothelial cell 318

value: Pdgfb ret/+


title: Brain endothelial cell 319

description: Brain endothelial cell 319

value: endothelial cell


title: PAVUGI-R-IgG control


title: PAVSYL-R-H3K27ac


title: PAVSYL-D-IgG control

value: blood


title: PAVSYL-R-H3K27me3

value: H3K27me3 Abcam #ab6002


title: Brain endothelial cell 316

description: Brain endothelial cell 316


title: PAVSYL-D-H3K27me3


title: Brain endothelial cell 317

description: Brain endothelial cell 317


title: Brain endothelial cell 315

description: Brain endothelial cell 315


title: PAVSYL-D-H3K27ac

value: H3K27ac Abcam #ab4729


title: Brain endothelial cell 324

description: Brain endothelial cell 324


title: Brain endothelial cell 314

description: Brain endothelial cell 314


title: PAVSGZ-R-IgG control

value: PAVSGZ


title: Brain endothelial cell 312

description: Brain endothelial cell 312


title: PAVSGZ-R-H3K9ac


title: PAVUGI-D-H3K27me3

value: diagnosis


title: PAVSGZ-R-H3K27me3

value: bone marrow


title: Brain endothelial cell 326

description: Brain endothelial cell 326


title: Brain endothelial cell 311

description: Brain endothelial cell 311


title: Brain endothelial cell 310

description: Brain endothelial cell 310


title: PAVSGZ-R-H3K27ac


title: PAVSGZ-D-IgG control


title: PAVSGZ-D-H3K9ac


title: Brain endothelial cell 309

description: Brain endothelial cell 309


title: Brain endothelial cell 307

description: Brain endothelial cell 307


title: PAVAYW-R-IgG control

value: PAVAYW


title: Brain endothelial cell 308

description: Brain endothelial cell 308


title: PAVSGZ-D-H3K27me3


title: Brain endothelial cell 304

description: Brain endothelial cell 304


title: PAVSGZ-D-H3K27ac


title: Brain endothelial cell 306

description: Brain endothelial cell 306


title: Brain endothelial cell 303

description: Brain endothelial cell 303


title: Brain endothelial cell 305

description: Brain endothelial cell 305


title: PAVAYW-R-H3K9ac


title: PAVAYW-R-H3K27me3


title: PAVAYW-R-H3K27ac


title: Brain endothelial cell 302

description: Brain endothelial cell 302


title: Brain endothelial cell 1187

description: Brain endothelial cell 1187

value: Pdgfb ret/ret


title: Brain endothelial cell 313

description: Brain endothelial cell 313


title: PAVAYW-D-IgG control

value: cohort B


title: Brain endothelial cell 1186

description: Brain endothelial cell 1186


title: PAVAYW-D-H3K27me3


title: PAVAYW-D-H3K9ac


title: Brain endothelial cell 1184

description: Brain endothelial cell 1184


title: PAUWBS-R-IgG control

value: PAUWBS

value: relapse


title: Brain endothelial cell 1182

description: Brain endothelial cell 1182


title: PAUWBS-R-H3K27me3


title: Brain endothelial cell 1183

description: Brain endothelial cell 1183


title: Brain endothelial cell 1185

description: Brain endothelial cell 1185


title: PAVAYW-D-H3K27ac


title: PAUWBS-D-IgG control

value: IgG Abcam #ab37415


title: Brain endothelial cell 1181

description: Brain endothelial cell 1181

value: brain


title: PAUWBS-R-H3K27ac


title: Brain endothelial cell 1179

description: Brain endothelial cell 1179

value: adult mice


title: Brain endothelial cell 1178

description: Brain endothelial cell 1178


title: Brain endothelial cell 1177

description: Brain endothelial cell 1177


title: PAUWBS-D-H3K27ac


title: PAUWBS-D-H3K27me3


title: PAUVZV-R-H3K9ac

value: PAUVZV

value: H3K9ac Millipore #Mi 06-942


title: PAUVZV-R-H3K27me3


title: PAUVZV-R-H3K27ac


title: PAUVZV-D-IgG control


title: Brain endothelial cell 1173

description: Brain endothelial cell 1173

value: endothelial cell


title: Brain endothelial cell 1174

description: Brain endothelial cell 1174


title: PAUVZV-D-H3K9ac


title: Brain endothelial cell 1172

description: Brain endothelial cell 1172


title: PAUVZV-D-H3K27me3


title: Brain endothelial cell 1170

description: Brain endothelial cell 1170


title: PAUVZV-D-H3K27ac


title: Brain endothelial cell 1171

description: Brain endothelial cell 1171


title: Brain endothelial cell 1169

description: Brain endothelial cell 1169


title: PAUVRA-R-IgG

value: PAUVRA


title: PAUVRA-R-H3K9ac


title: Brain endothelial cell 1168

description: Brain endothelial cell 1168


title: PAUVRA-R-H3K27me3

value: H3K27me3 Abcam #ab6002


title: PAUVZV-R-IgG control


title: Brain endothelial cell 1180

description: Brain endothelial cell 1180


title: Brain endothelial cell 1166

description: Brain endothelial cell 1166


title: Brain endothelial cell 1176

description: Brain endothelial cell 1176


title: Brain endothelial cell 1165

description: Brain endothelial cell 1165


title: PAUVRA-D-H3K9ac


title: PAUVRA-R-H3K27ac

value: H3K27ac Abcam #ab4729


title: Brain endothelial cell 1164

description: Brain endothelial cell 1164


title: Brain endothelial cell 1175

description: Brain endothelial cell 1175


title: Brain endothelial cell 1167

description: Brain endothelial cell 1167


title: PAUVRA-D-H3K27ac


title: PAUUDV-R-IgG control

value: PAUUDV


title: Brain endothelial cell 1161

description: Brain endothelial cell 1161


title: Brain endothelial cell 1163

description: Brain endothelial cell 1163


title: PAUUDV-R-H3K27me3


title: Brain endothelial cell 1160

description: Brain endothelial cell 1160


title: PAUVRA-D-H3K27me3

value: diagnosis


title: Brain endothelial cell 1162

description: Brain endothelial cell 1162


title: Brain endothelial cell 1159

description: Brain endothelial cell 1159


title: PAUUDV-R-H3K27ac

value: bone marrow


title: PAUUDV-D-IgG control


title: PAUUDV-D-H3K27me3


title: Brain endothelial cell 1158

description: Brain endothelial cell 1158


title: Brain endothelial cell 1157

description: Brain endothelial cell 1157


title: PAUVRA-D-IgG control


title: PAULEB-R-IgG control

value: PAULEB


title: Brain endothelial cell 1155

description: Brain endothelial cell 1155

value: Pdgfb ret/ret


title: PAUUDV-D-H3K27ac

value: cohort B


title: PAULEB-R-H3K9ac


title: Brain endothelial cell 1154

description: Brain endothelial cell 1154


title: PAWISV-R-H3K27me3

value: PAWISV


title: Brain endothelial cell 1153

description: Brain endothelial cell 1153


title: Brain endothelial cell 1152

description: Brain endothelial cell 1152


title: PAULEB-R-H3K27ac

value: relapse


title: PAULEB-D-IgG control

value: IgG Abcam #ab37415


title: PAULEB-R-H3K27me3


title: Brain endothelial cell 1151

description: Brain endothelial cell 1151

value: brain


title: PAULEB-D-H3K9ac


title: Brain endothelial cell 1150

description: Brain endothelial cell 1150

value: adult mice


title: Brain endothelial cell 1148

description: Brain endothelial cell 1148


title: PAUHHJ-R-H3K27ac

value: PAUHHJ


title: PAULEB-D-H3K27ac


title: PAUHHJ-D-IgG control


title: Brain endothelial cell 1156

description: Brain endothelial cell 1156


title: Brain endothelial cell 1146

description: Brain endothelial cell 1146


title: Brain endothelial cell 1147

description: Brain endothelial cell 1147


title: PAUHHJ-D-H3K27ac


title: Brain endothelial cell 1144

description: Brain endothelial cell 1144


title: Brain endothelial cell 1149

description: Brain endothelial cell 1149


title: PAUCYW-R-IgG control

value: PAUCYW


title: Brain endothelial cell 1143

description: Brain endothelial cell 1143

value: endothelial cell


title: PAUCYW-R-H3K27me3


title: Brain endothelial cell 1142

description: Brain endothelial cell 1142


title: PAUCYW-R-H3K27ac


title: Brain endothelial cell 1141

description: Brain endothelial cell 1141


title: Brain endothelial cell 1140

description: Brain endothelial cell 1140


title: PAUCYW-D-IgG control

value: Blood


title: PAULEB-D-H3K27me3

value: H3K27me3 Abcam #ab6002


title: Brain endothelial cell 1138

description: Brain endothelial cell 1138


title: Brain endothelial cell 1139

description: Brain endothelial cell 1139


title: PAUCYW-D-H3K27me3


title: PAUCYW-D-H3K27ac

value: H3K27ac Abcam #ab4729


title: Brain endothelial cell 1137

description: Brain endothelial cell 1137


title: PAUCYW-D-H3K9ac

value: H3K9ac Millipore #Mi 06-942


title: Brain endothelial cell 1136

description: Brain endothelial cell 1136


title: Brain endothelial cell 1135

description: Brain endothelial cell 1135


title: PATTJL-R-IgG control

value: PATTJL


title: Brain endothelial cell 1145

description: Brain endothelial cell 1145


title: PATTJL-R-H3K27ac

value: bone marrow


title: PATTJL-R-H3K9ac


title: Brain endothelial cell 1132

description: Brain endothelial cell 1132


title: PATTJL-D-IgG control

value: diagnosis


title: PATTJL-R-H3K27me3


title: PATTJL-D-H3K27me3


title: Brain endothelial cell 1134

description: Brain endothelial cell 1134

value: Pdgfb ret/ret


title: PAUCYW-R-H3K9ac

value: cohort B


title: Brain endothelial cell 1133

description: Brain endothelial cell 1133


title: PATTJL-D-H3K9ac


title: Brain endothelial cell 1130

description: Brain endothelial cell 1130


title: Brain endothelial cell 1131

description: Brain endothelial cell 1131


title: PATTJL-D-H3K27ac


title: Brain endothelial cell 1129

description: Brain endothelial cell 1129


title: Brain endothelial cell 1128

description: Brain endothelial cell 1128


title: PATRLY-R-IgG control

value: PATRLY


title: PATRLY-R-H3K27me3

value: relapse


title: PATRLY-R-H3K27ac


title: Brain endothelial cell 1127

description: Brain endothelial cell 1127


title: Brain endothelial cell 1125

description: Brain endothelial cell 1125


title: Brain endothelial cell 1124

description: Brain endothelial cell 1124


title: PATRLY-D-H3K27ac


title: Brain endothelial cell 1123

description: Brain endothelial cell 1123


title: PATRLY-D-H3K27me3


title: Brain endothelial cell 1126

description: Brain endothelial cell 1126


title: PARGVZ R_H3K9ac

value: PARGVZ

value: cohort A


title: PARGVZ  R_H3K9me3

value: H3K9me3 Abcam #ab8898


title: Brain endothelial cell 1121

description: Brain endothelial cell 1121

value: brain

value: adult mice


title: PARGVZ R_H3K27ac


title: Brain endothelial cell 1120

description: Brain endothelial cell 1120

value: endothelial cell


title: PARGVZ R_H3K4me3

value: H3K4me3 Abcam #ab8580


title: Brain endothelial cell 1122

description: Brain endothelial cell 1122


title: PARGVZ R_H3K27me3

value: H3K27me3 Abcam #ab6002


title: Brain endothelial cell 1119

description: Brain endothelial cell 1119


title: Brain endothelial cell 1118

description: Brain endothelial cell 1118


title: Brain endothelial cell 1117

description: Brain endothelial cell 1117


title: PARGVZ D_H3K9ac


title: PARGVZ D_H3K27me3


title: PARGVZ D_H3K9me3


title: Brain endothelial cell 1115

description: Brain endothelial cell 1115


title: Brain endothelial cell 1113

description: Brain endothelial cell 1113


title: PARGVZ D_H3K27ac

value: H3K27ac Abcam #ab4729


title: Brain endothelial cell 1112

description: Brain endothelial cell 1112


title: PARGVZ D_input


title: Brain endothelial cell 1114

description: Brain endothelial cell 1114


title: PARGVZ D_H3K4me3


title: PAPZGR R_H3K27ac

value: PAPZGR


title: Brain endothelial cell 1111

description: Brain endothelial cell 1111


title: Brain endothelial cell 1109

description: Brain endothelial cell 1109


title: Brain endothelial cell 1110

description: Brain endothelial cell 1110


title: PAPZGR R_input


title: PAPZGR D_H3K27ac


title: Brain endothelial cell 1108

description: Brain endothelial cell 1108


title: Brain endothelial cell 1107

description: Brain endothelial cell 1107


title: PAPZGR R_H3K4me3


title: PARGVZ R_input


title: PAPZGR D_input


title: Brain endothelial cell 1116

description: Brain endothelial cell 1116


title: PARPRW R_H3K27ac

value: PARPRW


title: Brain endothelial cell 1106

description: Brain endothelial cell 1106


title: PAPZGR D_H3K4me3

value: bone marrow


title: Brain endothelial cell 1103

description: Brain endothelial cell 1103


title: Brain endothelial cell 1102

description: Brain endothelial cell 1102


title: PARPRW D_H3K27ac

value: diagnosis


title: Brain endothelial cell 1101

description: Brain endothelial cell 1101

value: Pdgfb ret/ret


title: PARPRW R_input


title: Brain endothelial cell 1105

description: Brain endothelial cell 1105


title: PARPRW D_H3K4me3


title: PARPRW D_input


title: PASSRR R_H3K9me3

value: PASSRR


title: PASSRR R_H3K9ac

value: H3K9ac Millipore #Mi 06-942


title: PASSRR R_H3K27me3

value: relapse


title: Brain endothelial cell 1098

description: Brain endothelial cell 1098


title: Brain endothelial cell 1099

description: Brain endothelial cell 1099


title: Brain endothelial cell 1100

description: Brain endothelial cell 1100


title: Brain endothelial cell 1097

description: Brain endothelial cell 1097


title: PASSRR R_H3K4me3


title: Brain endothelial cell 1095

description: Brain endothelial cell 1095


title: PASSRR R_input


title: Brain endothelial cell 1096

description: Brain endothelial cell 1096


title: Brain endothelial cell 1104

description: Brain endothelial cell 1104


title: PARPRW R_H3K4me3


title: PASSRR D_H3K9me3


title: Brain endothelial cell 1093

description: Brain endothelial cell 1093


title: Brain endothelial cell 1092

description: Brain endothelial cell 1092


title: PASSRR D_H3K9ac


title: PASSRR D_H3K27me3


title: Brain endothelial cell 1094

description: Brain endothelial cell 1094


title: PASSRR D_H3K27ac


title: Brain endothelial cell 1091

description: Brain endothelial cell 1091


title: Brain endothelial cell 1090

description: Brain endothelial cell 1090


title: PASSRR D_H3K4me3


title: Brain endothelial cell 1089

description: Brain endothelial cell 1089


title: Brain endothelial cell 1087

description: Brain endothelial cell 1087


title: PAPIDY R_H3K27me3

value: PAPIDY


title: PAPIDY R_H3K27ac

value: cohort A


title: Brain endothelial cell 1088

description: Brain endothelial cell 1088


title: Brain endothelial cell 1085

description: Brain endothelial cell 1085


title: Brain endothelial cell 1086

description: Brain endothelial cell 1086


title: PAPIDY D_H3K27me3


title: PAPIDY R_input


title: PASSRR R_H3K27ac


title: PAPIDY D_H3K27ac


title: Brain endothelial cell 1083

description: Brain endothelial cell 1083


title: PAPIDY D_input


title: Brain endothelial cell 1082

description: Brain endothelial cell 1082


title: Brain endothelial cell 1081

description: Brain endothelial cell 1081


title: PAPDKJ R_H3K27me3

value: PAPDKJ


title: PAPDKJ R_H3K27ac


title: Brain endothelial cell 1079

description: Brain endothelial cell 1079

value: brain


title: Brain endothelial cell 1078

description: Brain endothelial cell 1078

value: adult mice


title: Brain endothelial cell 1080

description: Brain endothelial cell 1080

value: endothelial cell


title: PAPDKJ R_H3K4me3

value: H3K4me3 Abcam #ab8580


title: PAPDKJ R_input


title: PAPDKJ D_H3K27me3

value: H3K27me3 Abcam #ab6002


title: PASSRR D_input


title: Brain endothelial cell 1077

description: Brain endothelial cell 1077


title: Brain endothelial cell 1076

description: Brain endothelial cell 1076


title: PAPDKJ D_H3K4me3


title: Brain endothelial cell 1074

description: Brain endothelial cell 1074


title: Brain endothelial cell 1075

description: Brain endothelial cell 1075


title: Brain endothelial cell 1072

description: Brain endothelial cell 1072


title: PAPDKJ D_input


title: PAPAGK R_H3K27me3

value: PAPAGK


title: Brain endothelial cell 1070

description: Brain endothelial cell 1070


title: PAPAGK R_H3K27ac

value: H3K27ac Abcam #ab4729


title: PAPAGK R_H3K4me3


title: PAPAGK D_H3K9me3

value: H3K9me3 Abcam #ab8898


title: Brain endothelial cell 1069

description: Brain endothelial cell 1069


title: Brain endothelial cell 1068

description: Brain endothelial cell 1068


title: Brain endothelial cell 1067

description: Brain endothelial cell 1067


title: PAPAGK D_H3K27ac

value: bone marrow


title: Brain endothelial cell 1065

description: Brain endothelial cell 1065


title: Brain endothelial cell 1066

description: Brain endothelial cell 1066


title: PAPAGK D_H3K4me3

value: diagnosis


title: Brain endothelial cell 1064

description: Brain endothelial cell 1064

value: Pdgfb ret/ret


title: PAPAGK R_H3K9me3


title: PAPAGK D_input


title: Brain endothelial cell 1084

description: Brain endothelial cell 1084


title: Brain endothelial cell 1063

description: Brain endothelial cell 1063


title: PARGHW R_H3K9ac

value: PARGHW


title: Brain endothelial cell 1061

description: Brain endothelial cell 1061


title: PAPAGK R_input


title: PARGHW R_H3K4me3


title: Brain endothelial cell 1060

description: Brain endothelial cell 1060


title: PARGHW R_H3K27me3


title: PAPAGK D_H3K27me3


title: PARGHW D_H3K9me3


title: Brain endothelial cell 1073

description: Brain endothelial cell 1073


title: Brain endothelial cell 1062

description: Brain endothelial cell 1062


title: PARGHW R_H3K27ac


title: Brain endothelial cell 1059

description: Brain endothelial cell 1059


title: PARGHW D_H3K9ac

value: H3K9ac Millipore #Mi 06-942


title: PARGHW R_input

value: relapse


title: Brain endothelial cell 1058

description: Brain endothelial cell 1058


title: Brain endothelial cell 1056

description: Brain endothelial cell 1056


title: PAPDKJ D_H3K27ac


title: PARGHW D_H3K27me3


title: Brain endothelial cell 1055

description: Brain endothelial cell 1055


title: PARGHW  R_H3K9me3


title: PARGHW D_H3K27ac


title: Brain endothelial cell 1054

description: Brain endothelial cell 1054


title: Brain endothelial cell 1053

description: Brain endothelial cell 1053


title: PARCBK  R_H3K9me3

value: PARCBK


title: Brain endothelial cell 1051

description: Brain endothelial cell 1051


title: Brain endothelial cell 1057

description: Brain endothelial cell 1057


title: PARCBK R_H3K27ac

value: cohort A


title: Brain endothelial cell 1047

description: Brain endothelial cell 1047


title: Brain endothelial cell 1050

description: Brain endothelial cell 1050


title: PARCBK D_H3K27me3


title: PARCBK D_H3K9ac


title: Brain endothelial cell 1048

description: Brain endothelial cell 1048


title: Brain endothelial cell 1044

description: Brain endothelial cell 1044


title: PARCBK R_input


title: Brain endothelial cell 1049

description: Brain endothelial cell 1049


title: PARCBK R_H3K9ac


title: Brain endothelial cell 1043

description: Brain endothelial cell 1043


title: PARCBK D_H3K4me3


title: PARCBK R_H3K4me3


title: Brain endothelial cell 1040

description: Brain endothelial cell 1040


title: PARCBK R_H3K27me3


title: PARCBK D_input


title: Brain endothelial cell 1041

description: Brain endothelial cell 1041


title: Brain endothelial cell 1039

description: Brain endothelial cell 1039


title: PARFLV R_H3K9ac

value: PARFLV


title: PARGHW D_H3K4me3


title: Brain endothelial cell 1052

description: Brain endothelial cell 1052

value: brain


title: Brain endothelial cell 1042

description: Brain endothelial cell 1042

value: adult mice


title: PARFLV  R_H3K9me3


title: PARGHW D_input


title: Brain endothelial cell 1045

description: Brain endothelial cell 1045

value: endothelial cell


title: Brain endothelial cell 1046

description: Brain endothelial cell 1046


title: PARCBK D_H3K27ac


title: PARCBK D_H3K9me3


title: Brain endothelial cell 1038

description: Brain endothelial cell 1038


title: PARFLV R_H3K27me3


title: Brain endothelial cell 1037

description: Brain endothelial cell 1037


title: PARFLV R_H3K4me3

value: H3K4me3 Abcam #ab8580


title: Brain endothelial cell 1035

description: Brain endothelial cell 1035


title: Brain endothelial cell 1036

description: Brain endothelial cell 1036


title: PARFLV R_input


title: Brain endothelial cell 1032

description: Brain endothelial cell 1032


title: Brain endothelial cell 1034

description: Brain endothelial cell 1034


title: PARFLV D_H3K9me3


title: PARFLV D_H3K27me3

value: H3K27me3 Abcam #ab6002


title: PARFLV D_H3K9ac


title: Brain endothelial cell 1031

description: Brain endothelial cell 1031


title: Brain endothelial cell 1029

description: Brain endothelial cell 1029


title: Brain endothelial cell 1028

description: Brain endothelial cell 1028


title: PARFLV D_input


title: PARBVI  R_H3K9me3

value: PARBVI


title: Brain endothelial cell 1033

description: Brain endothelial cell 1033


title: PARFLV D_H3K4me3


title: Brain endothelial cell 1030

description: Brain endothelial cell 1030


title: PARFLV D_H3K27ac

value: H3K27ac Abcam #ab4729


title: Brain endothelial cell 1026

description: Brain endothelial cell 1026


title: Brain endothelial cell 1027

description: Brain endothelial cell 1027


title: PARBVI R_H3K9ac


title: PARFLV R_H3K27ac


title: PARBVI R_H3K27ac


title: Brain endothelial cell 1025

description: Brain endothelial cell 1025


title: PARBVI R_H3K27me3


title: Brain endothelial cell 1024

description: Brain endothelial cell 1024


title: PARBVI R_input


title: PARBVI R_H3K4me3


title: PARBVI D_H3K9me3

value: H3K9me3 Abcam #ab8898


title: Brain endothelial cell 1020

description: Brain endothelial cell 1020


title: PARBVI D_H3K27me3

value: bone marrow


title: PARBVI D_H3K27ac

value: diagnosis


title: Brain endothelial cell 1018

description: Brain endothelial cell 1018

value: Pdgfb ret/ret


title: Brain endothelial cell 1019

description: Brain endothelial cell 1019


title: PARBVI D_H3K4me3


title: Brain endothelial cell 1017

description: Brain endothelial cell 1017


title: Brain endothelial cell 1015

description: Brain endothelial cell 1015


title: PAPZNK R_H3K9me3

value: PAPZNK


title: PARBVI D_input


title: PAPZNK R_H3K9ac

value: H3K9ac Millipore #Mi 06-942


title: PAPZNK R_H3K27me3

value: relapse


title: Brain endothelial cell 1013

description: Brain endothelial cell 1013


title: Brain endothelial cell 1014

description: Brain endothelial cell 1014


title: PARBVI D_H3K9ac


title: PAPZNK R_H3K4me3


title: Brain endothelial cell 1011

description: Brain endothelial cell 1011


title: PAPZNK R_input


title: Brain endothelial cell 1010

description: Brain endothelial cell 1010


title: Brain endothelial cell 1022

description: Brain endothelial cell 1022


title: Brain endothelial cell 1021

description: Brain endothelial cell 1021


title: Brain endothelial cell 1012

description: Brain endothelial cell 1012


title: Brain endothelial cell 1071

description: Brain endothelial cell 1071


title: PAPZNK D_H3K9me3


title: Brain endothelial cell 1008

description: Brain endothelial cell 1008


title: PAPZNK D_H3K9ac


title: PAPZNK D_H3K27me3


title: Brain endothelial cell 1007

description: Brain endothelial cell 1007


title: Brain endothelial cell 1016

description: Brain endothelial cell 1016


title: Brain endothelial cell 1006

description: Brain endothelial cell 1006


title: PAPZNK D_H3K4me3


title: Brain endothelial cell 1005

description: Brain endothelial cell 1005


title: Brain endothelial cell 1004

description: Brain endothelial cell 1004


title: PAPZNK R_H3K27ac


title: PAPZNK D_input


title: Brain endothelial cell 1002

description: Brain endothelial cell 1002


title: PAPSPN R_H3K27me3

value: PAPSPN


title: PAPSPN R_H3K9me3

value: cohort A


title: PAPSPN R_H3K9ac


title: Brain endothelial cell 1023

description: Brain endothelial cell 1023


title: Brain endothelial cell 1003

description: Brain endothelial cell 1003


title: PAPZNK D_H3K27ac


title: PAPSPN R_H3K27ac


title: Brain endothelial cell 1001

description: Brain endothelial cell 1001


title: Brain endothelial cell 1000

description: Brain endothelial cell 1000


title: Brain endothelial cell 1009

description: Brain endothelial cell 1009


title: Brain endothelial cell 998

description: Brain endothelial cell 998


title: Brain endothelial cell 997

description: Brain endothelial cell 997


title: PAPSPN R_H3K4me3


title: Brain endothelial cell 999

description: Brain endothelial cell 999


title: PAPSPN D_H3K9me3


title: Brain endothelial cell 994

description: Brain endothelial cell 994


title: Brain endothelial cell 995

description: Brain endothelial cell 995


title: PAPSPN D_H3K27me3


title: PAPSPN D_H3K9ac


title: Brain endothelial cell 996

description: Brain endothelial cell 996


title: PAPSPN R_input


title: PAPSPN D_H3K4me3


title: PAPSPN D_H3K27ac


title: Brain endothelial cell 991

description: Brain endothelial cell 991


title: PAWUUS_D (eRRBS)

data_processing:
Raw reads alignment and CpG methylation call were formed by using an in-house pipeline described in Akalin et al., PLoSGenetics, 2012.
FASTQ files were generated by using the Illumina CASAVA 1.8.2 pipeline.
Genome_build: hg19
Supplementary_files_format_and_content: wig file format

extract_protocol:
Genomic DNA was extracted and digested with MspI and DNA fragments were ligated with Illumina kits following end repair. Library fragments of 150-250 b.p. and 250-400 b.p. were isolated and bisulfite treated
Enhanced Reduced Representation Bisulfite Sequencing

value: PAWUUS


title: PAWUUS_R (eRRBS)


title: Brain endothelial cell 992

description: Brain endothelial cell 992

value: brain


title: Brain endothelial cell 990

description: Brain endothelial cell 990

value: adult mice


title: PAWLKK_R (eRRBS)

value: PAWLKK


title: Brain endothelial cell 989

description: Brain endothelial cell 989

value: endothelial cell


title: PAWLKK_D (eRRBS)


title: Brain endothelial cell 988

description: Brain endothelial cell 988


title: PAWISV_R (eRRBS)

value: PAWISV


title: Brain endothelial cell 987

description: Brain endothelial cell 987


title: Brain endothelial cell 986

description: Brain endothelial cell 986


title: PAWISV_D (eRRBS)


title: PAWGDA_R (eRRBS)

value: PAWGDA


title: Brain endothelial cell 985

description: Brain endothelial cell 985


title: Brain endothelial cell 984

description: Brain endothelial cell 984


title: PAWGDA_D (eRRBS)


title: Brain endothelial cell 301

description: Brain endothelial cell 301

value: Pdgfb ret/+


title: PAVVBJ_R (eRRBS)

value: PAVVBJ


title: PAPSPN D_input

value: bone marrow


title: PAVVBJ_D (eRRBS)

value: diagnosis


title: Brain endothelial cell 993

description: Brain endothelial cell 993

value: Pdgfb ret/ret


title: PAVUJE_R (eRRBS)

value: PAVUJE


title: Brain endothelial cell 298

description: Brain endothelial cell 298


title: PAVUGI_R (eRRBS)

value: PAVUGI


title: Brain endothelial cell 300

description: Brain endothelial cell 300


title: Brain endothelial cell 297

description: Brain endothelial cell 297


title: PAVUGI_D (eRRBS)


title: Brain endothelial cell 296

description: Brain endothelial cell 296


title: PAVSYL_D (eRRBS)

value: Blood

value: PAVSYL


title: Brain endothelial cell 293

description: Brain endothelial cell 293


title: PAVSGZ_R (eRRBS)

value: PAVSGZ

value: relapse


title: PAVSGZ_D (eRRBS)


title: Brain endothelial cell 292

description: Brain endothelial cell 292

value: brain


title: PAVSYL_R (eRRBS)


title: Brain endothelial cell 294

description: Brain endothelial cell 294

value: adult mice


title: Brain endothelial cell 291

description: Brain endothelial cell 291


title: Brain endothelial cell 290

description: Brain endothelial cell 290


title: PAVIFZ_D (eRRBS)

value: PAVIFZ


title: PAVAYW_R (eRRBS)

value: PAVAYW


title: PAVIFZ_R (eRRBS)


title: PAUWBS_R (eRRBS)

value: PAUWBS


title: Brain endothelial cell 289

description: Brain endothelial cell 289

value: endothelial cell


title: Brain endothelial cell 288

description: Brain endothelial cell 288

value: Pdgfb ret/+


title: Brain endothelial cell 287

description: Brain endothelial cell 287


title: PAVUJE_D (eRRBS)


title: Brain endothelial cell 299

description: Brain endothelial cell 299


title: PAVAYW_D (eRRBS)


title: PAUWBS_D (eRRBS)


title: Brain endothelial cell 285

description: Brain endothelial cell 285


title: Brain endothelial cell 284

description: Brain endothelial cell 284


title: Brain endothelial cell 286

description: Brain endothelial cell 286


title: PAUVZV_D (eRRBS)

value: PAUVZV


title: Brain endothelial cell 295

description: Brain endothelial cell 295


title: PAUVRA_R (eRRBS)

value: bone marrow

value: PAUVRA


title: PAUVZV_R (eRRBS)


title: Brain endothelial cell 283

description: Brain endothelial cell 283


title: Brain endothelial cell 282

description: Brain endothelial cell 282


title: PAUVRA_D (eRRBS)

value: diagnosis


title: PAULEB_R (eRRBS)

value: PAULEB


title: Brain endothelial cell 281

description: Brain endothelial cell 281


title: Brain endothelial cell 280

description: Brain endothelial cell 280


title: PAUHHJ_R (eRRBS)

value: PAUHHJ


title: Brain endothelial cell 279

description: Brain endothelial cell 279


title: PAUCYW_R (eRRBS)

value: PAUCYW


title: Brain endothelial cell 277

description: Brain endothelial cell 277


title: Brain endothelial cell 278

description: Brain endothelial cell 278


title: PAUHHJ_D (eRRBS)


title: PAUCYW_D (eRRBS)

value: Blood


title: Brain endothelial cell 276

description: Brain endothelial cell 276


title: Brain endothelial cell 275

description: Brain endothelial cell 275


title: PATRLY_R (eRRBS)

value: PATRLY


title: Brain endothelial cell 274

description: Brain endothelial cell 274


title: PATTJL_R (eRRBS)

value: PATTJL

value: relapse


title: Brain endothelial cell 273

description: Brain endothelial cell 273

value: brain

value: adult mice


title: Brain endothelial cell 270

description: Brain endothelial cell 270


title: Brain endothelial cell 271

description: Brain endothelial cell 271


title: PATTJL_D (eRRBS)


title: Brain endothelial cell 269

description: Brain endothelial cell 269


title: Brain endothelial cell 272

description: Brain endothelial cell 272


title: PAWLKK.R (RNAseq)

data_processing:
adapters and low quality bases were trimmed using trimmomatic
data was aligned to reference genome (hg19) using STAR
Genes-samples count matrices were generated using featureCounts
Genome_build: hg19
Supplementary_files_format_and_content: xls files presenting normalized counts

extract_protocol:
RNA was extracted using the QIAGEN RNeasy Mini Kit and quality was verified by an Agilent Bioanalyzer 2100 (PICO chip).
RNAseq libraries were generated using TruSeq stranded total RNA, with RiboZero Gold. RNA-seq libraries were sequenced using 54 base pair reads on the Illumina HiSeq 2500

value: PAWLKK


title: PAWLKK.D (RNAseq)


title: PAWISV.R (RNAseq)

value: PAWISV


title: Brain endothelial cell 268

description: Brain endothelial cell 268

value: endothelial cell


title: PAWISV.D (RNAseq)


title: PAUUDV_R (eRRBS)

value: PAUUDV


title: PAWUUS.D (RNAseq)

value: PAWUUS


title: PAWGDA.D (RNAseq)

value: bone marrow

value: PAWGDA


title: Brain endothelial cell 266

description: Brain endothelial cell 266

value: Pdgfb ret/+


title: PAVVBJ.R (RNAseq)

value: PAVVBJ


title: Brain endothelial cell 265

description: Brain endothelial cell 265


title: PAWGDA.R (RNAseq)


title: Brain endothelial cell 263

description: Brain endothelial cell 263


title: Brain endothelial cell 264

description: Brain endothelial cell 264


title: PAVUJE.R (RNAseq)

value: PAVUJE


title: Brain endothelial cell 262

description: Brain endothelial cell 262


title: PAVUJE.D (RNAseq)

value: diagnosis


title: PAWUUS.R (RNAseq)


title: PAVUGI.R (RNAseq)

value: PAVUGI


title: PAVUGI.D (RNAseq)


title: PAVSGZ.R (RNAseq)

value: PAVSGZ


title: PAVSGZ.D (RNAseq)


title: Brain endothelial cell 258

description: Brain endothelial cell 258


title: Brain endothelial cell 260

description: Brain endothelial cell 260


title: Brain endothelial cell 259

description: Brain endothelial cell 259


title: Brain endothelial cell 267

description: Brain endothelial cell 267


title: Brain endothelial cell 261

description: Brain endothelial cell 261


title: PAVAYW.R (RNAseq)

value: PAVAYW


title: Brain endothelial cell 257

description: Brain endothelial cell 257


title: Brain endothelial cell 256

description: Brain endothelial cell 256


title: PAVAYW.D (RNAseq)

value: Blood


title: PAUVRA_R (RNAseq)

value: PAUVRA

value: relapse


title: Brain endothelial cell 255

description: Brain endothelial cell 255

value: brain

value: adult mice


title: PAUVRA_D (RNAseq)


title: Brain endothelial cell 253

description: Brain endothelial cell 253

value: endothelial cell


title: Brain endothelial cell 254

description: Brain endothelial cell 254


title: Whole_Blood_GR19_V7

city: Burnaby

first: Amy

middle: H.

last: Lee

state: BC

address: 8888 University Drive

department: Molecular Biology and Biochemistry

country: Canada

institute: Simon Fraser University

data_processing:
Reads were checked for quality using FastQC v0.11.7
Reads were aligned to the reference genome using STAR v2.5.4b
Reads were counted using HTSeq v0.10.0
Quality metrics were summarized using MultiQC v1.0
Genome_build: Ensembl Genome Build GRCh38 v91
Supplementary_files_format_and_content: Tab-delimited text files containing gene counts for each sample

molecule: polyA RNA

source_name: Whole Blood

extract_protocol:
PAXGene RNA purification kit was used on collected whole blood as per manufacturer's instructions
KAPA stranded RNA-Seq library preparation kit was used as per manufacturer's guidelines

value: Whole Blood

tag: Sex

value: Male

tag: participant id

tag: visit


title: Brain endothelial cell 252

description: Brain endothelial cell 252


title: Whole_Blood_GR19_V6


title: PAVVBJ.D (RNAseq)

value: bone marrow


title: Brain endothelial cell 250

description: Brain endothelial cell 250


title: Whole_Blood_GR19_V5


title: mot2∆ mamRNA∆_2

city: JOUY-EN-JOSAS

first: Alicia

last: Nevers

address: Domaine de Vilvert

department: Micalis

country: France

institute: Institut national de la recherche agronomique (Inrae)

data_processing:
Demultiplexing using bcl2fastq2-2.18.12
Adaptors trimming with Cutadapt 1.15
Read alignment to reference genome with Bowtie2 in Galaxy. Write unaligned reads (in fastq format) to separate file(s): False; Write aligned reads (in fastq format) to separate file(s): False; Do you want to set paired-end options?: no  Will you select a reference genome from your history or use a built-in index?: indexed; Select reference genome: Schizosaccharomyces_pombe_1.1; Set read groups information?: do_not_set; Select analysis mode: simple; Do you want to use presets?: Very fast end-to-end (--very-fast); Save the bowtie2 mapping statistics to the history: True
Read counting with MulticovBed in Galaxy. Calculation based on strandedness?: Only overlaps occurring on the **same** strand.; minimum overlap required as a fraction of A: 1e-09; Require that the fraction of overlap be reciprocal for A and B: False; Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage: False; Minimum mapping quality (MAPQ) allowed:0; Include duplicate reads: True; Include failed-QC reads: False; Only count proper pairs: False
Genome_build: Schizosaccharomyces_pombe_1.1 (Galaxy)
Supplementary_files_format_and_content: raw counts

organism: Schizosaccharomyces pombe

source_name: liquid culture in minimal medium

growth_protocol: Schizosaccharomyces pombe cells were cultured in minimal medium (EMM) for 2 days at 30°C . Samples were collected during exponential phase (OD = 0.6).

extract_protocol:
Total RNAs were extracted using the hot acid phenol method
After Ribosomal RNA depletion, NextSeq 500/550 Mid Output Kit v2 was used to construct library. Paired-end 75 sequencing

value: h90, mamRNA::hygTK, mot2::kanMX

tag: growth phase

value: Exponential phase


title: Brain endothelial cell 249

description: Brain endothelial cell 249

value: Pdgfb ret/+


title: Brain endothelial cell 251

description: Brain endothelial cell 251


title: Brain endothelial cell 248

description: Brain endothelial cell 248


title: Brain endothelial cell 247

description: Brain endothelial cell 247


title: Whole_Blood_GR19_V3


title: mot2∆ mamRNA∆_1


title: Whole_Blood_GR18_V7


title: Whole_Blood_GR18_V6


title: Brain endothelial cell 243

description: Brain endothelial cell 243


title: Brain endothelial cell 246

description: Brain endothelial cell 246


title: Brain endothelial cell 242

description: Brain endothelial cell 242


title: mamRNA∆_1

value: h90, mamRNA::natMX


title: Brain endothelial cell 244

description: Brain endothelial cell 244


title: Whole_Blood_GR18_V4


title: Brain endothelial cell 240

description: Brain endothelial cell 240


title: Brain endothelial cell 239

description: Brain endothelial cell 239


title: Brain endothelial cell 245

description: Brain endothelial cell 245


title: mamRNA∆_2


title: Brain endothelial cell 241

description: Brain endothelial cell 241


title: Brain endothelial cell 238

description: Brain endothelial cell 238


title: Whole_Blood_GR19_V4


title: Whole_Blood_GR18_V5


title: mot2∆_1

value: h90, mot2::natMX


title: Whole_Blood_GR18_V3


title: wt_2

value: h90, wild type


title: Brain endothelial cell 236

description: Brain endothelial cell 236


title: Whole_Blood_GR17_V7

value: Female


title: wt_1


title: Brain endothelial cell 235

description: Brain endothelial cell 235


title: Brain endothelial cell 234

description: Brain endothelial cell 234


title: Whole_Blood_GR17_V6


title: Brain endothelial cell 233

description: Brain endothelial cell 233


title: rsfG mutant - sample2

city: Porto

first: Marta

middle: V.

last: Mendes

address: Rua Alfredo Allen, 208

country: Portugal

institute: i3S - Instituto de Investigação e Inovação em Saúde

data_processing:
Reads were aligned to the S. tsukubaensis NRRL18448 genome using Bowtie2 (Langmead et al., 2009) to get bam files (.bam) for each fasta file. The function featureCounts (Liao et al., 2013) in the R packages Rsubread was used to count the number of reads mapping to every 30 nucleotide section of the genome where adjacent sections overlapped by 15 nucleotides. These counts were used as the starting point for differential enrichment analysis using the R package edgeR (Robinson et al., 2009). Counts were read into a DGEList object and the function calcNormFactors (Sun et al., 2013) was used to calculate the normalisation factors. A suitable design matrix was made and then the function glmQLFit was used to fit a quasi-likelihood negative binomial model to the count data. After making a ΔrsfG, ΔsigG1 contrast the function glmQLFTest was used to conduct section-wise statistical tests of differential binding between ΔrsfG and ΔsigG1 strains. A Perl script (Stajich et al., 2002) was used to make bedgraph files from the output of a topTags function table and the counts data.
Genome_build: NZ_AJSZ00000000.1
Supplementary_files_format_and_content: bedgraph files with log fold changes and associated P-vaues

organism: Streptomyces tsukubensis NRRL18488

source_name: Liquid culture-grown bacteria

growth_protocol: S. tsukubaensis grown for 72h in liquid MGm-2.5 medium

extract_protocol:
Immunoprecipitation of SigG1-DNA complexes was carried out as described in Bush et al. (2013), using an anti-SigG1V16-A39 antibody and a goat anti-chicken IgY agarose (ab76444, Abcam).
Libraries were prepared according to NEB's instructions accompanying the Next® Ultra™ DNA Library Prep Kit. Library fragments of ~100-500 bp (insert plus adaptor and PCR primer sequences) were selected. Libraries were sequenced on an Illumina Novaseq 6000 platform

tag: developmental stage

value: exponential phase

tag: antibody


title: mot2∆_2


title: Brain endothelial cell 232

description: Brain endothelial cell 232

extract_protocol:
Pdgfb ret mice were crossed with Cldn5-GFP; Cspg4-DsRed mice for endothelial cell (positive for GFP, negative for dsRed) isolation based on fluorescence-activated cell sorting (FACS),  followed by the SmartSeq2 methodology for the generation and sequencing of full length polyadenylated cDNAs
Libraries for RNA-seq were prepared by using SMART-seq2 methodology


title: Brain endothelial cell 231

description: Brain endothelial cell 231


title: Whole_Blood_GR17_V5


title: rsfG mutant - sample1


title: Brain endothelial cell 237

description: Brain endothelial cell 237


title: Brain endothelial cell 230

description: Brain endothelial cell 230


title: Brain endothelial cell 228

description: Brain endothelial cell 228


title: Brain endothelial cell 222

description: Brain endothelial cell 222


title: Brain endothelial cell 224

description: Brain endothelial cell 224


title: Brain endothelial cell 229

description: Brain endothelial cell 229


title: sigG1 mutant - sample2


title: Brain endothelial cell 227

description: Brain endothelial cell 227


title: Whole_Blood_GR17_V3


title: Brain endothelial cell 223

description: Brain endothelial cell 223


title: Whole_Blood_GR15_V6


title: Brain endothelial cell 219

description: Brain endothelial cell 219


title: Whole_Blood_GR15_V5


title: Brain endothelial cell 226

description: Brain endothelial cell 226


title: Brain endothelial cell 218

description: Brain endothelial cell 218


title: sigG1 mutant - sample1


title: Whole_Blood_GR15_V7


title: Brain endothelial cell 220

description: Brain endothelial cell 220


title: Whole_Blood_GR15_V3


title: Brain endothelial cell 217

description: Brain endothelial cell 217


title: Whole_Blood_GR17_V4


title: Brain endothelial cell 225

description: Brain endothelial cell 225


title: Brain endothelial cell 215

description: Brain endothelial cell 215


title: Brain endothelial cell 216

description: Brain endothelial cell 216


title: Whole_Blood_GR13_V7


title: Whole_Blood_GR15_V4


title: Brain endothelial cell 213

description: Brain endothelial cell 213


title: Brain endothelial cell 221

description: Brain endothelial cell 221


title: Whole_Blood_GR13_V6


title: Brain endothelial cell 214

description: Brain endothelial cell 214


title: Brain endothelial cell 208

description: Brain endothelial cell 208


title: Whole_Blood_GR13_V5


title: Brain endothelial cell 209

description: Brain endothelial cell 209


title: Whole_Blood_GR13_V3


title: Brain endothelial cell 211

description: Brain endothelial cell 211


title: Whole_Blood_GR13_V4


title: Whole_Blood_GR11_V7


title: Brain endothelial cell 207

description: Brain endothelial cell 207


title: Brain endothelial cell 212

description: Brain endothelial cell 212


title: Brain endothelial cell 203

description: Brain endothelial cell 203


title: Whole_Blood_GR11_V6


title: Brain endothelial cell 210

description: Brain endothelial cell 210


title: E7386-4

city: Tsukuba-shi

first: Kazuhiko

last: Yamada

address: 5-1-3 Tokodai

institute: Eisai Co., Ltd.

description: Gene expression after E7386 treatment in whisler follicle tissues of ApcMin/+ mice, replicate 4

hyb_protocol: Cy3-RNAs were hybridized to a SurePrint G3 Mouse GE 8×60K Microarray (Agilent Technologies).

scan_protocol: Hybridization images were obtained with a DNA Microarray Scanner (Agilent Technologies).

data_processing: Scanned images were quantified by using Feature Extraction software ver. 11 (Agilent Technologies).

source_name: Whisker follicle, E7386, replicate 4

label_protocol: An aliquot of total RNA (50 ng) was converted to cyanine-3-labeled cRNA by using a Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies).

extract_protocol: Total RNA was extracted from the whisker follicles of ApcMin/+ mice by using an RNeasy Kit (QIAGEN)

treatment_protocol: ApcMin/+ mice were administered with E7386 (30 mg/kg orally, twice daily) for 4 cycles (each cycle, 5 days on/2 days off) from 8 weeks of age.

value: ApcMin/+

tag: gender

value: female

tag: agent

value: whisker follicle


title: Brain endothelial cell 205

description: Brain endothelial cell 205

value: brain


title: Vehicle-3

description: Gene expression after vehicle treatment in whisler follicle tissues of ApcMin/+ mice, replicate 3

source_name: Whisker follicle, vehicle, replicate 3

value: vehicle


title: Vehicle-4

description: Gene expression after vehicle treatment in whisler follicle tissues of ApcMin/+ mice, replicate 4

source_name: Whisker follicle, vehicle, replicate 4


title: Brain endothelial cell 202

description: Brain endothelial cell 202

value: adult mice

value: endothelial cell


title: E7386-3

description: Gene expression after E7386 treatment in whisler follicle tissues of ApcMin/+ mice, replicate 3

source_name: Whisker follicle, E7386, replicate 3


title: E7386-1

description: Gene expression after E7386 treatment in whisler follicle tissues of ApcMin/+ mice, replicate 1

source_name: Whisker follicle, E7386, replicate 1


title: Brain endothelial cell 204

description: Brain endothelial cell 204

source_name: Brain


title: Brain endothelial cell 200

description: Brain endothelial cell 200


title: Whole_Blood_GR11_V4

value: Whole Blood


title: E7386-2

description: Gene expression after E7386 treatment in whisler follicle tissues of ApcMin/+ mice, replicate 2

source_name: Whisker follicle, E7386, replicate 2


title: Treated group [ex1]

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

description:
ex1
Group_2
mRNA stranded library sequencing
JF_12_A_mRNAseq_ProcessedFile.tsv

data_processing:
Quality Control of sequenced samples was performed by FASTQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ). Reads were mapped against the mouse (mm10) reference genome by STAR program to account for spliced junctions. The resulting BAM alignment files for the samples were then used to generate a table of raw counts by Rsubread. Raw counts Table was the input for the Differential Expression (DE) analysis, carried out by DESeq2, to detect differentially expressed genes among the different conditions.
Genome_build: Mus_musculus.GRCm38.94.gtf
Supplementary_files_format_and_content: A plain text file (*.tsv) was generated for the whole project, consisting in a matrix with two sort of columns: 1st column contains gene IDs (ENTREZ_GENE_ID), and then, from the 2nd to the 7th columns, the numbers of raw counts obtained by STAR per gene and per sample are depicted.

source_name: 3T3.L1 cell line

growth_protocol: Cells were plated in a p100, incubated o/n in 25 mM HEPES-containing complete DMEM medium (contaminating vesicles were first removed by overnight centrifugation at 110000×g).

extract_protocol:
After PBS and trypsinization, cells were pelleted, washed in PBS, and frozen. RNA extraction was performed with RNeasy (Qiagen) RNA isolation kit, including the step of DNase treatment for all the samples, and finally eluted in RNase free water.
Sequencing libraries were prepared following the protocol "TruSeq Stranded mRNA Sample Preparation Guide (Part#15031047Rev.E)" with the "TruSeq stranded mRNAseq library preparation kit” (Illumina Inc., Cat.#RS-122-2101orRS-122-2102 (SetA or B, respectively)).

treatment_protocol: Cells were treated with EVs or non-conditioned media Prep during 24 hours, in 25 mM HEPES-containing complete DMEM medium (contaminating vesicles were first removed by overnight centrifugation at 110000×g).

tag: cell line

value: Fibroblast

tag: treatment

value: EV from MLP29 cell line conditioned culture media


title: Whole_Blood_GR11_V3


title: Brain endothelial cell 198

description: Brain endothelial cell 198

data_processing:
The sequencing reads were first aligned to the mouse reference genome GRCm38 (mm10) with tophat (version 2.1.1). The duplicated reads were removed using samtools software (version 0.1.18). The raw read counts for each gene were then calculated using featureCounts function from the Subread package (version 1.4.6-p5)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each sample


title: Vehicle-1

description: Gene expression after vehicle treatment in whisler follicle tissues of ApcMin/+ mice, replicate 1

source_name: Whisker follicle, vehicle, replicate 1


title: Brain endothelial cell 196

description: Brain endothelial cell 196


title: Brain endothelial cell 199

description: Brain endothelial cell 199


title: Brain endothelial cell 193

description: Brain endothelial cell 193


title: Brain endothelial cell 197

description: Brain endothelial cell 197


title: Whole_Blood_GR10_V6


title: Brain endothelial cell 206

description: Brain endothelial cell 206


title: Whole_Blood_GR11_V5


title: Control group [bg3]

description:
bg3
Group_1
mRNA stranded library sequencing
JF_12_A_mRNAseq_ProcessedFile.tsv

value: EV prep from "non conditioned" media


title: Brain endothelial cell 194

description: Brain endothelial cell 194

value: Pdgfb ret/+


title: Treated group [ex4]

description:
ex4
Group_2
mRNA stranded library sequencing
JF_12_A_mRNAseq_ProcessedFile.tsv


title: Whole_Blood_GR10_V7


title: Control group [bg2]

description:
bg2
Group_1
mRNA stranded library sequencing
JF_12_A_mRNAseq_ProcessedFile.tsv


title: Treated group [ex2]

description:
ex2
Group_2
mRNA stranded library sequencing
JF_12_A_mRNAseq_ProcessedFile.tsv


title: Whole_Blood_GR10_V5


title: Control group [bg1]

description:
bg1
Group_1
mRNA stranded library sequencing
JF_12_A_mRNAseq_ProcessedFile.tsv


title: Brain endothelial cell 192

description: Brain endothelial cell 192


title: Brain endothelial cell 190

description: Brain endothelial cell 190


title: Vehicle-2

description: Gene expression after vehicle treatment in whisler follicle tissues of ApcMin/+ mice, replicate 2

source_name: Whisker follicle, vehicle, replicate 2


title: Whole_Blood_GR10_V4


title: Brain endothelial cell 195

description: Brain endothelial cell 195


title: Brain endothelial cell 188

description: Brain endothelial cell 188


title: Brain endothelial cell 191

description: Brain endothelial cell 191


title: E13.5_heart_Homo_H222P

city: Marseille

first: michel

last: PUCEAT

address: 27 bd Jean moulin

department: University aix marseille

institute: INSERM

data_processing:
Sequence alignment and quantification of gene expression
Fastq files were aligned to the reference Mouse genome mm10 with STAR1 (--twopassMode Basic --outReadsUnmapped None --chimSegmentMin 12 --chimJunctionOverhangMin 12 -alignSJDBoverhangMin 10 --alignMatesGapMax 200000 --alignIntronMax 200000 -chimSegmentReadGapMax parameter 3 --alignSJstitchMismatchNmax 5 -1 5 5 --quantMode GeneCounts --outWigType wiggle --sjdbGTFtagExonParentGene gene_name). We removed reads mapping to multiple locations. We quantified gene expression using the full Gencode vM24 annotation. We used also STAR to obtain the number of reads associated to each gene in the Gencode vM24 database (restricted to protein-coding genes, antisense and lincRNAs). We used the Bioconductor DESeq package2 to import raw HTSeq counts for each sample into R statistical software and extract the count matrix. After normalizing for library size, we normalized the count matrix by the coding length of genes to compute FPKM scores (number of fragments per kilobase of exon model and millions of mapped reads). Bigwig visualization files were generated using STAR and the bam2wig python script3.

source_name: embryonic E13.5 heart

extract_protocol:
RNA was extracted from embryonic hearts using a Zymo research RNA kit
total RNA library

value: heart

value: total RNA

tag: genotype/variation

value: Lmna H222P/H222P


title: Brain endothelial cell 187

description: Brain endothelial cell 187

tag: strain


title: E13.5_heart_wt

tag: tissue

value: wild type


title: Brain endothelial cell 186

description: Brain endothelial cell 186

tag: age


title: Brain endothelial cell 189

description: Brain endothelial cell 189

tag: genotype


title: Brain endothelial cell 185

description: Brain endothelial cell 185

tag: cell type


title: Whole_Blood_GR09_V7

value: Female


title: Whole_Blood_GR10_V3


title: Brain endothelial cell 184

description: Brain endothelial cell 184


title: Brain endothelial cell 183

description: Brain endothelial cell 183


title: Shmt2 knockdown oocytes 3

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

data_processing:
raw fastq files were trimmed using Trim Galore
Clean data were mapped to mm10 reference genome using Bismark
Methylation levels of CpG sites were extracted using Bismark suite
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph, the forth column contains the methylation level

source_name: Shmt2 knockdown oocytes

extract_protocol:
In brief, denuded oocytes (30 oocytes for each sample) were lysed in lysis buffer (10 mM Tris-Cl pH 7.4 and 2% SDS) with 0.5 μl protease K for 1 h at 37 °C. Bisulfite conversion was performed on cell lysates using the EZ DNA Methylation-Gold Kit (Zymo Research).
Purification was performed and DNA was eluted in 10 mM Tris-Cl and combined with oligo 1. Klenow were added and incubated at 4 °C for 5 min, 37 °C for 30 min. Following incubation at 95 °C for 1 min, samples were transferred to ice before addition of fresh oligo 1. This random priming and extension was repeated a further three times. Samples were then incubated with 40 U exonuclease I and M-280 Streptavidin Dynabeads. After washes and resuspension in oligo 2 and Blue Buffer, samples were incubated at 95 °C for 45 s, transferred immediately to ice before addition of 100 U Klenow. Libraries were amplified by PCR, and assessed for quality and quantity using Agilent Bioanalyzer and StepOnePlus Real-Time PCR System. Libraries were prepared for 125-bp paired-end sequencing on a HiSeq2500.

value: Shmt2 knockdown

value: MII oocytes


title: Whole_Blood_GR09_V6


title: Brain endothelial cell 182

description: Brain endothelial cell 182


title: Shmt2 knockdown oocytes 1


title: Whole_Blood_GR09_V5


title: Brain endothelial cell 180

description: Brain endothelial cell 180


title: Whole_Blood_GR09_V4


title: normal oocytes 3

source_name: normal oocytes

value: control


title: Brain endothelial cell 178

description: Brain endothelial cell 178

value: brain


title: Brain endothelial cell 179

description: Brain endothelial cell 179


title: Brain endothelial cell 181

description: Brain endothelial cell 181


title: Whole_Blood_GR09_V3


title: normal oocytes 2


title: Brain endothelial cell 176

description: Brain endothelial cell 176


title: Brain endothelial cell 177

description: Brain endothelial cell 177


title: Brain endothelial cell 175

description: Brain endothelial cell 175


title: normal oocytes 1


title: Whole_Blood_GR07_V7

value: Male


title: Brain endothelial cell 172

description: Brain endothelial cell 172

value: adult mice


title: Brain endothelial cell 174

description: Brain endothelial cell 174

value: endothelial cell


title: Double Knockout Replicate 3

city: Clayton

first: Nicholas

middle: C

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

country: Australia

institute: Monash University

description:
Megakaryocyte cells from mice with lineage specific knockout of both LYL and TAL1
946_S2

data_processing:
STAR v2.5.2b
RNASik v1.4.7
featurecounts (subread v1.5.2)
Degust
Genome_build: GRCm38.87
Supplementary_files_format_and_content: text table of read counts from featurecounts to gene models.

source_name: Primary megakaryocyte culture

growth_protocol: DMEM (Gibco) supplemented with 10% FBS, 1% penicillin/streptomycin (Gibco) and recombinant TPO

extract_protocol:
Qiagen Rneasy Mini Prep Kit
TruSeq mRNA

value: megakaryocytes

value: double Scl/Tal1/Lyl1 knockout


title: Brain endothelial cell 171

description: Brain endothelial cell 171


title: Double Knockout Replicate 2

description:
Megakaryocyte cells from mice with lineage specific knockout of both LYL and TAL1
930_S1


title: Whole_Blood_GR07_V5

source_name: Whole Blood

value: Whole Blood


title: Whole_Blood_GR07_V6


title: Shmt2 knockdown oocytes 2


title: Brain endothelial cell 170

description: Brain endothelial cell 170


title: Brain endothelial cell 168

description: Brain endothelial cell 168


title: Whole_Blood_GR07_V4


title: Whole_Blood_GR07_V3


title: Brain endothelial cell 169

description: Brain endothelial cell 169


title: Double Knockout Replicate 1

description:
Megakaryocyte cells from mice with lineage specific knockout of both LYL and TAL1
1027_S10


title: SCL/TAL1 Knockout Replicate 3

description:
Megakaryocyte cells from mice with lineage specific knockout of TAL1
987_S6

value: SCL/TAL1 Knockout


title: Brain endothelial cell 166

description: Brain endothelial cell 166

value: Pdgfb ret/+


title: SCL/TAL1 Knockout Replicate 2

description:
Megakaryocyte cells from mice with lineage specific knockout of TAL1
986_S5


title: Brain endothelial cell 164

description: Brain endothelial cell 164


title: Brain endothelial cell 165

description: Brain endothelial cell 165


title: Brain endothelial cell 163

description: Brain endothelial cell 163


title: SCL/TAL1 Knockout Replicate 1

description:
Megakaryocyte cells from mice with lineage specific knockout of TAL1
1052_S11


title: Whole_Blood_GR06_V6


title: Whole_Blood_GR06_V5


title: LYL Knockout Replicate 3

description:
Megakaryocyte cells from mice with lineage specific knockout of LYL
976_S4

value: LYL Knockout


title: Brain endothelial cell 160

description: Brain endothelial cell 160


title: Whole_Blood_GR06_V4


title: Brain endothelial cell 158

description: Brain endothelial cell 158


title: Brain endothelial cell 159

description: Brain endothelial cell 159


title: Whole_Blood_GR06_V3


title: LYL Knockout Replicate 1

description:
Megakaryocyte cells from mice with lineage specific knockout of LYL
1026_S9


title: Brain endothelial cell 157

description: Brain endothelial cell 157


title: Whole_Blood_GR05_V7


title: Brain endothelial cell 156

description: Brain endothelial cell 156


title: Whole_Blood_GR05_V6


title: Brain endothelial cell 153

description: Brain endothelial cell 153


title: WT Replicate 3

description:
Megakaryocyte cells from wildtype mice
1079_S12

value: wildtype


title: Whole_Blood_GR06_V7


title: LYL Knockout Replicate 2

description:
Megakaryocyte cells from mice with lineage specific knockout of LYL
975_S3


title: Brain endothelial cell 152

description: Brain endothelial cell 152


title: WT Replicate 2

description:
Megakaryocyte cells from wildtype mice
1021_S8


title: Whole_Blood_GR05_V5


title: Brain endothelial cell 155

description: Brain endothelial cell 155


title: WT Replicate 1

description:
Megakaryocyte cells from wildtype mice
1017_S7


title: Brain endothelial cell 167

description: Brain endothelial cell 167


title: Brain endothelial cell 162

description: Brain endothelial cell 162


title: Brain endothelial cell 151

description: Brain endothelial cell 151


title: Brain endothelial cell 161

description: Brain endothelial cell 161


title: Brain endothelial cell 201

description: Brain endothelial cell 201


title: Brain endothelial cell 150

description: Brain endothelial cell 150


title: Brain endothelial cell 149

description: Brain endothelial cell 149


title: Whole_Blood_GR05_V3


title: Whole_Blood_GR05_V4